pathogenicity_label,genome_id,genome_name,strain,species,genus,family,order,class,phylum,biosample_accession,taxon_id,serovar,biovar,pathovar,mlst,other_typing,culture_collection,type_strain,completion_date,publication,bioproject_accession,assembly_accession,genbank_accessions,refseq_accessions,sequencing_centers,sequencing_platform,sequencing_depth,assembly_method,chromosomes,plasmids,contigs,genome_length,gc_content,patric_cds,refseq_cds,isolation_source,isolation_comments,collection_date,isolation_country,geographic_location,other_environmental,host_gender,host_age,host_health,body_sample_site,other_clinical,antimicrobial_resistance,antimicrobial_resistance_evidence,gram_stain,cell_shape,motility,temperature_range,optimal_temperature,oxygen_requirement,habitat,disease,comments,additional_metadata,env_broad_scale,env_local_scale,env_medium,isol_growth_condt,project_name,pathogenicity_details,host_disease,host_health_state,host_disease_outcome,host_description,host_disease_stage,pathotype,subsource_note,note,description,biotic_relationship,biome,host_status,risk_group,Note_on_infection_mode,checkm_compl_final,checkm_contam_final,disease_category,disease_subcategory,isolation_source_category,disease_comb NHP,100886.347,Catenibacterium mitsuokai strain DSM 15897,DSM 15897,Catenibacterium mitsuokai,Catenibacterium,Coprobacillaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMN20222672,100886,,,,,,DSM:15897,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148785.1,CP102271,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2650196,34.67766,2673,2614,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,1017264.6,Bordetella pertussis CS,CS,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN22851881,1017264,,,,MLST.Bordetella_spp.1,,,,2022-05-31T00:00:00Z,,PRJNA777368,GCA_023612135.1,CP086368,,,PacBio Sequel,295.0x,SMRT Link v. v5.0.1,1,0,1,4141631,67.71542,4087,3912,nasal pharynx,,1951,China,China,,,,pertussis,,,,,,,,,,,,,,collected_by:China Institue for Food and Drug Control,,,,,,,pertussis,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,1018.121,Capnocytophaga ochracea KCOM 2191,KCOM 2191,Capnocytophaga ochracea,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN31453015,1018,,,,,,,,2022-11-06T00:00:00Z,,PRJNA894344,GCA_026013785.1,CP110228,,,PacBio RSII; Illumina HiSeq,1039.0x,RS HGAP v. 3.0; SPAdes v. 3.8.2,1,0,1,2672569,39.697533,2404,2256,"subgingival dental plaque, gingivitis",,2001-12-10,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,96.7,0.3,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1018.123,Capnocytophaga ochracea KCOM 26681,KCOM 26681,Capnocytophaga ochracea,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN31469266,1018,,,,,,,,2022-11-06T00:00:00Z,,PRJNA894794,GCA_026013805.1,CP110229,,,PacBio RSII,516.0x,RS HGAP v. 3.0,1,0,1,2779391,39.26968,2476,2362,"subgingival dental plaque, periimplantitis",,2003-09-29,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,96.4,1.3,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1019.50,Capnocytophaga sputigena strain NCTC11097,NCTC11097,Capnocytophaga sputigena,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA104200653,1019,not available: to be reported later,,,,,NCTC:11097,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638125.1,LR134489,,SC,,,,1,,1,2933908,38.733868,2726,2668,blood culture,,1974,United Kingdom,United Kingdom,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.52,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,1033732.50,Alistipes senegalensis JC50,JC50,Alistipes senegalensis,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222637,1033732,,,,,,DSM:25460,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025145645.1,CP102252,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4023197,58.313698,3453,3175,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.76,0.48,,,Other,- HP,103817.8,Janibacter terrae strain YFY001,YFY001,Janibacter terrae,Janibacter,Intrasporangiaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN04226596,103817,,,,,,,,2016-12-05T00:00:00Z,,PRJNA300616,GCF_001889125.1,CP013290,NZ_CP013290.1,The First Affiliated Hospital of NanChang University,PacBio RS II system,missing,SMRTAnalysis v. 2.3.0 HGAP2,1,,1,3401189,71.24,3358,3192,blood,"derived from a patient isolated from JiangXi province, China",2014-07,China,China: Nanchang,,,,sepsis,,,,,,,,,C,,,,"Janibacter terrae is an important pathogenic microorganism. We sequenced the genome of J. terrae YFY001, which was derived from a patient isolated from JiangXi province, China.",collected_by:Lingbing Zeng,,,,,,,sepsis,,,,,,,,,,,,,,99.5,0.5,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1038927.31,Escherichia coli O104:H4 strain FDAARGOS_348,FDAARGOS_348,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173361,1038927,O104:H4,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,FDA:FDAARGOS_348,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002209105.2,"CP022086,CP022085,CP022087",,US Food and Drug Administration,PacBio,18.1565653439553x,"SMRT v. 2.3.0, HGAP v. 3.0",1,2,3,5442181,50.58,5899,5662,stool,,2009,USA,USA: Georgia,,,,Bloody diarrhea complicated hemolytic uremic syndrome (HUS),,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < CDC-Atlanta,,,,,,,Bloody diarrhea complicated hemolytic uremic syndrome (HUS),Missing,Missing,Missing,Missing,,,,,,,,,,100,1.5,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1038927.40,Escherichia coli O104:H4 strain FDAARGOS_349,FDAARGOS_349,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173362,1038927,O104:H4,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,FDA:FDAARGOS_349,,2018-03-09T00:00:00Z,,PRJNA231221,GCA_002983645.1,"CP027394,CP027395,CP027392,CP027396,CP027393",,US Food and Drug Administration,PacBio; Illumina,13.6271677151539x,"SMRT v. 2.3.0, HGAP v. 3.0",1,4,5,5501145,50.640114,5925,5734,stool,,2001,Germany,Germany,,female,37Y,Hemolytic uremic syndrome,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < Bundeswehr Inst. Microbiology,,,,,,,Hemolytic uremic syndrome,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1038927.45,Escherichia coli O104:H4 strain FWSEC0009,FWSEC0009,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768110,1038927,O104:H4,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2019-05-01T00:00:00Z,,PRJNA287560,GCA_005014075.1,"CP031902,CP031903,CP031904,CP031905",,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,65.55x;110.27x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5442997,50.65053,5768,5654,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2011,Germany,Germany,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.93,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,105219.32,Ralstonia mannitolilytica strain Guangzhou-RMAB10,Guangzhou-RMAB10,Ralstonia mannitolilytica,Ralstonia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN14131005,105219,,,,,,,,2020-03-01T00:00:00Z,,PRJNA607372,GCA_011044515.1,"CP049132,CP049133",,South China University of Technology,PacBio,100.0x,HGAP v. 0,2,0,2,4838688,65.66358,4843,4492,blood,,2014-04-18,China,China: Guangzhou,,,,Acute exacerbation of chronic obstructive pulmonary disease severe pneumonia and type II respiratory failure,,,,,,,,,,,,,"This study reported the case and genome of a Ralstonia mannitolilytica strain causing bacteremia in an acute exacerbation of chronic obstructive pulmonary disease, confirming its pathogenic role in this disease.",collected_by:The First Affiliated Hospital of Guangzhou Medical University (FAHGMU),,,,,,,Acute exacerbation of chronic obstructive pulmonary disease severe pneumonia and type II respiratory failure,,,,,,,,,,,,,,98.82,0.92,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,105219.63,Ralstonia mannitolilytica SN82F48,SN82F48,Ralstonia mannitolilytica,Ralstonia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03295199,105219,,,,,,,,2015-03-19T00:00:00Z,,PRJNA273689,GCA_000954135.2,"CP010799,CP010800,CP010801",,,"Oxford Nanopore; Illumina, Nextera",,SPAdes v. v3.5,2,1,3,5072301,65.4861,4888,4472,bone marrow,,2002-10-16,USA,USA: San Francisco,,,,sepsis,,,,,,,,,,,,,,collected_by:UCSF,,,,,,,sepsis,,,,,,,,,,,,,,100,0.5,Bloodstream Infections,Sepsis,Bone and Joint,Bloodstream Infections-Sepsis NHP,105841.48,Anaerostipes caccae strain NBRC 114412,NBRC 114412,Anaerostipes caccae,Anaerostipes,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN21163588,105841,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181435.1,CP084016,,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore GridION,332.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,0,1,3284789,44.45905,3416,3243,human feces,,2019,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.33,4.03,,,Gastrointestinal,- HP,106648.173,Acinetobacter bereziniae AB839,AB839,Acinetobacter bereziniae,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN33465245,106648,,,,,,,,2023-03-13T00:00:00Z,,PRJNA939378,,"CP119245,CP119243,CP119244,CP119246",,,Oxford Nanopore MinION,49.0x,Flye v. Oct 2022,1,3,4,5092623,38.06111,5601,4842,blood,,2006,Taiwan,Taiwan,,,,Bacteremia,,,,,,,,,,,,,,collected_by:Jiunn-Jong Wu,,,,,,,Bacteremia,,,,,,,,,,,,,,100,4,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,106648.179,Acinetobacter bereziniae UCO-553,UCO-553,Acinetobacter bereziniae,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN34266403,106648,,,,,,,,2023-05-02T00:00:00Z,,PRJNA957799,,"CP123912,CP123913,CP123914,CP123915,CP123916,CP123917",,,Illumina NextSeq; Oxford Nanopore MinION,100X,SPAdes v. 0.5.0,1,5,6,4651239,38.068115,4453,,tracheal aspirate,,2021-02-16,Chile,Chile: Santiago,,,,Respiratory tract infection,,,,,,,,,,,,,,collected_by:Hospital de Urgencia Asistencia Pblica,,,,,,,Respiratory tract infection,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,106648.180,Acinetobacter bereziniae UCO-554,UCO-554,Acinetobacter bereziniae,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN34266404,106648,,,,,,,,2023-05-02T00:00:00Z,,PRJNA957799,,"CP123918,CP123919,CP123920,CP123921,CP123922",,,Illumina NextSeq; Oxford Nanopore MinION,100X,SPAdes v. 0.5.0,1,4,5,4651266,38.067657,4450,,blood,,2020-10-16,Chile,Chile: Santiago,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Hospital de Urgencia Asistencia Pblica,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,106654.118,Acinetobacter nosocomialis strain FDAARGOS_129,FDAARGOS_129,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN03996318,106654,,,,MLST.Acinetobacter_baumannii_2.433,,FDA:FDAARGOS_129,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002951295.1,CP014019,,US Food and Drug Administration,PacBio; Illumina,21x,Celera v. 8.2,1,,1,4002679,38.780853,3831,3744,abscess,,2014-12-26,USA,USA:DC,,female,12Y,Perforated appendicitis,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Perforated appendicitis,Missing,Missing,Missing,Missing,,,,,,,,,,99.4,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,106654.125,Acinetobacter nosocomialis strain NCTC 8102,NCTC 8102,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09197281,106654,,,,MLST.Acinetobacter_baumannii_2.74,,,,2018-05-20T00:00:00Z,,PRJNA471013,GCA_003143895.1,CP029351,,"Chungnam National University, College of medicine",PacBio,204.38x,PacBio SMRT Analysis v. 2.3.0,1,,1,4010110,38.70183,3888,3791,not applicable,,1950-01-01,USA,USA: Rhode Island,,,,"Bacteremia, pneumonia",,,,,,,,,,,,,"This is the whole genome sequence of Acinetobacter nosocomialis str. NCTC 8102 which is known to be a nosocomial pathogen. Here, we resequenced the A. nosocomialis str. NCTC 8102 to collect valuable genetic information as there is not much information available from the previously published genome sequence of the same. The information which could be drawn from the new whole genome sequence can be used for further studies at the genome level which might led to the invention of new strategies to effectively tackle this nosocomial pathogen.",collected_by:C A Stuart,,,,,,,"Bacteremia, pneumonia",,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,106654.152,Acinetobacter nosocomialis strain KAN02,KAN02,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10928940,106654,,,,,,,,2019-02-25T00:00:00Z,,PRJNA522344,GCA_004295305.1,CP036171,,Korea Basic Science Institute,PacBio RSII,240.0x,HGAP v. Jun-2016,1,,1,3958196,38.788654,3769,3702,blood,isolated from blood of chronic obstructive pulmonary disease patient,2015-02-27,South Korea,South Korea:Jeonju,,,,,,,,,,,,,,,,,Acinetobacter nosocomialis isolated from blood of chronic obstructive pulmonary disease patient.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,106654.153,Acinetobacter nosocomialis strain KAN01,KAN01,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11295118,106654,,,,MLST.Acinetobacter_baumannii_1.879,,,,2019-04-14T00:00:00Z,,PRJNA530095,GCA_004792395.1,CP038816,,Korea Basic Science Institute,PacBio RS,240.0x,HGAP v. Jun-2016,1,,1,3793191,38.82143,3661,3581,sputum,isolated from blood of chronic obstructive pulmonary disease patient,2015-03-18,South Korea,South Korea:Daejeon,,,,,,,,,,,,,,,,,Acinetobacter nosocomialis KAN01 isolated from blood of chronic obstructive pulmonary disease patient.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,106654.196,Acinetobacter nosocomialis strain AC1530,AC1530,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13066419,106654,,,,MLST.Acinetobacter_baumannii_2.224,,,,2019-11-05T00:00:00Z,,PRJNA576555,GCA_009588945.1,"CP045560,CP045561",,Universiti Sultan Zainal Abidin,PacBio RSII; Illumina HiSeq,256.0x,SPAdes v. 3.11.1,1,1,2,4154154,38.79779,4052,3969,blood,,2015,Malaysia,Malaysia,,,,"Infections, nosocomial",,,,,,,,,,,,,"Whole genome sequencing of non-baumannii Acinetobacter hospital isolates from Terengganu, Malaysia",collected_by:UniSZA,,,,,,,"Infections, nosocomial",,,,,,,,,,,,,,100,0.14,Nosocomial Infections,Other Nosocomial Infections,Blood and Circulatory System,Nosocomial Infections-Other Nosocomial Infections HP,106654.366,Acinetobacter nosocomialis 11J360,11J360,Acinetobacter nosocomialis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27553639,106654,,,,,,,,2023-06-22T00:00:00Z,,PRJNA826226,,"CP095867,CP095868,CP095869,CP095870",,,Oxford Nanopore PromethION,229.75x,Celera Assembler v. October-2019,1,3,4,4344035,38.75526,4271,4058,sputamentum,,2012,China,China: Guangzhou Province,,,,Infect,,,,,,,,,,,,,,collected_by:the Institute of Clinical Pharmacology of Peking University First Hospital,,,,,,,Infect,,,,,,,,,,,,,,100,2.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1071983.3,Legionella cardiaca H63,H63,Legionella cardiaca,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN33435349,1071983,,,,,,,,2023-03-08T00:00:00Z,,PRJNA938446,,CP119078,,,Illumina NovaSeq; PacBio RSII,4411.46x,HGAP v. 4,1,0,1,3477232,38.586063,3109,2955,resected aortic valve tissue,,2009-08,USA,USA: Chicago,,,,endocarditis,,,,,,,,,,,,,,collected_by:Northwestern Memorial Hospital,,,,,,,endocarditis,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,1077464.33,Streptococcus oralis subsp. tigurinus strain osk_001,osk_001,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00078884,1077464,,,,,,,,2017-07-14T00:00:00Z,,PRJDB5718,GCA_002356415.1,AP018338,,Osaka University,PacBio RS; Illumina MiSeq,675.9x,HGAP v. 3,1,,1,1889005,41.15,1869,1831,,,2016-10-03,Japan,"Japan:Osaka, Osaka, Higashisumiyoshi",env_biome:subtropical moist broadleaf forest,,,,,,,,,,,,,,,,"Severe infectious death is often diagnosed by the post-mortem examination. T he causative microorganism is not often identified due to technical difficulty. It is very important in public health to detect microorganisms in the infectious disease. We sample the specimens and perform the alternative updated gene analysis in addition to the conventional microbiological methods, to diagnose the cause of death is more useful in public health.",,subtropical moist broadleaf forest,carcass,fat,not provided,Microbiological diagnosis by post-mortem examination,,,,,,,,,,,,subtropical moist broadleaf forest,,,,99.8,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1078021.3,Escherichia coli O113:H21 strain FWSEC0010,FWSEC0010,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768111,1078021,O113:H21,,,MLST.Escherichia_coli_1.223,,,,2019-05-01T00:00:00Z,,PRJNA287560,GCA_005014055.1,"CP031898,CP031899,CP031900,CP031901",,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,94.45x;51.16x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5131000,50.785305,5319,5244,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",1991,Canada,Canada,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.93,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1078032.3,Escherichia coli O45:H2 strain FWSEC0003,FWSEC0003,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768104,1078032,O45:H2,,,MLST.Escherichia_coli_2.135,,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037845.2,NJGS00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,100.74x;244.02x,Unicycler;Canu v. 0.4.4.0;1.7,1,2,3,5680623,50.60373,6253,6018,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2005,Canada,"Canada:Nova Scotia,Halifax",,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.93,0.58,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1086030.18,Shigella flexneri 5a str. M90T,M90T,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10608416,1086030,,,,,,,,2019-04-18T00:00:00Z,,PRJNA510559,GCA_004799585.1,"CP037923,CP037924",,Umea University,PacBio RSII; Illumina HiSeq,155.0x,Canu v. V.1.7,1,1,2,4828909,50.665173,5428,4865,"walter reed collection. sansonetti, p. j., et al. (1982). involvement of a plasmid in the invasive ability of shigella flexneri. infect immun 35(3): 852-860.",,1981-07-09,USA,USA:MD,,,,dysentery,,,,,,,,,,,,,Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri 5a M90T and genome-wide transcription start site determination,collected_by:Samuel Formal,,,,,,,dysentery,,,,,,,,,,,,,,99.43,0.21,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,109328.5,Leptotrichia trevisanii strain JMUB3935,JMUB3935,Leptotrichia trevisanii,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMD00156220,109328,,,,,,,Yes,2019-07-24T00:00:00Z,,PRJDB7856,GCA_007990425.1,AP019840,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MinION; MiSeq,48X,Canu v. 1.8; Circlator v. 1.5.5;,1,,1,2903646,30.642475,2767,2686,blood,,2016,Japan,Japan,,,,,,,,,Negative,,,,,,,,We determined genome sequences of seven clinical isolates and four type strains of Leptotrichia.,,missing,missing,blood,11783691,Genome Sequence of Leptotrichia trevisanii Strain JMUB3935,,,,,,,,,,,,missing,,,,100,1.14,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,109328.6,Leptotrichia trevisanii strain JMUB4039,JMUB4039,Leptotrichia trevisanii,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMD00156225,109328,,,,,,,Yes,2019-07-24T00:00:00Z,,PRJDB7856,GCA_007990575.1,AP019845,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MinION; MiSeq,44X,Canu v. 1.8; Circlator v. 1.5.5;,1,,1,2685755,30.771347,2494,2387,blood,,2012,Japan,Japan,,,,,,,,,Negative,,,,,,,,We determined genome sequences of seven clinical isolates and four type strains of Leptotrichia.,,missing,missing,blood,11783691,Complete Genome Sequence of Leptotrichia trevisanii Strain JMUB4039,,,,,,,,,,,,missing,,,,100,1.14,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,109790.33,Lactobacillus jensenii strain SNUV360,SNUV360,Lactobacillus jensenii,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN06163224,109790,,,,,,,,2017-01-05T00:00:00Z,,PRJNA357991,GCF_001936235.1,CP018809,NZ_CP018809.1,"KoBioLabs, Inc.",PacBio,420.0x,HGAP3 v. 3.0,1,,1,1672949,34.44,1631,1562,vaginal environment,,2013-08,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,"Lactobacillus jensenii SNUV360, is a potential probiotic strain that shows antimicrobial activity for treatment of bacterial vaginosis",sample_type:vaginal fluid,,,,,,,,,,,,,,,,,,,,,100,0,,,Genitourinary,- HP,110505.9,Mycobacterium heckeshornense strain JCM 15655,JCM 15655,Mycobacterium heckeshornense,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00265704,110505,,,,,,,Yes,2020-12-25T00:00:00Z,,PRJDB10874,GCA_016592155.1,AP024237,,"Mycobacteriology, National Institute of Infectious Diseases",ONT MinION; Illumina Miniseq,192x,Canu v. 1.8; Shovill v. 1.0.4,1,0,1,4957188,65.9294,5019,4840,,,1994,Germany,Germany,,,,,,,,,Positive,Bacilli,,,,,,,"Mycobacterium (M.) heckeshornense is a slow growing, scotochromogenic, thermophilic non-tuberculous mycobacterial (NTM) species. Both biochemical and phylogenetic analyses indicated that M. heckeshornense is closely related to M. xenopi and M. botniense. We determined the complete genome sequence of M. heckeshornense type strain JCM 15655T, helping us to understand characteristics of this pathogen.",,not applicable,not applicable,not applicable,not applicable,Complete genome sequence of Mycobacterium heckeshornense type strain JCM 15655T,,,,,,,,,,,,not applicable,,,,97.73,0.34,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1117645.198,Elizabethkingia anophelis strain FDAARGOS_198,FDAARGOS_198,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN04875535,1117645,,,,,,FDA:FDAARGOS_198,,2017-08-30T00:00:00Z,,PRJNA231221,GCA_002277995.1,CP023010,,US Food and Drug Administration,PacBio,17.69x,CA v. 8.2,1,,1,4073991,35.82,3915,3668,blood,,,Sweden,Sweden,,,,Infection with Elizabethkingia meningoseptica,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC < CCUG < PHL,,,,,,,Infection with Elizabethkingia meningoseptica,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1117645.380,Elizabethkingia anophelis strain 296-96,296-96,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN13281618,1117645,,,,,,,,2019-11-23T00:00:00Z,,PRJNA589371,GCA_009697265.1,CP046080,,National Chung Hsing University,Illumina iSeq; Oxford Nanopore MiniION,130.0x,Unicycler v. v0.4.7,1,0,1,4203861,35.844856,4013,3808,blood sample,,2011,Taiwan,Taiwan,,male,82,bacteremia,,,,,,,,,,,,,"During 2011 to 2017, there is an increasing of patient numbers infected by Elizabethkingia anophelis in the respiratory care center and intensive care unit in Changhua Christian Hospital, a medical center in central Taiwan. E. anophelis strain 296-96 was collected from the blood sample from a patient in the respiratory care center in 2011. RFLP analysis on the genomic DNA samples using XhoI digestion indicated that almost all of the E. anophelis isolates collected in this outbreak have the same genomic pattern to 296-96.",collected_by:ChangHua Christian Hospital,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.406,Elizabethkingia anophelis strain JUNP 353 strain JUNP353,JUNP353,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMD00195183,1117645,,,,,,,,2019-12-21T00:00:00Z,,PRJDB9120,GCA_009810215.1,AP022313,,"Department of Microbiology, Juntendo University School of Medicine",Illuminia MiSeq; Oxford nanopore MinION,56x,Unicycler v. 0.4.8,1,0,1,4316163,35.841927,4158,3950,,,2019,Nepal,Nepal:Kathmandu,,,,,,,,,,,,,,,,,Elizabethkingia anophelis clinical isolates with pan-drug resistance were detected in a medical setting in Nepal.,,missing,missing,missing,missing,Multidrug-resistant Elizabethkingia anophelis clinicla isolate in Nepal,,,,,,,,,,,,missing,,,,100,1.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1117645.501,Elizabethkingia anophelis strain SUE,SUE,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN08166467,1117645,,,,,,,,2020-09-22T00:00:00Z,,PRJNA507867,GCA_014702245.1,CP034247,,National Chung Cheng University,Oxford Nanopore; Illumina,100.0x,Unicycler v. 0.4.7,1,0,1,4201198,35.842754,4014,3796,blood,,2015,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,Analysis of the genome in order to understand the genetic factors leading to virulence and antibiotic resistance,collected_by:Ching-Lin Shy,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1117645.679,Elizabethkingia anophelis strain SEA01,SEA01,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN17717915,1117645,,,,,,,,2021-02-09T00:00:00Z,,PRJNA698406,GCA_016838625.1,CP069277,,Sri Sathya Sai Institute of Higher Learning,Illumina HiSeq; Oxford Nanopore MinION,96.38x,Unicycler v. 0.4.8,1,0,1,3957392,35.62533,3667,3546,blood,"isolated from the blood culture of a 5-day old infant at Sri Sathya Sai General Hospital, Puttaparthi",2014-11,India,India:Puttaparthi,,,5-day old,blood Infection,,,,,,,,,,,,,"Elizabethkingia anophelis SEA01 was isolated from the blood culture of a 5-day old infant at Sri Sathya Sai General Hospital, Puttaparthi.","collected_by:Sri Sathya Sai General Hospital, Puttaparthi",,,,,,,blood Infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1117645.812,Elizabethkingia anophelis 362-2,362-2,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192331,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205105.1,CP071532,,,Illumina iSeq; Oxford Nanopore MinION,100.30x,Unicycler v. 0.4.8,1,0,1,4175258,35.84102,3972,3786,blood,,2017,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.813,Elizabethkingia anophelis 367-19,367-19,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192332,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205085.1,CP071531,,,Illumina iSeq; Oxford Nanopore MinION,69.35x,Unicycler v. 0.4.8,1,0,1,4194549,35.820347,3978,3793,blood,,2017,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.814,Elizabethkingia anophelis 356-17,356-17,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192330,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205125.1,CP071533,,,Illumina iSeq; Oxford Nanopore MinION,115.24x,Unicycler v. 0.4.8,1,0,1,4174898,35.840805,3972,3785,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.815,Elizabethkingia anophelis 355-58,355-58,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192329,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205145.1,CP071534,,,Illumina iSeq; Oxford Nanopore MinION,110.77x,Unicycler v. 0.4.8,1,0,1,4174387,35.84059,3974,3785,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.816,Elizabethkingia anophelis 354-87,354-87,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192328,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205165.1,CP071535,,,Illumina iSeq; Oxford Nanopore MinION,110.25x,Unicycler v. 0.4.8,1,0,1,4150716,35.86015,3937,3747,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.817,Elizabethkingia anophelis 354-72,354-72,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192327,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205185.1,CP071536,,,Illumina iSeq; Oxford Nanopore MinION,126.88x,Unicycler v. 0.4.8,1,0,1,4174699,35.84093,3974,3784,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.818,Elizabethkingia anophelis 351-72,351-72,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192326,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205425.1,CP071537,,,Illumina iSeq; Oxford Nanopore MinION,112.20x,Unicycler v. 0.4.8,1,0,1,4174868,35.840797,3975,3788,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.819,Elizabethkingia anophelis 349-83,349-83,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192325,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205445.1,CP071538,,,Illumina iSeq; Oxford Nanopore MinION,105.28x,Unicycler v. 0.4.8,1,0,1,4174743,35.84017,3978,3786,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.820,Elizabethkingia anophelis 348-50,348-50,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192324,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205485.1,CP071539,,,Illumina iSeq; Oxford Nanopore MinION,115.01x,Unicycler v. 0.4.8,1,0,1,4174896,35.840652,3971,3786,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.821,Elizabethkingia anophelis 347-96,347-96,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192323,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205465.1,CP071540,,,Illumina iSeq; Oxford Nanopore MinION,104.87x,Unicycler v. 0.4.8,1,0,1,4174562,35.840958,3976,3786,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.822,Elizabethkingia anophelis 347-10,347-10,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192321,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205525.1,CP071542,,,Illumina iSeq; Oxford Nanopore MinION,122.09x,Unicycler v. 0.4.8,1,0,1,4175073,35.841553,3972,3784,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.823,Elizabethkingia anophelis 347-50,347-50,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192322,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205505.1,CP071541,,,Illumina iSeq; Oxford Nanopore MinION,117.94x,Unicycler v. 0.4.8,1,0,1,4154020,35.859383,3936,3754,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.7,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.824,Elizabethkingia anophelis 346-66,346-66,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192319,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205565.1,CP071544,,,Illumina iSeq; Oxford Nanopore MinION,111.84x,Unicycler v. 0.4.8,1,0,1,4174894,35.840622,3976,3786,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.825,Elizabethkingia anophelis 346-72,346-72,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192320,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205545.1,CP071543,,,Illumina iSeq; Oxford Nanopore MinION,109.46x,Unicycler v. 0.4.8,1,0,1,4174905,35.841415,3971,3785,blood,,2016,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.826,Elizabethkingia anophelis 343-63,343-63,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192317,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205585.1,CP071546,,,Illumina iSeq; Oxford Nanopore MinION,137.36x,Unicycler v. 0.4.8,1,0,1,4174896,35.840485,3974,3787,blood,,2015,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.827,Elizabethkingia anophelis 313-22,313-22,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192316,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205605.1,CP071547,,,Illumina iSeq; Oxford Nanopore MinION,107.16x,Unicycler v. 0.4.8,1,0,1,4049143,35.772038,3809,3659,blood,,2013,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,99.2,2.8,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.828,Elizabethkingia anophelis 344-1,344-1,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192318,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205645.1,CP071545,,,Illumina iSeq; Oxford Nanopore MinION,949.59x,Unicycler v. 0.4.8,1,0,1,4202044,35.842724,4013,3817,blood,,2015,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.6,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.829,Elizabethkingia anophelis 277-17,277-17,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN18192315,1117645,,,,,,,,2022-07-11T00:00:00Z,,PRJNA707236,GCA_024205625.1,"CP071548,CP071549",,,Illumina iSeq; Oxford Nanopore MinION,86.34x,Unicycler v. 0.4.8,1,1,2,4019226,35.643356,3800,3619,blood,,2010,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,"collected_by:Yu-Lin Lee, MD. CCH",,,,,,,bacteremia,,,,,,,,,,,,,,98.5,3.3,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1117645.837,Elizabethkingia anophelis C08,C08,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN30929146,1117645,,,,,,,,2022-09-28T00:00:00Z,35852325,PRJNA882201,GCA_025449135.1,CP104875,,,PacBio Sequel,1348,HGAP v. not specified,1,0,1,4045260,35.762077,3799,3668,blood,,2012-12-08,Taiwan,Taiwan,,female,73,Penumonia,,"host_description:The E. anophelis C08 strain was obtained from the Microbial Infections Reference Laboratory of the National Health Research Institutes, Taiwan. The clinical isolate was obtained from a female patient with bacteremia;host_disease_outcome:death;host_disease_stage:ICU;host_health_state:ICU;host_subject_id:08",,,,,,,,,,,,collected_by:National Health Research Institutes,,,,,,,Penumonia,ICU,death,"The E. anophelis C08 strain was obtained from the Microbial Infections Reference Laboratory of the National Health Research Institutes, Taiwan. The clinical isolate was obtained from a female patient with bacteremia",ICU,,,,,,,,,,99.2,2.8,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1117645.874,Elizabethkingia anophelis Ytc,Ytc,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN34152478,1117645,,,,,,,,2023-06-26T00:00:00Z,,PRJNA954589,,CP128315,,,Illumina NovaSeq,112.0x,other (bwa) v. 07.17-r1188,1,0,1,4058535,35.464947,3861,3697,blood,,2022-09-10,Turkey,Turkey,,,,blood infection,,,,,,,,,,,,,,collected_by:Yeliz TANRIVERDI CAYCI,,,,,,,blood infection,,,,,,,,,,,,,,99.1,2.7,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1117645.876,Elizabethkingia anophelis EAV_VTKC53,EAV_VTKC53,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA12009939,1117645,,,,,,,,2023-06-01T00:00:00Z,,PRJEB49667,,OX596083,,,,,,1,0,1,4120123,35.63799,3858,3767,sputum,,2020-09-05,Viet Nam,Viet Nam,,,,,,host_health_state:diseased,,,,,,,,,,,,collected_by:108 Military Central Hospital,,,,,,,,diseased,,,,,,,,,,,,,98.1,3.4,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1117645.877,Elizabethkingia anophelis EAV_NNN508,EAV_NNN508,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA112835271,1117645,,,,,,,,2023-06-01T00:00:00Z,,PRJEB49667,,OX596082,,,,,,1,0,1,4139199,35.797867,3909,3818,sputum,,2021-04-07,Viet Nam,Viet Nam,,,,,,host_health_state:diseased,,,,,,,,,,,,collected_by:108 Military Central Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.3,2.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1117645.878,Elizabethkingia anophelis EAV_NVB490,EAV_NVB490,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA12009938,1117645,,,,,,,,2023-06-01T00:00:00Z,,PRJEB49667,,OX596081,,,,,,1,0,1,4139197,35.797935,3910,3820,bronchial fluid,,2021-04-02,Viet Nam,Viet Nam,,,,,,host_health_state:diseased,,,,,,,,,,,,collected_by:108 Military Central Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.3,2.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1117645.879,Elizabethkingia anophelis EAV_NVH72,EAV_NVH72,Elizabethkingia anophelis,Elizabethkingia,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA12009940,1117645,,,,,,,,2023-06-01T00:00:00Z,,PRJEB49667,,OX596084,,,,,,1,0,1,4167098,35.791527,3952,3849,sputum,,2021-03-29,Viet Nam,Viet Nam,,,,,,host_health_state:diseased,,,,,,,,,,,,collected_by:108 Military Central Hospital,,,,,,,,diseased,,,,,,,,,,,,,98.7,3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1118202.5,Cruoricaptor ignavus strain M1214,M1214,Cruoricaptor ignavus,Cruoricaptor,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN16424887,1118202,,,,,,,,2020-10-27T00:00:00Z,,PRJNA668829,GCA_014961145.1,CP063145,,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,35.0x,Unicycler v. SEP-2020; Flye v. SEP-2020,1,0,1,2120336,45.216137,2127,2012,blood culture,,2019,Australia,Australia,,,,Bacteremia,,,,,,,,,,,,,Cruoricaptor ignavus genome,collected_by:Queensland Health,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia NHP,1121115.14,Blautia wexlerae DSM 19850,DSM 19850,Blautia wexlerae,Blautia,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222668,1121115,,,,,,DSM:19850,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148125.1,CP102267,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4685728,41.496304,4681,4296,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.37,0,,,Other,- HP,1121364.5,Corynebacterium massiliense DSM 45435,DSM 45435,Corynebacterium massiliense,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13404539,1121364,,,,,,DSM:45435,,2023-02-13T00:00:00Z,,PRJNA532615,,CP063189,,,Illumina MiSeq; Oxford Nanopore MinION,121.0x,Newbler v. 2.8; canu v. 1.6,1,0,1,2237865,64.80364,1995,1987,osteoarticular infection,,,France,"France: Marseille, Timone Hospital",,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 45435,,,,,,,,,,,,,,,,,,,,,98.3,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1122984.13,Prevotella intermedia ATCC 25611 = DSM 20706 strain ATCC 25611,ATCC 25611,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN04529094,1122984,,,,,,ATCC: 25611,Yes,2017-01-18T00:00:00Z,,PRJNA313956,GCF_001953955.1,"CP019300,CP019301","NZ_CP019300.1,NZ_CP019301.1",The Forsyth Institute,PacBio,200.0x,Celera Assembler v. June 2016; HGAP v.,2,,2,2674170,43.44,2643,2283,empyema,,1984,USA,United States,,,,Empyema,,,,,,,,,C,,,,Re-sequencing of the Prevotella intermedia type strain ATCC25611 and clinical isolate Prevotella intermedia strain-17 (January 2016) using using a PacBio RS II system (Pacific Biosciences) on a single-molecule real-time (SMRT) cell using PacBio P6-C4 chemistry.,collected_by:LV Holdeman,,,,,,,Empyema,,,,,,,,,,,,,,100,2.5,Respiratory Diseases,Empyema,Other,Respiratory Diseases-Empyema HP,1134687.163,Klebsiella michiganensis strain C52,C52,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289379,1134687,,,,MLST.Klebsiella_oxytoca.108,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931605.1,"CP042545,CP042546,CP042547,CP042548,CP042549,CP042550",,University of Oxford,Oxford Nanopore MiniION,3273x,Unicycler v. SEP-2017,1,5,6,6312326,55.849747,6278,5998,clinical sample,,2014-06-01,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,1.95,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1134687.167,Klebsiella michiganensis strain F107,F107,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07411959,1134687,,,,,,,,2020-01-27T00:00:00Z,,PRJNA395651,GCA_009930855.1,"CP024643,CP024641,CP024642",,Peking University People's Hospital,PacBio,79.8x,SOAPdenovo v. 2.3.0,1,2,3,6152545,55.381634,6293,5963,sputum,,2014-11-07,China,China: Fujian Province,,female,,premature,,,,,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella michiganensis isolate F107,collected_by:Fujian Provincial Hospital,,,,,,,premature,,,,,,,,,,,,,,99.98,0.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1134687.254,Klebsiella michiganensis strain 7525,7525,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16931445,1134687,,,,,,,,2020-12-13T00:00:00Z,,PRJNA681062,GCA_015999385.1,"CP065474,CP065475",,Zhejiang Provincial People's Hospital,Oxford Nanopore MinION,200x,unicycler v. 0.4.8,1,1,2,6244801,55.272747,6247,5864,urine,,2020-09-25,China,China: Zhejiang,,,,Urinary tract infection,,,,,,,,,,,,,Chromosome and plasmid sequencing of Klebsiella oxytoca strain. Co-occurrence of blaNDM-1 and blaIMP-4 on a single plasmid,collected_by:Xi Li;sample_type:not applicable,hospital,urine,,,,,Urinary tract infection,,,,,,,,,,hospital,,,,100,1.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1134687.280,Klebsiella michiganensis strain Kmfe267,Kmfe267,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18138829,1134687,,,,,,,,2021-03-13T00:00:00Z,,PRJNA638288,GCA_017348855.1,"CP071393,CP071394,CP071395,CP071396,CP071397,CP071398",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore MinION; Illumina HiSeq,50.0x,Unicycler v. v0.4.8,1,5,6,6398286,55.5202,6332,5944,urine,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-05-14,China,China:Hengyang,,,,infection,,,,,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:XiaoTuan Zhang,,,,,,,infection,,,,,,,,,,,,,,100,0.71,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1134687.296,Klebsiella michiganensis strain CZ598,CZ598,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18753391,1134687,,,,,,,,2021-04-27T00:00:00Z,,PRJNA722384,GCA_018140945.1,"CP073305,CP073306,CP073307,CP073308,CP073309",,Charles University in Prague,PacBio Sequel,560X,Microbial assembly v. 1.1,1,4,5,6494581,55.41067,6465,6072,urine,,2019-12-02,Czech Republic,Czech Republic: Pilsen,,,,kidney failure,,,,,,,,,,,,,Molecular characterization of GES-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:FNP,,,,,,,kidney failure,,,,,,,,,,,,,,100,1.14,Urinary Tract Diseases,Upper UTI/Kidney Diseases,Urinary Tract,Urinary Tract Diseases-Upper UTI/Kidney Diseases HP,1134687.629,Klebsiella michiganensis Kox58,Kox58,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286118,1134687,,,,,,,,2021-12-19T00:00:00Z,,PRJNA781656,GCA_021228695.1,"CP089395,CP089396,CP089397,CP089398",,,Oxford Nanopore MinION; Illumina HiSeq,37x,Flye v. v2.8,1,3,4,6355275,55.728825,6298,5938,urine,,2018-04-17,Australia,Australia: Melbourne,,,,urinary tract infection,,,,,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1134687.630,Klebsiella michiganensis Kox101,Kox101,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286126,1134687,,,,MLST.Klebsiella_oxytoca.116,,,,2021-12-19T00:00:00Z,,PRJNA781656,GCA_021228755.1,"CP089407,CP089408,CP089409,CP089410",,,Oxford Nanopore MinION; Illumina HiSeq,17x,Flye v. v2.8,1,3,4,6472862,55.765812,6497,6115,urine,,2018-06-03,Australia,Australia: Melbourne,,,,urinary tract infection,,,,,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,99.7,0.65,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1134687.631,Klebsiella michiganensis K92,K92,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23799016,1134687,,,,MLST.Klebsiella_oxytoca.27,,,,2021-12-19T00:00:00Z,,PRJNA787404,GCA_021228855.1,CP089315,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,6108919,56.002903,6004,5690,sputum,,2017,China,China: Zhejiang,,,,Pulmonary infection,,,,,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,0.67,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1134687.637,Klebsiella michiganensis KO_408,KO_408,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25236446,1134687,,,,,genotype:ST-265,,,2022-02-10T00:00:00Z,,PRJNA800235,GCA_022163245.2,"CP091470,CP091471,CP091472,CP091473,CP091474,CP091475",,,Illumina; Oxford Nanopore,150.0x,Unicycler hybrid assembly v. 0.4.4,1,5,6,6475028,55.47298,6447,6068,respiratory culture,,2018,Japan,Japan,,male,71,Pnuemonia,,,,,,,,,,,,,,collected_by:TMDU_Hospital staff,,,,,,,Pnuemonia,,,,,,,,,,,,,,100,0.87,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1134687.670,Klebsiella michiganensis K342,K342,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26455295,1134687,,,,MLST.Klebsiella_oxytoca.85,,,,2022-03-15T00:00:00Z,,PRJNA813204,GCA_022569835.1,CP093010,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,6006113,56.00842,5869,5584,sputum,,2019,China,China: Zhejiang,,,,Pulmonary infection,,,,,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,1.02,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1134687.687,Klebsiella michiganensis K254,K254,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26455257,1134687,,,,,,,,2022-04-24T00:00:00Z,,PRJNA813202,GCA_023093835.1,CP095761,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,5884314,55.677094,5802,5521,urine,,2017,China,China: Zhejiang,,,,Urinary tract infection,,,,,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.9,0.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1134687.700,Klebsiella michiganensis 5088,5088,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174081,1134687,,,,MLST.Klebsiella_oxytoca.11,genotype:ST11,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917295.1,"CP103554,CP103555,CP103556",,,Oxford Nanopore GridION,88x,Flye v. 2.8.3-b1695,1,2,3,6243900,55.798733,6108,5800,blood,,2019-06-26,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1134687.750,Klebsiella michiganensis S4_CRE4,S4_CRE4,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387624,1134687,,,,MLST.Klebsiella_oxytoca.50,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074449,CP074450,CP074451,CP074452,CP074453",,,Illumina NextSeq; PacBio Sequel,395x,Unicycler v. v0.4.7,1,4,5,6149943,55.88195,6024,5685,"urine, clean catch",,2017-01-26,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,99.9,0.6,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1134687.752,Klebsiella michiganensis 2563,2563,Klebsiella michiganensis,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32737190,1134687,,,,MLST.Klebsiella_oxytoca.43,,,,2023-01-24T00:00:00Z,,PRJNA923778,,"CP116214,CP116215,CP116216,CP116217,CP116219,CP116218",,,Illumina NovaSeq; Oxford Nanopore GridION,100.0x,Unicycler v. 0.5.0,1,5,6,6720861,55.457047,6755,6317,sputum,,2018,China,China: Hangzhou,,,,pulmonary infection,,,,,,,,,,,,,,,,,,,,,pulmonary infection,,,,,,,,,,,,,,99.4,0.4,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1138383.22,Mycobacterium paraintracellulare strain M021,M021,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258723,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016755955.1,AP024259,,Niigata University School of Medicine,PacBio RS II,159x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5412210,68.078476,5184,5120,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.88,0.33,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.23,Mycobacterium paraintracellulare strain M001,M001,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258727,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756035.1,AP024240,,Niigata University School of Medicine,PacBio RS II,61x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5739349,67.97537,5549,5465,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.04,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.24,Mycobacterium paraintracellulare strain M019,M019,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258726,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756015.1,AP024257,,Niigata University School of Medicine,PacBio RS II,129x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5615686,67.99328,5435,5358,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.25,Mycobacterium paraintracellulare strain M011,M011,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258728,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756055.1,"AP024251,AP024252",,Niigata University School of Medicine,PacBio RS II,104x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5357612,68.11994,5132,5078,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.26,Mycobacterium paraintracellulare strain M003,M003,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258740,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756295.1,AP024243,,Niigata University School of Medicine,PacBio RS II,103x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5533584,68.05407,5267,5197,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.04,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.27,Mycobacterium paraintracellulare strain M020,M020,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258739,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756275.1,AP024258,,Niigata University School of Medicine,PacBio RS II,163x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5429978,68.035706,5254,5189,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1138383.28,Mycobacterium paraintracellulare strain M015,M015,Mycobacterium paraintracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258724,1138383,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016755975.1,AP024253,,Niigata University School of Medicine,PacBio RS II,98x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5588488,68.01181,5345,5281,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1151001.14,Salmonella enterica subsp. enterica serovar Napoli strain 16-174478,16-174478,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14150057,1151001,Napoli,,,MLST.Salmonella_enterica.2095,,,,2021-02-11T00:00:00Z,,PRJNA607884,GCA_016864955.1,CP063140,,IZSVenezie,Oxford Nanopore; Illumina MiSeq; Illumina,120.0x,UNICYCLER v. 0.4.9b,1,0,1,4691273,52.164944,4854,4442,"ospedale s. maria delle grazie (napoli, italy)",isolated in a human case,2012-11,Italy,Italy:Naples,,,,salmonellosis,,,,,,,,,,,,,"This study reports the WGS data of a S.Napoli strain carrying a plasmid encoding for blaCTX-M-15 gene isolated in a human case. The identification of S. Napoli isolates able to produce ESBLs would be of great concern, as this pathogen is frequently associated to invasive infections and a higher risk of bacteraemia especially in young patients, and its reservoir has not been clearly identified yet",collected_by:Carmen Losasso,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1160769.22,Salmonella enterica subsp. enterica serovar Worthington strain 7101.67,7101.67,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11445819,1160769,Worthington,,,MLST.Salmonella_enterica.592,,,,2019-04-30T00:00:00Z,,PRJNA533232,GCA_004923395.1,"CP039503,CP039504,CP039505,CP039506,CP039507,CP039508",,University of Bern,Oxford Nanopore MiniION; Illumina NovaSeq,40.0x,Canu v. 1.7.1; Pilon v. 1.22,1,5,6,4897162,52.222614,5016,4715,stools,,2018-11,Switzerland,Switzerland: Bern,,male,,Diarrhea,,,,,,,,,,,,,Whole genome sequencing of Salmonella enterica subsp. enterica serovar Worthington before and after blaDHA-1 gene acquisition,"collected_by:Insel Spital, Bern, Switzerland",,,,,,,Diarrhea,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1160769.23,Salmonella enterica subsp. enterica serovar Worthington strain 7102.58,7102.58,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11445820,1160769,Worthington,,,MLST.Salmonella_enterica.592,,,,2019-04-30T00:00:00Z,,PRJNA533232,GCA_004923415.1,"CP039509,CP039512,CP039511,CP039510,CP039515,CP039514,CP039513",,University of Bern,Oxford Nanopore MiniION; Illumina NovaSeq,40.0x,Canu v. 1.7.1; Pilon v. 1.22,1,6,7,4989762,52.235138,5167,4852,stools,,2018-11,Switzerland,Switzerland: Bern,,male,,Diarrhea,,,,,,,,,,,,,Whole genome sequencing of Salmonella enterica subsp. enterica serovar Worthington before and after blaDHA-1 gene acquisition,"collected_by:Insel Spital, Bern, Switzerland",,,,,,,Diarrhea,,,,,,,,,,,,,,100,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1173427.6,Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189,CFSAN000189,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04364135,1173427,Bareilly,,,MLST.Salmonella_enterica.909,,,,2019-11-15T00:00:00Z,31704961,PRJNA498670,GCA_009667855.1,"CP034177,CP034178",,USDA,Oxford Nanopore MiniION,599.0x,Unicycler v. 10-2018,1,1,2,4806620,52.210037,4892,4663,none,,,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Sequenced two of the most prominent foodborne pathogens that cause severe human illnesses worldwide, Enterohemorrhagic Escherichia coli O157:H7 and Salmonella enterica subsp. enterica serovar Bareilly with Oxford Nanopore’s MinION sequencer, and the whole genomes of both samples were assembled and polished with only a 0.1% error rate.",collected_by:PHE,,,,,,,Not available,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1177574.95,Prevotella jejuni strain F0106,F0106,Prevotella jejuni,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352180,1177574,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128105.1,"CP072365,CP072366",,The Forsyth Institute,PacBio Sequel,182x,Pacbio MA v. 9.0.0.92188,2,0,2,4115533,41.971695,3600,3048,human oral cavity,,1988-08,USA,"USA: Blacksberg, Virginia",,male,12,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02171;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,98.99,0,,,Oral,- NHP,1177574.96,Prevotella jejuni strain F0697,F0697,Prevotella jejuni,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352195,1177574,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128085.1,"CP072363,CP072364",,The Forsyth Institute,PacBio Sequel,175x,Flye v. 2.8,2,0,2,3944801,41.73019,3566,2986,human oral cavity,,1987-03,USA,"USA: Blacksberg, Virginia",,male,12,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02172;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.32,0,,,Oral,- HP,1185650.1046,Mycobacteroides abscessus subsp. abscessus strain GD38,GD38,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431561,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183555.1,CP063318,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,66x,Unicycler v. 0.4.8,1,0,1,5182416,64.16098,5168,5036,clinical patient,isolated from patients around the world,2019,Canada,"Canada: Hamilton, ON",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Hamilton General Hospital,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.08,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1047,Mycobacteroides abscessus subsp. abscessus strain GD22,GD22,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431558,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183775.1,"CP063324,CP063325,CP063326",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,51x,Unicycler v. 0.4.8,1,2,3,5111734,64.13984,5081,4976,clinical patient,isolated from patients around the world,2019,USA,"USA: Pittsburgh, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of Pittsburgh Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1048,Mycobacteroides abscessus subsp. abscessus strain GD25,GD25,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431559,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183655.1,"CP063320,CP063321,CP063322,CP063323",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,70x,Unicycler v. 0.4.8,1,3,4,5194754,64.185486,5209,5073,clinical patient,isolated from patients around the world,2019,USA,"USA: Anchorage, AL",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Alaska Regional Hospital,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1049,Mycobacteroides abscessus subsp. abscessus strain GD26,GD26,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431560,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183735.1,CP063319,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,86x,Unicycler v. 0.4.8,1,0,1,5098671,64.13248,5075,4969,clinical patient,isolated from patients around the world,2019,USA,"USA: Pittsburgh, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of Pittsburgh Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.33,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1050,Mycobacteroides abscessus subsp. abscessus strain GD19,GD19,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431556,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183815.1,"CP063328,CP063329",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,64x,Unicycler v. 0.4.8,1,1,2,4933928,64.212776,4921,4815,clinical patient,isolated from patients around the world,2019,USA,"USA: San Diego, CA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,"collected_by:University of California, San Diego Health",,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1051,Mycobacteroides abscessus subsp. abscessus strain GD20,GD20,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16431557,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183795.1,CP063327,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,52x,Unicycler v. 0.4.8,1,0,1,5026147,64.136604,4981,4881,clinical patient,isolated from patients around the world,2019,USA,"USA: Durham, NC",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of North Carolina Hospitals,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1052,Mycobacteroides abscessus subsp. abscessus strain GD17,GD17,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16428209,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA668996,GCA_017183835.1,CP063165,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,272.0x,Unicycler v. 0.4.8,1,0,1,5107403,64.127014,5094,4997,clinical patient,,2019,USA,"USA: Chapel Hill, NC",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,Genomes of clinically-isolated Mycobacterium abscessus strains,collected_by:University of North Carolina Hospitals,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1053,Mycobacteroides abscessus subsp. abscessus strain GD100B,GD100B,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828771,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183875.1,"CP065183,CP065184",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,117x,Unicycler v. 0.4.8,1,1,2,5150786,64.11616,5142,5027,clinical patient,isolated from patients around the world,2020,USA,"USA: Philadelphia, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Penn Medicine,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1054,Mycobacteroides abscessus subsp. abscessus strain GD100A,GD100A,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828770,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183895.1,"CP065263,CP065264",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,134x,Unicycler v. 0.4.8,1,1,2,5150786,64.116135,5142,5027,clinical patient,isolated from patients around the world,2020,USA,"USA: Philadelphia, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Penn Medicine,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1055,Mycobacteroides abscessus subsp. abscessus strain GD69B,GD69B,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828768,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183935.1,"CP065266,CP065267,CP065268",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,108x,Unicycler v. 0.4.8,1,2,3,5210349,64.17121,5236,5110,clinical patient,isolated from patients around the world,2019,USA,"USA: Long Beach, CA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Long Beach Memorial Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1056,Mycobacteroides abscessus subsp. abscessus strain GD69A,GD69A,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828767,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183955.1,"CP065269,CP065270,CP065271",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,77x,Unicycler v. 0.4.8,1,2,3,5210348,64.1712,5232,5111,clinical patient,isolated from patients around the world,2019,USA,"USA: Long Beach, CA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Long Beach Memorial Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1057,Mycobacteroides abscessus subsp. abscessus strain GD59,GD59,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828764,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017189355.1,CP065274,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,71x,Unicycler v. 0.4.8,1,0,1,5073623,64.13381,5039,4932,clinical patient,isolated from patients around the world,2019,USA,"USA: Chapel Hill, NC",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of North Carolina Hospitals,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1058,Mycobacteroides abscessus subsp. abscessus strain GD57,GD57,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828763,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017189375.1,CP065275,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,79x,Unicycler v. 0.4.8,1,0,1,5120346,64.1236,5114,5003,clinical patient,isolated from patients around the world,2019,Spain,Spain: Barcelona,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Vall d'Hebron University Hospital,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1059,Mycobacteroides abscessus subsp. abscessus strain GD54,GD54,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828762,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017189395.1,"CP065276,CP065277",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,125x,Unicycler v. 0.4.8,1,1,2,5186935,64.0983,5247,5096,clinical patient,isolated from patients around the world,2019,Australia,Australia: New South Wales,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:The Children's Hospital at Westmead,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1060,Mycobacteroides abscessus subsp. abscessus strain GD43B,GD43B,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828761,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017189415.1,CP065278,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,88x,Unicycler v. 0.4.8,1,0,1,5286951,64.05121,5387,5236,clinical patient,isolated from patients around the world,2019,Australia,Australia: New South Wales,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:New South Wales Health,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1061,Mycobacteroides abscessus subsp. abscessus strain GD43A,GD43A,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828760,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017189435.1,CP065279,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,93x,Unicycler v. 0.4.8,1,0,1,5377795,64.04556,5507,5359,clinical patient,isolated from patients around the world,2019,Australia,Australia: New South Wales,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:New South Wales Health,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1062,Mycobacteroides abscessus subsp. abscessus strain GD42,GD42,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828759,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017190595.1,"CP065280,CP065281,CP065282",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,54x,Unicycler v. 0.4.8,1,2,3,5232300,64.15185,5246,5142,clinical patient,isolated from patients around the world,2019,USA,"USA: Pittsburgh, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of Pittsburgh Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1063,Mycobacteroides abscessus subsp. abscessus strain GD05,GD05,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828756,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017190795.1,CP065287,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,88x,Unicycler v. 0.4.8,1,0,1,5352395,64.08273,5429,5300,clinical patient,isolated from patients around the world,2018,USA,"USA: Winston-Salem, NC",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Naval Medical Research Center/Wake Forest Baptist Health,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.67,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1064,Mycobacteroides abscessus subsp. abscessus strain GD41,GD41,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828758,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017190695.1,CP065283,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,75x,Unicycler v. 0.4.8,1,0,1,5074858,64.133026,5039,4933,clinical patient,isolated from patients around the world,2019,USA,"USA: Pittsburgh, PA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:University of Pittsburgh Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1185650.1065,Mycobacteroides abscessus subsp. abscessus strain GD21,GD21,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828757,1185650,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017190875.1,"CP065284,CP065285,CP065286",,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,107x,Unicycler v. 0.4.8,1,2,3,5486769,63.943806,5616,5421,clinical patient,isolated from patients around the world,2019,USA,"USA: Baton Rouge, LA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,"collected_by:Our Lady of the Lake Children's Hospital, Baton Rouge, LA",,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1190508.4,Corynebacterium aquatimens strain CNCTC,CNCTC,Corynebacterium aquatimens,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN17304831,1190508,,,,,,CNCTC:7651,,2021-08-03T00:00:00Z,,PRJNA691736,GCA_019443945.1,CP068278,,"NIPH, Prague",Oxford Nanopore,40.0x,CANU v. 2019,1,0,1,2426021,64.881676,2860,2333,blood,,2019,Czech Republic,Czech Republic,,,,bacteremia,,,,,,,,,,,,,Identification of bacteria,collected_by:P Jezek,,,,,,,bacteremia,,,,,,,,,,,,,,92.82,1.81,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,119602.1853,Streptococcus dysgalactiae subsp. equisimilis MGCS36089,MGCS36089,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257648,119602,stG62647,,,MLST.Streptococcus_dysgalactiae_equisimilis.20,genotype:ST20,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117284,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2151694,39.368282,2130,1944,patient clinical isolate,,2018-10-17,France,France:French Brittany,,,,osteitis,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,osteitis,,,,,,,,,,,,,,100,0,Bone and Joint Infections,Osteitis,Other,Bone and Joint Infections-Osteitis HP,119602.1854,Streptococcus dysgalactiae subsp. equisimilis MGCS36083,MGCS36083,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257647,119602,stG62647,,,MLST.Streptococcus_dysgalactiae_equisimilis.20,genotype:ST20,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117285,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2212841,39.608086,2189,2056,patient clinical isolate,,2018-09-15,France,France:French Brittany,,,,osteitis,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,osteitis,,,,,,,,,,,,,,100,0,Bone and Joint Infections,Osteitis,Other,Bone and Joint Infections-Osteitis HP,119602.1855,Streptococcus dysgalactiae subsp. equisimilis MGCS36044,MGCS36044,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257606,119602,stG62647,,,MLST.Streptococcus_dysgalactiae_equisimilis.20,genotype:ST20,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117287,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2158391,39.38985,2122,1943,patient clinical isolate,,2018-03-30,France,France:French Brittany,,,,osteitis,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,osteitis,,,,,,,,,,,,,,100,0,Bone and Joint Infections,Osteitis,Other,Bone and Joint Infections-Osteitis HP,119602.1856,Streptococcus dysgalactiae subsp. equisimilis MGGS36055,MGGS36055,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257614,119602,stC74a,,,MLST.Streptococcus_dysgalactiae_equisimilis.17,genotype:ST17,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117286,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2204518,39.487907,2182,2014,patient clinical isolate,,2018-06-11,France,France:French Brittany,,,,osteitis,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,osteitis,,,,,,,,,,,,,,100,0,Bone and Joint Infections,Osteitis,Other,Bone and Joint Infections-Osteitis HP,119602.1857,Streptococcus dysgalactiae subsp. equisimilis MGCS35957,MGCS35957,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257456,119602,stG62647,,,MLST.Streptococcus_dysgalactiae_equisimilis.20,genotype:ST20,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117288,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2233554,39.325623,2263,2117,patient clinical isolate,,2017-03-22,France,France:French Brittany,,,,angina,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,angina,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,119602.1858,Streptococcus dysgalactiae subsp. equisimilis MGCS35823,MGCS35823,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31257356,119602,stG62647,,,MLST.Streptococcus_dysgalactiae_equisimilis.20,genotype:ST20,,,2023-03-17T00:00:00Z,,PRJNA925803,,CP117289,,,Illumina NovaSeq;Oxford Nanopore GridION,complete,Unicycler v. v0.5.0,1,0,1,2189610,39.392403,2192,2035,patient,,2015-07-08,France,France:French Brittany,,,,Erysipelas,,,,,,,,,,,,,,collected_by:Universite de Rennes,,,,,,,Erysipelas,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Erysipelas,Other,Skin and Soft Tissue Infections-Erysipelas HP,119602.1924,Streptococcus dysgalactiae subsp. equisimilis TPCH-F37,TPCH-F37,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN35689118,119602,,,,MLST.Streptococcus_dysgalactiae_equisimilis.17,,,,2023-06-19T00:00:00Z,,PRJNA982186,,CP127842,,,Illumina; Oxford Nanopore MinION,21.0x,Unicycler v. 0.4.7,1,0,1,2117261,39.509346,2087,1985,blood,,2015-10,Japan,Japan:Toyama,,,,sepsis,,,,,,,,,,,,,,collected_by:Toyama Prefecture Central Hospital,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,119602.564,Streptococcus dysgalactiae subsp. equisimilis strain 89,89,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00238723,119602,,,,MLST.Streptococcus_dysgalactiae_equisimilis.29,,,,2020-08-08T00:00:00Z,,PRJDB10330,GCA_014192695.1,AP023393,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",Illumina MiSeq; Oxford Nanopore,362x,Unicycler v. 0.4.8,1,0,1,2158609,39.4316,2147,2075,,,1998,,,,,,,,,,,Positive,Cocci,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,missing,missing,missing,missing,Complete genome sequence of three Streptococcus species,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1196159.3,Listeria monocytogenes serotype 4b str. 81-0558 strain 81-0558,81-0558,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN02713777,1196159,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167872,GCA_002213985.1,CP007525,,Public Health Agency of Canada,454 Illumina,411_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2971543,37.96,2969,2911,csf,,1981-06-01,Canada,Canada: Halifax,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1196160.3,Listeria monocytogenes serotype 4b str. 81-0592 strain 81-0592,81-0592,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN02713778,1196160,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167873,GCA_002214005.1,CP007526,,Public Health Agency of Canada,454 Illumina,328_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2975864,37.96,2976,2925,fetal blood,,1981-07-01,Canada,Canada: Halifax,,,,,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1196162.3,Listeria monocytogenes serotype 4b str. 10-0809 strain 10-0809,10-0809,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124730,1196162,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-07-03T00:00:00Z,,PRJNA167875,GCA_002214065.1,CP007167,,Public Health Agency of Canada,454 Illumina,328_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2975853,37.96,2976,2925,stool,,1981,Canada,Canada: Nova Scotia,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196163.3,Listeria monocytogenes serotype 1/2b str. 10-0810 strain 10-0810,10-0810,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124731,1196163,1/2b,,,MLST.Listeria_monocytogenes.5,,,,2017-07-03T00:00:00Z,,PRJNA167876,GCA_002214085.1,CP007168,,Public Health Agency of Canada,454 Illumina,461_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3017944,37.96,3031,2962,stool,,1996,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196166.3,Listeria monocytogenes serotype 1/2a str. 10-0813 strain 10-0813,10-0813,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124734,1196166,1/2a,,,MLST.Listeria_monocytogenes.7,,,,2017-07-03T00:00:00Z,,PRJNA167879,GCA_002214145.1,CP007171,,Public Health Agency of Canada,454 Illumina,316_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2942234,37.96,2950,2884,blood,,2000,Canada,Canada: Manitoba,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Bureau of Microbial Hazards,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196167.3,Listeria monocytogenes serotype 1/2a str. 10-4754 strain 10-4754,10-4754,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124735,1196167,1/2a,,,MLST.Listeria_monocytogenes.37,,,,2017-06-30T00:00:00Z,,PRJNA167880,GCA_002213805.1,CP007197,,Public Health Agency of Canada,454 Illumina,796_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2910922,37.98,2907,2851,csf,,2002,Canada,Canada: Quebec,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Laboratoire de la sante publique du Quebec,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196169.3,Listeria monocytogenes serotype 1/2a str. 10-0933 strain 10-0933,10-0933,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124737,1196169,1/2a,,,MLST.Listeria_monocytogenes.394,,,,2017-06-30T00:00:00Z,,PRJNA167882,GCA_002213845.1,CP007199,,Public Health Agency of Canada,454 Illumina,166_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2870277,38.02,2846,2795,blood,,2008,Canada,Canada: Quebec,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Laboratoire de la sante publique du Quebec,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196171.3,Listeria monocytogenes serotype 4b str. 02-1103 strain 02-1103,02-1103,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124739,1196171,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167884,GCA_002213885.1,CP007459,,Public Health Agency of Canada,454 Illumina,1049_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2979105,37.95,2979,2918,csf,,2002,Canada,Canada: British Columbia,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:BC Centre for Disease Control Site,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196172.3,Listeria monocytogenes serotype 4b str. 02-1289 strain 02-1289,02-1289,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124740,1196172,4b,,,MLST.Listeria_monocytogenes.1,,,,2017-06-30T00:00:00Z,,PRJNA167885,GCA_002213925.1,CP007460,,Public Health Agency of Canada,454 Illumina,1086_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2979105,37.95,2979,2918,stool,,2002,Canada,Canada: British Columbia,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:BC Centre for Disease Control Site,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196174.3,Listeria monocytogenes serotype 4b str. 02-6679 strain 02-6679,02-6679,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN02944848,1196174,4b,,,MLST.Listeria_monocytogenes.388,,,,2017-06-30T00:00:00Z,,PRJNA167887,GCA_002213505.1,CP008821,,Public Health Agency of Canada,454 Illumina,1058x,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2908004,38,2873,2825,stool,,2002,Canada,Canada: Vancouver,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,collected_by:Public Health Agency of Canada,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196177.3,Listeria monocytogenes serotype 1/2a str. 95-0093 strain 95-0093,95-0093,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124743,1196177,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167890,GCA_002213685.1,CP007019,,Public Health Agency of Canada,454 Illumina,875_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3000273,37.96,3031,2950,blood,,1995,Canada,Canada: Alberta,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Provlab Alberta,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196178.3,Listeria monocytogenes serotype 1/2a str. 98-2035 strain 98-2035,98-2035,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124744,1196178,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167891,GCA_002213705.1,CP007020,,Public Health Agency of Canada,454 Illumina,418_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3032209,37.96,3071,2993,blood,,1998,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196179.3,Listeria monocytogenes serotype 1/2a str. 99-6370 strain 99-6370,99-6370,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124745,1196179,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167892,GCA_002213725.1,CP007021,,Public Health Agency of Canada,454 Illumina,758_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,3032209,37.96,3072,2993,blood,,1999,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196180.3,Listeria monocytogenes serotype 1/2a str. 02-5993 strain 02-5993,02-5993,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124746,1196180,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167893,GCA_002213545.1,CP007007,,Public Health Agency of Canada,454 Illumina,946_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999248,37.97,3028,2948,blood,,2002,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196181.4,Listeria monocytogenes serotype 1/2a str. 04-5457,04-5457,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124747,1196181,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167894,GCA_002213565.1,CP007008,,Public Health Agency of Canada,454 Illumina,795_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999326,37.97,3026,2948,blood,,2004,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196186.3,Listeria monocytogenes serotype 1/2a str. 08-7669 strain 08-7669,08-7669,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124750,1196186,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167899,GCA_002213625.1,CP007011,,Public Health Agency of Canada,454 Illumina,115_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2954577,38.01,2959,2889,blood,,2008,Canada,Canada: Saskatchewan,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196189.3,Listeria monocytogenes serotype 1/2a str. 10-1046 strain 10-1046,10-1046,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124751,1196189,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167902,GCA_002213645.1,CP007017,,Public Health Agency of Canada,454 Illumina,120_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2998206,37.97,3026,2941,blood,,2010,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1196191.3,Listeria monocytogenes serotype 1/2a str. 10-1321 strain 10-1321,10-1321,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07124752,1196191,1/2a,,,,,,,2017-06-30T00:00:00Z,,PRJNA167904,GCA_002213665.1,CP007018,,Public Health Agency of Canada,454 Illumina,315_X,Newbler v. 2.5.3 CLC genomics workbench v.,1,,1,2999326,37.97,3026,2947,blood,,2010,Canada,Canada: Ontario,,,,Listeriosis,,,,,,,,,,,,,Whole genome sequencing and comparison of Listeria monocytogenes Canadian food outbreaks,sample_type:Homo Sapien;collected_by:Public Health Agency of Canada;biomaterial_provider:Public Health Ontario,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,119857.200,Francisella tularensis subsp. holarctica strain B-8367,B-8367,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN12754423,119857,,,,,,,,2020-02-06T00:00:00Z,,PRJNA565628,GCA_010232785.1,CP044002,,Irkutsk Antiplague Research Institute of Siberia and Far East,Illumina MiSeq,212x,BWA v. 0.7.17,1,0,1,1892749,32.151966,2167,1886,far east of russian federation,isolated from Far East of Russian Federation,1975,Russia,Russia: Khabarovsk,,,,tularemia,,,,,,,,,,,,,Molecular genetic analysis of Francisella tularensis strains isolated from Far East of Russian Federation. Strains were isolated from various sources in the same region at the different time,collected_by:Irkutsk Antiplague Research Institute of Siberia and the Far East,,,,,,,tularemia,,,,,,,,,,,,,,99.82,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,119857.202,Francisella tularensis subsp. holarctica strain B-8365,B-8365,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN12754421,119857,,,,,,,,2020-02-06T00:00:00Z,,PRJNA565628,GCA_010233165.1,CP044004,,Irkutsk Antiplague Research Institute of Siberia and Far East,Illumina MiSeq,205x,BWA v. 0.7.17,1,0,1,1893151,32.146458,2162,1894,far east of russian federation,isolated from Far East of Russian Federation,1966,Russia,Russia: Khabarovsk,,,,tularemia,,,,,,,,,,,,,Molecular genetic analysis of Francisella tularensis strains isolated from Far East of Russian Federation. Strains were isolated from various sources in the same region at the different time,collected_by:Irkutsk Antiplague Research Institute of Siberia and the Far East,,,,,,,tularemia,,,,,,,,,,,,,,99.82,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,119857.297,Francisella tularensis subsp. holarctica strain 2015321842,2015321842,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737166,119857,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019134795.1,CP073125,,USAMRIID,PacBio,200x,HGAP v. 4,1,0,1,1890509,32.175358,2173,1849,pleural,,2015,USA,USA: KY,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:Minnesota Public Health,,,,,,,Tularemia,,,,,,,,,,,,,,99.41,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,119857.376,Francisella tularensis subsp. holarctica A-1341,A-1341,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMEA5971373,119857,,,,,,,,2022-11-28T00:00:00Z,,PRJEB33006,,CP098826,,,"Oxford Nanopore, Illumina MiSeq",100.0x,Unicycler v. 0.4.7,1,0,1,1893440,32.15122,2167,1942,human,,2018,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1200752.3,Escherichia coli NCCP15648,NCCP15648,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN02928551,1200752,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2017-08-02T00:00:00Z,,PRJNA168631,GCA_003433275.1,"CP009050,CP009051,CP009052,CP009053",,Yonsei University,HiSeq2000,"1,205x",CLC Genomics workbench v. 5.1,1,3,4,5588834,50.603848,5710,5343,stool,isolated from a patient with diarrhea and has Shiga-like toxin genes and eaeA,2001,South Korea,South Korea,,,,diarrhea,,,,,Negative,,,Mesophilic,,Facultative,HostAssociated,,Escherichia coli NCCP15648 was isolated from a patient with diarrhea and has Shiga-like toxin genes and eaeA. The genome sequence will be used for comparative analysis with those of other pathogenic E. coli strains.,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,120683.5,Treponema sp. OMZ 804,OMZ 804,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253843,69710,,,,,,ATCC:700766,,2020-02-10T00:00:00Z,,PRJNA602574,GCA_010365865.1,CP048020,,The University of Hong Kong,Illumina HiSeq; Oxford Nanopore MiniION,260.0x,Canu v. 1.8,1,0,1,2980180,44.319202,3149,2778,subgingival plaque,isolated from the dental plaque of a patient with periodontitis in Switzerland in 1994,1994,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,"Treponema sp. ATCC 700766 was isolated from the dental plaque of a patient with periodontitis in Switzerland in 1994. This strain is also known as T. vincentii (ex Brumpt) Smibert (ATCC 700766), OMZ 804[MH1F1].",,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,99.19,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases NHP,1211813.138,Alistipes ihumii AP11,AP11,Alistipes ihumii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222633,1211813,,,,,,,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025144665.1,CP102294,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2780015,57.88555,2703,2197,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:Laboratory of Didier Raoult,not applicable,not applicable,not applicable,https://www.ncbi.nlm.nih.gov/nuccore/NZ_ACOK01000005.3,,,,,,,,,,,,,not applicable,,,,100,0.48,,,Other,- HP,1214063.4,Mycobacterium intracellulare M.i.198,M.i.198,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258721,1214063,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016755915.1,AP024265,,Niigata University School of Medicine,PacBio RS II,73x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5445552,68.04785,5355,5277,sputum,,2005,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.62,0.05,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1226751.7,Mycolicibacterium monacense DSM 44395,DSM 44395,Mycolicibacterium monacense,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN10880098,1226751,,,,,,DSM:44395,,2020-01-27T00:00:00Z,,PRJNA521103,GCA_009931355.1,CP035734,,Uppsala University,PacBio,56.0x,SMART-HGAP v. v.3,1,0,1,6019539,68.41203,5886,5757,bronchial lavage sample,isolated from lung and open wound infections,1998,Germany,Germany:Munich,temperature:37,,,,,,,,,,,,,,,,"Mycolicibacterium monacense is a non-tuberculous, rapidly growing mycobacteria (RGM) that forms smooth, yellow, scotochromogenic colonies within 5-7 days on L-J medium. It has been isolated from lung and open wound infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.81,0.13,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1226753.6,Mycolicibacterium mucogenicum DSM 44124,DSM 44124,Mycolicibacterium mucogenicum,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08339096,1226753,,,,,,DSM:44124,,2020-12-18T00:00:00Z,"31215393,31848383",PRJNA429429,GCA_005670685.2,POTL00000000,,,PacBio,101.0x,SMART-analysis HGAP3 assembly pipeline v.,1,0,1,6099273,67.23395,5975,5879,cause of peritonitis,,,USA,USA: Seattle,temperature:37,,,,,,,,,,,,,,,,,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,99.9,0.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1232428.41,Megasphaera massiliensis strain NBRC 114414,NBRC 114414,Megasphaera massiliensis,Megasphaera,Veillonellaceae,Veillonellales,Negativicutes,Bacillota,SAMN21163591,1232428,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181515.1,CP084019,,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,328.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,0,1,2610024,50.591297,2431,2337,human feces,,2019,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.6,,,Gastrointestinal,- HP,1236517.6,Prevotella fusca JCM 17724 strain W1435,W1435,Prevotella fusca,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352204,1236517,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128145.1,"CP072370,CP072369",,The Forsyth Institute,PacBio Sequel,390x,Flye v. 2.8,2,0,2,3261788,44.12433,3036,2526,human oral cavity,,1985,United Kingdom,United Kingdom: Cardiff,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02169;collected_by:William Wade, King's College London",human oral cavity,,,,Genome analysis of human oral bacteria,,,periodontitis,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1236518.39,Prevotella scopos JCM 17725 strain W2052,W2052,Prevotella scopos,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352205,1236518,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127785.1,"CP072389,CP072390,CP072391",,The Forsyth Institute,PacBio Sequel,319x,Flye v. 2.8,2,1,3,3304345,40.74744,2790,2540,human oral cavity,,1988,United Kingdom,United Kingdom: Cardiff,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02186;collected_by:William Wade, King's College London",human oral cavity,,,,Genome analysis of human oral bacteria,,,periimplantitis,,,,,,,,,human oral cavity,,,,99.32,0.17,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,123899.25,Bordetella trematum strain CBM01,CBM01,Bordetella trematum,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10962613,123899,,,,,,,,2020-03-19T00:00:00Z,,PRJNA523013,GCA_011463375.1,CP036357,,Universidade Federal de Santa Maria,Illumina MiSeq,26.0x,SPAdes v. 3.13.0,1,0,1,4518493,65.76725,3976,3841,ulcer tissue; necrotic ulcer,"recovered from necrotic ulcer, aiming to describe its virulence and resistance genes",2016-02-12,Brazil,Brazil,,,,,,,,,,,,,,,,,"Bordetella trematum is an infrequent Gram-negative coccobacillus, with a reservoir, pathogenesis, a life cycle and a virulence level which has been poorly elucidated and understood. Related information is scarce due to the low frequency of isolates. We performed whole-genome sequencing of an isolate recovered from necrotic ulcer, aiming to describe its virulence and resistance genes.",sample_type:Bacteria;collected_by:Hospital staff,,,,,,,,,,,,,,,,,,,,,99.07,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1241982.8,Chryseobacterium nakagawai strain NCTC13529,NCTC13529,Chryseobacterium nakagawai,Chryseobacterium,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA24550918,1241982,not available: to be reported later,,,,,NCTC:13529,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900637665.1,LR134386,,SC,,,,1,,1,5602501,35.395317,5295,5135,kidney abscess,,1900-2013,United Kingdom,United Kingdom: Gloucester,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0.49,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1247414.3,Neisseria gonorrhoeae NG-k51.05,NG-k51.05,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN02380725,1247414,,,,,,,,2017-01-18T00:00:00Z,,PRJNA223523,GCA_001956715.1,"CP003974,CP003975",,RIPCM,454; IonTorrent,23,"Newbler, Sspace v. 2.6, 03.2013",1,1,2,2236743,52.37866,2783,2203,male,isolated in 2005,2005,Russia,Russia: Kaluga,,,,gonorrhea,,,,,Negative,Cocci,No,,,,,,"Neisseria gonorrhoeae NG-k51.05 was isolated in 2005. This is a multidrug-resistant strain and will be used to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism.;many frameshifted proteins",collected_by:RIPCM,,,,,,,gonorrhea,,,,,,,,,,,,,,99.4,0.36,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,1260.177,Finegoldia magna strain FDAARGOS_764 strain Not applicable,Not applicable,Finegoldia magna,Finegoldia,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMN11056479,1260,,,,,,FDA:FDAARGOS_764,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267535.1,CP054000,,US Food and Drug Administration,Pacbio; Illumina,1616.75x,"SMRT v. 2.3.0, HGAP v. 3",1,0,1,2090058,31.992174,1987,1944,vagina,,,USA,USA:VA,,female,,Bacterial vaginosis,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Bacterial vaginosis,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.39,0,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,126385.91,Providencia alcalifaciens 2939/90,2939/90,Providencia alcalifaciens,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32951864,126385,,,,,,,,2023-05-10T00:00:00Z,,PRJNA929094,,"CP116943,CP116944,CP116945,CP116946,CP116947",,,Oxford Nanopore,536.0x,dragonflye v. 1.0.13,1,4,5,4365872,41.739887,4330,4092,rectal swab,,1990,Bangladesh,Bangladesh,,,,Diarrhea,,host_disease_outcome:death;host_disease_stage:postmortem;host_health_state:postmortem,,,,,,,,,,,,collected_by:M. John Albert,,,,,,,Diarrhea,postmortem,death,,postmortem,,,,,,,,,,100,1.7,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases NHP,1280.10759,Staphylococcus aureus strain SA40TW,SA40TW,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04263915,1280,,,,,,,,2016-11-17T00:00:00Z,,PRJNA302097,GCF_001880265.1,CP013182,NZ_CP013182.1,Zhejiang University School of Medicine,PacBio RS II,50x,RS_HGAP v. 2; SMRT v. 2.3.0,1,,1,2771849,32.9,2693,2582,nasopharyngeal swab,,2005,Taiwan,Taiwan,,,,healthy,,,,,,,,,C,,,,SA40TW is a nasal colonization S. aureus isolate.,collected_by:Chih-Jung Chen,,,,,,,healthy,,,,,,,,,,,,,,100,0,,,Respiratory Tract,- HP,1280.11642,Staphylococcus aureus strain SR434,SR434,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06277866,1280,,,,MLST.Staphylococcus_aureus.88,,,,2017-02-06T00:00:00Z,,PRJNA369164,GCF_001986135.1,"CP019563,CP019564,CP019565,CP019566,CP019567","NZ_CP019563.1,NZ_CP019564.1,NZ_CP019565.1,NZ_CP019566.1,NZ_CP019567.1",Zhejiang University,PacBio,200.0x,HGAP v. Dec-2016,5,,5,2839706,32.84,2880,2891,skin,,2015-11-26,China,China:Hangzhou,,,,skin abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete Genome Sequence of a Community-Associated Methicillin-Resistant Staphylococcus aureus Strain of Sequence type 88 from China,collected_by:Yan Chen,,,,,,,skin abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.11675,Staphylococcus aureus strain USA300-SUR9,USA300-SUR9,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497603,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000565.1,"CP014392,CP014393,CP014394,CP014395,CP014396","NZ_CP014392.1,NZ_CP014393.1,NZ_CP014394.1,NZ_CP014395.1,NZ_CP014396.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2953985,32.76,2984,2972,nose,,2013-05-02,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.11676,Staphylococcus aureus strain USA300-SUR10,USA300-SUR10,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497604,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000585.1,"CP014397,CP014398,CP014399,CP014400,CP014401","NZ_CP014397.1,NZ_CP014398.1,NZ_CP014399.1,NZ_CP014400.1,NZ_CP014401.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2953985,32.76,2984,2972,nose,,2013-05-03,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.11677,Staphylococcus aureus strain USA300-SUR11,USA300-SUR11,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497605,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000605.1,"CP014402,CP014403,CP014404,CP014405,CP014406","NZ_CP014402.1,NZ_CP014403.1,NZ_CP014404.1,NZ_CP014405.1,NZ_CP014406.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2953985,32.76,2984,2972,perineum,,2013-05-03,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.11678,Staphylococcus aureus strain USA300-SUR12,USA300-SUR12,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497606,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000625.1,"CP014407,CP014408","NZ_CP014407.1,NZ_CP014408.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,1,2,2903423,32.74,2912,2903,wound left foot,,2013-05-09,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.11679,Staphylococcus aureus strain USA300-SUR13,USA300-SUR13,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497607,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000645.1,"CP014409,CP014410,CP014411","NZ_CP014409.1,NZ_CP014410.1,NZ_CP014411.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2949913,32.76,2975,2970,pus left axilla,,2013-05-09,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.11680,Staphylococcus aureus strain USA300-SUR14,USA300-SUR14,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497608,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000665.1,"CP014412,CP014413,CP014414","NZ_CP014412.1,NZ_CP014413.1,NZ_CP014414.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2950020,32.76,2973,2971,wound groin,,2013-05-14,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.11681,Staphylococcus aureus strain USA300-SUR15,USA300-SUR15,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497609,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000685.1,"CP014415,CP014416,CP014417,CP014418,CP014419","NZ_CP014415.1,NZ_CP014416.1,NZ_CP014417.1,NZ_CP014418.1,NZ_CP014419.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2985088,32.7,3019,3014,nose,,2013-05-17,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.11682,Staphylococcus aureus strain USA300-SUR16,USA300-SUR16,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497610,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000705.1,"CP014420,CP014421,CP014422","NZ_CP014420.1,NZ_CP014421.1,NZ_CP014422.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2950020,32.76,2973,2971,perineum,,2013-05-17,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.11683,Staphylococcus aureus strain USA300-SUR17,USA300-SUR17,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497611,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000725.1,"CP014423,CP014424,CP014425","NZ_CP014423.1,NZ_CP014424.1,NZ_CP014425.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2950019,32.76,2975,2972,throat,,2013-05-21,Suriname,Suriname: Paramaribo,,,,,,,Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.11685,Staphylococcus aureus strain USA300-SUR19,USA300-SUR19,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497613,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000765.1,"CP014429,CP014430,CP014431","NZ_CP014429.1,NZ_CP014430.1,NZ_CP014431.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2950021,32.76,2972,2971,perineum,,2013-05-21,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.11686,Staphylococcus aureus strain USA300-SUR20,USA300-SUR20,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497614,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000785.1,"CP014432,CP014433,CP014434","NZ_CP014432.1,NZ_CP014433.1,NZ_CP014434.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2945638,32.77,2972,2966,nose,,2013-05-23,Suriname,Suriname: Nickerie,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.11687,Staphylococcus aureus strain USA300-SUR21,USA300-SUR21,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497615,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000805.1,"CP014435,CP014436,CP014437","NZ_CP014435.1,NZ_CP014436.1,NZ_CP014437.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2949913,32.76,2975,2969,pus,,2013-05-27,Suriname,Suriname: Paramaribo,,,,,,,Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.11688,Staphylococcus aureus strain USA300-SUR22,USA300-SUR22,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497616,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000825.1,"CP014438,CP014439,CP014440","NZ_CP014438.1,NZ_CP014439.1,NZ_CP014440.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2945637,32.77,2969,2964,pus axilla,,2013-05-28,Suriname,Suriname: Nickerie,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.11689,Staphylococcus aureus strain USA300-SUR23,USA300-SUR23,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497617,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000845.1,"CP014441,CP014442,CP014443","NZ_CP014441.1,NZ_CP014442.1,NZ_CP014443.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2945637,32.77,2969,2964,perineum,,2013-05-28,Suriname,Suriname: Nickerie,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.11690,Staphylococcus aureus strain USA300-SUR24,USA300-SUR24,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497618,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCF_002000865.1,"CP014444,CP014445,CP014446,CP014447,CP014448","NZ_CP014444.1,NZ_CP014445.1,NZ_CP014446.1,NZ_CP014447.1,NZ_CP014448.1",University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2985088,32.7,3019,3014,perineum,,2013-05-28,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.12234,Staphylococcus aureus strain JE2,JE2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06677988,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-04-11T00:00:00Z,,PRJNA381486,GCA_002085525.1,CP020619,,Walter Reed Army Institute of Research,Illumina MiSeq; PacBio,136.0x,HGAP2 and Geneious v. Ja,1,,1,2874399,32.78,2919,2938,skin and soft tissue,,2013,USA,USA:Nebraska,,,,Soft Tissue Infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Sequence the genome of Staphylococcus aureus JE2,collected_by:Paul Fey,,,,,,,Soft Tissue Infections,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.12239,Staphylococcus aureus strain C2406,C2406,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN05860146,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-04-13T00:00:00Z,,PRJNA345240,GCA_002088995.1,CP019590,,University of Calgary,PacBio,346x,HGAP v. RS_HGAP Assembly.2,1,,1,2878854,32.78,2919,2948,lung,,2004-05,Canada,Canada: Calgary,,,,Necrotizing pneumonia,,host_disease_outcome:death,Resistant,Computational Prediction,,,,,,,,,Sequencing of a clinical MRSA USA300 isolate,collected_by:Kunyan Zhang,,,,,,,Necrotizing pneumonia,,death,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1280.12905,Staphylococcus aureus strain Seattle 1945,G477,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07212543,1280,,,pathovar L,MLST.Staphylococcus_aureus.243,genotype:CC30 / PVL+,ATCC:25923,,2017-06-20T00:00:00Z,,PRJNA390063,GCA_002202075.1,"CP021905,CP021906",,Alere Technologies Jena GmbH,Illumina MiSeq,146.0x,SeqMan NGen 12.1.0 v. July-2015,1,1,2,2806349,32.86,2638,,unknown,,2014-04-04,Germany,Germany: Saarbruecken,,,,,,,Susceptible,Computational Prediction,,,,,,,,,PVL overexpression in Staphylococcus aureus ATCC25923,"collected_by:Stefan Weber, MVZ Saarbruecken",,,,,,,missing,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.12906,Staphylococcus aureus strain Seattle 1945,G478,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07212544,1280,,,pathovar L,MLST.Staphylococcus_aureus.243,genotype:CC30 / PVL+,ATCC:25923,,2017-06-20T00:00:00Z,,PRJNA390063,GCA_002202095.1,"CP021907,CP021908",,Alere Technologies Jena GmbH,Illumina MiSeq,355.0x,SeqMan NGen 12.1.0 v. July-2015,1,1,2,2819703,32.84,2656,,unknown,,2013-11-07,Germany,Germany: Dresden,,,,,,,Susceptible,Computational Prediction,,,,,,,,,PVL overexpression in Staphylococcus aureus ATCC25923,"collected_by:Stefan Monecke, TU Dresden",,,,,,,missing,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.12910,Staphylococcus aureus strain FORC_045,FORC_045,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN05520967,1280,,,,MLST.Staphylococcus_aureus.1,,,,2017-06-27T00:00:00Z,,PRJNA338099,GCA_002209325.1,CP017115,,Seoul National University,PacBio,375.47x,SMRT Analysis v. 2.3.0,1,,1,2807171,32.84,2669,2630,blood,isolated from blood of patient in South Korea,2014-07-01,South Korea,South Korea: Seoul,,,,Not reported,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Staphylococcus aureus is one of the well-known food-borne pathogen. It was isolated from blood of patient in South Korea.,"collected_by:Samsung Medical Center, Seoul",,,,,,,Not reported,,,,,,,,,,,,,,100,3.5,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.14567,Staphylococcus aureus strain OC8,OC8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00043228,1280,,,,MLST.Staphylococcus_aureus.8,,,,2016-10-19T00:00:00Z,27741255,PRJDB4364,GCA_002355355.1,AP017377,,International Medical Education and Research Center,PacBio RS II system,259x,The assembler software SMRT Analysis v.,1,,1,2897106,32.87,2739,,,,2007,Russia,Russia:Krasnoyarsk,env_biome:not applicable,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"MRSA is a globally disseminated multidrug-resistant (MDR) pathogen that threatens the lives of patients and health of individuals not only in hospitals but also in the community. There are two types of MRSA, HA-MRSA and CA-MRSA. In this study, we investigated the whole genome of ST8 CA-MRSA in Siberian Russia (Krasnoyarsk), in which international research had never previously focused on MRSA and its invasive infections, focusing on the virulence potentials, drug resistance, and evolution. The obtained data will be employed for the diagnosis, treatment, and prevention of MRSA infections.",,not applicable,missing,missing,26047024,Whole genome analysis of methicillin-resistant Staphylococcus aureus (MRSA),,,,,,,,,,,,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.14573,Staphylococcus aureus strain HZW450,HZW450,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06703161,1280,,,,MLST.Staphylococcus_aureus.59,,,,2017-10-04T00:00:00Z,,PRJNA382289,GCA_002442975.1,CP020741,,"The First Affiliated Hospital of College of Medicine, Zhejiang University",PacBio,227.76x,SMRTanalysis v. R2.3.0,1,,1,2831958,32.9,2835,2848,pus,,2016-08-08,China,China: Hangzhou,,,,impetigo,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genomic analysis of Staphylococcus aureus isolated from pus of a patient with impetigo,collected_by:Chen Qiong,,,,,,,impetigo,,,,,,,,,,,,,,100,2.4,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.15138,Staphylococcus aureus strain USA400-0051,USA400-0051,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN05864218,1280,,,,MLST.Staphylococcus_aureus.1,,,,2017-11-24T00:00:00Z,,PRJNA345484,GCA_002795285.1,"CP019574,CP019575",,LNCC,IonTorrent; 454,57x,Newbler v. 3.0,1,1,2,2832530,32.76,2746,2473,,,2003-2006,USA,United States,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,3.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.16023,Staphylococcus aureus strain ST2594 strain 004,004,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08634544,1280,,,MRSA,,,,,2018-03-19T00:00:00Z,,PRJNA436877,GCA_003010475.1,"CP027486,CP027496,CP027495,CP027487,CP027488,CP027489,CP027490,CP027491,CP027492,CP027493,CP027494",,Universidade do Estado do Rio de Janeiro,Illumina MiSeq,40.0x,SPAdes v. 3.5; MAUVE v. 2.4.0,1,10,11,2809023,32.64186,2887,2883,wound fluid; femural surgical wound,,2015-03-11,Brazil,Brazil: Rio de Janeiro,,female,86 y/o,Surgical Wound Infection,,host_description:Subtrochanteric femoral fracture;host_disease_outcome:recovery;host_disease_stage:post-operative;host_subject_id:4,Resistant;Susceptible,Computational Prediction,,,,,,,,,Whole genome sequencing of ST2594 MRSA strain causing skin colonization and low-grade infection in surgical site.;missing ribosomal protein genes;missing tRNA genes,collected_by:Leonardo Bastos;passage_history:1,,,,,,,Surgical Wound Infection,,recovery,Subtrochanteric femoral fracture,post-operative,MRSA,,,,,,,,,100,1.2,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.16024,Staphylococcus aureus strain FORC59,FORC59,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06578843,1280,,,,MLST.Staphylococcus_aureus.188,,,,2018-03-19T00:00:00Z,,PRJNA379058,GCA_003010875.1,"CP020354,CP020355",,Seoul National University,PacBio,418.11x,SMRT Analysis HGAP.2 v. 2.3.0,1,1,2,2742918,32.806522,2585,2559,blood,isolated from the blood of a patient who suffered from food-poisoning,2016-01-01,South Korea,South Korea: Seoul,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Staphylococcus aureus is one of the most prevalent food-borne pathogens, and is very well known for its wide range of resistance against antibiotic agents. This sample was isolated from the blood of a patient who suffered from food-poisoning. (Seoul, Korea)",collected_by:Samsung Seoul Hospital,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.16063,Staphylococcus aureus strain SVH7513,SVH7513,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08999370,1280,,,,MLST.Staphylococcus_aureus.612,,,,2018-05-10T00:00:00Z,,PRJNA454172,GCA_003111725.1,"CP029166,CP029167,CP029165",,Curtin University,PacBio; Illumina MiSeq,616.0x,Canu v. 1.6,1,2,3,2945766,32.828167,3027,3039,vet hospital,,2009,Australia,Australia: New South Wales,,,,Cellulitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus ST612 , a close relative of ST8 USA300, is relatively rare. This isolate was identified during a screening of horses in a vet hospital and provides a high quality reference sequence for other ST612 genomes.",,,,,,,,Cellulitis,,,,,,,,,,,,,,100,3.5,Skin and Soft Tissue Infections,Cellulitis,Other,Skin and Soft Tissue Infections-Cellulitis HP,1280.16428,Staphylococcus aureus strain CC5,CC5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06480776,1280,,,,MLST.Staphylococcus_aureus.5,genotype:ST5,,,2018-04-03T00:00:00Z,,PRJNA378176,GCA_003031485.1,CP021105,,Federal University of Rio de Janeiro,Illumina,179.0x,Geneious v. 10,1,,1,2745711,32.855022,2721,2737,tracheal secretion,,2014-07-23,Brazil,Brazil: Rio de Janeiro,,female,,respiratory tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus clinical isolates from patients in Rio de Janeiro, Brazil.",collected_by:UFRJ,,,,,,,respiratory tract infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1280.16429,Staphylococcus aureus strain CR14-035,CR14-035,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06644991,1280,,,,MLST.Staphylococcus_aureus.5,genotype:ST5,,,2018-04-03T00:00:00Z,,PRJNA378176,GCA_003031465.1,CP020544,,Federal University of Rio de Janeiro,Illumina,114.0x,Geneious v. 10.0.6,1,,1,2989067,32.982704,3168,3098,nasal swab,,2014-09-22,Brazil,Brazil: Rio de Janeiro,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus clinical isolates from patients in Rio de Janeiro, Brazil.",collected_by:UFRJ,,,,,,,Unknown,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.16565,Staphylococcus aureus strain CHU15-056,CHU15-056,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06560523,1280,,,,MLST.Staphylococcus_aureus.5,genotype:ST5,,,2018-06-06T00:00:00Z,,PRJNA378176,GCA_003194405.1,CP021171,,Federal University of Rio de Janeiro,Illumina,102.0x,Geneious v. 10.0.6,1,,1,2773467,32.889393,2759,2771,blood,,2015,Brazil,Brazil: Rio de Janeiro,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus clinical isolates from patients in Rio de Janeiro, Brazil.",collected_by:UFRJ,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.16765,Staphylococcus aureus strain CMRSA-3,CMRSA-3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08717045,1280,,,,MLST.Staphylococcus_aureus.241,,,,2018-06-25T00:00:00Z,,PRJNA438470,GCA_003264775.1,CP029685,,University of Calgary,Illumina MiSeq; PacBio,234.0,Lordec v. 0.9; Canu v. 1.7; Spades v.,1,,1,2958212,32.905518,3030,3039,,,,Canada,Canada,,,,,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequence of the Canadian epidemic MRSA strain CMRS-3,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.16766,Staphylococcus aureus strain CMRSA-6,CMRSA-6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08717048,1280,,,,MLST.Staphylococcus_aureus.239,,,,2018-06-25T00:00:00Z,,PRJNA438472,GCA_003264815.1,CP027788,,University of Calgary,Illumina; PacBio,193x,Lordec v. 0.9; Canu v. 1.7; Spades v.,1,,1,3044721,32.780178,3135,3137,,,,Canada,Canada,,,,,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequence of the Canadian epidemic MRSA strain CMRSA-6,,,,,,,,,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.17679,Staphylococcus aureus strain E16SA093,E16SA093,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09668080,1280,,,,MLST.Staphylococcus_aureus.72,,,,2018-07-26T00:00:00Z,,PRJNA481439,GCA_003342735.1,CP031131,,Yonsei University College of medicine,PacBio,684x,HGAP v. 3,1,,1,2785564,32.88447,2795,2800,blood,,2016-09,South Korea,South Korea,,,,Blood stream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,pseudo SCCmec in MRSA ST72 from South Korea,collected_by:Kor-GLASS,,,,,,,Blood stream infection,,,,,,,,,,,,,,100,2.4,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.17680,Staphylococcus aureus strain F17SA003,F17SA003,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09668081,1280,,,,MLST.Staphylococcus_aureus.72,,,,2018-07-26T00:00:00Z,,PRJNA481439,GCA_003342775.1,CP031130,,Yonsei University College of medicine,PacBio,744x,HGAP v. 3,1,,1,2768346,32.85431,2778,2790,blood,,2017-01,South Korea,South Korea,,,,Blood stream infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,pseudo SCCmec in MRSA ST72 from South Korea,collected_by:Kor-GLASS,,,,,,,Blood stream infection,,,,,,,,,,,,,,100,1.8,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.17684,Staphylococcus aureus strain FORC_061,FORC_061,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07372047,1280,,,,MLST.Staphylococcus_aureus.72,,,,2018-07-31T00:00:00Z,,PRJNA395147,GCA_003347055.1,"CP022607,CP022608",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,341 x,PacBio SMRT Analysis v. 2.3.0,1,1,2,2749621,32.81245,2574,2518,stool; blood,isolated from human stool in South Korea,2017-01,South Korea,South Korea,,,,food poisoning,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Staphylococcus aureus FORC_061 Complete genome sequencingStaphylococcus aureus is one of the well-known food-borne pathogen. It was isolated from human stool in South Korea.,collected_by:samsunghospital,,,,,,,food poisoning,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1280.17686,Staphylococcus aureus strain FORC_062,FORC_062,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07407571,1280,,,,MLST.Staphylococcus_aureus.5,,,,2018-08-01T00:00:00Z,,PRJNA395485,GCA_003351925.1,CP022582,,"Food-borne Pathogen Omics Research Center, FORC",PacBio,453x,PacBio SMRT Analysis v. 2.3.0,1,,1,2905353,32.91717,2791,2721,blood,isolated from the human blood in South Korea,2017-01-01,South Korea,South Korea: Seoul,,,,Food Poisoning,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Staphylococcus aureus FORC_062 Complete genome sequencingStaphylococcus aureus is one of the well-known food-borne pathogen. It was isolated from the human blood in South Korea.,collected_by:Samsung hospital,,,,,,,Food Poisoning,,,,,,,,,,,,,,100,0.6,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1280.17721,Staphylococcus aureus strain WCH-SK2,WCH-SK2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN03799496,1280,,,,MLST.Staphylococcus_aureus.239,,,,2018-08-16T00:00:00Z,26458527,PRJNA261650,GCA_003394105.1,CP031537,,University of Adelaide,PacBio Sequel,159.6x,HGAP ASSEMBLY v. 2,1,,1,2914635,32.82133,2964,2976,bloodstream,,2009-01-01,Australia,Australia,,,,"pneumoniae, SSTI, custic fibrosis",,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This strain was selected as forming SCVs and biofilms in different conditions of host-specific stress,collected_by:WCH,,,,,,,"pneumoniae, SSTI, custic fibrosis",,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,1280.17973,Staphylococcus aureus strain CFBR-105,CFBR-105,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09847825,1280,,,,MLST.Staphylococcus_aureus.632,,,,2018-08-29T00:00:00Z,,PRJNA480016,GCA_003431365.1,CP031779,,Emory University,Illumina HiSeq; Oxford Nanopore MiniION,1.0x,Unicycler v. 0.4.0,1,,1,2782740,32.9039,2764,2776,sputum,,2011-10-25,USA,"USA: Atlanta, GA",,female,53,Cystic fibrosis,,host_disease_outcome:chronic disease,Susceptible;Resistant,Computational Prediction,,,,,,,,,Staphylococcus aureus is often an early colonizer of Cystic fibrosis (CF) patients that is later replaced by Pseudomonas aeruginosa. Co-infection with both bacteria is correlated with poor prognosis and decreases the lifespan of the patient. We have sequenced clinical isolates of S. aureus from patients co-infected with both pathogens. Isolates were obtained from the CF Biospecimen Registry (CFBR) at Emory University + Children's Center for Cystic Fibrosis and Airways Disease Research.,collected_by:Emory Cystic Fibrosis Biospecimen Registry (CFBR),,,,,,,Cystic fibrosis,,chronic disease,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,1280.18507,Staphylococcus aureus strain USA300-SUR1,USA300-SUR1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497595,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595365.1,"CP014362,CP014363,CP014364",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2935151,32.770546,2965,2956,perineum,,2013-03-26,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.18508,Staphylococcus aureus strain USA300-SUR2,USA300-SUR2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497596,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595385.1,"CP014365,CP014366,CP014367",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2935151,32.77051,2965,2956,groin,,2013-03-26,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.18509,Staphylococcus aureus strain USA300-SUR3,USA300-SUR3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497597,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595405.1,"CP014368,CP014369,CP014370",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2949899,32.758747,2974,2970,wound fluid,,2013-04-24,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.18510,Staphylococcus aureus strain USA300-SUR4,USA300-SUR4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497598,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595425.1,"CP014371,CP014372,CP014373,CP014374,CP014375",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2953985,32.759037,2982,2972,urine,,2013-04-25,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1280.18511,Staphylococcus aureus strain USA300-SUR5,USA300-SUR5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497599,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595445.1,"CP014376,CP014377,CP014378,CP014379,CP014380",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,4,5,2953985,32.759037,2982,2972,sputum,,2013-04-25,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.18514,Staphylococcus aureus strain USA300-SUR7,USA300-SUR7,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04497601,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-02-16T00:00:00Z,28106148,PRJNA312385,GCA_003595485.1,"CP014384,CP014385,CP014386",,University Medical Center Groningen,Illumina,missing,SeqMan NGen v. 12.1.0,1,2,3,2948930,32.758762,2971,2968,pus leg,,2013-04-30,Suriname,Suriname: Paramaribo,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,C,,,,The study characterizes a Staphylococcus aureus outbreak which took place in Paramaribo in the Republic of Suriname.,collected_by:Sandra Hermelijn,,,,,,,missing,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.18528,Staphylococcus aureus strain GN3,GN3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00043229,1280,,,,MLST.Staphylococcus_aureus.50,,,,2017-11-14T00:00:00Z,29117225,PRJDB4365,GCA_003609895.1,AP017891,,International Medical Education and Research Center,PacBio RS II system,443X,SMRT Analysis v. 2.3.0,1,,1,2809401,32.84878,2603,,,,2005,Japan,Japan:Niigata,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus is a most common pathogen that threatens the lives of patients and health of individuals not only in hospitals but also in the community. S. aureus causes skin and soft tissue infections such as bullous impetigo, furunculosis, and staphylococcal scalded skin syndrome\; life-threatening infections such as blood-stream infections, pneumonia and toxic shock syndrome. There are divergent global S. aureus lineages, and S. aureus evolution includes horizontal gene transfer, mediated by, for example, mobile DNA elements. In this study, we investigated the whole genome of S. aureus, which contained multiple copies of a mobile DNA, focusing on the new mechanisms, through which mobile DNAs can efficiently be transposed.",,not applicable,missing,missing,26047024,Whole genome analysis of Staphylococcus aureus carrying a mobile DNA with a new transposition mechanism,,,,,,,,,,,,not applicable,,,,98.95,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.18529,Staphylococcus aureus strain GN1,GN1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00089953,1280,,,,MLST.Staphylococcus_aureus.50,,,,2017-11-14T00:00:00Z,29117225,PRJDB6169,GCA_003609915.1,AP018349,,"International Medical Education and Research Center, Department of Epidemiology, Genomics, and Evolution, International Medical Education and Research Center",PacBio RS II system,500x,The assembler software SMRT Analysis v.,1,,1,2809565,32.84345,2602,,,,2005,Japan,Japan: Niigata,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus is a most common pathogen that threatens the lives of patients and health of individuals not only in hospitals but also in the community. S. aureus causes skin and soft tissue infections such as bullous impetigo, furunculosis, and staphylococcal scalded skin syndrome\; life-threatening infections such as blood-stream infections, pneumonia and toxic shock syndrome. There are divergent global S. aureus lineages, and S. aureus evolution includes horizontal gene transfer, mediated by, for example, mobile DNA elements. In this study, we investigated the whole genome of S. aureus, which contained multiple copies of a mobile DNA, focusing on the new mechanisms, through which mobile DNAs can efficiently be transposed.",,missing,missing,MSSA,"Nutrient agar, 37 C",Genome analysis of clinical S. aureus,,,,,,,,,,,,missing,,,,98.95,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.19051,Staphylococcus aureus strain ATCC BAA-39,ATCC BAA-39,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09635551,1280,,,,MLST.Staphylococcus_aureus.464,,ATCC:BAA-39,,2018-11-26T00:00:00Z,,PRJNA480363,GCA_003827835.1,CP033506,,University of Pretoria,PacBio,150x,HGAP v. 4,1,,1,2792888,32.877113,3075,2411,nose,,2017,Kazakhstan,Kazakhstan,,,,Infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study is to investigate the therapeutic effect of FS-1, a new antibacterial agent that reverses the sensitivity of drug resistant pathogens, through identifying DNA modifications. Long-read PacBio SMRT sequencing was performed on chromosomal DNA of the methicillin-resistant Staphylococcus aureus (MRSA) collection strain, Staphylococcus aureus ATCC BAA-39, under the effect of FS-1 as well as the control.",collected_by:Ilya Korotetskiy;passage_history:10,,,,,,,Infections,,,,,,FS culture; grown on experimental medium,,,,,,,,95.93,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.19052,Staphylococcus aureus strain ATCC BAA-39,ATCC BAA-39,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09635552,1280,,,,MLST.Staphylococcus_aureus.464,,ATCC:BAA-39,,2018-11-26T00:00:00Z,,PRJNA480363,GCA_003827735.1,CP033505,,University of Pretoria,PacBio,150x,HGAP v. 4,1,,1,2791218,32.884605,2818,2465,nose,,2017,Kazakhstan,Kazakhstan,,,,Infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study is to investigate the therapeutic effect of FS-1, a new antibacterial agent that reverses the sensitivity of drug resistant pathogens, through identifying DNA modifications. Long-read PacBio SMRT sequencing was performed on chromosomal DNA of the methicillin-resistant Staphylococcus aureus (MRSA) collection strain, Staphylococcus aureus ATCC BAA-39, under the effect of FS-1 as well as the control.",collected_by:Ilya Korotetskiy;passage_history:10,,,,,,,Infections,,,,,,NC culture; grown on normal medium,,,,,,,,97.46,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.19099,Staphylococcus aureus strain USA 100 strain 30-47,30-47,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09220587,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-01-03T00:00:00Z,,PRJNA471840,GCA_003991015.1,"CP029474,CP029475",,University of Illinois at Chicago,Oxford nanopore; Illumina HiSeq,400.0x,canu v. 1.5,1,1,2,2788097,32.806393,2799,2788,anterior nares,,2015,USA,"USA:Surgical Intensive Care Unit at Rush University Medical Center in Chicago, IL",,,,infection control,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome assembly of USA100 isolate,collected_by:Koh Okamoto MD MS,,,,,,,infection control,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1280.19106,Staphylococcus aureus strain PCFH-226,PCFH-226,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10659762,1280,,,,MLST.Staphylococcus_aureus.541,,,,2019-01-16T00:00:00Z,,PRJNA498007,GCA_004026165.1,"CP035005,CP035006",,Chung-Ang University,PacBio RSII,475x,HGAP v. v3.0,1,1,2,2815599,32.90252,2652,,left hand,,2017-08-28,South Korea,South Korea: Chungcheongnam-do,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The aim of this project was to investigate the genetic characteristics of methicillin-resistant Staphylococcus aureus strains isolated from pig farms in Korea,collected_by:Sanigen,,,,,,,healthy,,,,,,,,,,,,,,99.13,0.1,,,Other,- HP,1280.19117,Staphylococcus aureus strain NCTC11965,NCTC11965,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3529261,1280,not available: to be reported later,,,MLST.Staphylococcus_aureus.30,,NCTC:11965,,2018-12-20T00:00:00Z,,PRJEB6403,GCA_900635335.1,LR134093,,SC,,,,1,,1,2838411,32.804447,2676,2606,vagina,,1986,United Kingdom,United Kingdom,,,,,,host_health_state:Toxic Shock Syndrome,Susceptible;Resistant,Computational Prediction,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Toxic Shock Syndrome,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1280.20975,Staphylococcus aureus strain LAC,LAC,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10779666,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-01-30T00:00:00Z,,PRJNA515948,GCA_004118995.1,"CP035369,CP035370",,UC San Diego,Oxford Nanopore MiniION,50.0x,Unicycler v. 0.4.2,1,1,2,2878171,32.78478,2720,,blood,,2017-06,USA,USA: San Diego,,,,bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This is a hybrid assembly of the S. aureus LAC isolate. The assembly was performed by combining Illumina HiSeq short reads with Minion long reads.,collected_by:San Diego,,,,,,,bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.20976,Staphylococcus aureus strain NF25,NF25,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10712706,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-01-30T00:00:00Z,,PRJNA513421,GCA_004119935.1,"CP035415,CP035416",,Third Military Medical University,PacBio RSII,200.0x,Celera Assembler v. 16,1,1,2,2872188,32.878345,2911,2911,abdominal drainage tube,,2011-02-12,China,China,,,,abdominal infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,NF25,collected_by:Third Military Medical University,,,,,,,abdominal infection,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,1280.21013,Staphylococcus aureus strain C3948,C3948,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06830422,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-02-13T00:00:00Z,,PRJNA384205,GCA_004193875.1,CP020957,,University of Calgary,PacBio,368x,HGAP v. RS_HGAP Assembly.2,1,,1,2795888,32.846024,2823,2842,unknown,,2002-10,Canada,Canada: Calgary,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Complete genome sequence of a USA300 related clinical MSSA isolate, C3948",collected_by:Kunyan Zhang,,,,,,,unknown,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.21014,Staphylococcus aureus strain H489,H489,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06830441,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-02-13T00:00:00Z,,PRJNA384209,GCA_004193895.1,CP020959,,University of Calgary,PacBio,392x,HGAP v. RS_HGAP Assembly.2,1,,1,2757748,32.84952,2784,2789,sputum,,1993-04,Canada,Canada: Winnipeg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Complete genome sequence of USA300 related clinical MSSA isolate, H489",,,,,,,,unknown,,,,,,,,,,,,,,99.43,0.08,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.21017,Staphylococcus aureus strain 592,592,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10779665,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-02-17T00:00:00Z,,PRJNA515949,GCA_004208595.1,"CP035791,CP035792",,UC San Diego,Oxford Nanopore MiniION,50.0x,Unicycler v. 0.4.2,1,1,2,2847444,32.85364,2679,,blood,,2016-01-01,USA,USA: San Diego,,,,bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This is a hybrid assembly of the S. aureus 592 clinical isolate. The assembly was performed by combining Illumina HiSeq short reads with Minion long reads.,collected_by:George Sakoulas,,,,,,,bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.21046,Staphylococcus aureus strain C8879,C8879,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06830421,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-04-04T00:00:00Z,,PRJNA384204,GCA_004614295.1,CP020956,,University of Calgary,PacBio,348x,HGAP v. RS_HGAP Assembly.2,1,,1,2832897,32.814747,2872,2890,wound,,2002-10,Canada,Canada: Calgary,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Complete genome sequence of a USA300 related clinical MRSA isolate, C8879",collected_by:Kunyan Zhang,,,,,,,unknown,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.21047,Staphylococcus aureus strain JK3137,JK3137,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06830443,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-04-04T00:00:00Z,,PRJNA384212,GCA_004614315.1,CP020960,,University of Calgary,PacBio,366x,HGAP v. RS_HGAP Assembly.2,1,,1,2955000,32.81804,3070,3068,unknown,,2011-07,Canada,Canada: Calgary,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Complete genome sequence of a USA300 related clinical MRSA isolate, JK3137",collected_by:Kunyan Zhang,,,,,,,unknown,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.21137,Staphylococcus aureus strain J01,J01,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11823229,1280,,,,MLST.Staphylococcus_aureus.8,genotype:ST8-MRSA-IVg CC8 spa t064. PFGE type USA300. agr type 1.,,,2019-05-30T00:00:00Z,,PRJNA544229,GCA_005889995.1,"CP040619,CP040620,CP040621",,Wayne State University,PacBio; MiSeq,842.0x,Unicycler v. v0.4.6,1,2,3,2939272,32.753994,2974,2963,blood,,2011,USA,USA: California,,female,,Infective Endocarditis,,host_disease_outcome:clinical cure with daptomycin+nafcillin,Resistant;Susceptible,Computational Prediction,,,,,,,,,Daptomycin resistance development limits therapeutic options to treat Staphylococcus aureus infection. Daptomycin resistance development can be mitigated by combining daptomycin with beta lactams even in the setting of MRSA. This study explored the ability of different beta lactams to prevent daptomycin resistance development following in vitro serial passage in daptomycin.,collected_by:Sakoulas;passage_history:Sakoulas > Berti,,,,,,,Infective Endocarditis,,clinical cure with daptomycin+nafcillin,,,,clinical sample,,,,,,,,99.37,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.21138,Staphylococcus aureus strain JKD6004,JKD6004,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11823230,1280,,,,MLST.Staphylococcus_aureus.239,genotype:ST239-MRSA-III CC8 spa t574 agr type 1.,,,2019-05-30T00:00:00Z,,PRJNA544229,GCA_005890015.1,CP040622,,Wayne State University,PacBio; MiSeq,1499.0x,Unicycler v. v0.4.6,1,,1,2936830,32.87336,2951,2941,blood,,2004,Australia,Australia: Brisbane,,male,83,Pacemaker Abscess,,host_disease_outcome:death,Susceptible;Resistant,Computational Prediction,,,,,,,,,Daptomycin resistance development limits therapeutic options to treat Staphylococcus aureus infection. Daptomycin resistance development can be mitigated by combining daptomycin with beta lactams even in the setting of MRSA. This study explored the ability of different beta lactams to prevent daptomycin resistance development following in vitro serial passage in daptomycin.,collected_by:Howden;passage_history:Howden > Berti,,,,,,,Pacemaker Abscess,,death,,,,clinical sample,,,,,,,,99.51,0.08,Skin and Soft Tissue Infections,Wounds and Abscesses,Blood and Circulatory System,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.21143,Staphylococcus aureus strain D592,D592,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11823228,1280,,,,MLST.Staphylococcus_aureus.5,genotype:ST5-MRSA-II CC5 spa t002. PFGE type USA100. agr type 2.,,,2019-06-04T00:00:00Z,,PRJNA544229,GCA_005954685.1,"CP040665,CP040666",,Wayne State University,PacBio; MiSeq,1433.0x,Unicycler v. v0.4.6,1,1,2,2847448,32.853653,2845,2817,blood,,2010,USA,USA: California,,male,55,Osteomyelitis,,host_disease_outcome:clinical cure with daptomycin+nafcillin,Susceptible;Resistant,Computational Prediction,,,,,,,,,Daptomycin resistance development limits therapeutic options to treat Staphylococcus aureus infection. Daptomycin resistance development can be mitigated by combining daptomycin with beta lactams even in the setting of MRSA. This study explored the ability of different beta lactams to prevent daptomycin resistance development following in vitro serial passage in daptomycin.,collected_by:Dhand;passage_history:Dhand > Sakoulas > Berti,,,,,,,Osteomyelitis,,clinical cure with daptomycin+nafcillin,,,,human clinical,,,,,,,,99.51,0.08,Bone and Joint Infections,Osteomyelitis,Blood and Circulatory System,Bone and Joint Infections-Osteomyelitis HP,1280.21144,Staphylococcus aureus,aureus,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08969227,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-06-06T00:00:00Z,,PRJNA451378,GCA_006088835.1,"CP029198,CP029199",,Seoul National University,PacBio,350x,SMRT Analysis v. 2.3.0,1,1,2,3003628,32.870216,2869,2819,blood,"isolated from the blood of a food-poisoned patient in Seoul, Korea",2016,South Korea,South Korea: Seoul,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"As a food-borne pathogen, Staphylococcus aureus profound food-poisoning activities with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",collected_by:Samsung Seoul Hospital,,,,,,,,,,,,,,,,,,,,,99.01,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21153,Staphylococcus aureus strain JKD6009,JKD6009,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5047402,1280,,,,MLST.Staphylococcus_aureus.239,,,,2019-02-11T00:00:00Z,,PRJEB29322,GCA_900607245.1,LR027876,,UNIVERSITY OF MELBOURNE,,,,1,,1,2930439,32.874428,2801,,tissue,,2003,Australia,Australia,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA,,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.21154,Staphylococcus aureus strain BPH2019,BPH2019,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5047399,1280,,,,MLST.Staphylococcus_aureus.239,,,,2019-02-11T00:00:00Z,,PRJEB29322,GCA_900607255.1,"LR027870,LR027871,LR027872",,UNIVERSITY OF MELBOURNE,,,,1,2,3,2936483,32.783073,2783,,blood culture,,2005,Australia,Australia,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA,,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21155,Staphylococcus aureus strain BPH2003,BPH2003,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5047398,1280,,,,MLST.Staphylococcus_aureus.239,,,,2019-02-11T00:00:00Z,,PRJEB29322,GCA_900607265.1,"LR027878,LR027879",,UNIVERSITY OF MELBOURNE,,,,1,1,2,3079710,32.78984,2970,,blood culture,,2001,Australia,Australia,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA,,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21156,Staphylococcus aureus strain BPH2070,BPH2070,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5047401,1280,,,,MLST.Staphylococcus_aureus.239,,,,2019-02-11T00:00:00Z,,PRJEB29322,GCA_900607275.1,LR027873,,UNIVERSITY OF MELBOURNE,,,,1,,1,2930188,32.89178,2758,,blood culture,,1998,Australia,Australia,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA,,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21159,Staphylococcus aureus strain BPH2056,BPH2056,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5047400,1280,,,,MLST.Staphylococcus_aureus.239,,,,2019-02-11T00:00:00Z,,PRJEB29322,GCA_900607305.1,"LR027874,LR027875",,UNIVERSITY OF MELBOURNE,,,,1,1,2,3023304,32.718906,2889,,,,1981,Australia,Australia,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA,,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.21160,Staphylococcus aureus strain BPH2760,BPH2760,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5099550,1280,,,,MLST.Staphylococcus_aureus.1,,102.100.100.25745,,2019-01-10T00:00:00Z,,PRJEB29881,GCA_900620215.1,"LR130509,LR130510",,Bioplatforms Australia,,,,1,1,2,2750105,32.787292,2516,,blood,,2007-09-28,Australia,Australia,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Staphylococcus aureus.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21161,Staphylococcus aureus strain BPH2819,BPH2819,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5099551,1280,,,,MLST.Staphylococcus_aureus.5,,102.100.100.25746,,2019-01-10T00:00:00Z,,PRJEB29881,GCA_900620225.1,"LR130511,LR130512",,Bioplatforms Australia,,,,1,1,2,2760664,32.819424,2561,,blood,,2007-12-14,Australia,Australia,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Staphylococcus aureus.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21162,Staphylococcus aureus strain BPH2900,BPH2900,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5099552,1280,,,,MLST.Staphylococcus_aureus.22,,102.100.100.25747,,2019-01-10T00:00:00Z,,PRJEB29881,GCA_900620235.1,"LR130513,LR130514",,Bioplatforms Australia,,,,1,1,2,2825765,32.839672,2671,,blood,,2008-04-20,Australia,Australia,,,,,,host_health_state:diseased,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Staphylococcus aureus.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21163,Staphylococcus aureus strain BPH2947,BPH2947,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5099553,1280,,,,MLST.Staphylococcus_aureus.239,,102.100.100.25748,,2019-01-10T00:00:00Z,,PRJEB29881,GCA_900620245.1,"LR130515,LR130516,LR130517",,Bioplatforms Australia,,,,1,2,3,3079932,32.794327,2970,,blood,,2008-08-09,Australia,Australia,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Staphylococcus aureus.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21164,Staphylococcus aureus strain BPH2986,BPH2986,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA5099554,1280,,,,MLST.Staphylococcus_aureus.8,,102.100.100.25749,,2019-01-10T00:00:00Z,,PRJEB29881,GCA_900620255.1,"LR130518,LR130519,LR130520",,Bioplatforms Australia,,,,1,2,3,2919756,32.798527,2796,,blood,,2008-12-05,Australia,Australia,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Staphylococcus aureus.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.21676,Staphylococcus aureus strain BSN9S,BSN9S,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12476135,1280,,,,MLST.Staphylococcus_aureus.8,genotype:ST8-MRSA-IVa CC8 spa t008. PFGE type USA300. agr type 1.,,,2019-08-11T00:00:00Z,,PRJNA544229,GCA_007954445.1,"CP042346,CP042347",,Wayne State University,Oxford Nanopore MiniION; Illumina MiSeq,842.0x,Unicycler v. v0.4.2,1,1,2,2868644,32.743973,2872,2855,"heart valve; tricuspid valve, anterior leaflet",,2018-08-08,USA,USA: Detroit,,female,45,Infective Endocarditis,,host_disease_outcome:Valve Replacement,Susceptible;Resistant,Computational Prediction,,,,,,,,,Daptomycin resistance development limits therapeutic options to treat Staphylococcus aureus infection. Daptomycin resistance development can be mitigated by combining daptomycin with beta lactams even in the setting of MRSA. This study explored the ability of different beta lactams to prevent daptomycin resistance development following in vitro serial passage in daptomycin.,collected_by:Andrew Berti,,,,,,,Infective Endocarditis,,Valve Replacement,,,,,,,,,,,,99.51,0.67,Bloodstream Infections,Other Bloodstream Infections,Ear,Bloodstream Infections-Other Bloodstream Infections HP,1280.21677,Staphylococcus aureus strain BSN9R,BSN9R,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12476193,1280,,,,MLST.Staphylococcus_aureus.8,genotype:ST8-MRSA-IVa CC8 spa t008. PFGE type USA300. agr type 1.,,,2019-08-11T00:00:00Z,,PRJNA544229,GCA_007954465.1,"CP042348,CP042349",,Wayne State University,Oxford Nanopore MiniION; Illumina MiSeq,842.0x,Unicycler v. v0.4.2,1,1,2,2868644,32.74394,2873,2855,"heart valve; tricuspid valve, septal leaflet",,2018-08-08,USA,USA: Detroit,,female,45,Infective Endocarditis,,host_disease_outcome:Valve Replacement,Susceptible;Resistant,Computational Prediction,,,,,,,,,Daptomycin resistance development limits therapeutic options to treat Staphylococcus aureus infection. Daptomycin resistance development can be mitigated by combining daptomycin with beta lactams even in the setting of MRSA. This study explored the ability of different beta lactams to prevent daptomycin resistance development following in vitro serial passage in daptomycin.,collected_by:Andrew Berti,,,,,,,Infective Endocarditis,,Valve Replacement,,,,,,,,,,,,99.51,0.67,Bloodstream Infections,Other Bloodstream Infections,Ear,Bloodstream Infections-Other Bloodstream Infections HP,1280.21784,Staphylococcus aureus strain CFSAN082782,CFSAN082782,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09882578,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-09-09T00:00:00Z,,PRJNA278886,GCA_008329865.1,"CP031888,CP031889",,Brigham & Women's Hospital,PacBio,300x,HGAP v. 3,1,1,2,2893410,32.727646,2961,2972,nasal perirectal swab,,2018-04,USA,USA:MA,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.;MRSA,collected_by:Clinical Micorbiology Laboratory @ Brigham and Women's Hospital,,,,,,,missing,,,,,,,,MRSA,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1280.21785,Staphylococcus aureus strain CFSAN082781,CFSAN082781,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09882579,1280,,,,MLST.Staphylococcus_aureus.8,,,,2019-09-09T00:00:00Z,,PRJNA278886,GCA_008329885.1,"CP031890,CP031891",,Brigham & Women's Hospital,PacBio,210x,HGAP v. 3,1,1,2,2893422,32.727753,2962,2972,nasal perirectal swab,,2018-04,USA,USA:MA,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.;MRSA,collected_by:Clinical Micorbiology Laboratory @ Brigham and Women's Hospital,,,,,,,missing,,,,,,,,MRSA,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1280.21786,Staphylococcus aureus strain VGC1,VGC1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11431687,1280,,,,MLST.Staphylococcus_aureus.59,genotype:ST59,,,2019-09-09T00:00:00Z,,PRJNA533010,GCA_008330045.1,"CP039448,CP039449,CP039450",,National Health Research Institutes,Illumina HiSeq; Oxford Nanopore MiniION,445.0x,Canu v. 1.6; Unicycler v. 0.4.7,1,2,3,2889504,32.862907,2893,2881,blood,,2013-04,Taiwan,Taiwan: Taichung,,male,17,Pneumonia and Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,One strain isolated from a critical pneumonia and bacteremia patient was identified sharing the same genomic background of ST59-SCCmecV (“Taiwan clone”),collected_by:Pin-Kuei Fu,,,,,,,Pneumonia and Bacteremia,,,,,,,,,,,,,,99.51,0.22,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,1280.21787,Staphylococcus aureus strain CFSAN082783,CFSAN082783,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09882580,1280,,,,MLST.Staphylococcus_aureus.45,,,,2019-09-09T00:00:00Z,,PRJNA278886,GCA_008330585.1,"CP031886,CP031887",,Brigham & Women's Hospital,PacBio,170x,HGAP v. 3,1,1,2,2808051,32.91386,2847,2822,wound,,2018-05,USA,USA:MA,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.;MRSA,collected_by:Clinical Micorbiology Laboratory @ Brigham and Women's Hospital,,,,,,,missing,,,,,,,,MRSA,,,,,,99.49,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.21826,Staphylococcus aureus strain GHA12,GHA12,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722007,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630695.1,CP043912,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,166X,Geneious Prime v. Geneious Prime v,1,,1,2726530,32.945595,2615,2534,hospital,,2018-10-29,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.4,0.22,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21827,Staphylococcus aureus strain GHA13,GHA13,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722008,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630675.1,CP043911,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,352X,Geneious Prime v. Geneious Prime v,1,,1,2672245,32.659153,2655,2628,hospital,,2018-10-29,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,98,0.14,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21828,Staphylococcus aureus strain GHA11,GHA11,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722006,1280,,,,MLST.Staphylococcus_aureus.30,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630715.1,CP043913,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,175X,Geneious Prime v. Geneious Prime v,1,,1,2792580,32.90039,2700,2653,hospital,,2018-10-24,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.22,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21829,Staphylococcus aureus strain GHA9,GHA9,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722004,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630735.1,CP043915,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,74X,Geneious Prime v. Geneious Prime v,1,,1,2672254,32.65888,2666,2632,hospital,,2018-11-28,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,98,0.14,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21830,Staphylococcus aureus strain GHA6,GHA6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722001,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630755.1,CP043918,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,554X,Geneious Prime v. Geneious Prime v,1,,1,2778329,32.819912,2675,2649,hospital,,2018-10-29,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.22,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21831,Staphylococcus aureus strain GHA5,GHA5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722000,1280,,,,MLST.Staphylococcus_aureus.3249,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630775.1,CP043919,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,17X,Geneious Prime v. Geneious Prime v,1,,1,2735454,33.012215,2722,2612,hospital,,2018-11-19,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,94.27,0.56,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21832,Staphylococcus aureus strain GHA4,GHA4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12721999,1280,,,,,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630795.1,CP043920,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,24X,Geneious Prime v. Geneious Prime v,1,,1,2809532,32.953335,2795,2694,hospital,,2018-08-28,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,95.27,0.09,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21833,Staphylococcus aureus strain GHA7,GHA7,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722002,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630815.1,CP043917,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,551X,Geneious Prime v. Geneious Prime v,1,,1,2672282,32.643837,2594,2564,hospital,,2018-11-13,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,98,0.14,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21834,Staphylococcus aureus strain GHA3,GHA3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12721998,1280,,,,MLST.Staphylococcus_aureus.152,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630835.1,CP043921,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,208X,Geneious Prime v. Geneious Prime v,1,,1,2778348,32.843487,2704,2675,hospital,,2018-08-14,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.22,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21835,Staphylococcus aureus strain GHA2,GHA2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12721997,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630855.1,CP043922,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,379X,Geneious Prime v. Geneious Prime v,1,,1,2764963,32.90725,2698,2683,hospital,,2018-11-05,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21836,Staphylococcus aureus strain GHA1,GHA1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12721996,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-09-21T00:00:00Z,,PRJNA564764,GCA_008630875.1,CP043923,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,441X,Geneious Prime v. Geneious Prime v,1,,1,2848409,32.841152,2740,2699,hospital,,2018-07-09,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.4,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21838,Staphylococcus aureus strain GHA8,GHA8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722003,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-09-25T00:00:00Z,,PRJNA564764,GCA_008694145.1,CP043916,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,612X,Geneious Prime v. Geneious Prime v,1,,1,2787596,32.84393,2737,2716,hospital,,2018-09-06,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.21839,Staphylococcus aureus strain GHA10,GHA10,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12722005,1280,,,,MLST.Staphylococcus_aureus.3249,,,,2019-09-25T00:00:00Z,,PRJNA564764,GCA_008694165.1,CP043914,,Noguchi Memorial Institute for Medical Research,Illumina Miseq,233X,Geneious Prime v. Geneious Prime v,1,,1,2726612,32.89536,2664,2651,hospital,,2018-10-18,Ghana,Ghana: Accra,,,,Skin and soft tissue infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The study sought to determine the antimicrobial resistance patterns and to characterize strains of Staphylococcus aureus among patients with surgical site infections at two hospitals in Accra, Ghana. This study fills an important knowledge gap and will guide antimicrobial therapy and designing of potential interventions.","collected_by:NMIMR, Ghana",,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.51,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.22660,Staphylococcus aureus strain KG-03,KG-03,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00164374,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-10-11T00:00:00Z,31474962,PRJDB8056,GCA_009176765.1,AP019542,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Illumina NextSeq 500,200x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,,1,2945245,32.925682,2846,2787,blood specimens of a persistent bacteremia patient,isolated from blood specimens of a persistent bacteremia patient,2015,Japan,Japan:Tokyo,,,,,blood,,Susceptible;Resistant,Computational Prediction,,,,,,,,bacteremia,The purpose of this project is related to comparative omics analysis of vancomycin intermediate resistant Staphylococcus aureus strains sequentially isolated from blood specimens of a persistent bacteremia patient.,,not applicable,not applicable,blood,not applicable,DNAseq and RNAseq data of vancomycin intermediate resistant Staphylococcus aureus strains sequentially isolated from blood specimens of a persistent bacteremia patient.,persistent bacteremia,,,,,,,,,,,not applicable,,,,99.51,0.11,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.23629,Staphylococcus aureus strain ZY05,ZY05,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13011721,1280,,,,MLST.Staphylococcus_aureus.338,,,,2019-11-20T00:00:00Z,31682959,PRJNA576862,GCA_009684655.1,"CP045472,CP045473",,Zhejiang University,PacBio Sequel,100.0x,Unicycler v. 0.4.7,1,1,2,2848476,32.860695,2802,2785,blood,,2016-04-02,China,China:Hangzhou,,,,toxic shock syndrome,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This study focused on a sequence type 338 community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strain and revealed the relevance among MRSA strains from various lineages and areas.,collected_by:Yan Chen,,,,,,,toxic shock syndrome,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.23706,Staphylococcus aureus strain ST20130944,ST20130944,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10250996,1280,,,,MLST.Staphylococcus_aureus.30,,,,2019-12-04T00:00:00Z,,PRJNA497214,GCA_009728755.1,"CP033112,CP033113",,LNCC,IonTorrent; PacBio,100.0x,Newbler v. 3.0,1,1,2,2897766,32.849133,2854,2792,83-year-old man,,2005,France,France,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus is among the most important human pathogens associated with a wide variety of manifestations, ranging from superficial skin infections, such as folliculitis, furunculosis, carbuncles, abscesses or scalded skin syndrome, to life-threatening conditions, such as osteomyelitis, endocarditis, pneumonia and septicemia. Within the plethora of more severe conditions caused by S. aureus, are bone-joint infections (BJIs) caused by the invasion and progressive destruction of bone tissues and cartilages. This project was aimed to study the evolution of the bacterial genome during the course of BJIs.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,1280.23707,Staphylococcus aureus strain ST20130945,ST20130945,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10251108,1280,,,,MLST.Staphylococcus_aureus.30,,,,2019-12-04T00:00:00Z,,PRJNA497221,GCA_009728775.1,"CP033114,CP033115",,LNCC,PacBio; IonTorrent,100.0x,Newbler v. 3.0,1,1,2,2856204,32.83792,2794,2725,83-year-old man,,2005,France,France,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus is among the most important human pathogens associated with a wide variety of manifestations, ranging from superficial skin infections, such as folliculitis, furunculosis, carbuncles, abscesses or scalded skin syndrome, to life-threatening conditions, such as osteomyelitis, endocarditis, pneumonia and septicemia. Within the plethora of more severe conditions caused by S. aureus, are bone-joint infections (BJIs) caused by the invasion and progressive destruction of bone tissues and cartilages. This project was aimed to study the evolution of the bacterial genome during the course of BJIs.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,1280.23712,Staphylococcus aureus strain P1D14C1,P1D14C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374693,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739865.1,"CP033990,CP033988,CP033989",,Hebrew University,Illumina HiSeq,561x,Celera Assembler v. 1.7,1,2,3,2825707,32.880516,2836,2852,blood,,2017-05-17,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23713,Staphylococcus aureus strain P1D1C1,P1D1C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374685,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739845.1,"CP034014,CP034012,CP034013",,Hebrew University,PacBio + Illumina HiSeq,400x,Celera Assembler v. 1.7,1,2,3,2825900,32.879898,2836,2852,blood,,2017-05-04,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23714,Staphylococcus aureus strain P2D15C1,P2D15C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374696,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739715.1,"CP033977,CP033973,CP033974,CP033975,CP033976",,Hebrew University,Illumina HiSeq,1177x,Celera Assembler v. 1.7,1,4,5,2898198,32.802864,2932,2935,blood,,2017-10-17,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.95,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23715,Staphylococcus aureus strain P1D9C1,P1D9C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374691,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739735.1,"CP033996,CP033994,CP033995",,Hebrew University,Illumina HiSeq,548x,Celera Assembler v. 1.7,1,2,3,2825707,32.880444,2836,2852,blood,,2017-05-12,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23716,Staphylococcus aureus strain P1D7C1,P1D7C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374688,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739795.1,"CP034005,CP034003,CP034004",,Hebrew University,Illumina HiSeq,400x,Celera Assembler v. 1.7,1,2,3,2825899,32.87987,2836,2852,blood,,2017-05-10,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23717,Staphylococcus aureus strain P1D8C2,P1D8C2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374690,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739755.1,"CP033999,CP033997,CP033998",,Hebrew University,Illumina HiSeq,674x,Celera Assembler v. 1.7,1,2,3,2825900,32.87986,2836,2852,blood,,2017-05-11,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23718,Staphylococcus aureus strain P1D8C1,P1D8C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374689,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739775.1,"CP034002,CP034000,CP034001",,Hebrew University,Illumina HiSeq,600x,Celera Assembler v. 1.7,1,2,3,2825894,32.879826,2836,2852,blood,,2017-05-11,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.23719,Staphylococcus aureus strain P1D5C1,P1D5C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374686,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739825.1,"CP034011,CP034009,CP034010",,Hebrew University,Illumina HiSeq,592x,Celera Assembler v. 1.7,1,2,3,2825900,32.879898,2836,2852,blood,,2017-05-08,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.24172,Staphylococcus aureus strain P1D12C1,P1D12C1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374692,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009739885.1,"CP034259,CP034258,CP034257",,Hebrew University,Illumina HiSeq,549x,Celera Assembler v. 1.7,1,2,3,2825707,32.880444,2836,2852,blood,,2017-05-15,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.24173,Staphylococcus aureus strain P1D5C2,P1D5C2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10374687,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-12-11T00:00:00Z,,PRJNA503808,GCA_009740205.1,"CP034008,CP034006,CP034007",,Hebrew University,Illumina HiSeq,399x,Celera Assembler v. 1.7,1,2,3,2825900,32.879898,2836,2852,blood,,2017-05-08,Israel,Israel: Jerusalem,,,,ENDOCARDITIS,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Tolerance evolves fast under antibiotic treatments in patients with MRSA blood infection. We identified the mutations responsible for slow growth and tolerance.,collected_by:Shaare Zedek,,,,,,,ENDOCARDITIS,,,,,,,,,,,,,,98.9,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.24234,Staphylococcus aureus strain RJ1267,RJ1267,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13698767,1280,,,,MLST.Staphylococcus_aureus.630,genotype:ST630,,,2020-01-12T00:00:00Z,,PRJNA598122,GCA_009857055.1,"CP047321,CP047322",,USTC,PacBio RSII,1.0x,Unicycler v. 4.8,1,1,2,2901780,32.746864,2931,2878,sputum,"isolate from the Renji hospital affiliated to Shanghai Jiaotong University, China",2018-06-06,China,China: Shanghai,,female,,hyperbilirubinemia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Staphylococcus aureus multilocus sequence type 630 (ST630) is a human clinical isolate from the Renji hospital affiliated to Shanghai Jiaotong University, China.","collected_by:Renji hospital affiliated to Shanghai Jiaotong University, China",,,,,,,hyperbilirubinemia,,,,,,,,,,,,,,99.49,1.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.24256,Staphylococcus aureus strain WH3018,WH3018,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10135573,1280,,,,MLST.Staphylococcus_aureus.59,genotype:ST59,,,2020-01-15T00:00:00Z,,PRJNA493519,GCA_009883675.1,CP033085,,Wuhan Centers for Disease Prevention and Control,Hiseq,30x,MaSuRCA v. 3.2.8,1,0,1,2819961,32.93148,2891,2911,sputum,,2013-04-02,China,China: Wuhan,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Illumina HiSeq 2500 platform was used for whole-genome sequencing of this clone.,collected_by:Yuanshan Jiang,,,,,,,pneumonia,,,,,,PVL-Negative ST59,,,,,,,,99.51,1.73,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1280.24257,Staphylococcus aureus strain WH9628,WH9628,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10135572,1280,,,,,genotype:ST59,,,2020-01-15T00:00:00Z,,PRJNA493519,GCA_009883695.1,CP033086,,Wuhan Centers for Disease Prevention and Control,Hiseq,30x,MaSuRCA v. 3.2.8,1,0,1,2841969,33.021156,2921,2931,sputum,,2014-09-27,China,China: Wuhan,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Illumina HiSeq 2500 platform was used for whole-genome sequencing of this clone.,collected_by:Yuanshan Jiang,,,,,,,pneumonia,,,,,,PVL-Positive ST59,,,,,,,,99.51,1.65,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1280.24334,Staphylococcus aureus strain SAW1,SAW1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13025165,1280,,,,MLST.Staphylococcus_aureus.59,,,,2020-01-22T00:00:00Z,,PRJNA577395,GCA_009914455.1,"CP045468,CP045469,CP045470,CP045471",,Zhejiang University,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.7,1,3,4,2832410,32.83455,2845,2797,blood,,2018-01-25,China,China:Hangzhou,,,,endocarditis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,strain with daptomycin exposure,collected_by:Feng Zhao,,,,,,,endocarditis,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.25812,Staphylococcus aureus strain SR153,SR153,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13008646,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-02-17T00:00:00Z,,PRJNA576781,GCA_010669265.1,"CP048643,CP048644,CP048645,CP048646",,Zhejiang University,PacBio RSII,100.0x,Unicycler v. 0.4.7,1,3,4,2940975,32.731117,2951,2866,blood,,2013-06-01,China,China:Hangzhou,,,,acute pancreatitis and catheter related blood stream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A linezolid resistant staphylococcus aureus strain with cfr carrying in Chinese epidemic ST5-SCCmecII-t311 clone,collected_by:Wu Dandan,,,,,,,acute pancreatitis and catheter related blood stream infection,,,,,,,,,,,,,,99.32,0.13,Gastrointestinal Diseases,Pancreatic Disorders,Blood and Circulatory System,Gastrointestinal Diseases-Pancreatic Disorders HP,1280.25835,Staphylococcus aureus strain M2024,M2024,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13612188,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-02-27T00:00:00Z,,PRJNA596097,GCA_011035105.1,"CP047021,CP047022",,Hvidovre Hospital,Illumina MiSeq; Oxford Nanopore MiniION,150.0x,SPAdes v. 3.11,1,1,2,2811700,32.876194,2737,2709,hospital ward,,2011-08-06,Denmark,Denmark,,,,Skin infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Repeated introduction and spread of the MRSA clone t304/ST6 in Northern Europe,collected_by:Hvidovre Hospital,,,,,,,Skin infection,,,,,,,,,,,,,,99.51,0.1,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.28358,Staphylococcus aureus strain BLR-DV,BLR-DV,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15361562,1280,,,MRSA,MLST.Staphylococcus_aureus.239,,,,2020-07-06T00:00:00Z,,PRJNA641705,GCA_013389715.1,"CP058312,CP058313,CP058314",,Belarusian State Medical University,Oxford Nanopore MiniION; Illumina MiSeq,400.0x,Barapost v. v 3.14; Flye v. v.,1,2,3,2975033,32.872543,2954,2901,urine,,2016-12-10,Belarus,Belarus:Baranavichy,,male,71,Urologic Sepsis Syndrome,,host_disease_outcome:death;host_disease_stage:Urologic Sepsis Syndrome,Resistant,Computational Prediction,,,,,,,,,"Detection of geographical variation of Staphylococcus aureus circulating in Belarus and exhibiting drud resistance, and identification of genome variations associated with resistance.",collected_by:Slizen V.V.,,,,,,,Urologic Sepsis Syndrome,,death,,Urologic Sepsis Syndrome,MRSA,MRSA strain,,,,,,,,99.51,0.22,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,1280.28360,Staphylococcus aureus strain TPS3156,TPS3156,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00212273,1280,,,pathovar L,MLST.Staphylococcus_aureus.8,,,,2020-06-26T00:00:00Z,,PRJDB9398,GCA_013394425.1,"AP023034,AP023035",,Tokyo University of Pharmacy and Life Sciences,PacBio RSII,411x,RS HGAP Assembly v. 3.0,1,1,2,2877470,32.78109,2751,2715,,,2013,,,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Panton-Valentine leukocidin (PVL) is a one of virulence factor of Staphylococcus aureus. Among PVL-positive MRSAs, USA300 is known as a clone that is prevalent in various parts of the world. We have detected a number of USA300-Like strains in Japan. The whole genome analysis of TPS3156 was conducted and revealed that it belonged to USA300-LV.",,not applicable,not applicable,not applicable,aerobic,TPS3156,,,,,,,,,,,,not applicable,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.28364,Staphylococcus aureus strain 515798,515798,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13028851,1280,,,,MLST.Staphylococcus_aureus.1,,,,2020-07-14T00:00:00Z,,PRJNA577568,GCA_013414865.1,"CP045474,CP045475,CP045476",,LNCC,IonTorrent,80.0x,Newbler v. 2.9,1,2,3,2838852,32.768597,2843,2481,ca-mrsa blood site,,2005-03-28,Australia,Australia,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,98.66,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.28366,Staphylococcus aureus strain 08-028,08-028,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13025398,1280,,,,MLST.Staphylococcus_aureus.1,,,,2020-07-15T00:00:00Z,,PRJNA577414,GCA_013415955.1,"CP045435,CP045436,CP045437,CP045438",,LNCC,IonTorrent,159.0x,Newbler v. 2.9,1,3,4,2936025,32.83773,2893,2756,ha-mrsa blood clinical site,,2005-2009,Brazil,Brazil: Rio de Janeiro,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,99.46,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.28367,Staphylococcus aureus strain 111250134,111250134,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13028842,1280,,,,MLST.Staphylococcus_aureus.1,,,,2020-07-15T00:00:00Z,,PRJNA577563,GCA_013415995.1,"CP045442,CP045443",,LNCC,IonTorrent,62.0x,Newbler v. 2.9,1,1,2,2932476,32.79577,2926,2658,ca-mrsa blood site,,2011-2012,Canada,Canada,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,99.41,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.28368,Staphylococcus aureus strain 950122,950122,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13028840,1280,,,,MLST.Staphylococcus_aureus.1,,,,2020-07-15T00:00:00Z,,PRJNA577560,GCA_013415975.1,CP045441,,LNCC,IonTorrent,48.0x,Newbler v. 2.9,1,0,1,2809177,32.792202,2802,2480,ha-mrsa blood clinical site,,2009-2010,Canada,Canada,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,99.64,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.28375,Staphylococcus aureus strain 07-059,07-059,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13028838,1280,,,,MLST.Staphylococcus_aureus.1,,,,2020-07-20T00:00:00Z,,PRJNA577559,GCA_013426235.1,"CP045439,CP045440",,LNCC,IonTorrent,49.0x,Newbler v. 2.9,1,1,2,2910390,32.85127,2923,2647,ha-mrsa blood clinical site,,2005-2009,Brazil,Brazil: Rio de Janeiro,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"This genome sequencing is part of a genome project to sequencing the whole genome of the methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST1-SCCmecIV from different countries. In Brazil, ST1-SCCmecIV isolates have emerged as an important healthcare-associated pathogen.",sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,99.63,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1280.28540,Staphylococcus aureus strain 110900,110900,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15430096,1280,,,,MLST.Staphylococcus_aureus.630,,,,2020-07-28T00:00:00Z,,PRJNA643825,GCA_013836525.1,"CP058615,CP058616",,Statens Serum Institut,Illumina NextSeq; Oxford Nanopore MiniION,334x,SPAdes v. 3.9,1,1,2,2920712,32.700485,2912,2860,uberon:0002067,,2016-09-02,Denmark,Denmark,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus of sequence type 630 (ST630) and spa type t4549 is an emerging cause of infections in humans in Asia and since 2015 also in the Nordic countries including Denmark, where this lineage was among the most important community associated MRSA lineages in 2018. In this study, the emergence of MRSA ST630/t4549 in Denmark and other Nordic countries was investigated by comparative genomics in order to understand the recent emergence of this lineage in this area of generally low MRSA prevalence.",,UBERON:0000061,UBERON:0000061,UBERON:0002067,nose swab,,,,,,,,,,,,,UBERON:0000061,,,,99.51,1.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.29067,Staphylococcus aureus strain 128254,128254,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15430097,1280,,,,MLST.Staphylococcus_aureus.630,,,,2020-07-28T00:00:00Z,,PRJNA643825,GCA_013836745.1,"CP058613,CP058614",,Statens Serum Institut,Illumina NextSeq; Oxford Nanopore MiniION,219x,SPAdes v. 3.9,1,1,2,2879556,32.708134,2868,2822,uberon:0002067,,2018-11-06,Denmark,Denmark,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus of sequence type 630 (ST630) and spa type t4549 is an emerging cause of infections in humans in Asia and since 2015 also in the Nordic countries including Denmark, where this lineage was among the most important community associated MRSA lineages in 2018. In this study, the emergence of MRSA ST630/t4549 in Denmark and other Nordic countries was investigated by comparative genomics in order to understand the recent emergence of this lineage in this area of generally low MRSA prevalence.",,UBERON:0000061,UBERON:0000061,UBERON:0002067,nose swab,,,,,,,,,,,,,UBERON:0000061,,,,99.51,1.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1280.30704,Staphylococcus aureus strain K246,K246,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891915,1280,,,,MLST.Staphylococcus_aureus.291,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334395.1,CP060596,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814784,33.11375,2608,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.58,0.22,,,Other,- NHP,1280.30705,Staphylococcus aureus strain K245,K245,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891914,1280,,,,MLST.Staphylococcus_aureus.291,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334415.1,CP060597,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814788,33.11898,2601,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.79,0.22,,,Other,- NHP,1280.30706,Staphylococcus aureus strain K104,K104,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891913,1280,,,,MLST.Staphylococcus_aureus.7,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334435.1,CP060598,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814662,33.007217,2515,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,99.24,0.08,,,Other,- NHP,1280.30707,Staphylococcus aureus strain K099,K099,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891912,1280,,,,MLST.Staphylococcus_aureus.7,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334455.1,CP060599,,,Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814823,33.007202,2525,,nasal cavity,,2018,Germany,Germany,,,,,,,Susceptible,Computational Prediction,,,,,,,,healthy,,,,,,,,,,,,,,,,,,,,,,,99.26,0.08,,,Other,- NHP,1280.30708,Staphylococcus aureus strain K094,K094,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891911,1280,,,,,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334475.1,CP060600,,,Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814954,33.10317,2641,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,,collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.11,0.08,,,Other,- NHP,1280.30709,Staphylococcus aureus strain K152,K152,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891909,1280,,,,MLST.Staphylococcus_aureus.15,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334515.1,CP060602,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814854,32.97888,2558,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,98.03,0.08,,,Other,- NHP,1280.30710,Staphylococcus aureus strain K090,K090,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891910,1280,,,,,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334495.1,CP060601,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814929,33.108013,2638,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.39,0.08,,,Other,- NHP,1280.30711,Staphylococcus aureus strain K150,K150,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891908,1280,,,,MLST.Staphylococcus_aureus.15,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334535.1,CP060603,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814765,32.983334,2514,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,99.11,0.08,,,Other,- NHP,1280.30712,Staphylococcus aureus strain K112,K112,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891907,1280,,,,MLST.Staphylococcus_aureus.15,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334555.1,CP060604,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814919,32.984367,2499,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,98.92,0.08,,,Other,- NHP,1280.30713,Staphylococcus aureus strain K329,K329,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891906,1280,,,,MLST.Staphylococcus_aureus.913,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334575.1,CP060605,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814887,32.964005,2611,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.6,0.08,,,Other,- NHP,1280.30714,Staphylococcus aureus strain K276,K276,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891905,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334595.1,CP060606,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814869,32.992958,2577,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,97.97,0.08,,,Other,- NHP,1280.30715,Staphylococcus aureus strain K275,K275,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891904,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334615.1,CP060607,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814827,32.994102,2570,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,98.25,0.08,,,Other,- NHP,1280.30716,Staphylococcus aureus strain K084,K084,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891903,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334635.1,CP060608,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814903,32.996624,2527,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,99.12,0.08,,,Other,- NHP,1280.30717,Staphylococcus aureus strain K078,K078,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891902,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334655.1,CP060609,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814850,32.994736,2538,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,99.26,0.08,,,Other,- NHP,1280.30718,Staphylococcus aureus strain K076,K076,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891901,1280,,,,MLST.Staphylococcus_aureus.6,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334675.1,CP060610,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814919,32.99508,2528,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,99.26,0.08,,,Other,- NHP,1280.30719,Staphylococcus aureus strain K216,K216,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15891900,1280,,,,MLST.Staphylococcus_aureus.30,,,,2020-08-31T00:00:00Z,,PRJNA658858,GCA_014334695.1,CP060611,,"University of Bielefeld, Germany",Illumina MiSeq,80x,BWA v. MARCH-2020,1,0,1,2814892,33.053688,2770,,nasal cavity,,2018,Germany,Germany,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,healthy,"The FlueGe Health Study (University Bielefeld project aims to assess the health of a German Refugee Population by an interdisciplinary approach. In the microbiology subproject, nasal swabs of the refugees were screened for Staphylococcus aureus isolates. The isolates were typed (spa/MLST), experimentally characterized (resistances to antibiotics, biofilm formation) and Whole Genome Sequenced in order to evaluate their virulence potetial. Sampling was performed in context of the FlueGe study between January and August 2018. All participants are refugees, who came to Germany within five years before data acquisition. Each participant of the study has been asked to voluntarily provide a nasal swab.",collected_by:Ines Creutz and FlueGe-Team,,,,,,,,,,,,,,,,,,,,,90.08,0.22,,,Other,- HP,1280.30720,Staphylococcus aureus strain S6,S6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862863,1280,,,,,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014335265.1,CP060612,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,378x,Flye v. 2.8,1,0,1,2745419,32.85283,3608,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,94.59,0.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30721,Staphylococcus aureus strain S4,S4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862861,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014335435.1,CP060614,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,174x,Flye v. 2.8,1,0,1,2818135,32.797924,2691,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.81,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30722,Staphylococcus aureus strain S5,S5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862862,1280,,,,MLST.Staphylococcus_aureus.45,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014335605.1,CP060613,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,439x,Flye v. 2.8,1,0,1,2769829,33.004204,2637,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.76,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30723,Staphylococcus aureus strain S3,S3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862860,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014335755.1,CP060615,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,242x,Flye v. 2.8,1,0,1,2818112,32.798122,2673,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.95,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30724,Staphylococcus aureus strain S2,S2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862859,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014335895.1,CP060616,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,323x,Flye v. 2.8,1,0,1,2788374,32.84107,2667,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.95,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30725,Staphylococcus aureus strain S1,S1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862858,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336015.1,CP060617,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,315x,Flye v. 2.8,1,0,1,2788360,32.841057,2662,,clinical sample,,2020,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.43,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30726,Staphylococcus aureus strain R41,R41,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862856,1280,,,,MLST.Staphylococcus_aureus.772,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336195.1,CP060618,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,464x,Flye v. 2.8,1,0,1,2818610,32.82213,2720,,clinical sample,,2013,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.81,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30727,Staphylococcus aureus strain R40,R40,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862855,1280,,,,MLST.Staphylococcus_aureus.772,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336335.1,CP060619,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,540x,Flye v. 2.8,1,0,1,2831585,32.837433,2742,,clinical sample,,2013,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.88,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30728,Staphylococcus aureus strain R39,R39,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862854,1280,,,,MLST.Staphylococcus_aureus.772,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336505.1,CP060620,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,274x,Flye v. 2.8,1,0,1,2816027,32.825176,2727,,clinical sample,,2004,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.89,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30729,Staphylococcus aureus strain R34,R34,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862849,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336685.1,CP060621,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,448x,Flye v. 2.8,1,0,1,2822220,32.871494,2709,,clinical sample,,2011,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.81,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30730,Staphylococcus aureus strain R31,R31,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862846,1280,,,,MLST.Staphylococcus_aureus.1637,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336835.1,CP060622,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,591x,Flye v. 2.8,1,0,1,2782458,32.87057,2619,,clinical sample,,2009,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.95,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30731,Staphylococcus aureus strain R28,R28,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862843,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336965.1,CP060623,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,464x,Flye v. 2.8,1,0,1,2817267,32.881687,2687,,clinical sample,,2007,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.9,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30732,Staphylococcus aureus strain R27,R27,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862842,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014336995.1,CP060624,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,451x,Flye v. 2.8,1,0,1,2802192,32.88525,2654,,clinical sample,,2007,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.76,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30733,Staphylococcus aureus strain R26,R26,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862841,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337015.1,CP060625,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,523x,Flye v. 2.8,1,0,1,2807085,32.89604,2676,,clinical sample,,2007,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.9,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30734,Staphylococcus aureus strain R24,R24,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862839,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337035.1,CP060626,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,237x,Flye v. 2.8,1,0,1,2807011,32.89602,2677,,clinical sample,,2006,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.95,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30735,Staphylococcus aureus strain R21,R21,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862836,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337055.1,CP060627,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,431x,Flye v. 2.8,1,0,1,2836126,32.854424,2752,,clinical sample,,2012,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.81,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30736,Staphylococcus aureus strain R20,R20,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862835,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337075.1,CP060628,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,273x,Flye v. 2.8,1,0,1,2786373,32.875385,2692,,clinical sample,,2012,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.73,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30737,Staphylococcus aureus strain R16,R16,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862831,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337095.1,CP060629,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,946x,Flye v. 2.8,1,0,1,2881699,32.86842,2824,,clinical sample,,2011,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.89,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30738,Staphylococcus aureus strain R9,R9,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862824,1280,,,,,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337115.1,CP060630,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,772x,Flye v. 2.8,1,0,1,2880126,32.869183,2907,,clinical sample,,2007,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.57,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30739,Staphylococcus aureus strain R3,R3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15862819,1280,,,,MLST.Staphylococcus_aureus.8,,,,2020-08-31T00:00:00Z,,PRJNA658251,GCA_014337135.1,CP060631,,"Akershus University Hospital, University of Oslo",Oxford Nanopore GridION,137x,Flye v. 2.8,1,0,1,2880247,32.865196,2774,,clinical sample,,2005,Norway,Norway,,,,Staphylococcus aureus infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak investigations are essential to control and prevent the dissemination of pathogens. This project developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole genome sequencing,collected_by:Ahus,,,,,,,Staphylococcus aureus infection,,,,,,,,,,,,,,98.95,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30901,Staphylococcus aureus strain MRSA - AMRF 4,MRSA - AMRF 4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11974903,1280,,,,MLST.Staphylococcus_aureus.2066,,,,2020-11-03T00:00:00Z,,PRJNA547699,GCA_015219885.1,"CP062469,CP062470",,Aravind Medical Research Foundation,Oxford Nanopore MiniION,183.69x,Canu v. 1.8,1,1,2,2917593,32.81688,2938,2833,eye,,,India,India:Madurai,,,,Eye disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of Bacterial keratitis infection, causing significant morbidity and mortality in developing countries like India. Thus, MRSA ocular infections are diseases of emerging importance, which need our attention for best and effective therapeutics. Identification of its genetic determinants of pathogenesis in ocular infections is hindered by the unavailability of its complete genome sequence. Several studies reported that ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Here, we report the results of a de novo assembly using Oxford nanopore long reads, complemented with Illumina short reads for polishing and comparative study of clinically significant antibiotic-resistant MRSA Keratitis isolates.",collected_by:Aravind eye hospital,,,,,,,Eye disease,,,,,,,,,,,,,,99.48,1.2,Eye Conditions,,Eye,Eye Conditions- HP,1280.30902,Staphylococcus aureus strain MRSA - AMRF 5,MRSA - AMRF 5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11974904,1280,,,,MLST.Staphylococcus_aureus.772,,,,2020-11-03T00:00:00Z,,PRJNA547699,GCA_015219905.1,"CP062467,CP062468",,Aravind Medical Research Foundation,Oxford Nanopore MiniION,50.92x,Canu v. 1.8,1,1,2,2941588,32.881252,2960,2862,eye,,,India,India:Madurai,,,,Eye disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of Bacterial keratitis infection, causing significant morbidity and mortality in developing countries like India. Thus, MRSA ocular infections are diseases of emerging importance, which need our attention for best and effective therapeutics. Identification of its genetic determinants of pathogenesis in ocular infections is hindered by the unavailability of its complete genome sequence. Several studies reported that ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Here, we report the results of a de novo assembly using Oxford nanopore long reads, complemented with Illumina short reads for polishing and comparative study of clinically significant antibiotic-resistant MRSA Keratitis isolates.",collected_by:Aravind eye hospital,,,,,,,Eye disease,,,,,,,,,,,,,,99.41,0.08,Eye Conditions,,Eye,Eye Conditions- HP,1280.30903,Staphylococcus aureus strain MRSA - AMRF 6,MRSA - AMRF 6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11974905,1280,,,,MLST.Staphylococcus_aureus.2066,,,,2020-11-03T00:00:00Z,,PRJNA547699,GCA_015219925.1,"CP062465,CP062466",,Aravind Medical Research Foundation,Oxford Nanopore MiniION,193.26x,Canu v. 1.8,1,1,2,2892675,32.78571,2913,2820,eye,,,India,India:Madurai,,,,Eye disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of Bacterial keratitis infection, causing significant morbidity and mortality in developing countries like India. Thus, MRSA ocular infections are diseases of emerging importance, which need our attention for best and effective therapeutics. Identification of its genetic determinants of pathogenesis in ocular infections is hindered by the unavailability of its complete genome sequence. Several studies reported that ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Here, we report the results of a de novo assembly using Oxford nanopore long reads, complemented with Illumina short reads for polishing and comparative study of clinically significant antibiotic-resistant MRSA Keratitis isolates.",collected_by:Aravind eye hospital,,,,,,,Eye disease,,,,,,,,,,,,,,99.51,1.2,Eye Conditions,,Eye,Eye Conditions- HP,1280.30904,Staphylococcus aureus strain MRSA - AMRF 3,MRSA - AMRF 3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11974902,1280,,,,MLST.Staphylococcus_aureus.772,,,,2020-11-03T00:00:00Z,,PRJNA547699,GCA_015220695.1,"CP062471,CP062472",,Aravind Medical Research Foundation,Oxford Nanopore MiniION,178.11x,Canu v. 1.8,1,1,2,2853272,32.82428,2791,2710,eye,,,India,India:Madurai,,,,Eye disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of Bacterial keratitis infection, causing significant morbidity and mortality in developing countries like India. Thus, MRSA ocular infections are diseases of emerging importance, which need our attention for best and effective therapeutics. Identification of its genetic determinants of pathogenesis in ocular infections is hindered by the unavailability of its complete genome sequence. Several studies reported that ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Here, we report the results of a de novo assembly using Oxford nanopore long reads, complemented with Illumina short reads for polishing and comparative study of clinically significant antibiotic-resistant MRSA Keratitis isolates.",collected_by:Aravind eye hospital,,,,,,,Eye disease,,,,,,,,,,,,,,99.44,0.64,Eye Conditions,,Eye,Eye Conditions- HP,1280.30909,Staphylococcus aureus strain WH52,WH52,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15887715,1280,,,,MLST.Staphylococcus_aureus.630,,,,2020-11-05T00:00:00Z,,PRJNA658738,GCA_015244035.1,CP060584,,Zhongnan Hospital of Wuhan University,Illumina NovaSeq,1x,Pacbio RSII v. v1.10,1,0,1,2842754,32.74128,2803,2753,wound secretion,,2018-05-18,China,China,,,,Nosocomial infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We detected some Staphylococcus aureus collected from Wuhan, Ningxia, Hainan, and Beijing.",collected_by:Zhongnan Hospital of Wuhan University,,,,,,,Nosocomial infection,,,,,,,,,,,,,,99.51,0.64,Nosocomial Infections,Other Nosocomial Infections,Skin and Soft Tissue,Nosocomial Infections-Other Nosocomial Infections HP,1280.30926,Staphylococcus aureus strain KHS103,KHS103,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16435353,1280,,,,,,,,2020-11-07T00:00:00Z,,PRJNA636233,GCA_015277595.1,CP063801,,ICAR-National Institute of Veterinary Epidemiology and Disease Informatics,Illumina HiSeq,75x,Spades v. 3.14.1,1,0,1,2750408,32.700817,2719,2674,hand,,2019,India,India: Karnataka,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Does antimicrobial resistance (AMR) in livestock contribute to AMR in NE India? An interdisciplinary study investigating antibiotic use, drivers of AMR and transmission dynamics","sample_type:tissue sample;biomaterial_provider:B. R. Shome;collected_by:Kundavee, Vinay, Devi, Yogisharadya",,,,,,,,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.30927,Staphylococcus aureus strain WMC_NY,WMC_NY,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16574825,1280,,,,MLST.Staphylococcus_aureus.5,,,,2020-11-09T00:00:00Z,,PRJNA672694,GCA_015290965.1,CP063990,,NASA,Oxford Nanopore MinION,75x,Flye v. 2.6; Racon v. 1.4.7; Medaka v.,1,0,1,2826257,32.909462,2760,,clinical isolate,,2018-07-06,USA,"USA: New York, Westchester Medical Center",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"A rapid assembly protocol was leveraged to quickly generate genome assemblies of prokaryotes using minimal computational resources. These assemblies were passed to a pipeline to assemble genome-scale metabolic network reconstructions of these microorganisms. The genomes include a validation reference (E. coli K12 MG1655 BOP27) and three (3) clinical isolates of pathogenic bacteria (Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus faecium).",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.71,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.31203,Staphylococcus aureus strain MSSA01,MSSA01,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16093280,1280,,,,MLST.Staphylococcus_aureus.582,,,,2020-12-03T00:00:00Z,,PRJNA662727,GCA_015732455.1,CP061349,,University of central Florida,"Illumina MiSeq, Oxford Nanopore",50.0x,Unicycler v. 0.4.8,1,0,1,2792190,32.891994,2730,2687,missing,,2019,USA,USA: Pennsylvania,,,,Staphylococcal Scalded-Skin Syndrome,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete Genome Sequence of an Exfoliative Toxin Producing Staphylococcus aureus Strain MSSA_SSSS_01,,,,,,,,Staphylococcal Scalded-Skin Syndrome,,,,,,,,,,,,,,99.41,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.31569,Staphylococcus aureus strain WH39,WH39,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15854353,1280,,,,MLST.Staphylococcus_aureus.630,,,,2021-01-05T00:00:00Z,,PRJNA657972,GCA_016496025.1,"CP060491,CP060492",,Zhongnan Hospital of Wuhan University,Illumina NovaSeq; PacBio RSII,432.0x,flye v. v2.5; CANU v. v1.7.1,1,1,2,2893747,32.69042,2886,2829,wound secretion,,2018-05-11,China,China,,,,fracture,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The strain was collected from a hospital in Wuhan. We expect to explain its relationship with clinical practice by the whole genome sequence and analyze the composition of the virulence gene and drug resistance gene.,collected_by:Zhongnan Hospital of Wuhan University,,,,,,,fracture,,,,,,,,,,,,,,99.51,1.2,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,1280.32247,Staphylococcus aureus strain MEI001,MEI001,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13388595,1280,,,,MLST.Staphylococcus_aureus.97,,,,2021-03-03T00:00:00Z,,PRJNA591785,GCA_017161095.1,"CP046476,CP046477",,University of Bern,Oxford Nanopore MiniION and illumina,100x,Unicycler v. 0.4.4,1,1,2,2746973,32.85591,2685,2647,healthy human nose,,2019-10,Switzerland,Switzerland: Bern,,,,,,,Susceptible,Computational Prediction,,,,,,,,,WGS of Staphylococcus aureus from healthy human nose,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.51,0.08,,,Other,- NHP,1280.32988,Staphylococcus aureus strain 17Gst354,17Gst354,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12342460,1280,,,,MLST.Staphylococcus_aureus.398,,,,2021-04-23T00:00:00Z,,PRJNA721254,GCA_018135565.1,"CP073065,CP073064",,"Institute of Veterinary Bacteriology, University of Bern",PacBio Sequel; Illumina NextSeq,791.0x,Unicycler v. v0.4.4,1,1,2,2788328,32.93411,2725,2675,human nose,,2017-11-25,Switzerland,Switzerland,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Investigation of Staphylococcal phages.,collected_by:IVB,,,,,,,healthy,,,,,,,,,,,,,,99.51,0.08,,,Other,- HP,1280.32992,Staphylococcus aureus strain iso141,iso141,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN18317715,1280,,,,,,,,2021-05-06T00:00:00Z,33808095,PRJNA714681,GCA_018292225.1,CP071941,,Akershus University Hospital,Oxford Nanopore GridION,402x,flye v. 2.7.1,1,0,1,2883453,32.857445,3510,,tissue,,2017,Norway,Norway,,,,Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"S. aureus assemblies from a culture-independent shotgun metagenomic nanopore sequencing performed directly on tissue biopsies. The aim was to test a culture independent protocol for the genotyping, virulence and AMR gene detection of OIAI. These are S. auresus assemblies from the study.",collected_by:Akershus University Hospital,,,,,,,Infection,,,,,,,,,,,,,,96.19,0.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.32993,Staphylococcus aureus strain iso139,iso139,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN18317713,1280,,,,,,,,2021-05-06T00:00:00Z,33808095,PRJNA714681,GCA_018292245.1,CP071943,,Akershus University Hospital,Oxford Nanopore GridION,231x,flye v. 2.7.1,1,0,1,2816259,32.831463,3428,,tissue,,2017,Norway,Norway,,,,Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"S. aureus assemblies from a culture-independent shotgun metagenomic nanopore sequencing performed directly on tissue biopsies. The aim was to test a culture independent protocol for the genotyping, virulence and AMR gene detection of OIAI. These are S. auresus assemblies from the study.",collected_by:Akershus University Hospital,,,,,,,Infection,,,,,,,,,,,,,,96.14,0.38,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.32994,Staphylococcus aureus strain iso140,iso140,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN18317714,1280,,,,,,,,2021-05-06T00:00:00Z,33808095,PRJNA714681,GCA_018292265.1,CP071942,,Akershus University Hospital,Oxford Nanopore GridION,22x,flye v. 2.7.1,1,0,1,2736340,32.929314,3814,,tissue,,2017,Norway,Norway,,,,Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"S. aureus assemblies from a culture-independent shotgun metagenomic nanopore sequencing performed directly on tissue biopsies. The aim was to test a culture independent protocol for the genotyping, virulence and AMR gene detection of OIAI. These are S. auresus assemblies from the study.",collected_by:Akershus University Hospital,,,,,,,Infection,,,,,,,,,,,,,,93.44,0.93,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.32995,Staphylococcus aureus strain SR231,SR231,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13875136,1280,,,,MLST.Staphylococcus_aureus.965,,,,2021-05-11T00:00:00Z,,PRJNA601847,GCA_018336515.1,"CP047922,CP047923",,Zhejiang University,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,1,2,2929593,32.882214,2909,2861,secretions,,2013-10-22,China,China:Hangzhou,,,,arthritis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This study descripts the erm gene among MRSA strains.,collected_by:Feng Zhao,,,,,,,arthritis,,,,,,,,,,,,,,99.51,0.08,Bone and Joint Infections,Septic Arthritis,Other,Bone and Joint Infections-Septic Arthritis HP,1280.32996,Staphylococcus aureus strain SR130,SR130,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13875135,1280,,,,MLST.Staphylococcus_aureus.965,,,,2021-05-11T00:00:00Z,,PRJNA601847,GCA_018336535.1,"CP047924,CP047925",,Zhejiang University,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,1,2,2838668,32.88264,2779,2751,pus,,2013-03-15,China,China:Hangzhou,,,,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This study descripts the erm gene among MRSA strains.,collected_by:Feng Zhao,,,,,,,pneumonia,,,,,,,,,,,,,,99.51,0.08,Respiratory Diseases,Pneumonia,Skin and Soft Tissue,Respiratory Diseases-Pneumonia HP,1280.33000,Staphylococcus aureus strain PNID0137,PNID0137,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN18227822,1280,,,,MLST.Staphylococcus_aureus.977,,,,2021-05-19T00:00:00Z,,PRJNA708260,GCA_018399115.1,CP071594,,Pusan National University Hospital,PacBio RSII,326X,HGAP v. 2.3,1,0,1,2914236,32.85269,2901,2835,blood,,2015-03-08,South Korea,South Korea: Busan,,,,Vertebral osteomyelitis with bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To evaluate genomes of MSSAs which are clinically important,collected_by:PNUH ID Lab,,,,,,,Vertebral osteomyelitis with bacteremia,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.33504,Staphylococcus aureus strain ST59,ST59,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19700552,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-06-23T00:00:00Z,,PRJNA737582,GCA_018987365.1,CP076823,,University of Science and Technology of China,PacBio RSII,1.05x,"canu v. 1,3",1,0,1,2789576,32.883385,2713,2659,china: shanghai,,2012,China,China: Shanghai,,,,Skin and soft tissue infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Clinical isolate from skin and soft tissue infections,collected_by:Min Li,,,,,,,Skin and soft tissue infections,,,,,,,,,,,,,,99.42,0.22,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.34330,Staphylococcus aureus strain V8,V8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20227817,1280,,,,MLST.Staphylococcus_aureus.8,,ATCC:49775,,2021-07-25T00:00:00Z,,PRJNA746562,GCA_019334585.1,CP079715,,National Center for Toxicology Research,PacBio,150.0x,CANU v. 1.7.1,1,0,1,2835652,32.833576,2801,2781,human furuncles,,1936,United Kingdom,United Kingdom,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,S. aureus involved in Superinfections post influenza,,Human Furuncles,Human Furuncles,London Hospital,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082194/pdf/brjexppathol00380-0002.pdf,,,,,,,,,,,,,Human Furuncles,,,,99.51,0.36,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.34728,Staphylococcus aureus strain BSN14R1,BSN14R1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20178839,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-07-29T00:00:00Z,,PRJNA745996,GCA_019395185.1,CP080053,,UC San Diego,Illumina HiSeq,50x,SPAdes v. 3.12,1,0,1,2944341,32.83128,2970,2947,,,2020-01-01,USA,USA: Detroit,,,,MRSA Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Understating how antibiotic tolerance impacts subsequent resistance development in the clinical setting is important to identifying effective therapeutic interventions and prevention measures. This study describes a patient case of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia which rapidly developed resistance to three primary MRSA therapies and identifies genetic and metabolic changes selected in vivo that are associated with rapid resistance evolution. Index blood cultures displayed susceptibility to all (non-beta-lactam) antibiotics. One month after initial presentation, during the same encounter, blood cultures were again positive for MRSA, now displaying intermediate resistance to vancomycin and ceftaroline and resistance to daptomycin. Two weeks later, blood cultures were positive for a third time, still resistant to vancomycin and daptomycin but now ceftaroline-susceptible alongside a resistant-but-lower daptomycin MIC. Mutations in mprF and vraT were common to all multidrug resistant isolates whereas mutations in tagH, agrB and saeR and secondary mprF mutation emerged sequentially and transiently resulting in distinct in vitro phenotypes. The baseline mutation rate of the patient isolates was unremarkable ruling out the hypermutator phenotype as a contributor to the rapid emergence of resistance. However, the index isolates demonstrated pronounced tolerance to the antibiotic daptomycin, a phenotype that facilitates the subsequent development of resistance during antibiotic exposure. This study exemplifies the capacity of antibiotic-tolerant pathogens to rapidly develop both stable and transient genetic and phenotypic changes, over the course of a single patient encounter.",collected_by:A Berti,,,,,,,MRSA Infection,,,,,,,,,,,,,,99.37,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.34729,Staphylococcus aureus strain BSN14S3,BSN14S3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20178841,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-07-29T00:00:00Z,,PRJNA745996,GCA_019395225.1,CP080055,,UC San Diego,Illumina HiSeq,50x,SPAdes v. 3.12,1,0,1,2944342,32.8311,2969,2944,,,2020-01-01,USA,USA: Detroit,,,,MRSA Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Understating how antibiotic tolerance impacts subsequent resistance development in the clinical setting is important to identifying effective therapeutic interventions and prevention measures. This study describes a patient case of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia which rapidly developed resistance to three primary MRSA therapies and identifies genetic and metabolic changes selected in vivo that are associated with rapid resistance evolution. Index blood cultures displayed susceptibility to all (non-beta-lactam) antibiotics. One month after initial presentation, during the same encounter, blood cultures were again positive for MRSA, now displaying intermediate resistance to vancomycin and ceftaroline and resistance to daptomycin. Two weeks later, blood cultures were positive for a third time, still resistant to vancomycin and daptomycin but now ceftaroline-susceptible alongside a resistant-but-lower daptomycin MIC. Mutations in mprF and vraT were common to all multidrug resistant isolates whereas mutations in tagH, agrB and saeR and secondary mprF mutation emerged sequentially and transiently resulting in distinct in vitro phenotypes. The baseline mutation rate of the patient isolates was unremarkable ruling out the hypermutator phenotype as a contributor to the rapid emergence of resistance. However, the index isolates demonstrated pronounced tolerance to the antibiotic daptomycin, a phenotype that facilitates the subsequent development of resistance during antibiotic exposure. This study exemplifies the capacity of antibiotic-tolerant pathogens to rapidly develop both stable and transient genetic and phenotypic changes, over the course of a single patient encounter.",collected_by:A Berti,,,,,,,MRSA Infection,,,,,,,,,,,,,,99.37,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.34730,Staphylococcus aureus strain BSN14RB,BSN14RB,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20178840,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-07-29T00:00:00Z,,PRJNA745996,GCA_019395205.1,CP080054,,UC San Diego,Illumina HiSeq,50x,SPAdes v. 3.12,1,0,1,2944325,32.83122,2971,2948,,,2020-01-01,USA,USA: Detroit,,,,MRSA Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Understating how antibiotic tolerance impacts subsequent resistance development in the clinical setting is important to identifying effective therapeutic interventions and prevention measures. This study describes a patient case of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia which rapidly developed resistance to three primary MRSA therapies and identifies genetic and metabolic changes selected in vivo that are associated with rapid resistance evolution. Index blood cultures displayed susceptibility to all (non-beta-lactam) antibiotics. One month after initial presentation, during the same encounter, blood cultures were again positive for MRSA, now displaying intermediate resistance to vancomycin and ceftaroline and resistance to daptomycin. Two weeks later, blood cultures were positive for a third time, still resistant to vancomycin and daptomycin but now ceftaroline-susceptible alongside a resistant-but-lower daptomycin MIC. Mutations in mprF and vraT were common to all multidrug resistant isolates whereas mutations in tagH, agrB and saeR and secondary mprF mutation emerged sequentially and transiently resulting in distinct in vitro phenotypes. The baseline mutation rate of the patient isolates was unremarkable ruling out the hypermutator phenotype as a contributor to the rapid emergence of resistance. However, the index isolates demonstrated pronounced tolerance to the antibiotic daptomycin, a phenotype that facilitates the subsequent development of resistance during antibiotic exposure. This study exemplifies the capacity of antibiotic-tolerant pathogens to rapidly develop both stable and transient genetic and phenotypic changes, over the course of a single patient encounter.",collected_by:A Berti,,,,,,,MRSA Infection,,,,,,,,,,,,,,99.37,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.34757,Staphylococcus aureus strain HL18840,HL18840,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301235,1280,,,,MLST.Staphylococcus_aureus.72,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019550875.1,CP080551,,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,649x,SPAdes v. 3.14.0,1,0,1,2796963,32.854637,2720,2685,blood,,2016,South Korea,South Korea:Seoul,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34758,Staphylococcus aureus strain HL17064,HL17064,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301231,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019550945.1,"CP080560,CP080561",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,549x,SPAdes v. 3.14.0,1,1,2,2956278,32.941048,2943,2890,blood,,2015,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34759,Staphylococcus aureus strain HL18807,HL18807,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301234,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551315.1,CP080552,,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,435x,SPAdes v. 3.14.0,1,0,1,2903929,32.918503,2875,2828,blood,,2016,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34760,Staphylococcus aureus strain HL18883,HL18883,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301236,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551035.1,CP080550,,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,867x,SPAdes v. 3.14.0,1,0,1,2904018,32.92032,2874,2826,blood,,2016,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34761,Staphylococcus aureus strain HL17078,HL17078,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301232,1280,,,,,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551175.1,"CP080556,CP080557,CP080558,CP080559",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,515x,SPAdes v. 3.14.0,1,3,4,2988155,32.722164,2983,2945,blood,,2015,South Korea,South Korea:Seoul,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.64,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34762,Staphylococcus aureus strain HL18380,HL18380,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301233,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551235.1,"CP080553,CP080554,CP080555",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,607x,SPAdes v. 3.14.0,1,2,3,2947175,32.776745,2940,2894,blood,,2016,South Korea,South Korea:Seoul,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.64,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34763,Staphylococcus aureus strain HL21008,HL21008,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301239,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551095.1,"CP080562,CP080563",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,507x,SPAdes v. 3.14.0,1,1,2,2972739,32.894344,2970,2916,blood,,2017,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34764,Staphylococcus aureus strain HL18888,HL18888,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301237,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551375.1,"CP080548,CP080549",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,441x,SPAdes v. 3.14.0,1,1,2,2917929,32.850147,2884,2841,blood,,2016,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.09,0.13,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34765,Staphylococcus aureus strain HL20835,HL20835,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301238,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551415.1,"CP080566,CP080567",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,501x,SPAdes v. 3.14.0,1,1,2,2937977,32.872757,2921,2891,blood,,2017,South Korea,South Korea:Seoul,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.26,0.18,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34766,Staphylococcus aureus strain HL16278,HL16278,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17301230,1280,,,,MLST.Staphylococcus_aureus.72,,,,2021-08-11T00:00:00Z,,PRJNA693997,GCA_019551355.1,"CP080564,CP080565",,Hallym University College of Medicine,Oxford Nanopore MinION; Illumina MiSeq,817x,SPAdes v. 3.14.0,1,1,2,2760709,32.81215,2668,2633,blood,,2014,South Korea,South Korea:Seoul,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequencing and assembly of most prevalent Spa types among clinical isolates of methicillin-resistant Staphylococcus aureus in Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34770,Staphylococcus aureus strain HL23187,HL23187,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14846125,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-08-16T00:00:00Z,,PRJNA630831,GCA_019603375.1,"CP080770,CP080771",,Hallym University College of Medicine,Illumina MiSeq; Oxford Nanopore MinION,426.0x,SPAdes v. 3.14.0,1,1,2,2860005,32.88246,2786,2755,blood,,2019,South Korea,South Korea: Seoul,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequence of Staphylococcus aureus SCCmec type V isolated from Korea,collected_by:Kandong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.34772,Staphylococcus aureus strain RGB-095930,RGB-095930,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19770946,1280,,,,,"genotype:MLST: aroE-3, glpF-1, gmk-1, pta-4, tpi-4, yqil-3, RIDOM spa: 08-16-02-25-51-51-51-51, SCCmec IVg",,,2021-08-17T00:00:00Z,,PRJNA739061,GCA_019653615.1,CP077098,,Leibniz Institute of Photonic Technology (IPHT),Oxford Nanopore MinION; Illumina MiniSeq,169.0x,Flye v. 2.8-b1674,1,0,1,2904556,32.860962,2894,2850,swab,,2014,Germany,"Germany: Regensburg, Bavaria",,male,adult,Admission/pre-OP screening. Later sepsis,,host_disease_outcome:survived,Resistant;Susceptible,Computational Prediction,,,,,,,,,"This strain comprised of segments originating from two different clonal complexes (CC). While the backbone of the genome, i.e., roughly 2 megabases, belongs to CC8, a continuous insert of 894 kb (approx. 30% of the genome, including an SCCmec IV element) originated from CC140.","collected_by:Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany",,,,,,,Admission/pre-OP screening. Later sepsis,,survived,,,,,,,,,,,,99.48,0.64,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,1280.34801,Staphylococcus aureus strain S36,S36,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00269945,1280,,,,MLST.Staphylococcus_aureus.1232,genotype:ST1232,,,2021-05-08T00:00:00Z,,PRJDB11000,GCA_019669385.1,"AP024318,AP024319",,Tokyo University of Pharmacy and Life Sciences,MGI DNBSEQ; ONT GridION,2460x,Unicycler v. 0.4.7,1,1,2,2777124,32.943794,2629,2588,humans but also from livestock animals; the mrsa strains originated from livestock animals are termed as livestock-associated mrsa (la-mrsa),isolated not only from humans but also from livestock animals; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA),2019,Japan,Japan,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Methicillin-resistant Staphylococcus aureus (MRSA) has been isolated not only from humans but also from livestock animals\; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA). Although LA-MRSA strains are considered low virulent, they can colonize and infect humans. The major genotypes of LA-MRSA are sequence types (ST) 398 and ST9 in Europe and Asia, respectively. However, patient infected by ST398 and ST9 strains has not yet been reported in Japan and Korea. Recently, two cases of infectious disease caused by ST1232 strains were reported in Japan\; ST1232 is a single locus variant of ST398. Additionally, we identified two ST1232 strains in Vietnamese and Korean patients. In this project, comparative genomics analysis for those strains was conducted to investigate relationship between ST1232 strains isolated in Korea and Japan.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.34802,Staphylococcus aureus strain BDH17,BDH17,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00269944,1280,,,,MLST.Staphylococcus_aureus.1232,genotype:ST1232,,,2021-05-08T00:00:00Z,,PRJDB11000,GCA_019669345.1,"AP024315,AP024316,AP024317",,Tokyo University of Pharmacy and Life Sciences,MGI DNBSEQ; ONT GridION,1932x,Unicycler v. 0.4.7,1,2,3,2813111,32.916546,2661,2621,humans but also from livestock animals; the mrsa strains originated from livestock animals are termed as livestock-associated mrsa (la-mrsa),isolated not only from humans but also from livestock animals; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA),2019,South Korea,South Korea,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Methicillin-resistant Staphylococcus aureus (MRSA) has been isolated not only from humans but also from livestock animals\; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA). Although LA-MRSA strains are considered low virulent, they can colonize and infect humans. The major genotypes of LA-MRSA are sequence types (ST) 398 and ST9 in Europe and Asia, respectively. However, patient infected by ST398 and ST9 strains has not yet been reported in Japan and Korea. Recently, two cases of infectious disease caused by ST1232 strains were reported in Japan\; ST1232 is a single locus variant of ST398. Additionally, we identified two ST1232 strains in Vietnamese and Korean patients. In this project, comparative genomics analysis for those strains was conducted to investigate relationship between ST1232 strains isolated in Korea and Japan.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.34803,Staphylococcus aureus strain N1195,N1195,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00269943,1280,,,,MLST.Staphylococcus_aureus.1232,genotype:ST1232,,,2021-05-08T00:00:00Z,,PRJDB11000,GCA_019669245.1,"AP024313,AP024314",,Tokyo University of Pharmacy and Life Sciences,MGI DNBSEQ; ONT GridION,2305x,Unicycler v. 0.4.7,1,1,2,2853441,32.95109,2725,2684,humans but also from livestock animals; the mrsa strains originated from livestock animals are termed as livestock-associated mrsa (la-mrsa),isolated not only from humans but also from livestock animals; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA),2017,Japan,Japan,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Methicillin-resistant Staphylococcus aureus (MRSA) has been isolated not only from humans but also from livestock animals\; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA). Although LA-MRSA strains are considered low virulent, they can colonize and infect humans. The major genotypes of LA-MRSA are sequence types (ST) 398 and ST9 in Europe and Asia, respectively. However, patient infected by ST398 and ST9 strains has not yet been reported in Japan and Korea. Recently, two cases of infectious disease caused by ST1232 strains were reported in Japan\; ST1232 is a single locus variant of ST398. Additionally, we identified two ST1232 strains in Vietnamese and Korean patients. In this project, comparative genomics analysis for those strains was conducted to investigate relationship between ST1232 strains isolated in Korea and Japan.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.34804,Staphylococcus aureus strain THI2018-120,THI2018-120,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00269942,1280,,,,MLST.Staphylococcus_aureus.1232,genotype:ST1232,,,2021-05-08T00:00:00Z,,PRJDB11000,GCA_019669165.1,"AP024311,AP024312",,Tokyo University of Pharmacy and Life Sciences,MGI DNBSEQ; ONT GridION,1866x,Unicycler v. 0.4.7,1,1,2,2857437,32.955826,2730,2688,humans but also from livestock animals; the mrsa strains originated from livestock animals are termed as livestock-associated mrsa (la-mrsa),isolated not only from humans but also from livestock animals; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA),2018,Japan,Japan,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Methicillin-resistant Staphylococcus aureus (MRSA) has been isolated not only from humans but also from livestock animals\; the MRSA strains originated from livestock animals are termed as livestock-associated MRSA (LA-MRSA). Although LA-MRSA strains are considered low virulent, they can colonize and infect humans. The major genotypes of LA-MRSA are sequence types (ST) 398 and ST9 in Europe and Asia, respectively. However, patient infected by ST398 and ST9 strains has not yet been reported in Japan and Korea. Recently, two cases of infectious disease caused by ST1232 strains were reported in Japan\; ST1232 is a single locus variant of ST398. Additionally, we identified two ST1232 strains in Vietnamese and Korean patients. In this project, comparative genomics analysis for those strains was conducted to investigate relationship between ST1232 strains isolated in Korea and Japan.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.35615,Staphylococcus aureus strain SCAID OTT1-2021 (597/2) strain SCAID OTT1-2021 (597/2) strain SCAID OTT1-2021 (597/2),SCAID OTT1-2021 (597/2),Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20982456,1280,,,,MLST.Staphylococcus_aureus.508,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915405.1,"CP082813,CP082814",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,804x,Canu v. 2.0,1,1,2,2771008,32.911633,2696,2635,swab from ear,,2021-06-10,Kazakhstan,Kazakhstan: Almaty,,male,19,otitis,,host_disease_outcome:Recovery;host_disease_stage:Acute otitis,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,otitis,,Recovery,,Acute otitis,,,,,,,,,,99.37,0.13,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,1280.35616,Staphylococcus aureus strain SCAID WND1-2021 (598) strain SCAID WND1-2021 (598) strain SCAID WND1-2021 (598),SCAID WND1-2021 (598),Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20982455,1280,,,,MLST.Staphylococcus_aureus.30,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915425.1,CP082815,,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,654x,Canu v. 2.0,1,0,1,2889511,32.83206,2860,2791,swab from wound,,2021-06-18,Kazakhstan,Kazakhstan: Almaty,,male,20,wound discharge,,host_disease_outcome:Recovery;host_disease_stage:Burn wound,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,wound discharge,,Recovery,,Burn wound,,,,,,,,,,99.49,0.22,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.35617,Staphylococcus aureus strain HL24830,HL24830,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20667806,1280,,,,MLST.Staphylococcus_aureus.72,,,,2021-09-09T00:00:00Z,,PRJNA752931,GCA_019915585.1,"CP082789,CP082790",,Hallym University,Illumina MiSeq; Oxford Nanopore MinION,568.0x,SPAdes v. 3.14.0,1,1,2,2926847,32.781693,2900,2861,blood,,2020,South Korea,South Korea,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Whole genome sequence of Staphylococcus aureus SCCmec type V,collected_by:Kangdong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.35621,Staphylococcus aureus strain HL25274,HL25274,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20667807,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-09-18T00:00:00Z,,PRJNA752928,GCA_020034535.1,"CP083259,CP083260,CP083261",,Hallym University,Illumina MiSeq; Oxford Nanopore MinION,333.0x,SPAdes v. 3.14.0,1,2,3,2913602,32.87089,2851,2795,blood,,2020,South Korea,South Korea,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequence of Staphylococcus aureus SCCmec type V,collected_by:Kangdong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.35714,Staphylococcus aureus strain HL25870,HL25870,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN20667808,1280,,,,MLST.Staphylococcus_aureus.1232,,,,2021-09-23T00:00:00Z,,PRJNA752929,GCA_020097755.1,"CP083671,CP083672",,Hallym University,Illumina MiSeq; Oxford Nanopore MinION,262.0x,SPAdes v. 3.14.0,1,1,2,2809575,32.919533,2742,2690,blood,,2020,South Korea,South Korea,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequence of Staphylococcus aureus SCCmec type V,collected_by:Kangdong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.36235,Staphylococcus aureus strain N6,N6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550066,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020386595.1,CP077852,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766978,32.91309,2680,2653,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36236,Staphylococcus aureus strain N5,N5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550065,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388075.1,CP077853,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766976,32.91315,2682,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36237,Staphylococcus aureus strain N4,N4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550064,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388095.1,CP077854,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766976,32.91308,2683,2653,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36238,Staphylococcus aureus strain 282,282,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550033,1280,,,,MLST.Staphylococcus_aureus.15,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388965.1,CP077915,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2732780,32.869167,2629,2597,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36239,Staphylococcus aureus strain L6,L6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550063,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388115.1,CP077855,,,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766978,32.913162,2683,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,,,Atopic Dermatitis,"Skin, lesional, hand",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36240,Staphylococcus aureus strain L5,L5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550062,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388135.1,CP077856,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766975,32.913128,2684,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,"Skin, lesional, hand",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36241,Staphylococcus aureus strain L4,L4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550061,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388155.1,CP077857,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766975,32.913162,2680,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,"Skin, lesional, hand",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36242,Staphylococcus aureus strain AC6,AC6,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550060,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388175.1,CP077858,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766990,32.91324,2681,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,"Skin, control, AC",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36243,Staphylococcus aureus strain AC5,AC5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550059,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388195.1,CP077859,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766976,32.91315,2680,2654,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,"Skin, control, AC",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36244,Staphylococcus aureus strain AC4,AC4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550058,1280,,,,,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388215.1,CP077860,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2766976,32.91315,2680,2653,skin swab,,2018-09-11,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,"Skin, control, AC",Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36245,Staphylococcus aureus strain 367,367,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550054,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388295.1,CP077867,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2786390,32.888756,2704,2658,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.78,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36246,Staphylococcus aureus strain 371,371,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550056,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388255.1,"CP077863,CP077864",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2793848,32.85089,2715,2654,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36247,Staphylococcus aureus strain 372,372,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550057,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388235.1,"CP077861,CP077862",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2798879,32.86173,2710,2657,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,1.91,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36248,Staphylococcus aureus strain 370,370,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550055,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388275.1,"CP077865,CP077866",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2838117,32.895508,2759,2697,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,4.05,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36249,Staphylococcus aureus strain 366,366,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550053,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388315.1,CP077868,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2757281,32.888996,2651,2617,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36250,Staphylococcus aureus strain 365,365,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550052,1280,,,,MLST.Staphylococcus_aureus.59,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388335.1,CP077869,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2757494,32.890297,2652,2619,skin swab,,2019-03-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36251,Staphylococcus aureus strain 359,359,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550050,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388395.1,"CP077933,CP077934,CP077935",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2884333,32.73429,2849,2817,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.4,0.12,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36252,Staphylococcus aureus strain 360,360,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550051,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388355.1,"CP077870,CP077871",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2902129,32.762154,2887,2841,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36253,Staphylococcus aureus strain 355,355,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550046,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388695.1,"CP077885,CP077887,CP077886",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2912691,32.681633,2885,2851,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.17,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36254,Staphylococcus aureus strain 357,357,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550048,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388655.1,"CP077877,CP077879,CP077878",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2898286,32.726894,2868,2834,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.12,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36255,Staphylococcus aureus strain 356,356,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550047,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388675.1,"CP077880,CP077881,CP077884,CP077882,CP077883",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,4,5,2930327,32.67311,2910,2865,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.16,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36256,Staphylococcus aureus strain 358,358,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550049,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388555.1,"CP077872,CP077876,CP077875,CP077873,CP077874",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,4,5,2926152,32.6996,2924,2865,skin swab,,2019-01-17,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.16,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36257,Staphylococcus aureus strain 334,334,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550045,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388715.1,CP077888,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2745573,32.83464,2669,2643,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36258,Staphylococcus aureus strain 328,328,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550041,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388805.1,CP077897,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2764234,32.957485,2722,2664,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36259,Staphylococcus aureus strain 329,329,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550042,1280,,,,MLST.Staphylococcus_aureus.426,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388785.1,"CP077894,CP077896,CP077895",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2877025,32.88011,2810,2753,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.23,0.78,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36260,Staphylococcus aureus strain 332,332,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550043,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388765.1,CP077893,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2745575,32.83469,2665,2638,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36261,Staphylococcus aureus strain 333,333,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550044,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388735.1,"CP077889,CP077891,CP077890,CP077892",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,3,4,2840121,32.841347,2805,2722,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,3.45,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36262,Staphylococcus aureus strain 323,323,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550038,1280,,,,MLST.Staphylococcus_aureus.426,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388865.1,"CP077906,CP077907",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2873258,32.878143,2830,2751,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.23,3.25,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36263,Staphylococcus aureus strain 324,324,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550039,1280,,,,MLST.Staphylococcus_aureus.426,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388845.1,"CP077899,CP077900,CP077902,CP077904,CP077903,CP077901,CP077905",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,6,7,3123465,32.77328,3190,3002,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.23,4.15,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36264,Staphylococcus aureus strain 322,322,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550037,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388885.1,"CP077908,CP077910,CP077909",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2831656,32.84661,2820,2742,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36265,Staphylococcus aureus strain 327,327,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550040,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388825.1,CP077898,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2764236,32.957497,2723,2665,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36266,Staphylococcus aureus strain 281,281,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550032,1280,,,,MLST.Staphylococcus_aureus.7,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388985.1,CP077916,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2748821,32.894104,2644,2627,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,98.95,0.11,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36267,Staphylococcus aureus strain 318,318,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550035,1280,,,,MLST.Staphylococcus_aureus.1708,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388925.1,"CP077911,CP077912",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2952667,32.794487,2951,2867,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,2.5,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36268,Staphylococcus aureus strain 319,319,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550036,1280,,,,MLST.Staphylococcus_aureus.1708,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388905.1,"CP077936,CP077938,CP077937",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2952363,32.82452,2996,2888,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.48,0.62,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36269,Staphylococcus aureus strain 317,317,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550034,1280,,,,MLST.Staphylococcus_aureus.1708,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020388945.1,"CP077913,CP077914",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2955603,32.830276,2986,2891,skin swab,,2019-02-06,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.25,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36270,Staphylococcus aureus strain 276,276,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550028,1280,,,,MLST.Staphylococcus_aureus.15,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389265.1,CP077921,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2730804,32.87039,2625,2594,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36271,Staphylococcus aureus strain 280,280,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550031,1280,,,,MLST.Staphylococcus_aureus.7,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389005.1,CP077917,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2748827,32.894104,2645,2630,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,98.81,0.11,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36272,Staphylococcus aureus strain 277,277,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550029,1280,,,,MLST.Staphylococcus_aureus.7,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389165.1,CP077920,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2749120,32.896164,2645,2629,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,98.95,0.11,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36273,Staphylococcus aureus strain 278,278,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550030,1280,,,,MLST.Staphylococcus_aureus.15,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389025.1,"CP077918,CP077919",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2785715,32.835377,2698,2658,skin swab,,2018-11-18,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,1.77,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36274,Staphylococcus aureus strain 202,202,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550027,1280,,,,MLST.Staphylococcus_aureus.398,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389325.1,CP077922,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2719233,32.960285,2616,2572,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36275,Staphylococcus aureus strain 200,200,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550025,1280,,,,MLST.Staphylococcus_aureus.398,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389445.1,CP077924,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2719166,32.96029,2613,2569,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36276,Staphylococcus aureus strain 199,199,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550024,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389465.1,"CP077939,CP077940",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2793131,32.990612,2734,2666,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,98.9,1.54,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36277,Staphylococcus aureus strain 196,196,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550021,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389525.1,"CP077928,CP077930,CP077929",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,2,3,2828046,33.010178,2810,2729,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.97,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36278,Staphylococcus aureus strain 198,198,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550023,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389485.1,CP077925,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2754401,32.963757,2690,2634,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36279,Staphylococcus aureus strain 197,197,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550022,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389505.1,"CP077926,CP077927",,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,1,2,2788328,32.960434,2749,2661,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Nose,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36280,Staphylococcus aureus strain 194,194,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550019,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389565.1,CP077932,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2754399,32.96374,2690,2633,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36281,Staphylococcus aureus strain 195,195,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550020,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389545.1,CP077931,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2754414,32.96418,2697,2634,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Atopic Dermatitis,Skin,Skin swab,missing,,,,,,,,,,,,,Atopic Dermatitis,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36282,Staphylococcus aureus strain 201,201,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN19550026,1280,,,,MLST.Staphylococcus_aureus.398,,,,2021-10-08T00:00:00Z,,PRJNA732579,GCA_020389425.1,CP077923,,Helmholtz Center Munich,PacBio Sequel,200X,HGAP v. 4,1,0,1,2719235,32.960262,2615,2571,skin swab,,2018-07-23,Germany,Germany: Augsburg,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The main questions we set out to address in this study are 1) what are the phylogenetic relationships of individual S. aureus strains within- and across-host, 2) how do they disseminate and evolve within-host and 3) how do their metabolic functions change to adapt to new niches\; all this in the context of the role of S. aureus in the onset of Atopic Dermatitis.",,Health control,Nose,Skin swab,missing,,,,,,,,,,,,,Health control,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.36297,Staphylococcus aureus strain GS426,GS426,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN21905974,1280,,,,MLST.Staphylococcus_aureus.950,,,,2021-10-19T00:00:00Z,,PRJNA767475,GCA_020526105.1,CP084878,,Guangzhou Medical University,Oxford Nanopore,470.0x,SOAPnuke v. 1.5.6; porechop v. 0.2.4,1,0,1,2673223,32.86026,2570,2534,,,2020-01-01,China,China:GuangDong Province,,,,,,,Susceptible,Computational Prediction,,,,,,,,,To find the relevant genes for biofilms formation and study the evolutionary relationships among staphylococcus aureus,sample_type:tissue sample,,,,,,,,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37107,Staphylococcus aureus strain SA23-1,SA23-1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00256196,1280,,,,MLST.Staphylococcus_aureus.45,genotype:ST45,,,2021-09-30T00:00:00Z,34454396,PRJDB10723,GCA_020886635.1,"AP024203,AP024204",,Osaka Institute of Public Health,ONT MinION; Illumina MiSeq,100X,Flye v. 2.7,1,1,2,2845371,32.912895,2756,2723,patient of staphylococcal foodborne outbreak caused,derived from a patient of staphylococcal foodborne outbreak caused by egc2-related new SEs,2016,,Japan:Osaka,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,No,Mesophilic,37,Aerobic,HostAssociated,Foodborne diseases,The complete genome sequence of Staphylococcus aureus SA23-1 isolate. This isolate was derived from a patient of staphylococcal foodborne outbreak caused by egc2-related new SEs.,,not applicable,not applicable,not applicable,not applicable,"The complete genome sequence of Staphylococcus aureus isolate 23-1, associated with egc2-related foodborne outbreak",Enterotoxins,,gastroenteritis,,,,,,,,,not applicable,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37108,Staphylococcus aureus strain TPS5614,TPS5614,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00407004,1280,,,pathovar L,MLST.Staphylococcus_aureus.22,genotype:ST22,,,2021-10-08T00:00:00Z,,PRJDB12326,GCA_020887155.1,AP025176,,"Department of Microbiology School of Pharmacy, Tokyo University of Pharmacy and Life Sciences",MGI DNBSEQ; ONT GridION,3614x,Unicycler v. 0.4.7,1,0,1,2832400,32.812668,2701,2657,,isolated in many countries,2019,,Japan,,,,,,,Resistant;Susceptible,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Staphylococcus aureus is known to produce a wide range of virulence factors, including Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1). CC22 MRSA carrying SCCmec type IV is known as EMRSA-15 clone, and its PVL or TSST-1 positive variants have been isolated in many countries. However, reports of PVL and TSST-1 positive CC22 variants are few. In Japan, several PVL positive S. aureus variant have been isolated. Recently, PVL and TSST-1 positive CC22 strains have been isolated, and are beginning to be disseminated in both communities and healthcare settings. In this project, we conducted molecular epidemiological analysis and whole genome comparative analysis to characterize PVL and TSST-1 positive CC22 MRSA strains.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37109,Staphylococcus aureus strain TPS6281,TPS6281,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00407005,1280,,,pathovar L,MLST.Staphylococcus_aureus.22,genotype:ST22,,,2021-10-08T00:00:00Z,,PRJDB12326,GCA_020887215.1,"AP025177,AP025178",,"Department of Microbiology School of Pharmacy, Tokyo University of Pharmacy and Life Sciences",MGI DNBSEQ; ONT GridION,3647x,Unicycler v. 0.4.7,1,1,2,2819716,32.81483,2683,2640,,isolated in many countries,2020,,Japan,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,Yes,Mesophilic,37,Facultative,HostAssociated,infectious disease,"Staphylococcus aureus is known to produce a wide range of virulence factors, including Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1). CC22 MRSA carrying SCCmec type IV is known as EMRSA-15 clone, and its PVL or TSST-1 positive variants have been isolated in many countries. However, reports of PVL and TSST-1 positive CC22 variants are few. In Japan, several PVL positive S. aureus variant have been isolated. Recently, PVL and TSST-1 positive CC22 strains have been isolated, and are beginning to be disseminated in both communities and healthcare settings. In this project, we conducted molecular epidemiological analysis and whole genome comparative analysis to characterize PVL and TSST-1 positive CC22 MRSA strains.",,not applicable,not applicable,not applicable,not collected,Comparative genomics analysis for human variant of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Korea and Japan,,,,,,,,,,,commensal,not applicable,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37706,Staphylococcus aureus strain UNC_SaCF35,UNC_SaCF35,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701160,1280,,,,MLST.Staphylococcus_aureus.30,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172825.1,CP089156,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,8x,Flye v. 2.8.3,1,0,1,2854518,32.858788,2824,2754,missing,,,,,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.44,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37707,Staphylococcus aureus strain UNC_SaCF36,UNC_SaCF36,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701161,1280,,,,MLST.Staphylococcus_aureus.45,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172845.1,"CP089154,CP089155",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,18x,Flye v. 2.8.3,1,1,2,2758520,32.95912,2705,2661,missing,,,,,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37708,Staphylococcus aureus strain UNC_SaCF30,UNC_SaCF30,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701159,1280,,,,MLST.Staphylococcus_aureus.30,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172865.1,"CP089157,CP089158",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,34x,Flye v. 2.8.3,1,1,2,2771283,32.76035,2686,2618,op swab,,2019-07-02,USA,"USA: Boston, Massachusetts",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37709,Staphylococcus aureus strain UNC_SaCF18,UNC_SaCF18,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701158,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172885.1,"CP089159,CP089160",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,72x,Flye v. 2.8.3,1,1,2,2938416,32.789196,2939,2902,op swab,,2018-12-04,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37710,Staphylococcus aureus strain UNC_SaCF13,UNC_SaCF13,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701157,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172905.1,CP089161,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,163x,Flye v. 2.8.3,1,0,1,2780115,32.82591,2683,2649,op swab,,2018-09-07,USA,"USA: Boston, Massachusetts",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.37711,Staphylococcus aureus strain UNC_SaCF11,UNC_SaCF11,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701156,1280,,,,MLST.Staphylococcus_aureus.8,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172925.1,"CP089162,CP089163,CP089164",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,54x,Flye v. 2.8.3,1,2,3,2906470,32.73094,2889,2837,sputum,,2018-07-11,USA,"USA: Boston, Massachusetts",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.37712,Staphylococcus aureus strain UNC_SaCF07,UNC_SaCF07,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23701155,1280,,,,MLST.Staphylococcus_aureus.5,,,,2021-12-13T00:00:00Z,,PRJNA749299,GCA_021172945.1,"CP089165,CP089166",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,155x,Flye v. 2.8.3,1,1,2,2814225,32.908955,2751,2718,sputum,,2018-06-28,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.38012,Staphylococcus aureus SAUR_BFS17,SAUR_BFS17,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648096,1280,,,,MLST.Staphylococcus_aureus.152,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491695.1,CP090872,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2775374,32.834007,2701,2674,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38013,Staphylococcus aureus SAUR_BFS62,SAUR_BFS62,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648098,1280,,,,,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491715.1,CP090870,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2782272,32.894733,2723,2698,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38014,Staphylococcus aureus SAUR_BFS16,SAUR_BFS16,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648095,1280,,,,,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491735.1,CP090873,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2782265,32.89442,2719,2699,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38015,Staphylococcus aureus SAUR_BFS1,SAUR_BFS1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648088,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491755.1,CP090880,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2819460,32.927128,2786,2758,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38016,Staphylococcus aureus SAUR_BFS2,SAUR_BFS2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648089,1280,,,,MLST.Staphylococcus_aureus.1472,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491775.1,CP090879,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2828753,32.913372,2777,2731,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.25,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38017,Staphylococcus aureus SAUR_BFS14,SAUR_BFS14,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648094,1280,,,,MLST.Staphylococcus_aureus.1,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491795.1,CP090874,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2835347,32.860794,2770,2752,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.47,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38018,Staphylococcus aureus SAUR_BFS13,SAUR_BFS13,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648093,1280,,,,MLST.Staphylococcus_aureus.152,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491815.1,CP090875,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2735553,32.821346,2630,2607,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38019,Staphylococcus aureus SAUR_BFS11,SAUR_BFS11,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648091,1280,,,,MLST.Staphylococcus_aureus.2434,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491835.1,CP090877,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2807449,32.93381,2741,2722,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38020,Staphylococcus aureus SAUR_BFS4,SAUR_BFS4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648090,1280,,,,MLST.Staphylococcus_aureus.1,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491855.1,CP090878,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2818800,32.87113,2745,2724,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.47,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38021,Staphylococcus aureus SAUR_BFS21,SAUR_BFS21,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648097,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491875.1,CP090871,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2774014,32.86669,2715,2688,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38022,Staphylococcus aureus SAUR_BFS12,SAUR_BFS12,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24648092,1280,,,,MLST.Staphylococcus_aureus.152,,,,2022-01-17T00:00:00Z,,PRJNA794346,GCA_021491895.1,CP090876,,,Illumina MiSeq + Oxford Nanopore MiniION,30x,SPAdes v. 3.12.0,1,0,1,2731384,32.859314,2630,2607,skin wound,,2019,Burkina Faso,Burkina Faso,,,,Human_Disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,Human_Disease,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.38978,"Staphylococcus aureus Patient 14, Isolate 02","Patient 14, Isolate 02",Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN22513885,1280,,,,MLST.Staphylococcus_aureus.5,"genotype:MRSA, ST 5",,,2022-02-02T00:00:00Z,,PRJNA773815,GCA_021869805.1,CP086215,,,Illumina NextSeq & Oxford Nanopore,168.4x,de novo hybrid assembly v. Unicycler,1,0,1,2866462,32.906208,2822,2787,blood,,2018-01-31,USA,"USA:Pittsburgh, Pennsylvania",,,,persistent bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:clinical micro lab,,,,,,,persistent bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.38996,Staphylococcus aureus MN8,MN8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN25556620,1280,,,,MLST.Staphylococcus_aureus.30,,,,2022-02-10T00:00:00Z,,PRJNA802579,GCA_022163365.1,CP091875,,,PacBio Sequel; Illumina,1X,HGAP v. 3.0,1,0,1,2905879,32.868435,2902,2832,patient with toxic shock syndrome-1,,1980,USA,USA,,,,Toxic Shock Syndrome,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Gregory Bohach,,,,,,,Toxic Shock Syndrome,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.38997,Staphylococcus aureus FRI-1169,FRI-1169,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN25556619,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-02-10T00:00:00Z,,PRJNA802579,GCA_022163485.1,"CP091876,CP091877",,,PacBio Sequel; Illumina,1X,HGAP v. 3.0,1,1,2,2795298,32.775467,2727,2703,patient with toxic shock syndrome-1,,1981,USA,USA,,,,Toxic Shock Syndrome,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Merlin S. Bergdoll,,,,,,,Toxic Shock Syndrome,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1280.39032,Staphylococcus aureus USA600,USA600,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN25144898,1280,,,,MLST.Staphylococcus_aureus.45,,,,2022-02-15T00:00:00Z,,PRJNA799058,GCA_022226975.1,CP092055,,,Illumina NextSeq; Oxford Nanopore,1x,Unicycler v. v0.4.9,1,0,1,2700946,32.943718,2523,2479,skin,,2021,USA,USA: Colorado,,,,healthy,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Alexander R. Horswill,,,,,,,healthy,,,,,,,,,,,,,,99.51,0.13,,,Skin and Soft Tissue,- NHP,1280.39033,Staphylococcus aureus USA300,USA300,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN25144899,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-02-15T00:00:00Z,,PRJNA799058,GCA_022226995.1,"CP092052,CP092053,CP092054",,,Illumina NextSeq; Oxford Nanopore,1x,Unicycler v. v0.4.9,1,2,3,2833317,32.78479,2674,2613,skin,,2021,USA,USA: Colorado,,,,healthy,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Alexander R. Horswill,,,,,,,healthy,,,,,,,,,,,,,,99.51,0.64,,,Skin and Soft Tissue,- HP,1280.39424,Staphylococcus aureus 199,199,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23416073,1280,,,,MLST.Staphylococcus_aureus.88,genotype:st-88,,,2022-03-07T00:00:00Z,,PRJNA783074,GCA_022494545.1,CP088157,,,PacBio,120.0x,SMRT Link v. v5.0.1,1,0,1,2844011,32.89836,2815,2779,pus,,2018-01-23,China,China: Guangzhou,,female,26 year,SSTI,,host_disease_outcome:recovery;host_subject_id:#199,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Guangzhou Women and Children Medical Center,,,,,,,SSTI,,recovery,,,,,,,,,,,,99.51,0.08,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.40425,Staphylococcus aureus VMRSA-WC062,VMRSA-WC062,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026633,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691325.1,"CP092556,CP092557",,,Illumina MiSeq and Oxford Nanopore MinION,177x,Unicycler v. 0.4.8,1,1,2,2922786,32.882427,2888,2830,nephrostomy,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,1280.40426,Staphylococcus aureus MRSA-WC101,MRSA-WC101,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026631,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691365.1,"CP092561,CP092562",,,Illumina MiSeq and Oxford Nanopore MinION,395x,Unicycler v. 0.4.8,1,1,2,2842774,32.834442,2778,2733,urine,,2004-06-24,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40427,Staphylococcus aureus VMRSA-WC052,VMRSA-WC052,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026632,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691345.1,"CP092558,CP092559,CP092560",,,Illumina MiSeq and Oxford Nanopore MinION,236x,Unicycler v. 0.4.8,1,2,3,2918291,32.8862,2890,2825,urine,,2004-04-02,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40428,Staphylococcus aureus MRSA-WC090,MRSA-WC090,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026630,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691385.1,"CP092563,CP092564",,,Illumina MiSeq and Oxford Nanopore MinION,525x,Unicycler v. 0.4.8,1,1,2,2844782,32.830566,2783,2738,nephrostomy,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,1280.40429,Staphylococcus aureus MRSA-WC061,MRSA-WC061,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026629,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691405.1,"CP092565,CP092566",,,Illumina MiSeq and Oxford Nanopore MinION,325x,Unicycler v. 0.4.8,1,1,2,2844400,32.832054,2783,2736,nephrostomy,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,1280.40431,Staphylococcus aureus VMRSA-WC123,VMRSA-WC123,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026642,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693165.1,"CP092538,CP092539",,,Illumina MiSeq and Oxford Nanopore MinION,242x,Unicycler v. 0.4.8,1,1,2,2922894,32.87892,2891,2833,urine,,2004-08-18,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40432,Staphylococcus aureus VMRSA-WC121,VMRSA-WC121,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026641,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693185.1,"CP092540,CP092541",,,Illumina MiSeq and Oxford Nanopore MinION,185x,Unicycler v. 0.4.8,1,1,2,2923332,32.87615,2924,2836,urine,,2004-08-18,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40433,Staphylococcus aureus VRMSSA-WC113,VRMSSA-WC113,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026640,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693205.1,"CP092542,CP092543",,,Illumina MiSeq and Oxford Nanopore MinION,199x,Unicycler v. 0.4.8,1,1,2,2896630,32.901096,2857,2806,urine,,2004-06-24,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40434,Staphylococcus aureus VMRSA-WC102,VMRSA-WC102,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026638,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693245.1,"CP092544,CP092545,CP092546",,,Illumina MiSeq and Oxford Nanopore MinION,345x,Unicycler v. 0.4.8,1,2,3,2922171,32.879047,2897,2832,urine,,2004-06-24,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40435,Staphylococcus aureus VRMSSA-WC111,VRMSSA-WC111,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026639,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693225.1,"CP092581,CP092582",,,Illumina MiSeq and Oxford Nanopore MinION,81x,Unicycler v. 0.4.8,1,1,2,2897139,32.898834,2881,2804,urine,,2004-06-24,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40436,Staphylococcus aureus VMRSA-WC083,VMRSA-WC083,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026637,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693265.1,"CP092547,CP092548,CP092549",,,Illumina MiSeq and Oxford Nanopore MinION,79x,Unicycler v. 0.4.8,1,2,3,2923261,32.87808,2904,2832,urine,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40437,Staphylococcus aureus VMRSA-WC082,VMRSA-WC082,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026636,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693285.1,"CP092550,CP092551",,,Illumina MiSeq and Oxford Nanopore MinION,119x,Unicycler v. 0.4.8,1,1,2,2924145,32.87843,2889,2832,urine,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40438,Staphylococcus aureus VMRSA-WC081,VMRSA-WC081,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026635,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693305.1,"CP092552,CP092553",,,Illumina MiSeq and Oxford Nanopore MinION,152x,Unicycler v. 0.4.8,1,1,2,2920075,32.88152,2897,2829,urine,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40439,Staphylococcus aureus VMRSA-WC071,VMRSA-WC071,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26026634,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693325.1,"CP092554,CP092555",,,Illumina MiSeq and Oxford Nanopore MinION,181x,Unicycler v. 0.4.8,1,1,2,2922615,32.880074,2891,2832,urine,,2004-04-20,USA,USA,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1280.40440,Staphylococcus aureus WA121-2021_16354,WA121-2021_16354,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26754981,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-27T00:00:00Z,,PRJNA817299,GCA_022699265.1,"CP093935,CP093936,CP093937",,,Oxford Nanopore MinION; Illumina NextSeq,378.0x,Flye v. 2.7.1-b1590; racon v. 1.4.15;,1,2,3,2911855,32.829967,2892,2854,skin,,2021,Australia,Australia: Western Australia,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:PathWest Microbiology,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.40441,Staphylococcus aureus WA121-2021_15363,WA121-2021_15363,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26754980,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-27T00:00:00Z,,PRJNA817299,GCA_022699285.1,"CP093933,CP093934",,,Oxford Nanopore MinION; Illumina NextSeq,414.0x,Flye v. 2.7.1-b1590; racon v. 1.4.15;,1,1,2,2875541,32.85771,2857,2815,skin,,2021,Australia,Australia: Western Australia,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:PathWest Microbiology,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.40442,Staphylococcus aureus WA121-2010_15611,WA121-2010_15611,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26754767,1280,,,,MLST.Staphylococcus_aureus.5,,,,2022-03-27T00:00:00Z,,PRJNA817299,GCA_022699245.1,"CP093930,CP093931,CP093932",,,Oxford Nanopore MinION; Illumina NextSeq,261.0x,Flye v. 2.7.1-b1590; racon v. 1.4.15;,1,2,3,2911979,32.81459,2894,2855,skin,,2010,Australia,Australia: Western Australia,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:PathWest Microbiology,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.40446,Staphylococcus aureus NY2010,NY2010,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27065448,1280,,,,MLST.Staphylococcus_aureus.239,,,,2022-04-07T00:00:00Z,,PRJNA821321,GCA_022832835.1,"CP094853,CP094854",,,PacBio RSII,100.0x,HGAP v. v3.0,1,1,2,2965586,32.819046,2972,2905,sputum,,2014,China,China: Beijing,,,,Secondary tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,,,,,,,,Secondary tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1280.40449,Staphylococcus aureus TCH32767,TCH32767,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16710839,1280,,,,MLST.Staphylococcus_aureus.105,,,,2022-04-11T00:00:00Z,,PRJNA675653,GCA_022870625.1,CP064772,,,Illumina MiSeq; Oxford Nanopore GridION,193.0x,Unicycler v. 0.4.6,1,0,1,2832381,32.880253,2777,2735,blood,,2017,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:BCM/TCH,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.42145,Staphylococcus aureus MRSA1369,MRSA1369,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN29251701,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-07-06T00:00:00Z,,PRJNA851804,GCA_024172245.1,"CP099576,CP099577,CP099578",,,Illumina HiSeq; Oxford Nanopore GridION,57.0x,Unicycler v. v0.4.0,1,2,3,2898303,32.751305,2870,2832,,,,,not collected,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:Clinical,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.42151,Staphylococcus aureus N09CSA16,N09CSA16,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN25263540,1280,,,,MLST.Staphylococcus_aureus.764,,,,2022-07-11T00:00:00Z,,PRJNA800603,GCA_024205325.1,"CP091525,CP091526",,,Oxford Nanopore,100.0x,unicycler v. 0.4.0,1,1,2,2910209,32.82881,2875,2834,sputum,,2016-02,China,China,,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1280.42681,Staphylococcus aureus UMCG579,UMCG579,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN24919645,1280,,,,MLST.Staphylococcus_aureus.1633,,,,2022-08-10T00:00:00Z,,PRJNA796811,GCA_024612055.1,CP091066,,,Oxford Nanopore MinION; Illumina NextSeq,122.0x,DNASTAR SeqMan NGen v. version 18,1,0,1,2741379,32.855434,2639,2601,pus,,2021-12-09,Netherlands,Netherlands: Groningen,,,,fasciitis necroticans,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:University Medical Center Groningen,,,,,,,fasciitis necroticans,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Necrotizing fasciitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Necrotizing fasciitis HP,1280.42691,Staphylococcus aureus SCAID OTT1-2022 (150) strain SCAID OTT1-2022 (150),SCAID OTT1-2022 (150),Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30333622,1280,,,,MLST.Staphylococcus_aureus.78,,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734775.1,CP102945,,,PacBio Sequel,325x,Velvet v. 1.2.10,1,0,1,2781669,32.879757,2725,2698,ear discharge,,2022-03,Kazakhstan,Kazakhstan: Almaty,,,,otitis,,,Resistant;Susceptible;Intermediate,Computational Method,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,otitis,,,,,,,,,,,,,,100,0,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,1280.43036,Staphylococcus aureus strain NRL 02/947,NRL 02/947,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30496472,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-09-05T00:00:00Z,,PRJNA873286,GCA_024925485.1,"CP103850,CP103849",,"Masaryk University, Faculty of Science",Illumina; Oxford Nanopore,293.0x,Unicycler v. 0.4.8,1,1,2,2846055,32.81936,2785,2762,nose,,2002-07,,Czech Republic,,male,1,bronchitis acuta,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Staphylococcus aureus strain E48 harbouring gene for prophage-encoded protein PdpSau providing population immunity to myovirus,collected_by:Faculty Hospital Brno Czech Republic,,,,,,,bronchitis acuta,,,,,,,,,,,,,,99.51,0.08,Respiratory Diseases,COPD/Emphysema/Bronchitis,Other,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,1280.43056,Staphylococcus aureus strain 0831,0831,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30633109,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-09-12T00:00:00Z,,PRJNA875930,GCA_025152705.1,"CP104020,CP104021",,University of Alabama at Birmingham,Illumina NextSeq; Oxford Nanopore,500.0x,Unicycler v. 0.4.8,1,1,2,2906340,32.76014,2750,,lung,,2017-08-31,USA,"USA: Birmingham, AL",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Clinical isolate of methicillin resistant Staphylococcus aureus obtained from cystic fibrosis in-patient sputum sample at the University of Alabama at Birmingham,sample_type:CF sputum,,,,,,,,,,,,,,,,,,,,,99.51,0.64,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1280.43081,Staphylococcus aureus strain R3-8,R3-8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30550580,1280,,,,MLST.Staphylococcus_aureus.8,genotype:ST8,,,2022-09-16T00:00:00Z,,PRJNA874487,GCA_025232045.1,"CP103860,CP103861",,Sapporo Medical University,PacBio,2898000.0x,Flye v. 2.9,1,1,2,2918241,32.80401,2915,2879,venous blood,,2021-01-31,Japan,Japan: Hokkaido,,,,blood stream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To characterize genome of USA300-like MRSA clone in Japan,collected_by:Meiji Soe Aung,,,,,,,blood stream infection,,,,,,,,,,,,,,99.51,0.64,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.43123,Staphylococcus aureus strain TCH32929,TCH32929,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16710840,1280,,,,MLST.Staphylococcus_aureus.105,,,,2022-09-19T00:00:00Z,,PRJNA675653,GCA_025259685.1,CP072116,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,134.0x,Flye v. 2.4.2; Unicycler v. 0.4.6,1,0,1,2873962,32.883175,2836,2798,blood,,2017,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of ceftaroline resistant Staphylococcus aureus,collected_by:BCM/TCH,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.43354,Staphylococcus aureus SA2107,SA2107,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30822352,1280,,,,MLST.Staphylococcus_aureus.45,,,,2022-09-24T00:00:00Z,,PRJNA879981,GCA_025398055.1,"CP104559,CP104560,CP104561",,,Illumina HiSeq; PacBio,103.61x,Hifiasm v. 0.13-r308; Canu v. 2.2,1,2,3,2868576,32.795994,2842,2786,sputum,,2022-05,China,China:Zhuhai,,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1280.43481,Staphylococcus aureus NRL 02/947,NRL 02/947,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30496472,1280,,,,MLST.Staphylococcus_aureus.8,,,,2022-09-05T00:00:00Z,,PRJNA873286,GCA_024925485.1,"CP103850,CP103849",,,Illumina; Oxford Nanopore,293.0x,Unicycler v. 0.4.8,1,1,2,2846055,32.81936,2785,2762,nose,,2002-07,Czech Republic,Czech Republic,,male,1,bronchitis acuta,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Faculty Hospital Brno Czech Republic,,,,,,,bronchitis acuta,,,,,,,,,,,,,,100,0,Respiratory Diseases,COPD/Emphysema/Bronchitis,Other,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,1280.43552,Staphylococcus aureus R3-8,R3-8,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30550580,1280,,,,MLST.Staphylococcus_aureus.8,genotype:ST8,,,2022-09-16T00:00:00Z,,PRJNA874487,GCA_025232045.1,"CP103860,CP103861",,,PacBio,2898000.0x,Flye v. 2.9,1,1,2,2918241,32.80401,2915,2879,venous blood,,2021-01-31,Japan,Japan: Hokkaido,,,,blood stream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Meiji Soe Aung,,,,,,,blood stream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1280.43594,Staphylococcus aureus TCH32929,TCH32929,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16710840,1280,,,,MLST.Staphylococcus_aureus.105,,,,2022-09-19T00:00:00Z,,PRJNA675653,GCA_025259685.1,CP072116,,,Illumina MiSeq; Oxford Nanopore GridION,134.0x,Flye v. 2.4.2; Unicycler v. 0.4.6,1,0,1,2873962,32.883175,2836,2798,blood,,2017,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:BCM/TCH,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1280.44379,Staphylococcus aureus 55-99-44,55-99-44,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08024196,1280,,,,MLST.Staphylococcus_aureus.152,genotype:ST152,,,2017-12-04T00:00:00Z,,PRJNA418239,,"CP024998,CP024999",,,Oxford nanopore MinION,107.798x,SPAdes v. 2016-12-22,1,1,2,2784606,32.75433,2747,2759,infection,,08-Jun-2015,Denmark,Denmark,,male,30,MRSA infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Anders Rhod Larsen,,,,,,,MRSA infection,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1280.44425,Staphylococcus aureus RIVM_M044329,RIVM_M044329,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27760537,1280,,,,MLST.Staphylococcus_aureus.398,genotype:GG0398 (CC398),,,2022-12-07T00:00:00Z,36317053,PRJNA831673,,"CP096540,CP096541",,,"Illumina MiSeq and HiSeq 2500, Nanopore",30x,Unicycler v. v.0.4.4,1,1,2,2946843,33.001892,2929,2883,pus,,2018-08-27,Netherlands,Netherlands,,male,51,Abscess,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:RIVM,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.44465,Staphylococcus aureus BIAI 117,BIAI 117,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN31815270,1280,,,,MLST.Staphylococcus_aureus.39,,,,2022-12-04T00:00:00Z,,PRJNA903851,,CP113105,,,Oxford Nanopore GridION; Illumina NextSeq,100.0x,flye v. 2.9,1,0,1,2833462,32.87586,2793,2736,breast,,2019,USA,USA:St. Louis,,,,Breast Implant Associated Infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Margaret Olsen,,,,,,,Breast Implant Associated Infection,,,,,,,,,,,,,,100,0.2,Surgical Site Infections,,Other,Surgical Site Infections- HP,1280.44466,Staphylococcus aureus Alexandria_2020-19,Alexandria_2020-19,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN31868372,1280,,,,MLST.Staphylococcus_aureus.1,"genotype:CC1, ST1",,,2022-12-05T00:00:00Z,,PRJNA905238,,"CP113244,CP113245",,,Oxford Nanopore MinION,164.0x,Flye v. version 2.8.3-b1695,1,1,2,2872119,32.864655,2968,2787,aspirated pus,,2020,Egypt,Egypt: Alexandria,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"sample_type:Culture;biomaterial_provider:Department of Microbiology, Medical Research Institute, Alexandria University",,,,,,,,,,,,,CC1-MRSA,,,,,,,,100,3.3,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.44467,Staphylococcus aureus BIAI 158,BIAI 158,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN31815319,1280,,,,MLST.Staphylococcus_aureus.45,,,,2022-12-05T00:00:00Z,,PRJNA903852,,"CP113231,CP113232",,,Oxford Nanopore GridION; Illumina NextSeq,100.0x,flye v. 2.9,1,1,2,2775791,32.942177,2744,2695,breast,,2019,USA,USA: St. Louis,,,,Breast Implant Associated Infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Margaret Olsen,,,,,,,Breast Implant Associated Infection,,,,,,,,,,,,,,100,0.2,Surgical Site Infections,,Other,Surgical Site Infections- HP,1280.45017,Staphylococcus aureus C308,C308,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN32538168,1280,,,,MLST.Staphylococcus_aureus.22,,,,2023-01-19T00:00:00Z,,PRJNA914892,,"CP115887,CP115888",,,Oxford Nanopore MiniION and Illumina,80.0x,"Flye for Genome, plassembler (Unicycler)",1,1,2,2837359,32.795464,2795,2743,patient sinus swab,,2015-02-20,Australia,Australia: Adelaide,,,,Chronic Rhinosinusitis without nasal polyps,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:ENT Surgery Department at the Queen Elizabeth Hospital, Adelaide, Australia 1",,,,,,,Chronic Rhinosinusitis without nasal polyps,,,,,,,,,,,,,,100,0,Respiratory Diseases,Rhinosinusitis,Other,Respiratory Diseases-Rhinosinusitis HP,1280.45018,Staphylococcus aureus FJ0322,FJ0322,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27752664,1280,,,,MLST.Staphylococcus_aureus.7,,,,2023-01-23T00:00:00Z,36544989,PRJNA831318,,CP096274,,,Oxford Nanopore,100.0x,unicycler v. 0.4.0,1,0,1,2809462,32.87512,2736,2707,pus,,2021-03-22,China,China:Fuzhou,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.45595,Staphylococcus aureus N29CSA02,N29CSA02,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN33573404,1280,,,,MLST.Staphylococcus_aureus.9,,,,2023-03-14T00:00:00Z,,PRJNA940516,,"CP119341,CP119342,CP119343",,,Oxford Nanopore,100.0x,unicycler v. 0.4.0,1,2,3,2899390,32.756752,2860,2821,pus,,2015-10-24,China,China:hefei,,,,,,,Resistant;Susceptible,Computational Method,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.45790,Staphylococcus aureus SA0907,SA0907,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN33961605,1280,,,,MLST.Staphylococcus_aureus.45,,,,2023-04-09T00:00:00Z,,PRJNA949857,,"CP121204,CP121205,CP121206",,,Illumina NovaSeq; PacBio Sequel,127.18x,Hifiasm v. 0.13-r308; Canu v. 1.7,1,2,3,2986908,32.8292,2973,2915,eccrine,,2022-09,China,China: Zhuhai,,,,cutaneous infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Qinghuan Zhang,,,,,,,cutaneous infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.46451,Staphylococcus aureus CHAL4,CHAL4,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35018952,1280,,,,MLST.Staphylococcus_aureus.8,,,,2023-05-23T00:00:00Z,,PRJNA971005,,"CP125897,CP125898",,,Oxford Nanopore GridION,100x,Flye v. 2.9.2; Polypolish v. 0.5.0,1,1,2,2827954,32.802692,2799,2770,skin,,2022-06-19,United Kingdom,United Kingdom:Sheffield,,,,eczema herpeticum,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Northern General Hospital, Sheffield",,,,,,,eczema herpeticum,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1280.46452,Staphylococcus aureus CHAL3,CHAL3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35018951,1280,,,,MLST.Staphylococcus_aureus.45,,,,2023-05-23T00:00:00Z,,PRJNA971005,,"CP125899,CP125900",,,Oxford Nanopore GridION,100x,Flye v. 2.9.2; Polypolish v. 0.5.0,1,1,2,2758763,32.87401,2712,2648,skin,,2022-06-14,United Kingdom,United Kingdom:Sheffield,,,,cellulitis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Northern General Hospital, Sheffield",,,,,,,cellulitis,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Cellulitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Cellulitis HP,1280.46453,Staphylococcus aureus CHAL2,CHAL2,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35018950,1280,,,,MLST.Staphylococcus_aureus.5,,,,2023-05-23T00:00:00Z,,PRJNA971005,,"CP125901,CP125902",,,Oxford Nanopore GridION,100x,Flye v. 2.9.2; Polypolish v. 0.5.0,1,1,2,2806888,32.869995,2769,2720,skin,,2022-06-08,United Kingdom,United Kingdom:Sheffield,,,,abscess neck,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Northern General Hospital, Sheffield",,,,,,,abscess neck,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1280.46455,Staphylococcus aureus CHAL1,CHAL1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35018949,1280,,,,MLST.Staphylococcus_aureus.30,,,,2023-05-23T00:00:00Z,,PRJNA971005,,CP125903,,,Oxford Nanopore GridION,100x,Flye v. 2.9.2; Polypolish v. 0.5.0,1,0,1,2907971,32.85772,2900,2828,skin,,2022-06-08,United Kingdom,United Kingdom:Sheffield,,,,surgical site infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Northern General Hospital, Sheffield",,,,,,,surgical site infection,,,,,,,,,,,,,,100,0.2,Surgical Site Infections,,Skin and Soft Tissue,Surgical Site Infections- HP,1280.46904,Staphylococcus aureus SASWT1215,SASWT1215,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30089067,1280,,,,MLST.Staphylococcus_aureus.5,,,,2023-06-05T00:00:00Z,,PRJNA834886,,"CP109933,CP109934,CP109935",,,Oxford Nanopore,100.0x,unicycler v. 0.4.0,1,2,3,2944259,32.81797,2932,2891,intestinal mucosa,,2020-12-15,China,China:hangzhou,,,,enteritis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:feng zhao,,,,,,,enteritis,,,,,,,,,,,,,,100,0.2,Gastrointestinal Diseases,Diarrheal Diseases,Genitourinary,Gastrointestinal Diseases-Diarrheal Diseases HP,1280.47122,Staphylococcus aureus SA12-SX,SA12-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429652,1280,,,,MLST.Staphylococcus_aureus.25,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130537,,,DNBSEQ,461x,SOAPdenovo v. 1.5.6,1,0,1,2795768,32.80054,2652,,purulent fluid,,2022-03-09,China,China,,,,,,,Resistant;Susceptible,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47132,Staphylococcus aureus SA13-SX,SA13-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429653,1280,,,,MLST.Staphylococcus_aureus.59,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130536,,,DNBSEQ,457x,SOAPdenovo v. 1.5.6,1,0,1,2786813,32.915916,2584,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47133,Staphylococcus aureus SA04-SX,SA04-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429644,1280,,,,MLST.Staphylococcus_aureus.398,,,,2023-07-25T00:00:00Z,,PRJNA994481,,"CP130547,CP130548",,,DNBSEQ,433x,SOAPdenovo v. 1.5.6,1,1,2,2874130,33.0063,2783,,purulent fluid,,2021-05-04,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47136,Staphylococcus aureus SA14-SX,SA14-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429654,1280,,,,MLST.Staphylococcus_aureus.59,,,,2023-07-25T00:00:00Z,,PRJNA994481,,"CP130534,CP130535",,,DNBSEQ,438x,SOAPdenovo v. 1.5.6,1,1,2,2888817,32.843098,2717,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47139,Staphylococcus aureus SA18-SX,SA18-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429658,1280,,,,MLST.Staphylococcus_aureus.59,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130528,,,DNBSEQ,449x,SOAPdenovo v. 1.5.6,1,0,1,2815806,32.892857,2629,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47141,Staphylococcus aureus SA16-SX,SA16-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429656,1280,,,,MLST.Staphylococcus_aureus.59,,,,2023-07-25T00:00:00Z,,PRJNA994481,,"CP130531,CP130532",,,DNBSEQ,456x,SOAPdenovo v. 1.5.6,1,1,2,2821675,32.909107,2656,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47143,Staphylococcus aureus SA17-SX,SA17-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429657,1280,,,,MLST.Staphylococcus_aureus.22,,,,2023-07-25T00:00:00Z,,PRJNA994481,,"CP130529,CP130530",,,DNBSEQ,441x,SOAPdenovo v. 1.5.6,1,1,2,2841352,32.861996,2706,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47146,Staphylococcus aureus SA20-SX,SA20-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429660,1280,,,,MLST.Staphylococcus_aureus.22,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130525,,,DNBSEQ,433x,SOAPdenovo v. 1.5.6,1,0,1,2921768,32.867565,2814,,purulent fluid,,2022-03-09,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47147,Staphylococcus aureus SA03-SX,SA03-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429643,1280,,,,MLST.Staphylococcus_aureus.254,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130549,,,DNBSEQ,423x,SOAPdenovo v. 1.5.6,1,0,1,2976881,32.8994,2895,,purulent fluid,,2021-05-04,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47152,Staphylococcus aureus SA01-SX,SA01-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429641,1280,,,,,,,,2023-07-25T00:00:00Z,,PRJNA994481,,CP130551,,,DNBSEQ,455x,SOAPdenovo v. 1.5.6,1,0,1,2833694,32.948124,2663,,purulent fluid,,2021-05-04,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1280.47156,Staphylococcus aureus SA05-SX,SA05-SX,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36429645,1280,,,,MLST.Staphylococcus_aureus.5,,,,2023-07-25T00:00:00Z,,PRJNA994481,,"CP130545,CP130546",,,DNBSEQ,458x,SOAPdenovo v. 1.5.6,1,1,2,2778425,32.83418,2584,,purulent fluid,,2021-05-04,China,China,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,sample_type:purulent fluid,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.2244,Staphylococcus epidermidis strain ATCC 12228,ATCC 12228,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07291625,1282,,,,MLST.Staphylococcus_epidermidis.679,,ATCC:12228,,2017-07-06T00:00:00Z,,PRJNA392321,GCA_002215535.1,"CP022247,CP022249,CP022250,CP022251,CP022252,CP022248",,University of New Hampshire-Manchester,PacBio,25.0x,Celera Assembler v. 8.1,1,5,6,2570371,32.08,2528,2462,skin and mucous membranes,,1908,,,,,,Primary bacteremia and infections of indwelling medical devices,,,,,,,,,,,,,Sequencing of Staphylococcus epidermidis using long-read sequencing technology for scientific and educational purposes,collected_by:Winslow and Winslow,,,,,,,None,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1282.2268,Staphylococcus epidermidis strain SE90,SE90,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07702384,1282,,,,,,,,2017-11-03T00:00:00Z,,PRJNA412200,GCA_002749455.1,"CP024408,CP024409,CP024410",,EA7290,Illumina HiSeq,422.0x,SPAdes v. 3.11,1,2,3,2418596,32.04,2358,2306,blood cultures,,2014,Benin,Benin,,,,Bacteremia,,,,,,,,,,,,,Pathogenic strain of Staphylococcus epidermidis causing bacteremia and with enterotoxin-bearing-pathogenicity island,collected_by:Nanoukon,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1282.2269,Staphylococcus epidermidis strain SE95,SE95,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07702411,1282,,,,,,,,2017-11-03T00:00:00Z,,PRJNA412208,GCA_002749515.1,"CP024437,CP024438,CP024439,CP024440,CP024441",,EA7290,Illumina HiSeq,410.0x,SPAdes v. 3.11,1,4,5,2437836,31.94,2361,2320,blood cultures,,2014,Benin,Benin,,,,Bacteremia,,,,,,,,,,,,,"Staphylococcus epidermidis strain issued from bacteremia, that contains an enterotoxin-bearing pathogenicity island",collected_by:Nanoukon,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.7,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1282.2719,Staphylococcus epidermidis strain CSF41498,CSF41498,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09491332,1282,,,,MLST.Staphylococcus_epidermidis.297,,,,2018-07-17T00:00:00Z,,PRJNA478035,GCA_003325735.1,"CP030246,CP030247,CP030248,CP030249",,Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,89.0x,HGAP v. 2; Geneious v. 9,1,3,4,2535366,32.14088,2490,2427,cerebrospinal fluid,,2000,Ireland,Ireland,,,,Suspected or confirmed neurosurgical device related infection,,,Susceptible;Resistant;Intermediate,AMR Panel,,,,,,,,,This project was to sequence the Staphylococcus epidermidis CSF41498 complete genome.,collected_by:James P O'Gara,,,,,,,Suspected or confirmed neurosurgical device related infection,,,,,,,,,,,,,,100,0,Surgical Site Infections,,Central Nervous System,Surgical Site Infections- HP,1282.2966,Staphylococcus epidermidis strain NCTC13924,NCTC13924,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA104318201,1282,not available: to be reported later,,,MLST.Staphylococcus_epidermidis.2,,NCTC:13924,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638695.1,LR134536,,SC,,,,1,,1,2750807,31.986286,2706,2635,blood culture,,2013,United Kingdom,United Kingdom: Dublin,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.81,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1282.3356,Staphylococcus epidermidis strain HD66,HD66,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11953769,1282,,,,MLST.Staphylococcus_epidermidis.87,,,,2019-06-13T00:00:00Z,,PRJNA546129,GCA_006337185.1,"CP040868,CP040869,CP040870",,University Medical Center Hamburg-Eppendorf,Illumina,94.0x,SPAdes v. MAY-2019,1,2,3,2521715,32.091846,2537,2450,skin; prosthetic joint infection,,2018,Germany,Germany: Hamburg,,,,Prosthesis Related Infections,,,,,,,,,,,,,Inter- and intraclonal diversity in S. epidermidis prosthetic joint infection,collected_by:Anna Both,,,,,,,Prosthesis Related Infections,,,,,,,,,,,,,,99.77,0.09,Surgical Site Infections,,Skin and Soft Tissue,Surgical Site Infections- HP,1282.3357,Staphylococcus epidermidis strain HD43,HD43,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11953768,1282,,,,MLST.Staphylococcus_epidermidis.23,,,,2019-06-13T00:00:00Z,,PRJNA546129,GCA_006337205.1,CP040867,,University Medical Center Hamburg-Eppendorf,Illumina,150.0x,SPAdes v. MAY-2019,1,,1,2424890,32.015076,2385,2329,skin; prosthetic joint infection,,2018,Germany,Germany: Hamburg,,,,Prosthesis Related Infections,,,,,,,,,,,,,Inter- and intraclonal diversity in S. epidermidis prosthetic joint infection,collected_by:Anna Both,,,,,,,Prosthesis Related Infections,,,,,,,,,,,,,,99.81,0.04,Surgical Site Infections,,Skin and Soft Tissue,Surgical Site Infections- HP,1282.3358,Staphylococcus epidermidis strain HD33,HD33,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11953736,1282,,,,MLST.Staphylococcus_epidermidis.87,,,,2019-06-13T00:00:00Z,,PRJNA546129,GCA_006337225.1,"CP040864,CP040865,CP040866",,University Medical Center Hamburg-Eppendorf,Illumina,229.0x,SPAdes v. MAY-2019,1,2,3,2491048,32.082867,2504,2426,skin; prosthetic joint infection,,2018,Germany,Germany: Hamburg,,,,Prosthesis Related Infections,,,,,,,,,,,,,Inter- and intraclonal diversity in S. epidermidis prosthetic joint infection,collected_by:Anna Both,,,,,,,Prosthesis Related Infections,,,,,,,,,,,,,,99.81,0,Surgical Site Infections,,Skin and Soft Tissue,Surgical Site Infections- HP,1282.3617,Staphylococcus epidermidis strain IRL01,IRL01,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09103952,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2019-11-21T00:00:00Z,,PRJNA532483,GCA_009685135.1,"CP045648,CP045647",,University of Melbourne,PacBio RSII,149.0x,HGAP v. 3,1,1,2,2751032,31.980507,2760,2686,blood,,2016,Ireland,Ireland,,,,Staphylococcal Infection,,,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",collected_by:not collected,,,,,,,Staphylococcal Infection,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1282.3621,Staphylococcus epidermidis strain none strain Se_BPH0697,Se_BPH0697,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712729,1282,,,,MLST.Staphylococcus_epidermidis.89,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509485.1,"LR735421,LR735422,LR735423",,UNIVERSITY OF MELBOURNE,,,,1,2,3,2547194,32.079494,2386,,clinical,,2007,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.3622,Staphylococcus epidermidis strain none strain Se_BPH0723,Se_BPH0723,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712754,1282,,,,MLST.Staphylococcus_epidermidis.5,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509515.1,"LR735437,LR735438,LR735439",,UNIVERSITY OF MELBOURNE,,,,1,2,3,2598654,32.246387,2447,,clinical,,2009,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.3623,Staphylococcus epidermidis strain none strain Se_BPH0704,Se_BPH0704,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712735,1282,,,,MLST.Staphylococcus_epidermidis.368,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509495.1,"LR735429,LR735430",,UNIVERSITY OF MELBOURNE,,,,1,1,2,2541041,32.10027,2378,,clinical,,2008,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.3624,Staphylococcus epidermidis strain none strain Se_BPH0736,Se_BPH0736,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712766,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509505.1,"LR735434,LR735435,LR735436",,UNIVERSITY OF MELBOURNE,,,,1,2,3,2581001,32.02986,2439,,clinical,,2011,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.25,0.28,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.3626,Staphylococcus epidermidis strain none strain Se_BPH0711,Se_BPH0711,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712742,1282,,,,MLST.Staphylococcus_epidermidis.59,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509535.1,"LR735440,LR735441,LR735442",,UNIVERSITY OF MELBOURNE,,,,1,2,3,2561733,32.217762,2440,,clinical,,2008,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1282.3699,Staphylococcus epidermidis strain none strain Se_RP62a-WT,Se_RP62a-WT,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA3712772,1282,,,,MLST.Staphylococcus_epidermidis.10,,,,2019-11-22T00:00:00Z,,PRJEB35032,GCA_902509525.1,"LR735432,LR735433",,UNIVERSITY OF MELBOURNE,,,,1,1,2,2646468,32.15308,2509,,clinical,,1979,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Staphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and ways to combat these infections have been hindered by an inability to genetically manipulate the “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms by which S. epidermidis resists the uptake of foreign DNA and demonstrate these to be distinct to those described for S. aureus, that until now had been assumed to be the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.",,,,,,,,,diseased,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1282.3780,Staphylococcus epidermidis strain SESURV_p1_0557,SESURV_p1_0557,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12507996,1282,,,,MLST.Staphylococcus_epidermidis.487,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011306595.1,"CP043777,CP043775,CP043776,CP043778,CP043779,CP043780",,The Jackson Laboratory,PacBio Sequel System,545x,HGAP4 v. Release 6.0.0.47841,1,5,6,2569240,32.125458,2454,,r_nares,,2018,USA,USA: Connecticut,,,,,,host_subject_id:p1,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],external naris [UBERON:0005928],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.81,0.09,,,Other,- NHP,1282.3781,Staphylococcus epidermidis strain SESURV_p1_0563,SESURV_p1_0563,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508002,1282,,,,MLST.Staphylococcus_epidermidis.60,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011306775.1,"CP043781,CP043782,CP043783",,The Jackson Laboratory,PacBio Sequel System,633x,HGAP4 v. Release 6.0.0.47841,1,2,3,2555535,32.121304,2451,,r_cheek,,2018,USA,USA: Connecticut,,,,,,host_subject_id:p1,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of face [UBERON:1000021],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.67,0.28,,,Other,- NHP,1282.3782,Staphylococcus epidermidis strain SESURV_p1_0612,SESURV_p1_0612,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508047,1282,,,,,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307015.1,"CP043784,CP043785,CP043786,CP043787",,The Jackson Laboratory,PacBio Sequel System,535x,HGAP4 v. Release 6.0.0.47841,1,3,4,2641854,32.004494,2528,,toeweb,,2018,USA,USA: Connecticut,,,,,,host_subject_id:p1,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of pes [UBERON:0001513],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.67,0.65,,,Other,- NHP,1282.3783,Staphylococcus epidermidis strain SESURV_p4_1553,SESURV_p4_1553,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508927,1282,,,,MLST.Staphylococcus_epidermidis.218,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307715.1,"CP043804,CP043805,CP043806,CP043807",,The Jackson Laboratory,PacBio Sequel System,628x,HGAP4 v. Release 6.0.0.47841,1,3,4,2542477,32.11361,2393,,umbilicus,,2018,USA,USA:Connecticut,,,,,,host_subject_id:p4,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of trunk [UBERON:0001085],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.81,0,,,Other,- NHP,1282.3784,Staphylococcus epidermidis strain SESURV_p1_1200,SESURV_p1_1200,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508595,1282,,,,MLST.Staphylococcus_epidermidis.487,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307595.1,"CP043796,CP043797,CP043798,CP043799,CP043800",,The Jackson Laboratory,PacBio Sequel System,309x,HGAP4 v. Release 6.0.0.47841,1,4,5,2550919,32.192406,2424,,cubital_fossa,,2018,USA,USA: Connecticut,,,,,,host_subject_id:p1,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],arm skin [UBERON:0002427],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.81,0.09,,,Other,- NHP,1282.3785,Staphylococcus epidermidis strain SESURV_p3_1362,SESURV_p3_1362,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508754,1282,,,,,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307695.1,"CP043801,CP043802,CP043803",,The Jackson Laboratory,PacBio Sequel System,502x,HGAP4 v. Release 6.0.0.47841,1,2,3,2501908,32.120213,2372,,l_index,,2018,USA,USA:Connecticut,,,,,,host_subject_id:p3,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of manus [UBERON:0001519],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.67,0.28,,,Other,- NHP,1282.3786,Staphylococcus epidermidis strain SESURV_p2_0614,SESURV_p2_0614,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508049,1282,,,,,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307235.1,"CP043788,CP043789,CP043790,CP043791",,The Jackson Laboratory,PacBio Sequel System,647x,HGAP4 v. Release 6.0.0.47841,1,3,4,2600860,32.11142,2488,,r_thumb,,2018,USA,USA:Connecticut,,,,,,host_subject_id:p2,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of manus [UBERON:0001519],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.67,0,,,Other,- NHP,1282.3787,Staphylococcus epidermidis strain SESURV_p3_0825,SESURV_p3_0825,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12508243,1282,,,,MLST.Staphylococcus_epidermidis.73,,,,2020-03-16T00:00:00Z,32004459,PRJNA559376,GCA_011307475.1,"CP043792,CP043793,CP043794,CP043795",,The Jackson Laboratory,PacBio Sequel System,304x,HGAP4 v. Release 6.0.0.47841,1,3,4,2515051,32.15709,2380,,l_thumb,,2010-2020,USA,USA,,,,,,host_subject_id:p3,,,,,,,,,,,PACBIO sequences of selected skin S. epidermidis isolates,,skin of body [UBERON:0002097],skin of manus [UBERON:0001519],skin swab,Not provided,,,,healthy,,,,,,,,commensal,skin of body [UBERON:0002097],,,,99.67,0.28,,,Other,- HP,1282.4265,Staphylococcus epidermidis strain PH1-28,PH1-28,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16085533,1282,,,,MLST.Staphylococcus_epidermidis.387,,,,2020-12-27T00:00:00Z,,PRJNA662445,GCA_016406625.1,"CP066376,CP066375,CP066374,CP066373,CP066372,CP066371",,L'Oreal,Oxford Nanopore MinION; Illumina HiSeq,4828.0x,MaSuRCA v. v3.3.0; SPAdes v. v3.10.1;,1,5,6,2598183,32.04978,2508,2368,,,2012-06,France,France,,,,,,,,,,,,,,,,,Complete genome sequencing and assembly of this Staphylococcus epidermidis clinical monoisolate,sample_type:monoisolate from skin swab,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1282.4587,Staphylococcus epidermidis strain NBRC 113846,NBRC 113846,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN21163584,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2021-09-30T00:00:00Z,,PRJNA747117,,"CP084008,CP084009,CP084010,CP084011",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,362.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,3,4,2520735,32.148994,2380,2306,human skin,,2018,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.81,0,,,Skin and Soft Tissue,- NHP,1282.4787,Staphylococcus epidermidis AZ39,AZ39,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17983073,1282,,,,,,,,2022-01-10T00:00:00Z,,PRJNA715223,GCA_021398365.1,"CP071996,CP071997,CP071998,CP071999",,,Illumina MiSeq; Oxford Nanopore MinION,410.0x,Trycycler v. v0.3.3,1,3,4,2506991,32.12708,2467,2314,human skin swabs of healthy volunteers,,2015,Canada,Canada,,,,None,,host_health_state:healthy,,,,,,,,,,,,collected_by:Canadian Blood Services (Contact: Sandra Ramirez),,,,,,,None,healthy,,,,,,,,,,,,,98.79,0,,,Skin and Soft Tissue,- NHP,1282.4789,Staphylococcus epidermidis AZ22,AZ22,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17983072,1282,,,,MLST.Staphylococcus_epidermidis.73,,,,2022-01-10T00:00:00Z,,PRJNA715221,GCA_021398345.1,"CP071994,CP071995",,,Illumina MiSeq; Oxford Nanopore MinION,297.0x,Unicycler v. v0.4.8,1,1,2,2475286,32.229366,2375,2284,human skin swabs of healthy volunteers,,2015,Canada,Canada,,,,None,,host_health_state:healthy,,,,,,,,,,,,collected_by:Canadian Blood Services (Contact: Sandra Ramirez),,,,,,,None,healthy,,,,,,,,,,,,,99.67,0.28,,,Skin and Soft Tissue,- HP,1282.4871,Staphylococcus epidermidis C100,C100,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27161489,1282,,,,,,,,2022-04-07T00:00:00Z,,PRJNA821968,GCA_022832915.1,"CP094865,CP094866,CP094867,CP094868,CP094869,CP094870,CP094871",,,Illumina NextSeq; Oxford Nanopore MinION,1841.0x,Flye v. 2.9-b1774; Racon v. 1.4.15; Pilon,1,6,7,2541647,32.145847,2401,2327,pertoneal cavity,,2017-04-19,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,0.2,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.4872,Staphylococcus epidermidis C99,C99,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27160588,1282,,,,,,,,2022-04-07T00:00:00Z,,PRJNA821968,GCA_022832895.1,"CP094859,CP094860,CP094861,CP094862,CP094863,CP094864",,,Illumina NextSeq; Oxford Nanopore MinION,1552.0x,Flye v. 2.9-b1774; Racon v. 1.4.15; Pilon,1,5,6,2540715,32.148666,2401,2325,pertoneal cavity,,2017-04-14,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.4873,Staphylococcus epidermidis C101,C101,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27161490,1282,,,,,,,,2022-04-07T00:00:00Z,,PRJNA821968,GCA_022832935.1,"CP094872,CP094874,CP094873,CP094875,CP094876,CP094877,CP094878",,,Illumina NextSeq; Oxford Nanopore MinION,306.0x,Flye v. 2.9-b1774; Racon v. 1.4.15; Pilon,1,6,7,2541905,32.145733,2411,2327,pertoneal cavity,,2017-04-28,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,0.4,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.4875,Staphylococcus epidermidis SKN25lux,SKN25lux,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27305141,1282,,,,MLST.Staphylococcus_epidermidis.5,,,,2022-04-12T00:00:00Z,,PRJNA823545,GCA_022919195.1,CP095090,,,PacBio RS,450.0x,Flye v. 2.5,1,0,1,2539082,32.34149,2429,2358,bloodstream,,2018,Switzerland,Switzerland: Bern,,,,Infection,,,,,,,,,,,,,,collected_by:David Cameron,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1282.4936,Staphylococcus epidermidis C019,C019,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN28460870,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-05-25T00:00:00Z,,PRJNA821968,GCA_023547085.1,"CP097512,CP097513",,,Illumina NextSeq; Oxford Nanopore MinION,142.0x,Flye v. 2.9-b1778; Racon v. v1.4.17;,1,1,2,2634259,31.99765,2540,2433,pertoneal cavity,,2017,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,1.4,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.4937,Staphylococcus epidermidis C066,C066,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN28461093,1282,,,,MLST.Staphylococcus_epidermidis.6,,,,2022-05-25T00:00:00Z,,PRJNA821968,GCA_023547125.1,"CP097519,CP097520,CP097521,CP097522,CP097523",,,Illumina NextSeq; Oxford Nanopore MinION,210.0x,Flye v. 2.9-b1778; Racon v. v1.4.17;,1,4,5,2513271,32.13967,2393,2300,pertoneal cavity,,2017,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,2.3,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.4938,Staphylococcus epidermidis C034,C034,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN28460979,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-05-25T00:00:00Z,,PRJNA821968,GCA_023547105.1,"CP097514,CP097515,CP097516,CP097517,CP097518",,,Illumina NextSeq; Oxford Nanopore MinION,197.0x,Flye v. 2.9-b1778; Racon v. v1.4.17;,1,4,5,2654212,31.982298,2573,2458,pertoneal cavity,,2017,Australia,Australia: Perth,,,,peritonitis,,,,,,,,,,,,,,collected_by:Harry Perkins Institute of Medical Research,,,,,,,peritonitis,,,,,,,,,,,,,,100,1.2,Gastrointestinal Diseases,Peritoneal Conditions,Respiratory Tract,Gastrointestinal Diseases-Peritoneal Conditions HP,1282.5186,Staphylococcus epidermidis TMDU-41,TMDU-41,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26514226,1282,,,,MLST.Staphylococcus_epidermidis.5,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204705.1,"CP093165,CP093166,CP093167,CP093168,CP093169",,,Illumina MiSeq; Oxford Nanopore,283.0x,Unicycler hybrid assembley v. 0.4.8,1,4,5,2472870,32.202217,2323,2257,blood,,2015-01-21,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5187,Staphylococcus epidermidis TMDU-128,TMDU-128,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26515352,1282,,,,,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204725.1,"CP093170,CP093171,CP093172",,,Illumina MiSeq; Oxford Nanopore,486.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2558914,32.13324,2466,2374,blood,,2015-03-06,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0.4,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5188,Staphylococcus epidermidis TMDU-137,TMDU-137,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26515364,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204745.1,"CP093173,CP093174,CP093175,CP093176,CP093177,CP093178",,,Illumina MiSeq; Oxford Nanopore,249.0x,Unicycler hybrid assembley v. 0.4.8,1,5,6,2573209,32.181644,2468,2387,blood,,2015-03-09,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5189,Staphylococcus epidermidis TMDU-190,TMDU-190,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26515377,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204765.1,"CP093179,CP093180",,,Illumina MiSeq; Oxford Nanopore,469.0x,Unicycler hybrid assembley v. 0.4.8,1,1,2,2734660,32.079163,2674,2592,blood,,2015-04-19,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5190,Staphylococcus epidermidis TMDU-265,TMDU-265,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26517650,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204785.1,"CP093181,CP093182,CP093183,CP093184",,,Illumina MiSeq; Oxford Nanopore,838.0x,Unicycler hybrid assembley v. 0.4.8,1,3,4,2761052,32.105297,2692,2605,blood,,2015-06-12,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5191,Staphylococcus epidermidis TMDU-300,TMDU-300,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26517675,1282,,,,MLST.Staphylococcus_epidermidis.22,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204805.1,"CP093185,CP093186,CP093187",,,Illumina MiSeq; Oxford Nanopore,785.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2493311,32.181545,2367,2277,blood,,2015-07-09,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5192,Staphylococcus epidermidis TMDU-302,TMDU-302,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26517680,1282,,,,MLST.Staphylococcus_epidermidis.20,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204825.1,"CP093188,CP093189,CP093190,CP093191,CP093192",,,Illumina MiSeq; Oxford Nanopore,742.0x,Unicycler hybrid assembley v. 0.4.8,1,4,5,2556309,32.106525,2461,2359,blood,,2015-07-11,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5193,Staphylococcus epidermidis TMDU-323,TMDU-323,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26517682,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204845.1,"CP093193,CP093194,CP093195",,,Illumina MiSeq; Oxford Nanopore,521.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2485634,32.199512,2353,2273,blood,,2015-08-01,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5194,Staphylococcus epidermidis TMDU-2014-62,TMDU-2014-62,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26518685,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204865.1,"CP093196,CP093197",,,Illumina MiSeq; Oxford Nanopore,576.0x,Unicycler hybrid assembley v. 0.4.8,1,1,2,2646864,32.161644,2553,2479,blood,,2014-11-14,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:TMDU hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,99.6,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5195,Staphylococcus epidermidis TSM-31,TSM-31,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26520624,1282,,,,MLST.Staphylococcus_epidermidis.6,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204885.1,"CP093202,CP093203,CP093204",,,Illumina MiSeq; Oxford Nanopore,557.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2518699,32.12702,2359,2293,blood,,2012-04-19,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5196,Staphylococcus epidermidis TSM-36,TSM-36,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26520678,1282,,,,MLST.Staphylococcus_epidermidis.5,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204925.1,"CP093205,CP093206,CP093207",,,Illumina MiSeq; Oxford Nanopore,742.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2602631,32.24537,2471,2397,blood,,2012-09-28,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5197,Staphylococcus epidermidis TSM-18,TSM-18,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26519684,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204905.1,"CP093198,CP093199,CP093200,CP093201",,,Illumina MiSeq; Oxford Nanopore,706.0x,Unicycler hybrid assembley v. 0.4.8,1,3,4,2659990,32.08681,2610,2525,blood,,2010-10-05,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital,,,,,,,sepsis,,,,,,,,,,,,,,100,0.4,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5198,Staphylococcus epidermidis TSM-50,TSM-50,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26520718,1282,,,,MLST.Staphylococcus_epidermidis.5,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204965.1,"CP093210,CP093211",,,Illumina MiSeq; Oxford Nanopore,830.0x,Unicycler hybrid assembley v. 0.4.8,1,1,2,2503340,32.226505,2342,2275,blood,,2014-07-28,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5199,Staphylococcus epidermidis TSM-47,TSM-47,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26520700,1282,,,,MLST.Staphylococcus_epidermidis.59,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204945.1,"CP093208,CP093209",,,Illumina MiSeq; Oxford Nanopore,508.0x,Unicycler hybrid assembley v. 0.4.8,1,1,2,2501323,32.263687,2401,2330,blood,,2014-03-04,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1282.5200,Staphylococcus epidermidis TSM-51,TSM-51,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN26520719,1282,,,,MLST.Staphylococcus_epidermidis.2,,,,2022-07-11T00:00:00Z,,PRJNA800235,GCA_024204985.1,"CP093212,CP093213,CP093214",,,Illumina MiSeq; Oxford Nanopore,413.0x,Unicycler hybrid assembley v. 0.4.8,1,2,3,2748644,32.042492,2680,2593,blood,,2014-08-12,Japan,Japan,,,,sepsis,,,,,,,,,,,,,,collected_by:Toshima hospital staff,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis NHP,1282.5339,Staphylococcus epidermidis AH6072,AH6072,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN30996408,1282,,,,MLST.Staphylococcus_epidermidis.73,,,,2022-10-12T00:00:00Z,,PRJNA883761,GCA_025665415.1,"CP106834,CP106835,CP106836,CP106837",,,Oxford Nanopore MinION; Illumina NextSeq,312.0x,Unicycler v. 0.4.8,1,3,4,2507467,32.15512,2426,2348,skin,,2021,USA,USA: Colorado,,,,Healthy,,,,,,,,,,,,,,collected_by:Alexander R. Horswill,,,,,,,Healthy,,,,,,,,,,,,,,100,0,,,Skin and Soft Tissue,- HP,1282.5340,Staphylococcus epidermidis IVK83,IVK83,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23401985,1282,,,,,,,,2022-10-24T00:00:00Z,,PRJNA782842,GCA_025809335.1,"CP088002,CP088003",,,Illumina; PacBio Sequel,80.0x,Velvet v. Mar-2012; Hierarchical Genome,1,1,2,2553156,32.053898,2404,2324,human nose,,2009-05,Germany,Germany,,,,,,,,,,,,,,,,,,,human associated,human nasal swab,nasal mucosa,https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1005812&type=printable,,,,,,,,,,,,,human associated,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1282.5870,Staphylococcus epidermidis NG02,NG02,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35671194,1282,,,,MLST.Staphylococcus_epidermidis.490,,,,2023-06-20T00:00:00Z,,PRJNA981289,,"CP127869,CP127870",,,Illumina NovaSeq; Oxford Nanopore MinION,405.0x,Unicycler v. v0.4.8-beta,1,1,2,2497763,32.302345,2393,2324,fingertip,,2022-11-16,Hong Kong,Hong Kong: Telegraph Bay,temperature:37 deg celsius,,,,,,,,,,,,,,,,,sample_type:Bacterial isolate;collected_by:Sarah S. Q. Zhang,Skin microbiome,,,,,,,,,,,,,,,,Skin microbiome,,,,100,0,,,Other,- NHP,1282.5962,Staphylococcus epidermidis CCSH-141,CCSH-141,Staphylococcus epidermidis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36269256,1282,,,,,,,,2023-07-12T00:00:00Z,,PRJNA498007,,"CP129372,CP129373",,,Oxford Nanopore MinION; Illumina iSeq,453.0x,Prokka v. v1.14.6,1,1,2,2537768,32.06211,2362,,nasal cavity,,2019-05-19,South Korea,South Korea: Chungcheong,,,,Healthy,,,,,,,,,,,,,,collected_by:Chung-Ang University,,,,,,,Healthy,,,,,,,,,,,,,,100,0,,,Other,- HP,1283.1358,Staphylococcus haemolyticus CGMH-SH51,CGMH-SH51,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23247097,1283,,,,,genotype:ST42,,,2023-01-09T00:00:00Z,,PRJNA781382,,"CP092478,CP092479",,,PacBio,1x,Flye v. 2.9,1,1,2,2596982,32.742893,2509,2453,"chang-gung memorial hospital, linkou",,2015-07-03,Taiwan,Taiwan,,,20,Bacteremia,,,,,,,,,,,,,,collected_by:Jang-Jih Lu,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,1283.1359,Staphylococcus haemolyticus CGMH-SH53,CGMH-SH53,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23247098,1283,,,,,genotype:ST3,,,2023-01-09T00:00:00Z,,PRJNA781382,,"CP092476,CP092477",,,PacBio,1x,Flye v. 2.9,1,1,2,2586626,32.704178,2499,2439,"chang-gung memorial hospital, linkou",,2015-06-29,Taiwan,Taiwan,,,18,Bacteremia,,,,,,,,,,,,,,collected_by:Jang-Jih Lu,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia NHP,1283.1397,Staphylococcus haemolyticus CCSH-121,CCSH-121,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN36269253,1283,,,,,,,,2023-07-12T00:00:00Z,,PRJNA498007,,"CP129362,CP129363,CP129364",,,Oxford Nanopore MinION; Illumina iSeq,513.0x,Prokka v. v1.14.6,1,2,3,2490837,32.837597,2419,,nasal cavity,,2019-05-07,South Korea,South Korea: Chungcheong,,,,Healthy,,,,,,,,,,,,,,collected_by:Chung-Ang University,,,,,,,Healthy,,,,,,,,,,,,,,100,0,,,Other,- HP,1283.595,Staphylococcus haemolyticus strain 83131A,83131A,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08013134,1283,,,,MLST.Staphylococcus_haemolyticus.25,,,,2018-02-20T00:00:00Z,,PRJNA417990,GCA_002906595.1,"CP024809,CP024810",,UMCG,Illumina MiSeq; minION,196.0x,Unicycler v. v0.4.1,1,1,2,2610865,32.789055,2526,2472,hospital,,2016-10,Netherlands,Netherlands: Groningen,,,,Ascitis,,,,,,,,,,,,,Resolving SCCmec elements through hybrid assemblies.,collected_by:UMCG,,,,,,,Ascitis,,,,,,,,,,,,,,100,1.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1283.596,Staphylococcus haemolyticus strain 83131B,B,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN08161435,1283,,,,MLST.Staphylococcus_haemolyticus.25,,,,2018-02-20T00:00:00Z,,PRJNA417990,GCA_002906615.1,"CP025396,CP025397,CP025398",,UMCG,Illumina MiSeq; MinION,200.0x,Unicycler v. v0.4.1,1,2,3,2612666,32.792137,2528,2462,hospital,,2016,Netherlands,Netherlands: Groningen,,,,infection,,,,,,,,,,,,,Resolving SCCmec elements through hybrid assemblies.,collected_by:UMCG,,,,,,,infection,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1283.683,Staphylococcus haemolyticus strain PK-01,PK-01,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10838965,1283,,,,,,,,2019-05-23T00:00:00Z,,PRJNA517594,GCA_005706435.1,CP035541,,National University of Sciences and Technology,Illumina,30.0x,SPAdes v. 3.9,1,,1,2615683,32.820225,2670,2615,missing,,2018-03-16,Pakistan,Pakistan: Lahore,,male,48,Wound Infection,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis of methicillin-resistant Staphylococcus haemolyticus isolates from local hospitals of Pakistan.,"collected_by:IBGR, NUST",,,,,,,Wound Infection,,,,,,,,,,,,,,99.62,0.07,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1283.798,Staphylococcus haemolyticus strain SCAID URN1-2019,SCAID URN1-2019,Staphylococcus haemolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14667507,1283,,,,,,,,2020-05-03T00:00:00Z,,PRJNA627194,GCA_012955505.1,CP052055,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,19x,Bowtie v. 1.2.3,1,0,1,2256190,33.040203,2658,2279,urine,,2019-03-06,Kazakhstan,Kazakhstan: Almaty,,female,42,Chronic pyelonephritis,,host_disease_outcome:Chronic disease;host_disease_stage:Chronic pyelonephritis,Resistant;Susceptible,AMR Panel,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Chronic pyelonephritis,,Chronic disease,,Chronic pyelonephritis,,,,,,,,,,94.43,0,Urinary Tract Diseases,Upper UTI/Kidney Diseases,Urinary Tract,Urinary Tract Diseases-Upper UTI/Kidney Diseases HP,128780.25,Stenotrophomonas acidaminiphila strain SUNEO,SUNEO,Stenotrophomonas acidaminiphila,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN06335323,128780,,,,,,,,2018-02-06T00:00:00Z,,PRJNA374779,GCA_002951995.1,CP019797,,National Chung Cheng University,PacBio,358.062x,Canu v. 1.3,1,,1,3660864,69.74577,3439,3173,bile,,2015-11-16,Taiwan,Taiwan,,,,cholangitis,,,,,,,,,,,,,Exploring the resistance and evolutionary change of marine associated emerging zoonotic organisms.,collected_by:National Chung Cheng University,,,,,,,cholangitis,,,,,,,,,,,,,,99.1,3.4,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases NHP,1290.286,Staphylococcus hominis strain FDAARGOS_762 strain Not applicable,Not applicable,Staphylococcus hominis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11056477,1290,,,,,,FDA:FDAARGOS_762,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267575.1,"CP054006,CP054005,CP054007,CP054008,CP054009",,US Food and Drug Administration,Pacbio; Illumina,1357.12x,"Canu v. 1.7, SPAdes v. 3.11.1",1,4,5,2255507,31.537344,2224,2154,normal skin of the left arm,,,USA,USA:VA,,female,47Y,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.38,0,,,Skin and Soft Tissue,- HP,1290.488,Staphylococcus hominis C34847,C34847,Staphylococcus hominis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04515345,1290,,,,,,,,2018-02-26T00:00:00Z,,PRJNA313096,,CP014567,,,PacBio,166x,HGAP v. RS_HGAP Assembly.2,1,0,1,2273112,31.599148,2219,2136,blood,,Oct-2000,Canada,Canada,,,,Bacteremia,,,,,,,,,,,,,,collected_by:K. Zhang,,,,,,,Bacteremia,,,,,,,,,,,,,,100,1.8,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia NHP,1292.160,Staphylococcus warneri strain FDAARGOS_754 strain Not applicable,Not applicable,Staphylococcus warneri,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11056469,1292,,,,,,FDA:FDAARGOS_754,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267715.1,"CP054017,CP054016",,US Food and Drug Administration,Pacbio; Illumina,1331.87x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,2460001,32.78454,2394,2324,normal skin of the right arm,,,USA,USA:VA,,male,57Y,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.73,0,,,Skin and Soft Tissue,- HP,1296.224,Mammaliicoccus sciuri strain SSC-7107,SSC-7107,Mammaliicoccus sciuri,Mammaliicoccus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN17906023,1296,,,,,,,,2021-03-07T00:00:00Z,,PRJNA701729,GCA_017277335.1,CP071138,,Cardiff University,Illumina MiSeq; Oxford Nanopore MinION,100.0x,SPAdes v. JUL-2020; Miniasm v. JUL-2020,1,0,1,2932999,32.49159,2960,2907,blood from neonate,,2017-08-07,Pakistan,Pakistan,,,,Sepsis,,,,,,,,,,,,,"The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) is a network of 12 clinical sites distributed among four African (Ethiopia, Nigeria, Rwanda, South Africa) and three South-Asian (Bangladesh, India, Pakistan) countries aiming to assess the burden of AMR in neonates (www.barnards-group.com).We focus on the reporting of genomic diversity, genomic traits including virulence and resistance genes, and the phenotypic susceptibility profiles. We also report on an epidemiological cluster of neonatal sepsis caused by S. scuiri (recently reclassified) in Islamabad, Pakistan between July-November 2017.","collected_by:PIMS, Pakistan and Cardiff University",,,,,,,Sepsis,,,,,,,,,,,,,,99.45,3.78,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1296.381,Mammaliicoccus sciuri 82104,82104,Mammaliicoccus sciuri,Mammaliicoccus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16788958,1296,,,,,,,,2022-05-02T00:00:00Z,,PRJNA678127,GCA_023205995.1,"CP064868,CP064869",,,PacBio,393.0x,SMRT Link v. v5.0.1,1,1,2,3069055,32.608864,3064,,urine,,2014-08-21,China,"China: Quanzhou,Fujian",,,,urinary tract infection seconday to prostatic hyperplasia,,,,,,,,,,,,,,collected_by:Desong Ming,,,,,,,urinary tract infection seconday to prostatic hyperplasia,,,,,,,,,,,,,,99.9,0.2,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1296536.233,Enterobacter hormaechei subsp. xiangfangensis MDCL 3,MDCL 3,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21522362,1296536,,,,,,,,2023-02-21T00:00:00Z,,PRJNA721536,,"CP115150,CP115152,CP115151",,,Oxford Nanopore MinION; Illumina NovaSeq,250.0x,Unicycler v. v0.4.8,1,2,3,5000180,55.161953,4924,4749,blood,,2019-03-30,India,India: Kolkata,,,,Sepsis,,,,,,,,,,,,,,collected_by:ICMR-NICED,,,,,,,Sepsis,,,,,,,,,,,,,,99.9,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1296536.239,Enterobacter hormaechei subsp. xiangfangensis CNCI 7,CNCI 7,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26810699,1296536,,,,,,,,2023-05-22T00:00:00Z,,PRJNA721536,,"CP112980,CP112981",,,Oxford Nanopore MinION; Illumina NovaSeq,250.0x,Unicycler v. v0.4.8,1,1,2,4981346,54.821205,4889,4690,blood,,2021-11-23,India,India:Kolkata,,female,,sepsis,,,,,,,,,,,,,,collected_by:ICMR-NICED,,,,,,,sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1296536.67,Enterobacter hormaechei subsp. xiangfangensis strain UM_CRE-14,UM_CRE-14,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07611365,1296536,,,,,,,,2019-01-08T00:00:00Z,,PRJNA401926,GCA_003999755.1,CP023430,,Michigan State University,Illumina MiSeq,43.0x,SPAdes v. 3.7.1,1,,1,4924340,55.18531,4948,4820,"endoscope, bal",,2013-02-18,USA,USA: Michigan,,,,,,,,,,,,,,,,,Enterobacter xiangfangensis clinical isolate genome sequencing and annotation,collected_by:University of Michigan,,,,,,,not available,,,,,,,,,,,,,,99.77,0.79,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1299077.3,Salmonella enterica subsp. enterica serovar Paratyphi B str. CFSAN000541 strain SGSC 2239,SGSC 2239,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01933105,1299077,Paratyphi B,,,MLST.Salmonella_enterica.42,,SGSC:2239,,2021-05-24T00:00:00Z,,PRJNA186035,GCA_006519455.2,CP074609,,Center for Food Safety and Applied Nutrition,PacBio,132x,HGAP v. 4,1,0,1,4744898,52.168076,4769,4451,,,1981,France,France,,,,,,,,,,,,,,,,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1302.125,Streptococcus gordonii strain FDAARGOS_371,FDAARGOS_371,Streptococcus gordonii,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07312415,1302,,,,,,FDA:FDAARGOS_371,,2017-09-28T00:00:00Z,,PRJNA231221,GCA_002386285.1,CP023511,,US Food and Drug Administration,PacBio; Illumina,14.54x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,2121309,40.68,2089,2024,blood,,2014-02-16,USA,USA:DC,,male,74Y,Endocarditits,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Geroge Washington University,,,,,,,Endocarditits,Missing,Missing,Missing,Missing,,,,,,,,,,99.5,0.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1302.168,Streptococcus gordonii strain NCTC7865,NCTC7865,Streptococcus gordonii,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3594362,1302,Lancefield Group H,,,,,NCTC:7865,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900475015.1,LS483341,,SC,,,,1,,1,2187611,40.592957,2121,2054,not available: to be reported later,,1900-1946,,,,,,,,host_health_state:Sub Acute Bacterial Endocarditis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Sub Acute Bacterial Endocarditis,,,98.6,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1302.321,Streptococcus gordonii strain NCTC9124,NCTC9124,Streptococcus gordonii,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3643307,1302,Group H Serotypes,,,,,NCTC:9124,,2019-05-17T00:00:00Z,,PRJEB6403,GCA_901543415.1,LR594041,,SC,,,,1,,1,2223915,40.370697,2169,2099,blood,,1800-2018,United Kingdom,United Kingdom,,,,,,host_health_state:endocarditis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,endocarditis,,,99.81,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1302.557,Streptococcus gordonii CW,CW,Streptococcus gordonii,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31205635,1302,,,,,,,,2022-12-12T00:00:00Z,,PRJNA887960,,CP113953,,,Illumina NovaSeq,100.0x,SPAdes v. 3.15.0,1,0,1,2204031,40.278637,2190,2121,dental biofilm,,2008-03-31,Sweden,Sweden: Malmo,,,,,,,,,,,,,,,,,,sample_type:Clinical isolate;identified_by:Carolina Robertsson,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1302.83,Streptococcus gordonii strain FDAARGOS_257,FDAARGOS_257,Streptococcus gordonii,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04875583,1302,,,,,,FDA:FDAARGOS_257,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073435.2,CP020450,,US Food and Drug Administration,PacBio,24.23x,CA v. 8.2,1,,1,2222466,40.42,2265,2111,blood,,2014-08-22,USA,USA:DC,,female,,Infection with Streptococcus gordonii,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,,,,,,,Infection with Streptococcus gordonii,Missing,Missing,Missing,Missing,,,,,,,,,,99.5,4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,1303.1089,Streptococcus oralis CCUG 53468,CCUG 53468,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09081250,1303,,,,,,CCUG:53468,,2022-07-25T00:00:00Z,,PRJNA305687,GCA_024399415.1,CP029257,,,PacBio,395.0x,HGAP v. 3,1,0,1,2002022,41.38481,1902,1869,saliva,,2000-04-06,Sweden,"Sweden: Vastra Gotaland, Gothenburg",,,,None,,host_description:Healthy person;host_health_state:Healthy,,,,,,,,,,,,collected_by:Annika Alnstahl,,,,,,,None,Healthy,,Healthy person,,,,,,,,,,,100,0,,,Oral,- HP,1303.136,Streptococcus oralis strain S.MIT/ORALIS-351,S.MIT/ORALIS-351,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06179980,1303,,,,MLST.Streptococcus_oralis.65,,,,2017-02-03T00:00:00Z,,PRJNA358614,GCF_001983955.1,CP019562,NZ_CP019562.1,University of California San Francisco,PacBio,23.5x,SMRT v. 2.2;HGAP3 v. Sep 2014,1,,1,1966910,40.98,1880,1865,blood,,2001-10-09,Spain,Spain: Barcelona,,,,infective endocarditis,,,,,,,,,,,,,The goal of this project is to identify genes of oral streptococci that are important for human infection.,collected_by:Hospital Clinic of Barcelona Microbiology Laboratory,,,,,,,infective endocarditis,,,,,,,,,,,,,,99.8,0.8,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1303.167,Streptococcus oralis strain FDAARGOS_367,FDAARGOS_367,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07312411,1303,,,,,,FDA:FDAARGOS_367,,2017-09-28T00:00:00Z,,PRJNA231221,GCA_002386345.1,CP023507,,US Food and Drug Administration,PacBio; Illumina,14.79x,Celera v. 8.3,1,,1,2053209,40.94,2002,1968,blood,,2014-10-25,USA,USA:DC,,female,64Y,Endocarditits,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Geroge Washington University,,,,,,,Endocarditits,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1303.923,Streptococcus oralis strain SF100,SF100,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17082796,1303,,,,MLST.Streptococcus_oralis.75,,,,2021-01-06T00:00:00Z,,PRJNA685325,GCA_016549395.1,CP066172,,Korea Atomic Energy Research Institute,PacBio RSII,565.0x,CANU v. Oct-2020,1,0,1,1969104,41.493744,1887,1833,blood,,1980-11-22,USA,USA:San Francisco General Hospital,,,,endocarditis,,,,,,,,,,,,,Complete Genome Sequence,collected_by:John Mills,,,,,,,endocarditis,,,,,,,,,,,,,,99.87,0.2,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1303.927,Streptococcus oralis strain SF100,SF100,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07428910,1303,,,,MLST.Streptococcus_oralis.75,,,,2021-02-16T00:00:00Z,,PRJNA358614,GCA_016888845.1,"CP069427,CP069428",,University of California San Francisco,Pacbio,16.36x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,1985912,41.50083,1913,1889,blood,,2000,USA,USA: San Francisco,,,,endocarditis,,,,,,,,,,,,,The goal of this project is to identify genes of oral streptococci that are important for human infection.,collected_by:San Francisco General Hospital,,,,,,,endocarditis,,,,,,,,,,,,,,99.87,0.37,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,1304.1379,Streptococcus salivarius strain ICDC2,ICDC2,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06066184,1304,,,,,,,,2019-12-10T00:00:00Z,,PRJNA355056,GCA_009738225.1,"CP018187,CP018188",,"National Institute for Communicable Disease Control and Prevention, China CDC",PacBio RSII,232.0x,SMRT porta v. 2.3.0,1,1,2,2442990,39.53041,2299,2226,4-6 years old child with healthy oral,,2014-06-21,China,"China:Changping, Beijing",,,,,,,,,,,,,,,,,The potential of Streptococcus salivarius to inhibit the production of volatile sulphur compounds in the oral cavity,,,,,4-6 years old child with healthy oral,,,,,,,,,,,,,Beijing,,,,99.56,1.12,,,Ear,- NHP,1304.1380,Streptococcus salivarius strain ICDC3,ICDC3,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06066191,1304,,,,,,,,2019-12-10T00:00:00Z,,PRJNA355057,GCA_009738245.1,CP018189,,"National Institute for Communicable Disease Control and Prevention, China CDC",PacBio RSII,501.0x,SMRT porta v. 2.3.0,1,0,1,2193173,39.830647,2030,1993,4-6 years old child with healthy oral,,2014-06-21,China,"China:Changping, Beijing",,,,,,,,,,,,,,,,,The potential of Streptococcus salivarius to inhibit the production of volatile sulphur compounds in the oral cavity,,,,,4-6 years old child with healthy oral,,,,,,,,,,,,,Beijing,,,,99.65,0.15,,,Ear,- NHP,1304.1381,Streptococcus salivarius strain ICDC1,ICDC1,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06066182,1304,,,,,,,,2019-12-10T00:00:00Z,,PRJNA355044,GCA_009738205.1,CP018186,,"National Institute for Communicable Disease Control and Prevention, China CDC",PacBio RSII,232.0x,SMRT porta v. 2.3.0,1,0,1,2193178,39.831833,2023,1992,4-6 years old child with healthy oral,,2014-06-21,China,"China:Changping, Beijing",,,,,,,,,,,,,,,,,The potential of Streptococcus salivarius to inhibit the production of volatile sulphur compounds in the oral cavity.,,,,,4-6 years old child with healthy oral,,,,,,,,,,,,,City,,,,99.83,0.15,,,Ear,- NHP,1304.1560,Streptococcus salivarius strain FDAARGOS_771 strain Not applicable,Not applicable,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11056486,1304,,,,,,FDA:FDAARGOS_771,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267495.1,CP053998,,US Food and Drug Administration,Pacbio; Illumina,4237.14x,Canu v. 1.7,1,0,1,1999501,40.146866,1888,1840,normal skin of the right arm,,,USA,USA:VA,,female,47Y,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.84,0.15,,,Skin and Soft Tissue,- NHP,1304.1588,Streptococcus salivarius strain DB-B5,DB-B5,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15048692,1304,,,,,,,,2020-07-28T00:00:00Z,,PRJNA635659,GCA_013822985.1,"CP054153,CP054154,CP054155,CP054156",,Dose Biosystems,Illumina MiSeq; PacBio Sequel,1000.0x,Unicycler v. 0.4.8.0,1,3,4,2343299,39.90144,2130,2072,oral,,2017,Canada,Canada,,,,,,,,,,,,,,,,,Probiotics,sample_type:single culture,,,,,,,,,,,,,,,,,,,,,99.84,0.38,,,Oral,- HP,1304.1829,Streptococcus salivarius SALI-10,SALI-10,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN24172469,1304,,,,,,,,2022-04-12T00:00:00Z,,PRJNA789885,GCA_022936265.1,"CP090007,CP090008",,,PacBio,60.0x,Pacbio Smrtpipe v. December-2021,1,1,2,2261408,39.90054,2078,2015,human oral cavity,,2019-10-10,Canada,Canada,,,,,,,,,,,,,,,,,,,Oral Cavity,Tongue,-,"Mitis salivarius Agar, 37C with 5% CO2",,,,,,,,,,,,,Oral Cavity,,,,100,0.2,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1304.240,Streptococcus salivarius strain FDAARGOS_259,FDAARGOS_259,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04875585,1304,,,,,,FDA:FDAARGOS_259,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073835.2,CP020451,,US Food and Drug Administration,PacBio,24.94x,CA v. 8.2,1,,1,2259227,40.14,2142,2058,blood,,2014-09-07,USA,USA:DC,,male,85Y,Infection with Streptocoocus salivarius,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,,,,,,,Infection with Streptocoocus salivarius,Missing,Missing,Missing,Missing,,,,,,,,,,99.8,3.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,1304.245,Streptococcus salivarius strain ATCC 27945,ATCC 27945,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03140396,1304,,,,,,ATCC:27945,,2017-04-18T00:00:00Z,,PRJNA264747,GCA_002094955.1,CP015282,,Illinois Institute of Technology,PacBio,449.52x,SMRTportal v. 2.3.0,1,,1,2108274,40.24,1911,1847,saliva,,,,,env_biome:human oral microbiome,,,,,,,,Positive,Cocci,,,,,,,Streptococcus salivarius is a pioneer colonizer of the human oral microbiome,,,,,,,,,,,,,,,,,,human oral microbiome,,,,99.8,2.8,,,Oral,- NHP,1304.246,Streptococcus salivarius strain ATCC 25975,ATCC 25975,Streptococcus salivarius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN02401019,1304,,,,,,ATCC:25975,,2017-04-18T00:00:00Z,,PRJNA227252,GCA_002094975.1,"CP015283,CP015284",,Illinois Institute of Technology,PacBio,275.39x,SMRTportal v. 2.3.0,1,1,2,2326348,39.67,2132,2044,saliva,,,,,env_biome:oral microbiome,,,,,,,,Positive,Cocci,,,,,,,Streptococcus salivarius is a pioneer colonizer of the human oral microbiome,,,,,,,,,,,,,,,,,,oral microbiome,,,,99.8,2.1,,,Oral,- HP,1305.147,Streptococcus sanguinis strain NCTC7863,NCTC7863,Streptococcus sanguinis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3672886,1305,not available: to be reported later,,,,,NCTC:7863,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900475505.1,LS483385,,SC,,,,1,,1,2296927,43.32419,2248,2174,not available: to be reported later,,1900-1949,,,,,,,,host_health_state:Subacute bacterial endocarditis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Subacute bacterial endocarditis,,,99.5,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1305.692,Streptococcus sanguinis strain FDAARGOS_770 strain Not applicable,Not applicable,Streptococcus sanguinis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11056485,1305,,,,,,FDA:FDAARGOS_770,,2020-06-15T00:00:00Z,,PRJNA231221,GCA_013343115.1,CP054570,,US Food and Drug Administration,Pacbio; Illumina,1678.5x,Canu v. 1.7,1,0,1,2358846,43.320717,2324,2225,missing,,,USA,USA:VA,,,,subacute case of bacterial endocarditis,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.","collected_by:BEI Resources, American Type and Culture Collection (ATCC)",,,,,,,subacute case of bacterial endocarditis,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,100,0.37,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,1305738.8,Mycobacterium orygis strain MUHC/MB/EPTB/Orygis/51145,MUHC/MB/EPTB/Orygis/51145,Mycobacterium orygis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16564840,1305738,,,,,,,,2020-11-06T00:00:00Z,,PRJNA672657,GCA_015265495.1,CP063804,,Mc Gill University Health Centre,PacBio Sequel,13.0x,Canu v. 2.0,1,0,1,4352172,65.620316,4280,3988,cerebospinal fluid,"is from human highlight the need for implementation programmes, policies and research to achieve better public health outcomes and to combat this zoonoses",1997-09-23,Canada,Canada: Quebec,,not collected,,Tuberculosis,,host_disease_outcome:Chronic disease;host_disease_stage:extrapulmonary TB,,,,,,,,,,,"Mycobacterium orygis (M. orygis) a newly described MTBC member is known to cause infection in wide range of hosts including animals and humans (Van Ingen 2012). Identification of M. orygis from human highlight the need for implementation programmes, policies and research to achieve better public health outcomes and to combat this zoonoses. Considering this, we sequenced the complete genome of M. orygis for the first time, which in future will aid in understanding the genetic features and epidemiology of this human and veterinary pathogen.",collected_by:Laboratoire de Sante Publique du Quebec;passage_history:3,,,,,,,Tuberculosis,,Chronic disease,,extrapulmonary TB,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1307.1635,Streptococcus suis strain LSM102,LSM102,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05231907,1307,,,,MLST.Streptococcus_suis.658,,,,2017-06-12T00:00:00Z,,PRJNA325429,GCA_002189695.1,CP016175,,Huazhong Agricultural University,Pacific Biosciences,250,SMRT Analysis v. 2.3.0,1,,1,2067932,41.23,2037,1970,not collected,,2014,China,China,,,,,,,,,,,,,,,,,To investigate the prevention and control measures of the streptococcus disease,collected_by:Jinquan Li,,,,,,,not collected,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1307.2451,Streptococcus suis strain 861160,861160,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6227225,1307,2,,,MLST.Streptococcus_suis.20,,,,2019-11-20T00:00:00Z,,PRJEB35407,GCA_902702745.1,LR738722,,AMSTERDAM UMC,,,,1,0,1,2143438,41.092163,2103,,csf or blood culture,,1986,Netherlands,Netherlands,,,,,,host_health_state:diseased,,,,,,,,,,,"The zoonotic pathogen Streptococcus suis can cause septicemia and meningitis in humans. We report five complete genomes of Streptococcus suis serotype 2 and serotype 9, covering the complete phylogeny of serotype 9 Dutch porcine isolates and zoonotic isolates. The isolates include the model strain S10 and Dutch emerging zoonotic lineage.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1307.3420,Streptococcus suis strain ID33329,ID33329,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17277757,1307,24,,,MLST.Streptococcus_suis.221,genotype:ST221,,,2021-01-31T00:00:00Z,,PRJNA691075,GCA_016774475.1,CP068708,,Faculty of Public Health,Illumina; Oxford Nanopore MinION,300X,Unicycler v. v0.4.8,1,0,1,2138155,41.388298,2037,1975,blood,is from humans,2010-07,Thailand,Thailand: Phetchabul,,,,Septicemia,,,,,,,,,,,,,Characterization of genomic sequences of S. suis from humans.,collected_by:Anusak Kerdsin,,,,,,,Septicemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.3671,Streptococcus suis strain 39565,39565,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN19600291,1307,24,,,MLST.Streptococcus_suis.221,genotype:ST221,,,2021-06-15T00:00:00Z,,PRJNA691075,GCA_018885285.1,CP076517,,Faculty of Public Health,Illumina MiSeq; Oxford Nanopore MinION,132.0x,Unicycler v. v0.4.8,1,0,1,2169193,41.352566,2102,2028,blood,is from humans,2012-04-01,Thailand,Thailand: Bangkok,,,,Sepsis,,,,,,,,,,,,,Characterization of genomic sequences of S. suis from humans.,collected_by:Anusak,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.3747,Streptococcus suis strain ID41570,ID41570,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN20090113,1307,5,,,MLST.Streptococcus_suis.221,genotype:ST221,,,2021-07-21T00:00:00Z,,PRJNA691075,GCA_019297755.1,CP079193,,Faculty of Public Health,Illumina MiSeq; Oxford Nanopore MinION,230.0x,Unicycler v. v0.4.8,1,0,1,2128215,41.382095,2033,1973,blood,is from humans,2020-08,Thailand,Thailand: Phayao,,,,Septicemia,,,,,,,,,,,,,Characterization of genomic sequences of S. suis from humans.,collected_by:Anusak Kerdsin,,,,,,,Septicemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.3954,Streptococcus suis strain SZ1908,SZ1908,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN21240299,1307,2,,,MLST.Streptococcus_suis.7,,,,2021-09-14T00:00:00Z,,PRJNA760999,GCA_019967855.1,CP082948,,Nanjing agticultural university,Illumina HiSeq,100.0x,SPAdes v. 3.15,1,0,1,2137458,41.20848,2111,2007,intestinal,,2019,China,China: suzhou,,female,75,Meningitis,,,,,,,,,,,,,A streptococcus suis isolated from a human intestinal infection,collected_by:The Second Affiliated Hospital of Soochow University,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Genitourinary,Neurological Diseases-Meningitis HP,1307.4133,Streptococcus suis strain GX69,GX69,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18029937,1307,serovar 7,,,MLST.Streptococcus_suis.373,,,,2021-10-13T00:00:00Z,,PRJNA702910,GCA_020462325.1,CP071806,,National Institute for Communicable Disease Control and Prevention,Illumina NovaSeq,845x,SOAPdenovo v. SOAPdenovo 2.04,1,0,1,2388171,40.844143,2424,2277,,,2016,,China,,,,,,,,,,,,,,,,,Streptococcus suis serotype 7 genome sequences,"sample_type:pure cultures of bacteria;collected_by:State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,,,,,,,,,,,,,,,,,,,,100,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1307.5574,Streptococcus suis STC80,STC80,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401320,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206615.1,"CP100338,CP100339",,,Oxford Nanopore MiniION,96x,Unicycler v. 0.4.8,1,1,2,2253919,40.99695,2269,2183,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,female,72,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5575,Streptococcus suis STC78,STC78,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401318,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206595.1,"CP100340,CP100341",,,Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,2254043,40.996735,2277,2182,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,male,67,Sepsis,,host_disease_outcome:Death;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Death,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5576,Streptococcus suis STC84,STC84,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401323,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206635.1,"CP100332,CP100333",,,Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,2253842,40.997906,2276,2182,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,female,62,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5577,Streptococcus suis STC83,STC83,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401322,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206655.1,"CP100334,CP100335",,,Oxford Nanopore MiniION,96x,Unicycler v. 0.4.8,1,1,2,2254085,40.9961,2274,2183,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,male,75,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5578,Streptococcus suis STC90,STC90,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401328,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206695.1,"CP100326,CP100327",,,Oxford Nanopore MiniION,96x,Unicycler v. 0.4.8,1,1,2,2253851,40.997475,2272,2183,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,male,66,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5579,Streptococcus suis STC81,STC81,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401321,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206675.1,"CP100336,CP100337",,,Oxford Nanopore MiniION,96x,Unicycler v. 0.4.8,1,1,2,2251744,41.010967,2273,2180,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,male,68,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5580,Streptococcus suis STC85,STC85,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401324,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206735.1,"CP100330,CP100331",,,Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,2251579,41.0114,2268,2180,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,female,50,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5581,Streptococcus suis STC86,STC86,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401325,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206715.1,"CP100328,CP100329",,,Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,2251306,41.011883,2270,2180,blood,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,male,64,Sepsis,,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,Sepsis,Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5582,Streptococcus suis STC104,STC104,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN29401332,1307,2,,ST1656,,,,,2022-07-11T00:00:00Z,,PRJNA853715,GCA_024206755.1,"CP100418,CP100419",,,Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,2254065,40.99673,2274,2183,blood and csf,,2021-04,Thailand,Thailand:Nakhon Ratchasima,,female,67,"Meningitis, Septic arthritis",,host_disease_outcome:Recovery;host_health_state:Diseased,,,,,,,,,,,,collected_by:Kasetsart University,,,,,,,"Meningitis, Septic arthritis",Diseased,Recovery,,,ST1656,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5761,Streptococcus suis ID36054,ID36054,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31277174,1307,,,,MLST.Streptococcus_suis.94,,,,2022-11-01T00:00:00Z,,PRJNA691075,GCA_025946865.1,CP109939,,,Complete Genomics,100X,Unicycler v. v0.4.8,1,0,1,2215082,41.092564,2225,2127,blood,,2011-06,Thailand,Thailand: Lampang,,,,Septicaemia,,,,,,,,,,,,,,collected_by:Anusak,,,,,,,Septicaemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1307.5763,Streptococcus suis ID38828,ID38828,Streptococcus suis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31277172,1307,,,,MLST.Streptococcus_suis.105,,,,2022-11-01T00:00:00Z,,PRJNA691075,GCA_025946905.1,CP109941,,,Complete Genomics,100X,Unicycler v. v0.4.8,1,0,1,2074728,41.23866,2046,1963,blood,,2011-12,Thailand,Thailand: Chanthaburi,,,,Septicaemia,,,,,,,,,,,,,,collected_by:Anusak,,,,,,,Septicaemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis NHP,1308.1078,Streptococcus thermophilus strain EU01,EU01,Streptococcus thermophilus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13618337,1308,,,,MLST.Streptococcus_thermophilus.3,,,,2020-01-11T00:00:00Z,,PRJNA596306,GCA_009856565.1,CP047191,,Tianjin University of Traditional Chinese Medicine,PacBio,120.0x,HGAP v. 2.3,1,0,1,1948689,38.93659,2218,1957,,,2018-04-18,China,China: tianjin,,,,,,,,,,,,,,,,,"Eucommia ulmoides Oliv. (Du-zhong in Chinese), traditionally used as a dried bark, is a valuable and nourishing medicinal material in China. It nourishes the liver and the kidney, strengthens bones, and calms the fetus. E. ulmoides also promotes the growth of intestinal probiotics, especially Bifidobacteria and Lactobacillales, and regulates intestinal microflora disorder. According to the National Health Commission of China, E. ulmoides leaves have been added to the new list of Traditional Chinese Medicine that can be used as food and medicine. This progress contributes to the development and utilization of E. ulmoides leaves. The interaction between E. ulmoides and probiotics, along with the isolation of the potential probiotic strain EU01 from E. ulmoides, is worth studying. We tried to provide a basis for using the aqueous extract of E. ulmoides Oliv. leaves to increase the colonization quantity of probiotics, further promote intestinal and oral health, and expand the coproduction of Traditional Chinese Medicines and probiotics in vitro.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.89,1.02,,,Other,- NHP,1308.247,Streptococcus thermophilus strain ST3,ST3,Streptococcus thermophilus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05631197,1308,,,,MLST.Streptococcus_thermophilus.21,,,,2017-09-05T00:00:00Z,,PRJNA340075,GCA_002286255.1,CP017064,,Korea Food Research Institute,PacBio,369x,HGAP v. 3.0,1,,1,1865056,39.05,2101,1870,commercial dietary supplements,,2016-04-12,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,ST3 strain was isolated from Commercial dietary supplements,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.8,3,,,Other,- HP,1309.177,Streptococcus mutans strain MD,MD,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12440940,1309,,,,,,,,2019-10-07T00:00:00Z,,PRJNA525085,GCA_008831325.1,"CP044493,CP044494",,KUMC,PacBio,112.95x,Canu v. 1.7,1,1,2,2022536,36.938675,2046,1984,oral cavity,,,Brazil,Brazil: Sao Paolo,,,,Dental caries,,,,,,,,,,,,,Streptococcus mutans isolate producing Mutacin II lantibiotics.,,,,,,,,Dental caries,,,,,,,,,,,,,,100,1.31,Oral and Dental Diseases,Dental Caries,Oral,Oral and Dental Diseases-Dental Caries HP,1309.178,Streptococcus mutans strain T8,T8,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12440949,1309,,,,,,,,2019-10-07T00:00:00Z,,PRJNA525085,GCA_008831345.1,CP044492,,KUMC,PacBio,326.20x,Flye v. 2.4.1,1,,1,1976303,37.04209,1926,1877,oral cavity,,,Netherlands,Netherlands,,,,Dental caries,,,,,,,,,,,,,Streptococcus mutans isolate producing Mutacin II lantibiotics.,,,,,,,,Dental caries,,,,,,,,,,,,,,100,0.64,Oral and Dental Diseases,Dental Caries,Oral,Oral and Dental Diseases-Dental Caries HP,1309.179,Streptococcus mutans strain UA140,UA140,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12441283,1309,,,,,,,,2019-10-07T00:00:00Z,,PRJNA525085,GCA_008831365.1,CP044495,,KUMC,PacBio,195.44x,Flye v. 2.4.1,1,,1,2050049,37.041653,2007,1953,oral cavity,,,USA,USA: Alabama,,,,Dental caries,,,,,,,,,,,,,Streptococcus mutans isolate producing Mutacin II lantibiotics.,collected_by:Page Caufield,,,,,,,Dental caries,,,,,,,,,,,,,,100,0.26,Oral and Dental Diseases,Dental Caries,Oral,Oral and Dental Diseases-Dental Caries HP,1309.328,Streptococcus mutans strain S4,S4,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14397576,1309,c,,,,,,,2020-03-29T00:00:00Z,,PRJNA613248,GCA_011765485.1,CP050270,,University of Florida,PacBio,50x,Celera Assembler v. 8.3rc2,1,0,1,2085365,36.86573,2065,1966,root canal,,2018-03,Brazil,Brazil,,,,endodontic infection; Secondary endodontic infection - Patient #4,,,,,,,,,,,,,These strains were isolated from subjects with primary or secondary endodontic infections,collected_by:Augusto R. Lima,,,,,,,endodontic infection; Secondary endodontic infection - Patient #4,,,,,,,,,,,,,,99.63,0.19,Oral and Dental Diseases,Other Oral and Dental Diseases,Medical Device,Oral and Dental Diseases-Other Oral and Dental Diseases HP,1309.329,Streptococcus mutans strain S1,S1,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14397575,1309,c,,,,,,,2020-03-29T00:00:00Z,,PRJNA613248,GCA_011765505.1,CP050271,,University of Florida,PacBio,50x,Celera Assembler v. 8.3rc2,1,0,1,2080705,36.858517,2066,1960,root canal,,2018-03,Brazil,Brazil,,,,endodontic infection; Secondary endodontic infection - Patient #1,,,,,,,,,,,,,These strains were isolated from subjects with primary or secondary endodontic infections,collected_by:Augusto R. Lima,,,,,,,endodontic infection; Secondary endodontic infection - Patient #1,,,,,,,,,,,,,,99.63,0.19,Oral and Dental Diseases,Other Oral and Dental Diseases,Medical Device,Oral and Dental Diseases-Other Oral and Dental Diseases HP,1309.330,Streptococcus mutans strain P6,P6,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14397574,1309,k,,,,,,,2020-03-29T00:00:00Z,,PRJNA613248,GCA_011765525.1,CP050272,,University of Florida,PacBio,50x,Celera Assembler v. 8.3rc2,1,0,1,2085254,36.868412,2067,1965,root canal,,2015-03,Brazil,Brazil,,,,endodontic infection; primary endodontic infection - Patient #6,,,,,,,,,,,,,These strains were isolated from subjects with primary or secondary endodontic infections,collected_by:Augusto R. Lima,,,,,,,endodontic infection; primary endodontic infection - Patient #6,,,,,,,,,,,,,,99.63,0.19,Oral and Dental Diseases,Other Oral and Dental Diseases,Medical Device,Oral and Dental Diseases-Other Oral and Dental Diseases HP,1309.331,Streptococcus mutans strain P1,P1,Streptococcus mutans,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14397573,1309,c,,,,,,,2020-03-29T00:00:00Z,,PRJNA613248,GCA_011765545.1,CP050273,,University of Florida,PacBio,50x,Celera Assembler v. 8.3rc2,1,0,1,2085371,36.865864,2069,1962,root canal,,2015-03,Brazil,Brazil,,,,endodontic infection; primary endodontic infection - Patient #1,,,,,,,,,,,,,These strains were isolated from subjects with primary or secondary endodontic infections,collected_by:Augusto R. Lima,,,,,,,endodontic infection; primary endodontic infection - Patient #1,,,,,,,,,,,,,,99.63,0.19,Oral and Dental Diseases,Other Oral and Dental Diseases,Medical Device,Oral and Dental Diseases-Other Oral and Dental Diseases HP,1310.5,Streptococcus sobrinus strain 10919,10919,Streptococcus sobrinus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09214223,1310,,,,,,,,2018-06-04T00:00:00Z,,PRJNA471712,GCA_003172975.1,CP029491,,University of Illinois at Urbana-Champaign,Illumina MiSeq,300x,SPAdes v. 3.11.1,1,,1,2145290,43.60222,2156,2005,dental plaque,,,,,,,,,,,,,,,,,,,,,Streptococcus sobrinus is a Gram-positive oral pathogen. Lactic acid produced by Streptococcus sobrinus causes dental caries. The goal of this study was to assemble the first complete genomes of two strains of Streptococcus sobrinus.,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,98.8,1.2,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1310.6,Streptococcus sobrinus strain SL1,SL1,Streptococcus sobrinus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09214222,1310,,,,,,,,2018-06-04T00:00:00Z,,PRJNA471712,GCA_003172995.1,CP029490,,University of Illinois at Urbana-Champaign,Illumina MiSeq,300x,SPAdes v. 3.11.1,1,,1,2198571,43.507442,2209,2060,dental plaque,,1983,,,,,,,,,,,,,,,,,,,Streptococcus sobrinus is a Gram-positive oral pathogen. Lactic acid produced by Streptococcus sobrinus causes dental caries. The goal of this study was to assemble the first complete genomes of two strains of Streptococcus sobrinus.,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,98.8,1.2,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1310.7,Streptococcus sobrinus strain NIDR 6715-7,NIDR 6715-7,Streptococcus sobrinus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09232464,1310,,,,,,,,2018-05-30T00:00:00Z,,PRJNA471712,GCA_003176795.1,CP029560,,University of Illinois at Urbana-Champaign,Illumina MiSeq,300x,SPAdes v. 3.11.1,1,,1,2145017,43.66096,2150,1997,human dental plaque,,,,,,,,,,,,,,,,,,,,,Streptococcus sobrinus is a Gram-positive oral pathogen. Lactic acid produced by Streptococcus sobrinus causes dental caries. The goal of this study was to assemble the first complete genomes of two strains of Streptococcus sobrinus.,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,98.8,1.9,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1310.8,Streptococcus sobrinus strain NIDR 6715-15,NIDR 6715-15,Streptococcus sobrinus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09232465,1310,,,,,,,,2018-05-30T00:00:00Z,,PRJNA471712,GCA_003176815.1,CP029559,,University of Illinois at Urbana-Champaign,Illumina MiSeq,300x,SPAdes v. 3.11.1,1,,1,2144746,43.66023,2154,1996,human dental plaque,,,,,,,,,,,,,,,,,,,,,Streptococcus sobrinus is a Gram-positive oral pathogen. Lactic acid produced by Streptococcus sobrinus causes dental caries. The goal of this study was to assemble the first complete genomes of two strains of Streptococcus sobrinus.,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,98.8,1.9,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1311.1349,Streptococcus agalactiae strain FDAARGOS_254,FDAARGOS_254,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04875580,1311,,,,,,FDA:FDAARGOS_254,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073695.2,CP020449,,US Food and Drug Administration,PacBio,23.9x,CA v. 8.2,1,,1,2218541,35.75,2308,2191,blood,,2014-10-06,USA,USA:DC,,male,63Y,Infection with Streptococcus agalactiae,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,,,,,,,Infection with Streptococcus agalactiae,Missing,Missing,Missing,Missing,,,,,,,,,,98.7,4.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1311.1451,Streptococcus agalactiae strain CUGBS591,CUGBS591,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384056,1311,,,,MLST.Streptococcus_agalactiae.12,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197205.1,CP021862,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2227680,35.75,2287,2223,joint aspirate,,2008,Hong Kong,Hong Kong,,,,"arthritis, bacterial",,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,"arthritis, bacterial",,,,,,,,,,,,,,100,0.9,Bone and Joint Infections,Septic Arthritis,Bone and Joint,Bone and Joint Infections-Septic Arthritis HP,1311.1452,Streptococcus agalactiae strain SG-M50,SG-M50,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384208,1311,,,,MLST.Streptococcus_agalactiae.283,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197245.1,CP021865,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2116810,35.48,2173,2112,blood,,2013-09-13,Singapore,Singapore,,,,Meningitis; bacteremia,,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,Meningitis; bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.1453,Streptococcus agalactiae strain SG-M158,SG-M158,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384089,1311,,,,MLST.Streptococcus_agalactiae.283,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197265.1,CP021864,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2116811,35.48,2173,2113,blood,,2015-03-31,Singapore,Singapore,,,,Bacteremia,,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.1454,Streptococcus agalactiae strain SG-M29,SG-M29,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384163,1311,,,,MLST.Streptococcus_agalactiae.283,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197285.1,CP021866,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2116773,35.48,2175,2113,blood,,2012-10-30,Singapore,Singapore,,,,"arthritis, bacterial; cystitis; bacteremia",,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,"arthritis, bacterial; cystitis; bacteremia",,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Blood and Circulatory System,Urinary Tract Diseases-Lower UTI HP,1311.1455,Streptococcus agalactiae strain SG-M25,SG-M25,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384059,1311,,,,MLST.Streptococcus_agalactiae.19,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197305.1,CP021867,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2208337,35.71,2263,2210,blood,,2012-04-24,Singapore,Singapore,,,,"skin diseases, bacterial; soft tissue infections; Liver abscess; bacteremia",,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,"skin diseases, bacterial; soft tissue infections; Liver abscess; bacteremia",,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Blood and Circulatory System,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1311.1456,Streptococcus agalactiae strain SG-M8,SG-M8,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384054,1311,,,,MLST.Streptococcus_agalactiae.1,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197325.1,CP021868,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2167120,35.6,2179,2133,blood,,2011-04-11,Singapore,Singapore,,,,Bacteremia,,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.1457,Streptococcus agalactiae strain SG-M6,SG-M6,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384057,1311,,,,MLST.Streptococcus_agalactiae.17,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197365.1,CP021869,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2106018,35.64,2149,2084,blood,,2011-03-04,Singapore,Singapore,,,,Bacteremia,,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.1458,Streptococcus agalactiae strain SG-M4,SG-M4,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384060,1311,,,,MLST.Streptococcus_agalactiae.23,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197385.1,CP021870,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2072007,35.54,2057,2029,blood,,2011-02-18,Singapore,Singapore,,,,"skin diseases, bacterial; soft tissue infections; bacteremia",,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,"skin diseases, bacterial; soft tissue infections; bacteremia",,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Blood and Circulatory System,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1311.1459,Streptococcus agalactiae strain SG-M163,SG-M163,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05384092,1311,,,,MLST.Streptococcus_agalactiae.283,,,,2017-06-16T00:00:00Z,28475781,PRJNA293392,GCA_002197425.1,CP021863,,National University of Singapore and Genome Institute of Singapore,PacBio,150x,HGAP3 v. NOV-2015,1,,1,2116810,35.48,2174,2113,blood,,2015-04-01,Singapore,Singapore,,,,"arthritis, bacterial; bacteremia",,,,,,,,,C,,Multiple,,Genome sequencing of S. agalactiae strains from the Singapore Streptococcus agalactiae working group,collected_by:Singapore S. agalactiae working group,,,,,,,"arthritis, bacterial; bacteremia",,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.1504,Streptococcus agalactiae strain 874391,874391,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07374522,1311,III,,,MLST.Streptococcus_agalactiae.17,,,,2017-09-11T00:00:00Z,,PRJNA395243,GCA_002289205.1,CP022537,,Griffith University,PacBio,50.0x,Celera Assembler v. RS_HGAP_Assembly.3,1,,1,2153937,35.49,2145,2023,vagina,,1992,Japan,Japan,,female,,Streptococcal infectious disease,,,,,,,,,,,,,This report provides the complete genome sequence of Streptococcus agalactiae strain 874391. This Serotype III isolate is a member of the hyper-virulent Sequence Type 17 (ST-17) lineage that causes a disproportionate number of cases of invasive disease in humans.,collected_by:Shinji Takahashi,,,,,,,Streptococcal infectious disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1311.1671,Streptococcus agalactiae strain B509,B509,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07178061,1311,,,,MLST.Streptococcus_agalactiae.12,,,,2018-07-05T00:00:00Z,,PRJNA388485,GCA_003287995.1,CP021769,,Hunter College of City University of New York,PacBio,35.77x,Celera Assembler v. 1.4,1,,1,2060637,35.450108,2081,2031,vagina swab from a perinatal mother,"isolated from Shenzhen, China",2016,China,China: Shenzhen,,,,carrier,,,,,,,,,,,,,"We present complete genome sequences of five isolates of Streptococcus agalactiae isolated from Shenzhen, China. These genomes add to the existing publicly available group B Streptococcus (GBS) genomes and provide insights into GBS epidemiology as well as mechanisms of pathogenicity and antibiotic resistance of GBS in neonatal patients.",collected_by:Lijuan Wu,,,,,,,carrier,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1311.1672,Streptococcus agalactiae strain B508,B508,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07178060,1311,,,,MLST.Streptococcus_agalactiae.335,,,,2018-07-05T00:00:00Z,,PRJNA388485,GCA_003288015.1,CP021770,,Hunter College of City University of New York,PacBio,32.26x,Celera Assembler v. 1.4,1,,1,2199578,35.59828,2226,2164,vagina swab from a perinatal mother,"isolated from Shenzhen, China",2016,China,China: Shenzhen,,,,carrier,,,,,,,,,,,,,"We present complete genome sequences of five isolates of Streptococcus agalactiae isolated from Shenzhen, China. These genomes add to the existing publicly available group B Streptococcus (GBS) genomes and provide insights into GBS epidemiology as well as mechanisms of pathogenicity and antibiotic resistance of GBS in neonatal patients.",collected_by:Lijuan Wu,,,,,,,carrier,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1311.1673,Streptococcus agalactiae strain B105,B105,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07178057,1311,,,,MLST.Streptococcus_agalactiae.17,,,,2018-07-05T00:00:00Z,,PRJNA388485,GCA_003288035.1,CP021773,,Hunter College of City University of New York,PacBio,31.44x,Celera Assembler v. 1.4,1,,1,2273717,35.73413,2308,2230,blood sample from a newborn,"isolated from Shenzhen, China",2016,China,China: Shenzhen,,,,neonatal sepsis,,,,,,,,,,,,,"We present complete genome sequences of five isolates of Streptococcus agalactiae isolated from Shenzhen, China. These genomes add to the existing publicly available group B Streptococcus (GBS) genomes and provide insights into GBS epidemiology as well as mechanisms of pathogenicity and antibiotic resistance of GBS in neonatal patients.",collected_by:Lijuan Wu,,,,,,,neonatal sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.1674,Streptococcus agalactiae strain B507,B507,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07178059,1311,,,,MLST.Streptococcus_agalactiae.10,,,,2018-07-05T00:00:00Z,,PRJNA388485,GCA_003288055.1,CP021771,,Hunter College of City University of New York,PacBio,34.02x,Celera Assembler v. 1.4,1,,1,2082479,35.44852,2106,2057,vagina swab from a perinatal mother,"isolated from Shenzhen, China",2016,China,China: Shenzhen,,,,carrier,,,,,,,,,,,,,"We present complete genome sequences of five isolates of Streptococcus agalactiae isolated from Shenzhen, China. These genomes add to the existing publicly available group B Streptococcus (GBS) genomes and provide insights into GBS epidemiology as well as mechanisms of pathogenicity and antibiotic resistance of GBS in neonatal patients.",collected_by:Lijuan Wu,,,,,,,carrier,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1311.1675,Streptococcus agalactiae strain B111,B111,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07178058,1311,,,,MLST.Streptococcus_agalactiae.1,,,,2018-07-05T00:00:00Z,,PRJNA388485,GCA_003288075.1,CP021772,,Hunter College of City University of New York,PacBio,34.65x,Celera Assembler v. 1.4,1,,1,2150631,35.447086,2160,2122,blood sample from a newborn,"isolated from Shenzhen, China",2016,China,China: Shenzhen,,,,neonatal sepsis,,,,,,,,,,,,,"We present complete genome sequences of five isolates of Streptococcus agalactiae isolated from Shenzhen, China. These genomes add to the existing publicly available group B Streptococcus (GBS) genomes and provide insights into GBS epidemiology as well as mechanisms of pathogenicity and antibiotic resistance of GBS in neonatal patients.",collected_by:Lijuan Wu,,,,,,,neonatal sepsis,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.2499,Streptococcus agalactiae strain 32790-3A,32790-3A,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09229090,1311,III,,,MLST.Streptococcus_agalactiae.17,genotype:ST-17,,,2019-07-08T00:00:00Z,,PRJNA472222,GCA_006716245.1,CP029561,,The Eighth Affiliated Hospital of Sun Yat-sen University,PacBio,550.0x,Celera Assembler v. 8.3,1,,1,2148904,35.67707,2185,2128,blood,,2016-09,China,China,,female,1 M,Neonatal Sepsis,,,,,,,,,,,,,The whole genome of a ST-17 GBS strain isolated from was sequenced using the PacBio RSII and Illumina HiSeq 4000 platform,collected_by:Shenzhen Guangming New District Peoples Hospital,,,,,,,Neonatal Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.2500,Streptococcus agalactiae strain PLGBS13,PLGBS13,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09267180,1311,,,,MLST.Streptococcus_agalactiae.1,,,,2019-07-11T00:00:00Z,,PRJNA473176,GCA_006874565.1,CP029749,,University of Alberta,454 Roche & Illumina Misq,120.0x,clc genomic benchwork v. 7,1,,1,2095031,35.51567,2128,2095,soft tissue wound,,1997,Canada,Canada: Alberta,,,,wound infection,,,,,,,,,,,,,Streptococcus agalactiae Genome sequencing and assembly,collected_by:the National Center for Streptococcus (NCS),,,,,,,wound infection,,,,,,,,,,,,,,100,0.18,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1311.3229,Streptococcus agalactiae strain S9968,S9968,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15246708,1311,,,,MLST.Streptococcus_agalactiae.19,,,,2020-07-14T00:00:00Z,,PRJNA639694,GCA_013414325.1,CP058666,,Korea Atomic Energy Research Institute,PacBio RSII,376x,HGAP v. 3.0,1,0,1,2201113,35.73147,2198,2149,urine,,2013-03,South Korea,South Korea: Seoul,,,,meningitis,,,,,,,,,,,,,"Group B streptococcus (GBS) is the leading cause of meningitis in newborns and the adults with underlying diseases. Whole genome sequencing was performed to characterize the properties of clinical GBS isolates such as virulence, antibiotics resistance and infection",collected_by:Guro Hospital,,,,,,,meningitis,,,,,,,,,,,,,,99.29,0.53,Neurological Diseases,Meningitis,Urinary Tract,Neurological Diseases-Meningitis HP,1311.3252,Streptococcus agalactiae strain GBS7,GBS7,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355362,1311,serovar V,,,MLST.Streptococcus_agalactiae.1,,,,2020-08-17T00:00:00Z,,PRJNA556442,GCA_014218075.1,CP041998,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,130.0x,Unicycler v. 0.4.6,1,0,1,2090429,35.529167,2115,2083,blood,,1987,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,Whole genome sequencing of group B Streptococcus serotype V ST1 and ST2 perinatal strains,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.3253,Streptococcus agalactiae strain GBS11,GBS11,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355365,1311,serovar V,,,MLST.Streptococcus_agalactiae.1,,,,2020-08-17T00:00:00Z,,PRJNA556442,GCA_014218095.1,CP041999,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,450.0x,Unicycler v. 0.4.6,1,0,1,2140995,35.55786,2192,2154,blood,,1989,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,Whole genome sequencing of group B Streptococcus serotype V ST1 and ST2 perinatal strains,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.3254,Streptococcus agalactiae strain GBS19,GBS19,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355372,1311,serovar V,,,MLST.Streptococcus_agalactiae.1,,,,2020-08-17T00:00:00Z,,PRJNA556442,GCA_014218115.1,CP042000,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,315.0x,Unicycler v. 0.4.6,1,0,1,2100561,35.51975,2127,2098,blood,,1993,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,Whole genome sequencing of group B Streptococcus serotype V ST1 and ST2 perinatal strains,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.3255,Streptococcus agalactiae strain GBS28,GBS28,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355381,1311,serovar V,,,MLST.Streptococcus_agalactiae.1,,,,2020-08-17T00:00:00Z,,PRJNA556442,GCA_014218135.1,CP042001,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,250.0x,Unicycler v. 0.4.6,1,0,1,2137402,35.676254,2184,2153,blood,,1994,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,Whole genome sequencing of group B Streptococcus serotype V ST1 and ST2 perinatal strains,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.3256,Streptococcus agalactiae strain GBS30,GBS30,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355383,1311,serovar V,,,MLST.Streptococcus_agalactiae.1,,,,2020-08-17T00:00:00Z,,PRJNA556442,GCA_014218155.1,CP042002,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,395.0x,Unicycler v. 0.4.6,1,0,1,2075620,35.494263,2097,2067,blood,,1995,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,Whole genome sequencing of group B Streptococcus serotype V ST1 and ST2 perinatal strains,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.3462,Streptococcus agalactiae strain 2014-661,2014-661,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14644156,1311,,,,MLST.Streptococcus_agalactiae.17,,,,2020-12-31T00:00:00Z,33079049,PRJNA626549,GCA_016454885.1,CP051845,,Inserm,Illumina HiSeq,10x,SPAdes v. Galaxy version 3.9.1,1,0,1,2271271,35.21764,1912,,blood,,2014,France,France: La Rochelle,,,,streptococcal bacteremia,,,,,,,,,,,,,"Group B Streptococcus (Streptococcus agalactiae, GBS) is the leading cause of neonatal invasive diseases. Multidrug resistant (MDR) isolates of the hypervirulent neonatal CC17 clone have been decribed in China and Canada, and more recently in Europe. We provide the whole genome sequence of eight of these isolates responsible for neonatal invasive diseases in France. These isolates harbor large integrative and conjugative genetic elements carrying multiple resistance determinants.",collected_by:CNR-Strep,,,,,,,streptococcal bacteremia,,,,,,,,,,,,,,91.49,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1311.3467,Streptococcus agalactiae strain 2011-995,2011-995,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14644152,1311,,,,MLST.Streptococcus_agalactiae.17,,,,2020-12-31T00:00:00Z,33079049,PRJNA626549,GCA_016454945.1,CP051841,,Inserm,Illumina HiSeq,10x,SPAdes v. Galaxy version 3.9.1,1,0,1,2065471,35.145416,1948,,cerebrospinal fluid,,2011,France,France: Colombes,,,,streptococcal meningitis,,,,,,,,,,,,,"Group B Streptococcus (Streptococcus agalactiae, GBS) is the leading cause of neonatal invasive diseases. Multidrug resistant (MDR) isolates of the hypervirulent neonatal CC17 clone have been decribed in China and Canada, and more recently in Europe. We provide the whole genome sequence of eight of these isolates responsible for neonatal invasive diseases in France. These isolates harbor large integrative and conjugative genetic elements carrying multiple resistance determinants.",collected_by:CNR-Strep,,,,,,,streptococcal meningitis,,,,,,,,,,,,,,95.04,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,1311.3972,Streptococcus agalactiae strain CM45/1,CM45/1,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN23500515,1311,,,,,,,,2021-12-12T00:00:00Z,,PRJNA784761,GCA_021165795.1,"CP088933,CP088934",,University of Agriculture in Krakow,Oxford Nanopore MinION,698.0x,Miniasm v. 0.3_r179,1,1,2,2171738,35.6603,2406,2138,vagina,isolated form the vagina of mother of twins with early-onset disease GBS,2008,,Poland,,female,,GBS infection,,host_description:asymptomatic carriage of Streptococcus agalactiae cause sepsis and death of the newborn;host_disease_outcome:death of the newborn,,,,,,,,,,,Genome submission of Streptococcus agalactiae strain: CM45/1 isolated form the vagina of mother of twins with early-onset disease GBS.Genome characterization of the Streptococcus agalactiae strain CM45/1 isolated from a carrier of a woman whose twins developed GBS sepsis. One of the cases resulted in death.The strain genome was sequenced using MinION M1k system (Oxford Nanopore). Filtered reads were assembled into single contig using Unicycler software - implementing Miniasm assembler and repeated assembly polishing rounds using Racon software.,"collected_by:Dorota Pawlik, Clinic of Neonatology, Jagiellonian University Medical College, Krakow, Poland",,,,,,,GBS infection,,death of the newborn,asymptomatic carriage of Streptococcus agalactiae cause sepsis and death of the newborn,,,CM_45 isolated form the vagina of mother of twins with early-onset disease GBS,,,,,,,,98.77,0.18,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1311.3999,Streptococcus agalactiae GBS20,GBS20,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12355373,1311,,,,MLST.Streptococcus_agalactiae.1,,,,2022-01-18T00:00:00Z,,PRJNA556442,GCA_021496905.1,CP053891,,,Illumina MiSeq; ONT GridION,258x,Unicycler v. 0.4.6,1,0,1,2097492,35.535107,2081,2011,blood,,1993,USA,USA: Houston,,,,Sepsis,,,,,,,,,,,,,,collected_by:UTHSC/BCM,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1311.4784,Streptococcus agalactiae SA5087,SA5087,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31213618,1311,,,,MLST.Streptococcus_agalactiae.19,,,,2022-10-24T00:00:00Z,,PRJNA888255,GCA_025808195.1,CP107524,,,Illumina HiSeq; PacBio,221.33x,Hifiasm v. 0.13-r308; Canu v. 0.7; pilon,1,0,1,2278514,35.844723,2277,2209,urine,,2022-06,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1311.5370,Streptococcus agalactiae GBSIR0001,GBSIR0001,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33919071,1311,IV,,,MLST.Streptococcus_agalactiae.452,genotype:ST452,,,2023-06-22T00:00:00Z,,PRJNA948805,,CP120953,,,Illumina MiSeq; Oxford Nanopore GridION,560.0x,Trycycler v. 0.5.3,1,0,1,2136302,35.666073,2114,2060,spinal fluid,,2022-10-26,Japan,Japan: Shiga,,,,Meningitis,,,,,,,,,,,,,,collected_by:Japanese Red Cross Otsu Hospital,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,1311.5443,Streptococcus agalactiae NEM316,NEM316,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN35521428,1311,III,,,MLST.Streptococcus_agalactiae.23,,,,2023-07-17T00:00:00Z,,PRJNA977207,,CP129876,,,PacBio,842x,SMRTLink v. 1,1,0,1,2211485,35.62742,2179,,blood from neonate,,,,,,,,Fatal septicaemia,,,,,,,,,,,,,,,,,,,,,Fatal septicaemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,131111.13,Schaalia turicensis strain CT001,CT001,Schaalia turicensis,Schaalia,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMN14131124,131111,,,,,,,,2021-07-28T00:00:00Z,,PRJNA607374,GCA_019380255.1,CP048928,,"Faculty of Medicine Siriraj Hospital, Mahidol University",Illumina NovaSeq and Oxford Nanopore,1443.414545x,Unicycler v. 0.4.4,1,0,1,1912310,57.120342,1727,1630,urethra,,2010-01-15,Thailand,Thailand: Bangkok,,,15,gonorrhea,,,,,,,,,,,,,To explore the genomic dynamics of co-evolution between Neisseria gonorrhoeae and Schaalia turicensis,collected_by:Natakorn Nokchan,,,,,,,gonorrhea,,,,,,,,,,,,,,99.53,0.71,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,1313.13832,Streptococcus pneumoniae strain SP49,SP49,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN05981365,1313,,,,,,,,2016-12-09T00:00:00Z,,PRJNA352462,GCF_001896045.1,CP018136,NZ_CP018136.1,Helmholtz-Centre for Infection Research,PacBio; Illumina MiSeq,186x,HGAP SMRTPortal v. 2.3.0,1,,1,2206644,39.86,2345,2183,blood,,2008-08-20,Germany,Germany: Aachen,,,,bacterial pneumonia,,,,,,,,,,,,,Genome sequencing of a clinical Streptococcus pneumoniae isolate (SP49) with high susceptibility to the myxobacterial secondary metabolite Carolacton.,collected_by:National Reference Center for Streptococci RWTH Aachen University,,,,,,,bacterial pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,1313.13833,Streptococcus pneumoniae strain SP61,SP61,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06009945,1313,,,,,,,,2016-12-09T00:00:00Z,,PRJNA353112,GCF_001896065.1,CP018137,NZ_CP018137.1,Helmholtz-Centre for Infection Research,PacBio; Illumina MiSeq,200x,HGAP SMRTPortal v. 2.3.0,1,,1,2071812,39.85,2127,2025,thorax drainage,,2009-04-20,Germany,Germany: Aachen,,,,pleuritis,,,,,,,,,,,,,Genome sequencing of a clinical Streptococcus pneumoniae isolate (SP61) with high susceptibility to the myxobacterial secondary metabolite Carolacton.,collected_by:National Reference Center for Streptococci RWTH Aachen University,,,,,,,pleuritis,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1313.13835,Streptococcus pneumoniae strain SWU02,SWU02,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06109026,1313,,,,,,,,2016-12-13T00:00:00Z,,PRJNA354664,GCF_001902455.1,CP018347,NZ_CP018347.1,Southwest Medical University,Illumina Miseq and PacBio RS Sequencing,475.0x,SOAPdenovo v. v2.04,1,,1,2092148,39.77,2150,,sputum specimens,,2015-03,China,China,,,,infection,,,,,,,,,,,,,"Molecular characteristic of a high virulence streptococcuspneumoniae ST271 in Sichuan,China",collected_by:Yingshun Zhou,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1313.15185,Streptococcus pneumoniae strain KK0981,KK0981,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00073590,1313,,,,MLST.Streptococcus_pneumoniae.242,,,,2017-01-25T00:00:00Z,,PRJDB5486,GCA_002357995.1,AP017971,,"Department of Infectious Diseases, Keio University School of Medicine",PacBio RS II,278X,SMRT Analysis v. 2.3,1,,1,2148476,39.64,2273,2164,blood,,2011,Japan,Japan: Hyogo,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Elucidation fo capsular switching and drug resistance acceleration mechanism accompanying the spread of PCV7,,missing,Human (clinical patient),Blood,10.3201/eid2007.131485,Streptococcus pneumoniae KK0981 sequenceing,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1313.15186,Streptococcus pneumoniae strain KK1157,KK1157,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00073750,1313,,,,MLST.Streptococcus_pneumoniae.242,,,,2017-04-29T00:00:00Z,,PRJDB5486,GCA_002358035.1,AP018044,,"Department of Infectious Diseases, Keio University School of Medicine",PacBio RS II,370X,SMRT Analysis v. 2.3,1,,1,2267947,39.62,2437,2303,blood from clinical patient,,2011,Japan,Japan: Sapporo,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Elucidation fo capsular switching and drug resistance acceleration mechanism accompanying the spread of PCV7,,missing,Human (clinical patient),Blood,10.3201/eid2007.131485,Streptococcus pneumoniae KK1157 sequenceing,,,,,,,,,,,,missing,,,,100,4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1313.15386,Streptococcus pneumoniae strain 11A,11A,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06166933,1313,,,,MLST.Streptococcus_pneumoniae.8279,genotype:ST8279,,,2017-12-07T00:00:00Z,,PRJNA358150,GCA_002813955.1,CP018838,,Asia Pacific Foundation for Infectious Diseases,PacBio,427.9x,GS De Novo Assembler v. NOV-2016,1,,1,2079194,39.81,2307,2244,blood,,2012-05,Korea,Korea: Seoul,,male,81,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,to investigate genome of an XDR (extensively drug resistant) pneumococcal strain,collected_by:JinYang Baek,,,,,,,Pneumonia,,,,,,,,,,,,,,99.2,0.3,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,1313.15789,Streptococcus pneumoniae strain 335,335,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08501023,1313,,,,MLST.Streptococcus_pneumoniae.81,,,,2018-02-15T00:00:00Z,,PRJNA433539,GCA_002947575.1,CP026670,,University of Mississippi Medical Center,Illumina MiSeq,81.0x,BASys v. September-2017,1,,1,2221315,39.48859,2430,2301,vitreous humor,,2005-11,USA,USA: Pittsburgh,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Genome of Streptococcus pneumoniae clinical ocular isolate strain, E335",sample_type:culture;biomaterial_provider:Regis P. Kowalski;collected_by:Charles T. Campbell Eye Microbiology Lab,,,,,,,,,,,,,,,,,,,,,100,0.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.16000,Streptococcus pneumoniae strain SPN XDR SMC1710-32,SPN XDR SMC1710-32,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08323709,1313,15A,,,MLST.Streptococcus_pneumoniae.8279,genotype:ST8279,,,2018-08-03T00:00:00Z,,PRJNA428885,GCA_003354825.1,CP025838,,Asia Pacific Foundation for Infectious Diseases,PacBio,702.9x,GS De Novo Assembler v. JAN-2017,1,,1,2057144,39.830025,2313,2171,blood,,2017-10,South Korea,South Korea: Seoul,,female,65,Bacteremic meningitis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,To investigate genetic differences in the whole genome sequences among the isolates of S. pneumoniae with XDR phenotype,"collected_by:Jin Yang, Baek",,,,,,,Bacteremic meningitis,,,,,,,,,,,,,,99.1,3.2,Neurological Diseases,Meningitis,Blood and Circulatory System,Neurological Diseases-Meningitis HP,1313.16141,Streptococcus pneumoniae strain MDRSPN001,MDRSPN001,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00096762,1313,serovar 19F,,,MLST.Streptococcus_pneumoniae.10017,,,,2017-10-05T00:00:00Z,,PRJDB6379,GCA_003609935.1,AP018391,,Sapporo Medical University School of Medicine,PacBio SMRT; illumina MiSeq; Sanger,701x,HGAP v. 3,1,,1,2045062,39.900063,2081,1983,,,,Japan,Japan:Hokkaido:Sapporo,,,,,,,Susceptible;Resistant,Computational Prediction,Positive,Cocci,No,Mesophilic,37,Aerobic,HostAssociated,bacteremia,"The complete genome sequence of a multidrug resistant S. penumoinae serotype 19F strain MDRSPN001, isolated from a patient with invasive pneumococcal infection in Sapporo, Japan",,not applicable,not applicable,not applicable,not applicable,"Complete genome sequence of invasive multidrug-resistant Streptococcus pneumoniae serotype 19F in Sapporo, Japan",,,,,,,,,,,,not applicable,,,,99.42,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.16305,Streptococcus pneumoniae strain HKU1-14,HKU1-14,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06233407,1313,serovar 3,,,MLST.Streptococcus_pneumoniae.6011,,,,2019-01-07T00:00:00Z,,PRJNA361421,GCA_003994915.1,CP019299,,The University of Hong Kong,PacBio,455.0x,HGAP v. JUN-2015,1,,1,2038121,39.66408,2225,2130,blood,,2014-07,Hong Kong,Hong Kong,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Serotype 3 Streptococcus pneumoniae complete genome,collected_by:Pak Leung Ho,,,,,,,Bacteremia,,,,,,,,,,,,,,99.74,0.26,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1313.16308,Streptococcus pneumoniae strain 4496,4496,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5092020,1313,1,,,MLST.Streptococcus_pneumoniae.3018,,102.100.100.25785,,2018-12-18T00:00:00Z,,PRJEB29727,GCA_900618545.1,LR129840,,Bioplatforms Australia,,,,1,,1,2169270,39.61932,2294,,blood,,1988-06-07,Australia,Australia,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pneumoniae.",,,,,,,,,diseased,,,,,,,,,,,,,99.52,0.21,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1313.16309,Streptococcus pneumoniae strain 947,947,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5092021,1313,14,,,MLST.Streptococcus_pneumoniae.15,,102.100.100.25786,,2018-12-18T00:00:00Z,,PRJEB29727,GCA_900618555.1,LR129841,,Bioplatforms Australia,,,,1,,1,2109624,39.61308,2176,,ear,,1997-09-07,Australia,Australia,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pneumoniae.",,,,,,,,,diseased,,,,,,,,,,,,,99.81,0.21,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,1313.16310,Streptococcus pneumoniae strain 180-2,180-2,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5092023,1313,3,,,MLST.Streptococcus_pneumoniae.180,,102.100.100.25788,,2018-12-18T00:00:00Z,,PRJEB29727,GCA_900618575.1,LR129843,,Bioplatforms Australia,,,,1,,1,2038006,39.814064,2161,,ear,,1989-07-28,Australia,Australia,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pneumoniae.",,,,,,,,,diseased,,,,,,,,,,,,,99.82,0.2,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,1313.16311,Streptococcus pneumoniae strain 180-15,180-15,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5092024,1313,3,,,MLST.Streptococcus_pneumoniae.180,,102.100.100.25789,,2018-12-18T00:00:00Z,,PRJEB29727,GCA_900618585.1,LR129844,,Bioplatforms Australia,,,,1,,1,2037269,39.811974,2156,,blood,,1996-10-11,Australia,Australia,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pneumoniae.",,,,,,,,,diseased,,,,,,,,,,,,,99.82,0.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1313.17693,Streptococcus pneumoniae strain 521,521,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11032549,1313,,,,MLST.Streptococcus_pneumoniae.595,,,,2019-03-07T00:00:00Z,,PRJNA524762,GCA_004331935.1,CP036529,,Korea Basic Science Institute,PacBio RSII,259.0x,Unicycler v. DEC-2018,1,,1,2041494,39.718903,2294,2115,sputum,,2011-08,South Korea,South Korea,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,To determine the genomic sequence of S. pneumoniae clinical strain 521 and elucidate antibiotics resistance mechanisms of this stain using proteogenomic analysis.,collected_by:chungnam national university hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.49,0.21,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1313.17709,Streptococcus pneumoniae strain 2245STDY5605682 strain GPSC94,GPSC94,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA2203393,1313,23F,,,MLST.Streptococcus_pneumoniae.2174,mlst:7-16-8-8-6-142-14;mlst:7-16-8-8-6-142-14,,,2019-02-20T00:00:00Z,31196809,PRJEB31141,GCA_900692615.1,LR216018,,WTSI,Illumina HiSeq,,,1,,1,2129739,39.54031,2279,2133,csf,,19-07,Gambia,West Coast Banjul,,,,,,host_health_state:Meningitis,Resistant;Susceptible,AMR Panel,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,Meningitis,,,99.6,0.26,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17727,Streptococcus pneumoniae strain 2245STDY5983173 strain GPSC67,GPSC67,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA2797120,1313,18C,,,MLST.Streptococcus_pneumoniae.4350,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692795.1,LR216034,,WTSI,,,,1,,1,2097748,39.691414,2233,2115,csf,,1998,India,India,,,,,,host_health_state:Meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,Meningitis,,,99.47,0.2,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17728,Streptococcus pneumoniae strain GPS_ZA_821-sc-1950967 strain GPSC37,GPSC37,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA2553885,1313,6B,,,,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692805.1,LR216038,,WTSI,,,,1,,1,2147673,39.3768,2285,2143,csf,,2007,South Africa,South Africa,,,,,,host_health_state:Meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,Meningitis,,,99.6,0.37,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17740,Streptococcus pneumoniae strain 2245STDY6106337 strain GPSC40,GPSC40,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3390054,1313,6B,,,MLST.Streptococcus_pneumoniae.5266,mlst:2-18-526-10-17-1-19;mlst:2-18-526-10-17-1-19,,,2019-02-20T00:00:00Z,31196809,PRJEB31141,GCA_900692925.1,LR216051,,WTSI,Illumina HiSeq,,,1,,1,2082222,39.66016,2201,2055,csf,,20-04,Malawi,Southern Blantyre,,,,,,host_health_state:meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.36,0.21,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17741,Streptococcus pneumoniae strain GPS_US_PATH396-sc-2296505 strain GPSC10,GPSC10,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3431333,1313,19A,,,MLST.Streptococcus_pneumoniae.2013,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692935.1,LR216050,,WTSI,,,,1,,1,2074861,39.61259,2191,2059,csf,,2000,Egypt,Egypt,,,,,,host_health_state:meningitis,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.42,0.2,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17742,Streptococcus pneumoniae strain 2245STDY6106635 strain GPSC5,GPSC5,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3431348,1313,6A,,,MLST.Streptococcus_pneumoniae.90,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692945.1,LR216053,,WTSI,,,,1,,1,2240045,39.593616,2430,2280,csf,,2000,Egypt,Egypt,,,,,,host_health_state:meningitis,Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.18,0.29,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17746,Streptococcus pneumoniae strain 2245STDY6106384 strain GPSC91,GPSC91,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3389963,1313,24,,,MLST.Streptococcus_pneumoniae.5079,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692985.1,LR216057,,WTSI,,,,1,,1,2101669,39.481823,2232,2081,csf,,2005,Malawi,Malawi,,,,,,host_health_state:meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.81,0.63,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17747,Streptococcus pneumoniae strain 2245STDY6106637 strain GPSC68,GPSC68,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3431351,1313,18C,,,MLST.Streptococcus_pneumoniae.542,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900692995.1,LR216056,,WTSI,,,,1,,1,2087640,39.56925,2180,2046,csf,,2001,Egypt,Egypt,,,,,,host_health_state:meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.6,0.21,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17749,Streptococcus pneumoniae strain 2245STDY6105855 strain GPSC56,GPSC56,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3389261,1313,7F,,,MLST.Streptococcus_pneumoniae.4350,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900693015.1,LR216059,,WTSI,,,,1,,1,2097748,39.691414,2233,2115,csf,,2000,Malawi,Malawi,,,,,,host_health_state:meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.47,0.2,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17750,Streptococcus pneumoniae strain 2245STDY6178787 strain GPSC47,GPSC47,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3713867,1313,6B,,,,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900693025.1,LR216060,,WTSI,,,,1,,1,2202359,39.413074,2341,2210,clinical specimen,,1995,China,China,,,,,,host_health_state:IPD,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,IPD,,,99.6,0.32,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.17752,Streptococcus pneumoniae strain 2245STDY6178826 strain GPSC53,GPSC53,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3713960,1313,19A,,,,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900693035.1,LR216061,,WTSI,,,,1,,1,2154542,39.492653,2312,2160,clinical specimen,,1997,China,China,,,,,,host_health_state:IPD,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,IPD,,,99.6,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.17758,Streptococcus pneumoniae strain 2245STDY6178854 strain GPSC51,GPSC51,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3714019,1313,3,,,MLST.Streptococcus_pneumoniae.5706,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900693105.1,LR216068,,WTSI,,,,1,,1,2057332,39.61444,2198,2064,clinical specimen,,1999,China,China,,,,,,host_health_state:IPD,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,IPD,,,99.82,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.17759,Streptococcus pneumoniae strain 2245STDY6178828 strain GPSC19,GPSC19,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3713964,1313,42,,,MLST.Streptococcus_pneumoniae.1955,,,,2019-02-20T00:00:00Z,,PRJEB31141,GCA_900693115.1,LR216069,,WTSI,,,,1,,1,2122938,39.532402,2277,2131,clinical specimen,,1995,China,China,,,,,,host_health_state:IPD,Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,IPD,,,99.32,0.73,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.17762,Streptococcus pneumoniae strain GPS_ZA_821-sc-1950967 strain GPSC37,GPSC37,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA2553885,1313,6B,,,MLST.Streptococcus_pneumoniae.2421,,,,2019-03-26T00:00:00Z,,PRJEB31141,GCA_900795145.1,LR536845,,WTSI,,,,1,,1,2133955,39.64639,2276,2160,csf,,2007,South Africa,South Africa,,,,,,host_health_state:Meningitis,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,Meningitis,,,99.08,0.21,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17764,Streptococcus pneumoniae strain 2245STDY6106635 strain GPSC5,GPSC5,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3431348,1313,6A,,,,,,,2019-03-26T00:00:00Z,,PRJEB31141,GCA_900795165.1,LR536837,,WTSI,,,,1,,1,2126260,39.603626,2278,2141,csf,,2000,Egypt,Egypt,,,,,,host_health_state:meningitis,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.76,0.2,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.17766,Streptococcus pneumoniae strain 2245STDY6178854 strain GPSC51,GPSC51,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3714019,1313,3,,,MLST.Streptococcus_pneumoniae.458,,,,2019-03-26T00:00:00Z,,PRJEB31141,GCA_900795245.1,LR536841,,WTSI,,,,1,,1,2022764,39.718243,2177,2046,clinical specimen,,1999,China,China,,,,,,host_health_state:IPD,Susceptible;Resistant,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,IPD,,,99.37,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.17767,Streptococcus pneumoniae strain 2245STDY6105855 strain GPSC56,GPSC56,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3389261,1313,7F,,,MLST.Streptococcus_pneumoniae.8672,,,,2019-03-26T00:00:00Z,,PRJEB31141,GCA_900795265.1,LR536839,,WTSI,,,,1,,1,1995077,39.78893,2094,1951,csf,,2000,Malawi,Malawi,,,,,,host_health_state:meningitis,Susceptible,Computational Prediction,,,,,,,,,Reference genome for Global Pneumococcal Sequence (GPS ) project.,,,,,,,,,,,,,,,,,,,meningitis,,,99.82,0.2,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1313.18291,Streptococcus pneumoniae strain 4559,4559,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5092022,1313,14,,,MLST.Streptococcus_pneumoniae.15,,102.100.100.25787,,2019-06-07T00:00:00Z,,PRJEB29727,GCA_900622505.1,"LR595848,LR595849",,Bioplatforms Australia,,,,1,1,2,2156228,39.646595,2239,,blood,,1988-11-11,Australia,Australia,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pneumoniae.",,,,,,,,,diseased,,,,,,,,,,,,,99.81,0.21,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1313.21214,Streptococcus pneumoniae strain AUSMDU00010538,AUSMDU00010538,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13191652,1313,19A,,,,mlst:ST199,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664475.1,CP045931,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,710x,de novo,1,0,1,2090792,39.6676,2197,2064,missing,,2014,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.82,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1313.34732,Streptococcus pneumoniae strain PZ900701590,PZ900701590,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14380576,1313,12F-ST6945,,,MLST.Streptococcus_pneumoniae.6945,,,,2020-03-24T00:00:00Z,,PRJNA612713,GCA_011694695.1,"CP050175,CP050176",,Kyoto University,Illumina NextSeq; PacBio RSII,100.0x,Unicycler v. 0.4.8,1,1,2,2145834,39.5717,2294,2151,blood,,2017-11,Japan,Japan:Osaka,,,,bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Clinical isolate of Streptococcus pneumoniae serotype 12F ST6945 derived in Japan,collected_by:Satoshi Nakano,,,,,,,bacteremia,,,,,,,,,,,,,,99.6,0.21,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1313.34903,Streptococcus pneumoniae strain SCAID PHRX1-2019,SCAID PHRX1-2019,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14653009,1313,,,,MLST.Streptococcus_pneumoniae.377,,,,2020-05-03T00:00:00Z,,PRJNA627194,GCA_012955565.1,CP052060,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,13x,Bowtie v. 1.2.3,1,0,1,1963680,39.899876,2487,2001,oropharyngeal swab of pharynx,,2019-07-24,Kazakhstan,Kazakhstan: Almaty,,female,32,bronchitis,,host_disease_outcome:Recovery;host_disease_stage:acute bronchitis,Susceptible;Intermediate;Resistant,Computational Prediction,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,bronchitis,,Recovery,,acute bronchitis,,,,,,,,,,98.85,0,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,1313.35499,Streptococcus pneumoniae strain MDR-MM-0720-0522,MDR-MM-0720-0522,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17215543,1313,,,,MLST.Streptococcus_pneumoniae.97,,,,2021-01-17T00:00:00Z,,PRJNA689737,GCA_016653535.1,CP067363,,Aix Marseille univesity,Oxford Nanopore,93.0x,Canu assembler v. Galaxy Version 1.8,1,0,1,2220550,39.884514,2314,1993,,,2020-07-15,France,France: Marseille,,female,,Meningitis,,,Susceptible,Computational Prediction,,,,,,,,,"Streptococcus pneumoniae is responsible for deadly meningitis, diagnosed at the point-of-care. Improving the rapidity and the reliability of the metagenomic process, we developed an innovative protocol for the direct diagnosis of S. pneumoniae meningitis offering all the pathogen genetic information in less than 2 hours. Using Oxford Nanopore Technology, we identified 92.5% of the Streptococcus pneumoniae genome by real-time whole genome sequencing directly from the cerebrospinal fluid collected in a patient with meningitis",sample_type:homo sapiens,,,,,,,Meningitis,,,,,,,,,,,,,,99.42,0.2,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,1313.35611,Streptococcus pneumoniae strain BVJ1JL,BVJ1JL,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17602804,1313,1,,,MLST.Streptococcus_pneumoniae.5012,genotype:Serotype 1,,,2021-03-23T00:00:00Z,,PRJNA695191,GCA_017569245.1,CP071871,,UCL,PacBio RS;Illumina HiSeq,573,Unicycler v. 0.4.9b,1,0,1,2134668,39.725567,2254,2101,nasopharynx,,2015,Malawi,Malawi,,male,9 years,"pneumonia, meningitis",,host_description:Male;host_health_state:Healthy,Susceptible;Resistant,Computational Prediction,,,,,,,,,The aim of the project was to generate a high quality contiguous genome sequence of an African S. pneumonia serotype 1.,collected_by:Todd D Swarthout,,,,,,,"pneumonia, meningitis",Healthy,,Male,,,,,,,,,,,99.54,0.21,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1313.35815,Streptococcus pneumoniae strain D39_P0,D39_P0,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15858987,1313,,,,MLST.Streptococcus_pneumoniae.595,,,,2021-05-11T00:00:00Z,,PRJNA658145,GCA_018336875.1,CP061208,,University of Liverpool,PacBio,469.0x,Flye Assembler v. 2.4.2; Pilon v. 1.22,1,0,1,2046551,39.707928,2127,1998,,,1916,USA,USA,,,,Pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,In this study we carried out manual passage of pneumococci between mice in a model of asymptomatic nasopharyngeal carriage and in parallel we also performed the same process in a pneumonia model of infection. The sequence reads from the evolved lineages were compared to a complete whole genome of the ancestor strain used for the initial infection inoculum. Using this approach we aimed to determine how environmental differences between the upper and lower airways might shape the adaptation and evolution processes of the pneumococcus.,collected_by:Avery,,,,,,,Pneumonia,,,,,,Ancestor Isolate,,,,,,,,99.6,0.21,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,1313.38060,Streptococcus pneumoniae strain SCAID PHRX1-2021,SCAID PHRX1-2021,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN20982453,1313,,,,MLST.Streptococcus_pneumoniae.377,,,,2021-09-09T00:00:00Z,,PRJNA754843,GCA_019915285.1,CP082820,,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,386x,Canu v. 2.0,1,0,1,2098200,39.720524,2188,2032,swab from pharynx,,2021-05-18,Kazakhstan,Kazakhstan: Almaty,,male,69,pneumonia,,host_disease_outcome:Recovery;host_disease_stage:Acute pneumonia,Susceptible;Resistant;Intermediate,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,pneumonia,,Recovery,,Acute pneumonia,,,,,,,,,,99.42,3.65,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,1313.41788,Streptococcus pneumoniae PZ900700608,PZ900700608,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783364,1313,15B,,,,,,,2022-03-14T00:00:00Z,,PRJNA656385,GCA_022558605.1,CP060156,,,Illumina NextSeq; PacBio RSII,318.0x,Unicycler v. 0.4.8,1,0,1,2210224,39.5131,2334,2164,middle ear fluid,,2014-05,Japan,Japan:Yamaguchi,,,,otitis media,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Satoshi Nakano,,,,,,,otitis media,,,,,,,,,,,,,,99.82,0.25,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,1313.43074,Streptococcus pneumoniae strain 19A-ST320_99-176,19A-ST320_99-176,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16580452,1313,19A,,,,genotype:ST320,,,2021-01-21T00:00:00Z,,PRJNA672899,GCA_025136435.1,CP063829,,Asia Pacific Foundation for Infectious Diseases,PacBio RSII; Illumina,350.0x,HGAP v. v3.0,1,0,1,2089994,39.835617,2197,2064,sputum,,1999,South Korea,South Korea: Seoul,,,69,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,to examine temporal genetic change of 19A ST320 S. pneumoniae isolates from Korea by genome-wide analysis,"collected_by:Jinyang, Baek",,,,,,,pneumonia,,,,,,,,,,,,,,99.42,0.2,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1313.43094,Streptococcus pneumoniae 19A-ST320_99-176,19A-ST320_99-176,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16580452,1313,19A,,,,genotype:ST320,,,2021-01-21T00:00:00Z,,PRJNA672899,GCA_025136435.1,CP063829,,,PacBio RSII; Illumina,350.0x,HGAP v. v3.0,1,0,1,2089994,39.835617,2197,2064,sputum,,1999,South Korea,South Korea: Seoul,,,69,pneumonia,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Jinyang, Baek",,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1313.43095,Streptococcus pneumoniae 3238/09,3238/09,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN25149806,1313,19F,,,,,,,2022-10-11T00:00:00Z,,PRJNA799231,GCA_025643295.1,CP091451,,,Illumina MiSeq; Oxford Nanopore GridION,311x,Unicycler v. v. 0.4.6,1,0,1,2103144,39.75881,2215,2089,hospital,,2009,Poland,Poland: malopolskie,,male,,pneumonia,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:National Medicines Institute,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,1313.43096,Streptococcus pneumoniae 3641/15,3641/15,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN25149807,1313,19A,,,,,,,2022-10-11T00:00:00Z,,PRJNA799231,GCA_025643315.1,CP091450,,,Illumina MiSeq; Oxford Nanopore GridION,211x,Unicycler v. v. 0.4.8,1,0,1,2069241,39.866936,2160,2025,hospital,,2015,Poland,Poland: podkarpackie,,male,,bacterial sepsis,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:National Medicines Institute,,,,,,,bacterial sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,1313.43256,Streptococcus pneumoniae SP007,SP007,Streptococcus pneumoniae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN27647185,1313,19F,,,,,,,2023-01-03T00:00:00Z,,PRJNA828336,,CP096809,,,Oxford Nanopore PromethION; DNBseq,670.0x,Canu v. v1.5; GATK v. v1.6-13,1,0,1,2088456,39.780346,2188,2054,cerebrospinal fluid,,2021,China,China:Hangzhou,,,,Meningitis,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Ai-Hua Sun,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,1314.1001,Streptococcus pyogenes strain emm58,emm58,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793311,1314,,,,MLST.Streptococcus_pyogenes.176,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005161985.1,CP035443,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1888806,38.40188,1934,1845,blood,,1995,Australia,Australia,,,,Invasive disease,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Invasive disease,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1006,Streptococcus pyogenes strain emm230,emm230,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793303,1314,,,,MLST.Streptococcus_pyogenes.205,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005162865.1,CP035451,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1826832,38.484657,1846,1775,skin,,2005,Australia,Australia,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.1008,Streptococcus pyogenes strain emm54,emm54,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793300,1314,,,,MLST.Streptococcus_pyogenes.302,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005163245.1,CP035454,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1742565,38.564186,1739,1664,skin,,1994,Australia,Australia,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.1011,Streptococcus pyogenes strain emm65,emm65,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793321,1314,,,,MLST.Streptococcus_pyogenes.716,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005163705.1,CP035433,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1789855,38.566364,1785,1709,blood,,1998,Kenya,Kenya,,,,Invasive disease,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Invasive disease,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1012,Streptococcus pyogenes strain emm75.1,emm75.1,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793320,1314,,,,MLST.Streptococcus_pyogenes.607,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005163865.1,CP035434,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1887700,38.604755,1906,1814,skin,,1991,Australia,Australia,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Skin sore / abscess / burns / IV Site,,,,,,,,,,,,,,99.85,0.11,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.1015,Streptococcus pyogenes strain emm1,emm1,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793313,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005164585.1,CP035441,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1834762,38.52914,1874,1801,blood,,,India,India,,,,Invasive disease,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Invasive disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1017,Streptococcus pyogenes strain emm90.5,emm90.5,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793310,1314,,,,MLST.Streptococcus_pyogenes.184,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005164885.1,CP035444,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1764969,38.54402,1745,1666,blood,,2014,New Zealand,New Zealand,,,,Invasive disease,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Invasive disease,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1019,Streptococcus pyogenes strain emm100,emm100,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793301,1314,,,,MLST.Streptococcus_pyogenes.119,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005165265.1,CP035453,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1839531,38.546566,1889,1800,blood,,2006,Fiji,Fiji,,,,Invasive disease,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Invasive disease,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1020,Streptococcus pyogenes strain emm197,emm197,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793299,1314,,,,,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005165385.1,CP035455,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1797172,38.612553,1842,1763,throat,,2013,New Zealand,New Zealand,,,,Rheumatic fever,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Rheumatic fever,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.1021,Streptococcus pyogenes strain emm68.2,emm68.2,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793308,1314,,,,,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005222545.1,CP035446,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1747924,38.533024,1729,1659,throat,,2004,Brazil,Brazil,,,,Pharyngitis,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.1045,Streptococcus pyogenes strain 5448,5448,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5096233,1314,M1T1,,,MLST.Streptococcus_pyogenes.28,,102.100.100.25705,,2019-01-10T00:00:00Z,,PRJEB29800,GCA_900619585.1,LR130236,,Bioplatforms Australia,,,,1,,1,1829838,38.50084,1826,,blood,,1994,Canada,Canada,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pyogenes.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1046,Streptococcus pyogenes strain SP444,SP444,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5096234,1314,M4,,,MLST.Streptococcus_pyogenes.39,,102.100.100.25706,,2019-01-10T00:00:00Z,,PRJEB29800,GCA_900619595.1,LR130237,,Bioplatforms Australia,,,,1,,1,1823047,38.545742,1799,,blood,,2008-04-28,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pyogenes.",,,,,,,,,diseased,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.1047,Streptococcus pyogenes strain HKU419,HKU419,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5096235,1314,M1T1,,,MLST.Streptococcus_pyogenes.28,,102.100.100.25707,,2019-01-10T00:00:00Z,,PRJEB29800,GCA_900619605.1,LR130238,,Bioplatforms Australia,,,,1,,1,1943295,38.452267,1963,,throat,,2012-02-23,China,China,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pyogenes.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.1048,Streptococcus pyogenes strain PS003,PS003,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5096236,1314,M77,,,,,102.100.100.25708,,2019-01-10T00:00:00Z,,PRJEB29800,GCA_900619615.1,LR130239,,Bioplatforms Australia,,,,1,,1,1909563,38.466915,1873,,urine,,2010-07-05,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pyogenes.",,,,,,,,,diseased,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1314.1049,Streptococcus pyogenes strain PS006,PS006,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5096237,1314,M28,,,MLST.Streptococcus_pyogenes.52,,102.100.100.25709,,2019-01-10T00:00:00Z,,PRJEB29800,GCA_900619625.1,LR130240,,Bioplatforms Australia,,,,1,,1,1854706,38.349743,1832,,urine,,2010-07-06,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Streptococcus pyogenes.",,,,,,,,,diseased,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1314.2390,Streptococcus pyogenes strain NCTC8318,NCTC8318,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3597581,1314,group a,,,,,NCTC:8318,,2019-05-11T00:00:00Z,,PRJEB6403,GCA_901482645.1,LR590483,,SC,,,,1,,1,1819777,38.558517,1799,1720,not available: not collected,,1800-1934,United Kingdom,United Kingdom,,,,,,host_health_state:Scarlet fever Outbreak,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Scarlet fever Outbreak,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2403,Streptococcus pyogenes strain 14GA0832 strain DMG1800716,DMG1800716,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08714459,1314,,,,MLST.Streptococcus_pyogenes.330,genotype:emm81;genotype:emm81,,,2019-08-08T00:00:00Z,,PRJNA438376,GCA_003352145.1,CP027771,,University of Melbourne,PacBio,105.0x,SMRTpipe v. 2.1.0,1,,1,1869673,38.37008,1876,1795,blood,,2014,New Zealand,New Zealand: Christchurch,,,,Invasive disease,,host_description:Aged care facility resident,,,,,,,,,,,This study examined genetic drivers of a Streptococcus pyogenes invasive disease outbreak,"collected_by:Institute of Environmental Science and Research, New Zealand",,,,,,,Invasive disease,,,Aged care facility resident,,,,NZ invasive outbreak isolate,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.2534,Streptococcus pyogenes strain AUSMDU00010539,AUSMDU00010539,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13191653,1314,EMM89.0,,,MLST.Streptococcus_pyogenes.101,mlst:ST101,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664495.1,CP045930,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,202x,de novo,1,0,1,1746807,38.55864,1709,1628,missing,,2013,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2536,Streptococcus pyogenes strain STAB09023,STAB09023,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11029189,1314,,,,MLST.Streptococcus_pyogenes.101,,,,2019-12-10T00:00:00Z,,PRJNA524538,GCA_009738475.1,CP036530,,university of rennes1,Illumina HiSeq + PCR + sanger,817.0x,CLC genomics workbench v. 6,1,0,1,1741943,38.521122,1727,1662,genital,,2009,France,France,,,,,,,,,,,,,,,,,Genomics comparative and determination of virulence factors,sample_type:cell culture;collected_by:S.Kayal,,,,,,,,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,1314.2770,Streptococcus pyogenes strain MGAS2221,MGAS2221,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12657656,1314,emm1,,,MLST.Streptococcus_pyogenes.28,genotype:M1T1,,,2020-04-20T00:00:00Z,,PRJNA562873,GCA_012572265.1,CP043530,,Houston Methodist Research Institute,Oxford Nanopore GridION & Illumina,1875.0x,Unicycler v. 0.4.8-beta,1,0,1,1835779,38.53514,1824,1741,not collected,,1988,Australia,Australia,,,,septic scarlet fever,,,,,,,,,,,,,"Streptococcus pyogenes (aka Group A Streptococcus, GAS) strain MGAS2221 is genetically representative of global pandemic M1T1 strains and is wild-type forall major global virulence regulators",collected_by:not collected;passage_history:minamal,,,,,,,septic scarlet fever,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,1314.2775,Streptococcus pyogenes strain 4063-05,4063-05,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14547667,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2020-06-09T00:00:00Z,,PRJNA623467,GCA_013306985.1,CP051138,,"College of Medicine, National Taiwan University",PacBio Sequel,4333.0x,Flye v. v2.7,1,0,1,1890399,38.487694,1913,,,,2005,USA,USA,,,,,,,,,,,,,,,,,draft genome of GAS strain 4063-05,sample_type:clinical isolate,,,,,,,,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2826,Streptococcus pyogenes strain KUN-0012590,KUN-0012590,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00238719,1314,,,,,,,,2020-08-08T00:00:00Z,,PRJDB10330,GCA_014192005.1,AP023389,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",Illumina MiSeq; Oxford Nanopore,526x,Unicycler v. 0.4.8,1,0,1,1854597,38.5384,1870,1780,,,2007,Japan,Japan:Kyoto,,,,,,,,,Positive,Cocci,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,missing,missing,missing,missing,Complete genome sequence of three Streptococcus species,,,,,,,,,,,,missing,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2831,Streptococcus pyogenes strain NIH34,NIH34,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00238717,1314,,,,MLST.Streptococcus_pyogenes.15,,,,2020-08-08T00:00:00Z,,PRJDB10330,GCA_014191695.1,AP023387,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",Illumina MiSeq; Oxford Nanopore,514x,Unicycler v. 0.4.8,1,0,1,1900555,38.58636,1957,1866,,,,Japan,Japan:Kochi,,,,,,,,,Positive,Cocci,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,missing,missing,missing,missing,Complete genome sequence of three Streptococcus species,,,,,,,,,,,,missing,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2832,Streptococcus pyogenes strain NIH35,NIH35,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00238718,1314,,,,MLST.Streptococcus_pyogenes.52,,,,2020-08-08T00:00:00Z,,PRJDB10330,GCA_014191835.1,AP023388,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",Illumina MiSeq; Oxford Nanopore,598x,Unicycler v. 0.4.8,1,0,1,1853362,38.34545,1834,1750,,,,Japan,Japan:Kochi,,,,,,,,,Positive,Cocci,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,missing,missing,missing,missing,Complete genome sequence of three Streptococcus species,,,,,,,,,,,,missing,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2833,Streptococcus pyogenes strain KUN-0014944,KUN-0014944,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00238720,1314,,,,MLST.Streptococcus_pyogenes.646,,,,2020-08-08T00:00:00Z,,PRJDB10330,GCA_014192175.1,AP023390,,"Department of Microbiology, Graduate School of Medicine, Kyoto University",Illumina MiSeq; Oxford Nanopore,547x,Unicycler v. 0.4.8,1,0,1,1747400,38.558887,1688,1611,,,2009,Japan,Japan:Kyoto,,,,,,,,,Positive,Cocci,,,,,,,"We determined complete genome sequence of three Streptococcus species, S. pyogenes, S. suis, and S. dysgalactiae. Among these three species, S. pyogenes and S. dysagalactiae have recognized as causative agents occasionally causing sever disease (ex. toxic shock syndrome) to human. On the other hand, S. suis is one of the major zoonotic agent and cause a variety of infections in individuals working in close contact with swine or pork products. In this study, we focus on the gene sets or genomic regions contributing to their pathogenicity, based on the complete genome sequence of three Streptococcus species.",,missing,missing,missing,missing,Complete genome sequence of three Streptococcus species,,,,,,,,,,,,missing,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2843,Streptococcus pyogenes strain emm9ST603,emm9ST603,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17054563,1314,,,,MLST.Streptococcus_pyogenes.603,,,,2020-12-20T00:00:00Z,,PRJNA684347,GCA_016126835.1,CP065927,,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,100.0x,Unicycler v. DEC-2020,1,0,1,1862424,38.544605,1836,1727,bone,,2020,Australia,Australia,,,,Streptococcal Infections,,,,,,,,,,,,,Streptococcus pyogenes WGS,collected_by:Queensland Health,,,,,,,Streptococcal Infections,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,1314.2848,Streptococcus pyogenes strain iGAS426,iGAS426,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17141635,1314,,,,MLST.Streptococcus_pyogenes.99,,,,2021-01-06T00:00:00Z,,PRJNA685009,GCA_016549335.1,CP067008,,University of Glasgow,Illumina; Oxford Nanopore MinION,199x,Unicycler hybrid assembly v. 0.4.8,1,0,1,1897111,38.60122,1936,1824,blood,,2015-02-27,United Kingdom,United Kingdom: Scotland,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,Complete genomes of three invasive isolates of S. pyogenes emm5.23,"collected_by:Scottish Haemophilus, Legionella, Meningococcus & Pneumococcus Reference Laboratory",,,,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.2849,Streptococcus pyogenes strain iGAS376,iGAS376,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17141633,1314,,,,MLST.Streptococcus_pyogenes.99,,,,2021-01-06T00:00:00Z,,PRJNA685009,GCA_016549355.1,CP067010,,University of Glasgow,Illumina; Oxford Nanopore MinION,101x,Unicycler hybrid assembly v. 0.4.8,1,0,1,1897124,38.60138,1936,1824,blood,,2018-06-07,United Kingdom,United Kingdom: Scotland,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,Complete genomes of three invasive isolates of S. pyogenes emm5.23,"collected_by:Scottish Haemophilus, Legionella, Meningococcus & Pneumococcus Reference Laboratory",,,,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.2850,Streptococcus pyogenes strain iGAS391,iGAS391,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17141634,1314,,,,MLST.Streptococcus_pyogenes.99,,,,2021-01-06T00:00:00Z,,PRJNA685009,GCA_016549375.1,CP067009,,University of Glasgow,Illumina; Oxford Nanopore MinION,237x,Unicycler hybrid assembly v. 0.4.8,1,0,1,1897129,38.600906,1933,1824,blood,,2019-03-21,United Kingdom,United Kingdom: Scotland,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,Complete genomes of three invasive isolates of S. pyogenes emm5.23,"collected_by:Scottish Haemophilus, Legionella, Meningococcus & Pneumococcus Reference Laboratory",,,,,,,Invasive group A Streptococcus infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.2925,Streptococcus pyogenes strain M11318,M11318,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18034722,1314,,,,MLST.Streptococcus_pyogenes.28,genotype:emm1ST28,,,2021-03-02T00:00:00Z,,PRJNA684347,GCA_017132795.1,CP070994,,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,50.0x,Unicycler v. V0.4.8,1,0,1,1831274,38.498936,1836,1743,tissue,,2018,Australia,Australia,,,,Streptococcal infections,,,,,,,,,,,,,Streptococcus pyogenes WGS,collected_by:Queensland Health,,,,,,,Streptococcal infections,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.2962,Streptococcus pyogenes strain M08500,M08500,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18435893,1314,,,,,genotype:emm66ST874,,,2021-03-30T00:00:00Z,,PRJNA684347,GCA_017638465.1,CP072112,,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,248.0x,Unicycler v. v0.4.9b,1,0,1,1852911,38.553444,1850,1752,blood culture,,2020,Australia,Australia,,,,Sepsis,,,,,,,,,,,,,Streptococcus pyogenes WGS,collected_by:Queensland Health,,,,,,,Sepsis,,,,,,,,,,,,,,99.85,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1314.2969,Streptococcus pyogenes strain TSPY1687,TSPY1687,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14162572,1314,,,,MLST.Streptococcus_pyogenes.36,,,,2021-04-27T00:00:00Z,,PRJNA608028,GCA_018140985.1,CP049187,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,120.0x,Unicycler v. 0.4.6,1,0,1,1866140,38.467907,1847,1759,pharyngeal,,2018,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing of emm12 group A streptococcal strains derived from multiple disease states,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3067,Streptococcus pyogenes strain TSPY806,TSPY806,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14235221,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2021-07-26T00:00:00Z,,PRJNA609136,GCA_019342845.1,CP049685,,UTHSC/McGovern Medical School,Illumina MiSeq; ONT GridION,513x,Unicycler v. 0.4.6,1,0,1,1866006,38.561024,1878,1772,cellulitis,,2016,USA,USA,,,,SSTI,,,,,,,,,,,,,Emergence of a novel emm4 GAS clone in the human population,collected_by:BCM/UTHSC,,,,,,,SSTI,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1314.3068,Streptococcus pyogenes strain TSPY637,TSPY637,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14235203,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2021-07-26T00:00:00Z,,PRJNA609136,GCA_019342865.1,CP049686,,UTHSC/McGovern Medical School,Illumina MiSeq; ONT GridION,130x,Unicycler v. 0.4.6,1,0,1,1823857,38.54019,1820,1715,throat,,2015,USA,USA,,,,Pharyngitis,,,,,,,,,,,,,Emergence of a novel emm4 GAS clone in the human population,collected_by:BCM/UTHSC,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3081,Streptococcus pyogenes strain TSPY767,TSPY767,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN14235217,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2021-08-04T00:00:00Z,,PRJNA609136,GCA_019448315.1,CP055246,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,750.0x,Unicycler v. 0.4.6,1,0,1,1860158,38.507805,1882,1771,throat,,2015,USA,USA,,,,Pharyngitis,,,,,,,,,,,,,Emergence of a novel emm4 GAS clone in the human population,collected_by:BCM/UTHSC,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3162,Streptococcus pyogenes strain TSPY141,TSPY141,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824172,1314,serovar s,,,MLST.Streptococcus_pyogenes.184,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020826915.1,CP060638,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,102x,Unicycler v. 0.4.6,1,0,1,1878218,38.412262,1872,1768,throat,,2013,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3163,Streptococcus pyogenes strain TSPY153,TSPY153,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824171,1314,serovar s,,,MLST.Streptococcus_pyogenes.75,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020826935.1,CP060639,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,186x,Unicycler v. 0.4.6,1,0,1,1970284,38.53424,1989,1866,throat,,2013,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3164,Streptococcus pyogenes strain TSPY764,TSPY764,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824170,1314,serovar s,,,,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020826955.1,CP060640,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,111x,Unicycler v. 0.4.6,1,0,1,1758170,38.558956,1705,1604,throat,,2015,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0.08,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3166,Streptococcus pyogenes strain TSPY1312,TSPY1312,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824167,1314,serovar s,,,MLST.Streptococcus_pyogenes.378,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020826995.1,CP060642,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,147x,Unicycler v. 0.4.6,1,0,1,1845647,38.508987,1828,1728,throat,,2017,USA,USA:Houston,,,,Abscess,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Abscess,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Respiratory Tract,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.3167,Streptococcus pyogenes strain TSPY416,TSPY416,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824166,1314,serovar s,,,,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827015.1,CP060643,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,1090x,Unicycler v. 0.4.6,1,0,1,1791351,38.482742,1749,1651,skin,,2014,USA,USA:Houston,,,,Cellulitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Cellulitis,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Cellulitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Cellulitis HP,1314.3168,Streptococcus pyogenes strain TSPY1309,TSPY1309,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824165,1314,serovar s,,,,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827035.1,CP060644,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,290x,Unicycler v. 0.4.6,1,0,1,1781254,38.614986,1732,1634,skin,,2017,USA,USA:Houston,,,,Abscess,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.3169,Streptococcus pyogenes strain TSPY1349,TSPY1349,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824164,1314,serovar s,,,MLST.Streptococcus_pyogenes.161,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827055.1,CP060645,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,260x,Unicycler v. 0.4.6,1,0,1,1902845,38.422836,1901,1793,throat,,2017,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3170,Streptococcus pyogenes strain TSPY1026,TSPY1026,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824163,1314,serovar s,,,,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827075.1,CP060646,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,270x,Unicycler v. 0.4.6,1,0,1,1890384,38.44023,1868,1757,skin,,2016,USA,USA:Houston,,,,Cellulitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Cellulitis,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Cellulitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Cellulitis HP,1314.3171,Streptococcus pyogenes strain TSPY136,TSPY136,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824162,1314,serovar s,,,MLST.Streptococcus_pyogenes.46,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827095.1,CP060647,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,420x,Unicycler v. 0.4.6,1,0,1,1780403,38.63597,1753,1666,throat,,2013,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3172,Streptococcus pyogenes strain TSPY383,TSPY383,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15824161,1314,serovar s,,,MLST.Streptococcus_pyogenes.28,,,,2021-11-10T00:00:00Z,,PRJNA657283,GCA_020827115.1,CP060648,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,130x,Unicycler v. 0.4.6,1,0,1,1827693,38.463352,1838,1744,throat,,2014,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Genome sequencing and assembly of multiple serotypes of group A Streptococcus for epigenetic studies,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.3302,Streptococcus pyogenes 52SS1,52SS1,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN26993930,1314,,,,MLST.Streptococcus_pyogenes.37,,,,2022-04-11T00:00:00Z,,PRJNA820333,GCA_022869745.1,CP094944,,,Illumina NovaSeq,100.0x,SPAdes v. May2021,1,0,1,1860753,38.372498,1917,1812,oropharynx,,,Saudi Arabia,Saudi Arabia,,,,pharyngitis,,,,,,,,,,,,,,collected_by:Galal Esmail and Badr AlDawood,,,,,,,pharyngitis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,1314.3322,Streptococcus pyogenes 21SPY7071,21SPY7071,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN28104815,1314,,,,MLST.Streptococcus_pyogenes.46,genotype:emm 21,,,2022-05-17T00:00:00Z,,PRJNA835576,GCA_023380045.1,CP097251,,,Illumina HiSeq,728.0x,SOAPdenovo v. 2.04,1,0,1,1910967,38.514427,1939,1842,cerebral abscess pus,,2021-12-09,China,China: Hangzhou,,female,2 years and 3 months,cerebral abscess,,host_description:She had a small abscess in the skin of the left lower limb and his mother squeezed the pus out of the abscess about 12 days before the onset of the disease.;host_disease_outcome:Recovery;host_disease_stage:Acute stage;host_health_state:Had decreased muscle strength in the left limbs;host_subject_id:Medical record ID was 65146224,,,,,,,,,,,,"collected_by:Hua CZ, Shen ZP, Zhou MM, Hu WL, Shu Q",,,,,,,cerebral abscess,Had decreased muscle strength in the left limbs,Recovery,She had a small abscess in the skin of the left lower limb and his mother squeezed the pus out of the abscess about 12 days before the onset of the disease.,Acute stage,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1314.3940,Streptococcus pyogenes SP1448,SP1448,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783175,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060267,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1837335,38.53576,1834,1741,blood,,2019,Australia,Australia,,,,invasive disease,,,,,,,,,,,,,,,,,,,,,invasive disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.3941,Streptococcus pyogenes SP1450,SP1450,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783176,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060266,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1831250,38.498512,1838,1741,blood,,2019,Australia,Australia,,,,invasive disease,,,,,,,,,,,,,,,,,,,,,invasive disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.3942,Streptococcus pyogenes SP1380,SP1380,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783172,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060269,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1883075,38.527515,1907,1808,throat,,2019,Australia,Australia,,,,scarlet fever,,,,,,,,,,,,,,collected_by:Gold Coast University Hospital,,,,,,,scarlet fever,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.3943,Streptococcus pyogenes SP1426,SP1426,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783174,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060268,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1872024,38.506878,1893,1791,throat,,2019,Australia,Australia,,,,scarlet fever,,,,,,,,,,,,,,,,,,,,,scarlet fever,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.3944,Streptococcus pyogenes SP1451,SP1451,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783177,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060265,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1902947,38.423878,1913,1808,blood,,2019,Australia,Australia,,,,invasive disease,,,,,,,,,,,,,,,,,,,,,invasive disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.3945,Streptococcus pyogenes SP1384,SP1384,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15783173,1314,,,,MLST.Streptococcus_pyogenes.28,,,,2023-02-01T00:00:00Z,,PRJNA656382,,CP060270,,,Oxford Nanopore,100x,Unicycler v. 0.4.7,1,0,1,1837261,38.534534,1841,1741,throat,,2019,Australia,Australia,,,,scarlet fever,,,,,,,,,,,,,,collected_by:Gold Coast University Hospital,,,,,,,scarlet fever,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.470,Streptococcus pyogenes strain NCTC8198,NCTC8198,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA2479569,1314,group a,,,MLST.Streptococcus_pyogenes.28,,,,2015-05-02T00:00:00Z,,PRJEB6403,GCA_002055535.1,LN831034,,SC,,,,1,,1,1914862,38.5,1967,1891,throat,,1950,United Kingdom,United Kingdom,,,,,,host_health_state:disease: scarlet fever,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,disease: scarlet fever,,,,,,,,,,disease: scarlet fever,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.492,Streptococcus pyogenes strain STAB14018,STAB14018,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04500791,1314,,,,MLST.Streptococcus_pyogenes.150,,,,2017-06-02T00:00:00Z,,PRJNA312571,GCA_002163545.1,CP014542,,university of rennes1,Illumina,2000,CLC genomic workbench v. 6,1,,1,1890465,38.6,1934,1804,blood,,2014-05-09,France,France: Brittany,,female,81,"Bacteriemia, sepcis",,host_disease_stage:sepsis,,,,,,,C,,,sepsis,sequencing of virulent strains,collected_by:Samer kayal,,,,,,,"Bacteriemia, sepcis",,,,sepsis,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.509,Streptococcus pyogenes strain STAB090229,STAB090229,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06473357,1314,,,,MLST.Streptococcus_pyogenes.150,genotype:emm75,,,2017-08-01T00:00:00Z,,PRJNA377855,GCA_002238295.1,CP020027,,university of rennes1,Illumina; PCR + Sanger,800.0x,CLC Genomics v. 6.5,1,,1,1846347,38.57,1913,1810,hospital,,2009-02-28,France,France,,female,28,endometritisis,,,,,,,,,,,,,virulence factor determination,collected_by:S. Kayal,,,,,,,endometritisis,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.534,Streptococcus pyogenes strain M3-b,M3-b,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00000355,1314,serovar s,,,MLST.Streptococcus_pyogenes.15,,,,2016-02-26T00:00:00Z,,PRJDB1740,GCA_002355175.1,AP014596,,National Center for Global Health and Medicine,,20x,GS De Novo Assembler v. 2.7,1,,1,1893821,38.54,1958,1926,patient of a stss case,derived from a patient of a STSS case,1994,Japan,Japan:Aichi,env_biome:clinical,,,,,,,,,,,,,,,,"Streptococcus pyogenes cause a wide variety of infectious diseases, from relatively benign to life threatening. S. pyogenes can be subtyped according to the serotypes of the M proteins expressed on the cell surface. Particular M types of GAS have been associated with certain diseases, which suggests that there are differences in the expression of pathogenic traits among S. pyogeneswith different M types. M1 and M3 S. pyogenes have been found predominantly in patients with streptococcal toxic shock syndrome (STSS), a life-threatening in Japan, the United States, and Europe S. pyogenes str. M3-b is one of the isolates derived from a patient of a STSS case. In this study, complete whole genome sequence of S. progenes str. M3-b to analyze genes related to the virulence.",,clinical,streptococcal toxic shock syndrome,Human blood,15942900,Complete whole genome sequence of Streptococcus pyogenes,,,,,,,,,,,,clinical,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.536,Streptococcus pyogenes strain HarveyGAS,HarveyGAS,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07757765,1314,M28,,,MLST.Streptococcus_pyogenes.52,genotype:M28,,,2017-10-16T00:00:00Z,,PRJNA413555,GCA_002557755.1,CP023769,,Houston Methodist Hospital,Illumina MiSeq; Oxford Nanopore MinION,501.0x,Unicycler v. 0.4.1,1,,1,1852980,38.34,1869,1788,wound,,2017-08-30,USA,"USA: Houston, Texas",,,,necrotizing fasciitis,,,,,,,,,,,,,Whole genome sequencing of a Group A Streptococcus causing necrotizing fasciitis acquired contemporaneously with Hurricane Harvey.,collected_by:Houston Methodist Hospital,,,,,,,necrotizing fasciitis,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Necrotizing fasciitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Necrotizing fasciitis HP,1314.548,Streptococcus pyogenes strain JS12,JS12,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07174848,1314,,,,MLST.Streptococcus_pyogenes.619,,,,2017-12-18T00:00:00Z,,PRJNA388295,GCA_002844355.1,CP021640,,National University of Singapore and Genome Institute of Singapore,PacBio,200.0x,HGAP3 v. JUL-2016,1,,1,1810283,38.46,1782,1721,csf,"isolate from a meningitis patient in Jerusalem, Israel to gain insights into its pathogenicity",1997,Israel,Israel,,,,Meningitis,,,,,,,,,,,,,"Sequencing of Group A Streptococcus strain JS12, a sil-positive isolate from a meningitis patient in Jerusalem, Israel to gain insights into its pathogenicity.","collected_by:Ministry of Health Streptococcal Reference Laboratory, Jerusalem, Israel",,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,1314.663,Streptococcus pyogenes strain TJ11-001,TJ11-001,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08793275,1314,,,,MLST.Streptococcus_pyogenes.36,,,,2018-03-30T00:00:00Z,,PRJNA445523,GCA_003025365.1,CP028148,,"National Institute for Communicable Disease Control and Prevention, China CDC",Illumina HiSeq; Oxford Nanopore,320.0x,Unicycler v. MAR-2018,1,,1,1939844,38.47995,1927,,swab throat,,2011-07,China,China,,,,scarlet fever,,,,,,,,,,,,,complete genome of a scarlet fever isolate from China,"collected_by:ICDC, China CDC",,,,,,,scarlet fever,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.759,Streptococcus pyogenes strain NCTC13744,NCTC13744,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3879490,1314,"Lancefield Group A, emm 108",,,MLST.Streptococcus_pyogenes.1088,,NCTC:13744,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900475705.1,LS483407,,SC,,,,1,,1,1808803,38.635273,1784,1702,blood culture,,2013,United Kingdom,United Kingdom: London,,,,,,host_health_state:Throat Infection,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Throat Infection,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.845,Streptococcus pyogenes strain KS030,KS030,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00084336,1314,,,,MLST.Streptococcus_pyogenes.15,genotype:emm3/ST15,,,2017-12-15T00:00:00Z,,PRJDB5912,GCA_003609955.1,AP018337,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",NextSeq; PacBio RSII,700x,HGAP Assembly v. 3.0; Pilon v1.18,1,,1,1900008,38.578102,2002,1898,"endotracheal aspirates culture, the strain was designated as ks030","isolated from endotracheal aspirates culture, the strain was designated as KS030",2017,Japan,Japan,,,,,,,,,,,,,,,,streptococcal toxic shock syndrome (STSS),"A young patient was diagnosed as Streptococcal Toxic Shock Syndrome (STSS) with severe pneumonia, impaired renal function, and rhabdomyolysis. Streptococcus pyogenes (GAS) was isolated from endotracheal aspirates culture, the strain was designated as KS030.",,missing,trachea,endotracheal aspirates,missing,complete genome sequence of emm3/ST15 invasive Streptococcus pyogenes str. KS030 isolated from a patient with streptococcal toxic shock syndrome (STSS),streptococcal toxic shock syndrome (STSS),,,,,,,,,,,missing,,,,99.85,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.846,Streptococcus pyogenes strain SASM4-Duke,SASM4-Duke,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04230441,1314,serovar M4,,,MLST.Streptococcus_pyogenes.39,,,,2018-10-12T00:00:00Z,,PRJNA300859,GCA_003640605.1,CP031770,,Baylor College of Medicine,Illumina MiSeq; PacBio,200.0x,SPAdes v. 3.12.0,1,,1,1903997,38.541344,1976,1875,blood,,,USA,USA: North Carolina,,female,48,Bacteremia,,,,,,,,,C,,,,Clinical isolates of serotype M4 GAS,collected_by:Duke University Medical Center,,,,,,,Bacteremia,,,,,,,,,,,,,,99.85,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1314.847,Streptococcus pyogenes strain ABC020055975,ABC020055975,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09284928,1314,serovar M3,,,MLST.Streptococcus_pyogenes.15,,,,2018-10-30T00:00:00Z,,PRJNA473837,GCA_003698205.1,CP029694,,UTHSC/McGovern Medical School,Illumina HiSeq; PacBio,1000.0x,SPAdes v. 3.11.1,1,,1,1866513,38.593086,1956,1858,not collected,,2011,,,,,,STSS,,,,,,,,,,,,,Complete genome sequence of serotype M3 group A Streptococcus,collected_by:Centers for Disease Control,,,,,,,STSS,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.850,Streptococcus pyogenes strain Duke-Large,Duke-Large,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10416086,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2018-11-23T00:00:00Z,,PRJNA505351,GCA_003814365.1,CP033907,,UTHSC/McGovern Medical School,Illumina MiSeq; PacBio,51.0x,SPAdes v. 3.10.0,1,,1,1903852,38.540863,1975,1874,blood,,,USA,USA: North Carolina,,female,48,Bacteremia,,,,,,,,,,,,,Whole genome sequencing of type emm4 GAS clinical strains,collected_by:Duke University Medical Center,,,,,,,Bacteremia,,,,,,,,,,,,,,99.85,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1314.851,Streptococcus pyogenes strain RLGH,RLGH,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10416088,1314,,,,MLST.Streptococcus_pyogenes.39,,,,2018-11-23T00:00:00Z,,PRJNA505351,GCA_003814385.1,CP033908,,UTHSC/McGovern Medical School,Illumina MiSeq; PacBio,50.0x,SPAdes v. 3.10.0,1,,1,1903972,38.541584,1975,1875,not collected,,,USA,USA: North Carolina,,male,38,Cellulitis,,,,,,,,,,,,,Whole genome sequencing of type emm4 GAS clinical strains,collected_by:Duke University Medical Center,,,,,,,Cellulitis,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Cellulitis,Other,Skin and Soft Tissue Infections-Cellulitis HP,1314.893,Streptococcus pyogenes strain MGAS27961,MGAS27961,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555909,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-01-10T00:00:00Z,,PRJNA434389,GCA_004010855.1,CP032665,,Houston Methodist Research Institute,Oxford Nanopore MiniION; Illumina NextSeq,110.0x,Unicycler/SPAdes/PILON v. 0.4.6/3.12/1.22,1,,1,1853912,38.34303,1880,1789,normally sterile site,,2005,USA,USA: Minnesota,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.894,Streptococcus pyogenes strain MGAS28085,MGAS28085,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556030,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-01-10T00:00:00Z,,PRJNA434389,GCA_004010875.1,CP032666,,Houston Methodist Research Institute,Oxford Nanopore MiniION; Illumina NextSeq,244.0x,Unicycler/SPAdes/PILON v. 0.4.6/3.12/1.22,1,,1,1851471,38.34227,1867,1783,normally sterile site,,2009,USA,USA: New Mexico,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.895,Streptococcus pyogenes strain S119,S119,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4805863,1314,emm1,,,MLST.Streptococcus_pyogenes.28,,,Yes,2018-11-30T00:00:00Z,,PRJEB27939,GCA_900608505.1,LR031521,,IP,,,,1,,1,1877450,38.5451,1885,1816,blood culture,isolated from a blood culture,2008,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,The streptococcus pyogenes strain S119 is an invasive emm1 type strain isolated from a blood culture. Its complete genome sequence was performed using Illumina sequencing and served as reference sequence to characterize the transcriptional landscape in S. pyogenes by using dRNA-sequencing and strand-specific RNA-sequencing. ncRNAs and promoters were annotated;Invasive strain isolated from a blood culture,,,,,,,,,diseased,,,,,,,,,,,,,99.65,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1314.951,Streptococcus pyogenes strain CCUG 4207,CCUG 4207,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08915690,1314,"Lancefield group A, Griffith serotype 1",,,MLST.Streptococcus_pyogenes.28,,CCUG:4207,,2019-01-17T00:00:00Z,,PRJNA302716,GCA_004028355.1,CP028841,,University of Gothenburg - CCUG,Illumina HiSeq; Oxford Nanopore MinION,185.6; 576.4,SPAdes v. 3.11,1,,1,1914862,38.503246,2017,1921,throat swab,,,United Kingdom,United Kingdom:Manchester,,,,Scarlet fever,,,,,,,,,,,,,Identification of protein biomarkers for proteotyping pathogenic bacteria and their metabolic functions.,collected_by:Frederick Griffith,,,,,,,Scarlet fever,,,,,,,isolated before 1926,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.963,Streptococcus pyogenes strain TSPY453,TSPY453,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10172674,1314,,,,MLST.Streptococcus_pyogenes.63,,,,2019-01-31T00:00:00Z,,PRJNA494557,GCA_004124075.1,CP033337,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,211.0x,Unicycler v. 0.4.6; Canu v. 1.7.1,1,,1,1976011,38.422207,2026,1931,cellulitis,,2014,USA,USA:Houston,,,,SSTI,,,,,,,,,,,,,Whole genome sequencing of antibiotic resistant strains of group A Streptococcus,collected_by:UTHSC/BCM,,,,,,,SSTI,,,,,,,,,,,,,,99.85,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1314.964,Streptococcus pyogenes strain TSPY208,TSPY208,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10172651,1314,,,,MLST.Streptococcus_pyogenes.49,,,,2019-01-31T00:00:00Z,,PRJNA494557,GCA_004124115.1,CP033335,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,250.0x,Unicycler v. 0.4.6; Canu v. 1.7.1,1,,1,1801696,38.688046,1828,1735,pharyngeal,,2014,USA,USA:Houston,,,,Pharyngitis,,,,,,,,,,,,,Whole genome sequencing of antibiotic resistant strains of group A Streptococcus,collected_by:UTHSC/BCM,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.965,Streptococcus pyogenes strain TSPY165,TSPY165,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10172669,1314,,,,MLST.Streptococcus_pyogenes.133,,,,2019-01-31T00:00:00Z,,PRJNA494557,GCA_004124135.1,CP033336,,UTHSC/McGovern Medical School,Illumina MiSeq; Oxford Nanopore GridION,263.0x,Unicycler v. 0.4.6; Canu v. 1.7.1,1,,1,1812036,38.51204,1844,1765,otitis media,,2013,USA,USA:Houston,,,,Invasive,,,,,,,,,,,,,Whole genome sequencing of antibiotic resistant strains of group A Streptococcus,collected_by:UTHSC/BCM,,,,,,,Invasive,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,1314.966,Streptococcus pyogenes strain M75,M75,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10397505,1314,,,,MLST.Streptococcus_pyogenes.150,,,,2019-02-04T00:00:00Z,,PRJNA504701,GCA_004135875.1,CP033621,,University of Melbourne,PacBio,105.0x,PacBio SMRT Pipe v. 2.3.0,1,,1,1852894,38.60604,1910,1810,throat,,2011,Australia,Australia: Melbourne,,,,Pharyngitis,,,,,,,,,,,,,"A multifaceted characterisation of a controlled human infection model candidate strain, M75 611024, compared to two other GAS strains: GAS M12 611025, and CDC SS-496, an M1 strain administered to 88 subjects in 1970s pharyngitis controlled human infection model studies (‘SS-496’). This study provides the rationale for the initial deployment of M75 611025 in a modern controlled human infection model, with the aim of safely and successfully causing pharyngitis in healthy adult volunteers.",collected_by:Murdoch Children's Research Institute,,,,,,,Pharyngitis,,,,,,,,,,,,,,99.85,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.967,Streptococcus pyogenes strain MGAS8347,MGAS8347,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555653,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004153945.1,CP031638,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,162.3 (15.4 & 146.9)x,Unicycler/SPAdes/PILON v.,1,,1,1833822,38.41714,1822,1741,normally sterile site,,1995,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.968,Streptococcus pyogenes strain MGAS10786,MGAS10786,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555729,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004153965.1,CP031637,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,189.5 (6.5 & 183.0)x,Unicycler/SPAdes/PILON v.,1,,1,1937069,38.380203,1999,1895,normally sterile site,,1998,Canada,Canada: Ontario,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:Public Health Ontario,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.969,Streptococcus pyogenes strain MGAS7914,MGAS7914,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555548,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004153985.1,CP031639,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,167.3 (19.9 & 147.4)x,Unicycler/SPAdes/PILON v.,1,,1,1885126,38.370857,1914,1832,normally sterile site,,1995,Canada,Canada: Ontario,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:Public Health Ontario,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.970,Streptococcus pyogenes strain MGAS7888,MGAS7888,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555522,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154005.1,CP031640,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,204.5 (27.9 & 176.6)x,Unicycler/SPAdes/PILON v.,1,,1,1962429,38.161533,1995,1898,normally sterile site,,1994,Canada,Canada: Ontario,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:Public Health Ontario,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.971,Streptococcus pyogenes strain MGAS29409,MGAS29409,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08563099,1314,Emm28,,,MLST.Streptococcus_pyogenes.458,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154025.1,CP031617,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,279.5 (15.7 & 263.8)x,Unicycler/SPAdes/PILON v.,1,,1,1894040,38.374584,1932,1839,normally sterile site,,2008,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.972,Streptococcus pyogenes strain MGAS29326,MGAS29326,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08563018,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154045.1,CP031618,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,106.0 (64.7 & 41.3)x,Unicycler/SPAdes/PILON v.,1,,1,1940684,38.272278,1969,1883,normally sterile site,,2010,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.973,Streptococcus pyogenes strain MGAS29284,MGAS29284,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562978,1314,Emm28,,,MLST.Streptococcus_pyogenes.458,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154065.1,CP031619,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,352.2 (10.7 & 341.5)x,Unicycler/SPAdes/PILON v.,1,,1,1946265,38.37047,2008,1918,normally sterile site,,2011,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.974,Streptococcus pyogenes strain MGAS28746,MGAS28746,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562542,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154085.1,CP031621,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,147.1 (27.7 & 119.4)x,Unicycler/SPAdes/PILON v.,1,,1,1853620,38.343998,1874,1785,normally sterile site,,2012,USA,USA: New Mexico,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.975,Streptococcus pyogenes strain MGAS28686,MGAS28686,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562482,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154105.1,CP031622,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,246.0 (121.0 & 125.0)x,Unicycler/SPAdes/PILON v.,1,,1,1894087,38.347553,1937,1851,normally sterile site,,2008,USA,USA: New Mexico,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.976,Streptococcus pyogenes strain MGAS28669,MGAS28669,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562467,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154125.1,CP031623,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,186.4 (57.7 & 128.7)x,Unicycler/SPAdes/PILON v.,1,,1,1905059,38.343063,1949,1858,normally sterile site,,2008,USA,USA: Maryland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.977,Streptococcus pyogenes strain MGAS28650,MGAS28650,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562449,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154145.1,CP031624,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,474.7 (71.3 & 403.4)x,Unicycler/SPAdes/PILON v.,1,,1,1851876,38.339554,1870,1784,normally sterile site,,2008,USA,USA: Oregon,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.978,Streptococcus pyogenes strain MGAS28533,MGAS28533,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556433,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154165.1,CP031625,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,156.4 (28.7 & 127.7)x,Unicycler/SPAdes/PILON v.,1,,1,1893263,38.349136,1935,1851,normally sterile site,,2006,USA,USA: New Mexico,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.979,Streptococcus pyogenes strain MGAS28360,MGAS28360,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556272,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154185.1,CP031627,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,127.6 (25.1 & 102.5)x,Unicycler/SPAdes/PILON v.,1,,1,1893041,38.372757,1930,1833,normally sterile site,,2000,USA,USA: New York,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.980,Streptococcus pyogenes strain MGAS28330,MGAS28330,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556245,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154205.1,CP031628,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,126.9 (16.7 & 110.1)x,Unicycler/SPAdes/PILON v.,1,,1,1851619,38.35184,1865,1776,normally sterile site,,1998,USA,USA: Maryland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.981,Streptococcus pyogenes strain MGAS28278,MGAS28278,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556197,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154225.1,CP031629,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,152.2 (6.8 & 145.4)x,Unicycler/SPAdes/PILON v.,1,,1,1893446,38.375957,1921,1832,normally sterile site,,2011,USA,USA: New York,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.982,Streptococcus pyogenes strain MGAS28271,MGAS28271,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556190,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154245.1,CP031630,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,201.7 (18.1 & 183.7)x,Unicycler/SPAdes/PILON v.,1,,1,1842830,38.362736,1856,1771,normally sterile site,,2011,USA,USA: Minnesota,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.983,Streptococcus pyogenes strain MGAS28191,MGAS28191,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556116,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154265.1,CP031631,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,188.5 (22.3 & 166.2)x,Unicycler/SPAdes/PILON v.,1,,1,1892473,38.36155,1919,1832,normally sterile site,,1999,USA,USA: Connecticut,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.984,Streptococcus pyogenes strain MGAS11115,MGAS11115,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555801,1314,Emm28,,,MLST.Streptococcus_pyogenes.456,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154285.1,CP031633,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,186.9 (32.3 & 154.7)x,Unicycler/SPAdes/PILON v.,1,,1,1851403,38.338924,1873,1788,normally sterile site,,2002,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.985,Streptococcus pyogenes strain MGAS11108,MGAS11108,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555796,1314,Emm28,,,MLST.Streptococcus_pyogenes.456,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154305.1,CP031634,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,221.0 (50.1 & 170.9)x,Unicycler/SPAdes/PILON v.,1,,1,1853812,38.346607,1866,1783,normally sterile site,,2001,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.986,Streptococcus pyogenes strain MGAS29064,MGAS29064,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08562766,1314,Emm28,,,MLST.Streptococcus_pyogenes.458,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154325.1,CP031620,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,226.3 (107.8 & 118.5)x,Unicycler/SPAdes/PILON v.,1,,1,1839848,38.360615,1844,1759,normally sterile site,,2015,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.987,Streptococcus pyogenes strain MGAS28386,MGAS28386,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556297,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154345.1,CP031626,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,192.7 (80.4 & 112.2)x,Unicycler/SPAdes/PILON v.,1,,1,1837594,38.356026,1841,1758,normally sterile site,,2002,USA,USA: Minnesota,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.988,Streptococcus pyogenes strain MGAS28078,MGAS28078,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08556024,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154365.1,CP031632,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,194.2 (45.5 & 148.8)x,Unicycler/SPAdes/PILON v.,1,,1,1880780,38.37222,1894,1811,normally sterile site,,2010,USA,USA: Georgia,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:CDC Active Bacterial Core Surveillance,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.989,Streptococcus pyogenes strain MGAS11052,MGAS11052,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555770,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154385.1,CP031635,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,267.8 (25.1 & 242.7)x,Unicycler/SPAdes/PILON v.,1,,1,1907750,38.24348,1917,1832,normally sterile site,,2000,Finland,Finland,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:National Public Health Laboratory,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.990,Streptococcus pyogenes strain MGAS10826,MGAS10826,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08555766,1314,Emm28,,,MLST.Streptococcus_pyogenes.52,,,,2019-02-11T00:00:00Z,,PRJNA434389,GCA_004154405.1,CP031636,,Houston Methodist Research Institute,Oxford Nanopore MinION & Illumina,265.2 (44.1 & 221.1)x,Unicycler/SPAdes/PILON v.,1,,1,1852263,38.33543,1866,1782,normally sterile site,,2000,Canada,Canada: Ontario,,,,invasive infection,,,,,,,,,,,,,"Population genomic sequencing of 2,101 Streptococcus pyogenes Emm-type 28 strains",collected_by:Public Health Ontario,,,,,,,invasive infection,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1314.991,Streptococcus pyogenes strain SP1336,SP1336,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09867132,1314,M12,,,MLST.Streptococcus_pyogenes.36,,,,2019-02-13T00:00:00Z,30721938,PRJNA486857,GCA_004193935.1,CP031738,,University of Melbourne,PacBio,105.0x,PacBio SMRT Pipe v. 2.3.0,1,,1,1878827,38.525208,1936,1843,throat,,2017,Australia,"Australia: Gold Coast, QLD",,,,Scarlet Fever,,,,,,,,,,,,,Complete genome of M12 Streptococcus pyogenes associated with Scarlet Fever in an Australian patient,collected_by:Gold Coast Health,,,,,,,Scarlet Fever,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.993,Streptococcus pyogenes strain emm74,emm74,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793327,1314,,,,MLST.Streptococcus_pyogenes.120,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005160565.1,CP035427,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1861037,38.46576,1903,1827,throat,,2014,New Zealand,New Zealand,,,,Rheumatic fever,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Rheumatic fever,,,,,,,,,,,,,,100,0.35,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1314.995,Streptococcus pyogenes strain emm55,emm55,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793324,1314,,,,MLST.Streptococcus_pyogenes.100,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005160925.1,CP035430,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1899479,38.51946,1940,1848,skin,,2005,Australia,Australia,,,,Acute post-streptococcal glomerulonephritis,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Acute post-streptococcal glomerulonephritis,,,,,,,,,,,,,,99.85,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1314.997,Streptococcus pyogenes strain emm64.3,emm64.3,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793319,1314,,,,,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005161325.1,CP035435,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1779766,38.563663,1811,1743,throat,,2003,Brazil,Brazil,,,,Pharyngitis,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Pharyngitis,,,,,,,,,,,,,,100,0.35,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1314.998,Streptococcus pyogenes strain emm78.3,emm78.3,Streptococcus pyogenes,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10793317,1314,,,,,,,,2019-05-06T00:00:00Z,,PRJNA454341,GCA_005161465.1,CP035437,,University of Melbourne,PacBio,80x,HGAP v. 2,1,,1,1806521,38.44035,1799,1723,throat,,2002,New Zealand,New Zealand,,,,Rheumatic fever,,,,,,,,,,,,,Complete genomes of 30 globally distributed Group A Streptococcus isolates,collected_by:Davies_et_al,,,,,,,Rheumatic fever,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1328.351,Streptococcus anginosus 47S1,47S1,Streptococcus anginosus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN23380299,1328,Group C,,S. anginosus,,genotype:not applicable,not applicable,,2021-12-15T00:00:00Z,,PRJNA782455,GCA_021184285.1,CP088916,,,Illumina NovaSeq,800.0x,SPAdes v. May2021,1,0,1,1981612,38.600925,2110,1977,king khalid university hospital at king saud university,,2020-09-14,Saudi Arabia,Saudi Arabia,,male,63,Pharyngitis,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,"collected_by:Galal A. Esmail, Badr Aldawood;specimen_voucher:not applicable",,,,,,,Pharyngitis,not applicable,not applicable,not applicable,not applicable,S. anginosus,,,,,,,,,99.53,0.21,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,13373.58,Burkholderia mallei strain FMH,FMH,Burkholderia mallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03174435,13373,,,,"MLST.Burkholderia_cepacia_complex.734,MLST.Burkholderia_pseudomallei.40",,,,2017-09-22T00:00:00Z,,PRJNA264186,GCA_002346045.1,"CP009929,CP009930",,USAMRIID,PacBio,160x,HGAP v. 3.3,2,,2,5835466,68.49,5821,4970,,,2000-05,USA,USA:Maryland,,,,Glanders,,,,,,,,,,,,,Whole genome sequencing of ten Burkholderia mallei isolates,collected_by:USAMRIID,,,,,,,Glanders,,,,,,,,,,,,,,99.7,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,13373.65,Burkholderia mallei strain JHU,JHU,Burkholderia mallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03174429,13373,,,,"MLST.Burkholderia_cepacia_complex.734,MLST.Burkholderia_pseudomallei.40",,,,2017-09-22T00:00:00Z,,PRJNA264186,GCA_002346205.1,"CP009931,CP009932",,USAMRIID,PacBio,,HGAP v. 3.3,2,,2,5736590,68.44,5761,4913,,,2000-05,USA,USA:Maryland,,,,Glanders,,,,,,,,,,,,,Whole genome sequencing of ten Burkholderia mallei isolates,collected_by:USAMRIID,,,,,,,Glanders,,,,,,,,,,,,,,99.5,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,13373.94,Burkholderia mallei strain FDAARGOS_590 strain Not applicable,Not applicable,Burkholderia mallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10228570,13373,,,,"MLST.Burkholderia_cepacia_complex.734,MLST.Burkholderia_pseudomallei.40",genotype:UNK,FDA:FDAARGOS_590,,2018-12-14T00:00:00Z,,PRJNA231221,GCA_003933045.1,RKJU00000000,,US Food and Drug Administration,Pacbio; Illumina,37.30x,Canu v. 1.7,2,,2,5864677,68.48184,6265,6174,clinical isolate,,,China,China,,male,,Glanders-melioidosis,,host_description:Not applicable;host_disease_outcome:fatal,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,,,,,,,Glanders-melioidosis,Unknown,fatal,Not applicable,Unknown,,,,,,,,,,100,0.43,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,1338.30,Streptococcus intermedius strain FDAARGOS_233,FDAARGOS_233,Streptococcus intermedius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN04875570,1338,,,,,,FDA:FDAARGOS_233,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073355.2,CP020433,,US Food and Drug Administration,PacBio,18.3295368x,HGAP v. 3,1,,1,1913894,37.66,1985,1843,abscess,,2014-09-14,USA,USA:DC,,female,15M,Abdominal abscess,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,,,,,,,Abdominal abscess,Missing,Missing,Missing,Missing,,,,,,,,,,97.4,2.5,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1338.31,Streptococcus intermedius strain TYG1620,TYG1620,Streptococcus intermedius,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00031898,1338,,,,,,,,2017-06-15T00:00:00Z,27895128,PRJDB3973,GCA_002356055.1,AP014880,,"Pathogen Genomics Center, National Institute of Infectious Diseases",Illumina GAIIx; MiSeq; ABI 3730xl,1000x,CLC De Novo Assembler v. 6.5; Platanus v.,1,,1,2006877,37.55,2060,2020,the brain abscess,isolated from the brain abscess in infant,2011,,,env_biome:not applicable,,,,,,,,Positive,Cocci,No,,,Anaerobic,,brain abscess,"Streptococcus intermedius belongs to a group of S. anginosus group, and is intraoral commensal bacteria. However, S. intermedius is known to cause periodontitis and pyogenic infection in brain and liver, strain TYG1620 was isolated from the brain abscess in infant. TYG1620 can be grown under anaerobic cultivation, and it shows strong auto aggregation. To elucidate the virulence factors for streptococcal brain abscess formation, complete genome sequencing of TYG1620 was performed, and revealed that whole genome size is 2,006,877 bp (GC, 37.55 %).",,not applicable,brain,abscess,missing,Complete genome sequence of Streptococcus intermedius str. TYG1620,brain abscess,,,,,,,,,,commensal,not applicable,,,,97.4,0.7,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,134034.17,Corynebacterium freneyi DSM 44506,DSM 44506,Corynebacterium freneyi,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13404523,134034,,,,,,DSM:44506,,2023-07-05T00:00:00Z,,PRJNA454156,,CP047357,,,Illumina MiSeq; Oxford Nanopore GridION,82.0x,Newbler v. 2.8; canu v. 1.8,1,0,1,2880330,68.85708,2594,2498,pus from a toe,,,France,"France: E. Herriot Hospital, Lyon",,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 44506,,,,,,,,,,,,,,,,,,,,,97.1,0.7,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,134534.15,Acinetobacter gyllenbergii strain NCCP 16015,NCCP 16015,Acinetobacter gyllenbergii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12340933,134534,,,,,,NCCP:16015,,2020-01-15T00:00:00Z,,PRJNA556124,GCA_009884295.1,CP041971,,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,357.0x,SPAdes v. 3.1,1,0,1,4091186,41.35121,3866,3757,unknown,,2013-01-01,South Korea,South Korea: Incheon,,,,,,,,,,,,,,,,,A clinical isolate of the genus Acinetobacter,collected_by:Korea National Institute of Health,,,,,,,unknown,,,,,,,,,,,,,,100,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1349.244,Streptococcus uberis strain NCTC4674,NCTC4674,Streptococcus uberis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3956095,1349,not available: to be reported later,,,,,NCTC:4674,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900475695.1,LS483408,,SC,,,,1,,1,2024265,36.52852,1979,1951,not available: to be reported later,,1900-1932,United Kingdom,United Kingdom: London,,,,,,host_health_state:Mastitis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Mastitis,,,100,1.9,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1351.2070,Enterococcus faecalis strain SCAID PHRX1-2018 strain Swab from oropharyngeal of the woman with tonsillitis,Swab from oropharyngeal of the woman with tonsillitis,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12301878,1351,,,,MLST.Enterococcus_faecalis.6,,,,2019-07-30T00:00:00Z,,PRJNA555137,GCA_007632055.1,"CP041877,CP041878",,SCAID,IonTorrent,17.0x,Velvet v. 1.2.10,1,1,2,2695820,37.84477,2791,2698,pharynx,,2018-08-28,Kazakhstan,Kazakhstan: Almaty,,female,32,Tonsillitis,,host_disease_outcome:Recovery;host_disease_stage:Acute phase of tonsillitis,Intermediate;Resistant;Susceptible,AMR Panel,,,,,,,,,"Creating experimental models based on clinical isolates that are characterized by multiple drug resistance, to clarify the universality of the reversion phenomenon.","collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Tonsillitis,,Recovery,,Acute phase of tonsillitis,,,,,,,,,,98.72,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases NHP,1351.2355,Enterococcus faecalis strain 4928STDY7071355,4928STDY7071355,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567465,1351,,,,MLST.Enterococcus_faecalis.30,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164645.1,LR607334,,SC,,,,1,,1,3380663,37.76527,2807,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97.75,0,,,Other,- NHP,1351.2356,Enterococcus faecalis strain 4928STDY7071325,4928STDY7071325,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567435,1351,,,,MLST.Enterococcus_faecalis.72,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164695.1,LR607329,,SC,,,,1,,1,3380441,37.837414,2738,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97.38,0.19,,,Other,- NHP,1351.2431,Enterococcus faecalis strain 4928STDY7071263,4928STDY7071263,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567373,1351,,,,MLST.Enterococcus_faecalis.40,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166395.1,LR607346,,SC,,,,1,,1,3398119,37.726833,2822,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.25,0,,,Other,- NHP,1351.2433,Enterococcus faecalis strain 4928STDY7071765,4928STDY7071765,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4608511,1351,,,,MLST.Enterococcus_faecalis.19,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166575.1,LR607359,,SC,,,,1,,1,3392575,37.86133,2682,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,98.88,0,,,Other,- NHP,1351.2434,Enterococcus faecalis strain 4928STDY7071766,4928STDY7071766,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4608512,1351,,,,MLST.Enterococcus_faecalis.19,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166605.1,LR607356,,SC,,,,1,,1,3375521,37.86695,2675,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,98.88,0,,,Other,- NHP,1351.2435,Enterococcus faecalis strain 4928STDY7387674,4928STDY7387674,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694312,1351,,,,MLST.Enterococcus_faecalis.145,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166645.1,LR607354,,SC,,,,1,,1,3378277,37.78353,2768,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.25,0,,,Other,- NHP,1351.2436,Enterococcus faecalis strain 4928STDY7387719,4928STDY7387719,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694356,1351,,,,MLST.Enterococcus_faecalis.179,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166665.1,LR607365,,SC,,,,1,,1,3384564,37.782715,2800,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.88,0,,,Other,- NHP,1351.2437,Enterococcus faecalis strain 4928STDY7387718,4928STDY7387718,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694355,1351,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166685.1,LR607371,,SC,,,,1,,1,3460686,37.58153,3191,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,95.88,0,,,Other,- NHP,1351.2438,Enterococcus faecalis strain 4928STDY7387713,4928STDY7387713,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694350,1351,,,,MLST.Enterococcus_faecalis.472,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166695.1,LR607361,,SC,,,,1,,1,3396661,37.526127,2835,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.63,0.37,,,Other,- NHP,1351.2439,Enterococcus faecalis strain 4928STDY7387888,4928STDY7387888,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4623312,1351,,,,MLST.Enterococcus_faecalis.133,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166775.1,LR607376,,SC,,,,1,,1,2870977,37.76496,2627,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.63,0,,,Other,- NHP,1351.2440,Enterococcus faecalis strain 4928STDY7387896,4928STDY7387896,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4623320,1351,,,,MLST.Enterococcus_faecalis.102,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166815.1,LR607378,,SC,,,,1,,1,3093718,37.44204,2753,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.53,0.15,,,Other,- HP,1351.496,Enterococcus faecalis strain CLB21560,CLB21560,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06270347,1351,,,,MLST.Enterococcus_faecalis.28,,,,2017-02-07T00:00:00Z,,PRJNA368724,GCF_001989555.1,"CP019512,CP019513,CP019514","NZ_CP019512.1,NZ_CP019513.1,NZ_CP019514.1",Merck Research Laboratory,PacBio,100.0x,Velvet v. Jun-2016,1,2,3,3243539,37.11,3364,3332,clinical,,2017-01-25,USA,United States,,,,,,,,,,,,,,,,,Enterococcus faecalis CLB21560 Strain,sample_type:single cell;collected_by:Paul Mann,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1351.5086,Enterococcus faecalis strain 18-243,18-243,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988090,1351,,,,MLST.Enterococcus_faecalis.41,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517125.1,"CP065784,CP065785,CP065786",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,3097453,37.531548,3091,2975,digestive,is from clinical origin in France between 2016-20,2018-04,France,France: Nice,,,,Eneterococcus faecalis,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Eneterococcus faecalis,,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1351.5087,Enterococcus faecalis strain TM6294,TM6294,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595200,1351,,,,MLST.Enterococcus_faecalis.585,,,,2021-04-29T00:00:00Z,,PRJEB36950,GCA_906464835.1,"OD940431,OD940432,OD940433",,UNIVERSITY OF ST ANDREWS,,,,1,2,3,2934591,37.375294,2805,2737,urine,,2017,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.5088,Enterococcus faecalis strain WE0438,WE0438,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595199,1351,,,,MLST.Enterococcus_faecalis.330,,,,2021-04-29T00:00:00Z,,PRJEB36950,GCA_906464865.1,"OD940420,OD940421",,UNIVERSITY OF ST ANDREWS,,,,1,1,2,3030851,37.245445,2922,2831,urine,,2016,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.5089,Enterococcus faecalis strain BX5936,BX5936,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595201,1351,,,,,,,,2021-04-29T00:00:00Z,,PRJEB36950,GCA_906464925.1,"OD940434,OD940435,OD940436",,UNIVERSITY OF ST ANDREWS,,,,1,2,3,2927246,37.47741,2820,2747,semen,,2017,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1351.5090,Enterococcus faecalis strain BX8117,BX8117,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595202,1351,,,,MLST.Enterococcus_faecalis.16,,,,2021-04-29T00:00:00Z,,PRJEB36950,GCA_906464875.1,"OD940437,OD940438,OD940439",,UNIVERSITY OF ST ANDREWS,,,,1,2,3,3019890,37.417126,2917,2836,urine,,2017,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.53,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.5091,Enterococcus faecalis strain WE0851,WE0851,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595197,1351,,,,MLST.Enterococcus_faecalis.480,,,,2021-04-29T00:00:00Z,,PRJEB36950,GCA_906464895.1,"OD940422,OD940426,OD940427,OD940428,OD940429,OD940430,OD940423,OD940424,OD940425",,UNIVERSITY OF ST ANDREWS,,,,6,3,9,2866641,37.56822,2784,2695,urine,,2014,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.5338,Enterococcus faecalis strain WE0254,WE0254,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA6595198,1351,,,,MLST.Enterococcus_faecalis.19,,,,2021-08-18T00:00:00Z,,PRJEB36950,GCA_906464915.2,"OD940440,OU538996,OU538997,OU538998",,UNIVERSITY OF ST ANDREWS,,,,1,3,4,2994227,37.465565,2966,2890,urine,,2015,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"Short and long read sequence data was performed to generate complete chromosome and plasmid hybrid asssemblies of optrA positive, linezolid resistant Enterococcus faecalis.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.6410,Enterococcus faecalis VSE-WC032,VSE-WC032,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN26026625,1351,,,,,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691465.1,"CP092574,CP092575",,,Illumina MiSeq and Oxford Nanopore MinION,158x,Unicycler v. 0.4.8,1,1,2,3100993,37.39599,3140,2982,rectum,,2004-04-02,USA,USA,,,,UTI,,,,,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0.2,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,1351.6411,Enterococcus faecalis VRE-WC031,VRE-WC031,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN26026624,1351,,,,,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691485.1,"CP092576,CP092577,CP092578,CP092579,CP092580",,,Illumina MiSeq and Oxford Nanopore MinION,153x,Unicycler v. 0.4.8,1,4,5,3245651,37.318832,3352,3146,rectum,,2004-04-02,USA,USA,,,,UTI,,,,,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,2.5,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,1351.6814,Enterococcus faecalis strain SJ82,SJ82,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN30551391,1351,,,,,,,,2022-09-05T00:00:00Z,,PRJNA874495,GCA_024927865.1,"CP103863,CP103862",,Sapporo Medical University,PacBio,2880000.0x,Flye v. 2.9,1,1,2,2907997,37.58343,2840,2774,urine,,2018-02-25,,Bangladesh,,,,urinary tract infection (UTI),,,,,,,,,,,,,To characterize the molecular epidemiology of oxazolidinone resistant Enterococcus faecalis clinical isolate in Bangladesh,collected_by:Meiji Soe Aung,,,,,,,urinary tract infection (UTI),,,,,,,,,,,,,,99.16,0.37,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.6878,Enterococcus faecalis SJ82,SJ82,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN30551391,1351,,,,,,,,2022-09-05T00:00:00Z,,PRJNA874495,GCA_024927865.1,"CP103863,CP103862",,,PacBio,2880000.0x,Flye v. 2.9,1,1,2,2907997,37.58343,2840,2774,urine,,2018-02-25,Bangladesh,Bangladesh,,,,urinary tract infection (UTI),,,,,,,,,,,,,,collected_by:Meiji Soe Aung,,,,,,,urinary tract infection (UTI),,,,,,,,,,,,,,99.5,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8192,Enterococcus faecalis SVJ-EF01,SVJ-EF01,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31723118,1351,,,,MLST.Enterococcus_faecalis.314,,,,2023-04-12T00:00:00Z,,PRJNA901658,,JAQRFZ000000000,,,Illumina NovaSeq,130.0x,Unicycler v0.4.8.1 v. AUGUST-2022,1,0,1,2819823,37.610622,2735,2673,urine,,2022-05-09,India,India,,female,,Pauci-immune crescentic glomerulonephritis (PICGN),,host_subject_id:SUHRC0228391,,,,,,,,,,,,collected_by:Dr. Savita Jadhav,,,,,,,Pauci-immune crescentic glomerulonephritis (PICGN),,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1351.8337,Enterococcus faecalis NY13412,NY13412,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN30932864,1351,,,,MLST.Enterococcus_faecalis.16,,,,2023-04-25T00:00:00Z,,PRJNA882356,,"CP104856,CP104857",,,PacBio RSII,100.0x,HGAP v. v3.0,1,1,2,3098898,37.187283,3034,2935,hydrothorax,,2020,China,China: Shanghai,,,,interstitial pneumonia,,,,,,,,,,,,,,collected_by:a public hospital,,,,,,,interstitial pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,1351.8357,Enterococcus faecalis EfsPNK7,EfsPNK7,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741222,1351,,,,,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124887,CP124888",,,"Illumina NextSeq, ONT MinION",312x,Unicycler v. v.0.4.8,1,1,2,2918219,37.459595,2797,2723,urine,,2017-10,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8358,Enterococcus faecalis EfsPF2,EfsPF2,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741213,1351,,,,MLST.Enterococcus_faecalis.397,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124890,,,"Illumina NextSeq, ONT MinION","472x, 382x",Unicycler v. v.0.4.8,1,0,1,2833818,37.537167,2668,2614,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8360,Enterococcus faecalis EfsPF13,EfsPF13,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741215,1351,,,,,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124886,,,"Illumina NextSeq, ONT MinION","303x, 498x",Unicycler v. v.0.4.8,1,0,1,2870187,37.573895,2802,2714,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8361,Enterococcus faecalis EfsPF5,EfsPF5,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741214,1351,,,,MLST.Enterococcus_faecalis.19,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124889,,,"Illumina NextSeq, ONT MinION","151x, 136x",Unicycler v. v.0.5.0,1,0,1,2904543,37.56894,2860,2785,urine,,2018-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8362,Enterococcus faecalis EfsPF20,EfsPF20,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741217,1351,,,,MLST.Enterococcus_faecalis.40,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124882,CP124883",,,"Illumina NextSeq, ONT MinION","625x, 198x",Unicycler v. v.0.5.0,1,1,2,3013361,37.495575,2933,2856,urine,,2018-08,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8363,Enterococcus faecalis EfsC123,EfsC123,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741210,1351,,,,MLST.Enterococcus_faecalis.16,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124893,,,"Illumina NextSeq, ONT MinION","402x, 322x",Unicycler v. v.0.4.8,1,0,1,2894553,37.57195,2771,2699,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8365,Enterococcus faecalis EfsC109-2,EfsC109-2,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741208,1351,,,,MLST.Enterococcus_faecalis.16,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124898,CP124899",,,"Illumina NextSeq, ONT MinION","437x, 337x",Unicycler v. v.0.4.8,1,1,2,2978196,37.30594,2899,2815,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8366,Enterococcus faecalis EfsC94,EfsC94,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741206,1351,,,,MLST.Enterococcus_faecalis.79,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124901,CP124902,CP124903,CP124904",,,"Illumina NextSeq, ONT MinION","439x, 346x",Unicycler v. v.0.4.8,1,3,4,2953867,37.438618,2888,2795,urine,,2019-03,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8367,Enterococcus faecalis EfsC108,EfsC108,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741207,1351,,,,MLST.Enterococcus_faecalis.534,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124900,,,"Illumina NextSeq, ONT MinION","437x, 413x",Unicycler v. v.0.4.8,1,0,1,2764125,37.619717,2608,2549,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8368,Enterococcus faecalis EfsC85,EfsC85,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741205,1351,,,,MLST.Enterococcus_faecalis.16,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124905,,,"Illumina NextSeq, ONT MinION","484x, 337x",Unicycler v. v.0.4.8,1,0,1,2859274,37.45755,2723,2649,urine,,2019-03,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,99.8,0.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8369,Enterococcus faecalis EfsC61,EfsC61,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741203,1351,,,,MLST.Enterococcus_faecalis.40,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124911,CP124912",,,"Illumina NextSeq, ONT MinION","542x, 330x",Unicycler v. v.0.4.8,1,1,2,3039738,37.36085,3011,2924,urine,,2019-01,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8370,Enterococcus faecalis EfsC49,EfsC49,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741202,1351,,,,MLST.Enterococcus_faecalis.21,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124906,CP124907",,,"Illumina NextSeq, ONT MinION","369x, 439x",Unicycler v. v.0.4.8,1,1,2,2845302,37.622192,2725,2664,urine,,2018-12,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8371,Enterococcus faecalis EfsC33,EfsC33,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741200,1351,,,,,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124908,CP124909,CP124910",,,"Illumina NextSeq, ONT MinION","91x, 103x",Unicycler v. v.0.4.8,1,2,3,3112897,37.423885,3061,2964,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8372,Enterococcus faecalis EfsC17,EfsC17,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741196,1351,,,,MLST.Enterococcus_faecalis.25,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124916,CP124917",,,"Illumina NextSeq, ONT MinION","97x, 215x",Unicycler v. v.0.4.8,1,1,2,2954172,37.47571,2946,2848,urine,,2018-07,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8373,Enterococcus faecalis EfsC11,EfsC11,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741193,1351,,,,MLST.Enterococcus_faecalis.30,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124923,CP124924",,,"Illumina NextSeq, ONT MinION","81x, 381x",Unicycler v. v.0.4.8,1,1,2,3004778,37.440834,2950,2849,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8374,Enterococcus faecalis EfsC12,EfsC12,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741194,1351,,,,MLST.Enterococcus_faecalis.81,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124921,CP124922",,,"Illumina NextSeq, ONT MinION","395x, 316x",Unicycler v. v.0.4.8,1,1,2,2945592,37.413498,2803,2739,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8376,Enterococcus faecalis EfsC20,EfsC20,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741197,1351,,,,MLST.Enterococcus_faecalis.179,,,,2023-05-16T00:00:00Z,,PRJNA944190,,CP124913,,,"Illumina NextSeq, ONT MinION","301x, 239x",Unicycler v. v.0.4.8,1,0,1,2904406,37.466145,2816,2734,urine,,2018-07,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8377,Enterococcus faecalis EfsC8,EfsC8,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741191,1351,,,,MLST.Enterococcus_faecalis.165,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124914,CP124915",,,"Illumina NextSeq, ONT MinION","94x, 243x",Unicycler v. v.0.5.0,1,1,2,2753347,37.588215,2595,2544,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8713,Enterococcus faecalis EfsC1,EfsC1,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741190,1351,,,,MLST.Enterococcus_faecalis.179,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124960,CP124961,CP124962",,,"Illumina NextSeq, ONT MinION","75x, 51x",Unicycler v. v.0.4.8,2,1,3,3077295,37.28125,3064,2930,urine,,2018-05,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8721,Enterococcus faecalis EfsPF23,EfsPF23,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741218,1351,,,,,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124935,CP124936,CP124937,CP124938",,,"Illumina NextSeq, ONT MinION","102x, 514x",Unicycler v. v.0.4.8,2,2,4,3138108,37.203243,3143,2997,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8722,Enterococcus faecalis EfsPF36,EfsPF36,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741221,1351,,,,MLST.Enterococcus_faecalis.179,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124925,CP124926,CP124927",,,"Illumina NextSeq, ONT MinION","506x, 353x",Unicycler v. v.0.4.8,2,1,3,3138260,37.23726,3140,3000,urine,,2019-02,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8724,Enterococcus faecalis EfsC43,EfsC43,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741201,1351,,,,MLST.Enterococcus_faecalis.30,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124947,CP124948,CP124949",,,"Illumina NextSeq, ONT MinION","741x, 98x",Unicycler v. v.0.4.8,2,1,3,3035886,37.39317,3018,2856,urine,,2018-12,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8730,Enterococcus faecalis EfsC13,EfsC13,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741195,1351,,,,,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124956,CP124957,CP124958,CP124959",,,"Illumina NextSeq, ONT MinION","398x, 370x",Unicycler v. v.0.5.0,2,2,4,3118388,37.225323,3128,2983,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1351.8731,Enterococcus faecalis EfsPF27,EfsPF27,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741220,1351,,,,MLST.Enterococcus_faecalis.40,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124928,CP124929,CP124930",,,"Illumina NextSeq, ONT MinION","577x, 361x",Unicycler v. v.0.4.8,2,1,3,3013507,37.44086,2956,2829,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI NHP,1351.8733,Enterococcus faecalis HL1,HL1,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN34473392,1351,,,,MLST.Enterococcus_faecalis.387,,,,2023-07-20T00:00:00Z,,PRJNA964481,,CP124778,,,PacBio Sequel,286.0x,HGAP v. APIRL-2023,1,0,1,2695805,37.70829,2522,2472,microbiome,,2022-07-18,South Korea,South Korea,,,,,,,,,,,,,,,,,,,gut microbiome,gut microbiome,microbiome,BL medium,,,,,,,,,,,,,gut microbiome,,,,100,0,,,Other,- HP,1351.8734,Enterococcus faecalis EfsPF24-2,EfsPF24-2,Enterococcus faecalis,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN33741219,1351,,,,MLST.Enterococcus_faecalis.40,,,,2023-05-16T00:00:00Z,,PRJNA944190,,"CP124931,CP124932,CP124933,CP124934",,,"Illumina NextSeq, ONT MinION","136x, 704x",Unicycler v. v.0.4.8,2,2,4,3114654,37.40515,3069,2936,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1352.12103,Enterococcus faecium strain AML0158,AML0158,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15643624,1352,,,,MLST.Enterococcus_faecium.203,,,,2020-09-07T00:00:00Z,,PRJNA648658,GCA_014489995.1,"CP060857,CP060858,CP060859,CP060860",,University of Cologne,Illumina MiSeq; Oxford Nanopore MiniION,100x,Other Unicycler v. v0.4.9b,1,3,4,3182731,37.833416,3228,,clinical,,2016-11,Germany,Germany:Cologne,,,,Bloodstream infection,,,,,,,,,,,,,Characterization of a vancomycin-resistant and a vancomycin-susceptible Enterococcus faecium isolate from the same blood culture,collected_by:University Hospital of Cologne,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.44,0.37,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,1352.12104,Enterococcus faecium strain AML0157,AML0157,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15643623,1352,,,,MLST.Enterococcus_faecium.203,,,,2020-09-07T00:00:00Z,,PRJNA648658,GCA_014490015.1,"CP060861,CP060862,CP060863,CP060864,CP060865",,University of Cologne,Illumina MiSeq; Oxford Nanopore MiniION,100x,Other Unicycler v. v0.4.9b,1,4,5,3317988,37.67102,3374,,clinical,,2016-11,Germany,Germany:Cologne,,,,Bloodstream infection,,,,,,,,,,,,,Characterization of a vancomycin-resistant and a vancomycin-susceptible Enterococcus faecium isolate from the same blood culture,collected_by:University Hospital of Cologne,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.44,0.37,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,1352.12139,Enterococcus faecium strain VB3338,VB3338,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16287686,1352,,,,MLST.Enterococcus_faecium.80,,,,2020-10-10T00:00:00Z,,PRJNA666302,GCA_014874615.1,"CP062265,CP062266,CP062275,CP062276,CP062277,CP062267,CP062268,CP062269,CP062270,CP062271,CP062272,CP062273",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,45.0x,CANU v. v. 1.7; UNICYCLER HYBRID v. v.,1,12,13,3206679,37.514202,3252,3078,blood,,2019,India,India,,,,sepsis,,,,,,,,,,,,,Complete genome of vancomycin resistant Enterococcus faecium,collected_by:Christian Medical College,,,,,,,sepsis,,,,,,,,,,,,,,99.63,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12160,Enterococcus faecium strain Cairo,Cairo,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16574827,1352,,,,MLST.Enterococcus_faecium.18,,,,2020-11-12T00:00:00Z,,PRJNA672694,GCA_015356095.1,"CP064279,CP064280,CP064281,CP064282,CP064291,CP064283,CP064284,CP064285,CP064286,CP064287,CP064288,CP064289",,NASA,Oxford Nanopore MinION,46x,Flye v. 2.6; Racon v. 1.4.7; Medaka v.,1,12,13,3156539,37.776184,3631,,clinical isolate,,2018-07-06,Egypt,Egypt: Cairo,,,,,,,,,,,,,,,,,"A rapid assembly protocol was leveraged to quickly generate genome assemblies of prokaryotes using minimal computational resources. These assemblies were passed to a pipeline to assemble genome-scale metabolic network reconstructions of these microorganisms. The genomes include a validation reference (E. coli K12 MG1655 BOP27) and three (3) clinical isolates of pathogenic bacteria (Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus faecium).",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.13,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1352.12529,Enterococcus faecium strain WGS1811-4-7,WGS1811-4-7,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12930511,1352,,,,MLST.Enterococcus_faecium.117,,,,2021-02-11T00:00:00Z,,PRJNA576159,GCA_016864255.1,"CP046166,CP046167,CP046168,CP046169,CP046170",,Haukeland University Hospital,Illumina MiSeq; Oxford Nanopore MiniION,119.0x,UniCycler v. v0.4.8,1,4,5,3211076,37.9091,3272,3082,urine,,2017-02-03,Norway,Norway:bergen,,,,bacteriuria,,,,,,,,,,,,,"VRE-outbreak, Haukeland University Hospital",collected_by:Haukeland University Hospital,,,,,,,bacteriuria,,,,,,,,,,,,,,99.63,0.37,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,1352.12579,Enterococcus faecium strain AUSMDU00011555,AUSMDU00011555,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18082828,1352,,,,,,,,2021-03-08T00:00:00Z,,PRJNA565795,GCA_017301355.1,"CP071271,CP071272,CP071273,CP071274,CP071275",,Microbiological Diagnostic Unit,Illumina NextSeq; Oxford Nanopore GridION,74.0x,Unicycler v. 0.4.8beta,1,4,5,3263630,37.72048,3469,3116,rectal swab,,2017,Australia,Australia,,,,,,,,,,,,,,,,,Prospective whole-genome sequencing of multidrug-resistant pathogens from hospital inpatients to detect transmission and inform infection control interventions.,,,,,,,,missing,,missing,missing,missing,missing,,,,,,,,,99.63,0.44,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12694,Enterococcus faecium strain VB13828,VB13828,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18353823,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-03-29T00:00:00Z,,PRJNA715591,GCA_017603725.1,"CP071958,CP071968,CP071969,CP071959,CP071960,CP071961,CP071962,CP071963,CP071964,CP071965,CP071966,CP071967",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,59.0x,CANU v. v.1.7; UNICYCLER HYBRID v.,1,11,12,3095842,37.77089,3177,2992,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Vancomycin-Resistant Enterococcus faecium_VB13828,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.63,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12699,Enterococcus faecium strain VB12993,VB12993,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533867,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-07T00:00:00Z,,PRJNA718447,GCA_017815655.1,"CP072579,CP072580,CP072581,CP072582,CP072583,CP072584,CP072585",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,98.7x,UNICYCLER v. v0.4.8,1,6,7,3151778,37.784008,3202,3025,blood,,2018,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Vancomycin Resistant Enterococcus faecium_VB12993,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.63,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12700,Enterococcus faecium strain VB3895,VB3895,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533866,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-07T00:00:00Z,,PRJNA718444,GCA_017815675.1,"CP072567,CP072568,CP072577,CP072578,CP072569,CP072570,CP072571,CP072572,CP072573,CP072574,CP072575,CP072576",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,44.3x,UNICYCLER v. v0.4.8,1,11,12,3106441,37.844627,3118,2945,blood,,2019,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Vancomycin Resistant Enterococcus faecium_VB3895,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.63,0.12,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12701,Enterococcus faecium strain VB976,VB976,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533868,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-07T00:00:00Z,,PRJNA718448,GCA_017815695.1,"CP072586,CP072587,CP072588,CP072589,CP072590,CP072591,CP072592,CP072593,CP072594,CP072595",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,124.4x,UNICYCLER v. v0.4.8,1,9,10,3210490,37.67917,3283,3098,blood,,2019,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Vancomycin Resistant Enterococcus faecium_VB976,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.63,0.37,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12702,Enterococcus faecium strain VB6521,VB6521,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533757,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-11T00:00:00Z,,PRJNA718440,GCA_017898005.1,"CP072720,CP072721,CP072730,CP072722,CP072723,CP072724,CP072725,CP072726,CP072727,CP072728,CP072729",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,72.3x,UNICYCLER v. V.0.4.8,1,10,11,3248079,37.70364,3282,3087,blood,,2019,India,India,,,,sepsis,,,,,,,,,,,,,Complete genome of vancomycin resistant Enterococcus faecium_VB6521,collected_by:Christian Medical College,,,,,,,sepsis,,,,,,,,,,,,,,99.63,0.12,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12703,Enterococcus faecium strain VB6171,VB6171,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533763,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-11T00:00:00Z,,PRJNA718441,GCA_017897965.1,"CP072731,CP072732,CP072741,CP072733,CP072734,CP072735,CP072736,CP072737,CP072738,CP072739,CP072740",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,87.2x,UNICYCLER v. V.0.4.8,1,10,11,3248079,37.70364,3282,3087,blood,,2019,India,India,,,,sepsis,,,,,,,,,,,,,Complete genome of vancomycin resistant Enterococcus faecium_VB6171,collected_by:Christian Medical College,,,,,,,sepsis,,,,,,,,,,,,,,99.63,0.12,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12704,Enterococcus faecium strain VB3378,VB3378,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18533778,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-04-11T00:00:00Z,,PRJNA718443,GCA_017898025.1,"CP072707,CP072708,CP072717,CP072718,CP072719,CP072709,CP072710,CP072711,CP072712,CP072713,CP072714,CP072715",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,93.4x,UNICYCLER v. v0.4.8,1,12,13,3206679,37.514202,3251,3071,blood,,2019,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Vancomycin Resistant Enterococcus faecium_VB3378,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.63,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1352.12855,Enterococcus faecium strain 18-276,18-276,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988099,1352,,,,MLST.Enterococcus_faecium.80,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018516925.1,"CP065754,CP065755,CP065756,CP065757,CP065758,CP065759,CP065760,CP065761,CP065762,CP065763",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,9,10,2942453,37.95466,2930,2786,rectal swab,is from clinical origin in France between 2016-20,2018-05,France,France: Corbeil-Essonnes,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12856,Enterococcus faecium strain 18-133,18-133,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988096,1352,,,,MLST.Enterococcus_faecium.168,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517025.1,"CP065764,CP065765,CP065766",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,2873307,38.014038,3044,2730,urine,is from clinical origin in France between 2016-20,2018-03,France,France: Ales,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,98.2,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1352.12857,Enterococcus faecium strain 17-508,17-508,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988094,1352,,,,MLST.Enterococcus_faecium.168,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517045.1,"CP065767,CP065768,CP065769",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,2874010,38.010307,2900,2724,urine,is from clinical origin in France between 2016-20,2017-11,France,France: Amiens,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1352.12858,Enterococcus faecium strain 18-465,18-465,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988100,1352,,,,,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018516845.1,"CP065752,CP065753",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,1,2,2581780,38.267475,2565,2404,digestive,is from clinical origin in France between 2016-20,2018-08,France,France: Bordeaux,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0.12,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12859,Enterococcus faecium strain 16-164,16-164,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988092,1352,,,,MLST.Enterococcus_faecium.650,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517085.1,"CP065773,CP065774,CP065775,CP065776",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,3,4,2782002,37.980923,2814,2644,urine,is from clinical origin in France between 2016-20,2016-07,France,France: Chambery,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1352.12860,Enterococcus faecium strain 16-021,16-021,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988091,1352,,,,MLST.Enterococcus_faecium.323,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517105.1,"CP065777,CP065778,CP065779,CP065780,CP065781,CP065782,CP065783",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,6,7,2908103,38.160545,2902,2746,rectal swab,is from clinical origin in France between 2016-20,2016-02,France,France: Caen,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0.44,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12861,Enterococcus faecium strain 17-318,17-318,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988093,1352,,,,MLST.Enterococcus_faecium.324,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517065.1,"CP065770,CP065771,CP065772",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,2914615,37.806435,2946,2785,digestive,is from clinical origin in France between 2016-20,2017-06,France,France: Rennes,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12862,Enterococcus faecium strain 18-204,18-204,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988098,1352,,,,MLST.Enterococcus_faecium.18,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517145.1,"CP066205,CP066206,CP066207,CP066208,CP066209,CP066210,CP066211",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,6,7,2982571,37.858982,3306,2836,rectal swab,is from clinical origin in France between 2016-20,2018-04,France,France: Creteil,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,97.68,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12863,Enterococcus faecium strain 18-201,18-201,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988097,1352,,,,MLST.Enterococcus_faecium.168,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517165.1,"CP066212,CP066213,CP066214",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,2949262,37.99093,3450,2800,digestive,is from clinical origin in France between 2016-20,2018-04,France,France: Nantes,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,97.43,1.81,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12864,Enterococcus faecium strain 18-042,18-042,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16988095,1352,,,,,,,,2021-05-26T00:00:00Z,33895846,PRJNA682333,GCA_018517185.1,"CP066215,CP066216,CP066217",,U1230,Oxford Nanopore MiniION; Illumina MiSeq,250x,Unicycler v. v0.4.8,1,2,3,2665360,38.174206,2631,2503,digestive,is from clinical origin in France between 2016-20,2018-01,France,France: Tourcoing,,,,Enterococcus faecium,,,,,,,,,,,,,"Acquired resistance to linezolid (LZD) is rising among enterococci due to the spread of resistance genes (cfr, optrA and poxtA) carried by genetic mobile elements that are transferable between gram-positive bacteria. In this study, we aimed to characterize the genetic support and environment of poxtA(+) isolates of Enterococcus faecium and Enterococcus faecalis from clinical origin in France between 2016-20.",collected_by:NRC for Enterococci,,,,,,,Enterococcus faecium,,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12875,Enterococcus faecium strain USZ_VRE32_P32,USZ_VRE32_P32,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8659956,1352,,,,MLST.Enterococcus_faecium.117,,,,2021-05-10T00:00:00Z,,PRJEB44616,GCA_907165365.1,"OU015708,OU015710,OU015709,OU015711,OU015712,OU015713,OU015714,OU015715,OU015716",,University of Zurich,,,,1,8,9,3297824,37.604675,3304,,inguinal/rectal swab,,2017,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,"Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of healthcare-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this timeframe and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or indirect transmission networks, not detectable by traditional surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N acetyl galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work provides an example of the potential of the integration of epidemiological, functional genomic and evolutionary perspectives to understand adaptation strategies contributing to the successful spread of VREfm.",,,,,,,,,diseased,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.12876,Enterococcus faecium strain USZ_VRE5_P5,USZ_VRE5_P5,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8659929,1352,,,,MLST.Enterococcus_faecium.203,,,,2021-05-12T00:00:00Z,,PRJEB44616,GCA_907176135.1,"OU015946,OU015947,OU015948,OU015949,OU015950,OU015951,OU015952,OU015953,OU015954",,University of Zurich,,,,1,8,9,3156640,37.755177,3145,,superficial wound,,2015,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,"Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of healthcare-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this timeframe and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or indirect transmission networks, not detectable by traditional surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N acetyl galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work provides an example of the potential of the integration of epidemiological, functional genomic and evolutionary perspectives to understand adaptation strategies contributing to the successful spread of VREfm.",,,,,,,,,diseased,,,,,,,,,,,,,99.44,0.37,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1352.12877,Enterococcus faecium strain USZ_VRE53_P46,USZ_VRE53_P46,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8659977,1352,,,,MLST.Enterococcus_faecium.203,,,,2021-05-12T00:00:00Z,,PRJEB44616,GCA_907177285.1,"OU016036,OU016038,OU016037,OU016039,OU016040,OU016041,OU016042,OU016043,OU016044,OU016045",,University of Zurich,,,,1,9,10,3281836,37.642284,3298,,superficial wound,,2018,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,"Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of healthcare-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this timeframe and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or indirect transmission networks, not detectable by traditional surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N acetyl galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work provides an example of the potential of the integration of epidemiological, functional genomic and evolutionary perspectives to understand adaptation strategies contributing to the successful spread of VREfm.",,,,,,,,,diseased,,,,,,,,,,,,,99.44,0.37,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1352.12878,Enterococcus faecium strain USZ_VRE67_P60,USZ_VRE67_P60,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8659991,1352,,,,MLST.Enterococcus_faecium.203,,,,2021-05-12T00:00:00Z,,PRJEB44616,GCA_907176815.1,"OU016027,OU016028,OU016029,OU016030,OU016031,OU016032,OU016033,OU016034,OU016035",,University of Zurich,,,,1,8,9,3173120,37.75316,3168,,superficial wound,,2018,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,"Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of healthcare-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this timeframe and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or indirect transmission networks, not detectable by traditional surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N acetyl galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work provides an example of the potential of the integration of epidemiological, functional genomic and evolutionary perspectives to understand adaptation strategies contributing to the successful spread of VREfm.",,,,,,,,,diseased,,,,,,,,,,,,,99.44,0.37,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1352.13178,Enterococcus faecium strain AUS2001,AUS2001,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8520472,1352,,,,MLST.Enterococcus_faecium.203,,,,2021-07-30T00:00:00Z,,PRJEB42923,GCA_907163255.1,"OU015345,OU015346,OU015347,OU015348,OU015349",,THE UNIVERSITY OF MELBOURNE,,,,1,4,5,3096160,37.74782,3073,,blood,,2012,New Zealand,New Zealand,,,,,,host_health_state:diseased,,,,,,,,,,,De novo emergence of vanD vancomycin resistant Enterococcus faecium,,,,,,,,,diseased,,,,,,,,,,,,,99.44,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1352.13179,Enterococcus faecium strain AUS2002,AUS2002,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA8520473,1352,,,,,,,,2021-07-30T00:00:00Z,,PRJEB42923,GCA_907163315.1,"OU015350,OU015351,OU015352,OU015353,OU015354",,THE UNIVERSITY OF MELBOURNE,,,,1,4,5,3241449,38.02935,3286,,hepatic abscess,,2012,New Zealand,New Zealand,,,,,,host_health_state:diseased,,,,,,,,,,,De novo emergence of vanD vancomycin resistant Enterococcus faecium,,,,,,,,,diseased,,,,,,,,,,,,,99.44,0.81,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1352.13372,Enterococcus faecium strain V1225,V1225,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5367970,1352,,,,MLST.Enterococcus_faecium.18,,,,2021-09-28T00:00:00Z,,PRJNA764087,GCA_020162155.1,"CP083912,CP083913,CP083914,CP083915,CP083916,CP083917,CP083918,CP083919",,Copenhagen University Hospital Hvidovre,Illumina MiSeq and Oxford Nanopore MinION,154x,Unicycler v. 4.0.7,1,7,8,3003650,37.92359,3098,2886,hospitalized patient,,2015,,Denmark,,,,,,host_health_state:diseased,,,,,,,,,,,Resistance mechanisms of daptomycin are not fully understood. In this project we analysed the genomic changes leading to a daptomycin-susceptible vancomycin-resistant Enterococcus faecium (VREfm) isolate becoming resistant after 40 days of daptomycin and linezolid combination therapy. The two isogenic VREfm isolates (daptomycin-susceptible and daptomycin-resistant) were closed using whole genome sequencing with Illumina and Nanopore.,,,,,,,,,diseased,,,,,,,,,,,,,99.25,0.75,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1352.13376,Enterococcus faecium strain V1164,V1164,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA5367917,1352,,,,MLST.Enterococcus_faecium.18,,,,2021-09-28T00:00:00Z,,PRJNA764087,GCA_020162175.1,"CP083920,CP083921,CP083922,CP083923,CP083924,CP083925,CP083926,CP083927,CP083928,CP083929",,Copenhagen University Hospital Hvidovre,Illumina MiSeq and Oxford Nanopore MinION,254.19410228420895x,Unicycler v. 4.0.7,1,9,10,3028274,37.901985,3074,2901,hospitalized patient,,2015,,Denmark,,,,,,host_health_state:diseased,,,,,,,,,,,Resistance mechanisms of daptomycin are not fully understood. In this project we analysed the genomic changes leading to a daptomycin-susceptible vancomycin-resistant Enterococcus faecium (VREfm) isolate becoming resistant after 40 days of daptomycin and linezolid combination therapy. The two isogenic VREfm isolates (daptomycin-susceptible and daptomycin-resistant) were closed using whole genome sequencing with Illumina and Nanopore.,,,,,,,,,diseased,,,,,,,,,,,,,99.5,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1352.13416,Enterococcus faecium strain 4995/20,4995/20,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN21850488,1352,,,,MLST.Enterococcus_faecium.18,,,,2021-10-04T00:00:00Z,,PRJNA766534,GCA_020221735.1,"CP084178,CP084179,CP084180,CP084181,CP084182,CP084183,CP084184,CP084185,CP084186,CP084187",,National Medicines Institute,Oxford Nanopore MinION; Illumina MiSeq,670.0x,Unicycler v. 0.4.7,1,9,10,3185029,37.94292,3225,3054,hematoma,,2020-09-25,Poland,Poland: Bydgoszcz,,male,35,wound infection,,,,,,,,,,,,,"MDR enterococci constitute a great therapeutic challenge in hospitals due to limited treatment options. Isolates resistant to last-resort antimicrobials, i.e. glycopeptides, linezolid and tigecycline are of special concern and should be investigated in detail.",collected_by:National Medicines Institute,,,,,,,wound infection,,,,,,,,,,,,,,99.63,0.75,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1352.1406,Enterococcus faecium strain E1,E1,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06019998,1352,,,,MLST.Enterococcus_faecium.117,,,,2016-11-28T00:00:00Z,,PRJNA353757,GCF_001886635.1,"CP018065,CP018068,CP018066,CP018067,CP018069","NZ_CP018065.1,NZ_CP018068.1,NZ_CP018066.1,NZ_CP018067.1,NZ_CP018069.1",Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS),Illumina HiSeq; PacBio,800.0x,SPAdes v. 3.5.0,1,4,5,3208737,37.72,3249,3063,blood,,2010-01-11,Spain,Spain: Madrid,,female,82,Bloodstream infection,,,,,,,,,,,,,"Five ST117 isolates associated with bloodstream (n=4) and urinary tract (n=1) and one ST17 (bloodstream isolate) infections were selected for this study based on their antibiotic susceptibility, virulence/colonization traits and origin (community and hospital)",collected_by:Hospital Ramon y Cajal. Microbiology Department,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1352.1408,Enterococcus faecium strain VRE001,VRE001,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06018903,1352,,,,MLST.Enterococcus_faecium.203,,,,2016-12-09T00:00:00Z,,PRJNA353653,GCF_001895905.1,"CP018071,CP018070,CP018072,CP018073","NZ_CP018071.1,NZ_CP018070.1,NZ_CP018072.1,NZ_CP018073.1",St Jude Children's Research Hospital,PacBio,100.0x,CLC NGS Cell v. October 2014,1,3,4,3242672,37.85,3306,3102,blood,,2013,USA,United States,,,,Bacteremia,,host_health_state:TENNESSEE,,,,,,,,,,,Initial isolate of vancomycin resistant enterococcus faecium from prolonged bloodstream infection.,collected_by:SJCRH,,,,,,,Bacteremia,TENNESSEE,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.14140,Enterococcus faecium NMVRE-001,NMVRE-001,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN23828484,1352,,,,MLST.Enterococcus_faecium.584,,,,2021-12-19T00:00:00Z,,PRJNA787599,GCA_021228615.1,"CP089319,CP089320,CP089321,CP089322,CP089323,CP089324",,,Illumina MiSeq; Oxford Nanopore MinION,60.0x,Unicycler v. 0.4.8,1,5,6,3173447,37.777626,3204,3034,blood,,2021-02,USA,"USA: Chicago, Illinois",,,,"Bacteremia, Intraabdominal Abscess",,,,,,,,,,,,,,collected_by:Clinical Microbiology Laboratory at Northwestern,,,,,,,"Bacteremia, Intraabdominal Abscess",,,,,,,,,,,,,,99.63,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Blood and Circulatory System,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1352.14402,Enterococcus faecium VRE-WC072,VRE-WC072,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN26026626,1352,,,,MLST.Enterococcus_faecium.280,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022691445.1,"CP092569,CP092570,CP092571,CP092572,CP092573",,,Illumina MiSeq and Oxford Nanopore MinION,157x,Unicycler v. 0.4.8,1,4,5,3157285,37.884132,3194,2954,urine,,2004-04-20,USA,USA,,,,UTI,,,,,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1352.14403,Enterococcus faecium VRE-WC084,VRE-WC084,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN26026627,1352,,,,MLST.Enterococcus_faecium.280,,,,2022-03-24T00:00:00Z,,PRJNA808078,GCA_022693745.1,"CP092583,CP092584,CP092585,CP092586",,,Illumina MiSeq and Oxford Nanopore MinION,57x,Unicycler v. 0.4.8,1,3,4,3239747,37.79644,3344,3071,urine,,2004-04-20,USA,USA,,,,UTI,,,,,,,,,,,,,,collected_by:NYS DOH,,,,,,,UTI,,,,,,,patient,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1352.14514,Enterococcus faecium UCH5,UCH5,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN27728132,1352,,,,MLST.Enterococcus_faecium.584,,,,2022-05-02T00:00:00Z,,PRJNA830504,GCA_023204975.1,"CP096219,CP096220,CP096221,CP096222,CP096223,CP096224,CP096225,CP096226",,,Illumina; Oxford Nanopore,247.0x,Unicycler v. 0.5.0,1,7,8,3073918,37.795284,3087,2919,blood,,2019,USA,USA,,,,Enterococcus infection,,,,,,,,,,,,,,collected_by:Bruce McCollister,,,,,,,Enterococcus infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1352.14515,Enterococcus faecium UCH1,UCH1,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN27725314,1352,,,,MLST.Enterococcus_faecium.752,,,,2022-05-02T00:00:00Z,,PRJNA830484,GCA_023204955.1,"CP096211,CP096212,CP096213,CP096214,CP096215,CP096216,CP096217,CP096218",,,Oxford Nanopore; Illumina,225.8x,Unicycler v. 0.5.0,1,7,8,3334275,37.763203,3371,3183,blood,,2019,USA,USA,,,,Enterococcus infection,,,,,,,,,,,,,,collected_by:Bruce McCollister,,,,,,,Enterococcus infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1352.15085,Enterococcus faecium Efaecium_ER04120.3A,Efaecium_ER04120.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679729,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023784,CP023785,CP023786,CP023787,CP023788",,,PacBio,22.31065672x,HGAP v. 2.2.0,1,4,5,3125083,37.81426,3136,3008,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15086,Enterococcus faecium Efaecium_ER03933.3A,Efaecium_ER03933.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679728,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023780,CP023781,CP023782,CP023783",,,PacBio,26.0x,HGAP v. 2.2.0,1,3,4,3078193,37.839863,3074,2957,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15087,Enterococcus faecium Efaecium_ER04484.3A,Efaecium_ER04484.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679731,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023794,CP023795,CP023796,CP023797,CP023798",,,PacBio,25.79616617x,HGAP v. 2.2.0,1,4,5,3127550,37.80755,3132,3011,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15088,Enterococcus faecium Efaecium_ER04462.3A,Efaecium_ER04462.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679730,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023789,CP023790,CP023791,CP023792,CP023793",,,PacBio,31.2611278x,HGAP v. 2.2.0,1,4,5,3122770,37.813736,3133,3007,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15089,Enterococcus faecium Efaecium_ER04619.3A,Efaecium_ER04619.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679734,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023804,CP023805,CP023806,CP023807",,,PacBio,26.13171707x,HGAP v. 2.2.0,1,3,4,3086625,37.83459,3087,2967,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15090,Enterococcus faecium Efaecium_ER04526.5A,Efaecium_ER04526.5A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679733,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023799,CP023800,CP023801,CP023802,CP023803",,,PacBio,28.10666784x,HGAP v. 2.,1,4,5,3126139,37.809258,3130,3011,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15091,Enterococcus faecium Efaecium_ER04526.3A,Efaecium_ER04526.3A,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07679732,1352,not applicable,,not applicable,MLST.Enterococcus_faecium.736,genotype:not applicable,not applicable,,2017-12-28T00:00:00Z,,PRJNA407447,,"CP023808,CP023809,CP023810,CP023811,CP023812",,,PacBio,25.04034924x,HGAP v. 2.2.0,1,4,5,3170042,37.781013,3193,3067,blood,,2015,USA,"USA: New York, NY",,not applicable,not applicable,Bacteremia,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,,collected_by:Icahn School of Medicine at Mount Sinai;specimen_voucher:not applicable,,,,,,,Bacteremia,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.15163,Enterococcus faecium DVT1681,DVT1681,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31742645,1352,,,,MLST.Enterococcus_faecium.17,,,,2022-11-26T00:00:00Z,,PRJNA901969,,"CP112862,CP112863,CP112864,CP112865",,,Illumina; Oxford Nanopore MinION,100.0x,Unicycler v. v0.5.0,1,3,4,3267914,37.70454,3326,3153,clinical,,2019,USA,USA,,,,Clinical,,,,,,,,,,,,,,collected_by:University of Pittsburgh,,,,,,,Clinical,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1352.15589,Enterococcus faecium EF0656,EF0656,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN32302292,1352,,,,MLST.Enterococcus_faecium.80,,,,2022-12-26T00:00:00Z,,PRJNA913624,,"CP114617,CP114618,CP114619,CP114620,CP114621,CP114622,CP114623",,,Illumina HiSeq; PacBio,58.82x,HGAP v. 4; FALCON v. 0.3; Canu v. 0.7,1,6,7,3060378,37.74622,3091,2942,urine,,2022,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Wenfang Tian,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1352.1610,Enterococcus faecium strain ISMMS_VRE_12,ISMMS_VRE_12,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988631,1352,,,,MLST.Enterococcus_faecium.736,,,,2017-01-17T00:00:00Z,,PRJNA292809,GCF_001953235.1,"CP018828,CP018827,CP018825,CP018829,CP018826","NZ_CP018828.1,NZ_CP018827.1,NZ_CP018825.1,NZ_CP018829.1,NZ_CP018826.1",Mount Sinai School of Medicine,PacBio; Illumina,278.48; 196.4,HGAP3 v. v2.2.0,1,4,5,3130591,37.75,3302,3276,blood,,2011-05-05,USA,USA: New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,VRE transmission during a liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,Vancomycin-resistant Enterococcus faecium from an infection of the liver of the donor of a liver transplant,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1611,Enterococcus faecium strain ISMMS_VRE_9,ISMMS_VRE_9,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988627,1352,,,,MLST.Enterococcus_faecium.736,,,,2017-01-17T00:00:00Z,,PRJNA292804,GCF_001953255.1,"CP018830,CP018832,CP018831,CP018834,CP018833","NZ_CP018830.1,NZ_CP018832.1,NZ_CP018831.1,NZ_CP018834.1,NZ_CP018833.1",Mount Sinai School of Medicine,PacBio; Illumina,140.00; 191.57,HGAP3 v. v2.2.0,1,4,5,3126703,37.76,3301,3274,blood,,2011-05-19,USA,USA: New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,VRE transmission during a liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.16255,Enterococcus faecium A2,A2,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN35725530,1352,,,,MLST.Enterococcus_faecium.117,,,,2023-06-21T00:00:00Z,,PRJNA983092,,"CP128188,CP128189",,,PacBio Sequel,10.0x,PBMM2 v. Jun-2021,1,1,2,2913126,37.991318,2844,,blood,,2019-02-02,South Korea,South Korea,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Gangnam Severance Hosapital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1352.1708,Enterococcus faecium strain ISMMS_VRE_1,ISMMS_VRE_1,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988632,1352,,,,,,,,2017-03-22T00:00:00Z,28301471,PRJNA292786,GCA_001720945.1,"CP012430,CP012432,CP012431,CP012435,CP012434,CP012433",,Mount Sinai School of Medicine,PacBio,218,HGAP v. 2014,1,5,6,3259287,37.69,3360,3057,human blood,,2011-05-05,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,Transmission of VRE infection during liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1709,Enterococcus faecium strain ISMMS_VRE_2,ISMMS_VRE_2,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988550,1352,,,,MLST.Enterococcus_faecium.656,,,,2017-03-22T00:00:00Z,28301471,PRJNA292790,GCA_001720965.1,"CP012436,CP012437,CP012439,CP012438",,Mount Sinai School of Medicine,PacBio,104,HGAP v. 2014,1,3,4,3285170,37.64,3415,3041,human blood,,2011-05-05,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,Transmission of VRE in liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,2.7,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1711,Enterococcus faecium strain ISMMS_VRE_4,ISMMS_VRE_4,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988559,1352,,,,MLST.Enterococcus_faecium.412,,,,2017-03-22T00:00:00Z,28301471,PRJNA292795,GCA_001721005.1,"CP012447,CP012450,CP012448,CP012449,CP012451,CP012452,CP012453",,Mount Sinai School of Medicine,PacBio,83,HGAP v. 2014,1,6,7,3223081,37.75,3341,3003,human blood,,2011-05-23,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,Transmission of VRE during a liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1712,Enterococcus faecium strain ISMMS_VRE_5,ISMMS_VRE_5,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988560,1352,,,,MLST.Enterococcus_faecium.736,,,,2017-03-22T00:00:00Z,28301471,PRJNA292797,GCA_001721025.1,"CP012454,CP012455,CP012458,CP012456,CP012457,CP012459",,Mount Sinai School of Medicine,PacBio,181,HGAP v. 2014,1,5,6,3161146,37.73,3232,2942,human blood,,2011-05-23,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,VRE transmission during liver transmission,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1713,Enterococcus faecium strain ISMMS_VRE_7,ISMMS_VRE_7,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988624,1352,,,,MLST.Enterococcus_faecium.736,,,,2017-03-22T00:00:00Z,28301471,PRJNA292801,GCA_001721065.1,"CP012460,CP012461,CP012462,CP012463,CP012464",,Mount Sinai School of Medicine,PacBio,144,HGAP v. 2014,1,4,5,3221354,37.69,3302,3026,human blood,,2011-05-24,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,VRE transmission during liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,2.7,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1714,Enterococcus faecium strain ISMMS_VRE_8,ISMMS_VRE_8,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988626,1352,,,,MLST.Enterococcus_faecium.17,,,,2017-03-22T00:00:00Z,28301471,PRJNA292803,GCA_001721085.1,"CP012465,CP012467,CP012468,CP012466,CP012469,CP012470",,Mount Sinai School of Medicine,PacBio,117,HGAP v. 2014,1,5,6,3415428,37.63,3557,3250,human blood,,2011-05-19,USA,USA:New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,Transmission of VRE during liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.1716,Enterococcus faecium strain ISMMS_VRE_11,ISMMS_VRE_11,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN03988630,1352,,,,MLST.Enterococcus_faecium.18,,,,2017-03-21T00:00:00Z,28301471,PRJNA292807,GCA_001721905.1,"CP016163,CP016164,CP016165,CP016166,CP016167,CP016168,CP016169",,Mount Sinai School of Medicine,PacBio,38.0x,HGAP v. May-2014,1,6,7,3140297,37.77,3247,2997,blood,,2011-05-24,USA,USA: New York City,,,,Enterococcus bacteremia,,,,,,,,,C,,,,VRE transmission during liver transplant,collected_by:Shirish Huprikar,,,,,,,Enterococcus bacteremia,,,,,,,,,,,,,,100,4.4,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.2590,Enterococcus faecium strain K60-39,K60-39,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07638053,1352,,,,MLST.Enterococcus_faecium.192,,,,2017-09-21T00:00:00Z,,PRJNA407052,GCA_002334625.1,"CP023423,CP023424,CP023425,CP023426,CP023427",,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance,PacBio,256.0x,HGAP v. V3,1,4,5,3071612,37.74,3224,3072,blood,,2008,Norway,Norway,,,,bacteremia,,,,,,,,,,,,,The goal is to characterize large plasmids that carry virulence and resistance factors among clinical Enterococcus faecium.,collected_by:Norwegian Monitoring System for Antibiotic Resistance in Microbes,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1352.3591,Enterococcus faecium strain CFSAN059071,CFSAN059071,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06621457,1352,,,,MLST.Enterococcus_faecium.203,,,,2018-04-25T00:00:00Z,,PRJNA243331,GCA_003071445.1,"CP020488,CP020489,CP020490,CP020491",,FDA/CFSAN,PacBio,460x,HGAP v. 3,1,3,4,3152365,37.776337,3167,,urine,,2014-12-05,Denmark,Denmark,,,,,,,,,,,,,,,,,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.;ST203,collected_by:Statens Serum Institut,,,,,,,bacteriuria,,,,,,,,ST203,,,,,,100,0,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,1352.3592,Enterococcus faecium strain CFSAN059070,CFSAN059070,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06621458,1352,,,,MLST.Enterococcus_faecium.203,,,,2018-04-25T00:00:00Z,,PRJNA243331,GCA_003071425.1,"CP020484,CP020485,CP020486,CP020487",,FDA/CFSAN,PacBio,550x,HGAP v. 3,1,3,4,3149315,37.776405,3166,,urine,,2014-10-18,Denmark,Denmark,,,,,,,,,,,,,,,,,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.;ST203,collected_by:Statens Serum Insitut,,,,,,,bacteriuria,,,,,,,,ST203,,,,,,100,0,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,1352.4246,Enterococcus faecium strain RBWH1,RBWH1,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10273305,1352,,,,MLST.Enterococcus_faecium.203,,,,2018-12-21T00:00:00Z,30538186,PRJNA497960,GCA_003957785.1,"CP033206,CP033207,CP033208,CP033209,CP033210,CP033211,CP033212",,University of Melbourne,PacBio,105.0x,PacBio SMRT Pipe v. 2.3.0,1,6,7,3158418,37.949158,3290,3153,urine,,2016,Australia,Australia: Brisbane,,,,Urinary tract infection,,,,,,,,,,,,,Here we report the synergy between ionophore-induced physiological stress in Gram positive bacteria and antibiotic treatment,collected_by:Royal Brisbane Women's Hospital,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.63,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1352.7940,Enterococcus faecium strain V24,V24,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10935273,1352,,,,MLST.Enterococcus_faecium.80,,,,2019-02-26T00:00:00Z,,PRJNA522366,GCA_004302885.1,"CP036151,CP036152,CP036161,CP036153,CP036154,CP036155,CP036156,CP036157,CP036158,CP036159,CP036160",,Hvidovre Hospital,PacBio; Illumina MiSeq,76.0x,SPAdes v. v3.6.2,1,10,11,3172186,37.636776,3336,3196,gastrointestinal tract,,2013-04-15,Denmark,Denmark: Copenhagen,,,,Colonisation in the gastrointestinal tract,,,,,,,,,,,,,"The goal of the study was to close the genome of a vancomycin-resistant E. faecium (VREfm) responsible for a VREfm outbreak in Copenhagen, Denmark",collected_by:Hvidovre Hospital,,,,,,,Colonisation in the gastrointestinal tract,,,,,,,,,,,,,,99.63,0.5,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Genitourinary,Gastrointestinal Diseases-Other Gastrointestinal Diseases NHP,1352.7952,Enterococcus faecium strain NM213,NM213,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10697318,1352,,,,MLST.Enterococcus_faecium.1054,,,,2019-05-06T00:00:00Z,,PRJNA513159,GCA_005166365.1,"CP034949,CP034950,CP034945,CP034946,CP034947,CP034948",,University of Nottingham,Illumina MiSeq,234.0x,clc genomics workbench v. 11.0.1,1,5,6,2857122,37.992638,3033,2892,infant feces,,2012,Egypt,Egypt:Cairo,,,,,,,,,,,,,,,,,Isolation and characterisation of prospective probiotic bacteria from healthy Egyptian infants.,sample_type:whole organism;collected_by:N M Mansour,,,,,,,,,,,,,,,,,,,,,99.63,0.12,,,Gastrointestinal,- HP,1352.8070,Enterococcus faecium strain VB3025,VB3025,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11490474,1352,,,,MLST.Enterococcus_faecium.80,,,,2019-05-20T00:00:00Z,,PRJNA534441,GCA_005517315.1,"CP040236,CP040237,CP040238",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,99.6x,CANU v. 1.7; UNICYCLER HYBRID v. 0.4.6,1,2,3,3209271,37.69233,3452,3222,pus,,2019,India,India,,,,Abscess,,,,,,,,,,,,,Linezolid and vancomycin resistant Enterococcus faecium,collected_by:Christian Medical College,,,,,,,Abscess,,,,,,,,,,,,,,99.63,0.12,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1352.8071,Enterococcus faecium strain VB3240,VB3240,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11633508,1352,,,,MLST.Enterococcus_faecium.17,,,,2019-05-22T00:00:00Z,,PRJNA542561,GCA_005576735.1,"CP040368,CP040369,CP040370,CP040371,CP040372,CP040373",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,136.8x,CANU v. 1.7; UNICYCLER HYBRID v. 0.4.6,1,5,6,3072272,37.76902,3265,3076,pus,,2019,India,India,,,,Abscess,,,,,,,,,,,,,Linezolid and vancomycin resistant Enterococcus faecium,collected_by:Christian Medical College,,,,,,,Abscess,,,,,,,,,,,,,,99.63,0.06,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1352.8079,Enterococcus faecium strain VRE1,VRE1,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11890391,1352,,,,MLST.Enterococcus_faecium.78,,,,2019-06-05T00:00:00Z,,PRJNA545358,GCA_006007925.1,"CP040740,CP040741,CP040743,CP040744,CP040742",,Zhejiang Provincial People's Hospital,Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. v. 0.4.7,1,4,5,3098023,37.75611,3229,3129,urine,,2018-12-03,China,China:Hangzhou,,,,urinary tract infection,,,,,,,,,,,,,Enterococcus faecium VRE1 whole genome sequence,collected_by:Fang He,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.63,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1352.8224,Enterococcus faecium strain 515,515,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12141647,1352,,,,MLST.Enterococcus_faecium.549,,,,2019-07-04T00:00:00Z,,PRJNA551139,GCA_006575625.1,"CP041257,CP041254,CP041256,CP041258,CP041255",,Rice University,PacBio,10.0x,SPAdes v. 2017,1,4,5,3115663,37.71778,3142,,infection,,2015,USA,USA: Houston,,,,endocarditis,,,,,,,,,,,,,Enterococcus faecium with liaR deleted from the genome,collected_by:Amy Prater,,,,,,,endocarditis,,,,,,,,,,,,,,99.63,0,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections NHP,1352.8356,Enterococcus faecium strain 4928STDY7071283,4928STDY7071283,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567393,1352,,,,MLST.Enterococcus_faecium.39,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166385.1,LR607353,,SC,,,,1,,1,2775175,38.619328,2625,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.31,0.02,,,Other,- NHP,1352.8357,Enterococcus faecium strain 4928STDY7071282,4928STDY7071282,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567392,1352,,,,MLST.Enterococcus_faecium.39,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166525.1,LR607349,,SC,,,,1,,1,2774396,38.639885,2610,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.25,0,,,Other,- NHP,1352.8358,Enterococcus faecium strain 4928STDY7071735,4928STDY7071735,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4608481,1352,,,,MLST.Enterococcus_faecium.39,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166655.1,LR607355,,SC,,,,1,,1,2776457,38.652363,2576,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,98.79,0.01,,,Other,- NHP,1352.8359,Enterococcus faecium strain 4928STDY7387800,4928STDY7387800,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694439,1352,,,,MLST.Enterococcus_faecium.361,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166835.1,LR607382,,SC,,,,1,,1,2789811,38.322342,2712,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.62,0,,,Other,- HP,1352.8557,Enterococcus faecium strain V1836,V1836,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12818007,1352,,,,MLST.Enterococcus_faecium.787,,,,2019-09-30T00:00:00Z,,PRJNA573568,GCA_008728455.1,"CP044264,CP044265,CP044266,CP044267,CP044268,CP044269,CP044270,CP044271,CP044272,CP044273",,Copenhagen University Hospital Hvidovre,Illumina MiSeq; Oxford Nanopore MinION,20.0x,Unicycler v. Version 0.4.7,1,9,10,3274751,37.554764,3484,3249,rectum,,2017,Denmark,Denmark:Copenhagen,,,,Infection,,,,,,,,,,,,,The association between vancomycin-resistant Enterococcus faecium colonization and infection: A retrospective WGS study,collected_by:Copenhagen University Hospital Hvidovre,,,,,,,Infection,,,,,,,,,,,,,,99.63,0.56,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.8558,Enterococcus faecium strain V2937,V2937,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN12818041,1352,,,,MLST.Enterococcus_faecium.117,,,,2019-09-30T00:00:00Z,,PRJNA573568,GCA_008728475.1,"CP044274,CP044275,CP044276,CP044277,CP044278,CP044279,CP044280,CP044281,CP044282",,Copenhagen University Hospital Hvidovre,Illumina MiSeq; Oxford Nanopore MinION,69.0x,Unicycler v. Version 0.4.7,1,8,9,3170487,37.813908,3259,3122,rectum,,2018,Denmark,Denmark:Copenhagen,,,,Infection,,,,,,,,,,,,,The association between vancomycin-resistant Enterococcus faecium colonization and infection: A retrospective WGS study,collected_by:Copenhagen University Hospital Hvidovre,,,,,,,Infection,,,,,,,,,,,,,,99.63,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1352.8996,Enterococcus faecium strain VRE,VRE,Enterococcus faecium,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13283502,1352,,,,,genotype:VanA,,,2019-11-23T00:00:00Z,,PRJNA589567,GCA_009697285.1,"CP046077,CP046079,CP046074,CP046075,CP046078,CP046076",,Public Health Agency of Canada,Illumina; Oxford Nanopore MiniION,73.0x,SPAdes v. 1.6,1,5,6,3347130,37.67658,3434,3245,,,2017-08-11,Canada,Canada,,,,BSI,,,,,,,,,,,,,"Enterococcus faecium, ST1478",collected_by:CNISP,,,,,,,BSI,,,,,,,,,,,,,,99.63,0.37,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1353.23,Enterococcus gallinarum strain FDAARGOS_375,FDAARGOS_375,Enterococcus gallinarum,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN07312419,1353,,,,,,FDA:FDAARGOS_375,,2017-09-28T00:00:00Z,,PRJNA231221,GCA_002393265.1,"CP023515,CP023514,CP023513",,US Food and Drug Administration,PacBio; Illumina,15.78x,"SMRT v. 2.3.0, HGAP v. 3",1,2,3,3549293,42.26,3613,3415,tissue grind,,2015-03-28,USA,USA:DC,,female,15Y,Abscess,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Abscess,Missing,Missing,Missing,Missing,,,,,,,,,,99.8,0.5,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,135487.48,Nocardia cyriacigeorgica FMUBM48,FMUBM48,Nocardia cyriacigeorgica,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00548746,135487,,,,,,,,2022-11-16T00:00:00Z,,PRJDB14512,,AP026979,,,MGISEQ; GridION,87.8x,Unicycler v. 0.4.8,1,0,1,6134265,68.46949,5791,5680,clinical sample of a patient suspected with bacterial infection; sputum of a patient suspected with respiratory tract infection,,2008,Japan,Japan,,,,,,,,,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.7,2.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,135487.8,Nocardia cyriacigeorgica strain MDA3349 strain MDA3349 ancestor,MDA3349 ancestor,Nocardia cyriacigeorgica,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08458266,135487,,,,,,,,2018-02-22T00:00:00Z,,PRJNA432572,GCA_002949635.1,"CP026746,CP026745",,Rice University,PacBio; Illumina HiSeq,43.0x,Canu v. 1.4,1,1,2,6462637,68.284355,6114,5803,laboratory,,2016,USA,USA: Texas,,,,nocardiosis,,,,,,,,,,,,,Multiple pathogenic isolates of Nocardia nova and Nocardia cyriageorgica were adapted to trimethoprim-sulfamethoxazole using experimental evolution. Whole genome sequencing was used to identify mutations conferring resistance.,collected_by:Heer Mehta,,,,,,,nocardiosis,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1363.322,Lactococcus garvieae strain LG728,LG728,Lactococcus garvieae,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086910,1363,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309485.1,"CP071285,CP071286,CP071287,CP071288,CP071289",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,4,5,2130387,38.61256,2120,2036,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0.57,,,Gastrointestinal,- NHP,1363.323,Lactococcus garvieae strain LG791,LG791,Lactococcus garvieae,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086911,1363,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309505.1,"CP071290,CP071291,CP071292",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,2,3,2014168,38.669315,2042,1956,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,1363.335,Lactococcus garvieae strain Lg-Granada,Lg-Granada,Lactococcus garvieae,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN21462875,1363,,,,,,,,2021-10-07T00:00:00Z,,PRJNA763925,GCA_020341655.1,"CP084377,CP084378",,University of Valencia,PacBio RSII,380.0x,HGAP v. 3.0; Celera Assembler v. 7.0,1,1,2,2149617,38.62251,2204,,mitral valve,,2015,Spain,Spain: Granada,,male,68,Infective endocarditis,,host_health_state:deceased,,,,,,,,,,,Complete genome of Lactococcus garvieae strain Lg-Granada with pLG50 plasmid,collected_by:Hospital Universitario Virgen de las Nieves,,,,,,,Infective endocarditis,deceased,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections NHP,137591.32,Weissella cibaria strain CMS2,CMS2,Weissella cibaria,Weissella,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN04328345,137591,,,,,,,,2017-01-04T00:00:00Z,16946611,PRJNA305557,GCF_001932695.1,CP013726,NZ_CP013726.1,Oradentics,PacBio,210x,HGAP v. 2,1,,1,2342914,45.32,2117,2104,infant saliva,,2001-11,South Korea,South Korea: Gwangju,,,,,,,,,,,,,C,,,,Genome sequencing helps to provide more genome insights of probiotic properties,sample_type:bacterial,,,,,,,,,,,,,,,,,,,,,100,0.5,,,Oral,- NHP,137591.34,Weissella cibaria strain CMS3,CMS3,Weissella cibaria,Weissella,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN04328350,137591,,,,,,,,2017-01-13T00:00:00Z,16288835,PRJNA305558,GCA_001951095.1,"CP013934,CP013935","NZ_CP013934.1,NZ_CP013935.1",Oradentics,PacBio,225x,HGAP v. 2,1,1,2,2363492,45.26,2147,2129,infant saliva,,2001-11,South Korea,South Korea: Gwangju,env_biome:food;temperature:37,,,,,,,,,,,,C,,,,Genome sequencing helps to provide more genomic insights of probiotic properties,sample_type:bacterial;biomaterial_provider:Oradentics;collected_by:Oradentics;identified_by:Dr. Oh JS,,,,,,,,,,,,,,,,,food,,,,100,0.5,,,Oral,- NHP,137591.37,Weissella cibaria strain CMS1,CMS1,Weissella cibaria,Weissella,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07414780,137591,,,,,,,,2017-08-08T00:00:00Z,,PRJNA395775,GCA_002243305.1,CP022606,,"Oradentics Co., Ltd.",PacBio,353.0x,HGAP v. 3,1,,1,2342849,45.32,2127,2099,infant saliva,,2003,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,To commercialize it as an industrial strain,sample_type:Whole organism;biomaterial_provider:Jongsuk Oh;collected_by:Chonnam National University;identified_by:Misun Kang,,,,,,,,,,,,,,,,,,,,,100,0.5,,,Oral,- HP,139.3242,Borreliella burgdorferi Am293,Am293,Borreliella burgdorferi,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10141357,139,,,,,,,,2023-07-12T00:00:00Z,,PRJNA431102,,"CP124092,CP124090,CP124089,CP124091",,,PacBio RSII,10-12x,HGAP v. HGAP3,1,3,4,1007753,28.418472,950,926,not collected,,2016,,not collected,,,,,,,,,,,,,,,,,,"sample_type:Bacterial isolate;biomaterial_provider:Adriana Marques, Lyme Disease Studies Unit, NIH/NIAID, USA",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,139.3243,Borreliella burgdorferi Am315,Am315,Borreliella burgdorferi,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10141358,139,,,,,,,,2023-07-12T00:00:00Z,,PRJNA431102,,"CP124088,CP124086,CP124085,CP124087",,,PacBio RSII,10-12x,HGAP v. HGAP3,1,3,4,1006503,28.430218,953,924,not collected,,2016,,not collected,,,,,,,,,,,,,,,,,,"sample_type:Bacterial isolate;biomaterial_provider:Adriana Marques, Lyme Disease Studies Unit, NIH/NIAID, USA",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,139.3246,Borreliella burgdorferi Am388,Am388,Borreliella burgdorferi,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10141359,139,,,,,,,,2023-07-12T00:00:00Z,,PRJNA431102,,"CP124084,CP124082,CP124081,CP124083",,,PacBio RSII,10-12x,HGAP v. HGAP3,1,3,4,1007632,28.416327,948,925,not collected,,2016,,not collected,,,,,,,,,,,,,,,,,,"sample_type:Bacterial isolate;biomaterial_provider:Adriana Marques, Lyme Disease Studies Unit, NIH/NIAID, USA",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,139.377,Borreliella burgdorferi strain B500,B500,Borreliella burgdorferi,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18927101,139,,,,,,,,2021-08-09T00:00:00Z,,PRJNA342676,GCA_019464575.1,"CP074054,CP074063,CP074072,CP074059,CP074055,CP074060,CP074061,CP074062,CP074071,CP074065,CP074066,CP074067",,New York Medical College,Illumina MiSeq; PacBio,150.0x,HGAP v. 3,1,18,19,1429304,28.213383,1513,1411,skin,,2000,USA,"USA: New York, Westchester county",,,,Lyme disease,,,,,,,,,,,,,Whole genome sequencing of clinical isolates of Borrelia burgdorferi,collected_by:New York Medical College,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Skin and Soft Tissue,Specific Bacterial Infections-Lyme Disease HP,1392.1029,Bacillus anthracis PNO2,PNO2,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN25416578,1392,,,,MLST.Bacillus_cereus.1,,,,2022-02-06T00:00:00Z,,PRJNA801913,GCA_022014755.1,"CP091762,CP091763,CP091764",,,PacBio Sequel; Illumina NovaSeq,890.0x,Canu v. 1.6; pilon v. 1.22,1,2,3,5505963,35.246586,5992,5609,,,1935,China,China: Beijing,,,,Anthrax,,,,,,,,,,,,,,collected_by:Shoushen Yang,,,,,,,Anthrax,,,,,,derived from Pasteur II which was introduced into China from the Pasteur Institute in France in 1934,,,,,,,,99.23,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1031,Bacillus anthracis ChBA30D,ChBA30D,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN25419190,1392,,,,MLST.Bacillus_cereus.1,,,,2022-02-06T00:00:00Z,,PRJNA801920,GCA_022014795.1,"CP091767,CP091768",,,PacBio Sequel; Illumina NovaSeq,470.0x,Canu v. 1.6; pilon v. 1.22,1,1,2,5323031,35.33825,5789,5447,missing,,1965,China,China: Heibei province,,,,Anthrax,,,,,,,,,,,,,,collected_by:the Institute of Lanzhou Biological Products,,,,,,,Anthrax,,,,,,,,,,,,,,99.23,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1047,Bacillus anthracis A178,A178,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN13164747,1392,,,,MLST.Bacillus_cereus.1,,,,2022-02-14T00:00:00Z,35076271,PRJNA695105,GCA_022220985.1,"CP076173,CP076174,CP076175",,,Illumina MiSeq; Oxford Nanopore GridION,62x,flye; unicycler v. 2.7; 0.4.8,1,2,3,5501188,35.24915,5951,5595,not applicable,,2008,France,France: Moselle (Lorraine),,,,Anthrax,,,,,,,,,,,,,,collected_by:P. Goosens,,,,,,,Anthrax,,,,,,,,,,,,,,99.2,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1050,Bacillus anthracis A27,A27,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN13164726,1392,,,,MLST.Bacillus_cereus.1,,,,2022-02-14T00:00:00Z,35076271,PRJNA695105,GCA_022221045.1,"CP076181,CP076182,CP076183",,,Illumina MiSeq; Oxford Nanopore GridION,80x,flye; unicycler v. 2.7; 0.4.8,1,2,3,5506783,35.24702,5954,5611,not applicable,,,Germany,Germany: Giessen,,,,Anthrax,,,,,,,,,,,,,,collected_by:W. Beyer,,,,,,,Anthrax,,,,,,,,,,,,,,99.23,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1053,Bacillus anthracis UR-1,UR-1,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN18241472,1392,,,,MLST.Bacillus_cereus.1,,,,2022-02-14T00:00:00Z,35076271,PRJNA695105,GCA_022221125.1,"CP076192,CP076193,CP076194",,,Illumina MiSeq; Oxford Nanopore GridION,76x,flye; unicycler v. 2.7; 0.4.8,1,2,3,5506410,35.24596,5959,5612,missing,,2012,Germany,Germany,,,,anthrax,,,,,,,,,,,,,,"collected_by:University Hospital, Regensburg",,,,,,,anthrax,,,,,,,,,,,,,,99.23,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1064,Bacillus anthracis Vollum,Vollum,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN18241461,1392,,,,MLST.Bacillus_cereus.1,,ATCC:14578,,2022-02-14T00:00:00Z,35076271,PRJNA695105,GCA_022221345.1,"CP076225,CP076226,CP076227",,,Illumina MiSeq; Oxford Nanopore GridION,97x,flye; unicycler v. 2.7; 0.4.8,1,2,3,5506524,35.24701,5957,5597,missing,,1951,USA,USA,,,,anthrax,,,,,,,,,,,,,,,,,,,,,anthrax,,,,,,,,,,,,,,99.23,0.15,Specific Bacterial Infections,anthrax,Other,Specific Bacterial Infections-anthrax HP,1392.1278,Bacillus anthracis BHY1401,BHY1401,Bacillus anthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN35323095,1392,,,,MLST.Bacillus_cereus.1,,,,2023-06-05T00:00:00Z,,PRJNA975313,,"CP126463,CP126464,CP126465",,,PacBio Sequel; Illumina NovaSeq,456.0x,Canu v. 1.6,1,2,3,5504346,35.245804,6000,5618,skin eschar,,2021-06-12,China,China:Hongyuan,,,,skin disease,,,,,,,,,,,,,,collected_by:Dongshu Wang,,,,,,,skin disease,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,140.38,Borrelia hermsii ML2,ML2,Borrelia hermsii,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN21374108,140,,,,,,,,2021-10-12T00:00:00Z,,PRJNA762107,,"CP084623,CP084624",,,Oxford Nanopore MinION; Illumina HiSeq,1000.0x,CLC NGS Cell v. 21.04,1,1,2,1104639,30.036963,1045,1001,mountain cabin,,2018-08-03,USA,"USA: Mono Co., CA",,,adult,relapsing fever,,host_disease_outcome:recovered;host_disease_stage:relapse of fever,,,,,,,,,,,,collected_by:Saahir Khan,,,,,,,relapsing fever,,recovered,,relapse of fever,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,140.41,Borrelia hermsii ML2,ML2,Borrelia hermsii,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN21374108,140,,,,,,,,2021-10-12T00:00:00Z,,PRJNA762107,GCA_020422925.2,"CP084623,OL311417,CP084624",,,Oxford Nanopore MinION; Illumina HiSeq,1000.0x,CLC NGS Cell v. 21.04,1,2,3,1161689,30.068632,1110,1059,mountain cabin,,2018-08-03,USA,"USA: Mono Co., CA",,,adult,relapsing fever,,host_disease_outcome:recovered;host_disease_stage:relapse of fever,,,,,,,,,,,,collected_by:Saahir Khan,,,,,,,relapsing fever,,recovered,,relapse of fever,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1402.452,Bacillus licheniformis strain KS28,KS28,Bacillus licheniformis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN12501148,1402,,,,,,,,2020-09-21T00:00:00Z,,PRJNA558883,GCA_014672855.1,CP043490,,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,181.0x,SPAdes v. 3.1,1,0,1,4384483,45.813587,5556,4481,blood,,2016-06,South Korea,South Korea,,,,Absorbent pulmonary edema,,,,,,,,,,,,,A clinical isolate of Bacillus licheniformis,collected_by:Gyeongsang National University,,,,,,,Absorbent pulmonary edema,,,,,,,,,,,,,,97.37,0,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases NHP,1408.387,Bacillus pumilus strain UAMX,UAMX,Bacillus pumilus,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN15498547,1408,,,,,,,,2020-07-19T00:00:00Z,27018166,PRJNA645214,GCA_013423765.1,CP058951,,Universidad Autonoma Metropolitana,PacBio RSII,2.0x,CANU v. 1.8,1,0,1,3854893,41.70772,4046,3850,feces,,2005-01-01,Mexico,Mexico,,,,,,,,,,,,,,,,,The aim of this study is know role of Bacillus pumilus on gut human microbiota.Actualy Bacillus genus is not considerated that part of normal gut human microbiota. We want know influence of Bacillus over gut human microbiota.,sample_type:SINGLE STRAIN,,,,,,,,,,,,,,,,,,,,,99.59,0.62,,,Gastrointestinal,- HP,1431450.3,Helicobacter pylori PMSS1 strain PMSS1,PMSS1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN04362855,1431450,,,Type I cagPAI positive,MLST.Helicobacter_pylori.31,,,,2017-02-10T00:00:00Z,,PRJNA306775,GCF_001991095.1,"CP018823,CP018824","NZ_CP018823.1,NZ_CP018824.1","University of California, Davis","PacBio, HiSeq",>500x,SMRT Analysis pipeline (HGAP & QUIVER) v.,1,1,2,1624538,39.01,1605,1462,stomach; gastric tissue biopsy,,1994,Australia,Australia: Sydney,,,,Duodenal ulcer,,host_description:Greek immigrant with family history of peptic ulcer disease,,,,,,Mesophilic,37 C,Microaerophilic,HostAssociated,Duodenal ulcer,"Characterization of the genome for H. pylori PMSS1, which is commonly used in animal models of infection",collected_by:Adrian Lee,,,,,,,Duodenal ulcer,,,Greek immigrant with family history of peptic ulcer disease,,Type I cagPAI positive,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,143221.89,Salmonella enterica subsp. enterica serovar Tennessee strain CFSAN076210,CFSAN076210,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10272908,143221,Tennessee,,,MLST.Salmonella_enterica.319,,,,2018-11-03T00:00:00Z,,PRJNA186035,GCA_003710185.1,"CP033345,CP033346",,Center for Food Safety and Applied Nutrition,PacBio,169x,HGAP v. 3,1,1,2,4943973,52.14365,5104,4890,patient in 2006 peanut associated outbreak,,,USA,United States,,,,,,,,,,,,,,,,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,100,0.42,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1433513.3,Streptococcus sp. ChDC B345 strain KCOM 1679 (=ChDC B345),KCOM 1679 (=ChDC B345),Streptococcus gwangjuense,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10135937,1433513,,,,,,KCOM:1679,,2018-10-07T00:00:00Z,,PRJNA493538,GCA_003627155.1,CP032621,,Korean Collection for Oral Microbiology,PacBio; Illumina HiSeq,639.3x,RS HGAP v. 3.0; SPAdes v. 3.8.2,1,,1,1972481,40.20216,1937,1917,pericoronitis,,2002-03-25,Korea,Korea: Gwangju,,,,Pericoronitis,,,,,,,,,,,,,Genome sequencing of Streptococcus sp. KCOM 1679 (=ChDC B345),collected_by:Korean Collection for Oral Microbiology,,,,,,,Pericoronitis,,,,,,,,,,,,,,99.82,0.28,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,143387.62,Fusobacterium necrophorum subsp. funduliforme strain F1291,F1291,Fusobacterium necrophorum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN06055349,143387,,,,,,,,2018-11-15T00:00:00Z,,PRJNA354964,GCA_003732505.1,CP018196,,Aarhus University,PacBio,281.0x,HGAP v. 2,1,,1,2135983,35.267696,2080,1987,blood,,1998,Denmark,Denmark,,,,Lemierre's syndrome,,,,,,,,,,,,,Closed genome of a human strain of Fusobacterium necrophorum subsp. funduliforme,collected_by:Lena Hagelskjaer Kristensen,,,,,,,Lemierre's syndrome,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases HP,143387.63,Fusobacterium necrophorum subsp. funduliforme strain F1260,F1260,Fusobacterium necrophorum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN06234847,143387,,,,,,,,2018-11-15T00:00:00Z,,PRJNA354964,GCA_003732525.1,CP019306,,Aarhus University,PacBio,300.0x,HGAP v. 3,1,,1,2288480,35.214333,2336,2219,blood,,2000,Denmark,Denmark,,,,Lemierre's syndrome,,,,,,,,,,,,,Closed genome of a human strain of Fusobacterium necrophorum subsp. funduliforme,collected_by:Lena Hagelskjaer,,,,,,,Lemierre's syndrome,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases HP,144549.4,Mycolicibacterium fortuitum subsp. fortuitum JCM6387,JCM6387,Mycolicibacterium fortuitum,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00436749,144549,,,,,,JCM:6387,,2022-01-28T00:00:00Z,,PRJDB12810,GCA_022179545.1,AP025518,,,ONT MinION; Illumina MiniSeq,200x,Canu v. 2.2,1,0,1,6406072,66.192665,6218,6171,,,1987,,not applicable,,,,,,,,,,,,,,,,,,,not applicable,not applicable,not applicable,not applicable,"Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum JCM 6837T, a type strain of human pathogenic mycobacteria showing inducible macrolide resistance.",,,,,,,,,,,,not applicable,,,,99.81,1.26,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1446600.3,Escherichia coli O15:H18 ST69,ST69,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30184957,1446600,O15:H18,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2022-08-15T00:00:00Z,,PRJNA867133,GCA_024662075.1,"CP102488,CP102489",,,Illumina iSeq; Oxford Nanopore MinION,150.0x,Unicycler v. 0.5.0,1,1,2,5437935,50.672085,5509,5178,cerebrospinal fluid,,2020-09-28,Italy,Italy: Bologna,,male,,Escherichia coli infection,,,,,,,,,,,,,,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,Escherichia coli infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1463164.100,Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603,ATCC 700603,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245763,1463164,ST498,,,MLST.Klebsiella_pneumoniae.489,,ATCC:700603,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181175.1,"CP029597,CP029598,CP029599",,Uppsala University,PacBio; Illumina HiSeq 2000,50.0x,CLC Genomics workbench v. 11.0.1,1,2,3,5514898,57.733723,5576,5456,urine,,1994,USA,"USA: Richmond, VA",,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1463164.187,Klebsiella quasipneumoniae subsp. similipneumoniae strain 12A476,12A476,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024807,1463164,,,,MLST.Klebsiella_pneumoniae.384,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525525.1,"CP084779,CP084780,CP084781,CP084782",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,3,4,5482753,57.760635,5382,5228,blood,,1998,,Netherlands,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,99.99,0.97,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1463164.188,Klebsiella quasipneumoniae subsp. similipneumoniae strain 09A323,09A323,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024806,1463164,,,,MLST.Klebsiella_pneumoniae.414,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525585.1,"CP084783,CP084784,CP084785,CP084786",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,3,4,5449678,57.734734,5351,5192,blood,,1997,,Greece,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.29,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1463164.190,Klebsiella quasipneumoniae subsp. similipneumoniae strain 07A044T,07A044T,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024805,1463164,,,,MLST.Klebsiella_pneumoniae.1215,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525685.1,"CP084787,CP084788",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5189735,58.128365,5031,4915,blood,,1997,,Germany,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,99.99,0.37,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1463165.1007,Klebsiella quasipneumoniae M7,M7,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34510250,1463165,,,,,,,,2023-05-16T00:00:00Z,,PRJNA965942,,"CP124866,CP124867,CP124868,CP124869,CP124870,CP124871,CP124872",,,Illumina; Oxford Nanopore,150.0x,SPAdes v. v3.15.5,1,6,7,5443711,57.621887,5391,5195,urine,,,Singapore,Singapore,,,,Bacterial infection,,,,,,,,,,,,,,collected_by:National University of Singapore Hospital,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1463165.315,Klebsiella quasipneumoniae strain N18-04101,N18-04101,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506050,1463165,,,,,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189245.1,"CP047281,CP047282",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,48.0x,Unicycler v. 0.4.7,1,1,2,5494076,57.667786,5413,5213,rectum,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,99.98,0.48,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1463165.317,Klebsiella quasipneumoniae strain N18-04116,N18-04116,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506065,1463165,,,,,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189265.1,"CP047283,CP047284",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,51.0x,Unicycler v. 0.4.7,1,1,2,5298079,57.825695,5175,4972,anal,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,99.99,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1463165.409,Klebsiella quasipneumoniae strain KqPF9,KqPF9,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016746,1463165,,,,,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016066695.1,"CP065841,CP065842,CP065843,CP065844,CP065845",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","359x, 153x",Unicycler v. v.0.4.8,1,4,5,5685062,57.352108,5675,5431,urine,,2018-05,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,1.41,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1463165.411,Klebsiella quasipneumoniae strain KqPF26,KqPF26,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016750,1463165,,,,,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016415705.1,"CP065838,CP065839,CP065840",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","271x, 39x",Unicycler v. v.0.4.8,1,2,3,5391123,57.847687,5269,5098,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,99.99,0.14,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1463165.420,Klebsiella quasipneumoniae strain KqPF42,KqPF42,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016751,1463165,,,,MLST.Klebsiella_pneumoniae.1535,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016510335.1,"CP065846,CP065847",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","420x, 147x",Unicycler v. v.0.4.8,1,1,2,5502071,57.70131,5427,5227,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,99.99,0.94,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,1463165.454,Klebsiella quasipneumoniae strain B2663,B2663,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17911902,1463165,,,,MLST.Klebsiella_pneumoniae.196,,,,2021-02-24T00:00:00Z,,PRJNA701805,GCA_016925255.1,"CP070420,CP070421,CP070422,CP070423,CP070424",,Christian Medical College,Illumina; Oxford Nanopore,101.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5604444,57.898376,5545,5310,blood,,2015,India,India: Vellore,,,,Bacteremia,,,,,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B2663,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,99.99,0.63,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1463165.456,Klebsiella quasipneumoniae strain B25110,B25110,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17915108,1463165,,,,MLST.Klebsiella_pneumoniae.196,,,,2021-02-24T00:00:00Z,,PRJNA701850,GCA_016925395.1,"CP070454,CP070455,CP070456,CP070457,CP070458",,Christian Medical College,Illumina; Oxford Nanopore,106.0x,Canu v. 1.8,1,4,5,5603348,57.89935,5539,5308,blood,,2014,India,India: Vellore,,,,Bacteremia,,,,,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B25110,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,99.99,0.63,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1463165.466,Klebsiella quasipneumoniae strain B6885,B6885,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18478622,1463165,,,,MLST.Klebsiella_pneumoniae.196,,,,2021-04-04T00:00:00Z,,PRJNA717120,GCA_017743035.1,"CP072468,CP072469,CP072470,CP072471,CP072472",,Christian Medical College,Illumina; Oxford Nanopore,93.65x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,5604518,57.898483,5547,5309,blood,,2015,India,India: Vellore,,,,Bacteremia,,,,,,,,,,,,,Complete genome sequencing of K. quasipneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,99.99,0.63,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1463165.484,Klebsiella quasipneumoniae strain JNQH473,JNQH473,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19186366,1463165,,,,MLST.Klebsiella_pneumoniae.571,,,,2021-06-01T00:00:00Z,,PRJNA702614,GCA_018604125.1,"CP075885,CP075884,CP075888,CP075886,CP075887",,The First Affiliated Hospital of Shandong First Medical University,Illumina NovaSeq; Oxford Nanopore MinION,200x,Flye v. 2.8.3; SPAdes v. 3.14,1,4,5,6035238,57.112114,6093,5779,urine,isolated from China,2019-08,China,China: Xiamen,,,,uninary infection,,,,,,,,,,,,,"The studies are aimed at determining the characteristics of epidemiology, antimicrobial resistance and pathogenicity for carbapenem resistant enterobacteriaceae, especially for strains isolated from China.",collected_by:Bo Zhu,,,,,,,uninary infection,,,,,,,,,,,,,,100,0.8,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1463165.70,Klebsiella quasipneumoniae strain ATCC 700603,ATCC 700603,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03996259,1463165,,,ESBL,MLST.Klebsiella_pneumoniae.489,,ATCC:700603,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002953295.1,"CP014071,CP014072,CP014073",,US Food and Drug Administration,PacBio; Illumina,25.45x,Celera v. 8.2,1,2,3,5513032,57.73627,5572,5451,urine,,1994,USA,USA:VA,,,,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC <-- JM Swenson <-- MJ Ferraro <-- G Jacoby <-- H Dalton,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,ESBL,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,1463165.707,Klebsiella quasipneumoniae NKP7,NKP7,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24972760,1463165,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028975.1,CP091825,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5158670,58.34838,4915,4692,blood,,2020-11-20,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.79,0.29,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1463165.74,Klebsiella quasipneumoniae strain KPC142,KPC142,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06767172,1463165,,,,,,,,2018-03-27T00:00:00Z,,PRJNA383559,GCA_003020825.1,"CP023478,CP023479,CP023480",,LNCC,Illumina MiSeq,115.0x,Newbler v. 3.0,1,2,3,5418654,57.59541,5268,4945,tracheal secretion isolated from an uncertain age woman,,2011,Brazil,"Brazil: City of Belo Horizonte, State of Minas Gerais",,,,,,,,,,,,,,,,,Whole genome sequencing of carbapenem-resistant Klebsiella quasipneumoniae isolate recovered after nosocomial infections in the Brazilian southeast region.,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.7,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1463165.76,Klebsiella quasipneumoniae strain CAV2013,CAV2013,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09205469,1463165,,,,MLST.Klebsiella_pneumoniae.196,,,,2018-05-22T00:00:00Z,,PRJNA411762,GCA_003146655.1,"CP029437,CP029435,CP029433,CP029434,CP029436",,Oxford University,PacBio,124x,HGAP v. MAY-2015,1,4,5,6084196,57.317616,6288,6061,peri-rectal,,2013-11-01,USA,USA:Virginia,,,,,,,,,,,,,,,,,A collection of Gammaproteobacteria isolated from environmental and patient sources originating from a single hospital in the United States,collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,Not Applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1463165.773,Klebsiella quasipneumoniae EF262,EF262,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26096228,1463165,,,,,,,,2022-06-27T00:00:00Z,,PRJNA473419,GCA_023920245.1,"CP092512,CP092513,CP092514,CP092516,CP092517,CP092518,CP092515",,,Illumina MiniSeq; Oxford Nanopore,53.0x,Unicycler hybrid assembly v. 0.4.8,1,6,7,5638936,57.541637,5630,5425,hvs,,2018,Ghana,Ghana,,,,UTI,,,,,,,,,,,,,,collected_by:ENRH_Hospital staff,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,1463165.82,Klebsiella quasipneumoniae strain L22,L22,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09708445,1463165,K1,,,MLST.Klebsiella_pneumoniae.367,,,,2018-09-04T00:00:00Z,,PRJNA482505,GCA_003443835.1,"CP031257,CP031258,CP031259,CP031260,CP031261,CP031262",,Peking University People 's Hospital,PacBio,106.0x,HGAP v. SMRT Link v5.1.0,1,5,6,5631032,57.198166,5545,,bronchoalveolar lavage fluid,,2014-09-02,China,China,,male,70y,pneumoniae,,host_disease_outcome:death,,,,,,,,,,,research Klebsiella quasipneumoniae Genome,collected_by:Yatao Guo,,,,,,,pneumoniae,,death,,,,,,,,,,,,100,0.7,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia NHP,147206.16,Collinsella stercoris strain DSM 13279,DSM 13279,Collinsella stercoris,Collinsella,Coriobacteriaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMN20222685,147206,,,,,,DSM:13279,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149625.1,CP102276,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2460746,63.349693,2249,2030,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- NHP,147802.102,Lactobacillus iners strain KY,KY,Lactobacillus iners,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN13943229,147802,,,,,,,,2020-02-19T00:00:00Z,,PRJNA603871,GCA_010748955.1,CP048798,,Seoul National Univerisity,Oxford Nanopore Flongle,165.87x,Guppy v. 3.4.3; Porechop v. 0.2.4; CANU,1,0,1,1339101,33.352303,1422,1218,vaginal flora,,2019-05-15,South Korea,South Korea:Daejeon,,,,,,,,,,,,,,,,,Lactobacillus iners is one of the main vaginal Lactobacillus species. The goal of this study is constructing the first complete genome of Lactobacillus iners.,sample_type:single isolated culture;biomaterial_provider:Kim Tae Hyun;identified_by:Hyaekang Kim,,,,,,,,,,,,,,,,,,,,,98.03,0.44,,,Genitourinary,- NHP,147802.103,Lactobacillus iners strain C0322A1,C0322A1,Lactobacillus iners,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN14165694,147802,,,,,,,,2020-03-03T00:00:00Z,,PRJNA608123,GCA_011058775.1,CP049230,,University of Maryland Baltimore,PacBio Sequel II,2000x,Canu v. 1.8,1,0,1,1318700,33.085766,1229,1210,vagina; mid-vagina,isolated from vaginal swab specimens,2019,USA,USA: Baltimore,,,,,,,,,,,,,,,,,Lactobacillus iners is a frequent member of the human vaginal microbiota and has a reduced genome. We sequenced the genomes of six Lactobacillus iners strains isolated from vaginal swab specimens. Three of the strains were further found to harbor plasmids.,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.41,0.44,,,Genitourinary,- NHP,147802.106,Lactobacillus iners strain C0059G1,C0059G1,Lactobacillus iners,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN14165697,147802,,,,,,,,2020-03-03T00:00:00Z,,PRJNA608123,GCA_011058715.1,CP049225,,University of Maryland Baltimore,PacBio Sequel II,2000x,Canu v. 1.8,1,0,1,1379123,33.269695,1302,1277,vagina; mid-vagina,isolated from vaginal swab specimens,2019,USA,USA: Baltimore,,,,,,,,,,,,,,,,,Lactobacillus iners is a frequent member of the human vaginal microbiota and has a reduced genome. We sequenced the genomes of six Lactobacillus iners strains isolated from vaginal swab specimens. Three of the strains were further found to harbor plasmids.,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.41,0.44,,,Genitourinary,- NHP,147802.108,Lactobacillus iners strain C0254C1,C0254C1,Lactobacillus iners,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN14165693,147802,,,,,,,,2020-03-03T00:00:00Z,,PRJNA608123,GCA_011058795.1,CP049231,,University of Maryland Baltimore,PacBio Sequel II,2000x,Canu v. 1.8,1,0,1,1314822,33.01656,1258,1230,vagina; mid-vagina,isolated from vaginal swab specimens,2019,USA,USA: Baltimore,,,,,,,,,,,,,,,,,Lactobacillus iners is a frequent member of the human vaginal microbiota and has a reduced genome. We sequenced the genomes of six Lactobacillus iners strains isolated from vaginal swab specimens. Three of the strains were further found to harbor plasmids.,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.41,0.44,,,Genitourinary,- HP,148942.549,Streptococcus equi subsp. equi strain NCTC12091,NCTC12091,Streptococcus equi,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3572409,148942,not available: to be reported later,,,MLST.Streptococcus_zooepidemicus.212,,NCTC:12091,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900636415.1,LR134273,,SC,,,,1,,1,2081938,41.578663,2077,1881,blood culture,,1987,United Kingdom,United Kingdom: Northallerton,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1491.1045,Clostridium botulinum strain CFSAN034200,CFSAN034200,Clostridium botulinum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN03769220,1491,,,,MLST.Clostridium_botulinum.7,,,,2018-07-30T00:00:00Z,,PRJNA243331,GCA_003345335.1,"CP031097,CP031095,CP031096",,FDA/CFSAN,Illumina MiSeq; Oxford Nanopore Minion,85.0x,Canu v. 1.7; SPAdes v. 3.11.1,1,2,3,4202171,28.068205,4220,4059,missing,,,,,,,,,,,,,,,,,,,,,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1491.1811,Clostridium botulinum strain IBCA10-7060,IBCA10-7060,Clostridium botulinum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN17763437,1491,BH,,,MLST.Clostridium_botulinum.87,,,,2021-02-09T00:00:00Z,24106295,PRJNA698972,GCA_016838665.1,CP069280,,California Dept. of Public Health,Oxford Nanopore MinION; Illumina MiSeq,200.0x,Trycycler v. OCT-2020,1,0,1,4090796,28.151587,4041,3843,infant stool,,2010,USA,USA:CA,,,,Infant Botulism,,,,,,,,,,,,,Closed genome of dual-toxin-producing (bivalent) Clostridium botulinum strain IBCA10-7060 type Bh. IBCA10-7060 is the only Clostridium botulinum strain known that produces botulinum toxin type H.,collected_by:CDPH/IBTPP,,,,,,,Infant Botulism,,,,,,,,,,,,,,99.31,0.69,Specific Bacterial Infections,Botulism,Gastrointestinal,Specific Bacterial Infections-Botulism HP,1491.2402,Clostridium botulinum FE9504ACG,FE9504ACG,Clostridium botulinum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN21169058,1491,A,,,MLST.Clostridium_botulinum.6,,,,2022-08-08T00:00:00Z,,PRJNA759433,GCA_024584665.1,CP096041,,,Illumina MiSeq; Oxford Nanopore MinION,380.0x,Unicycler v. v0.4.8,1,0,1,4086687,28.14593,3880,3717,fecal sample from infant botulism case,,1995,Canada,Canada,,,,infant botulism,,host_description:infant,,,,,,,,,,,,collected_by:Health Canada - Bureau of Microbial Hazards,,,,,,,infant botulism,,,infant,,,,,,,,,,,100,0.4,Specific Bacterial Infections,Botulism,Gastrointestinal,Specific Bacterial Infections-Botulism HP,1491.2647,Clostridium botulinum FE9508BRB,FE9508BRB,Clostridium botulinum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN25937291,1491,B,,,,,,,2023-02-02T00:00:00Z,,PRJNA806856,,"CP102913,CP102914,CP102915,CP102916",,,Illumina MiSeq; Oxford Nanopore MinION,265x,Trycycler v. 0.3.3,1,3,4,4180934,28.05232,4115,3920,fecal sample from botulism case,,1995-11-09,Canada,Canada,,,,botulism,,,,,,,,,,,,,,collected_by:Health Canada - Bureau of Microbial Hazards,,,,,,,botulism,,,,,,,,,,,,,,100,0.4,Specific Bacterial Infections,Botulism,Gastrointestinal,Specific Bacterial Infections-Botulism HP,1491.2649,Clostridium botulinum FE9508BPD,FE9508BPD,Clostridium botulinum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN25937292,1491,B,,,,,,,2023-02-02T00:00:00Z,,PRJNA806856,,"CP102909,CP102910,CP102911,CP102912",,,Illumina MiSeq; Oxford Nanopore MinION,225x,Unicycler v. 0.4.8,1,3,4,4180934,28.05232,4115,3920,fecal sample from botulism case,,1995-11-09,Canada,Canada,,,,botulism,,,,,,,,,,,,,,collected_by:Health Canada - Bureau of Microbial Hazards,,,,,,,botulism,,,,,,,,,,,,,,100,0.4,Specific Bacterial Infections,Botulism,Gastrointestinal,Specific Bacterial Infections-Botulism HP,1492.178,Clostridium butyricum strain CFSA3987,CFSA3987,Clostridium butyricum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN10285205,1492,,,,,,,,2019-11-12T00:00:00Z,,PRJNA498210,GCA_009650315.1,"CP033247,CP033246",,CFSA,PacBio RSII,163.19x,HGAP v. 27-Dec-2017,1,1,2,4746849,28.807636,4331,4144,stool,,2017,China,China,,,,,,,,,,,,,,,,,To confirm the relationship between the bacteria and disease.,,,,,37C,,,,,,,,,,,,,stool,,,,99.19,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1492.266,Clostridium butyricum CFSA-TJ-E,CFSA-TJ-E,Clostridium butyricum,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN14908714,1492,,,,,,,,2022-07-25T00:00:00Z,,PRJNA632418,GCA_024399875.1,"CP053374,CP053375",,,PacBio RSII,251.0x,HGAP v. Jan-2020,1,1,2,4697138,28.713783,4303,4183,stool from infant,,2019-09,China,China,,,,botulism,,,,,,,,,,,,,,collected_by:China national center for food safety risk assessment,,,,,,,botulism,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Botulism,Gastrointestinal,Specific Bacterial Infections-Botulism HP,149388.4,Salmonella enterica subsp. enterica serovar Mikawasima strain RSE15,RSE15,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10638899,149388,Mikawasima,,,MLST.Salmonella_enterica.2030,,,,2019-01-06T00:00:00Z,,PRJNA510422,GCA_003994575.1,"CP034713,CP034714",,Pennsylvania State University,IonTorrent & Oxford Nanopore MiniION,131x,Unicycler v. 0.4.7,1,1,2,4777004,52.254154,5046,4675,hospital,,2018-02-19,Rwanda,Rwanda:Rulindo,,female,,gastroenteritis,,,,,,,,,,,,,Complete genome sequencing of Salmonella isolates from Rwanda,collected_by:Maurice Byukusenge,,,,,,,gastroenteritis,,,,,,,,,,,,,,99.37,0.73,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,149388.5,Salmonella enterica subsp. enterica serovar Mikawasima strain RSE13,RSE13,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10638897,149388,Mikawasima,,,MLST.Salmonella_enterica.2030,,,,2019-01-06T00:00:00Z,,PRJNA510422,GCA_003994595.1,CP034715,,Pennsylvania State University,IonTorrent & Oxford Nanopore MiniION,81x,Unicycler v. 0.4.7,1,,1,4649621,52.29394,5023,4518,hospital,,2018-02-19,Rwanda,Rwanda:Rulindo,,female,,gastroenteritis,,,,,,,,,,,,,Complete genome sequencing of Salmonella isolates from Rwanda,collected_by:Maurice Byukusenge,,,,,,,gastroenteritis,,,,,,,,,,,,,,98.41,0.58,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,149390.29,Salmonella enterica subsp. enterica serovar London N18-04674,N18-04674,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20990803,149390,London,,,MLST.Salmonella_enterica.155,genotype:OXA-48,,,2022-10-11T00:00:00Z,,PRJNA758050,GCA_025643195.1,"CP082929,CP082930,CP082932,CP082933,CP082934,CP082935,CP082931",,,Illumina NextSeq; Oxford Nanopore MinION,79.0x,Unicycler v. 2020-01-18,1,6,7,4916758,52.091255,5007,4649,stool,,2018,Canada,Canada,,,,Salmonellosis,,,,,,,,,,,,,,collected_by:Public Health Agency of Canada,,,,,,,Salmonellosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,149539.1428,Salmonella enterica subsp. enterica serovar Enteritidis strain RM4283,RM4283,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768800,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2018-06-04T00:00:00Z,,PRJNA443261,GCA_003184325.1,"CP028157,CP028156,CP028155",,"United States Department of Agriculture, Agricultural Research Service",PacBio; Illumina MiSeq,195.0x,HGAP v.3 as available in the SMRT,1,2,3,4785531,52.007164,5008,4799,feces,isolated from a patient in British Columbia during the 2001 outbreak associated with consumption of raw almonds,2001-04,Canada,Canada: Vancouver,,,,gasteroenteritis,,,,,,,,,,,,,Salmonella enterica subsp. enterica serovar Enteritidis str. RM4283.This strain is phage type 30 (PT30) and was isolated from a patient in British Columbia during the 2001 outbreak associated with consumption of raw almonds.,"collected_by:BC Centre for Disease Control, Vancouver, Canada",,,,,,,gasteroenteritis,,,,,,,,,,,,,,99.7,0.5,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.1432,Salmonella enterica subsp. enterica serovar Enteritidis strain FORC_075,FORC_075,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07580859,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2018-08-28T00:00:00Z,,PRJNA400838,GCA_003429365.1,"CP023475,CP023476",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,158x,SMRT Analysis v. 2.3.0,1,1,2,4742259,52.100044,4753,4504,human stool,isolated from the human stool in South Korea,2017-05-31,South Korea,South Korea,,,,Salmonellosis,,,,,,,,,,,,,Salmonella Enteritidis is one of the well-known food-borne pathogen. It was isolated from the human stool in South Korea.,collected_by:National Culture Collection for Pathogens,,,,,,,Salmonellosis,,,,,,,,,,,,,,100,0.5,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,149539.1478,Salmonella enterica subsp. enterica serovar Enteritidis strain SEO,SEO,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10250222,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2018-10-27T00:00:00Z,,PRJNA497164,GCA_003691385.1,"CP033090,CP033089",,Chinese PLA general hospital,PacBio RSII,266.0x,Celera Assembler v. 8.3,1,1,2,4735694,52.169037,4725,,feces,,2016-09-18,China,China: Beijing,,,,gastroenteritis,,,,,,,,,,,,,"To find the relevant genes for virulence, drug resistance, motility and biofilm formation.","collected_by:Nanlou Respiratory Diseases Department, Chinese PLA General Hospital",,,,,,,gastroenteritis,,,,,,,,,,,,,,99.9,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.1592,Salmonella enterica subsp. enterica serovar Enteritidis strain AUSMDU00010528,AUSMDU00010528,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191644,149539,Enteritidis,,,MLST.Salmonella_enterica.1972,genotype:ST1972;mlst:ST1972,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664795.1,CP045955,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,269x,de novo,1,0,1,4703625,52.258205,4699,4408,missing,,2017,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.1593,Salmonella enterica subsp. enterica serovar Enteritidis strain AUSMDU00010527,AUSMDU00010527,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191643,149539,Enteritidis,,,,genotype:ST3304;mlst:ST3304,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664895.1,"CP045956,CP045957",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,240x,de novo,1,1,2,4683671,52.244747,4670,4365,missing,,2017,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.1644,Salmonella enterica subsp. enterica serovar Enteritidis strain NCCP 16206,NCCP 16206,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12340930,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,NCCP:16206,,2020-01-15T00:00:00Z,,PRJNA556121,GCA_009884355.1,"CP041973,CP041972",,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,271.0x,SPAdes v. 3.1,1,1,2,4774005,52.17372,4938,4576,stool,,2011,South Korea,South Korea: Gyeongnam,,,,diarrhea,,,,,,,,,,,,,Pathogen genome project of Salmonella Enteritidis,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,100,0.13,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.1794,Salmonella enterica subsp. enterica serovar Enteritidis strain SE109,SE109,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450173,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050205.1,"CP050709,CP050710,CP050711",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,81x,Unicycler v. 0.4.8,1,2,3,4829486,52.168865,4929,4596,diarrheal patient,,2013-09-29,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,149539.1795,Salmonella enterica subsp. enterica serovar Enteritidis strain SE95,SE95,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450171,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050385.1,"CP050716,CP050717,CP050718,CP050719,CP050720",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,34x,Unicycler v. 0.4.8,1,4,5,4839384,52.175854,4940,4610,diarrheal patient,,2013-06-19,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,149539.1796,Salmonella enterica subsp. enterica serovar Enteritidis strain SE104,SE104,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450172,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050525.1,"CP050712,CP050713,CP050714,CP050715",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,113x,Unicycler v. 0.4.8,1,3,4,4848540,52.186947,4954,4624,diarrheal patient,,2013-07-10,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,149539.1797,Salmonella enterica subsp. enterica serovar Enteritidis strain SE81,SE81,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450170,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050745.1,"CP050721,CP050722",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,75x,Unicycler v. 0.4.8,1,1,2,4797988,52.159676,4873,4552,human blood,,2012-06-25,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,149539.1798,Salmonella enterica subsp. enterica serovar Enteritidis strain SE74,SE74,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450169,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050905.1,"CP050723,CP050724,CP050725",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,2,3,4859063,52.14606,4964,4623,diarrheal patient,,2012-09-15,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,149539.2310,Salmonella enterica subsp. enterica serovar Enteritidis strain CP255,CP255,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16552337,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-11-05T00:00:00Z,,PRJNA671837,GCA_015240995.1,"CP063705,CP063707,CP063706",,University of Liverpool,Illumina HiSeq; PacBio Sequel,200x,Unicycler v. v0.4.4,1,2,3,4840946,52.271786,4873,,blood,,1991,Democratic Republic of the Congo,Democratic Republic of the Congo,,,,iNTS,,,,,,,,,,,,,"Invasive strains of non-typhoidal salmonellae have emerged as a prominent cause of bloodstream infection in African adults and children, with an associated case fatality of 20-25%. While serovar Typhimurium was determined to be the main cause of iNTS in Africa, serovar Enteritidis was responsible for approximately 2/3 of cases in Latin America. Here we describe finished genome assemblies of 4 strains, 2 invasive and 2 non-invasive.",collected_by:MLW,,,,,,,iNTS,,,,,,,,,,,,,,99.98,0.11,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,149539.2311,Salmonella enterica subsp. enterica serovar Enteritidis strain P125109,P125109,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16552335,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-11-05T00:00:00Z,,PRJNA671837,GCA_015240635.1,"CP063700,CP063701",,University of Liverpool,Illumina HiSeq; PacBio Sequel,200x,Unicycler v. v0.4.4,1,1,2,4745224,52.164555,4732,,stool,,1991,United Kingdom,United Kingdom,,,,food poisoning,,,,,,,,,,,,,"Invasive strains of non-typhoidal salmonellae have emerged as a prominent cause of bloodstream infection in African adults and children, with an associated case fatality of 20-25%. While serovar Typhimurium was determined to be the main cause of iNTS in Africa, serovar Enteritidis was responsible for approximately 2/3 of cases in Latin America. Here we describe finished genome assemblies of 4 strains, 2 invasive and 2 non-invasive.",collected_by:Wellcome Trust Sanger Institute,,,,,,,food poisoning,,,,,,,,,,,,,,100,0.13,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,149539.2312,Salmonella enterica subsp. enterica serovar Enteritidis strain A1636,A1636,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16552338,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-11-05T00:00:00Z,,PRJNA671837,GCA_015241115.1,"CP063708,CP063710,CP063709",,University of Liverpool,Illumina HiSeq; PacBio Sequel,200x,Unicycler v. v0.4.4,1,2,3,4748456,52.159798,4744,,blood,,1998,Malawi,Malawi,,,,iNTS,,,,,,,,,,,,,"Invasive strains of non-typhoidal salmonellae have emerged as a prominent cause of bloodstream infection in African adults and children, with an associated case fatality of 20-25%. While serovar Typhimurium was determined to be the main cause of iNTS in Africa, serovar Enteritidis was responsible for approximately 2/3 of cases in Latin America. Here we describe finished genome assemblies of 4 strains, 2 invasive and 2 non-invasive.",collected_by:MLW,,,,,,,iNTS,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,149539.2313,Salmonella enterica subsp. enterica serovar Enteritidis strain D7795,D7795,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16552336,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2020-11-05T00:00:00Z,,PRJNA671837,GCA_015240855.1,"CP063702,CP063704,CP063703",,University of Liverpool,Illumina HiSeq; PacBio Sequel,200x,Unicycler v. v0.4.4,1,2,3,4869504,52.265816,4921,,blood,,2000,Malawi,Malawi,,,,iNTS,,,,,,,,,,,,,"Invasive strains of non-typhoidal salmonellae have emerged as a prominent cause of bloodstream infection in African adults and children, with an associated case fatality of 20-25%. While serovar Typhimurium was determined to be the main cause of iNTS in Africa, serovar Enteritidis was responsible for approximately 2/3 of cases in Latin America. Here we describe finished genome assemblies of 4 strains, 2 invasive and 2 non-invasive.",collected_by:MLW,,,,,,,iNTS,,,,,,,,,,,,,,99.98,0.11,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,149539.3083,Salmonella enterica subsp. enterica serovar Enteritidis PS_Ent_3_2022,PS_Ent_3_2022,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33677890,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2023-05-26T00:00:00Z,,PRJNA942086,,"CP120315,CP120316,CP120317",,,Oxford Nanopore MiniION,57x,Trycycler v. 0.5.3,1,2,3,4817178,52.069115,4958,4603,state of palestine: west bank,,2022-07,,State of Palestine: West Bank,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Swiss Tropical and Public Health Institute,,,,,Salmonella enterica subsp. enterica genome sequencing for One Health Surveillance in Palestine,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Genitourinary,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.3084,Salmonella enterica subsp. enterica serovar Enteritidis PS_Ent_1_2022,PS_Ent_1_2022,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33677888,149539,Enteritidis,,,,,,,2023-05-26T00:00:00Z,,PRJNA942086,,"CP120322,CP120323,CP120324,CP120321",,,Oxford Nanopore MiniION,23x,Trycycler v. 0.5.3,1,3,4,4834585,52.077377,5012,4624,state of palestine: west bank,,2022-07,,State of Palestine: West Bank,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Swiss Tropical and Public Health Institute,,,,,Salmonella enterica subsp. enterica genome sequencing for One Health Surveillance in Palestine,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,2.4,Gastrointestinal Diseases,Diarrheal Diseases,Genitourinary,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.3085,Salmonella enterica subsp. enterica serovar Enteritidis PS_Ent_2_2022,PS_Ent_2_2022,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33677889,149539,Enteritidis,,,,,,,2023-05-26T00:00:00Z,,PRJNA942086,,"CP120318,CP120319,CP120320",,,Oxford Nanopore MiniION,46x,Trycycler v. 0.5.3,1,2,3,4817182,52.069073,4957,4603,state of palestine: west bank,,2022-07,,State of Palestine: West Bank,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Swiss Tropical and Public Health Institute,,,,,Salmonella enterica subsp. enterica genome sequencing for One Health Surveillance in Palestine,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Genitourinary,Gastrointestinal Diseases-Diarrheal Diseases HP,149539.883,Salmonella enterica subsp. enterica serovar Enteritidis strain 56-3991,56-3991,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050726,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002760915.1,"CP018635,CP018636",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4737486,52.17,4912,4715,human,,1956,USA,United States,,,,,,,Susceptible;Resistant,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.885,Salmonella enterica subsp. enterica serovar Enteritidis strain 74-1357,74-1357,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050729,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002760955.1,"CP018642,CP018643",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4816868,52.11,4993,4805,human,,1974,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.886,Salmonella enterica subsp. enterica serovar Enteritidis strain 77-2980,77-2980,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050730,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002760975.1,CP018644,,FDA,PacBio,missing,HGAP v. 3.0,1,,1,4686089,52.19,4897,4635,human,,1977,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,99.7,2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.887,Salmonella enterica subsp. enterica serovar Enteritidis strain 79-2359,79-2359,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050731,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002760995.1,"CP018645,CP018646",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4739705,52.18,4926,4703,human,,1979,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.888,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1435,81-1435,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050732,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761015.1,CP018647,,FDA,PacBio,missing,HGAP v. 3.0,1,,1,4699764,52.25,4859,4667,human,,1981,USA,United States,,,,,,,Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.889,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1706,81-1706,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050735,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761035.1,"CP018655,CP018656",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4944010,52.04,5235,4969,human,,1981,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.890,Salmonella enterica subsp. enterica serovar Enteritidis strain 92-0392,92-0392,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050736,149539,Enteritidis,,,MLST.Salmonella_enterica.19,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761055.1,"CP018657,CP018658",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,5028552,52.13,5320,5082,human,,1992,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,99.2,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.891,Salmonella enterica subsp. enterica serovar Enteritidis strain 93-0639,93-0639,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050737,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761075.1,"CP018659,CP018660",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4738679,52.17,4940,4714,human,,1993,USA,United States,,,,,,,Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.892,Salmonella enterica subsp. enterica serovar Enteritidis strain 95-0621,95-0621,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050738,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761095.1,"CP018661,CP018662,CP018663",,FDA,PacBio,missing,HGAP v. 3.0,1,2,3,4790958,52.1,5016,4771,human,,1995,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.893,Salmonella enterica subsp. enterica serovar Enteritidis strain 49-2444,49-2444,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050725,149539,Enteritidis,,,MLST.Salmonella_enterica.136,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761115.1,"CP018633,CP018634",,FDA,PacBio,missing,HGAP v. 3.0,1,1,2,4754716,52.2,4967,4726,human,,1949,USA,United States,,,,,,,Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.894,Salmonella enterica subsp. enterica serovar Enteritidis strain 69-3861,69-3861,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050727,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761135.1,"CP018637,CP018638,CP018639",,FDA,PacBio,missing,HGAP v. 3.0,1,2,3,4845989,52.11,5096,4874,human,,1969,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.895,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1607,81-1607,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050733,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002761155.1,"CP018648,CP018649,CP018650",,FDA,PacBio,missing,HGAP v. 3.0,1,2,3,4802885,52.19,4995,4776,human,,1981,USA,United States,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,0.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,149539.896,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1705,81-1705,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06050734,149539,Enteritidis,,,MLST.Salmonella_enterica.11,,,,2017-11-07T00:00:00Z,29301885,PRJNA354706,GCA_002763415.1,"CP018651,CP018652,CP018653,CP018654",,FDA,PacBio,missing,HGAP v. 3.0,1,3,4,4991608,52.03,5273,5022,human,,1981,USA,United States,,,,,,,Resistant,AMR Panel,,,,,,,,missing,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,,,,,,,,,,,,,,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,1496.1556,Clostridioides difficile strain BR81,BR81,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN06286529,1496,,,,,,,,2017-02-28T00:00:00Z,,PRJNA369458,GCF_002007885.1,CP019870,NZ_CP019870.1,Kyung Hee University,PacBio; Illumina HiSeq,275.0x,RS HGAP Assembly v. 3.0,1,,1,4124384,28.71,3741,3658,human feces,,2016-04-01,South Korea,South Korea,,,8 months,nope,,host_description:Infant,,,,,,,,,,,Clostridium difficile isolated from feces of healthy infant,collected_by:June-Young Lee,,,,,,,nope,,,Infant,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,1496.16373,Clostridioides difficile CDB,CDB,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN24220739,1496,,,,,,,,2022-03-25T00:00:00Z,,PRJNA790702,GCA_022695655.1,CP090060,,,PacBio RS,391.0x,Unicycler v. SEPT-2021,1,0,1,4234172,29.083868,3836,3757,hospital,,2020-11-30,China,China,,,,Blood sepsis,,,,,,,,,,,,,,"collected_by:Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine",,,,,,,Blood sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,1496.17243,Clostridioides difficile strain SH,SH,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598405,1496,,,,,genotype:ST37,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972115.1,"CP081017,CP081018",,"Ruijin Hospital, Shanghai Jiao Tong University School of Medicine",Illumina HiSeq PacBio; PacBio,1117x,SOAPdenovo v. 2.21,1,1,2,4287439,28.770578,3935,3842,stool,,2018-05,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,Our study aimed to conduct comparative analysis between Clostridioides difficile ST37 and ST81 isolates by performing whole genome sequencing.,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,99.51,0.45,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17244,Clostridioides difficile strain CD099,CD099,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598404,1496,,,,,genotype:ST37,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972275.1,"CP081019,CP081020",,"Ruijin Hospital, Shanghai Jiao Tong University School of Medicine",Illumina HiSeq PacBio; PacBio,638x,SOAPdenovo v. 2.21,1,1,2,4302821,28.800129,3953,3855,stool,,2017-01,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,Our study aimed to conduct comparative analysis between Clostridioides difficile ST37 and ST81 isolates by performing whole genome sequencing.,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,99.51,0.45,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17245,Clostridioides difficile strain CD060,CD060,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598402,1496,,,,,genotype:ST81,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972555.1,"CP081023,CP081024",,"Ruijin Hospital, Shanghai Jiao Tong University School of Medicine",Illumina HiSeq PacBio; PacBio,274x,SOAPdenovo v. 2.21,1,1,2,4338261,28.765028,4043,3956,stool,,2016-11,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,Our study aimed to conduct comparative analysis between Clostridioides difficile ST37 and ST81 isolates by performing whole genome sequencing.,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,99.18,0.78,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17246,Clostridioides difficile strain G89,G89,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598403,1496,,,,,genotype:ST81,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972415.1,"CP081021,CP081022",,"Ruijin Hospital, Shanghai Jiao Tong University School of Medicine",Illumina HiSeq PacBio; PacBio,318x,SOAPdenovo v. 2.21,1,1,2,4288937,28.760857,3960,3871,stool,,2018-07,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,Our study aimed to conduct comparative analysis between Clostridioides difficile ST37 and ST81 isolates by performing whole genome sequencing.,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,99.18,0.78,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17314,Clostridioides difficile CD099,CD099,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598404,1496,,,,,genotype:ST37,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972275.1,"CP081019,CP081020",,,Illumina HiSeq PacBio; PacBio,638x,SOAPdenovo v. 2.21,1,1,2,4302821,28.800129,3953,3855,stool,,2017-01,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17315,Clostridioides difficile SH,SH,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598405,1496,,,,,genotype:ST37,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972115.1,"CP081017,CP081018",,,Illumina HiSeq PacBio; PacBio,1117x,SOAPdenovo v. 2.21,1,1,2,4287439,28.770578,3935,3842,stool,,2018-05,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17319,Clostridioides difficile G89,G89,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598403,1496,,,,,genotype:ST81,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972415.1,"CP081021,CP081022",,,Illumina HiSeq PacBio; PacBio,318x,SOAPdenovo v. 2.21,1,1,2,4288937,28.760857,3960,3871,stool,,2018-07,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17322,Clostridioides difficile CD060,CD060,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20598402,1496,,,,,genotype:ST81,,,2022-09-06T00:00:00Z,,PRJNA752438,GCA_024972555.1,"CP081023,CP081024",,,Illumina HiSeq PacBio; PacBio,274x,SOAPdenovo v. 2.21,1,1,2,4338261,28.765028,4043,3956,stool,,2016-11,China,China: Shanghai,,,,Clostridioides difficile infection,,,,,,,,,,,,,,collected_by:dangfeng Dong,,,,,,,Clostridioides difficile infection,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.17442,Clostridioides difficile,Clostridioides difficile,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMEA110232939,1496,,,,,,,,2022-08-14T00:00:00Z,,PRJEB52887,GCA_945861085.1,OX244046,,,,,,1,0,1,4108918,28.711842,3762,,feces,,2021-01-01,Netherlands,Netherlands,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.2126,Clostridioides difficile strain DH/NAP11/106/ST-42,DH/NAP11/106/ST-42,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN07339707,1496,DH/NAP11/106/ST-42,,,,genotype:ST-42,,,2017-07-27T00:00:00Z,,PRJNA393704,GCA_002234355.1,CP022524,,Northwestern University,PacBio,25.2x,HGAP assembler v. SMRTAnalysis 2.3.0;,1,,1,4087127,28.62,3694,3615,stool; stool from hospitalized pediatric patient,isolated from the stool of a hospitalized pediatric patient with frequent relapses of C. difficile infection,2012-03-08,USA,USA: Chicago,,,,Clostridium difficile-associated diarrhea,,host_disease_outcome:frequently relapsing C difficile infection;host_subject_id:LC5624,Susceptible;Not defined;Intermediate,AMR Panel,,,,,,,,,"We report the complete genome of Clostridium difficile strain DH/NAP11/106, which is now the most common strain causing CDI among US adults. This strain was isolated from the stool of a hospitalized pediatric patient with frequent relapses of C. difficile infection.",collected_by:Children's Memorial Hospital,,,,,,,Clostridium difficile-associated diarrhea,,frequently relapsing C difficile infection,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1496.2355,Clostridioides difficile strain W0023a,W0023a,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08104990,1496,,,,,,,,2017-12-08T00:00:00Z,,PRJNA420067,GCA_002812605.1,CP025045,,New York Medical College,PacBio and Illumina MiSeq,50x,HGAP and SPAdes v. HGAP 2.3.0 & SPAdes,1,,1,4110080,28.69,3755,3676,stool,,2014-02-02,USA,"USA: NY, Westchester Medical Center, adult oncology unit",,,,Clostridium difficile infection,,,,,,,,,,,,,"Complete genome sequences of toxigenic Clostridium difficile clinical isolates from patients of Lower Hudson Valley, New York, USA. These genomes will enable a more comprehensive toxigenic evaluation of the Clostridium difficile.",,,,,,,,Clostridium difficile infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.2356,Clostridioides difficile strain R0104a,R0104a,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08104991,1496,,,,,,,,2017-12-08T00:00:00Z,,PRJNA420067,GCA_002812585.1,CP025044,,New York Medical College,PacBio and Illumina MiSeq,50x,HGAP and SPAdes v. HGAP 2.3.0 & SPAdes,1,,1,4190038,28.73,3873,3792,stool,,2014-07-19,USA,"USA: NY, Orange Regional Medical Center, adult med surg unit",,,,Clostridium difficile infection,,,,,,,,,,,,,"Complete genome sequences of toxigenic Clostridium difficile clinical isolates from patients of Lower Hudson Valley, New York, USA. These genomes will enable a more comprehensive toxigenic evaluation of the Clostridium difficile.",,,,,,,,Clostridium difficile infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.2357,Clostridioides difficile strain W0022a,W0022a,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08104989,1496,,,,,,,,2017-12-08T00:00:00Z,,PRJNA420067,GCA_002812625.1,CP025046,,New York Medical College,PacBio and Illumina MiSeq,50x,HGAP and SPAdes v. HGAP 2.3.0 & SPAdes,1,,1,4188456,28.85,3896,3818,stool,,2014-02-01,USA,"USA: NY, Westchester Medical Center, peds med surg unit",,,,Clostridium difficile infection,,,,,,,,,,,,,"Complete genome sequences of toxigenic Clostridium difficile clinical isolates from patients of Lower Hudson Valley, New York, USA. These genomes will enable a more comprehensive toxigenic evaluation of the Clostridium difficile.",,,,,,,,Clostridium difficile infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.2358,Clostridioides difficile strain W0003a,W0003a,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08104988,1496,,,,,,,,2017-12-08T00:00:00Z,,PRJNA420067,GCA_002812645.1,CP025047,,New York Medical College,PacBio and Illumina MiSeq,50x,HGAP and SPAdes v. HGAP 2.3.0 & SPAdes,1,,1,4075361,28.56,3715,3638,stool,,2014-01-05,USA,"USA: NY, Westchester Medical Center, adult oncology unit",,,,Clostridium difficile infection,,,,,,,,,,,,,"Complete genome sequences of toxigenic Clostridium difficile clinical isolates from patients of Lower Hudson Valley, New York, USA. These genomes will enable a more comprehensive toxigenic evaluation of the Clostridium difficile.",,,,,,,,Clostridium difficile infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.2554,Clostridioides difficile strain AK,AK,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08474965,1496,,,,,,,,2018-02-27T00:00:00Z,,PRJNA433329,GCA_002954015.1,"CP027014,CP027015,CP027016",,Los Alamos National Laboratory,PacBio,268.0x,HGAP v. 2.2.0,1,2,3,4315250,28.728664,4079,3947,,,,,,,,,,,,,,,,,,,,,,Clostridium difficile human clinical isolate,sample_type:Clinical,,,,,,,,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1496.3136,Clostridioides difficile strain CD10010,CD10010,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN10274208,1496,,,,,,,,2018-10-30T00:00:00Z,,PRJNA497978,GCA_003697205.1,CP033213,,BGI,PacBio RSII,138.0x,Celera Assembler v. 8.3,1,,1,4049580,28.740017,3671,,stool,,2015-12,China,China:beijing,,,,Diarrhea caused by clostridium difficile,,,,,,,,,,,,,Genetic character of three ST11 Clostridium difficile isolates with different RTs: tcdC deletion is not the unique feature of RT078 indicated by complete whole genome sequencing,"collected_by:ICDC, China CDC",,,,,,,Diarrhea caused by clostridium difficile,,,,,,,,,,,,,,98.03,0.34,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1496.3137,Clostridioides difficile strain 12038,12038,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN10274224,1496,,,,,,,,2018-10-30T00:00:00Z,,PRJNA497978,GCA_003697225.1,"CP033214,CP033215",,BGI,PacBio RSII,214.0x,Celera Assembler v. 8.4,1,1,2,4077502,28.817791,3682,,stool,,2015-12,China,China: Beijing,,,,Diarrhea caused by clostridium difficile,,,,,,,,,,,,,Genetic character of three ST11 Clostridium difficile isolates with different RTs: tcdC deletion is not the unique feature of RT078 indicated by complete whole genome sequencing,"collected_by:ICDC, China CDC",,,,,,,Diarrhea caused by clostridium difficile,,,,,,,,,,,,,,98.03,0.34,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1496.32583,Clostridioides difficile,Clostridioides difficile,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMEA110232938,1496,,,,,,,,2022-08-14T00:00:00Z,,PRJEB52887,,"OX246690,OX246691,OX246692",,,,,,1,2,3,4361491,28.66522,4064,,feces,,2016-01-01,Netherlands,Netherlands,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.7,1.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.4688,Clostridioides difficile strain Mta-79,Mta-79,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN12370807,1496,,,,,,,,2019-09-03T00:00:00Z,,PRJNA556848,GCA_008245165.1,CP042267,,Baylor College of Medicine,Illumina MiSeq; Oxford Nanopore MiniION,100.0x,Unicycler v. v0.4.8-beta,1,,1,4123685,28.681385,3827,3721,stool,isolate from an elderly patient with recurrent C. difficile infection (CDI),2018-11-30,USA,"USA: Houston, TX",,,,C. difficile Infection,,,,,,,,,,,,,Hybrid de novo assembly of Illumina/Nanopore sequence data produced a complete circular sequence of the chromosome for Clostridioides difficile ribotype (RT) 255 isolate from an elderly patient with recurrent C. difficile infection (CDI). This provides a high-quality representative sequence for the RT255 lineage.,collected_by:University of Houston,,,,,,,C. difficile Infection,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5450,Clostridioides difficile strain DSM 105001,DSM 105001,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN08744682,1496,,,,,,DSM:105001,,2020-08-18T00:00:00Z,30247587,PRJNA439324,GCA_014236775.1,CP028361,,University Medical Center Goettingen,PacBio; Illumina,99x,HGAP SMRTPortal v. 2.3.0,1,0,1,4198599,28.832855,3813,3715,stool,,2015,Germany,Germany: Goettingen,,female,,acute diarrhea,,host_disease_outcome:recovery,,,,,,,,,,,Genome sequence of a Fidaxomycin resistant Clostridioides difficile isolate,collected_by:Ortrud Zimmermann,,,,,,,acute diarrhea,,recovery,,,,,,,,,,,,99.51,0.37,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,1496.5909,Clostridioides difficile strain 2015,2015,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN18882462,1496,,,,,,,,2021-05-04T00:00:00Z,,PRJNA725530,GCA_018255775.1,CP073752,,University of Nebraska-Lincoln,Oxford Nanopore; Illumina NextSeq,50.0x,Unicycler v. May 5 2020,1,0,1,4208592,28.817833,3820,3717,human feces,,2007-12-07,USA,USA: Michigan,,,,Clostridium difficile colitis,,,,,,,,,,,,,Whole genome sequence from ribotype 027 clinical isolate from Michigan Department of Community Health,collected_by:Michigan Department of Community Health,,,,,,,Clostridium difficile colitis,,,,,,,,,,,,,,99.51,0.37,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,1496.5981,Clostridioides difficile strain MT5121,MT5121,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19317498,1496,,,,,,,,2021-05-31T00:00:00Z,,PRJNA732388,GCA_018603475.1,CP075685,,"Instructor, Baylor College of Medicine",Illumina,100x,SPAdes v. v3.13.0,1,0,1,3998712,28.681711,3646,3518,stool,,2018-11-30,USA,"USA: Houston, TX",,,,C. difficile Infection,,,,,,,,,,,,,"Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.",collected_by:University of Houston,human gut,stool,,,,,C. difficile Infection,,,,,,,,,,human gut,,,,97.72,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5982,Clostridioides difficile strain MHS-156,MHS-156,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19317495,1496,,,,,,,,2021-05-31T00:00:00Z,,PRJNA732388,GCA_018603455.1,CP075683,,"Instructor, Baylor College of Medicine",Illumina,76x,SPAdes v. v3.13.0,1,0,1,3998707,28.681997,3647,3526,stool,,2018-11-30,USA,"USA: Houston, TX",,,,C. difficile Infection,,,,,,,,,,,,,"Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.",collected_by:University of Houston,human gut,stool,,,,,C. difficile Infection,,,,,,,,,,human gut,,,,97.72,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5983,Clostridioides difficile strain MT4854,MT4854,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19317496,1496,,,,,,,,2021-05-31T00:00:00Z,,PRJNA732388,GCA_018603395.1,CP075684,,"Instructor, Baylor College of Medicine",Illumina,127x,SPAdes v. v3.13.0,1,0,1,3998618,28.68181,3646,3527,stool,,2018-11-30,USA,"USA: Houston, TX",,,,C. difficile Infection,,,,,,,,,,,,,"Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.",collected_by:University of Houston,human gut,stool,,,,,C. difficile Infection,,,,,,,,,,human gut,,,,97.72,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5984,Clostridioides difficile strain Cd28,Cd28,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021926,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884625.1,"CP037798,CP037799,CP037800",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,302x,nanoflow v. AUG-2018,1,2,3,4307593,28.63038,4108,3938,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2018-02-20,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.16,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5985,Clostridioides difficile strain Cd24,Cd24,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021922,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884645.1,CP037801,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,352x,nanoflow v. AUG-2018,1,0,1,4071445,28.620739,3730,3637,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-12-31,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.45,0.88,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5986,Clostridioides difficile strain Cd29,Cd29,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021927,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884605.1,CP037797,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,328x,nanoflow v. AUG-2018,1,0,1,4186793,28.7441,3961,3825,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2015-12-09,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.16,0.38,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5987,Clostridioides difficile strain Cd18,Cd18,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021916,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884705.1,"CP037806,CP037807,CP037808,CP037809,CP037810",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,202x,nanoflow v. AUG-2018,1,4,5,4356569,28.682594,4133,3968,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-10-15,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.18,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5988,Clostridioides difficile strain Cd23,Cd23,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021921,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884665.1,"CP037802,CP037803,CP037804",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,305x,nanoflow v. AUG-2018,1,2,3,4149746,28.548952,3842,3722,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-12-28,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.18,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5989,Clostridioides difficile strain Cd21,Cd21,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021919,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884685.1,CP037805,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,137x,nanoflow v. AUG-2018,1,0,1,4113713,28.69001,3764,3671,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-11-14,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.45,0.55,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5990,Clostridioides difficile strain Cd17,Cd17,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021915,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884725.1,CP037811,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,264x,nanoflow v. AUG-2018,1,0,1,3936124,28.548313,3682,3554,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-08-16,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,97.69,0.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5991,Clostridioides difficile strain Cd16,Cd16,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021914,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884745.1,CP037812,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,228x,nanoflow v. AUG-2018,1,0,1,4203966,28.744595,3930,3836,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-05-08,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.52,0.38,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5992,Clostridioides difficile strain Cd15,Cd15,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021913,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884785.1,"CP037813,CP037814,CP037815,CP037816,CP037817",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,151x,nanoflow v. AUG-2018,1,4,5,4393991,28.438347,4215,4039,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-05-03,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.48,0.48,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5993,Clostridioides difficile strain Cd14,Cd14,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021912,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884765.1,"CP037818,CP037819",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,329x,nanoflow v. AUG-2018,1,1,2,4240901,28.75547,3979,3895,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-02-12,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5994,Clostridioides difficile strain Cd12,Cd12,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021910,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884825.1,CP037821,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,231x,nanoflow v. AUG-2018,1,0,1,4100358,28.70347,3724,3652,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-03-06,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.45,0.55,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5995,Clostridioides difficile strain Cd13,Cd13,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021911,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884805.1,CP037820,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,181x,nanoflow v. AUG-2018,1,0,1,4102642,28.703886,3760,3658,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-03-06,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.42,0.88,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5996,Clostridioides difficile strain Cd11,Cd11,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021909,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884845.1,"CP037822,CP037823,CP037824,CP037825,CP037826",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,123x,nanoflow v. AUG-2018,1,4,5,4404202,28.479939,4153,4038,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2017-01-01,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5997,Clostridioides difficile strain Cd10,Cd10,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021908,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884865.1,"CP037827,CP037828,CP037829",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,153x,nanoflow v. AUG-2018,1,2,3,4245736,28.490208,3951,3857,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-03-28,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5998,Clostridioides difficile strain Cd9,Cd9,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021907,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884885.1,CP037830,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,187x,nanoflow v. AUG-2018,1,0,1,4121924,28.56945,3767,3684,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-07-27,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.32,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.5999,Clostridioides difficile strain Cd8,Cd8,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021906,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884905.1,"CP037831,CP037832,CP037833,CP037834",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,202x,nanoflow v. AUG-2018,1,3,4,4274902,28.541613,3988,3877,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-07-19,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6000,Clostridioides difficile strain Cd4,Cd4,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021902,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884985.1,CP037848,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,276x,nanoflow v. AUG-2018,1,0,1,4184598,28.76572,3885,3811,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2015-12-09,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.52,0.38,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6001,Clostridioides difficile strain Cd2,Cd2,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021900,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018885025.1,"CP037853,CP037854,CP037855,CP037856",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,334x,https://github.com/zhaoc1/nanoflow v.,1,3,4,4261386,28.497595,4012,3879,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2015-09-14,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,98.86,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6002,Clostridioides difficile strain Cd7,Cd7,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021905,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884925.1,"CP037835,CP037836,CP037837,CP037838",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,121x,nanoflow v. AUG-2018,1,3,4,4292701,28.578417,4011,3906,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-04-24,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6003,Clostridioides difficile strain Cd6,Cd6,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021904,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884965.1,CP037839,,University of Pennsylvania,Illumina and Oxford Nanopore MinION,305x,nanoflow v. AUG-2018,1,0,1,4321901,29.301598,4031,3968,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-04-08,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.53,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6004,Clostridioides difficile strain Cd5,Cd5,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021903,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018884945.1,"CP037840,CP037841,CP037842,CP037843",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,253x,nanoflow v. AUG-2018,1,3,4,4272298,28.437296,3973,3870,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2016-02-26,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.51,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6005,Clostridioides difficile strain Cd1,Cd1,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021899,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018885045.1,"CP037844,CP037845,CP037846,CP037847",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,330x,https://github.com/zhaoc1/nanoflow v.,1,3,4,4282853,28.612446,4051,3944,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2015-10-13,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,98.86,0.75,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6006,Clostridioides difficile strain Cd3,Cd3,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN11021901,1496,,,,,,,,2021-06-15T00:00:00Z,,PRJNA524299,GCA_018885005.1,"CP037849,CP037850,CP037851,CP037852",,University of Pennsylvania,Illumina and Oxford Nanopore MinION,173x,https://github.com/zhaoc1/nanoflow v.,1,3,4,4641978,28.453127,4426,4294,feces,isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms,2015-11-10,USA,"USA: Philadelphia, PA",,,,Clostridium difficile,,,,,,,,,,,,,C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.,collected_by:Children's Hospital of Philadelphia,,,,,,,Clostridium difficile,,,,,,,,,,,,,,99.41,0.83,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1496.6007,Clostridioides difficile strain S-0942,S-0942,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19491761,1496,,,,,,,Yes,2021-06-15T00:00:00Z,,PRJNA734443,GCA_018885105.1,CP076376,,University of Western Australia,MinION Mk1c and Illumina NovaSeq 6000,1505x MinION +,Unicycler v. v0.4.8,1,0,1,4129159,28.705942,3749,3648,"clinical, pcr+ stool swab",,2016-09-09,Australia,Australia: South Australia,,male,56,Clostridioides difficile infection,,,,,,,,,,,,,"C. difficile reference genomes are currently very limited, primarily being drawn from European or North American strains with none from Australian strains within the last decade. Due to the distinct and diverse nature of Australian C. difficile, strains from the three most prevalent ribotype strains were sequenced and assembled to provide more appropriate reference genomes.",collected_by:South Australia Pathology,,,,,,,Clostridioides difficile infection,,,,,,"Ribotype 056, Sequence type 34",,,,,,,,99.51,0.37,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.6008,Clostridioides difficile strain S-0253,S-0253,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19491759,1496,,,,,,,Yes,2021-06-15T00:00:00Z,,PRJNA734443,GCA_018885085.1,"CP076401,CP076402",,University of Western Australia,MinION Mk1c and Illumina NovaSeq 6000,563x MinION +,Unicycler v. v0.4.8,1,1,2,4095894,28.516705,3695,3591,"clinical, pcr+ stool swab",,2014-04-02,Australia,Australia: South Australia,,female,77,Clostridioides difficile infection,,,,,,,,,,,,,"C. difficile reference genomes are currently very limited, primarily being drawn from European or North American strains with none from Australian strains within the last decade. Due to the distinct and diverse nature of Australian C. difficile, strains from the three most prevalent ribotype strains were sequenced and assembled to provide more appropriate reference genomes.",collected_by:South Australia Pathology,,,,,,,Clostridioides difficile infection,,,,,,"Ribotype 002, Sequence type 8",,,,,,,,99.46,0.53,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.6009,Clostridioides difficile strain S-0352,S-0352,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN19491760,1496,,,,,,,Yes,2021-06-15T00:00:00Z,,PRJNA734443,GCA_018885065.1,CP076377,,University of Western Australia,MinION Mk1c and Illumina NovaSeq 6000,448x MinION +,Unicycler v. v0.4.8,1,0,1,4251987,28.961706,3908,3790,"clinical, pcr+ stool swab",,2014-09-12,Australia,Australia: Victoria,,male,28,Clostridioides difficile infection,,,,,,,,,,,,,"C. difficile reference genomes are currently very limited, primarily being drawn from European or North American strains with none from Australian strains within the last decade. Due to the distinct and diverse nature of Australian C. difficile, strains from the three most prevalent ribotype strains were sequenced and assembled to provide more appropriate reference genomes.",collected_by:Monash Health,,,,,,,Clostridioides difficile infection,,,,,,"Ribotype 014, Sequence type 2",,,,,,,,99.47,0.38,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1496.6058,Clostridioides difficile strain MAR286,MAR286,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMEA7490727,1496,,,,,,,,2021-07-02T00:00:00Z,,PRJNA679085,GCA_019095765.1,CP072118,,The University of Western Australia,Oxford Nanopore MinION; Illumina HiSeq,39.0x,Unicycler v. 0.4.8,1,0,1,4242261,28.841671,3853,3761,human,,2018-07-17,Thailand,Thailand,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aimed to characterise AMR among clinical C. difficile strains in Thailand, a country where the use of antimicrobials remains inadequately regulated.",,,,,,,,,diseased,,,,,,,,,,,,,99.51,0.45,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,150053.30,Yersinia enterocolitica subsp. palearctica strain Y1,Y1,Yersinia enterocolitica,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09641678,150053,O:3,,,MLST.Yersinia_spp.18,,,,2019-03-25T00:00:00Z,,PRJNA480560,GCA_004368055.1,"CP030980,CP030981",,Helmholtz Centre for Infection Research,PacBio; Illumina MiSeq,159x,HGAP SMRTPortal v. 2.3.0,1,1,2,4594706,46.95382,4575,4258,missing,,2007,Germany,Germany,,,,Yersiniosis,,,,,,,,,,,,,"The aim of the study was to sequence and annotate the genome of the clinical isolate of Y. enterocolitica Y1 (O:3/4). Additionally, the transcriptome of this isolate was compared to the transcriptome of Y. enterocolitica 8081v (O:8/1B).","collected_by:E. Strauch, BfR",,,,,,,Yersiniosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1501662.7,Streptococcus parasuis strain BS26,BS26,Streptococcus parasuis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17516902,1501662,,,,,,,,2021-06-30T00:00:00Z,,PRJNA694315,GCA_019076885.1,CP069079,,"Institute for Communicable Disease Control and Prevention,Chinese Center for Disease Control and Pr",Illumina HiSeq; PacBio; ABI3730,200X,SPAdes v. v3.13.0,1,0,1,1932292,39.75419,2047,1893,blood,,2018,China,China: Guangxi,,,,peritonitis,,,,,,,,,,,,,Investigate the genomic and pathogenic features of emerging zoonotic Streptococcus parasuis,"collected_by:Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,,,,,,peritonitis,,,,,,,,,,,,,,100,0.37,Gastrointestinal Diseases,Peritoneal Conditions,Blood and Circulatory System,Gastrointestinal Diseases-Peritoneal Conditions NHP,1502.1084,Clostridium perfringens strain 4928STDY7387940,4928STDY7387940,Clostridium perfringens,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMEA4623349,1502,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166765.1,LR607374,,SC,,,,1,,1,3382360,28.288553,2766,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.19,0,,,Other,- NHP,1502.1085,Clostridium perfringens strain 4928STDY7387880,4928STDY7387880,Clostridium perfringens,Clostridium,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMEA4623304,1502,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166825.1,LR607381,,SC,,,,1,,1,4006058,27.889894,3747,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,96.77,0,,,Other,- HP,1507806.50,Campylobacter fetus subsp. testudinum strain 772,772,Campylobacter fetus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN08618845,1507806,,,,MLST.Campylobacter_fetus.17,,,,2018-03-07T00:00:00Z,,PRJNA436182,GCA_002973655.1,CP027287,,Guangzhou Center for Disease Control and Prevention,Illumina HiSeq,1547.0x,SOAPdenovo v. v2.04,1,,1,1863540,33.13334,1875,1815,ascites,,2015-04-01,China,China: Guangzhou,,,,Peritonitis,,,,,,,,,,,,,"C. fetus subsp testudinum strain 772, complete genome",collected_by:Panyu central hospital,,,,,,,Peritonitis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,152480.137,Burkholderia ambifaria CEP0996,CEP0996,Burkholderia ambifaria,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN31539757,152480,,,,MLST.Burkholderia_cepacia_complex.924,,,,2022-12-06T00:00:00Z,,PRJNA896258,,"CP113272,CP113271,CP113270",,,Oxford Nanopore - Illumia,262 - 154x,Flye v. 1.3,3,0,3,7391553,66.713264,7040,,cystic fibrosis sputum,,2001,Canada,Canada,,,,,,,,,,,,,,,,,,,Clinical Isolate,Unknown,Cystic fibrosis Sputum,Burkholderia selective medium,,,,,,,,,,,,,Clinical Isolate,,,,99.8,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1528099.141,Lawsonella clevelandensis strain X1698,X1698,Lawsonella clevelandensis,Lawsonella,Lawsonellaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN03943545,1528099,,,,,,,,2017-10-11T00:00:00Z,"26659691,27130323",PRJNA256353,GCA_001281505.1,CP012390,,CDC,Illumina HiSeq,625.0x,CLC Genomics Workbench v. October 2014;,1,,1,1915154,58.611736,1682,1378,peritoneal abscess,derived from human clinical specimens,2013-10,USA,"USA: Cleveland, OH",,,,,,,,,,,,,,,,,CDC's Special Bacteriology Reference Laboratory (SBRL) has a vast collection of strains derived from human clinical specimens. These are their genomes.,sample_type:isolate,,,,,,,,,,,,,,,,,,,,,95,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1528099.142,Lawsonella clevelandensis strain X1036,X1036,Lawsonella clevelandensis,Lawsonella,Lawsonellaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN02943398,1528099,,,,,,,,2017-09-21T00:00:00Z,26659691,PRJNA256353,GCA_001293125.1,CP009312,,CDC,Illumina HiSeq,600.0x,CLC NGS Cell v. V7.04,1,,1,1860551,58.59327,1627,1164,abscess,derived from human clinical specimens,2011-06,USA,"USA: Cleveland, OH",,,,,,,,,,,,,,,,,CDC's Special Bacteriology Reference Laboratory (SBRL) has a vast collection of strains derived from human clinical specimens. These are their genomes.,,,,,,,,,,,,,,,,,,,,,,95,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1530123.47,Acinetobacter seifertii strain AS79,AS79,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092246,1530123,,,,"MLST.Acinetobacter_baumannii_2.554,MLST.Acinetobacter_baumannii_1.1039",,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014717515.1,CP061550,,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,0,1,3900615,38.583607,3618,3521,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:CCH,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.48,Acinetobacter seifertii strain AS80,AS80,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092247,1530123,,,,MLST.Acinetobacter_baumannii_2.548,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014717695.1,"CP061543,CP061544,CP061545,CP061546,CP061547,CP061548,CP061549",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,6,7,4002993,38.55605,4040,3692,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:CCH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.63,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.50,Acinetobacter seifertii strain AS78,AS78,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092245,1530123,,,,MLST.Acinetobacter_baumannii_2.548,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014718155.1,"CP061551,CP061552,CP061553,CP061554,CP061555",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,4,5,4021324,38.596714,4006,3723,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:CCH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.32,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.51,Acinetobacter seifertii strain AS73,AS73,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092243,1530123,,,,MLST.Acinetobacter_baumannii_1.262,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014718355.1,"CP061561,CP061562,CP061563,CP061564",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,3,4,4154390,38.624252,4165,3959,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TSGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.73,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.52,Acinetobacter seifertii strain AS72,AS72,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092242,1530123,,,,MLST.Acinetobacter_baumannii_2.90,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014718535.1,"CP061565,CP061566,CP061567",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,2,3,3969919,38.610184,4176,3699,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TSGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,98.8,1,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.57,Acinetobacter seifertii strain AS61,AS61,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092237,1530123,,,,MLST.Acinetobacter_baumannii_2.544,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014719655.1,"CP061589,CP061590,CP061591",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,2,3,4086212,38.60612,4177,3803,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.68,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.59,Acinetobacter seifertii strain AS59,AS59,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092235,1530123,,,,,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014720075.1,"CP061596,CP061597",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,1,2,3903769,38.644424,3683,3583,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.62,Acinetobacter seifertii strain AS52,AS52,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092231,1530123,,,,,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014720715.1,"CP061609,CP061610,CP061611,CP061612",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,3,4,3893187,38.650776,4128,3613,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.44,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.65,Acinetobacter seifertii strain AS48,AS48,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092228,1530123,,,,MLST.Acinetobacter_baumannii_2.551,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014721215.1,"CP061626,CP061627,CP061628",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,2,3,4000660,38.70984,3825,3712,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.86,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.68,Acinetobacter seifertii strain AS39,AS39,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092223,1530123,,,,"MLST.Acinetobacter_baumannii_2.554,MLST.Acinetobacter_baumannii_1.1039",,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014722015.1,"CP061646,CP061647,CP061648,CP061649",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,3,4,4091819,38.426918,3880,3739,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.73,Acinetobacter seifertii strain AS28,AS28,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092219,1530123,,,,MLST.Acinetobacter_baumannii_1.1039,,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014723035.1,"CP061664,CP061665",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,1,2,4071624,38.31245,3840,3690,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.73,0.94,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1530123.79,Acinetobacter seifertii strain AS9,AS9,Acinetobacter seifertii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16092213,1530123,,,,"MLST.Acinetobacter_baumannii_2.553,MLST.Acinetobacter_baumannii_1.262",,,,2020-09-24T00:00:00Z,,PRJNA662665,GCA_014723155.1,"CP061681,CP061682",,Taipei Veterans General Hospital,Oxford Nanopore MinION,80x,CCBGpipe v. 1,1,1,2,4084907,38.628075,3904,3785,blood,,2010-2017,Taiwan,Taiwan,,,,bloodstream infection,,,,,,,,,,,,,Clinical and molecular characterization of Acinetobacter seifertii in Taiwan,collected_by:TVGH,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.73,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,154046.361,Hungatella hathewayi strain DSM 13479,DSM 13479,Hungatella hathewayi,Hungatella,Clostridiaceae,Eubacteriales,Clostridia,Bacillota,SAMN20222677,154046,,,,,,DSM:13479,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149285.1,CP102274,,Stanford University,Illumina HiSeq; PacBio,100x,Unicycler v. 0.4.8,1,0,1,6931886,48.1088,6714,6246,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.37,0.95,,,Other,- NHP,1547448.3,Arachnia rubra strain DSMZ 100122,DSMZ 100122,Arachnia rubra,Arachnia,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN18352173,1547448,,,,,,DSMZ:100122,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128325.1,CP072384,,The Forsyth Institute,PacBio Sequel,185x,Pacbio MA v. 9.0.0.92188,1,0,1,3316958,64.202324,3145,2949,human oral cavity,,2014-06-16,Japan,Japan:Matsudo,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:DSMZ German Collection of Microorganisms;collected_by:M. Saito, Nihon University",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,96.95,1.22,,,Oral,- HP,155615.5,Fusobacterium nucleatum subsp. vincentii strain KCOM 2931,KCOM 2931,Fusobacterium vincentii,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07837329,155615,,,,,,,,2017-11-13T00:00:00Z,,PRJNA415900,GCA_002764055.1,CP024749,,Korean Collection for Oral Microbiology,PacBio,467.0x,RS HGAP v. 3.0,1,,1,2087706,27.21,1985,1962,subgingival dental plaque,,2015-04-24,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium nucleatum subsp. vincentii KCOM 2931,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,155864.210,Escherichia coli O157:H7 str. EDL933,EDL933,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196157,155864,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028715.1,CP028305,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4709911,50.763325,4635,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,96.8,1.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,155864.360,Escherichia coli O157:H7 str. EDL933,EDL933,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15296135,155864,O157:H7,,,MLST.Escherichia_coli_1.11,"genotype:ST11, O157:H7",,,2023-04-05T00:00:00Z,,PRJNA639799,,"CP120944,CP120945,CP120946",,,Illumina MiSeq; Oxford Nanopore GridION,110.0x,Unicycler v. 0.4.8,1,2,3,5549910,50.427807,5635,,missing,,,,,,,,,,,,,,,,,,,,,,"collected_by:Roberson, Dwayne",,,,,,,missing,,,,,,clinical,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1563222.9,Citrobacter pasteurii strain UMH17,UMH17,Citrobacter pasteurii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729549,1563222,,,,MLST.Citrobacter_freundii.128,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665575.1,CP024676,,University of Michigan,PacBio,213x,HGAP v. 2,1,,1,4654874,51.89728,4540,4469,,,2013-10,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,99.55,0.07,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,156980.9,Arthrobacter woluwensis strain QTS,QTS,Arthrobacter woluwensis,Arthrobacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN14299268,156980,,,,,,,,2021-03-24T00:00:00Z,,PRJNA610462,GCA_017579825.1,CP049819,,National Chung Cheng University,Oxford Nanopore GridION,122.0x,Flye v. 2.6,1,0,1,3680971,68.395325,3395,3301,blood,,2019-09-19,Taiwan,Taiwan,,,,sepsis,,,,,,,,,,,,,Analysis of the genome in order to understand the genetic factors leading to virulence and antibiotic resistance,collected_by:PO-YU LIU,,,,,,,sepsis,,,,,,,,,,,,,,99.31,0.46,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,157687.176,Leptotrichia wadei strain JMUB3933,JMUB3933,Leptotrichia wadei,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMD00156218,157687,,,,,,,Yes,2019-07-24T00:00:00Z,,PRJDB7856,GCA_007990385.1,AP019834,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MinION; MiSeq,91X,Canu v. 1.8; Circlator v. 1.5.5;,1,,1,2361227,29.591988,2262,2205,blood,,2017,Japan,Japan,,,,,,,,,Negative,,,,,,,,We determined genome sequences of seven clinical isolates and four type strains of Leptotrichia.,,missing,missing,blood,11783691,Complete Genome Sequence of Leptotrichia wadei Strain JMUB3933,,,,,,,,,,,,missing,,,,100,2.84,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1578165.6,Mycobacterium saopaulense strain EPM10906,EPM10906,Mycobacteroides saopaulense,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN03225541,1578165,,,,,,,,2015-12-03T00:00:00Z,,PRJNA268854,GCA_001456355.1,CP010271,,Universidade de Sao Paulo,454 Titanium XL+,100x,Newbler v. 2.6,1,,1,4649175,64.8,4602,4349,eye,,1998-01-01,Brazil,"Brazil: Sao Paulo,SP",,,,"Eye abscess, hospital infection",,,,,Positive,Bacilli,,,,,,Hospital Infection,Sequencing and analysis of new mycobacterium species,collected_by:Hospital staff,,,,,,,"Eye abscess, hospital infection",,,,,,,,,,,,,,94.7,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Eye,Skin and Soft Tissue Infections-Wounds and Abscesses NHP,1579.364,Lactobacillus acidophilus strain LA-G80-111,LA-G80-111,Lactobacillus acidophilus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN15165794,1579,,,,,,,,2020-06-15T00:00:00Z,,PRJNA638040,GCA_013342945.1,CP054559,,"Institute of Microbiology, Belarus National Academy of Sciences",Oxford Nanopore MiniION,157.0x,Barapost v. 3.13.a; Flye v. 2.7.1-b1590,1,0,1,1991976,34.70639,1908,1847,missing,,,,,,,,,,,,,,,,,,,,,"Genome analysis of probiotic strain Lactobacillus acidophilus LA-G80 from the Chinese company BIOGROWING CO., LTD.","sample_type:cell culture;biomaterial_provider:BIOGROWING CO., LTD.",,,,,,,,,,,,,,,,,,,,,98.94,0,,,Other,- HP,158.80,Treponema denticola OT2B,OT2B,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253866,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181425.1,CP051303,,,Illumina HiSeq; Oxford Nanopore MiniION,376.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2841718,37.879868,2699,2581,subgingival plaque,,,USA,USA,,,,Periodontitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,158.81,Treponema denticola OMZ 910,OMZ 910,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253862,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181465.1,CP051522,,,Illumina HiSeq; Oxford Nanopore MiniION,1595.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2728386,38.006573,2587,2460,subgingival plaque,,2000-06,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,158.82,Treponema denticola OMZ 852,OMZ 852,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253859,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181485.1,CP051523,,,Illumina HiSeq; Oxford Nanopore MiniION,869.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2882651,37.83736,2802,2693,subgingival plaque,,1999-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,158.84,Treponema denticola OMZ 850,OMZ 850,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253858,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181545.1,CP051634,,,Illumina HiSeq; Oxford Nanopore MiniION,1136.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2747952,37.894184,2610,2503,subgingival plaque,,1998-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,158.85,Treponema denticola OMZ 905,OMZ 905,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253861,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181565.1,CP051635,,,Illumina HiSeq; Oxford Nanopore MiniION,904.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2728291,38.005917,2598,2461,subgingival plaque,,2000-05,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,158.87,Treponema denticola OMZ 823,OMZ 823,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253855,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181605.1,CP054477,,,Illumina HiSeq; Oxford Nanopore MiniION,1213.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2759770,37.79322,2649,2517,subgingival plaque,,2007-11,Switzerland,Switzerland,,,,localized aggressive periodontits,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,localized aggressive periodontits,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Other Oral and Dental Diseases,Oral,Oral and Dental Diseases-Other Oral and Dental Diseases HP,158.88,Treponema denticola OMZ 854,OMZ 854,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN14933810,158,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181645.1,CP058624,,,Illumina HiSeq; Oxford Nanopore MiniION,998.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2782312,37.661663,2670,2556,acute necrotizing ulcerative gingivitis lesion,,1998-05,China,China,,,,,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],acute necrotizing ulcerative gingivitis lesion,27864174,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,158.89,Treponema denticola ATCC 700768,ATCC 700768,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253853,158,,,,,,ATCC:700768,,2022-07-25T00:00:00Z,,PRJNA284866,GCA_024400535.1,CP038800,,,Oxford Nanopore MiniION and illumina,1596x,"Celera Assembler v. Canu 1.8,",1,0,1,2920478,37.62408,2880,2707,subgingival plaque,,1998-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,158.91,Treponema denticola KCOM 3500,KCOM 3500,Treponema denticola,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31203232,158,,,,,,,,2022-10-29T00:00:00Z,,PRJNA887932,GCA_025905525.1,CP109619,,,PacBio Sequel,259.4x,Microbial Assembly Application from,1,0,1,2778422,38.05484,2631,2531,subgingival plaque of chronic periodontitis lesion,,2018-05-02,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,1582.99,Lactobacillus casei strain LC5,LC5,Lacticaseibacillus casei,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN05631198,1582,,,,,,,,2017-06-13T00:00:00Z,28439274,PRJNA340077,GCA_002192215.1,CP017065,,Korea Food Research Institute,PacBio,246x,HGAP v. 3.0,1,,1,3132867,47.92,3060,2848,commercial dietary supplements,,2016-06-22,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,LC5 strain was isolated from Commercial dietary supplements,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Other,- HP,1583098.7,Fusobacterium hwasookii strain KCOM 1249,KCOM 1249,Fusobacterium hwasookii,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN15742258,1583098,,,,,,,,2020-08-17T00:00:00Z,,PRJNA655549,GCA_014217355.1,"CP060112,CP060113,CP060114",,Korean Collection for Oral Microbiology,Illumina HiSeq,394.0x,SPAdes v. 3.6.2; SSPACE-PREMIUM v. 2.3.1;,1,2,3,2378155,27.179726,2335,2204,subgingival dental plaque,,2003-02-13,South Korea,South Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium hwasookii KCOM 1249 (ChDC F128),collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,1583098.8,Fusobacterium hwasookii strain KCOM 1253,KCOM 1253,Fusobacterium hwasookii,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN15742288,1583098,,,,,,,,2020-08-17T00:00:00Z,,PRJNA655553,GCA_014217375.1,"CP060115,CP060116",,Korean Collection for Oral Microbiology,Illumina HiSeq,1347.0x,SPAdes v. 3.6.2; SSPACE-PREMIUM v. 2.3.1;,1,1,2,2363187,27.199286,2185,2155,subgingival dental plaque,,2003-02-13,South Korea,South Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium hwasookii KCOM 1253 (ChDC F145),collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,1585976.13,Bergeyella cardium BC,BC,Bergeyella cardium,Bergeyella,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN34037267,1585976,,,,,,,,2023-05-12T00:00:00Z,,PRJNA951281,,CP121693,,,PacBio,100.0x,GS De Novo Assembler v. Jan-2020,1,0,1,2036890,39.626095,1938,1819,blood culture,,2020-01-20,China,China: Shandong,,,,infective endocarditis,,,,,,,,,,,,,,collected_by:Hongwei Pan,,,,,,,infective endocarditis,,,,,,,,,,,,,,97.9,1.3,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1585976.14,Bergeyella cardium BCP,BCP,Bergeyella cardium,Bergeyella,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN32105916,1585976,,,,,,,,2023-05-15T00:00:00Z,,PRJNA909954,,CP114055,,,PacBio,100.0x,SOAPdenovo v. January-2020,1,0,1,2036969,39.625835,1927,1818,blood culture,,2019-12-12,China,China,,,,infective endocarditis,,,,,,,,,,,,,,collected_by:hongwei Pan,,,,,,,infective endocarditis,,,,,,,,,,,,,,97.9,0.9,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1585976.7,Bergeyella cardium strain HPQL,HPQL,Bergeyella cardium,Bergeyella,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN08913567,1585976,,,,,,,,2020-01-22T00:00:00Z,,PRJNA449612,GCA_009914665.1,CP029149,,Shandong University,PacBio,524.0x,HGAP v. 3.0,1,0,1,2036890,39.626095,1941,1808,blood,,2016-05-31,China,China,,,,Infective Endocarditis,,,,,,,,,,,,,"Bergeyella cardium is an important human pathogen. However, studies regarding the genetic feathers of this species are very rare. Here, we characterized the complete genome sequences of Bergeyella cardium strain QL-PH to further understand the pathogenic mechanism of Bergeyella cardium strains.","collected_by:Qilu Hospital, Shandong University",,,,,,,Infective Endocarditis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,1587.304,Lactobacillus helveticus strain D75,D75,Lactobacillus helveticus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN05417795,1587,,,,,,,,2017-03-13T00:00:00Z,,PRJNA330602,GCA_001746265.2,MJGB00000000,,State Research Institute of Highly Pure Biopreparations,PacBio,422,SMRT Portal v. 2_3_0,1,,1,2053066,37.028034,2294,2019,intestine of a healthy child,,1991,Russia,Russia:Leningrad,,,,,,,,,,,,,,,,,"Initially, our isolates were attributed to Lactobacillus acidophilus. The following studies cast doubt on the correctness of this. With this aim, we sequenced two genomes.",sample_type:bacterial culture,,,,,,,,,,,,,,,,,,,,,99.03,0,,,Genitourinary,- HP,158836.1072,Enterobacter hormaechei strain 14280161202,14280161202,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999974,158836,,,,MLST.Enterobacter_cloacae.392,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864135.1,CP045450,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,118.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,4662942,55.684223,4377,,,,2014,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.47,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.1073,Enterobacter hormaechei strain 14102KSN,14102KSN,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999969,158836,,,,MLST.Enterobacter_cloacae.97,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864035.1,"CP045312,CP045313,CP045314,CP045315,CP045316",,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,96.0x,CLC Genomics Workbench v. 11; Unicycler,1,4,5,4827906,55.11052,4629,,,,2017,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.97,0.66,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.1074,Enterobacter hormaechei strain 14320055602,14320055602,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999995,158836,,,,MLST.Enterobacter_cloacae.150,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864155.1,CP045451,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,115.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,4583965,55.761093,4272,,,,2014,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.47,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.1088,Enterobacter hormaechei strain EC48293,EC48293,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933270,158836,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939555.1,"CP070534,CP070533,CP070532,CP070531,CP070530",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,4,5,5331528,54.887005,5257,5031,sputum-aspirate,,2019-01-02,Czech Republic,Czech Republic: Praha,,,,"Thoracic aortic aneurysm, ruptured",,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Krlovsk Vinohrady,,,,,,,"Thoracic aortic aneurysm, ruptured",,,,,,,,,,,,,,99.47,0.73,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,158836.1089,Enterobacter hormaechei strain EC49583,EC49583,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933280,158836,,,,,,,,2021-03-01T00:00:00Z,,PRJNA700516,GCA_017114585.1,JAFIQG000000000,,Charles University in Prague,PacBio Sequel,250x,Microbial Assembly v. 1.1,2,3,5,5306834,54.863087,5235,4998,mouth swab,,2019-03-15,Czech Republic,Czech Republic: st nad Labem,,,,Acute and subacute endocarditis,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Masarykova nemocnice,,,,,,,Acute and subacute endocarditis,,,,,,,,,,,,,,99.47,0.73,Bloodstream Infections,Other Bloodstream Infections,Oral,Bloodstream Infections-Other Bloodstream Infections HP,158836.1107,Enterobacter hormaechei strain IR5283,IR5283,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561277,158836,,,,MLST.Enterobacter_cloacae.418,,,,2021-03-09T00:00:00Z,,PRJNA672237,GCA_017310485.1,"CP064113,CP064114,CP064115,CP064116",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,3,4,4808700,55.312496,4670,4509,,,2015-08-21,China,China: Beijing,,,,,,,,,,,,,,,,,"aimed to investigate the molecular epidemiology, transmission and evolution of XA-48-producing Enterobacterales and pOXA-48",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.32,1.05,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.1365,Enterobacter hormaechei strain 60214CZ,60214CZ,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22377434,158836,,,,MLST.Enterobacter_cloacae.92,,,,2021-11-01T00:00:00Z,,PRJNA772913,GCA_020695365.1,"CP085743,CP085744,CP085745,CP085746,CP085747",,Charles University in Prague,PacBio Sequel,281x,Microbial assembly v. v.1,1,4,5,5124730,54.782867,5114,4900,tracheal aspirate,,2020-10,Czech Republic,Czech Republic: Prague,,,,Acute cholecystitis,,,,,,,,,,,,,Molecular characterization of VIM-producing Enterobacterales from Czech hospitals,collected_by:Nemocnice Na Homolce,,,,,,,Acute cholecystitis,,,,,,,,,,,,,,99.72,0.23,Urinary Tract Diseases,Lower UTI,Respiratory Tract,Urinary Tract Diseases-Lower UTI HP,158836.1536,Enterobacter hormaechei TUECL19001,TUECL19001,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24341409,158836,,,,MLST.Enterobacter_cloacae.78,,,,2022-01-10T00:00:00Z,,PRJNA791797,GCA_021397695.1,"CP090146,CP090147,CP090148,CP090149",,,Illumina MiSeq; Oxford Nanopore MinION,100.0x,unicycler v. 0.4.8,1,3,4,5039781,54.930264,4910,4754,sputum,,2018-02-28,Taiwan,Taiwan: Taichung,,male,79,Healthcare-Associated Pneumonia,,,,,,,,,,,,,,collected_by:Tungs' Taichung MetroHarbor Hospital (TTMHH),,,,,,,Healthcare-Associated Pneumonia,,,,,,,,,,,,,,99.87,0.78,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,158836.1537,Enterobacter hormaechei TUECL19003,TUECL19003,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24425646,158836,,,,MLST.Enterobacter_cloacae.78,,,,2022-01-10T00:00:00Z,,PRJNA791797,GCA_021398115.1,"CP090192,CP090193,CP090194,CP090195",,,Illumina MiSeq; Oxford Nanopore MinION,100.0x,unicycler v. 0.4.8,1,3,4,5034377,54.9292,4907,4745,pus,,2018-04-07,Taiwan,Taiwan: Taichung,,male,67,Surgical Wound Infection,,,,,,,,,,,,,,collected_by:Tungs' Taichung MetroHarbor Hospital (TTMHH),,,,,,,Surgical Wound Infection,,,,,,,,,,,,,,99.87,0.78,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,158836.1965,Enterobacter hormaechei P7538,P7538,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18255044,158836,,,,,,,,2022-07-05T00:00:00Z,,PRJNA713619,GCA_024138915.1,"CP071833,CP071832,CP071830,CP071831",,,Illumina MiSeq; Oxford Nanopore MinION,21.0x,SPAdes v. May 2020,1,3,4,5653758,54.454548,5698,5404,rectal swab,,2018,France,France: Marseille,,,,disease carrier,,,,,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,disease carrier,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,158836.2037,Enterobacter hormaechei 1074,1074,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173991,158836,,,,,genotype:ST1044,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917315.1,"CP103674,CP103675",,,Oxford Nanopore GridION,176x,Flye v. 2.8.3-b1695,1,1,2,4764181,55.552822,4535,4424,blood,,2017-12-29,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2038,Enterobacter hormaechei 4285,4285,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174055,158836,,,,MLST.Enterobacter_cloacae.141,genotype:ST141,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917395.1,"CP103577,CP103578",,,Oxford Nanopore GridION,460x,Flye v. 2.8.3-b1695,1,1,2,4950435,54.964058,4866,4699,blood,,2019-04-17,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.7,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2039,Enterobacter hormaechei 4453,4453,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174063,158836,,,,MLST.Enterobacter_cloacae.190,genotype:ST190,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917635.1,"CP103642,CP103643,CP103644",,,Oxford Nanopore GridION,36x,Flye v. 2.8.3-b1695,1,2,3,4954006,55.08217,4867,4701,blood,,2018-07-09,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2040,Enterobacter hormaechei 70,70,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173982,158836,,,,MLST.Enterobacter_cloacae.106,genotype:ST106,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917775.1,"CP103494,CP103495,CP103496,CP103497,CP103498",,,Oxford Nanopore GridION,163x,Flye v. 2.8.3-b1695,1,4,5,4918774,55.457375,4778,4627,blood,,2019-12-07,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2041,Enterobacter hormaechei MB4528 Variant,MB4528 Variant,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174038,158836,,,,,genotype:ST90,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918215.1,"CP103679,CP103680,CP103681,CP103682",,,Oxford Nanopore GridION,97x,Flye v. 2.8.3-b1695,1,3,4,5191592,55.199734,5089,4896,blood,,2017-10-22,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2042,Enterobacter hormaechei ST90,ST90,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174037,158836,,,,,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918255.1,"CP103683,CP103684,CP103685,CP103686",,,Oxford Nanopore GridION,127x,Flye v. 2.8.3-b1695,1,3,4,5229427,55.23921,5142,4950,blood,,2017-10-22,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2043,Enterobacter hormaechei 3131,3131,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174019,158836,,,,,genotype:ST461,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918795.1,"CP103722,CP103723,CP103724,CP103725,CP103726",,,Oxford Nanopore GridION,135x,Flye v. 2.8.3-b1695,1,4,5,5068472,55.31168,4976,4804,blood,,2016-12-25,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.2060,Enterobacter hormaechei ECC2783,ECC2783,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31455096,158836,,,,,,,,2022-11-07T00:00:00Z,,PRJNA894355,GCA_026015945.1,"CP110354,CP110355,CP110356,CP110357,CP110358",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,4,5,5388025,54.595627,5385,5153,blood,,2017-09-30,China,China:Hanzghou,,,,pancreatitis,,,,,,,,,,,,,,collected_by:Wenhao Wu,,,,,,,pancreatitis,,,,,,,,,,,,,,100,0.1,Gastrointestinal Diseases,Pancreatic Disorders,Blood and Circulatory System,Gastrointestinal Diseases-Pancreatic Disorders HP,158836.2081,Enterobacter hormaechei K432,K432,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31691762,158836,,,,,,,,2022-11-20T00:00:00Z,,PRJNA900428,,CP110857,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,4862801,55.14026,4765,4613,urine,,2020,China,China: Zhejiang,,,,urinary tract infection,,,,,,,,,,,,,,collected_by:a tertiary hospital,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.9,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,158836.22,Enterobacter hormaechei strain CAV1176,CAV1176,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03733727,158836,,,,,,,,2016-07-15T00:00:00Z,,PRJNA246471,GCA_001874505.1,"CP011662,CP011658,CP011659,CP011661,CP011660",,University of Oxford,PacBio,81X,HGAP3 v. 2.2.0,1,3,5,5043091,55.17,4934,4649,perirectal,,2010-05,USA,USA:Virginia,,,,,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,158836.2644,Enterobacter hormaechei Eh202_LBHALD,Eh202_LBHALD,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35822989,158836,,,,,,,,2023-07-10T00:00:00Z,,PRJNA986271,,"CP129250,CP129251",,,Illumina,60.0x,SPAdes v. 3.15.4,1,1,2,4791394,55.212532,4727,4574,leg pus,,2018-01-25,Senegal,Senegal: Dakar,,,,Hospital-acquired infection after surgery,,,,,,,,,,,,,,collected_by:Bacteriology laboratory of Aristide Le Dantec National University teaching hospital in Dakar Senegal,,,,,,,Hospital-acquired infection after surgery,,,,,,,,,,,,,,99.9,0.1,Nosocomial Infections,Other Nosocomial Infections,Skin and Soft Tissue,Nosocomial Infections-Other Nosocomial Infections HP,158836.282,Enterobacter hormaechei strain S11_16,S11_16,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10755318,158836,,,,,,,,2019-01-30T00:00:00Z,,PRJNA515436,GCA_004118875.1,"CP035385,CP035386,CP035387,CP035388,CP035389",,University of Birmingham,Illumina; Oxford Nanopore,100.0x,Unicycler v. 0.4.7,1,4,5,5038853,55.107403,4980,4852,n/a,,2016,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,Closed chromosome and plasmid sequences for a single clinical strain of E. hormaechei,collected_by:S. Dunn,,,,,,,N/A,,,,,,,,,,,,,,99.97,0.49,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.416,Enterobacter hormaechei strain C44,C44,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289368,158836,,,,MLST.Enterobacter_cloacae.113,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931325.1,"CP042566,CP042567,CP042568,CP042569,CP042570",,University of Oxford,Oxford Nanopore MiniION,1438x,Unicycler v. SEP-2017,1,4,5,4962392,55.38857,4835,4731,clinical sample,,2013-04-15,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,99.47,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.417,Enterobacter hormaechei strain C15,C15,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289339,158836,,,,MLST.Enterobacter_cloacae.114,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931405.1,"CP042488,CP042489,CP042490,CP042491,CP042492",,University of Oxford,Oxford Nanopore MiniION,1043x,Unicycler v. SEP-2017,1,4,5,5188104,54.74314,5141,4969,clinical sample,,2009-02-23,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,99.77,1.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.420,Enterobacter hormaechei strain C45,C45,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289303,158836,,,,,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931645.1,"CP042551,CP042552,CP042553,CP042554,CP042555",,University of Oxford,Oxford Nanopore MiniION,2580x,Unicycler v. SEP-2017,1,4,5,5538473,54.83582,5560,5369,clinical sample,,2013-04-27,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,99.47,0.18,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.434,Enterobacter hormaechei strain C4,C4,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289289,158836,,,,MLST.Enterobacter_cloacae.113,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931585.1,"CP042540,CP042541,CP042542,CP042543,CP042544",,University of Oxford,Oxford Nanopore MiniION,3051x,Unicycler v. SEP-2017,1,4,5,4972056,55.388092,4856,4745,clinical sample,,2007-06-28,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,99.47,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.490,Enterobacter hormaechei strain BW,BW,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07692716,158836,,,,MLST.Enterobacter_cloacae.110,,,,2020-01-27T00:00:00Z,,PRJNA411992,GCA_009930835.1,"CP023569,CP023572,CP023570,CP023571",,Penn State University,PacBio; Illumina HiSeq,150.0x,Canu for assembly of PacBio reads v. 1.6;,1,3,4,5248533,54.90713,5160,5023,blood and wound,,2013-08-24,USA,USA: University of Michigan University Hospital,,,,Enterobacter bacteremia,,,,,,,,,,,,,"This whole genome sequencing project involves a patient who had a reoccurring Enterobacter hormaechei bacteremia. The infection spanned about 10 months, from the onset of the infection to the death of the patient. During that time, the infection evolved resistance to the multiple antibiotics used to treat it, including the very important class of carbapenems. Bacterial isolates with progressively higher levels of resistance were drawn from the patient at different time points. Later, these isolates were sequenced in order to identify the genetic determinants of the resistance. While all the isolates were sequenced on an Illumina platform, the first isolate to be drawn from the patient, called 24, was also sequenced on a PacBio platform. Because both PacBio and Illumina reads were available, the de novo assembly of the reads from 24 yielded a complete ungapped genomic sequence, consisting of a chromosome and three plasmids. The complete genomic sequence of 24 was used as a template for the assembly of the Illumina reads from the other isolates.","collected_by:Robert Wood, MD",,,,,,,Enterobacter bacteremia,,,,,,,,,,,,,,99.47,1.25,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.491,Enterobacter hormaechei strain BW,BW,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08554725,158836,,,,MLST.Enterobacter_cloacae.110,,,,2020-01-27T00:00:00Z,,PRJNA434358,GCA_009930935.1,"CP027111,CP027112,CP027113",,Penn State University,PacBio; Illumina HiSeq,150.0x,Canu for assembly of PacBio reads v. 1.6;,1,2,3,5255981,54.9045,5194,5056,missing,,2014-05-30,USA,"USA: Ann Arbor, Michigan",,,,Enterobacter bacteremia,,,,,,,,,,,,,"This whole genome sequencing project involves a patient who had a reoccurring Enterobacter hormaechei bacteremia. The infection spanned about 10 months, from the onset of the infection to the death of the patient. During that time, the infection evolved resistance to the multiple antibiotics used to treat it, including the very important class of carbapenems. Bacterial isolates with progressively higher levels of resistance were drawn from the patient at different time points. Later, these isolates were sequenced in order to identify the genetic determinants of the resistance. While all the isolates were sequenced on an Illumina platform, the last isolate to be drawn from the patient, called 56, was also sequenced on a PacBio platform. Because both PacBio and Illumina reads were available, the de novo assembly of the reads from 56 yielded a complete ungapped genomic sequence, consisting of a chromosome and two plasmids.",collected_by:Robert Wood,,,,,,,Enterobacter bacteremia,,,,,,,,,,,,,,99.32,1.25,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,158836.591,Enterobacter hormaechei strain AMS-38,AMS-38,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14492121,158836,,,,,,,,2020-04-20T00:00:00Z,,PRJNA616711,GCA_012562255.1,"CP051132,CP051133,CP051134,CP051135,CP051136",,Academy of Hiroshima University,Oxford Nanopore GridION,166x,flye v. 2.6,1,4,5,5316620,54.90923,5181,,clinical,isolated in Africa and The Middle East,2015-04,Egypt,Egypt: Cairo,,,,,,,,,,,,,,,,,"E. hormaechei clinical isolate, which carries mcr-9 and blaVIM-4 on IncHI2 plasmid had been sequenced. It was isolated in Africa and The Middle East.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.47,0.32,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,158836.608,Enterobacter hormaechei strain AKB48,AKB48,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10107915,158836,,,,MLST.Enterobacter_cloacae.174,,,,2020-05-05T00:00:00Z,,PRJNA492847,GCA_012975085.1,"CP044335,CP044336,CP044337",,National Chung Cheng University,Oxford Nanopore,40.0x,Unicycler v. 0.4.7,1,2,3,4876334,55.53383,4741,4594,tissue,,2014-07-18,Taiwan,Taiwan,,,,sepsis,,,,,,,,,,,,,Analysis of the genome in order to understand the genetic factors leading to virulence and antibiotic resistance,collected_by:Ching-Lin Shy,,,,,,,sepsis,,,,,,,,,,,,,,99.47,0.25,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,158836.811,Enterobacter hormaechei strain ENCL48880,ENCL48880,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15589926,158836,,,,,,,,2020-07-29T00:00:00Z,,PRJNA647548,GCA_013873515.1,"CP059419,CP059420,CP059418,CP059421",,Charles University in Prague,PacBio Sequel,386.0x,Microbial Assembly v. SMRT Link v.9,1,3,4,5132301,54.661427,5067,4811,sputum,,2019,Czech Republic,Czech Republic: Kolin,,,,pneumonia,,,,,,,,,,,,,VIM/MCR producers in the Czech republic,collected_by:Nemocnice Kolin,,,,,,,pneumonia,,,,,,,,,,,,,,99.97,1.17,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,158836.822,Enterobacter hormaechei strain ZHH,ZHH,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15648651,158836,,,,MLST.Enterobacter_cloacae.97,,,,2020-08-09T00:00:00Z,,PRJNA648784,GCA_014117285.1,"CP059711,CP059712,CP059713,CP059714,CP059715,CP059716",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore MiniION,200.0x,Unicycler v. 0.4.0,1,5,6,5415820,54.509808,5449,5187,blood,,2019-08-08,China,China: Hangzhou,,,,Bacteremia,,,,,,,,,,,,,Multidrug resistance bacteria,collected_by:Xu Qian,,,,,,,Bacteremia,,,,,,,,,,,,,,99.97,1.36,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,158836.850,Enterobacter hormaechei strain NJGLYY90-CR,NJGLYY90-CR,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450178,158836,,,,MLST.Enterobacter_cloacae.418,,,,2020-09-28T00:00:00Z,,PRJNA659615,GCA_014771415.1,"CP061744,CP061745,CP061746,CP061747,CP061748",,Nanjing Drum Tower Hospital,Oxford Nanopore PromethION; Illumina,177.47x,Unicycler v. v0.4.8,1,4,5,5091488,54.92312,5061,4856,secretion,,,China,"China: Jiangsu, Nanjing",,,,Acute pneumonia,,,,,,,,,,,,,"Genome sequencing of pathogenic bacteria (Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, etc.)",collected_by:Xiaoli Cao;sample_type:cell culture,,,,,,,Acute pneumonia,,,,,,,,,,,,,,99.77,0.9,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia NHP,1589.89,Lactobacillus pentosus strain ZFM94,ZFM94,Lactiplantibacillus pentosus,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07302932,1589,,,,,,,,2018-10-08T00:00:00Z,,PRJNA392489,GCA_003627375.1,"CP032659,CP032660,CP032661,CP032662",,Zhejiang Gongshang University,PacBio RSII; Illumina HiSeq,46.0x,GATK v. v1.6-13; Celera Assembler v.,1,3,4,3687169,46.19273,3613,3343,healthy infant fecal samples,,2011-07-14,China,China:Zhejiang Maternal and Child Health Hospital,,,,,,,,,,,,,,,,,The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties. And it also can provide the information compared with other related species.,sample_type:thallus,,,,,,,,,,,,,,,,,,,,,99.38,2.78,,,Gastrointestinal,- NHP,1590.1174,Lactobacillus plantarum strain ZFM55,ZFM55,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07305427,1590,,,,,,,,2018-09-23T00:00:00Z,,PRJNA392731,GCA_003589725.1,"CP032359,CP032360,CP032361,CP032362",,Zhejiang Gongshang University,PacBio RSII; Illumina HiSeq,47.0x,FALCON v. v0.3.0; proovread v. 2.12;,1,3,4,3412302,44.32685,3414,3253,healthy infant fecal samples,,2011-07-28,China,China:Zhejiang maternal and child health hospital,,,,,,,,,,,,,,,,,The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties.And it also can provide the information compared with other related species.,sample_type:thallus,,,,,,,,,,,,,,,,,,,,,100,2,,,Gastrointestinal,- NHP,1590.1209,Lactobacillus plantarum strain ZFM9,ZFM9,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07303085,1590,,,,,,,,2018-10-08T00:00:00Z,,PRJNA392582,GCA_003627335.1,"CP032642,CP032643,CP032644,CP032645,CP032646,CP032647",,Zhejiang Gongshang University,PacBio RSII; Illumina HiSeq,44.0x,GATK v. v1.6-13; Celera Assembler v. 8.3;,1,5,6,3434010,44.256218,3480,3280,healthy infant fecal samples,,2005-04-03,China,China:Zhejiang maternal and child health hospital,,,,,,,,,,,,,,,,,The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties.And it also can provide the information compared with other related species.,sample_type:thallus,,,,,,,,,,,,,,,,,,,,,99.38,2.78,,,Gastrointestinal,- NHP,1590.1210,Lactobacillus plantarum strain ZFM4,ZFM4,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07303049,1590,,,,,,,,2018-10-08T00:00:00Z,,PRJNA392545,GCA_003627355.1,"CP032648,CP032649,CP032650,CP032651",,Zhejiang Gongshang University,PacBio RSII; Illumina HiSeq,46.0x,GATK v. v1.6-13; Celera Assembler v. 8.3;,1,3,4,3303780,44.50351,3371,3143,healthy infant fecal samples,,2005-03-01,China,China:Zhejiang maternal and child health hospital,,,,,,,,,,,,,,,,,The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties.And it also can provide the information compared with other related species.,sample_type:thallus,,,,,,,,,,,,,,,,,,,,,99.38,2.78,,,Gastrointestinal,- NHP,1590.1541,Lactobacillus plantarum strain pc-26,pc-26,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07620858,1590,,,,,,,,2019-07-09T00:00:00Z,,PRJNA403769,GCA_006770485.1,"CP023301,CP023302,CP023303",,BGI,PacBio,200.0x,Celera Assembler v. canu-1.4,1,2,3,3303360,44.465122,3284,3114,healthy adult fecal sample,,2014,China,China,,,,,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis were used to reveal its genetic adaptation and probiotic properties.,sample_type:fecal sample,,,,,,,,,,,,,,,,,,,,,99.07,2.78,,,Gastrointestinal,- NHP,1590.1542,Lactobacillus plantarum strain LLY-606,LLY-606,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07620857,1590,,,,,,,,2019-07-09T00:00:00Z,,PRJNA403768,GCA_006770505.1,"CP023306,CP023307",,BGI,PacBio,200.0x,Celera Assembler v. canu-1.4,1,1,2,3259255,44.472004,3224,3069,healthy adult fecal sample,,2014,China,China,,,,,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis were used to reveal its genetic adaptation and probiotic properties.,sample_type:fecal sample,,,,,,,,,,,,,,,,,,,,,99.07,2.93,,,Gastrointestinal,- NHP,1590.2253,Lactiplantibacillus plantarum strain ATCC 202195,ATCC 202195,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN14169821,1590,,,,,,ATCC:202195,,2021-05-13T00:00:00Z,,PRJNA611725,GCA_018351295.1,"CP063750,CP063751,CP063752",,DuPont Nutrition and Biosciences,Illumina NextSeq; Oxford Nanopore GridION,79.68x,Unicycler v. 0.4.7,1,2,3,3353701,44.35094,3297,3092,healthy infant feces,,2017-10,USA,USA,,,,,,,,,,,,,,,,,Lactobacillus plantarum ATCC202195,sample_type:freeze dried sample;biomaterial_provider:ATCC;collected_by:DuPont Nutrition and Biosciences,,,,,,,,,,,,,,,,,,,,,99.07,3.09,,,Gastrointestinal,- NHP,1590.548,Lactobacillus plantarum strain LP3,LP3,Lactiplantibacillus plantarum,Lactiplantibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN05631073,1590,,,,,,,,2017-09-05T00:00:00Z,,PRJNA340346,GCA_002286275.1,"CP017066,CP017067,CP017068",,Korea Food Research Institute,PacBio,97,CANU v. 1.3,1,2,3,3329954,44.44,3247,3009,commercial dietary supplements,,2015-09-08,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,LP3 strain was isolated from Commercial dietary supplements,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,1,,,Other,- NHP,1596.441,Lactobacillus gasseri strain Lg1266,Lg1266,Lactobacillus gasseri,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN23313748,1596,,,,,,,,2021-11-28T00:00:00Z,,PRJNA761982,GCA_020991185.1,"CP087761,CP087762",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","569x, 714x",Unicycler v. v.0.4.8,1,1,2,1819909,35.114998,1750,1679,urine,isolated from the urine of postmenopausal women with different histories of rUTI,2019-05,USA,"USA: Dallas, Texas",,,,,,,,,,,,,,,,,"Lactobacilli are commonly found in the urine of healthy women, hinting at a possible protective role in the female urinary tract. Recurrent urinary tract infections (rUTIs) are often associated with microbial dysbiosis in the bladder, involving depletion of lactobacilli. Here, we report the complete genome sequences of several Lactobacillus spp. isolated from the urine of postmenopausal women with different histories of rUTI.",sample_type:Whole organism;collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,,,,,,,,,,,,,,,99.22,0,,,Urinary Tract,- NHP,1596.442,Lactobacillus gasseri strain Lg637,Lg637,Lactobacillus gasseri,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN23313746,1596,,,,,,,,2021-11-28T00:00:00Z,,PRJNA761982,GCA_020991205.1,"CP087763,CP087764",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","590x, 443x",Unicycler v. v.0.4.8,1,1,2,1941578,34.87189,1906,1804,urine,isolated from the urine of postmenopausal women with different histories of rUTI,2019-03,USA,"USA: Dallas, Texas",,,,,,,,,,,,,,,,,"Lactobacilli are commonly found in the urine of healthy women, hinting at a possible protective role in the female urinary tract. Recurrent urinary tract infections (rUTIs) are often associated with microbial dysbiosis in the bladder, involving depletion of lactobacilli. Here, we report the complete genome sequences of several Lactobacillus spp. isolated from the urine of postmenopausal women with different histories of rUTI.",sample_type:Whole organism;collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,,,,,,,,,,,,,,,99.03,0.78,,,Urinary Tract,- NHP,1596.443,Lactobacillus gasseri strain Lg1199,Lg1199,Lactobacillus gasseri,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN23313747,1596,,,,,,,,2021-11-29T00:00:00Z,,PRJNA761982,GCA_020995385.1,"CP087959,CP087960,CP087961,CP087962",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","532x, 613x",Unicycler v. v.0.4.8,1,3,4,2081630,34.667496,2023,1954,urine,isolated from the urine of postmenopausal women with different histories of rUTI,2019-06,USA,"USA: Dallas, Texas",,,,,,,,,,,,,,,,,"Lactobacilli are commonly found in the urine of healthy women, hinting at a possible protective role in the female urinary tract. Recurrent urinary tract infections (rUTIs) are often associated with microbial dysbiosis in the bladder, involving depletion of lactobacilli. Here, we report the complete genome sequences of several Lactobacillus spp. isolated from the urine of postmenopausal women with different histories of rUTI.",sample_type:Whole organism;collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,,,,,,,,,,,,,,,99.22,0.15,,,Urinary Tract,- NHP,1597.275,Lactobacillus paracasei strain ZFM54,ZFM54,Lacticaseibacillus paracasei,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN07305422,1597,,,,,,,,2018-10-08T00:00:00Z,,PRJNA392728,GCA_003627255.1,"CP032637,CP032638,CP032639",,Zhejiang Gongshang University,PacBio RSII; Illumina HiSeq,42.0x,Celera Assembler v. 8.3; SMRT Analysis v.,1,2,3,3048677,46.33574,3245,3101,healthy infant fecal samples,,2011-08-03,China,China:Zhejiang maternal and child health hospital,,,,,,,,,,,,,,,,,The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties.And it also can provide the information compared with other related species.,sample_type:thallus,,,,,,,,,,,,,,,,,,,,,99.4,0,,,Gastrointestinal,- HP,1597.435,Lactobacillus paracasei strain 10266,10266,Lacticaseibacillus paracasei,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN09874024,1597,,,,,,,,2019-09-09T00:00:00Z,,PRJNA487125,GCA_008329845.1,"CP031785,CP031786",,Shandong Provincial Hospital Affiliated to Shandong University,PacBio,450.0x,HGAP v. 2.3.0,1,1,2,3044908,46.325077,3226,3068,blood,isolated and sequenced,2017-06-28,China,China,,,,endocarditis,,,,,,,,,,,,,"In this study, we report the endocarditis case dued to Lactobacillus paracasei and the strain were isolated and sequenced. As the first full whole genome of Lactobacillus paracasei from clinical infections,we will proved the genomic information for further in-depth analysis and a better understanding of functions of L. paracasei strains for the prevention of invasive infections.",collected_by:Yingying Hao,,,,,,,endocarditis,,,,,,,,,,,,,,99.46,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,1598.1793,Limosilactobacillus reuteri M2021619,M2021619,Limosilactobacillus reuteri,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN24114820,1598,,,,,,,,2022-01-13T00:00:00Z,,PRJNA789472,GCA_021459965.1,CP090476,,,Illumina; Nanopore,895.0x,CANU v. v1.5; Racon v. v3.4.3,1,0,1,2229645,39.06734,2205,2107,fecal sample from healthy young woman,,2020-09-15,China,China:Shanghai,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.46,0,,,Gastrointestinal,- NHP,1598.864,Lactobacillus reuteri,reuteri,Limosilactobacillus reuteri,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN12990932,1598,,,,,,,,2019-10-20T00:00:00Z,,PRJNA576342,GCA_009184725.1,"CP045049,CP045050",,Guangxi University,Illumina HiSeq+nanopore,330.0x,Unicycler v. 0.4.6 OR SEP-2018,1,1,2,2047619,38.97693,2060,,,,2015-07,China,China:Bama,,,,,,,,,,,,,,,,,Pan-genome analysis was performed on the complete genome sequence of Lactobacillus reuteri1318 and other strains of Lactobacillus reuteri to explore its strain specificity and probiotic potential.,sample_type:faeces,,,,,,,,,,,,,,,,,,,,,99.45,0,,,Other,- HP,160.24,Treponema pallidum strain UW-148B,UW-148B,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11476981,160,,,,,,,,2019-10-13T00:00:00Z,,PRJNA534087,GCA_009017435.1,CP045005,,University of Washington,Illumina MiSeq,192.3x,SPAdes v. v3.13.0,1,,1,1139562,52.786198,1027,1015,rabbit,,2003,USA,USA: Washington,,,,syphilis,,,,,,,,,,,,,WGS of two Treponema pallidum isolates from a single patient,collected_by:Christina Marra,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,160.25,Treponema pallidum strain UW-148B2,UW-148B2,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11476982,160,,,,,,,,2019-10-13T00:00:00Z,,PRJNA534087,GCA_009017475.1,CP045004,,University of Washington,Illumina MiSeq,275.1x,SPAdes v. v3.13.0,1,,1,1139560,52.78594,1030,1015,rabbit,,2009,USA,USA: Washington,,,,syphilis,,,,,,,,,,,,,WGS of two Treponema pallidum isolates from a single patient,collected_by:Christina Marra,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,160.66,Treponema pallidum UW15939,UW15939,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN30221409,160,,,,,,,,2023-05-17T00:00:00Z,,PRJNA961304,,CP125285,,,Illumina,87.7x,Unicycler v. v0.4.4,1,0,1,1145086,52.771187,1036,985,swab,,2021,USA,USA,,,,syphilis,,,,,,,,,,,,,,,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,160.67,Treponema pallidum UW15953,UW15953,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN30221410,160,,,,,,,,2023-05-17T00:00:00Z,,PRJNA961304,,CP125284,,,Illumina,34x,Unicycler v. v0.4.4,1,0,1,1145082,52.771694,1029,987,swab,,2021,USA,USA,,,,syphilis,,,,,,,,,,,,,,,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,160.69,Treponema pallidum EM211ph,EM211ph,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN30221343,160,,,,,,,,2023-07-02T00:00:00Z,,PRJNA974070,,CP128600,,,Illumina NovaSeq,19.4x,SPAdes v. 3.15,1,0,1,1139534,52.795757,1063,1017,swab,,2021,USA,USA,,,,syphilis,,,,,,,,,,,,,,,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,160.70,Treponema pallidum UAB09TUH034,UAB09TUH034,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN30221376,160,,,,,,,,2023-07-02T00:00:00Z,,PRJNA974070,,CP128599,,,Illumina NovaSeq,447.6x,SPAdes v. 3.15,1,0,1,1139633,52.789112,1027,987,swab,,2021,USA,USA,,,,syphilis,,,,,,,,,,,,,,,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.100,Treponema pallidum subsp. pallidum TpN-CL2,TpN-CL2,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502669,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016445.1,CP095419,,,Illumina MiSeq,57.62x,Snippy v. 4.3.6,1,0,1,1139537,52.790913,1027,984,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,,Male,,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis HP,161.101,Treponema pallidum subsp. pallidum strain Madras,Madras,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN19986645,161,,,,,,,,2022-09-06T00:00:00Z,,PRJNA742901,GCA_024971635.1,CP078121,,"Masaryk University, Faculty of Medicine",Illumina MiSeq,1087x,IDBA_UD v. v. 1.1.1,1,0,1,1139672,52.789864,1032,972,lession,,1954,India,India: Madras,,,,syphilis,,,,,,,,,,,,,The goal of this study was to obtain the complete genome sequence of Treponema pallidum subsp. pallidum strain Madras. A high-quality genome sequence of Treponema pallidum subsp. pallidum strain Madras was assembled using a pooled segment genome sequencing technique and Illumina sequencing.,collected_by:CDC,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.102,Treponema pallidum subsp. pallidum Madras,Madras,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN19986645,161,,,,,,,,2022-09-06T00:00:00Z,,PRJNA742901,GCA_024971635.1,CP078121,,,Illumina MiSeq,1087x,IDBA_UD v. v. 1.1.1,1,0,1,1139672,52.789864,1032,972,lession,,1954,India,India: Madras,,,,syphilis,,,,,,,,,,,,,,collected_by:CDC,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.104,Treponema pallidum subsp. pallidum Strasbourg_6715,Strasbourg_6715,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32270356,161,,,,,,,,2023-01-26T00:00:00Z,,PRJNA912995,,CP115658,,,Illumina MiSeq,13.99x,EAGER v. 2.4.5,1,0,1,1139553,52.69727,1096,1044,autopsy case 6715 ffpe,,1947,France,France: Strasbourg,,male,9 days,Congenital Syphilis,,host_disease_outcome:death,,,,,,,,,,,,collected_by:Institute of Pathological Anatomy of the Faculty of Medicine of the University of Strasbourg,,,,,,,Congenital Syphilis,,death,,,,,,,,,,,,100,4,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.105,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097693,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111128,,,Illumina MiSeq,253.0x,SPAdes v. 3.15,1,0,1,1139542,52.768696,1035,989,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.106,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097692,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111129,,,Illumina MiSeq,287.0x,SPAdes v. 3.15,1,0,1,1139545,52.76888,1036,992,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.107,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097691,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111130,,,Illumina MiSeq,136.0x,SPAdes v. 3.15,1,0,1,1139546,52.769306,1041,993,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.108,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097690,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111131,,,Illumina MiSeq,37.0x,SPAdes v. 3.15,1,0,1,1139545,52.768936,1041,992,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.109,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097687,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111132,,,Illumina MiSeq,125.0x,SPAdes v. 3.15,1,0,1,1139545,52.768757,1038,990,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.110,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097685,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111133,,,Illumina MiSeq,83.0x,SPAdes v. 3.15,1,0,1,1139547,52.773476,1058,1011,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,4,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.111,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097684,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111134,,,Illumina MiSeq,483.0x,SPAdes v. 3.15,1,0,1,1139539,52.768764,1038,992,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.112,Treponema pallidum subsp. pallidum SS14,SS14,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN31097683,161,,,,,,,,2023-03-14T00:00:00Z,,PRJNA885511,,CP111135,,,Illumina MiSeq,61.7x,SPAdes v. 3.15,1,0,1,1139544,52.768612,1032,990,in vitro culture,,2021,,not applicable,,,,Syphilis,,,,,,,,,,,,,,"collected_by:Lorenzo Giacani, University of Washington;sample_type:coculture with SfEP1",,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.67,Treponema pallidum subsp. pallidum strain Haiti B,Haiti B,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN07780978,161,,,,,,,,2018-10-07T00:00:00Z,,PRJNA414170,GCA_003627115.1,CP032623,,"Masaryk University, Faculty of Medicine",Illumina MiSeq; Sanger,3504.0x,SeqMan NGen v. 4.1.0.,1,,1,1139526,52.78498,1038,1015,lesions on the lower abdomen,isolated in 1951 on Haiti,1951,Haiti,Haiti: Cotes-de-Fer,,male,11,syphilis,,,,,,,,,,,,,Complete genome sequencing of Treponema pallidum subsp. pallidum strain Haiti B isolated in 1951 on Haiti.,collected_by:Dr S. Levitan,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.68,Treponema pallidum subsp. pallidum strain CW88,CW88,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534861,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311045.1,CP034912,,Masaryk University,Illumina NextSeq,68x,SPAdes v. 3.11.1,1,,1,1139445,52.78267,1042,969,genital smear,,2017,Czech Republic,Czech Republic,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.69,Treponema pallidum subsp. pallidum strain CW83,CW83,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534856,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311085.1,CP034917,,Masaryk University,Illumina NextSeq,35x,SPAdes v. 3.11.1,1,,1,1139543,52.785637,1037,973,genital smear,,2015,Cuba,Cuba,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.70,Treponema pallidum subsp. pallidum strain CW86,CW86,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534859,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311065.1,CP034914,,Masaryk University,Illumina NextSeq,38x,SPAdes v. 3.11.1,1,,1,1139665,52.786186,1034,972,genital smear,,2013,France,France,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.71,Treponema pallidum subsp. pallidum strain CW82,CW82,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534855,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311105.1,CP034972,,Masaryk University,Illumina NextSeq,127x,SPAdes v. 3.11.1,1,,1,1139773,52.792435,1034,970,genital smear,,2016,Cuba,Cuba,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.72,Treponema pallidum subsp. pallidum strain CW65,CW65,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534854,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311125.1,CP034918,,Masaryk University,Illumina NextSeq,27x,SPAdes v. 3.11.1,1,,1,1139123,52.78213,1034,971,anal smear,,2014,Australia,Australia,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.73,Treponema pallidum subsp. pallidum strain CW56,CW56,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534852,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311145.1,CP034920,,Masaryk University,Illumina NextSeq,84x,SPAdes v. 3.11.1,1,,1,1139415,52.783318,1040,972,genital smear,,2013,Cuba,Cuba,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.74,Treponema pallidum subsp. pallidum strain CW30,CW30,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534851,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311165.1,CP034921,,Masaryk University,Illumina NextSeq,500x,SPAdes v. 3.11.1,1,,1,1139568,52.785915,1039,971,genital smear,,2014,Czech Republic,Czech Republic,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.75,Treponema pallidum subsp. pallidum strain CW85,CW85,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534858,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311185.1,CP034915,,Masaryk University,Illumina NextSeq,221x,SPAdes v. 3.11.1,1,,1,1139522,52.78411,1037,970,genital smear,,2016,France,France,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.76,Treponema pallidum subsp. pallidum strain CW84,CW84,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534857,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311205.1,CP034916,,Masaryk University,Illumina NextSeq,216x,SPAdes v. 3.11.1,1,,1,1139423,52.78282,1040,971,genital smear,,2015,France,France,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.77,Treponema pallidum subsp. pallidum strain CW59,CW59,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534853,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005311445.1,CP034919,,Masaryk University,Illumina NextSeq,199x,SPAdes v. 3.11.1,1,,1,1139301,52.78409,1034,971,anal smear,,2012,France,France,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.78,Treponema pallidum subsp. pallidum strain CW87,CW87,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10534860,161,,,,,,,,2019-05-14T00:00:00Z,,PRJNA508872,GCA_005341485.1,CP034913,,Masaryk University,Illumina NextSeq,42x,SPAdes v. 3.11.1,1,,1,1139592,52.78203,1040,969,bucal smear,,2016,France,France,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Ear,Sexually Transmitted Infections (STIs)-Syphilis HP,161.79,Treponema pallidum subsp. pallidum strain Philadelphia 1,Philadelphia 1,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10581167,161,,,,,,,,2019-05-16T00:00:00Z,,PRJNA508872,GCA_005408385.1,CP035193,,Masaryk University,Illumina MiSeq; Sanger,2577.28x,SeqMan NGen v. 4.1.0,1,,1,1139569,52.785774,1039,975,unknown,,1988,USA,USA: Philadelphia,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",collected_by:CDC,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.80,Treponema pallidum subsp. pallidum strain Grady,Grady,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN10581168,161,,,,,,,,2019-05-16T00:00:00Z,,PRJNA508872,GCA_005408405.1,CP035104,,Masaryk University,Illumina MiSeq; Sanger,1510.37x,SeqMan NGen v. 4.1.0,1,,1,1139058,52.77803,1034,973,unknown,,1980,USA,USA: Atlanta,,,,syphilis,,,,,,,,,,,,,"This study aimed at obtaining complete genome sequences of Treponema pallidum subsp. pallidum strains causing contemporary syphilis infection. To achieve this aim, a new DpnI enrichment approach was used based on selective binding of prokaryotic DNA in samples containing eukaryotic DNA.",collected_by:CDC,,,,,,,syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.81,Treponema pallidum subsp. pallidum strain X-4,X-4,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11812273,161,not applicable,,not applicable,,,not applicable,,2019-05-29T00:00:00Z,,PRJNA544173,GCA_005885795.1,CP040555,,"Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China",Illumina HiSeq,4201.0x,SOAPdenovo v. unspecified,1,,1,1139838,52.794785,1029,1015,skin lesion,,2017-05-22,China,China: Xiamen,,male,62,Syphilis,,host_description:not collection;host_disease_outcome:not collection;host_disease_stage:primary syphilis;host_health_state:not collection;host_subject_id:not collection,,,,,,,,,,,"The overlap among human pathogenic treponemas in transmission and clinical manifestations reminds us need to be careful to characteristic a isolate with a novel or unusual molecular sequence-type. Recently, we identified a novel tp0548 subtype from a patient X-4 who attended the outpatient department of Zhongshan Hospital, Xiamen University for indurated painful genital ulceration. Out of careful consideration, we conduct further molecular analysis in genome-scale to fully characterize the isolate and determine whether the infection agent of the X-4 isolate was a novel TPA strain or other treponemas which was misdiagnosed clinically.","collected_by:Zhongshan Hospital, Xiamen University;passage_history:not applicable;specimen_voucher:not applicable",,,,,,,Syphilis,not collection,not collection,not collection,primary syphilis,not applicable,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Skin and Soft Tissue,Sexually Transmitted Infections (STIs)-Syphilis HP,161.85,Treponema pallidum subsp. pallidum strain SMUTp_01,SMUTp_01,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN12638753,161,,,,,,,,2020-11-05T00:00:00Z,,PRJNA562373,GCA_015239315.1,CP051885,,Southern Medical University,Illumina MiSeq,325.0x,Bwa-mem v. 0.7.15-r1140,1,0,1,1139569,52.772083,1030,,chancre,,2018-06-13,China,China: Guangzhou,,,,Syphilis,,,,,,,,,,,,,"Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis. This study presents six TPA genomes of Chinese isolates, four of them obtained directly from the clinical material (strain SMUTp_04, SMUTp_07, SMUTp_08, and SMUTp_09) and two obtained from a multiplication in rabbits(strain SMUTp_01 and SMUTp_02).",collected_by:Dermatology hospital of Southern Medical University;lab_host:rabbit testicle,,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.86,Treponema pallidum subsp. pallidum strain SMUTp_07,SMUTp_07,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN12638759,161,,,,,,,,2020-11-05T00:00:00Z,,PRJNA562373,GCA_015239415.1,CP051890,,Southern Medical University,Illumina MiSeq,9.0x,Bwa-men v. 0.7.15-r1140,1,0,1,1139633,52.73765,1050,,chancre,,2018-03-02,China,China: Guangzhou,,,,Syphilis,,,,,,,,,,,,,"Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis. This study presents six TPA genomes of Chinese isolates, four of them obtained directly from the clinical material (strain SMUTp_04, SMUTp_07, SMUTp_08, and SMUTp_09) and two obtained from a multiplication in rabbits(strain SMUTp_01 and SMUTp_02).",collected_by:Dermatology hospital of Southern Medical University,,,,,,,Syphilis,,,,,,,,,,,,,,98.34,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.87,Treponema pallidum subsp. pallidum strain SMUTp_02,SMUTp_02,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN12638754,161,,,,,,,,2020-11-05T00:00:00Z,,PRJNA562373,GCA_015239335.1,CP051886,,Southern Medical University,Illumina MiSeq,908.0x,Bwa-men v. 0.7.15-r1140,1,0,1,1139569,52.767693,1032,,rabbit testicles,,2017-08-12,China,China: Guangzhou,,,,Syphilis,,,,,,,,,,,,,"Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis. This study presents six TPA genomes of Chinese isolates, four of them obtained directly from the clinical material (strain SMUTp_04, SMUTp_07, SMUTp_08, and SMUTp_09) and two obtained from a multiplication in rabbits(strain SMUTp_01 and SMUTp_02).",collected_by:Dermatology hospital of Southern Medical University,,,,,,,Syphilis,,,,,,,,,,,,,,99.17,0,Sexually Transmitted Infections (STIs),Syphilis,Genitourinary,Sexually Transmitted Infections (STIs)-Syphilis HP,161.88,Treponema pallidum subsp. pallidum strain SMUTp_04,SMUTp_04,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN12638756,161,,,,,,,,2020-11-05T00:00:00Z,,PRJNA562373,GCA_015239355.1,CP051887,,Southern Medical University,Illumina MiSeq,202.0x,Bwa-men v. 0.7.15-r1140,1,0,1,1139569,52.77208,1039,,chancre,,2018-01-10,China,China: Guangzhou,,,,Syphilis,,,,,,,,,,,,,"Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis. This study presents six TPA genomes of Chinese isolates, four of them obtained directly from the clinical material (strain SMUTp_04, SMUTp_07, SMUTp_08, and SMUTp_09) and two obtained from a multiplication in rabbits(strain SMUTp_01 and SMUTp_02).",collected_by:Dermatology hospital of Southern Medical University,,,,,,,Syphilis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,161.95,Treponema pallidum subsp. pallidum TpN-CL8,TpN-CL8,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502673,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016345.1,CP095415,,,Illumina MiSeq,29.7x,Snippy v. 4.3.6,1,0,1,1139539,52.791084,1030,986,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,,Male,,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis HP,161.96,Treponema pallidum subsp. pallidum TpN-CL5,TpN-CL5,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502672,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016365.1,CP095416,,,Illumina MiSeq,52.35x,Snippy v. 4.3.6,1,0,1,1139582,52.791813,1024,985,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,,Male,,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis HP,161.97,Treponema pallidum subsp. pallidum TpN-CL1,TpN-CL1,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502668,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016385.1,CP095420,,,Illumina MiSeq,19.59x,Snippy v. 4.3.6,1,0,1,1138497,52.785206,1025,985,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male;host_disease_outcome:Recovery;host_disease_stage:Tertiary Syphilis,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,Recovery,Male,Tertiary Syphilis,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis HP,161.98,Treponema pallidum subsp. pallidum TpN-CL4,TpN-CL4,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502671,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016405.1,CP095417,,,Illumina MiSeq,51.19x,Snippy v. 4.3.6,1,0,1,1139647,52.790382,1028,986,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,,Male,,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis HP,161.99,Treponema pallidum subsp. pallidum TpN-CL3,TpN-CL3,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN27502670,161,,,,,,Not applicable,,2022-04-17T00:00:00Z,,PRJNA825109,GCA_023016425.1,CP095418,,,Illumina MiSeq,32.53x,Snippy v. 4.3.6,1,0,1,1139665,52.79104,1025,986,cerebrospinal fluid,,1912-06-30,USA,"USA: DC, Washington",,male,25,syphilis,,host_description:Male,,,,,,,,,,,,"identified_by:Diane G. Edmondson, Steven J. Norris;collected_by:H. J. Nichols, W. H. Hough",,,,,,,syphilis,,,Male,,,Nichols clone,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Syphilis,Central Nervous System,Sexually Transmitted Infections (STIs)-Syphilis NHP,1613.127,Lactobacillus fermentum strain SNUV175,SNUV175,Limosilactobacillus fermentum,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN06174220,1613,,,,,,,,2017-01-10T00:00:00Z,,PRJNA358449,GCF_001941785.1,"CP019030,CP019031,CP019032,CP019033","NZ_CP019030.1,NZ_CP019031.1,NZ_CP019032.1,NZ_CP019033.1","KoBioLabs, Inc.",PacBio,276.0x,HGAP v. 3.0,1,3,4,2272328,51.02,2379,2236,vaginal tract,,2014-06,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,"Complete Genome Sequencing of Lactobacillus fermentum Strain SNUV175, a probiotic for Treatment of Bacterial Vaginosis",sample_type:Culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Genitourinary,- NHP,1613.133,Lactobacillus fermentum strain FTDC 8312,FTDC 8312,Limosilactobacillus fermentum,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN06703219,1613,,,,,,,,2017-05-09T00:00:00Z,,PRJNA382300,GCA_002119645.1,CP021104,,Universiti Sains Malaysia,PacBio,146.0x,HGAP v. APRIL-2017,1,,1,2239921,50.99,2311,,fecal sample,,2010,Malaysia,Malaysia,,,,,,,,,,,,,,,,,Here we describe the genome sequence of L. fermentum FTDC 8312 which is a probiotic strain that reduce serum cholesterol level via alteration of gut microbiota,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,1613.429,Lactobacillus fermentum strain MTCC 5898,MTCC 5898,Limosilactobacillus fermentum,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN10868412,1613,,,,,,,,2019-02-18T00:00:00Z,,PRJNA520814,GCA_004208815.1,CP035904,,ICAR-National Dairy Research Institute,Illumina NextSeq,85.0x,BWA-Mem Version 0.7.12 v.,1,,1,2098685,52.508724,2018,1782,infant fecal sample,,2013-10,India,India: Karnal,temperature:Room temperature,,,,,,,,,,,,,,,,Whole Genome Sequencing of Probiotic Strain Lactobacillus fermentum MTCC 5898,sample_type:Bacterial plate;collected_by:National Dairy Research Institute,Human feces,Toilet,None,http://dx.doi.org/10.1016/j.nutres.2014.09.006,,,,,,,,,,,,,Human feces,,,,99.18,0.55,,,Gastrointestinal,- NHP,1613.511,Lactobacillus fermentum strain HFD1,HFD1,Limosilactobacillus fermentum,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN14470504,1613,,,,,,,,2020-04-12T00:00:00Z,,PRJNA615901,GCA_012273035.1,CP050919,,Kazan Federal University,Illumina MiSeq; Oxford Nanopore MiniION,1100.0x,Unicycler v. v.0.4.8-beta,1,0,1,2101878,51.752007,2112,2042,,,2015-02,Russia,Russia: Kazan,,,,,,,,,,,,,,,,,"Characterization and de novo assembly of novel Lactobacillus Fermentum strain, producer of antimicrobial peptides.",sample_type:feces of healthy woman,,,,,,,,,,,,,,,,,,,,,99.18,0.82,,,Other,- HP,161879.62,Corynebacterium kroppenstedtii strain yu01,yu01,Corynebacterium kroppenstedtii,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30698500,161879,,,,,,,,2022-09-19T00:00:00Z,,PRJNA877407,GCA_025252365.1,CP104321,,Hohai University,Illumina NovaSeq; Oxford Nanopore MinION,200.0x,Unicycler v. 0.4.0,1,0,1,2536825,56.844955,2283,2101,interstitial fluid,,2021-10-05,China,China: Nanjing City,,,,mastitis,,,,,,,,,,,,,Potential pathogeny of breast infection,collected_by:Ying Huang,,,,,,,mastitis,,,,,,,,,,,,,,97.41,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,161879.63,Corynebacterium kroppenstedtii yu01,yu01,Corynebacterium kroppenstedtii,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30698500,161879,,,,,,,,2022-09-19T00:00:00Z,,PRJNA877407,GCA_025252365.1,CP104321,,,Illumina NovaSeq; Oxford Nanopore MinION,200.0x,Unicycler v. 0.4.0,1,0,1,2536825,56.844955,2283,2101,interstitial fluid,,2021-10-05,China,China: Nanjing City,,,,mastitis,,,,,,,,,,,,,,collected_by:Ying Huang,,,,,,,mastitis,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- NHP,1623.283,Ligilactobacillus ruminis strain ATCC 25644,ATCC 25644,Ligilactobacillus ruminis,Ligilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN20222695,1623,,,,,,ATCC:25644,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150895.1,CP102284,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2187892,43.86981,2349,2054,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.37,0,,,Other,- NHP,1624.628,Ligilactobacillus salivarius strain AR809,AR809,Ligilactobacillus salivarius,Ligilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN22202533,1624,,,,,,,,2021-10-20T00:00:00Z,,PRJNA770025,GCA_020535185.1,"CP084925,CP084926,CP084927,CP084928,CP084929",,University of Shanghai for Science and Technology,Illumina; PacBio,2312.64x,SOAPdenovo v. v2.04; GapCloser v. v1.12,1,4,5,2028711,32.86688,1889,1853,,isolated habitats,2021-03,China,China:Shanghai,,,,,,,,,,,,,,,,,"it is not clear about the genes related to probiotic properties of L. salivarius AR809. To gain an insight into genetic elements, we sequenced the whole genome of this strain and compared with other strains of the same species from different isolated habitats. This work will provide insight for a deeper understanding of molecular mechanisms which are responsible for its probiotic properties of L. salivarius.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.48,0,,,Other,- NHP,1633.112,Limosilactobacillus vaginalis LV1494_C165,LV1494_C165,Limosilactobacillus vaginalis,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN33053617,1633,,,,,,,,2023-02-13T00:00:00Z,,PRJNA930673,,CP117295,,,Illumina; Oxford Nanopore MinION,1x,unicycler v. v0.4.8,1,0,1,1837310,40.59032,1788,1744,urine,,2020-08-13,,not applicable,,,,,,,,,,,,,,,,,,,urogenital microbiome,urine sample,urine,5% Sheep Blood Agar,,,,,,,,,,,,,urogenital microbiome,,,,99.3,0,,,Urinary Tract,- HP,1639.11794,Listeria monocytogenes 20-05651,20-05651,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN26535716,1639,,,,MLST.Listeria_monocytogenes.394,,,,2022-03-23T00:00:00Z,,PRJNA814010,GCA_022682045.1,CP093220,,,Illumina MiSeq; Oxford Nanopore MinION,94.0x,SPAdes v. 3.13.1,1,0,1,2920067,37.99632,2901,2847,blood culture,,2020-10-20,Germany,Germany,,,,listeriosis,,,,,,,,,,,,,,collected_by:Robert Koch Institute,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.12145,Listeria monocytogenes s2020TJ,s2020TJ,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN23176672,1639,,,,,,,,2022-05-20T00:00:00Z,,PRJNA780773,GCA_023515845.1,"CP087264,CP087265",,,Illumina,543.0x,Fyle v. V2.5,1,1,2,3023666,38.054436,2976,2919,cerebrospinal fluid,,2020-09-20,China,China:Tianjin,,,,Infection of the central nervous system,,,,,,,,,,,,,,collected_by:WANG YUE,,,,,,,Infection of the central nervous system,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,1639.12735,Listeria monocytogenes FSCNU_000110,FSCNU_000110,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN29673611,1639,,,,MLST.Listeria_monocytogenes.224,,,,2022-07-25T00:00:00Z,,PRJNA858193,GCA_024399455.1,CP101619,,,Illumina MiSeq; Oxford Nanopore MinION,322.92x,Unicycler v. 0.4.8,1,0,1,2933635,37.992115,2875,2824,school cafeteria,,2018-09,South Korea,South Korea: Seoul,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Seoul Health and Environment Research Institute,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13128,Listeria monocytogenes MKELm2_2022,MKELm2_2022,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31888656,1639,,,,MLST.Listeria_monocytogenes.391,genotype:ST391,,,2023-01-02T00:00:00Z,,PRJNA906001,,CP115041,,,Illumina MiSeq; Oxford Nanopore GridION,1x,Unicycler v. 0.4.9b,1,0,1,2966007,37.944042,2961,2901,blood or cerebrospinal fluid,,,,Not collected,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Satens Serum Institut,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13129,Listeria monocytogenes MKELm6_2022,MKELm6_2022,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31888655,1639,,,,MLST.Listeria_monocytogenes.224,genotype:ST224,,,2023-01-02T00:00:00Z,,PRJNA906001,,CP115042,,,Illumina MiSeq; Oxford Nanopore GridION,1x,Unicycler v. 0.9.4b,1,0,1,2950586,37.969913,2912,2860,blood or cerebrospinal fluid,,,,Not collected,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Satens Serum Institut,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13130,Listeria monocytogenes MKELm8_2022,MKELm8_2022,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31888654,1639,,,,MLST.Listeria_monocytogenes.8,genotype:ST8,,,2023-01-02T00:00:00Z,,PRJNA906001,,CP115043,,,Illumina MiSeq; Oxford Nanopore GridION,1x,Unicycler v. 0.4.9b,1,0,1,2952502,37.960686,2957,2904,blood or cerebrospinal fluid,,,,Not collected,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Satens Serum Institut,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13131,Listeria monocytogenes MKELm391_2022,MKELm391_2022,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31888652,1639,,,,MLST.Listeria_monocytogenes.2,genotype:ST2,,,2023-01-02T00:00:00Z,,PRJNA906001,,CP115045,,,Illumina MiSeq; Oxford Nanopore GridION,1x,Unicycler v. 0.4.9b,1,0,1,2995020,37.97337,2960,2904,blood or cerebrospinal fluid,,,,Not collected,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Satens Serum Institut,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13132,Listeria monocytogenes MKELm224_2022,MKELm224_2022,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31888653,1639,,,,MLST.Listeria_monocytogenes.6,genotype:ST6,,,2023-01-02T00:00:00Z,,PRJNA906001,,CP115044,,,Illumina MiSeq; Oxford Nanopore GridION,1x,Unicycler v. 0.4.9b,1,0,1,2948313,38.008957,2927,2874,blood or cerebrospinal fluid,,,,Not collected,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Satens Serum Institut,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13305,Listeria monocytogenes 19-02390,19-02390,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA112128949,1639,IVb,,,MLST.Listeria_monocytogenes.6,,,,2023-02-17T00:00:00Z,,PRJNA902331,,CP111150,,,Illumina MiSeq; Oxford Nanopore MinION,37.0x,Unicycler v. v0.4.8,1,0,1,2956565,37.993687,2943,2888,human listeriosis,,2019,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.13306,Listeria monocytogenes 21-03201,21-03201,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA112128947,1639,IVb,,,MLST.Listeria_monocytogenes.1,,,,2023-02-17T00:00:00Z,,PRJNA902324,,CP111149,,,Illumina NextSeq; Oxford Nanopore MinION,290.0x,Unicycler v. v0.4.8,1,0,1,2946483,38.010403,2929,2871,human listeriosis,,2021,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.13307,Listeria monocytogenes 16-02236,16-02236,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA112128948,1639,,,,MLST.Listeria_monocytogenes.249,,,,2023-02-17T00:00:00Z,,PRJNA902326,,CP111148,,,Illumina MiSeq; Oxford Nanopore MinION,140.0x,Unicycler v. v0.4.8,1,0,1,2976730,37.95393,2922,2874,human listeriosis,,2016,Germany,Germany,,,,,,,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.13308,Listeria monocytogenes 19-07394,19-07394,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN31954760,1639,IVb,,,MLST.Listeria_monocytogenes.1,,,,2023-02-17T00:00:00Z,,PRJEB57450,,CP113891,,,Illumina MiSeq; Oxford Nanopore MinION,151.0x,Unicycler v. v0.4.8,1,0,1,2947414,38.019802,2932,2874,blood,,2019,Germany,Germany,,,,Listeriosis,,,,,,,,,,,,,,collected_by:Robert Koch Institute,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13604,Listeria monocytogenes FSL J1-0049,FSL J1-0049,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620975,1639,3c,,,,,,,2023-06-05T00:00:00Z,,PRJNA664209,,"CP096159,CP096160",,,"Illumina NextSeq 500, Oxford Nanopore",319x,Unicyler v. v0.4.8-beta,1,1,2,3051531,37.932434,3040,2982,human,,,,,,,,listeriosis,,,,,,,,,,,,,,collected_by:CDC,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13605,Listeria monocytogenes FSL J1-0094,FSL J1-0094,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620977,1639,1/2c,,,,,,,2023-06-05T00:00:00Z,,PRJNA664209,,CP096156,,,"Illumina NextSeq 2000, Oxford Nanopore",166x,Unicyler v. v0.4.8-beta,1,0,1,2973834,37.963516,2971,2917,human,,1982,United Kingdom,United Kingdom,,,,listeriosis,,,,,,,,,,,,,,collected_by:WHO,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13607,Listeria monocytogenes FSL J1-0169,FSL J1-0169,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620974,1639,3b,,,MLST.Listeria_monocytogenes.5,,,,2023-06-05T00:00:00Z,,PRJNA664209,,"CP096161,CP096162",,,"Illumina NextSeq 500, Oxford Nanopore",156x,Unicyler v. v0.4.8-beta,1,1,2,3074714,37.954163,3061,3002,human,,1996-12,USA,USA:NY,,,,listeriosis,,,,,,,,,,,,,,collected_by:NYSDOH,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13609,Listeria monocytogenes FSL C1-0115,FSL C1-0115,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620978,1639,3a,,,MLST.Listeria_monocytogenes.370,,,,2023-06-05T00:00:00Z,,PRJNA664209,,CP096155,,,"Illumina NextSeq 500, Oxford Nanopore",255x,Unicyler v. v0.4.8-beta,1,0,1,2977399,37.923637,2968,2922,human,,1998,USA,USA:CT,,,,listeriosis,,,,,,,,,,,,,,collected_by:CTDOH,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13611,Listeria monocytogenes FSL F2-0501,FSL F2-0501,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620980,1639,4b,,,,,,,2023-06-05T00:00:00Z,,PRJNA664209,,CP096153,,,"Illumina NextSeq 2000, Oxford Nanopore",72x,Unicyler v. v0.4.8-beta,1,0,1,2878613,38.24564,2813,2767,human,,2000-08,USA,USA: OH,,,,listeriosis,,,,,,,,,,,,,,collected_by:OHDOH,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.13614,Listeria monocytogenes FSL F2-0695,FSL F2-0695,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN27620979,1639,4a,,,,,,,2023-06-05T00:00:00Z,,PRJNA664209,,CP096154,,,"Illumina NextSeq 2000, Oxford Nanopore",157x,Unicyler v. v0.4.8-beta,1,0,1,2838519,38.27841,2776,2731,human,,2001-10,USA,USA:NY,,,,listeriosis,,,,,,,,,,,,,,collected_by:NYCDOH,,,,,,,listeriosis,,,,,,,,,,,,,,100,0.2,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.2298,Listeria monocytogenes strain VIMHA007,VIMHA007,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN05291441,1639,4b,,,MLST.Listeria_monocytogenes.2,genotype:ST2,,,2016-12-06T00:00:00Z,,PRJNA326717,GCF_001889645.1,CP018149,,N.F.Gamaleya Research Center for Epidemiology and Microbiology,454,28.0,GS De Novo Assembler v. 3,,,1,2991300,37.73,3025,2913,aborted fetus,,2005,Russia,Russia:Khabarovsk,,,,listeriosis,,,,,,,,,,,,,Genetic features analysis of Listeria monocytogenes human isolate,"collected_by:Zaytseva E.A., G.P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia",,,,,,,listeriosis,,,,,,,,,,,,,,99.4,1.8,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.2421,Listeria monocytogenes strain CFSAN042079,CFSAN042079,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN04277002,1639,,,,MLST.Listeria_monocytogenes.120,,,,2017-01-17T00:00:00Z,,PRJNA355549,GCF_001952795.1,CP019170,NZ_CP019170.1,Food and Drug Administration,PacBio,355.43x,HGAP2 v. September 2016,1,,1,3005348,37.99,3049,3005,blood,,2008,Canada,Canada,,,,,,,,,,,,,,,,,This Listeria monocytogenes dataset was developed to provide real groundtruth genome sequence data for validating bioinformatic pipelines.,collected_by:Listeriosis Reference Service for Canada,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.2613,Listeria monocytogenes strain ICDC-LM188,ICDC-LM188,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN04884549,1639,,,,MLST.Listeria_monocytogenes.87,,,,2017-03-20T00:00:00Z,,PRJNA319288,GCA_002043045.1,CP015593,,National Institute for Communicable Disease Control and Prevention,Illumina HiSeq 2000,85x,Velvet v. 1.2.10,1,,1,2982685,38,2969,2893,blood,,2008-12-17,China,China: Beijing,,,,septicemia,,,,,,,,,,,,,to understand the gemonic characters of Listeria monocytogenes,collected_by:Yan Wang,,,,,,,septicemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1639.2624,Listeria monocytogenes strain H34,H34,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN06681248,1639,1/2b,,,MLST.Listeria_monocytogenes.489,,,,2017-04-20T00:00:00Z,,PRJNA381593,GCA_002101275.1,CP020774,,University of Zuerich,PacBio,945.0x,HGAP-3 v. 3,1,,1,2892474,38.05,2872,2823,blood and lung culture,,2016-10-18,Uruguay,Uruguay,,,,neonatal sepsis,,,,,,,,,,,,,human clinical strain,"collected_by:Instituto de Higiene, Universidad de la Republica, Montevideo, Uruguay",,,,,,,neonatal sepsis,,,,,,,,,,,,,,100,0.6,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,1639.4404,Listeria monocytogenes strain 2015TE17781-7,2015TE17781-7,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693612,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045625.1,CP028410,,IZSAM,Illumina Next 500,112x,Spades v. 3.8,1,,1,2894816,38.03603,2885,2861,blood,,2015-06-02,Italy,"Italy: Marche, Ancona",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4405,Listeria monocytogenes strain 2015TE17781-8,2015TE17781-8,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693613,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045605.1,CP028409,,IZSAM,Illumina Next 500,116x,Spades v. 3.8,1,,1,2894813,38.036137,2883,2860,cerebrospinal fluid,,2015-06-07,Italy,"Italy: Marche, Osimo",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4406,Listeria monocytogenes strain 2015TE34286,2015TE34286,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693620,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045585.1,CP028404,,IZSAM,Illumina Next 500,201x,Spades v. 3.8,1,,1,2894816,38.0362,2885,2861,blood,,2015-12-07,Italy,"Italy: Marche, Pesaro- Urbino, San Costanzo",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4407,Listeria monocytogenes strain 2016TE337,2016TE337,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693624,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045565.1,CP028401,,IZSAM,Illumina Next 500,172x,Spades v. 3.8,1,,1,2894816,38.036167,2885,2861,blood,,2015-12-28,Italy,"Italy: Marche, Ancona, Filottrano",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4408,Listeria monocytogenes strain 2016TE3767-1-1,2016TE3767-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693627,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045545.1,CP028398,,IZSAM,Illumina Next 500,213x,Spades v. 3.8,1,,1,2894815,38.036144,2882,2859,cerebrospinal fluid,,2016-02-08,Italy,"Italy: Marche, Macerata, Recanati",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4409,Listeria monocytogenes strain 2016TE340,2016TE340,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693625,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045525.1,CP028400,,IZSAM,Illumina Next 500,229x,Spades v. 3.8,1,,1,2894816,38.036133,2885,2861,blood,,2015-12-28,Italy,"Italy: Marche, Pesaro-Urbino, Fano",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4410,Listeria monocytogenes strain 2016TE3765-1-1,2016TE3765-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693626,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045505.1,CP028399,,IZSAM,Illumina Next 500,165x,Spades v. 3.8,1,,1,2894817,38.036118,2884,2861,blood,,2016-02-08,Italy,"Italy: Marche, Ancona-Falcanora marittima",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4411,Listeria monocytogenes strain 2016TE4965-1-1,2016TE4965-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693631,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045485.1,CP028394,,IZSAM,Illumina Next 500,242x,Spades v. 3.8,1,,1,2894814,38.036194,2885,2861,blood,,2016-02-24,Italy,"Italy: Marche, Macerata, Montecosero",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4412,Listeria monocytogenes strain 2016TE840-1-1,2016TE840-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693632,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045465.1,CP028393,,IZSAM,Illumina Next 500,341x,Spades v. 3.8,1,,1,2894816,38.036133,2885,2861,blood,,2016-01-04,Italy,"Italy: Marche,Macerata, Castefidardo",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4413,Listeria monocytogenes strain 2015TE17781-3,2015TE17781-3,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693608,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045445.1,CP028413,,IZSAM,Illumina Next 500,189x,Spades v. 3.8,1,,1,2894810,38.036175,2885,2861,blood,,2015-05-16,Italy,"Italy: Marche, Macerata, Recanati",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4414,Listeria monocytogenes strain 2015TE17781-5,2015TE17781-5,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693610,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045425.1,CP028412,,IZSAM,Illumina Next 500,91x,Spades v. 3.8,1,,1,2894815,38.036144,2885,2861,blood,,2015-05-18,Italy,"Italy: Marche, Macerata",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4415,Listeria monocytogenes strain 2015TE17781-6,2015TE17781-6,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693611,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045405.1,CP028411,,IZSAM,Illumina Next 500,90x,Spades v. 3.8,1,,1,2894811,38.03613,2885,2861,blood,,2015-06-06,Italy,"Italy: Marche, Macerata, Morrovalle",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4416,Listeria monocytogenes strain 2015TE17781-9,2015TE17781-9,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693614,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045385.1,CP028408,,IZSAM,Illumina Next 500,150x,Spades v. 3.8,1,,1,2894813,38.036205,2885,2861,blood,,2015-06-16,Italy,"Italy: Marche, Macerata",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4417,Listeria monocytogenes strain 2015TE22590,2015TE22590,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693615,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045365.1,CP028407,,IZSAM,Illumina Next 500,217x,Spades v. 3.8,1,,1,2894817,38.036186,2883,2860,blood,,2015-07-14,Italy,"Italy: Marche, Pesaro- Urbino, Pesaro",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4418,Listeria monocytogenes strain 2015TE24968,2015TE24968,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693616,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045345.1,CP028406,,IZSAM,Illumina Next 500,160x,Spades v. 3.8,1,,1,2894710,38.03566,2885,2861,not collected,,2015-05-07,Italy,"Italy: Marche, Ancona, Monte San Vito",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4419,Listeria monocytogenes strain 2015TE24980,2015TE24980,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693617,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045325.1,CP028405,,IZSAM,Illumina Next 500,166x,Spades v. 3.8,1,,1,2863306,38.04536,2840,2817,not collected,,2015-03-03,Italy,"Italy: Marche, Ancona",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4420,Listeria monocytogenes strain 2016TE1560,2016TE1560,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693621,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045305.1,CP028403,,IZSAM,Illumina Next 500,182x,Spades v. 3.8,1,,1,2894816,38.036167,2885,2861,blood,,2016-01-19,Italy,"Italy: Marche, Ancona, Loreto",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4421,Listeria monocytogenes strain 2016TE2143,2016TE2143,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693623,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045285.1,CP028402,,IZSAM,Illumina Next 500,211x,Spades v. 3.8,1,,1,2894816,38.0362,2885,2861,blood,,2016-01-20,Italy,"Italy: Marche, Ancona",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4422,Listeria monocytogenes strain 2016TE3770-1-1,2016TE3770-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693628,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045255.1,CP028397,,IZSAM,Illumina Next 500,305x,Spades v. 3.8,1,,1,2894816,38.0361,2885,2861,cerebrospinal fluid,,2016-02-01,Italy,"Italy: Marche, Ancona, Jesi",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4423,Listeria monocytogenes strain 2016TE3773-1-1,2016TE3773-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693629,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045225.1,CP028396,,IZSAM,Illumina Next 500,353x,Spades v. 3.8,1,,1,2894816,38.036167,2885,2861,cerebrospinal fluid,,2016-02-12,Italy,"Italy: Marche, Ancona",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4424,Listeria monocytogenes strain 2016TE4526-1-1,2016TE4526-1-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693630,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045205.1,CP028395,,IZSAM,Illumina Next 500,101x,Spades v. 3.8,1,,1,2894816,38.0361,2885,2861,blood,,2016-02-16,Italy,"Italy: Marche, Macerata, Treia",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4425,Listeria monocytogenes strain 2016TE2013,2016TE2013,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08693622,1639,,,,MLST.Listeria_monocytogenes.7,,,,2018-04-09T00:00:00Z,,PRJNA261392,GCA_003045185.1,CP028392,,IZSAM,Illumina Next 500,144x,Spades v. 3.8,1,,1,2894711,38.035683,2885,2861,cerebrospinal fluid,,2016-01-22,Italy,"Italy: Marche: Pesaro, Urbino, Cagli",,,,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Central Nervous System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4444,Listeria monocytogenes strain 2018TE5305-1-4,2018TE5305-1-4,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN09197734,1639,1/2a,,,MLST.Listeria_monocytogenes.7,,,,2018-05-21T00:00:00Z,,PRJNA261392,GCA_003144075.1,CP029372,,IZSAM,Illumina NextSeq 500,70.0x,SPAdes v. 3.11,1,,1,2894782,38.036026,2883,2860,blood,,2018-04-03,Italy,Italy:Potenza Picena,,female,8 months,listeriosis,,,,,Positive,Bacilli,,,,,,,"This BioProject has the goal of studying the genetic variance, with particular emphasis in the analysis of virulence factors and antibiotic resistance genes, of Listeria monocytogenes strains circulating in Italy. It has relevance both in environmental/food area and clinical fields. In",collected_by:Francesco Pomilio;passage_history:3,,,,,,,listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4701,Listeria monocytogenes strain CIIMS-NV-3,CIIMS-NV-3,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08177723,1639,,,,MLST.Listeria_monocytogenes.328,,,,2018-08-20T00:00:00Z,,PRJNA422425,GCA_003409075.1,CP031674,,"Dr. G.M. Taori, Central India Institute of Medical Sciences",Illumina HiSeq,615.0x,SPAdes v. 3.10.1,1,,1,2954075,37.873074,3020,2967,vaginal swab of female,,2016-03-30,India,India: Nagpur,,,,Listeriosis,,,,,,,,,,,,,Listeriosis infection caused by pathogenic bacteria Listeria monocyotogenes. To reveal variable genetic islands responsible for pathogenesis is goal of study.,collected_by:Nagpur Veterinary College,,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Genitourinary,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.4711,Listeria monocytogenes strain CIIMS-PH-1,CIIMS-PH-1,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN07612368,1639,,,,MLST.Listeria_monocytogenes.308,,,,2018-01-25T00:00:00Z,,PRJNA401967,GCA_003433415.1,CP023321,,Central India Institute of Medical Sciences,Illumina HiSeq,615x,SPAdes v. 3.10.1,1,,1,2941368,37.99113,2936,2886,blood,,2016-07-07,India,India: Chandigarh,,,,Listeriosis,,,,,,,,,,,,,The microorganism cause zoonotic infection Listeriaosis in Humans. Genes/Protiens responsible for transmission from animal to human is objective of study.,"collected_by:PGIMER, Chandigarh",,,,,,,Listeriosis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.6581,Listeria monocytogenes strain N16-0044,N16-0044,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN10745353,1639,,,,MLST.Listeria_monocytogenes.6,,,,2019-01-22T00:00:00Z,,PRJNA515219,GCA_004101665.1,CP035187,,"University of Zurich, Vetsuisse Faculty",PacBio,412.0x,SMRT analysis v. 2.3.0,1,,1,2908718,38.028267,2894,2853,blood,recovered from a patient during the 2016 listeriosis outbreak linked to contaminated meat products in southern Switzerland,2016-01,Switzerland,Switzerland: Bellinzona,,,,Listeriosis,,,,,,,,,,,,,Listeria monocytogenes is a foodborne pathogen with a significant impact on public health and food safety. Strain Listeria monocytogenes N16-0044 is a clinical isolate recovered from a patient during the 2016 listeriosis outbreak linked to contaminated meat products in southern Switzerland. The genome of this strain will be used for comparative analysis with other sequenced Listeria monocytogenes genomes.,collected_by:Swiss National Reference Laboratory for Enteropathogenic Bacteria and Listeria,,,,,,,Listeriosis,,,,,,,,,,,,,,99.45,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.6586,Listeria monocytogenes strain N12-0935,N12-0935,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN11311853,1639,,,,MLST.Listeria_monocytogenes.403,,,,2019-04-10T00:00:00Z,,PRJNA530344,GCA_004768685.1,"CP038642,CP038643",,"University of Zurich, Vetsuisse Faculty",PacBio,366.0x,PacBio SMRT analysis v. 2.3.0,1,1,2,2991072,37.934795,2990,2945,blood,recovered from a human listeriosis case during 2012 in Switzerland,2012,Switzerland,Switzerland: Zurich,,,,Listeriosis,,,,,,,,,,,,,Listeria monocytogenes is a foodborne pathogen with a significant public health and food safety impacts. Listeria monocytogenes N12-0935 strain is a clinical isolate that was recovered from a human listeriosis case during 2012 in Switzerland. The genome of this strain will be used for comparative analysis with other sequenced Listeria monocytogenes genomes.,collected_by:Swiss National Reference Laboratory for Enteropathogenic Bacteria and Listeria,,,,,,,Listeriosis,,,,,,,,,,,,,,99.45,0.82,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.6587,Listeria monocytogenes strain NCCP 14714,NCCP 14714,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08939835,1639,,,,,,NCCP:14714,,2019-04-11T00:00:00Z,,PRJNA450488,GCA_004771175.1,CP031141,,Seoul National University,PacBio,,"SMRT Analysis v. 2,3.0",1,,1,2935813,38.00382,2898,2824,blood,,2017-01-01,South Korea,South Korea,,,,listeriosis,,,,,,,,,,,,,"As a food-borne pathogen, Listeria exhibits profound food-poisoning activites which high prevalence, every year. This sample was isolated form a food-poisoned patient in Seoul, Korea",collected_by:NCCP,,,,,,,listeriosis,,,,,,,,,,,,,,99.45,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.6588,Listeria monocytogenes strain NCCP 15743,NCCP 15743,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN08939842,1639,,,,MLST.Listeria_monocytogenes.101,,NCCP:15743,,2019-04-11T00:00:00Z,,PRJNA450492,GCA_004771195.1,CP029175,,Seoul National University,PacBio,,"SMRT Analysis v. 2,3.0",1,,1,2911466,37.983063,2882,2882,blood,,2012,South Korea,South Korea,,,,listeriosis,,,,,,,,,,,,,"As a food-borne pathogen, Listeria can exhibit profound food-poisoning. This sample was islated from the blood of patient in Korea.",collected_by:NCCP,,,,,,,listeriosis,,,,,,,,,,,,,,99.45,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.7177,Listeria monocytogenes strain AUSMDU00007774,AUSMDU00007774,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN13191637,1639,"1/2a,3a:155",,,MLST.Listeria_monocytogenes.155,mlst:ST155,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664735.1,CP045969,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,542x,de novo,1,0,1,2964538,37.978733,2954,2891,missing,,2013,Australia,Australia,,,,,,,,,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.7178,Listeria monocytogenes strain AUSMDU00000235,AUSMDU00000235,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN13191636,1639,"1/2a,3a:178",,,MLST.Listeria_monocytogenes.14,mlst:ST14,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664755.1,"CP045970,CP045971",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,518x,de novo,1,1,2,3007802,37.881584,2977,2912,missing,,2009,Australia,Australia,,,,,,,,,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.7180,Listeria monocytogenes strain N843_10,N843_10,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN13341854,1639,,,,MLST.Listeria_monocytogenes.412,,,,2019-12-05T00:00:00Z,,PRJNA590889,GCA_009730615.1,CP046361,,"University of Zurich, Vetsuisse Faculty",PacBio,140.0x,PacBio SMRT analysis 2.3.0 v. 2.3.0,1,0,1,2897260,37.955967,2859,2803,hip prosthetic joint fluid,recovered from a persistent recurrent case of a human prosthetic hip joint listeriosis infection in Switzerland,2010,Switzerland,Switzerland: Zurich,,,,Hip prosthetic joint listeriosis,,,,,,,,,,,,,Listeria monocytogenes N843_10 is a clinical isolate recovered from a persistent recurrent case of a human prosthetic hip joint listeriosis infection in Switzerland. The genome of this strain will be used for comparative analysis with other sequenced Listeria monocytogenes genomes.,collected_by:Swiss National Reference Laboratory for Enteropathogenic Bacteria and Listeria,,,,,,,Hip prosthetic joint listeriosis,,,,,,,,,,,,,,99.45,0.27,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Bone and Joint,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.7181,Listeria monocytogenes strain N843_15,N843_15,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN13341946,1639,,,,MLST.Listeria_monocytogenes.412,,,,2019-12-05T00:00:00Z,,PRJNA590892,GCA_009730635.1,CP046362,,"University of Zurich, Vetsuisse Faculty",PacBio,177.0x,PacBio SMRT analysis v. 2.3.0,1,0,1,2896666,37.95032,2861,2803,septic hip prosthetic joint fluid,recovered from a recurrent human prosthetic hip joint listeriosis infection during 2015 in Switzerland,2015,Switzerland,Switzerland: Zurich,,,,Hip prosthetic joint listeriosis,,,,,,,,,,,,,Listeria monocytogenes N843_15 is a clinical isolate recovered from a recurrent human prosthetic hip joint listeriosis infection during 2015 in Switzerland. The genome of this strain will be used for comparative analysis with other sequenced Listeria monocytogenes genomes.,collected_by:Swiss National Reference Laboratory for Enteropathogenic Bacteria and Listeria,,,,,,,Hip prosthetic joint listeriosis,,,,,,,,,,,,,,99.45,0.27,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Bone and Joint,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,1639.8503,Listeria monocytogenes strain GIMC2009:LmcUH4,GIMC2009:LmcUH4,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN14074479,1639,,,,MLST.Listeria_monocytogenes.7,,,,2020-08-26T00:00:00Z,,PRJNA605697,GCA_014304735.1,CP060435,,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq,217x,clc genomics workbench v. 20,1,0,1,2925782,38.017754,2879,2877,urine,,2019-02-13,Russia,Russia: Moscow,,female,23,premature birth,,,,,,,,,,,,,Monitoring the sources of Listeria mocytogenes infection.,"collected_by:Burmistrova E.N.;biomaterial_provider:N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia",,,,,,,premature birth,,,,,,,,,,,,,,99.45,0.27,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,1639.8504,Listeria monocytogenes strain GIMC2010:LmcUH8,GIMC2010:LmcUH8,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN14074480,1639,,,,MLST.Listeria_monocytogenes.7,,,,2020-08-26T00:00:00Z,,PRJNA605697,GCA_014304755.1,CP060434,,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq,183x,clc genomics workbench v. 20,1,0,1,2925387,38.017227,2880,2878,skin swab,,2019-02-13,Russia,Russia: Moscow,,male,,congenital pneumonia,,,,,,,,,,,,,Monitoring the sources of Listeria mocytogenes infection.,"collected_by:Burmistrova E.N.;biomaterial_provider:N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia",,,,,,,congenital pneumonia,,,,,,,,,,,,,,99.45,0.27,Respiratory Diseases,Pneumonia,Skin and Soft Tissue,Respiratory Diseases-Pneumonia HP,1639.8505,Listeria monocytogenes strain 24618,24618,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMN14074485,1639,,,,MLST.Listeria_monocytogenes.7,,,,2020-08-26T00:00:00Z,,PRJNA605697,GCA_014304775.1,CP060429,,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq,192x,clc genomics workbench v. 20,1,0,1,2865353,38.058975,2808,2808,necrotizing tonsils,,1971,Russia,Russia: Moscow,,,,not data,,,,,,,,,,,,,Monitoring the sources of Listeria mocytogenes infection.,"collected_by:no data;biomaterial_provider:Federal Research Center For Virology And Microbiology, Volginsky, Russia",,,,,,,not data,,,,,,,,,,,,,,99.45,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.8551,Listeria monocytogenes strain 15-01121 strain clinical isolate of L. monocytogenes,clinical isolate of L. monocytogenes,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA104485140,1639,4b,,,MLST.Listeria_monocytogenes.2,,,,2020-10-27T00:00:00Z,29643197,PRJEB24496,GCA_014983505.1,CP063382,,ROBERT KOCH INSTITUT,PacBio RS; Illumina,84x,SPAdes v. 3.13.1,1,0,1,2995602,37.978577,2987,2917,human listeriosis,,2015,Germany,Germany,,,,,,,,,,,,,,,,,Listeria monocyctogenes genome sequencing project on 424 strains isolated from human infection in Germany 2007-2017;isolate obtained from a human listeriosis case in Germany,,,,,,,,,not provided,,,,,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.8552,Listeria monocytogenes strain 18-04540 strain clinical isolate of L. monocytogenes,clinical isolate of L. monocytogenes,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA5041142,1639,IVb,,,MLST.Listeria_monocytogenes.6,,,,2020-10-27T00:00:00Z,32568037,PRJEB29295,GCA_014983645.1,"CP063383,CP063384",,ROBERT KOCH INSTITUT,Illumina; Oxford Nanopore MinION,59x,SPAdes v. 3.13.1,1,1,2,2996964,37.975132,3006,2946,human listeriosis,,2018,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,Whole genome sequencing of Listeria monocytogenes by the German consiliary laboratory for Listeria;isolate obtained from a human listeriosis case in Germany,,,,,,,,,diseased,,,,,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.8553,Listeria monocytogenes strain 12-05460 strain clinical isolate of L. monocytogenes,clinical isolate of L. monocytogenes,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA104485072,1639,2a,,,MLST.Listeria_monocytogenes.8,,,,2020-10-27T00:00:00Z,29643197,PRJEB24496,GCA_014983945.1,CP063381,,ROBERT KOCH INSTITUT,PacBio RS; Illumina,123x,SPAdes v. 3.13.1,1,0,1,2986724,37.94726,3004,2943,human listeriosis,,2012,Germany,Germany,,,,,,,,,,,,,,,,,Listeria monocyctogenes genome sequencing project on 424 strains isolated from human infection in Germany 2007-2017;isolate obtained from a human listeriosis case in Germany,,,,,,,,,not provided,,,,,,,,,,,,,99.45,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.8554,Listeria monocytogenes strain 19-05816 strain single colony,single colony,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA7376280,1639,,,,MLST.Listeria_monocytogenes.8,,,,2020-10-27T00:00:00Z,,PRJEB29295,GCA_014987905.1,CP063240,,ROBERT KOCH INSTITUT,Illumina MiniSeq; Oxford Nanopore MinION,165x,SPAdes v. 3.13.1,1,0,1,2951169,37.96292,2956,2898,clinical isolate,,2019-09-27,Germany,Germany,,,,,,,,,,,,,,,,,Whole genome sequencing of Listeria monocytogenes by the German consiliary laboratory for Listeria,,,,,,,,,not provided,,,,,,,,,,,,,99.45,0.82,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639.8577,Listeria monocytogenes strain clinical isolate of L. monocytogenes,clinical isolate of L. monocytogenes,Listeria monocytogenes,Listeria,Listeriaceae,Bacillales,Bacilli,Bacillota,SAMEA6798783,1639,IIa,,,MLST.Listeria_monocytogenes.8,,,,2020-11-18T00:00:00Z,,PRJEB37937,GCA_015583955.1,"CP064843,CP064844",,ROBERT KOCH INSTITUT,Illumina MiSeq; Oxford Nanopore MinION,140x,SPAdes v. 3.13.1,1,1,2,3038549,37.934456,3050,2987,human listeriosis,,2018,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,"Nationwide Outbreak of invasive Listeriosis associated with Consumption of Meat Products in Health Care Facilities (HCF), Germany, 2014-2019",,,,,,,,,diseased,,,,,,,,,,,,,99.45,0.82,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639133.23,Citrobacter portucalensis strain IOMTU157,IOMTU157,Citrobacter portucalensis,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00201481,1639133,,,,MLST.Citrobacter_freundii.15,,,,2020-01-28T00:00:00Z,,PRJDB9230,GCA_010319905.1,AP022378,,"Department of Microbiology, Juntendo University Graduate School of Medicine",Illuminia MiSeq; Oxford nanopore MinION,62x,Unicycler v. 0.4.8,1,0,1,4987090,52.067577,4868,4687,,,2012,Nepal,Nepal:Kathmandu,,,,,,,,,,,,,,,,,Highly drug-resistant Citrobacter spp. clinical isolates were detected in medical settings in Nepal. These isolates harbored genes encoding carbapenem- and aminoglycoside-resistant factors.,,missing,missing,missing,missing,Drug-resistant Citrobacter spp. clinicla isolates in Nepal,,,,,,,,,,,,missing,,,,99.87,0.72,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1639133.89,Citrobacter portucalensis K218,K218,Citrobacter portucalensis,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23799674,1639133,,,,,,,,2021-12-19T00:00:00Z,,PRJNA787413,GCA_021228875.1,CP089316,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,5082363,51.836063,5049,4821,blood,,2017,China,China: Zhejiang,,,,bloodstream infection,,,,,,,,,,,,,,collected_by:a teaching hospital,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.91,0.23,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,1648.276,Erysipelothrix rhusiopathiae 319078,319078,Erysipelothrix rhusiopathiae,Erysipelothrix,Erysipelotrichaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMN28202791,1648,,,,,,,,2022-06-13T00:00:00Z,,PRJNA837423,GCA_023650665.1,CP098031,,,Illumina MiniSeq; Oxford Nanopore MinION,100.0x,Unicycler v. v0.4.8,1,0,1,1780614,36.51858,1662,1634,wound swab,,2020-12-16,Germany,Germany: Magdeburg,,female,,Erysipeloid,,,,,,,,,,,,,,collected_by:Andreas Zautner,,,,,,,Erysipeloid,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,165179.2609,Prevotella copri strain YF2,YF2,Segatella copri,Segatella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN12321477,165179,,,,,,,,2020-09-21T00:00:00Z,,PRJNA555508,GCA_015074785.1,"CP042464,CP042465",,Xiamen University,PacBio RSII,350.0x,SMRT Link v. v5.0.1,1,1,2,3864035,44.936935,3392,3087,feces,,2018-01-20,,,,,,,,,,,,,,,,,,,The complete genome of P. copri YF2,,human gut microbiome,feces,feces,YCFA medium and,,Xiamen,,Fujian Province,,,,,,,,,human gut microbiome,,,,98.99,2.14,,,Gastrointestinal,- HP,1655.276,Actinomyces naeslundii CW,CW,Actinomyces naeslundii,Actinomyces,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMN31205636,1655,,,,,,,,2022-12-11T00:00:00Z,,PRJNA887960,,CP113787,,,Illumina NovaSeq,100.0x,SPAdes v. 3.15.0,1,0,1,3104561,67.58394,2795,2608,dental biofilm,,2008-03-31,Sweden,Sweden: Malmo,,,,,,,,,,,,,,,,,,sample_type:Clinical isolate;identified_by:Carolina Robertsson,,,,,,,,,,,,,,,,,,,,,100,0.8,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1659.4,Actinomyces israelii strain NCTC12972,NCTC12972,Actinomyces israelii,Actinomyces,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMEA4364212,1659,not available: to be reported later,,,,,NCTC:12972,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900637225.1,LR134357,,SC,,,,1,,1,2572997,64.12013,2206,2145,brain abscess,,1948,USA,United States,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.53,1.54,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,1660.163,Schaalia odontolytica strain FDAARGOS_732 strain Not applicable,Not applicable,Schaalia odontolytica,Schaalia,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMN11056447,1660,,,,,,FDA:FDAARGOS_732,,2019-12-05T00:00:00Z,,PRJNA231221,GCA_009730335.1,CP046315,,US Food and Drug Administration,Pacbio; Illumina,1020.91x,canu v. 1.4,1,0,1,2432635,65.25911,2140,2044,human oral cavity,,,USA,USA:VA,,,,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,100,0.71,,,Oral,- NHP,166486.1019,Roseburia intestinalis strain L1 82,L1 82,Roseburia intestinalis,Roseburia,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222706,166486,,,,,,,,2022-09-12T00:00:00Z,,PRJNA746600,,CP102289,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4482541,42.666515,4339,4069,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.03,1.57,,,Other,- HP,1667168.3,Dermabacter jinjuensis strain 32T,32T,Dermabacter jinjuensis,Dermabacter,Dermabacteraceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN07665299,1667168,,,,,,,,2017-10-04T00:00:00Z,27088668,PRJNA407870,GCA_002443115.1,CP023482,,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,300.0x,SPAdes v. v3.1,1,,1,2398786,62.898483,2242,2119,closed pus,,2011-12-05,South Korea,South Korea: Jinju,,,,finger necrosis,,,,,,,,,,,,,"Dermabcter jinjuensis sp. nov., a novel species of the genus Dermabcter isolated from a clinical specimen",collected_by:Geongsang National University Hospital,,,,,,,finger necrosis,,,,,,,,,,,,,,94.15,0.29,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1667327.31,Klebsiella quasipneumoniae subsp. quasipneumoniae strain M17277,M17277,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12744724,1667327,,,,MLST.Klebsiella_pneumoniae.526,,,,2019-09-22T00:00:00Z,,PRJNA499048,GCA_008632435.1,"CP043928,CP043927",,"Servicio Antimicrobianos, INEI-ANLIS Dr. Carlos G. Malbran",Illumina MiSeq; Oxford Nanopore MiniION,100.0x,Unicycler v. v0.4.7,1,1,2,5638612,57.39469,5707,5474,rectal swab,,2014,Argentina,Argentina,,,,Erythrodermic psoriasis,,host_disease_outcome:death,,,,,,,,,,,"NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae M17277 was obtained from a rectal swab of a paediatric patient co-infected with other four NDM-1-producing enterobacteria species and was characterized by whole genome sequencing. M17277 also harboured three plasmid-mediated quinolone resistance genes: qnrB4, qnrB52 and aac(6’)-Ib-cr1.",collected_by:Hospital de Ninos Dr. Ricardo Gutierrez,,,,,,,Erythrodermic psoriasis,,death,,,,,,,,,,,,99.99,0.86,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1667327.39,Klebsiella quasipneumoniae subsp. quasipneumoniae strain 01A030T,01A030T,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024800,1667327,,,,MLST.Klebsiella_pneumoniae.1528,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525925.1,"CP084876,CP084877",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5507230,58.001953,5391,5169,blood,,1997,,Austria,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,99.99,0.88,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1667327.40,Klebsiella quasipneumoniae subsp. quasipneumoniae strain 18A069,18A069,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024801,1667327,,,,MLST.Klebsiella_pneumoniae.1118,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525805.1,"CP084818,CP084819,CP084820,CP084821,CP084822",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,4,5,5507945,57.879246,5475,5263,blood,,1997,,Spain,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,99.99,0.79,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1667327.86,Klebsiella quasipneumoniae subsp. quasipneumoniae 5463,5463,Klebsiella quasipneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174098,1667327,,,,MLST.Klebsiella_pneumoniae.571,genotype:ST571,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917695.1,"CP103487,CP103488,CP103489,CP103490,CP103491,CP103492,CP103493",,,Oxford Nanopore GridION,278x,Flye v. 2.8.3-b1695,1,6,7,5591370,57.74188,5563,5327,blood,,2019-12-12,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1674146.69,Borreliella mayonii MN14-1539,MN14-1539,Borreliella mayonii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN04979182,1674146,,,,,,,,2017-01-05T00:00:00Z,28030649,PRJNA321302,GCA_001936295.1,"CP015796,CP015962,CP015803,CP015804,CP015797,CP015805,CP015806,CP015807,CP015798,CP015799,CP015800,CP015801",,,PacBio,missing,"HGAP, SMRTAnalysis v. 2.3.0",1,14,15,1302058,27.836472,1389,1221,blood,,not applicable,,not applicable,,,,Lyme Borreliosis,,,,,,,,,,,,,,collected_by:not applicable,,,,,,,Lyme Borreliosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Blood and Circulatory System,Specific Bacterial Infections-Lyme Disease NHP,1679.313,Bifidobacterium longum subsp. longum strain NBRC 114494,NBRC 114494,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21163593,1679,,,,,,,,2021-10-07T00:00:00Z,,PRJNA747117,GCA_020353915.1,"CP084020,CP084021,CP084022",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore GridION,509.0x,Flye v. 2.8.3; Unicycler v. 0.4.7,1,2,3,2534372,60.111893,2240,2134,human feces,,2018,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,1679.51,Bifidobacterium longum subsp. longum strain BORI,BORI,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN09691177,1679,,,,,,,,2018-07-26T00:00:00Z,29747442,PRJNA481853,GCA_003342655.1,CP031133,,"BIFIDO Co., LTD",PacBio,386.51x,SMRT analysis v. 2.3,1,,1,2311020,59.93864,1976,1915,korean infant,isolated from the feces of healthy Korean infants and has been characterized to have inhibitory effect against Rotavirus infection of children and has been commercially used as food ingredients since 2000,1998-10-01,South Korea,South Korea,,,,,,,,,,,,,,,,,Bifidobacterium longum BORI was isolated from the feces of healthy Korean infants and has been characterized to have inhibitory effect against Rotavirus infection of children and has been commercially used as food ingredients since 2000.,sample_type:Bacteria,,,,,,,,,,,,,,,,,,,,,100,1.4,,,Other,- HP,168.10,Treponema pallidum subsp. pertenue strain Kampung Dalan K363,Kampung Dalan K363,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN07709919,168,,,,,,,,2018-10-03T00:00:00Z,,PRJNA412353,GCA_003611295.1,CP024088,,"Masaryk University, Faculty of Medicine",Illumina MiSeq,995x,IDBA_UD v. 1.1.1,1,,1,1139764,52.787197,1035,1064,skin lesion,"isolated in 1990 in Pariaman region in Sumatra, Indonesia",1990-01-05,Indonesia,Indonesia: Pariaman region in Sumatra,,,,yaws,,,,,,,,,,,,,"Complete genome sequencing of two Treponema pallidum subsp. pertenue strains Sei Geringging K403 and Kampung Dalan K363 isolated in 1990 in Pariaman region in Sumatra, Indonesia.",,,,,,,,yaws,,,,,,,,,,,,,,99.97,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,168.11,Treponema pallidum subsp. pertenue strain Sei Geringging K403,Sei Geringging K403,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN07709936,168,,,,,,,,2018-10-03T00:00:00Z,,PRJNA412353,GCA_003611315.1,CP024089,,"Masaryk University, Faculty of Medicine",Illumina MiSeq,542x,IDBA_UD v. 1.1.1,1,,1,1139464,52.781517,1037,1062,skin lesion,"isolated in 1990 in Pariaman region in Sumatra, Indonesia",1990-05-14,Indonesia,Indonesia: Pariaman region in Sumatra,,,,yaws,,,,,,,,,,,,,"Complete genome sequencing of two Treponema pallidum subsp. pertenue strains Sei Geringging K403 and Kampung Dalan K363 isolated in 1990 in Pariaman region in Sumatra, Indonesia.",,,,,,,,yaws,,,,,,,,,,,,,,99.97,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,168.12,Treponema pallidum subsp. pertenue strain CDC-1,CDC-1,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN07967415,168,,,,,,,,2018-12-18T00:00:00Z,,PRJNA416916,GCA_003952805.1,CP024750,,"Masaryk University, Faculty of Medicine",Illumina MiSeq,460.0x,IDBA_UD v. 1.1.1,1,,1,1139578,52.785446,1036,1064,papillomatous lesion,isolated from a 5-year old patient with yaws infection in Ghana in 1980,1980-11,Ghana,Ghana: Densuso,,male,5 years,yaws,,host_disease_outcome:yaws,,,,,,,,,,,Complete genome sequencing of Treponema pallidum subsp. pertenue strain CDC-1. Strain CDC-1 was isolated from a 5-year old patient with yaws infection in Ghana in 1980.,,,,,,,,yaws,,yaws,,,,,,,,,,,,99.97,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections NHP,1680.2411,Bifidobacterium adolescentis iVS-1,iVS-1,Bifidobacterium adolescentis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN34156685,1680,,,,,,,,2023-04-24T00:00:00Z,,PRJNA954850,,CP123050,,,PacBio Sequel II,1473.0x,Canu v. 1.6; Flye v. 2.8.3-b1695,1,0,1,2306390,59.61975,1969,1839,stool,,2010-04-25,USA,"USA: Lincoln, NE",,,,,,,,,,,,,,,,,,,Human gut microbiome,Stool,Stool,Isolated on Rogosa SL plate,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,1681.137,Bifidobacterium bifidum strain TMC 3115,TMC 3115,Bifidobacterium bifidum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMD00078313,1681,,,,,,,,2017-10-03T00:00:00Z,,PRJDB5666,GCA_003573895.1,AP018132,,"Graduate School of Biostudies, Kyoto University",PacBio RSII,266x,SMRT Analysis v. 2.3.0,1,,1,2178894,62.787773,1863,1876,infant feces,isolated from infant feces,,,,env_biome:human infant feces,,,,,,,,,,,,,,,,"Bifidobacterium bifidum TMC 3115 was isolated from infant feces. As a symbiotic species in breast-fed infants' gut, Bifidobacterium bifidum is characterized by its unique properties in the ability to degrade complex carbohydrates such as human milk oligosaccharides and mucin glycans. Comprehension from the genome analysis of B. bifidum strain may be useful for the unveiling mechanisms of symbiosis between Bifidobacteria and human.","biomaterial_provider:Takanashi milk products Co., Ltd.",human infant feces,missing,missing,missing,Genome sequencing of Bifidobacterium bifidum TMC 3115,,,,,,,,,,,,human infant feces,,,,99.7,2.5,,,Gastrointestinal,- NHP,1681.94,Bifidobacterium bifidum strain PRI 1,PRI 1,Bifidobacterium bifidum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN06140833,1681,,,,,,,,2017-12-20T00:00:00Z,,PRJNA257684,GCA_002845845.1,CP018757,,Institute for Basic Science (IBS) and Pohang University of Science and Technology (POSTECH),PacBio,168.0x,PACBIO SMRT analysis v. 2.3,1,,1,2243572,62.74,1919,,,,2009-04-01,South Korea,"South Korea: Gyeonggido, Giheung",,,,,,,,,Positive,,,,,,,,"This strain could act nutraceutical immunomodulatory for hyper-immune disorders such as rheumatoid arthritis, atopic dermatitis and inflammatory bowel diseases.",sample_type:Bacteria,,,,,,,,,,,,,,,,,,,,,100,0,,,Other,- NHP,1682.213,Bifidobacterium longum subsp. infantis PI_003,PI_003,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077327,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023205815.1,CP054525,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2612005,59.25295,2424,2234,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.214,Bifidobacterium longum subsp. infantis PI_002,PI_002,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077326,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023205835.1,CP054526,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2604549,59.316757,2426,2242,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.215,Bifidobacterium longum subsp. infantis BB-02,BB-02,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077325,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023205855.1,CP054527,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2758198,59.869595,2630,2434,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.5,,,Other,- NHP,1682.216,Bifidobacterium longum subsp. infantis PI_004,PI_004,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077328,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023205795.1,CP054524,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2604558,59.31655,2412,2224,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.217,Bifidobacterium longum subsp. infantis PI_010,PI_010,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077334,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208035.1,CP054519,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2609031,59.283733,2417,2234,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.2,,,Other,- NHP,1682.218,Bifidobacterium longum subsp. infantis PI_009,PI_009,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077333,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208055.1,CP054520,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2604570,59.316433,2417,2227,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.219,Bifidobacterium longum subsp. infantis PI_008,PI_008,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077332,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208075.1,CP054521,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2612382,59.2524,2423,2233,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.220,Bifidobacterium longum subsp. infantis PI_007,PI_007,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077331,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208095.1,CP054522,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2604585,59.31659,2422,2226,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.221,Bifidobacterium longum subsp. infantis PI_006,PI_006,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077330,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208155.1,CP054596,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2610477,59.21546,2425,2233,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.222,Bifidobacterium longum subsp. infantis NLS,NLS,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077324,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208135.1,CP054528,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2598286,59.31876,2414,2228,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- NHP,1682.223,Bifidobacterium longum subsp. infantis PI_005,PI_005,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15077329,1682,,,,,,,,2022-05-02T00:00:00Z,33114073,PRJNA636403,GCA_023208115.1,CP054523,,,Illumina NextSeq,130x,SPAdes v. 3.14.1,1,0,1,2614802,59.21783,2431,2237,probiotic prodcut,,2018,USA,USA,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- HP,168471.7,Laribacter hongkongensis strain LHGZ1,HLGZ1,Laribacter hongkongensis,Laribacter,Aquaspirillaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07204264,168471,,,,,,,,2017-07-06T00:00:00Z,,PRJNA389628,GCA_002215055.1,CP022115,,The First Affiliated Hospital of Guangzhou Medical University,PacBio; Illumina MiSeq,33750.0x,Celera Assembler v. 8.3rc2,1,,1,3424272,62.29,3504,3497,feces,,2012-05,China,"China: Guangong, Guangzhou",,,,diarrhea,,,,,,,,,,,,,Whole genome sequence of Laribacter hongkongensis HLGZ1 and comparing with HLHK9 strain,collected_by:Dingqiang Chen,,,,,,,diarrhea,,,,,,,,,,,,,,98.3,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases NHP,1685.199,Bifidobacterium breve strain lw01,lw01,Bifidobacterium breve,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN10484345,1685,,,,,,,,2018-12-04T00:00:00Z,,PRJNA507053,GCA_003860285.1,CP034192,,Peking University,Illumina HiSeq,200.0x,SOAPdenovo v. 2.04,1,,1,2313172,58.766838,2097,2014,infant fecal,,2017-10-10,China,China,,,,,,,,,,,,,,,,,Detection of extracellular polysaccharide production by phenol-sulfuric acid method showed that this strain could produce extracellular polysaccharide. It can be used in the development of starter or probiotics.,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,1685.568,Bifidobacterium breve strain JTL,JTL,Bifidobacterium breve,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN15028705,1685,,,,,,,,2020-06-04T00:00:00Z,,PRJNA635210,GCA_013267755.1,CP053940,,KHEPRIOME,PacBio,98.0x,Celera Assembler v. Canu ver. 1.7,1,0,1,2289549,58.525894,1947,,infant feces,,2017-08-24,South Korea,South Korea,,,,,,,,,,,,,,,,,development of novel potentially probiotic,sample_type:feces,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,1685.775,Bifidobacterium breve 1101A,1101A,Bifidobacterium breve,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN14967674,1685,,,,,,,,2022-08-29T00:00:00Z,,PRJNA633614,GCA_024760465.1,CP053655,,,Illumina HiSeq,1234.3x,SPAdes v. 3.9,1,0,1,2371121,58.777306,2063,1974,feces,,2012,Brazil,Brazil: Belo Horizonte,,,,,,,,,,,,,,,,,,,feces of a healthy child,feces,feces,doi: 10.3920/BM2012.0052,,,,,,,,,,,,,feces of a healthy child,,,,100,0,,,Gastrointestinal,- HP,1689.18,Bifidobacterium dentium strain NCTC11816,NCTC11816,Bifidobacterium dentium,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMEA4076722,1689,not available: to be reported later,,,,,NCTC:11816,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900637175.1,LR134349,,SC,,,,1,,1,2635828,58.538986,2240,2138,dental caries,,1900-1974,,,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,169292.166,Corynebacterium aurimucosum DSM 44532,DSM 44532,Corynebacterium aurimucosum,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18253773,169292,,,,,,,,2022-07-05T00:00:00Z,,PRJNA713536,GCA_024138775.1,CP071874,,,Illumina MiSeq,68.0x,SPAdes v. 3.13.1,1,0,1,2683765,60.4532,2580,2480,blood culture,,2001-01-02,Germany,Germany,,,,Bronchitis,,,,,,,,,,,,,,"collected_by:A. F. Yassin, University of Bonn",,,,,,,Bronchitis,,,,,,,,,,,,,,98.8,2.2,Respiratory Diseases,COPD/Emphysema/Bronchitis,Blood and Circulatory System,Respiratory Diseases-COPD/Emphysema/Bronchitis NHP,169435.95,Anaerotruncus colihominis strain DSM 17241,DSM 17241,Anaerotruncus colihominis,Anaerotruncus,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222640,169435,,,,,,DSM:17241,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146135.1,CP102255,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3563916,54.15829,4112,3511,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,96.64,0.22,,,Other,- HP,170573.39,Staphylococcus pettenkoferi SP165,SP165,Staphylococcus pettenkoferi,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN22027592,170573,,,,,,,,2022-01-10T00:00:00Z,34948410,PRJNA768314,GCA_021398525.1,CP085279,,,Illumina MiSeq,54.05x,SHOVILL v. 1.1.0,1,0,1,2435720,38.993423,2367,2273,envo_01001110;bfo_0000040;obi_0100026,,2018-07-18,France,France: Nimes,,,,,,,,,,,,,,,,,,,CHEBI_72813;ENVO_01001110,BFO_0000040;OBI_0100026,ENVO_01001110;BFO_0000040;OBI_0100026,strain was isolated on blood agar gelose from diabetic foot osteomyelitis cultivated during 5 days at 37 degree Celsius,,,,,,,,,,,,,CHEBI_72813;ENVO_01001110,,,,98.9,1.24,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1706820.3,Treponema sp. OMZ 806,OMZ 806,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253842,69710,,,,,,DSM:16787,,2021-05-11T00:00:00Z,,PRJNA602573,GCA_018336815.1,CP050497,,The University of Hong Kong,Illumina HiSeq; Oxford Nanopore MiniION,700.0x,Canu v. 1.8,1,0,1,2711688,44.89436,2798,2427,subgingival plaque,isolated from the dental plaque biofilm of a periodontitis patient in Switzerland in 1995,1995,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,"Treponema sp. ATCC 700767 was isolated from the dental plaque biofilm of a periodontitis patient in Switzerland in 1995. This strain is also known as T. vincentii (ex Brumpt) Smibert ATCC 700767, DSM 16787, OMZ 806 [HA1B7].",,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,99.46,1.21,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases NHP,1710.44,Cellulosimicrobium cellulans strain ORNL-0100,ORNL-0100,Cellulosimicrobium cellulans,Cellulosimicrobium,Promicromonosporaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN18352201,1710,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128265.1,"CP072387,CP072388",,The Forsyth Institute,PacBio Sequel,107x,Flye v. 2.8,1,1,2,4411608,74.43118,4058,3944,human oral cavity,,2018-09-10,USA,"USA: Oak Ridge, Tennessee",,male,51,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Mircea Podar, Oak Ridge National Laboratory;collected_by:Mircea Podar, Oak Ridge National Laboratory",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,100,0.67,,,Oral,- HP,1717.285,Corynebacterium diphtheriae strain B-D-16-78,B-D-16-78,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06099113,1717,,,,MLST.Corynebacterium_diphtheriae.453,,,,2016-12-13T00:00:00Z,,PRJNA355958,GCF_001902275.1,CP018331,NZ_CP018331.1,University of Malaya,PacBio,808.11x,HGAP v. 2,1,,1,2474151,53.56,2507,2341,nasopharyngeal swab,,2016-06-27,Malaysia,Malaysia: Malacca,,female,7 years old,Diphtheria,,host_disease_outcome:Death,,,,,,,,,,,A Corynebacterium diphtheriae which cause diphtheria,collected_by:Malaysian National Public Health Laboratory,,,,,,,Diphtheria,,Death,,,,,,,,,,,,100,0.6,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.335,Corynebacterium diphtheriae strain FDAARGOS_197,FDAARGOS_197,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN04875534,1717,Gravis,,,MLST.Corynebacterium_diphtheriae.8,,FDA:FDAARGOS_197,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073375.2,CP020410,,US Food and Drug Administration,PacBio,15.7717179501426x,HGAP v. 3,1,,1,2489000,53.48,2468,2305,pharyngeal membrane,,1997,United Kingdom,United Kingdom,,,72Y,Clinical diptheria,,host_description:Patient returned to UK from Baltic cruise;host_disease_outcome:Alive,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:ATCC < NCTC,,,,,,,Clinical diptheria,Missing,Alive,Patient returned to UK from Baltic cruise,Missing,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1717.440,Corynebacterium diphtheriae strain BQ11,BQ11,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN09269643,1717,,,,MLST.Corynebacterium_diphtheriae.125,,,,2018-06-06T00:00:00Z,,PRJNA473263,GCA_003194045.1,CP029644,,The University of Queensland,PacBio,96.0x,HGAP v. 3.0,1,,1,2557381,53.614067,2505,2360,pharyngeal swab,isolated from an unvaccinated adult female in April 2011 in Australia,2011,Australia,Australia,,female,,Diphtheria,,host_description:Adult;host_disease_outcome:death,,,,,,,,,,,"Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Diphtheria is rare in developed countries but remains endemic in parts of Asia, the South Pacific, the Middle East, Eastern Europe and the Caribbean. Although resistance to erythromycin has been recognised, Penicillin and beta -lactam resistance in toxigenic diphtheria has not yet been described. Here we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and other beta-lactam antibiotics. Toxigenic C. diphtheriae strain BQ11 was isolated from an unvaccinated adult female in April 2011 in Australia. Using long-read whole genome sequencing we assembled the genome sequence of C. dipththeriae BQ11 to determine the genetic mechanisms of resistance. We found a 6,682 bp beta-lactam resistance gene cassette that is not found in the genomes of beta-lactam susceptible C. diphtheriae. Surprisingly, this element has been mobilised into the genome of BQ11 as a novel transposon. Remarkably, we found that transposon copy number was highly dynamic. When cultured with exposure to meropenem, selective pressure drives a rapid increase in transposon copy number and a corresponding change from a carbapenem susceptible to a carbapenem resistant phenotype. This case of fatal respiratory toxigenic diphtheria caused by beta-lactam resistant C. diphtheriae highlights the ongoing threat posed by the potential introduction of diphtheria from endemic regions to non-immune or partially immune individuals and demonstrates threat of emergent antimicrobial resistance within this species.",,,,,,,,Diphtheria,,death,Adult,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.441,Corynebacterium diphtheriae strain CHUV2995,CHUV2995,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA104679569,1717,,,,MLST.Corynebacterium_diphtheriae.360,,CCUG 5865,,2018-06-29T00:00:00Z,,PRJEB24256,GCA_900312965.1,LT990688,,CHUV-UNIL,,,,1,,1,3060363,53.940563,3269,3145,broncho-alveolar lavage,recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi,2012-01-20,Switzerland,Switzerland,,,,past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi,,host_health_state:diseased,,,,,,,,,,,"Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel of the PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703, shared a lower average nucleotide identity (ANI) (95.24% to 95.39%) with C. diphtheriae reference genome NCTC 11397 than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two distinct clades. Based on these findings, we propose here two new subspecies: C. diphtheriae subsp. lausannense subsp. nov., regrouping strains CHUV2995, CCUG 5865 and CMCNS703) and C. diphtheriae subsp. diphtheriae subsp. nov, regrouping all other C. diphtheriae in the dataset. Interestingly, subspecies lausannense displayed a larger genome size than subspecies diphtheriae and was enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, it lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, CHUV2995 genome was particularly enriched in mobility genes and harbored several prophages. It encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks csn2 or cas4, which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.;genome length too large",,,,,,,,,diseased,,,,,,,,,,,,,100,3.4,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1717.780,Corynebacterium diphtheriae CD1009,CD1009,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612662,1717,,,,MLST.Corynebacterium_diphtheriae.363,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560115.1,"CP091095,CP091096",,,PacBio RSII; Illumina HiSeq,413x,HGAP v. 3,1,1,2,2407586,53.316185,2326,2189,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.781,Corynebacterium diphtheriae CD1040,CD1040,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612666,1717,,,,,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560235.1,CP040520,,,PacBio RSII; Illumina HiSeq,708x,HGAP v. 3,1,0,1,2532323,53.64367,2545,2384,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.782,Corynebacterium diphtheriae CD1075,CD1075,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612667,1717,,,,MLST.Corynebacterium_diphtheriae.123,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560215.1,CP040519,,,PacBio RSII; Illumina MiSeq,488x,HGAP v. 3,1,0,1,2403985,53.47101,2369,2247,nasal swab,,2018,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.01,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,1717.783,Corynebacterium diphtheriae CD1036,CD1036,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612665,1717,,,,MLST.Corynebacterium_diphtheriae.258,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560255.1,CP040521,,,PacBio RSII; Illumina HiSeq,603x,HGAP v. 3,1,0,1,2564229,53.577587,2599,2443,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.784,Corynebacterium diphtheriae CD1033,CD1033,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612664,1717,,,,,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560275.1,CP040522,,,PacBio RSII; Illumina HiSeq,639x,HGAP v. 3,1,0,1,2530672,53.641087,2546,2382,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.4,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.785,Corynebacterium diphtheriae CD1032,CD1032,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612663,1717,,,,,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560295.1,CP040523,,,PacBio RSII; Illumina HiSeq,650x,HGAP v. 3,1,0,1,2457803,53.595753,2481,2329,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.786,Corynebacterium diphtheriae CD1008,CD1008,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612661,1717,,,,,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560315.1,CP040525,,,PacBio RSII; Illumina HiSeq,589x,HGAP v. 3,1,0,1,2474411,53.554604,2503,2335,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1717.787,Corynebacterium diphtheriae CD1005,CD1005,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11612660,1717,,,,,,,,2022-01-24T00:00:00Z,,PRJNA541851,GCA_021560335.1,CP040526,,,PacBio RSII; Illumina HiSeq,612x,HGAP v. 3,1,0,1,2474408,53.55467,2502,2335,throat swab,,2017,Bangladesh,Bangladesh,,,,diphtheria,,,,,,,,,,,,,,,,,,,,,diphtheria,,,,,,,,,,,,,,99.45,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1720349.100,Corynebacterium diphtheriae bv. gravis 4795/21,4795/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508173,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969385.1,CP103881,,,Oxford Nanopore GridION,185 x,CLC NGS Cell v. 22,1,0,1,2452503,53.498363,2520,2258,unk,,2021,Poland,Poland,,,60,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.6,4.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1720349.101,Corynebacterium diphtheriae bv. gravis 7072/17,7072/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508154,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969425.1,CP103900,,,Oxford Nanopore GridION; MiSeq,382 x,Unicycler v. not specified,1,0,1,2450063,53.496216,2374,2228,unk,,2017,Poland,Poland,,,63,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1720349.102,Corynebacterium diphtheriae bv. gravis 5521/17,5521/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508153,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969465.1,CP103901,,,Oxford Nanopore GridION; MiSeq,601 x,Unicycler v. not specified,1,0,1,2452932,53.497814,2373,2228,wound,,2017,Poland,Poland,,,31,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.103,Corynebacterium diphtheriae bv. gravis 5379/19,5379/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508161,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969485.1,CP103893,,,Oxford Nanopore GridION; MiSeq,199 x,Unicycler v. not specified,1,0,1,2446723,53.485416,2366,2226,blood,,2019,Poland,Poland,,,59,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.104,Corynebacterium diphtheriae bv. gravis 4674/18,4674/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508158,1720349,,,,MLST.Corynebacterium_diphtheriae.8,,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969525.1,CP103896,,,Oxford Nanopore GridION; MiSeq,170 x,Unicycler v. not specified,1,0,1,2447241,53.48664,2362,2225,blood,,2018,Poland,Poland,,,,,,,,,,,,,,,,,,,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.105,Corynebacterium diphtheriae bv. gravis 6211/17,6211/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508151,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969565.1,CP103903,,,Oxford Nanopore GridION; MiSeq,210 x,Unicycler v. not specified,1,0,1,2446364,53.485172,2361,2223,blood,,2017,Poland,Poland,,,18,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.67,Corynebacterium diphtheriae bv. gravis strain 3302/22,3302/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508180,1720349,,,non-toxigenic,,genotype:ST-32,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968165.1,CP103904,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,198 x,CLC NGS Cell v. 22,1,0,1,2408912,53.450645,2449,2220,respiratory tracks,isolated in Poland in 2017-2022,2022,,Poland,,,21,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.86,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1720349.68,Corynebacterium diphtheriae bv. gravis strain 1269/21,1269/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508169,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968205.1,CP103885,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,124 x,CLC NGS Cell v. 22,1,0,1,2437577,53.48881,2464,2223,blood,isolated in Poland in 2017-2022,2021,,Poland,,,55,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.77,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.69,Corynebacterium diphtheriae bv. gravis strain 576/21,576/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508167,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968225.1,CP103887,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,126 x,CLC NGS Cell v. 22,1,0,1,2449609,53.487354,2489,2247,blood,isolated in Poland in 2017-2022,2021,,Poland,,,65,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.55,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.70,Corynebacterium diphtheriae bv. gravis strain 5790/18,5790/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508156,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968245.1,CP103898,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,91 x,Unicycler v. not specified,1,0,1,2435912,53.487812,2347,2206,blood,isolated in Poland in 2017-2022,2018,,Poland,,,59,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.71,Corynebacterium diphtheriae bv. gravis strain 2736/18,2736/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508157,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968265.1,CP103897,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,211 x,Unicycler v. not specified,1,0,1,2437238,53.488457,2348,2198,blood,isolated in Poland in 2017-2022,2018,,Poland,,,45,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.72,Corynebacterium diphtheriae bv. gravis strain 49390/20,49390/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508165,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968285.1,CP103889,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,167 x,Unicycler v. not specified,1,0,1,2451330,53.48688,2380,2227,wound,isolated in Poland in 2017-2022,2020,,Poland,,,72,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.73,Corynebacterium diphtheriae bv. gravis strain 3745/21,3745/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508172,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968325.1,CP103882,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,200 x,CLC NGS Cell v. 22,1,0,1,2451250,53.486954,2532,2247,blood,isolated in Poland in 2017-2022,2021,,Poland,,,39,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.74,Corynebacterium diphtheriae bv. gravis strain 648/22,648/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508175,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968365.1,CP103880,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,203 x,CLC NGS Cell v. 22,1,0,1,2435954,53.47749,2497,2234,blood,isolated in Poland in 2017-2022,2022,,Poland,,,42,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.9,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.75,Corynebacterium diphtheriae bv. gravis strain 453/18,453/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508155,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968405.1,CP103899,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,183 x,Unicycler v. not specified,1,0,1,2456329,53.49837,2377,2234,wound,isolated in Poland in 2017-2022,2018,,Poland,,,64,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.76,Corynebacterium diphtheriae bv. gravis strain 2232/21,2232/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508171,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969025.1,CP103883,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,204 x,CLC NGS Cell v. 22,1,0,1,2450955,53.497105,2490,2249,wound,isolated in Poland in 2017-2022,2021,,Poland,,,17,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.05,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.77,Corynebacterium diphtheriae bv. gravis strain 8259/19,8259/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508162,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969205.1,CP103892,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,249 x,Unicycler v. not specified,1,0,1,2437088,53.485962,2350,2198,respiratory tracks,isolated in Poland in 2017-2022,2019,,Poland,,,66,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1720349.78,Corynebacterium diphtheriae bv. gravis strain 14225/20,14225/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508166,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969365.1,CP103888,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,148 x,Unicycler v. not specified,1,0,1,2450753,53.486988,2373,2219,blood,isolated in Poland in 2017-2022,2020,,Poland,,,42,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.79,Corynebacterium diphtheriae bv. gravis strain 4795/21,4795/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508173,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969385.1,CP103881,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,185 x,CLC NGS Cell v. 22,1,0,1,2452503,53.498363,2520,2258,unk,isolated in Poland in 2017-2022,2021,,Poland,,,60,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.71,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1720349.80,Corynebacterium diphtheriae bv. gravis strain 1784/21,1784/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508170,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969405.1,CP103884,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,187 x,CLC NGS Cell v. 22,1,0,1,2451395,53.48771,2532,2248,wound,isolated in Poland in 2017-2022,2021,,Poland,,,41,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.29,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.81,Corynebacterium diphtheriae bv. gravis strain 7072/17,7072/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508154,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969425.1,CP103900,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,382 x,Unicycler v. not specified,1,0,1,2450063,53.496216,2374,2228,unk,isolated in Poland in 2017-2022,2017,,Poland,,,63,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1720349.82,Corynebacterium diphtheriae bv. gravis strain 5521/17,5521/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508153,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969465.1,CP103901,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,601 x,Unicycler v. not specified,1,0,1,2452932,53.497814,2373,2228,wound,isolated in Poland in 2017-2022,2017,,Poland,,,31,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.83,Corynebacterium diphtheriae bv. gravis strain 5379/19,5379/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508161,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969485.1,CP103893,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,199 x,Unicycler v. not specified,1,0,1,2446723,53.485416,2366,2226,blood,isolated in Poland in 2017-2022,2019,,Poland,,,59,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.84,Corynebacterium diphtheriae bv. gravis strain 4674/18,4674/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508158,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969525.1,CP103896,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,170 x,Unicycler v. not specified,1,0,1,2447241,53.48664,2362,2225,blood,isolated in Poland in 2017-2022,2018,,Poland,,,54,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.85,Corynebacterium diphtheriae bv. gravis strain 6211/17,6211/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508151,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969565.1,CP103903,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,210 x,Unicycler v. not specified,1,0,1,2446364,53.485172,2361,2223,blood,isolated in Poland in 2017-2022,2017,,Poland,,,18,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.86,Corynebacterium diphtheriae bv. gravis strain 647/22,647/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508174,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024970245.1,"CP103905,CP103906",,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,201 x,CLC NGS Cell v. 22,1,1,2,2475879,53.512672,2560,2264,blood,isolated in Poland in 2017-2022,2022,,Poland,,,40,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.88,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.87,Corynebacterium diphtheriae bv. gravis 3302/22,3302/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508180,1720349,,,non-toxigenic,,genotype:ST-32,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968165.1,CP103904,,,Oxford Nanopore GridION,198 x,CLC NGS Cell v. 22,1,0,1,2408912,53.450645,2449,2220,respiratory tracks,,2022,Poland,Poland,,,21,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.9,4.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1720349.88,Corynebacterium diphtheriae bv. gravis 576/21,576/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508167,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968225.1,CP103887,,,Oxford Nanopore GridION,126 x,CLC NGS Cell v. 22,1,0,1,2449609,53.487354,2489,2247,blood,,2021,Poland,Poland,,,65,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.9,4.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.89,Corynebacterium diphtheriae bv. gravis 1269/21,1269/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508169,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968205.1,CP103885,,,Oxford Nanopore GridION,124 x,CLC NGS Cell v. 22,1,0,1,2437577,53.48881,2464,2223,blood,,2021,Poland,Poland,,,55,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.3,3.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.90,Corynebacterium diphtheriae bv. gravis 2736/18,2736/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508157,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968265.1,CP103897,,,Oxford Nanopore GridION; MiSeq,211 x,Unicycler v. not specified,1,0,1,2437238,53.488457,2348,2198,blood,,2018,Poland,Poland,,,45,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.91,Corynebacterium diphtheriae bv. gravis 5790/18,5790/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508156,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968245.1,CP103898,,,Oxford Nanopore GridION; MiSeq,91 x,Unicycler v. not specified,1,0,1,2435912,53.487812,2347,2206,blood,,2018,Poland,Poland,,,59,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1720349.92,Corynebacterium diphtheriae bv. gravis 49390/20,49390/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508165,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968285.1,CP103889,,,Oxford Nanopore GridION; MiSeq,167 x,Unicycler v. not specified,1,0,1,2451330,53.48688,2380,2227,wound,,2020,Poland,Poland,,,72,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.95,Corynebacterium diphtheriae bv. gravis 453/18,453/18,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508155,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968405.1,CP103899,,,Oxford Nanopore GridION; MiSeq,183 x,Unicycler v. not specified,1,0,1,2456329,53.49837,2377,2234,wound,,2018,Poland,Poland,,,64,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.96,Corynebacterium diphtheriae bv. gravis 2232/21,2232/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508171,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969025.1,CP103883,,,Oxford Nanopore GridION,204 x,CLC NGS Cell v. 22,1,0,1,2450955,53.497105,2490,2249,wound,,2021,Poland,Poland,,,17,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.9,4.8,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1720349.97,Corynebacterium diphtheriae bv. gravis 8259/19,8259/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508162,1720349,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969205.1,CP103892,,,Oxford Nanopore GridION; MiSeq,249 x,Unicycler v. not specified,1,0,1,2437088,53.485962,2350,2198,respiratory tracks,,2019,Poland,Poland,,,66,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1720349.99,Corynebacterium diphtheriae bv. gravis 14225/20,14225/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508166,1720349,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.8,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969365.1,CP103888,,,Oxford Nanopore GridION; MiSeq,148 x,Unicycler v. not specified,1,0,1,2450753,53.486988,2373,2219,blood,,2020,Poland,Poland,,,42,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,173.208,Leptospira interrogans strain FMAS_KW1,FMAS_KW1,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11289419,173,,,,MLST.Leptospira_spp.44,,,,2019-05-07T00:00:00Z,,PRJNA528695,GCA_005222565.1,"CP039258,CP039259,CP039260",,Rajarata University of Sri lanka,PacBio RSII,30x,Canu 1.8 v. 1.0,2,1,3,4740090,35.01507,4791,4069,blood,,2017-07-04,Sri Lanka,Sri Lanka: Karawanalla,,male,48 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.209,Leptospira interrogans strain FMAS_KW2,FMAS_KW2,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11289420,173,,,,,,,,2019-05-07T00:00:00Z,,PRJNA528695,GCA_005222585.1,"CP039256,CP039257",,Rajarata University of Sri lanka,PacBio RSII,30x,Canu 1.8 v. 1.0,2,,2,4651137,35.03666,4691,3997,blood,,2017-08-11,Sri Lanka,Sri Lanka: Karawanalla,,male,45 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.210,Leptospira interrogans strain FMAS_AW1,FMAS_AW1,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11289421,173,,,,,,,,2019-05-07T00:00:00Z,,PRJNA528695,GCA_005222625.1,"CP039283,CP039284,CP039285,CP039286",,Rajarata University of Sri lanka,PacBio RSII,30x,Canu 1.8 v. 1.0,2,2,4,5071735,35.18082,5290,4491,blood,,2017-06-22,Sri Lanka,Sri Lanka: Awissawella,,female,38 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.414,Leptospira interrogans UI29382,UI29382,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN18642399,173,,,,MLST.Leptospira_spp.34,,,,2022-01-06T00:00:00Z,34962921,PRJNA720173,GCA_021378355.1,"CP072853,CP072854,CP072855",,,PacBio RSII,121.0x,Unicycler v. 0.4.8,2,1,3,4727163,35.037758,4641,3795,blood,,2014,Laos,Laos: Vientiane,,,,Leptospirosis,,,,,,,,,,,,,,collected_by:Lao-Oxford-Mahosot-Hospital-Wellcome Trust-Research Unit,,,,,,,Leptospirosis,,,,,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.418,Leptospira interrogans FMAS_PN2,FMAS_PN2,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919591,173,,,,,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022343745.1,"CP092151,CP092149,CP092150",,,PacBio Sequel System,1477x,canu v. 2.1,2,1,3,4734467,35.041115,4722,3813,blood,,2018-05-11,Sri Lanka,Sri Lanka:Polonnaruwa,,male,40 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,1.18,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.419,Leptospira interrogans FMAS_AP7,FMAS_AP7,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919589,173,,,,MLST.Leptospira_spp.43,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022343765.1,"CP092152,CP092153,CP092154,CP092155",,,PacBio Sequel System,666x,canu v. 2.1,2,2,4,4831992,35.01045,4729,3885,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,39 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.420,Leptospira interrogans FMAS_AP6,FMAS_AP6,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919588,173,,,,MLST.Leptospira_spp.49,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022343785.1,"CP092156,CP092157,CP092158,CP092159,CP092160",,,PacBio Sequel System,1380x,canu v. 2.1,2,3,5,5190059,35.227962,5265,4353,blood,,2018-01-25,Sri Lanka,Sri Lanka:Anuradhapura,,male,21 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.421,Leptospira interrogans FMAS_AP5,FMAS_AP5,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919587,173,,,,MLST.Leptospira_spp.49,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022343805.1,"CP092161,CP092162,CP092163,CP092164,CP092165",,,PacBio Sequel System,956x,canu v. 2.1,2,3,5,5116342,35.21217,5145,4228,blood,,2018-01-05,Sri Lanka,Sri Lanka:Anuradhapura,,male,40 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.422,Leptospira interrogans FMAS_RT2,FMAS_RT2,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919578,173,,,,,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022343825.1,"CP092166,CP092167,CP092168,CP092169,CP092170",,,PacBio Sequel System,1465x,canu v. 2.1,2,3,5,5015483,35.119926,5001,4082,blood,,2017-09-13,Sri Lanka,Sri Lanka:Rathnapura,,male,28 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.426,Leptospira interrogans FMAS_AP1,FMAS_AP1,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919583,173,,,,MLST.Leptospira_spp.43,,,,2022-03-03T00:00:00Z,,PRJNA528695,GCA_022453705.1,"CP092681,CP092678,CP092679,CP092680",,,PacBio Sequel System,1300x,canu v. 2.1,2,2,4,4787426,34.99722,4691,3845,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,37 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.428,Leptospira interrogans FMAS_PD1,FMAS_PD1,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919579,173,,,,MLST.Leptospira_spp_3.72,,,,2022-03-06T00:00:00Z,,PRJNA528695,GCA_022488465.1,"CP092743,CP092741,CP092742,CP092744,CP092745,CP092746,CP092747",,,PacBio Sequel System,2504x,canu v. 2.1,2,5,7,5267693,35.246815,5351,4398,blood,,2017-09-04,Sri Lanka,Sri Lanka:Peradeniya,,male,52 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.429,Leptospira interrogans FMAS_AW3,FMAS_AW3,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919577,173,,,,MLST.Leptospira_spp.75,,,,2022-03-03T00:00:00Z,,PRJNA528695,GCA_022453725.1,"CP092676,CP092673,CP092674,CP092675,CP092677",,,PacBio Sequel System,1472x,canu v. 2.1,2,3,5,5121101,35.271126,5206,4312,blood,,2017-09-27,Sri Lanka,Sri Lanka:Awissawella,,male,41 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.430,Leptospira interrogans FMAS_AW2,FMAS_AW2,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919576,173,,,,,,,,2022-03-06T00:00:00Z,,PRJNA528695,GCA_022488445.1,"CP092739,CP092736,CP092737,CP092738,CP092740",,,PacBio Sequel System,1356x,canu v. 2.1,2,3,5,5292334,35.303345,5411,4383,blood,,2017-08-22,Sri Lanka,Sri Lanka:Awissawella,,male,41 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.431,Leptospira interrogans FMAS_KG1,FMAS_KG1,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919581,173,,,,,,,,2022-03-03T00:00:00Z,,PRJNA528695,GCA_022453745.1,"CP092672,CP092666,CP092665,CP092667,CP092668,CP092669,CP092670,CP092671",,,PacBio Sequel System,1652x,canu v. 2.1,2,6,8,5440099,35.276234,5634,4582,blood,,2017-12-27,Sri Lanka,Sri Lanka:Kegalle,,male,30 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,173.441,Leptospira interrogans FMAS_PN3,FMAS_PN3,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919592,173,,,,MLST.Leptospira_spp.43,,,,2022-03-10T00:00:00Z,,PRJNA528695,GCA_024526695.1,"CP092663,CP092664,CP092662",,,PacBio Sequel System,1231x,"canu v. 2,1",2,1,3,4721089,35.007366,4596,3783,blood,,Not collected,Sri Lanka,Sri Lanka:Polonnaruwa,,male,37 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,100,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis NHP,1734925.67,Cutibacterium acnes subsp. acnes strain NBRC 113869,NBRC 113869,Cutibacterium acnes,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN21163589,1734925,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181495.1,CP084017,,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,327.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,0,1,2560907,60.019867,2497,2415,human skin,,2018,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Skin and Soft Tissue,- HP,174.74,Leptospira borgpetersenii strain FMAS_PN4,FMAS_PN4,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919593,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018399095.1,"CP072622,CP072623",,Rajarata University of Sri lanka,PacBio Sequel System,1086x,Canu v. 2.1,2,0,2,3917202,40.09303,4180,3329,blood,,,Sri Lanka,Sri Lanka:Polonnaruwa,,male,66 yrs,Leptospirosis,,host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,Missing,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.75,Leptospira borgpetersenii strain FMAS_AP9,FMAS_AP9,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919595,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018402805.1,"CP072618,CP072619",,Rajarata University of Sri lanka,PacBio Sequel System,804x,Canu v. 2.1,2,0,2,3916909,40.092278,4190,3336,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.76,Leptospira borgpetersenii strain FMAS_AP8,FMAS_AP8,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919594,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018402785.1,"CP072620,CP072621",,Rajarata University of Sri lanka,PacBio Sequel System,1065x,Canu v. 2.1,2,0,2,3917353,40.09358,4186,3331,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,37 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.77,Leptospira borgpetersenii strain FMAS_AP2,FMAS_AP2,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919584,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018402825.1,"CP072630,CP072631",,Rajarata University of Sri lanka,PacBio Sequel System,1683x,Canu v. 2.1,2,0,2,3916918,40.091545,4185,3331,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,37 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.78,Leptospira borgpetersenii strain FMAS_AP3,FMAS_AP3,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919585,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018402845.1,"CP072628,CP072629",,Rajarata University of Sri lanka,PacBio Sequel System,925x,Canu v. 2.1,2,0,2,3917379,40.09316,4195,3326,blood,,,Sri Lanka,Sri Lanka:Anuradhapura,,male,24 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.79,Leptospira borgpetersenii strain FMAS_PN2,FMAS_PN2,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919590,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-21T00:00:00Z,,PRJNA528695,GCA_018403805.1,"CP072624,CP072625",,Rajarata University of Sri lanka,PacBio Sequel System,1228x,Canu v. 2.1,2,0,2,3917612,40.092945,4193,3331,blood,,2018-05-18,Sri Lanka,Sri Lanka:Polonnaruwa,,male,56 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,174.80,Leptospira borgpetersenii strain FMAS_AP4,FMAS_AP4,Leptospira borgpetersenii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919586,174,,,,MLST.Leptospira_spp_3.132,,,,2021-05-18T00:00:00Z,,PRJNA528695,GCA_018403825.1,"CP072626,CP072627",,Rajarata University of Sri lanka,PacBio Sequel System,1229x,Canu v. 2.1,2,0,2,3916982,40.090992,4181,3325,blood,,2017-12-19,Sri Lanka,Sri Lanka:Anuradhapura,,male,21 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,"This is a collaborative project to culture, isolation and genomic analysis of Sri Lankan Leptospira isolates","collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,1747.1370,Cutibacterium acnes W81,W81,Cutibacterium acnes,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN35448567,1747,,,,,,,,2023-06-05T00:00:00Z,,PRJNA977060,,CP126744,,,"Illumina NovaSeq, Oxford Nanopore GridION",103x,B-assembler v. December 2022,1,0,1,2560819,60.009277,2503,2417,irrigation and debridement,,2020,USA,USA: Salt Lake City,,,,,,,,,,,,,,,,,,,human skin,surgical site infection,irrigation and debridement,"anaerobic Brucella plates, 37C",,,,,,,,,,,,,human skin,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1747.1372,Cutibacterium acnes W80,W80,Cutibacterium acnes,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN35448566,1747,,,,,,,,2023-06-05T00:00:00Z,,PRJNA977060,,CP126745,,,"Illumina NovaSeq, Oxford Nanopore GridION",91x,B-assembler v. December 2022,1,0,1,2560578,60.009148,2504,2413,irrigation and debridement,,2020,USA,USA: Salt Lake City,,,,,,,,,,,,,,,,,,,human skin,surgical site infection,irrigation and debridement,"anaerobic Brucella plates, 37C",,,,,,,,,,,,,human skin,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1747.283,Cutibacterium acnes strain KCOM 1315,KCOM 1315,Cutibacterium acnes,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN09759490,1747,,,,,,KCOM:1315,,2018-08-14T00:00:00Z,,PRJNA484093,GCA_003390995.1,CP031442,,Korean Collection for Oral Microbiology,PacBio; Illumina HiSeq,1108.5x,RS HGAP v. 3.0,1,,1,2560321,60.01017,2562,2513,"pus, osteomyelitis",,2005-01-11,South Korea,South Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Cutibacterium acnes KCOM 1315,,,,,,,,gingivitis,,,,,,,,,,,,,,100,0.7,Oral and Dental Diseases,Gingivitis,Skin and Soft Tissue,Oral and Dental Diseases-Gingivitis NHP,1750.408,Pseudopropionibacterium propionicum strain F0231,F0231,Arachnia propionica,Arachnia,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN18352184,1750,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128345.1,CP072386,,The Forsyth Institute,PacBio Sequel,163x,Pacbio MA v. 9.0.0.92188,1,0,1,3404402,66.15855,3199,3006,human oral cavity,,1987-11,USA,"USA: Blacksberg, Virginia",,male,12,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02156;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,97.47,1.75,,,Oral,- HP,1750.409,Pseudopropionibacterium propionicum strain F0714,F0714,Arachnia propionica,Arachnia,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN18352198,1750,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128365.1,CP072385,,The Forsyth Institute,PacBio Sequel,150x,Pacbio MA v. 9.0.0.92188,1,0,1,3448470,66.06289,3264,3050,human oral cavity,,1984-01,USA,"USA: Blacksberg, Virginia",,male,6,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02157;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,gingivitis,,,,,,,,,human oral cavity,,,,97.47,1.22,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,1766.41,Mycolicibacterium fortuitum strain W4,W4,Mycolicibacterium fortuitum,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15806909,1766,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,GCA_020227715.1,CP060409,,University of Wisconsin-Madison,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,0,1,6674224,66.04717,6638,6463,sputum,,,,USA,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),,,,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,99.43,0.75,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1766.42,Mycolicibacterium fortuitum strain W6,W6,Mycolicibacterium fortuitum,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15806911,1766,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,GCA_020227835.1,CP060410,,University of Wisconsin-Madison,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,0,1,6555851,66.0852,6492,6306,sputum,,,,USA,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),,,,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,99.81,0.5,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1766.91,Mycolicibacterium fortuitum MF GZ001,MF GZ001,Mycolicibacterium fortuitum,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN31235336,1766,,,,,,,,2022-12-23T00:00:00Z,,PRJNA889243,,CP107719,,,Illumina HiSeq; PacBio,100.0x,FALCON v. 0.3; HGAP v. 4.0; Canu v. 0.7,1,0,1,6413573,66.18068,6232,6114,missing,,2022-01-05,China,China,,,,Pulmonary infection,,,,,,,,,,,,,,"collected_by:Guangzhou Chest Hospital, Guangzhou, China",,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,1767.24,Mycobacterium intracellulare strain M.i.27,M.i.27,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258722,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016755935.1,"AP024266,AP024267",,Niigata University School of Medicine,PacBio RS II,196x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5947382,67.55634,5803,5687,sputum,,2005,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.23,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.25,Mycobacterium intracellulare strain M016,M016,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258725,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016755995.1,AP024254,,Niigata University School of Medicine,PacBio RS II,76x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5476270,68.02486,5258,5206,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.05,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.26,Mycobacterium intracellulare strain M006,M006,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258732,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756135.1,"AP024245,AP024246",,Niigata University School of Medicine,PacBio RS II,74x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5657763,67.85236,5428,5339,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.27,Mycobacterium intracellulare strain M008,M008,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258731,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756115.1,"AP024248,AP024249",,Niigata University School of Medicine,PacBio RS II,129x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5850003,67.68678,5652,5553,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.28,Mycobacterium intracellulare strain M002,M002,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258730,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756095.1,"AP024241,AP024242",,Niigata University School of Medicine,PacBio RS II,76x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5489550,68.00769,5285,5233,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.29,Mycobacterium intracellulare strain M018,M018,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258729,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756075.1,"AP024255,AP024256",,Niigata University School of Medicine,PacBio RS II,80x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5572808,67.91522,5397,5313,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.78,0.04,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.30,Mycobacterium intracellulare strain M023,M023,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258733,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756155.1,"AP024260,AP024261",,Niigata University School of Medicine,PacBio RS II,129x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5762339,67.75098,5525,5433,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.31,Mycobacterium intracellulare strain M007,M007,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258738,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756255.1,AP024247,,Niigata University School of Medicine,PacBio RS II,122x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5532113,67.944565,5342,5276,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.32,Mycobacterium intracellulare strain M009,M009,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258737,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756235.1,AP024250,,Niigata University School of Medicine,PacBio RS II,137x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5730364,67.80077,5527,5447,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.33,Mycobacterium intracellulare strain M005,M005,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258735,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756195.1,AP024244,,Niigata University School of Medicine,PacBio RS II,137x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5519879,67.9475,5370,5294,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.05,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.34,Mycobacterium intracellulare strain M025,M025,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258734,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756175.1,"AP024262,AP024263",,Niigata University School of Medicine,PacBio RS II,142x,RS_HGAP_Assembly.3 v. 2.3.0,1,1,2,5669131,67.86714,5446,5386,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1767.35,Mycobacterium intracellulare strain M026,M026,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00258736,1767,,,,,,,,2020-12-26T00:00:00Z,,PRJDB10771,GCA_016756215.1,AP024264,,Niigata University School of Medicine,PacBio RS II,116x,RS_HGAP_Assembly.3 v. 2.3.0,1,0,1,5888633,67.66146,5704,5600,sputum,,2019,,,,,,,,,,,,,,,,,,,Comparative genome sequence analysis of Mycobacterium intracellulare strains isolated from patients with pulmonary Mycobacterium avium-intracellulare complex disease,,not applicable,not applicable,not applicable,https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=6384,Genome sequence of M. intracellulare clinical strains,,,,,,,,,,,,not applicable,,,,99.94,0.07,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.17700,Mycobacterium tuberculosis strain DKC2,DKC2,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA104027311,1773,,,,,,,,2018-11-09T00:00:00Z,,PRJEB20214,GCA_900520315.1,LR027516,,STATENS SERUM INSTITUT,,,,1,,1,4409544,65.62132,4294,4052,sputum,"derived from only 12% of the isolates, we have been able to extract important key information, such as mutation rate, conserved single-nucleotide polymorphisms to identify discrete transmission chains, and finally, the possible historical origins of the outbreak",1993,Denmark,Denmark,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Since 1992, Denmark has experienced the largest sustained outbreak of tuberculosis (TB) in Scandinavia ascribed to a single genotype. Based on nationwide strain-typing of every Mycobacterium tuberculosis culture-positive case, the ‘1112-15’ outbreak has been documented to progress at a surprisingly high rate, despite an overall declining trend in total Danish TB cases. As of Spring 2017, the International Reference Laboratory of Mycobacteriology (IRLM) in Copenhagen has collected and identified isolates from more than a thousand cases belonging to this outbreak via routine MIRU-VNTR typing. In 2015, we began a project of whole-genome sequencing every available ‘1112-15’ isolate identified between 1992 – 2014 (n=989), which is currently ~80% complete. Here, we present our first retrospective analysis of the 1112-15 dataset, based on whole-genome data from a sparse time-series consisting of five randomly selected isolates from each of the 23 years. Even if these data are derived from only 12% of the isolates, we have been able to extract important key information, such as mutation rate, conserved single-nucleotide polymorphisms to identify discrete transmission chains, and finally, the possible historical origins of the outbreak. In addition to helping us to put the outbreak in a global context, these data therefor also provide us with relevant information for future classification of new cases and ongoing monitoring of discrete transmission chains.;M. tuberculosis isolate DKC2-0PP1 from IRLM strain collection",,,,,,,,,diseased,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.17915,Mycobacterium tuberculosis strain L,L,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12816907,1773,,,,,,,,2019-10-01T00:00:00Z,,PRJNA573545,GCA_008761675.1,CP044345,,University of Otago,Illumina MiSeq; PacBio,50.0x,CANU v. 1.8,1,,1,4416671,65.61512,4386,4135,sputum,,2006,New Zealand,New Zealand,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequence of a New Zealand Mycobacterium tuberculosis strain,collected_by:Waikato DHB,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,0.33,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.18095,Mycobacterium tuberculosis strain AUSMDU00018547,AUSMDU00018547,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13191639,1773,,,,,genotype:ST215;mlst:ST215,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664875.1,CP045962,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,220x,de novo,1,0,1,4414769,65.60425,4291,4076,missing,,2017,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1773.21129,Mycobacterium tuberculosis strain 5005,5005,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN14150054,1773,,,,,,,,2020-03-01T00:00:00Z,,PRJNA607885,GCA_011044455.1,CP049108,,Belarusian State Medical University,Illumina MiSeq; Oxford Nanopore MiniION,200.0x,SPAdes v. 3.14; A5-miseq v. 20160825;,1,0,1,4418311,65.60774,4397,4070,sputum,,2019-03-12,Belarus,Belarus: Minsk,,male,53,Respiratory Tract Tuberculosis,,host_disease_outcome:recovery,Resistant,Computational Prediction,,,,,,,,,"Goals: detection of the geographical variation of Mycobacterium tuberculosis circulating in Republic of Belarus and exhibiting drug resistance to anti-TB drugs, and identification of genome variations associated with resistance.",collected_by:Bushma T.V.,,,,,,,Respiratory Tract Tuberculosis,,recovery,,,,,,,,,,,,98.92,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.22795,Mycobacterium tuberculosis strain 4860,4860,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN14598146,1773,,,MDR,,,,,2020-05-11T00:00:00Z,,PRJNA625312,GCA_013010385.1,CP053092,,Belarusian State Medical University,Illumina MiSeq; Oxford Nanopore MiniION,200.0x,Flye v. v. 2.7b; Unicycler v. v0.4.9b,1,0,1,4394156,65.60561,4258,4072,sputim from lungs,,2019-04-19,Belarus,Belarus:Minsk,,male,45,lung tuberculosis,,host_disease_outcome:recovery;host_subject_id:4860-2019,Susceptible;Resistant,Computational Prediction,,,,,,,,,genetic diversity of Mycobacterium tuberculosis resistant to anti-TB drugs,"collected_by:Bushma T.;biomaterial_provider:Republic Scientific and Practical center of Pulmonology and Tuberculosis\; Republican Reference-Laboratory: Phone +37517-2898452, Nikolenko Helena N.",,,,,,,lung tuberculosis,lung tuberculosis,recovery,,,MDR,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Urinary Tract,Respiratory Diseases-Tuberculosis HP,1773.22837,Mycobacterium tuberculosis strain FDAARGOS_757 strain Not applicable,Not applicable,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11056472,1773,,,,,,FDA:FDAARGOS_757,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267635.1,CP054013,,US Food and Drug Administration,Pacbio; Illumina,736.95x,Canu v. 1.7,1,0,1,4417931,65.61764,4289,4084,sputum,,,USA,USA:VA,,,,Chronic pulmonary tuberculosis,,host_description:Not applicable,Susceptible;Resistant,Computational Prediction,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Chronic pulmonary tuberculosis,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23590,Mycobacterium tuberculosis strain 4-0041P6C4,4-0041P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325246,1773,,,,,,,,2020-10-13T00:00:00Z,,PRJNA555636,GCA_014884625.1,CP043995,,San Diego State University,PacBio RSII,81x,Canu v. 1.6,1,0,1,4400017,65.61436,4325,4236,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23591,Mycobacterium tuberculosis strain 1-0072P6C4,1-0072P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325211,1773,,,,,,,,2020-10-13T00:00:00Z,,PRJNA555636,GCA_014884645.1,CP043996,,San Diego State University,PacBio RSII,110x,Canu v. 1.6,1,0,1,4421012,65.5957,4373,4267,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0.67,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23592,Mycobacterium tuberculosis strain 1-0066P6C4,1-0066P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325208,1773,,,,,,,,2020-10-13T00:00:00Z,,PRJNA555636,GCA_014884665.1,CP043997,,San Diego State University,PacBio RSII,118x,Canu v. 1.6,1,0,1,4416715,65.6077,4340,4257,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23593,Mycobacterium tuberculosis strain SEA17020028P6C4,SEA17020028P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325279,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899225.1,CP041789,,San Diego State University,PacBio RSII,136x,Canu v. 1.6,1,0,1,4415138,65.61099,4352,4250,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23594,Mycobacterium tuberculosis strain SEA15230P6C4,SEA15230P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325276,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899265.1,CP041792,,San Diego State University,PacBio RSII,165x,HGAP v. 2,1,0,1,4412837,65.60056,4334,4240,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23595,Mycobacterium tuberculosis strain SEA17020024P6C4,SEA17020024P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325278,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899245.1,CP041790,,San Diego State University,PacBio RSII,115x,Canu v. 1.6,1,0,1,4420315,65.60118,4369,4251,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23596,Mycobacterium tuberculosis strain SEA17020030P6C4,SEA17020030P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325280,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899205.1,CP041788,,San Diego State University,PacBio RSII,116x,Canu v. 1.6,1,0,1,4405198,65.628426,4331,4237,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23597,Mycobacterium tuberculosis strain SEA17020023P6C4,SEA17020023P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325277,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899285.1,CP041791,,San Diego State University,PacBio RSII,136x,Canu v. 1.6,1,0,1,4420316,65.60113,4373,4251,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23598,Mycobacterium tuberculosis strain SEA15228P6C4,SEA15228P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325274,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899325.1,CP041794,,San Diego State University,PacBio RSII,158x,HGAP v. 2,1,0,1,4407803,65.60688,4329,4232,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23599,Mycobacterium tuberculosis strain SEA15229P6C4,SEA15229P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325275,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899305.1,CP041793,,San Diego State University,PacBio RSII,158x,HGAP v. 2,1,0,1,4431110,65.60483,4348,4252,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23600,Mycobacterium tuberculosis strain SEA14333P6C4,SEA14333P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325273,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899345.1,CP041795,,San Diego State University,PacBio RSII,131x,HGAP v. 2,1,0,1,4408229,65.615395,4328,4234,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23601,Mycobacterium tuberculosis strain SEA14318P6C4,SEA14318P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325272,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899365.1,CP041796,,San Diego State University,PacBio RSII,128x,HGAP v. 2,1,0,1,4426614,65.59982,4353,4245,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23602,Mycobacterium tuberculosis strain SEA14117P6C4,SEA14117P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325271,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899385.1,CP041797,,San Diego State University,PacBio RSII,153x,Canu v. 1.6,1,0,1,4397372,65.61487,4317,4232,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23603,Mycobacterium tuberculosis strain SEA13111P6C4,SEA13111P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325270,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899405.1,CP041798,,San Diego State University,PacBio RSII,87x,HGAP v. 2,1,0,1,4410956,65.597275,4324,4234,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23604,Mycobacterium tuberculosis strain SEA13020298P6C4,SEA13020298P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325269,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899425.1,CP041799,,San Diego State University,PacBio RSII,130x,HGAP v. 2,1,0,1,4406587,65.61902,4332,4236,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23605,Mycobacterium tuberculosis strain SEA12334P6C4,SEA12334P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325268,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899445.1,CP041800,,San Diego State University,PacBio RSII,151x,Canu v. 1.6,1,0,1,4427826,65.61821,4366,4248,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23606,Mycobacterium tuberculosis strain SEA12202P6C4,SEA12202P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325267,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899465.1,CP041801,,San Diego State University,PacBio RSII,158x,HGAP v. 2,1,0,1,4433058,65.61419,4380,4255,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23607,Mycobacterium tuberculosis strain SEA12126P6C4,SEA12126P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325266,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899485.1,CP041802,,San Diego State University,PacBio RSII,124x,HGAP v. 2,1,0,1,4410647,65.60548,4331,4231,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23608,Mycobacterium tuberculosis strain SEA11020038P6C4,SEA11020038P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325261,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899585.1,CP041807,,San Diego State University,PacBio RSII,88x,HGAP v. 2,1,0,1,4397139,65.61098,4316,4228,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23609,Mycobacterium tuberculosis strain SEA11020057P6C4,SEA11020057P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325262,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899565.1,CP041806,,San Diego State University,PacBio RSII,126x,HGAP v. 2,1,0,1,4402162,65.60429,4327,4239,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23610,Mycobacterium tuberculosis strain SEA11020068P6C4,SEA11020068P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325263,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899545.1,CP041805,,San Diego State University,PacBio RSII,90x,HGAP v. 2,1,0,1,4402473,65.63457,4334,4244,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23611,Mycobacterium tuberculosis strain SEA11278P6C4,SEA11278P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325265,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899505.1,CP041803,,San Diego State University,PacBio RSII,94x,HGAP v. 2,1,0,1,4410029,65.602135,4325,4227,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23612,Mycobacterium tuberculosis strain SEA11020092P6C4,SEA11020092P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325264,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899525.1,CP041804,,San Diego State University,PacBio RSII,87x,HGAP v. 2,1,0,1,4406516,65.60276,4357,4245,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23613,Mycobacterium tuberculosis strain SEA08162P6C4,SEA08162P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325258,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899645.1,CP041810,,San Diego State University,PacBio RSII,124x,HGAP v. 2,1,0,1,4408888,65.61532,4344,4251,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23614,Mycobacterium tuberculosis strain SEA09020048P6C4,SEA09020048P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325259,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899625.1,CP041809,,San Diego State University,PacBio RSII,138x,HGAP v. 2,1,0,1,4391433,65.59563,4317,4228,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23615,Mycobacterium tuberculosis strain SEA09167P6C4,SEA09167P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325260,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899605.1,CP041808,,San Diego State University,PacBio RSII,115x,HGAP v. 2,1,0,1,4368671,65.630714,4301,4217,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.88,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23616,Mycobacterium tuberculosis strain SEA08151P6C4,SEA08151P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325257,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899665.1,CP041811,,San Diego State University,PacBio RSII,161x,Canu v. 1.6,1,0,1,4413498,65.60035,4342,4239,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23617,Mycobacterium tuberculosis strain SEA07020250P6C4,SEA07020250P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325256,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899685.1,CP041812,,San Diego State University,PacBio RSII,118x,Canu v. 1.6,1,0,1,4407077,65.61099,4329,4251,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23618,Mycobacterium tuberculosis strain SEA07010354P6C4,SEA07010354P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325255,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899705.1,CP041813,,San Diego State University,PacBio RSII,113x,HGAP v. 2,1,0,1,4438102,65.6133,4372,4270,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23619,Mycobacterium tuberculosis strain SEA06535P6C4,SEA06535P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325254,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899725.1,CP041814,,San Diego State University,PacBio RSII,108x,HGAP v. 2,1,0,1,4408176,65.629364,4320,4229,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23620,Mycobacterium tuberculosis strain 4-0077P6C4,4-0077P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325249,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899825.1,CP041819,,San Diego State University,PacBio RSII,158x,HGAP v. 2,1,0,1,4401396,65.626495,4331,4244,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23621,Mycobacterium tuberculosis strain 4-0087P6C4,4-0087P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325250,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899805.1,CP041818,,San Diego State University,PacBio RSII,128x,HGAP v. 2,1,0,1,4428457,65.62751,4365,4269,lung,,,South Africa,South Africa,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23622,Mycobacterium tuberculosis strain 4-0073P6C4,4-0073P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325248,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899845.1,CP041820,,San Diego State University,PacBio RSII,102x,HGAP v. 2,1,0,1,4414542,65.62019,4326,4241,lung,,,South Africa,South Africa,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23623,Mycobacterium tuberculosis strain 4-0062P6C4,4-0062P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325247,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899865.1,CP041821,,San Diego State University,PacBio RSII,75x,HGAP v. 2,1,0,1,4399842,65.62722,4326,4241,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23624,Mycobacterium tuberculosis strain 4-0024P6C4,4-0024P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325245,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899885.1,CP041822,,San Diego State University,PacBio RSII,130x,Canu v. 1.6,1,0,1,4399945,65.614204,4325,4233,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23625,Mycobacterium tuberculosis strain 4-0019P6C4,4-0019P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325244,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899905.1,CP041823,,San Diego State University,PacBio RSII,89x,Canu v. 1.6,1,0,1,4400017,65.61431,4319,4235,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23626,Mycobacterium tuberculosis strain 4-0012P6C4,4-0012P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325243,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899925.1,CP041824,,San Diego State University,PacBio RSII,116x,HGAP v. 2,1,0,1,4401614,65.636375,4302,4229,lung,,,South Africa,South Africa,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23627,Mycobacterium tuberculosis strain SEA02010036P6C4,SEA02010036P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325253,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899745.1,CP041815,,San Diego State University,PacBio RSII,140x,Canu v. 1.6,1,0,1,4416761,65.610725,4341,4249,missing,,,Belgium,Belgium,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,"collected_by:Institute of Tropical Medicine (Antwerp, Belgium)",,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23628,Mycobacterium tuberculosis strain SEA00042P6C4,SEA00042P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325252,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899765.1,CP041816,,San Diego State University,PacBio RSII,88x,HGAP v. 2,1,0,1,4424310,65.624695,4361,4249,missing,,,Sweden,Sweden,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Public Health Agency of Sweden,,,,,,,tuberculosis,,,,,,,,,,,,,,99.53,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.23629,Mycobacterium tuberculosis strain 4-0096P6C4,4-0096P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325251,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899785.1,CP041817,,San Diego State University,PacBio RSII,150x,HGAP v. 2,1,0,1,4408117,65.61741,4331,4247,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23630,Mycobacterium tuberculosis strain 4-0010P6C4,4-0010P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325242,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899945.1,CP041825,,San Diego State University,PacBio RSII,64x,Canu v. 1.6,1,0,1,4400007,65.614235,4330,4237,lung,,,South Africa,South Africa,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:South African National Health Laboratory Service,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23631,Mycobacterium tuberculosis strain 3-0124P6C4,3-0124P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325241,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899965.1,CP041826,,San Diego State University,PacBio RSII,51x,HGAP v. 2,1,0,1,4447644,65.5988,4423,4281,lung,,,Philippines,Philippines,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Tropical Disease Foundation,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23632,Mycobacterium tuberculosis strain 3-0090P6C4,3-0090P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325239,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900005.1,CP041828,,San Diego State University,PacBio RSII,131x,HGAP v. 2,1,0,1,4433503,65.59398,4375,4260,lung,,,Philippines,Philippines,,,,tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Tropical Disease Foundation,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23633,Mycobacterium tuberculosis strain 3-0059P6C4,3-0059P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325238,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900055.1,CP041829,,San Diego State University,PacBio RSII,78x,HGAP v. 2,1,0,1,4376753,65.62434,4302,4222,lung,,,Philippines,Philippines,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Tropical Disease Foundation,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23634,Mycobacterium tuberculosis strain 3-0096P6C4,3-0096P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325240,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014899985.1,CP041827,,San Diego State University,PacBio RSII,92x,HGAP v. 2,1,0,1,4450340,65.604744,4381,4280,lung,,,Philippines,Philippines,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Tropical Disease Foundation,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23635,Mycobacterium tuberculosis strain 2-0068P6C4,2-0068P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325237,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900075.1,CP041830,,San Diego State University,PacBio RSII,140x,HGAP v. 2,1,0,1,4417769,65.61004,4353,4253,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23636,Mycobacterium tuberculosis strain 2-0059P6C4,2-0059P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325236,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900095.1,CP041831,,San Diego State University,PacBio RSII,58x,HGAP v. 2,1,0,1,4425172,65.58615,4344,4254,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23637,Mycobacterium tuberculosis strain 2-0052P6C4,2-0052P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325235,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900115.1,CP041832,,San Diego State University,PacBio RSII,138x,HGAP v. 2,1,0,1,4404274,65.61592,4327,4250,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23638,Mycobacterium tuberculosis strain 2-0046P6C4,2-0046P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325234,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900135.1,CP041833,,San Diego State University,PacBio RSII,85x,HGAP v. 2,1,0,1,4438223,65.60887,4300,,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23639,Mycobacterium tuberculosis strain 2-0043-unknownP6C4,2-0043-unknownP6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325233,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900155.1,CP041834,,San Diego State University,PacBio RSII,137x,HGAP v. 2,1,0,1,4409038,65.62493,4245,,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23640,Mycobacterium tuberculosis strain 2-0034P6C4,2-0034P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325232,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900175.1,CP041835,,San Diego State University,PacBio RSII,145x,HGAP v. 2,1,0,1,4410873,65.61415,4336,4250,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23641,Mycobacterium tuberculosis strain 1-0160P6C4,1-0160P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325223,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900355.1,CP041844,,San Diego State University,PacBio RSII,96x,HGAP v. 2,1,0,1,4431494,65.62031,4374,4262,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23642,Mycobacterium tuberculosis strain 1-0168P6C4,1-0168P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325224,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900335.1,CP041843,,San Diego State University,PacBio RSII,90x,HGAP v. 2,1,0,1,4405183,65.60967,4334,4247,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23643,Mycobacterium tuberculosis strain 2-0013P6C4,2-0013P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325225,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900315.1,CP041842,,San Diego State University,PacBio RSII,102x,HGAP v. 2,1,0,1,4414962,65.61148,4346,4254,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23644,Mycobacterium tuberculosis strain 2-0022P6C4,2-0022P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325227,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900275.1,CP041840,,San Diego State University,PacBio RSII,71x,HGAP v. 2,1,0,1,4438339,65.60923,4297,,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23645,Mycobacterium tuberculosis strain 2-0028P6C4,2-0028P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325229,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900235.1,CP041838,,San Diego State University,PacBio RSII,158x,Canu v. 1.6,1,0,1,4438281,65.60937,4375,4275,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23646,Mycobacterium tuberculosis strain 2-0029P6C4,2-0029P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325230,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900215.1,CP041837,,San Diego State University,PacBio RSII,147x,Canu v. 1.6,1,0,1,4438363,65.60926,4375,4274,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23647,Mycobacterium tuberculosis strain 2-0031P6C4,2-0031P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325231,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900195.1,CP041836,,San Diego State University,PacBio RSII,64x,HGAP v. 2,1,0,1,4418552,65.609436,4362,4253,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.28,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23648,Mycobacterium tuberculosis strain 2-0023P6C4,2-0023P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325228,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900255.1,CP041839,,San Diego State University,PacBio RSII,117x,HGAP v. 2,1,0,1,4438366,65.60908,4378,4275,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23649,Mycobacterium tuberculosis strain 1-0156P6C4,1-0156P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325222,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900375.1,CP041845,,San Diego State University,PacBio RSII,49x,HGAP v. 2,1,0,1,4419404,65.61919,4346,4253,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23650,Mycobacterium tuberculosis strain 2-0021P6C4,2-0021P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325226,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900295.1,CP041841,,San Diego State University,PacBio RSII,108x,HGAP v. 2,1,0,1,4438299,65.60894,4372,4276,lung,,,Moldova,Moldova,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:Phthisiopneumology Institute,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23651,Mycobacterium tuberculosis strain 1-0153P6C4,1-0153P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325221,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900395.1,CP041846,,San Diego State University,PacBio RSII,93x,HGAP v. 2,1,0,1,4419030,65.61302,4357,4251,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23652,Mycobacterium tuberculosis strain 1-0110P6C4,1-0110P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325215,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900515.1,CP041852,,San Diego State University,PacBio RSII,83x,HGAP v. 2,1,0,1,4425422,65.600975,4366,4251,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23653,Mycobacterium tuberculosis strain 1-0116P6C4,1-0116P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325217,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900475.1,CP041850,,San Diego State University,PacBio RSII,132x,Canu v. 1.6,1,0,1,4416797,65.607025,4356,4257,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23654,Mycobacterium tuberculosis strain 1-0112P6C4,1-0112P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325216,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900495.1,CP041851,,San Diego State University,PacBio RSII,87x,HGAP v. 2,1,0,1,4413235,65.59374,4363,4251,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23655,Mycobacterium tuberculosis strain 1-0149P6C4,1-0149P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325220,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900415.1,CP041847,,San Diego State University,PacBio RSII,120x,HGAP v. 2,1,0,1,4418657,65.60145,4355,4256,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23656,Mycobacterium tuberculosis strain 1-0137P6C4,1-0137P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325219,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900435.1,CP041848,,San Diego State University,PacBio RSII,106x,Canu v. 1.6,1,0,1,4419694,65.606445,4352,4259,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23657,Mycobacterium tuberculosis strain 1-0123P6C4,1-0123P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325218,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900455.1,CP041849,,San Diego State University,PacBio RSII,110x,HGAP v. 2,1,0,1,4420004,65.61614,4349,4264,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23658,Mycobacterium tuberculosis strain 1-0107P6C4,1-0107P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325214,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900555.1,CP041853,,San Diego State University,PacBio RSII,124x,HGAP v. 2,1,0,1,4444842,65.61261,4372,4275,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23659,Mycobacterium tuberculosis strain 1-0084P6C4,1-0084P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325212,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900615.1,CP041855,,San Diego State University,PacBio RSII,125x,HGAP v. 2,1,0,1,4419973,65.60092,4360,4258,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23660,Mycobacterium tuberculosis strain 1-0102P6C4,1-0102P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325213,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900595.1,CP041854,,San Diego State University,PacBio RSII,133x,Canu v. 1.6,1,0,1,4421377,65.60083,4358,4260,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23661,Mycobacterium tuberculosis strain 1-0071P6C4,1-0071P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325210,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900635.1,CP041856,,San Diego State University,PacBio RSII,109x,HGAP v. 2,1,0,1,4416231,65.61337,4340,4251,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23662,Mycobacterium tuberculosis strain 1-0069P6C4,1-0069P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325209,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900655.1,CP041857,,San Diego State University,PacBio RSII,91x,HGAP v. 2,1,0,1,4416165,65.6132,4351,4253,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.28,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23663,Mycobacterium tuberculosis strain 1-0056P6C4,1-0056P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325205,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900715.1,CP041860,,San Diego State University,PacBio RSII,159x,Canu v. 1.6,1,0,1,4413638,65.59187,4361,4251,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23664,Mycobacterium tuberculosis strain 1-0054P6C4,1-0054P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325204,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900735.1,CP041861,,San Diego State University,PacBio RSII,143x,Canu v. 1.6,1,0,1,4419916,65.60088,4354,4257,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23665,Mycobacterium tuberculosis strain 1-0061P6C4,1-0061P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325206,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900695.1,CP041859,,San Diego State University,PacBio RSII,154x,HGAP v. 2,1,0,1,4413879,65.61736,4343,4233,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23666,Mycobacterium tuberculosis strain 1-0044P6C4,1-0044P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325201,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900795.1,CP041864,,San Diego State University,PacBio RSII,90x,Canu v. 1.6,1,0,1,4387956,65.60558,4310,4225,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23667,Mycobacterium tuberculosis strain 1-0047P6C4,1-0047P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325203,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900755.1,CP041862,,San Diego State University,PacBio RSII,150x,HGAP v. 2,1,0,1,4434707,65.623276,4370,4265,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23668,Mycobacterium tuberculosis strain 1-0064P6C4,1-0064P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325207,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900675.1,CP041858,,San Diego State University,PacBio RSII,142x,HGAP v. 2,1,0,1,4417680,65.601494,4354,4254,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.83,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23669,Mycobacterium tuberculosis strain 1-0039P6C4,1-0039P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325200,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900815.1,CP041865,,San Diego State University,PacBio RSII,142x,Canu v. 1.6,1,0,1,4411261,65.59648,4359,4254,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23670,Mycobacterium tuberculosis strain 1-0045P6C4,1-0045P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325202,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900775.1,CP041863,,San Diego State University,PacBio RSII,168x,HGAP v. 2,1,0,1,4416971,65.6072,4350,4256,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23671,Mycobacterium tuberculosis strain 1-0036P6C4,1-0036P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325199,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900835.1,CP041866,,San Diego State University,PacBio RSII,172x,HGAP v. 2,1,0,1,4404858,65.620865,4327,4243,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23672,Mycobacterium tuberculosis strain 1-0031P6C4,1-0031P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325198,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900855.1,CP041867,,San Diego State University,PacBio RSII,105x,Canu v. 1.6,1,0,1,4419967,65.6009,4360,4259,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23673,Mycobacterium tuberculosis strain 1-0030P6C4,1-0030P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325197,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900895.1,CP041868,,San Diego State University,PacBio RSII,158x,HGAP v. 2,1,0,1,4430047,65.60953,4348,4254,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23674,Mycobacterium tuberculosis strain 1-0021P6C4,1-0021P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325194,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901055.1,CP041871,,San Diego State University,PacBio RSII,63x,HGAP v. 2,1,0,1,4429476,65.615074,4382,4267,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0.33,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23675,Mycobacterium tuberculosis strain 1-0023P6C4,1-0023P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325195,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901035.1,CP041870,,San Diego State University,PacBio RSII,111x,HGAP v. 2,1,0,1,4419801,65.615326,4351,4259,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23676,Mycobacterium tuberculosis strain 1-0028P6C4,1-0028P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325196,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014900965.1,CP041869,,San Diego State University,PacBio RSII,93x,HGAP v. 2,1,0,1,4412588,65.60116,4349,4252,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23677,Mycobacterium tuberculosis strain 1-0017P6C4,1-0017P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325193,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901075.1,CP041872,,San Diego State University,PacBio RSII,101x,Canu v. 1.6,1,0,1,4418318,65.60189,4353,4254,lung,,,India,India,,,,tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23678,Mycobacterium tuberculosis strain 1-0013P6C4,1-0013P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325192,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901095.1,CP041873,,San Diego State University,PacBio RSII,119x,HGAP v. 2,1,0,1,4410415,65.62308,4343,4243,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23679,Mycobacterium tuberculosis strain 1-0006P6C4,1-0006P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325189,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901155.1,CP041876,,San Diego State University,PacBio RSII,99x,Canu v. 1.6,1,0,1,4419608,65.61541,4348,4254,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23680,Mycobacterium tuberculosis strain 1-0007P6C4,1-0007P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325190,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901135.1,CP041875,,San Diego State University,PacBio RSII,155x,HGAP v. 2,1,0,1,4432141,65.63009,4362,4259,lung,,,India,India,,,,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.23681,Mycobacterium tuberculosis strain 1-0009P6C4,1-0009P6C4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12325191,1773,,,,,,,,2020-10-20T00:00:00Z,,PRJNA555636,GCA_014901115.1,CP041874,,San Diego State University,PacBio RSII,113x,HGAP v. 2,1,0,1,4418159,65.60189,4362,4256,lung,,,India,India,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,This project presents 97 circularized reference-quality clinical M. tuberculosis genomes.,collected_by:PD Hinduja National Hospital,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.24178,Mycobacterium tuberculosis strain 11502,11502,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN17832565,1773,,,,,,,,2021-02-22T00:00:00Z,,PRJNA700485,GCA_016917775.1,CP070338,,Belarusian State Medical University,Illumina MiSeq; Oxford Nanopore MiniION,560.0x,Flye v. v. 2.8.2; SPAdes v. 3.14.1;,1,0,1,4420561,65.60692,4295,4053,sputum,,2019-06-25,Belarus,Belarus:Minsk,,male,42,Tuberculosis of lung,,host_disease_outcome:recovery;host_subject_id:#11502-2019,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genetic diversity of Mycobacterium tuberculosis resistant to anti-TB drugs,collected_by:Bushma T.V.,,,,,,,Tuberculosis of lung,,recovery,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.24179,Mycobacterium tuberculosis strain 120/26CAO,120/26CAO,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18056856,1773,,,,,,,,2021-03-04T00:00:00Z,,PRJNA704837,GCA_017164035.1,CP071127,,National Medical Research Center of Phthisiopulmonology and Infectious Diseases,Complete Genomics,164.0x,bwa v. 0.7.17-r1188,1,0,1,4411524,65.62177,4281,4041,sputum,,2018-06-22,Russia,Russia: Moscow,,male,36,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Study of the virulence of Mycobacterium tuberculosis strains of Beijing Central Asia Outbreak sublineage,collected_by:National Medical Research Center of Phthisiopulmonology and Infectious Diseases,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.24180,Mycobacterium tuberculosis strain 267/47W148,267/47W148,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18056929,1773,,,,,,,,2021-03-04T00:00:00Z,,PRJNA704837,GCA_017164055.1,CP071128,,National Medical Research Center of Phthisiopulmonology and Infectious Diseases,Complete Genomics,197.0x,bwa v. 0.7.17-r1188,1,0,1,4411528,65.62198,4279,4037,sputum,,2018-06-18,Russia,Russia: Moscow,,male,41,tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Study of the virulence of Mycobacterium tuberculosis strains of Beijing Central Asia Outbreak sublineage,collected_by:National Medical Research Center of Phthisiopulmonology and Infectious Diseases,,,,,,,tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.26080,Mycobacterium tuberculosis strain 2.2,2.2,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18928235,1773,,,,,,,,2021-08-05T00:00:00Z,,PRJNA726345,GCA_019454365.1,CP074075,,New York Presbyterian Queens Hospital,Illumina HiSeq,63.0x,MEGAHIT v. 1.1.3,1,0,1,4411505,65.80844,4258,,,,2019-07-01,USA,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Identification of co-infection by multiple mycobacteria species using Next Generation Sequencing,sample_type:Tissue Sample,,,,,,,,,,,,,,,,,,,,,98.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1773.27118,Mycobacterium tuberculosis I0003447-5,I0003447-5,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18614372,1773,,,,,,,,2022-02-07T00:00:00Z,,PRJNA719670,GCA_022023995.1,CP072790,,,PacBio RSII; Illumina HiSeq,203.0x,Flye v. 2.6,1,0,1,4397821,65.61472,4265,4039,,,2012-01-01,Peru,Peru,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Socios en Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.27119,Mycobacterium tuberculosis 060827,060827,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15348336,1773,,,,,,,,2022-01-24T00:00:00Z,,PRJNA641267,GCA_021559895.1,CP058236,,,PacBio RS,107.0x,HGAP v. 2016-11-01,1,0,1,4438262,65.59327,4338,,sputum,,2006,Benin,Benin,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:Laboratoire de Reference des Mycobacteries, Cotonou, Benin",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.94,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29743,Mycobacterium tuberculosis N0091,N0091,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406476,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870185.1,CP069065,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4387551,65.598694,4259,,human sputum,,2002-06-14,Gambia,Gambia,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.6,0.6,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29744,Mycobacterium tuberculosis N0069,N0069,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406479,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870125.1,CP069062,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4419191,65.599815,4284,,human sputum,,1998-09-11,China,China,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29745,Mycobacterium tuberculosis N3913,N3913,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406478,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870145.1,CP069063,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4408017,65.59521,4283,,human sputum,,2011-11-06,Ethiopia,Ethiopia,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.6,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29746,Mycobacterium tuberculosis N1202,N1202,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406477,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870165.1,CP069064,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4391569,65.59555,4255,,human sputum,,2008-02-05,Ghana,Ghana,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,0.6,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29747,Mycobacterium tuberculosis N1268,N1268,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406474,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870225.1,CP069067,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4428969,65.58508,4327,,human sputum,,2011-11-15,Sierra Leone,Sierra Leone,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.8,0.5,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29748,Mycobacterium tuberculosis N1201,N1201,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406475,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870205.1,CP069066,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4386429,65.594086,4243,,human sputum,,2009-02-17,Ghana,Ghana,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,1.2,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29749,Mycobacterium tuberculosis N1272,N1272,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406473,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870245.1,CP069068,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4420832,65.58702,4310,,human sputum,,2011-11-15,Ghana,Ghana,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.8,0.6,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29750,Mycobacterium tuberculosis N1176,N1176,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406472,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870265.1,CP069069,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4425207,65.59078,4317,,human sputum,,2009-09-11,Ghana,Ghana,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,0.4,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29751,Mycobacterium tuberculosis N1216,N1216,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406469,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870325.1,CP069072,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4393016,65.607,4288,,human sputum,,2011-02-15,Ghana,Ghana,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.8,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29752,Mycobacterium tuberculosis N1283,N1283,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406471,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870285.1,CP069070,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4419495,65.586296,4292,,human sputum,,2011-11-15,Germany,Germany,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29753,Mycobacterium tuberculosis N0136,N0136,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406470,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870305.1,CP069071,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4395562,65.613815,4253,,human sputum,,1991-07-19,USA,USA,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29754,Mycobacterium tuberculosis N0054,N0054,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406468,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870345.1,CP069073,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4431518,65.6091,4317,,human sputum,,1999-06-15,Ethiopia,Ethiopia,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29755,Mycobacterium tuberculosis N1274,N1274,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406467,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870365.1,CP069074,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4438446,65.61957,4325,,human sputum,,2011-11-15,Afghanistan,Afghanistan,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29756,Mycobacterium tuberculosis N0004,N0004,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406466,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870385.1,CP069075,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4422216,65.60788,4305,,human sputum,,2010-03-01,India,India,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29757,Mycobacterium tuberculosis N0031,N0031,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406464,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870405.1,CP069076,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4399032,65.61928,4237,,human sputum,,1994-06-15,China,China,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.8,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29758,Mycobacterium tuberculosis N0157,N0157,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406462,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870445.1,CP069078,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4410121,65.61754,4283,,human sputum,,1999-06-15,Philippines,Philippines,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29759,Mycobacterium tuberculosis N0072,N0072,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16406463,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA668291,GCA_022870425.1,CP069077,,,Oxford Nanopore MinION,50x,Flye v. 2.5,1,0,1,4420471,65.60955,4266,,human sputum,,1997-06-15,India,India,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:University of Basel, Switzerland",,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.29760,Mycobacterium tuberculosis SGF0232017,SGF0232017,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN27028218,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA820632,GCA_022871085.1,CP095020,,,PacBio RSII,83x,Celera Assembler v. 8.3,1,0,1,4413076,65.60471,4291,4089,skin biopsy,,2017,China,China:Jiangsu,,,,Mycobacterium tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,Mycobacterium tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Skin and Soft Tissue,Respiratory Diseases-Tuberculosis HP,1773.29761,Mycobacterium tuberculosis SGF0422017,SGF0422017,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN27028219,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA820632,GCA_022871105.1,CP095021,,,PacBio RSII,43x,Celera Assembler v. 8.3,1,0,1,4402590,65.61272,4285,4082,skin biopsy,,2017,China,China:Jiangsu,,,,Mycobacterium tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,Mycobacterium tuberculosis,,,,,,,,,,,,,,99.8,0.1,Respiratory Diseases,Tuberculosis,Skin and Soft Tissue,Respiratory Diseases-Tuberculosis HP,1773.29762,Mycobacterium tuberculosis SGF0472017,SGF0472017,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN27028220,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA820632,GCA_022871125.1,CP095022,,,PacBio RSII,42x,Celera Assembler v. 8.3,1,0,1,4417237,65.610405,4323,4100,skin biopsy,,2017,China,China:Jiangsu,,,,Mycobacterium tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,Mycobacterium tuberculosis,,,,,,,,,,,,,,99.9,0.5,Respiratory Diseases,Tuberculosis,Skin and Soft Tissue,Respiratory Diseases-Tuberculosis HP,1773.29763,Mycobacterium tuberculosis SGF0702019,SGF0702019,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN27028221,1773,,,,,,,,2022-04-11T00:00:00Z,,PRJNA820632,GCA_022871145.1,CP095023,,,PacBio RSII,43x,Celera Assembler v. 8.3,1,0,1,4419329,65.62143,4294,4086,skin biopsy,,2019,China,China:Jiangsu,,,,Mycobacterium tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,Mycobacterium tuberculosis,,,,,,,,,,,,,,99.9,0.4,Respiratory Diseases,Tuberculosis,Skin and Soft Tissue,Respiratory Diseases-Tuberculosis HP,1773.29764,Mycobacterium tuberculosis Lineage 1.1.2,Lineage 1.1.2,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188688,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932527315.1,OW052188,,,,,,1,0,1,4422327,65.597595,4256,,sputum,,2013-01-17,Madagascar,Madagascar,,,,,,host_health_state:diseased,Resistant;Susceptible,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.29765,Mycobacterium tuberculosis Lineage 2.2.7,Lineage 2.2.7,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188731,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932527325.1,OW052189,,,,,,1,0,1,4415120,65.61398,4262,,sputum,,2016-04-21,Madagascar,Madagascar,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.29766,Mycobacterium tuberculosis Lineage 3.1.1,Lineage 3.1.1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188685,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932527465.1,OW052302,,,,,,1,0,1,4428693,65.62236,4278,,sputum,,2015-03-23,Madagascar,Madagascar,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.29767,Mycobacterium tuberculosis Lineage 4.1.2.1,Lineage 4.1.2.1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188674,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932530255.1,OW052573,,,,,,1,0,1,4408536,65.63179,4245,,sputum,,2016-11-29,Madagascar,Madagascar,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.29768,Mycobacterium tuberculosis Lineage 4.1,Lineage 4.1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188689,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932530315.1,OW052571,,,,,,1,0,1,4394726,65.60832,4242,,sputum,,2017-02-02,Madagascar,Madagascar,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.8,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.29769,Mycobacterium tuberculosis Lineage 1.1.2,Lineage 1.1.2,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA13188715,1773,,,,,,,,2022-03-21T00:00:00Z,,PRJEB49093,GCA_932530395.1,OW052570,,,,,,1,0,1,4412157,65.607544,4255,,sputum,,2013-05-08,Madagascar,Madagascar,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,99.9,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.30122,Mycobacterium tuberculosis BLR-31d,BLR-31d,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN31644110,1773,,,,,,,,2022-11-14T00:00:00Z,,PRJNA899055,,CP110674,,,Illumina MiSeq; Oxford Nanopore MinION,48.0x,Barapost v. v. 1-11-19-edition; Flye v.,1,0,1,4418534,65.60977,4296,4084,sputum,,2019-12-24,Belarus,Belarus,,male,,lung tuberculosis,,host_description:male;host_disease_outcome:recovery;host_disease_stage:treated with delamanid and badaquiline;host_subject_id:N 231-24-12-2019,Resistant,Computational Method,,,,,,,,,,collected_by:Mogilev anti-tuberculosis clinic,,,,,,,lung tuberculosis,,recovery,male,treated with delamanid and badaquiline,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30190,Mycobacterium tuberculosis BLR 9248 2019,BLR 9248 2019,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN32350377,1773,,,,,,,,2023-01-18T00:00:00Z,,PRJNA916936,,CP115447,,,Illumina MiSeq; Oxford Nanopore MinION,160.0x,Barapost v. v. 2021-11-19-edition; Flye,1,0,1,4419959,65.609474,4293,4086,sputum,,2019-08-09,Belarus,Belarus,,male,43,Respiratory Tract Tuberculosis,,host_disease_outcome:recovery,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Ramaneika A.N.,,,,,,,Respiratory Tract Tuberculosis,,recovery,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30422,Mycobacterium tuberculosis I0004240-3,I0004240-3,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24038646,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089611,,,PacBio RSII; Illumina HiSeq,194.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4400005,65.63597,4270,4076,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios en salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30423,Mycobacterium tuberculosis I0004290-8,I0004290-8,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24039411,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089610,,,PacBio RSII; Illumina HiSeq,195.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4420979,65.61583,4307,4099,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30424,Mycobacterium tuberculosis 01-R1430,01-R1430,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24039564,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089773,,,PacBio RSII; Illumina HiSeq,227.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4409225,65.61339,4292,4102,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30425,Mycobacterium tuberculosis I0003165-3,I0003165-3,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24039456,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089772,,,PacBio RSII; Illumina HiSeq,172.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4396361,65.614746,4284,4083,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30426,Mycobacterium tuberculosis 02-R0894,02-R0894,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24039598,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089774,,,PacBio RSII; Illumina HiSeq,191.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4422503,65.63566,4309,4102,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30427,Mycobacterium tuberculosis 02-R1708,02-R1708,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24039640,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089775,,,PacBio RSII; Illumina HiSeq,193.0x,Flye v. 2.6; ilon (For Assembly,1,0,1,4427007,65.62974,4316,4102,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30428,Mycobacterium tuberculosis 02-R1896,02-R1896,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24040382,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089776,,,PacBio RSII; Illumina HiSeq,195.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4407304,65.60999,4302,4091,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30429,Mycobacterium tuberculosis I0003270-1,I0003270-1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24040385,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089777,,,PacBio RSII; Illumina HiSeq,162.0x,Flye v. 2.6,1,0,1,4431508,65.619514,4323,4115,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.4,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30430,Mycobacterium tuberculosis I0003758-5,I0003758-5,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24040410,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089778,,,PacBio RSII; Illumina HiSeq,163.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4416715,65.616165,4287,4088,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30431,Mycobacterium tuberculosis BLR 4299 2019,BLR 4299 2019,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN32238502,1773,,,,,,,,2023-05-20T00:00:00Z,,PRJNA912384,,CP125620,,,Illumina MiSeq; Oxford Nanopore MinION,375.0x,Barapost v. v. 2021-11-19-edition; Flye,1,0,1,4391403,65.60664,4256,4076,sputum,,2019-04-24,Belarus,Belarus,,male,49,Respiratory Tract Tuberculosis,,host_disease_outcome:recovery,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Bushma T.V.,,,,,,,Respiratory Tract Tuberculosis,,recovery,,,,,,,,,,,,99.9,0.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30432,Mycobacterium tuberculosis 01-R1134,01-R1134,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24040618,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089779,,,PacBio RSII; Illumina HiSeq,138.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4406184,65.615715,4294,4073,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.8,0.4,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30433,Mycobacterium tuberculosis 02-R1179,02-R1179,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24042990,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089781,,,PacBio RSII; Illumina HiSeq,249.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4393775,65.61435,4274,4078,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30434,Mycobacterium tuberculosis M0003941-3,M0003941-3,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN24042982,1773,,,,,,,,2023-04-25T00:00:00Z,,PRJNA719670,,CP089780,,,PacBio RSII; Illumina HiSeq,206.0x,Flye v. 2.6; Pilon (For Assembly,1,0,1,4421169,65.60962,4317,4091,patient,,2012-01-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Socios En Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.30515,Mycobacterium tuberculosis 6721,6721,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN35655918,1773,,,,,,,,2023-06-18T00:00:00Z,,PRJNA980952,,CP127275,,,Oxford Nanopore MinION,39.0x,minimap2 v. 2.24,1,0,1,4386759,65.62122,4288,4072,sputum,,2021-04-07,Russia,Russia: Ekaterinburg,,,,tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Umpeleva,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30516,Mycobacterium tuberculosis 5521,5521,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN35655919,1773,,,,,,,,2023-06-18T00:00:00Z,,PRJNA980952,,CP127276,,,Oxford Nanopore MinION,286.0x,minimap2 v. 2.24,1,0,1,4396200,65.61453,4287,4084,sputum,,2021-03-24,Russia,Russia: Ekaterinburg,,,,tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Umpeleva,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30517,Mycobacterium tuberculosis 17221,17221,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN35655917,1773,,,,,,,,2023-06-18T00:00:00Z,,PRJNA980952,,CP127274,,,Oxford Nanopore MinION,70.0x,minimap2 v. 2.24,1,0,1,4395387,65.609764,4273,4081,sputum,,2021-06-25,Russia,Russia: Ekaterinburg,,,,tuberculosis,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Umpeleva,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30518,Mycobacterium tuberculosis 3320,3320,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN35654954,1773,,,,,,,,2023-06-18T00:00:00Z,,PRJNA980952,,CP127273,,,Oxford Nanopore MinION,298.0x,minimap2 v. 2.24,1,0,1,4394501,65.61425,4287,4075,sputum,,2019-11-20,Russia,Russia: Ekaterinburg,,,,tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Umpeleva,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.30519,Mycobacterium tuberculosis 25421,25421,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN35655980,1773,,,,,,,,2023-06-18T00:00:00Z,,PRJNA980952,,CP127277,,,Oxford Nanopore MinION,222.0x,minimap2 v. 2.24,1,0,1,4393403,65.61429,4281,4073,sputum,,2021-10-18,Russia,Russia: Ekaterinburg,,,,tuberculosis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Umpeleva,,,,,,,tuberculosis,,,,,,,,,,,,,,99.9,0.3,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.6742,Mycobacterium tuberculosis strain I0004241-1,I0004241-1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010135,1773,,,,,,,,2016-12-09T00:00:00Z,,PRJNA343736,GCF_001895765.1,CP018303,NZ_CP018303.1,Texas A&M University,Illumina HiSeq,202.8x,software developed in-house v.,1,,1,4386132,65.6,4264,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6743,Mycobacterium tuberculosis strain M0018684-2,M0018684-2,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010493,1773,,,,,,,,2016-12-09T00:00:00Z,31086182,PRJNA343736,GCF_001895785.1,CP018305,NZ_CP018305.1,Texas A&M University,Illumina HiSeq,70.9x,software developed in-house v.,1,,1,4359825,65.62,4257,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,sputum,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6744,Mycobacterium tuberculosis strain I0004000-1,I0004000-1,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010122,1773,,,,,,,,2016-12-09T00:00:00Z,,PRJNA343736,GCF_001895805.1,CP018302,NZ_CP018302.1,Texas A&M University,Illumina HiSeq,158.2x,software developed in-house v.,1,,1,4365724,65.61,4278,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6745,Mycobacterium tuberculosis strain I0002801-4,I0002801-4,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010171,1773,,,,,,,,2016-12-09T00:00:00Z,,PRJNA343736,GCF_001895825.1,CP018301,NZ_CP018301.1,Texas A&M University,Illumina HiSeq,163.7x,software developed in-house v.,1,,1,4376067,65.59,4266,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6746,Mycobacterium tuberculosis strain I0002353-6,I0002353-6,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010490,1773,,,,,,,,2016-12-09T00:00:00Z,,PRJNA343736,GCF_001895845.1,CP018300,NZ_CP018300.1,Texas A&M University,Illumina HiSeq,62.3x,software developed in-house v.,1,,1,4385578,65.62,4259,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6747,Mycobacterium tuberculosis strain M0002959-6,M0002959-6,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06010343,1773,,,,,,,,2016-12-09T00:00:00Z,31086182,PRJNA343736,GCF_001895865.1,CP018304,NZ_CP018304.1,Texas A&M University,Illumina HiSeq,120.9x,software developed in-house v.,1,,1,4386447,65.6,4260,,patient,,2012-01-01,Peru,Peru: Lima,,,,tuberculosis,sputum,,,,,,,,,,,,"Clinical isolates of M. tuberculosis from Lima, Peru",collected_by:Roger Calderon,,,,,,,tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.6748,Mycobacterium tuberculosis strain DK9897,DK9897,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06141171,1773,,,,,,,,2016-12-29T00:00:00Z,,PRJNA357378,GCF_001922485.1,CP018778,NZ_CP018778.1,Statens Serum Institut,Illumina MiSeq,365.0x,BWA-backtrack v. 0.6.2-r126,1,,1,4411511,65.61,4400,4258,sputum,,1998-02-06,Denmark,Denmark:Aarhus,,,,Tuberculosis,,,,,,,,,,,,,Characterizing a clinical isolate extracted from a patient with extrapulmonary TB and not protected by a recombinant vaccine,collected_by:International Reference Laboratory of Mycobacteriology,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8213,Mycobacterium tuberculosis strain Beijing-like/35049,Beijing-like/35049,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833360,1773,,,,,genotype:Beijing-like,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116755.1,CP017593,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,810.9x,Canu & Pilon v. Julio-2016,1,,1,4427062,65.61,4377,4100,,,2008,Colombia,Colombia: Buenaventura,,male,,Tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM),,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8214,Mycobacterium tuberculosis strain Beijing-like/36918,Beijing-like/36918,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833361,1773,,,,,genotype:Beijing-like,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116775.1,CP017594,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,825.2x,Canu & Pilon v. Julio-2016,1,,1,4441591,65.61,4377,4108,,,2007,Colombia,Colombia: Buenaventura,,female,16,Tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM),,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8215,Mycobacterium tuberculosis strain Beijing-like/38774,Beijing-like/38774,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833362,1773,,,,,genotype:Beijing-like,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116795.1,CP017595,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,433.4x,Canu & Pilon v. Julio-2016,1,,1,4431885,65.6,4373,4100,,,2007,Colombia,Colombia: Buenaventura,,female,5,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM),,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8216,Mycobacterium tuberculosis strain Beijing/391,Beijing/391,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833364,1773,,,,,genotype:Beijing,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116815.1,CP017596,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,360.4x,Canu & Pilon v. Julio 2016,1,,1,4406925,65.58,4442,4101,,,2013,Colombia,Colombia: Buenaventura,,male,52,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Instituto Nacional de Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8217,Mycobacterium tuberculosis strain Beijing-like/50148,Beijing-like/50148,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833363,1773,,,,,genotype:Beijing-like,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116835.1,CP017597,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,616.5x,Canu & Pilon v. Julio 2016,1,,1,4444417,65.59,4379,4114,,,2008,Colombia,Colombia: Buenaventura,,male,44,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM),,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8218,Mycobacterium tuberculosis strain Beijing-like/1104,Beijing-like/1104,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05833359,1773,,,,,genotype:Beijing-like,,,2017-05-01T00:00:00Z,,PRJNA269967,GCA_002116855.1,CP017598,,Universidad Nacional de Colombia - Sede Bogota,Illumina; PacBio,496.3x,Canu & Pilon v. JUL-2016,1,,1,4380156,65.55,4327,4067,,,2012,Colombia,Colombia:Bogota,,male,61,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Identification of diagnostic/therapeutic targets of Colombian Mycobacterium tuberculosis Beijing-like isolates,collected_by:Instituto Nacional de Salud,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.8650,Mycobacterium tuberculosis strain HN-024,HN-024,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00076259,1773,,,,,,,,2017-08-11T00:00:00Z,28619797,PRJDB5608,GCA_002356255.1,AP018033,,"International Health, Institute of Tropical Medicine",PacBio SMRT;Illumina MiSeq;Sanger,166.96X,Hierarchical Genome Assembly Process v. 3,1,,1,4399916,65.61,4275,4027,sputum,"isolated from a tuberculosis patient in Vietnam, was determined as a reference sequence",2007-09-05,Viet Nam,Viet Nam: Hanoi,env_biome:not applicable,,,Pulmonary tuberculosis,,,Susceptible,Computational Prediction,Positive,Bacilli,No,Mesophilic,37,Aerobic,HostAssociated,tuberculosis,"The complete genome sequence of Mycobacterium tuberculosis clinical strain, HN-024, isolated from a tuberculosis patient in Vietnam, was determined as a reference sequence. The strain belongs to EAI clade, Indo-Oceanic lineage of the species.",,not applicable,not applicable,not applicable,not applicable,Complete genome sequence of Mycobacterium tuberculosis in Vietnam,,,,,,,,,,,,not applicable,,,,98.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.8651,Mycobacterium tuberculosis strain HN-205,HN-205,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00076256,1773,,,,,,,,2017-05-11T00:00:00Z,,PRJDB5607,GCA_002357935.1,AP018034,,"Department of International Health, Institute of Tropical Medicine, Nagasaki University",PacBio SMRT,179.51X,Hierarchical Genome Assembly Process v. 3,1,,1,4411033,65.61,4293,4059,sputum,isolated from Vietnamese tuberculosis patients in Hanoi,2008-04-18,Viet Nam,Viet Nam: Hanoi,env_biome:not applicable,,,Pulmonary tuberculosis,,,Susceptible;Resistant,Computational Prediction,Positive,Bacilli,No,Mesophilic,37,Aerobic,HostAssociated,tuberculosis,"The complete genome sequences of Mycobacterium tuberculosis clinical strains, HN-205, HN-321, and HN-506. These strains were isolated from Vietnamese tuberculosis patients in Hanoi. Their genotypes were those of three major clusters in a surveillance study, which means that they might be prevalent in the area.",,not applicable,not applicable,not applicable,not applicable,Complete genome sequence of Mycobacterium tuberculosis in Vietnam,,,,,,,,,,,,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.8652,Mycobacterium tuberculosis strain HN-321,HN-321,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00076257,1773,,,,,,,,2017-05-11T00:00:00Z,,PRJDB5607,GCA_002357955.1,AP018035,,"Department of International Health, Institute of Tropical Medicine, Nagasaki University",PacBio SMRT,170.68X,Hierarchical Genome Assembly Process v. 3,1,,1,4421540,65.62,4297,4066,sputum,isolated from Vietnamese tuberculosis patients in Hanoi,2008-07-18,Viet Nam,Viet Nam: Hanoi,env_biome:not applicable,,,Pulmonary tuberculosis,,,Susceptible;Resistant,Computational Prediction,Positive,Bacilli,No,Mesophilic,37,Aerobic,HostAssociated,tuberculosis,"The complete genome sequences of Mycobacterium tuberculosis clinical strains, HN-205, HN-321, and HN-506. These strains were isolated from Vietnamese tuberculosis patients in Hanoi. Their genotypes were those of three major clusters in a surveillance study, which means that they might be prevalent in the area.",,not applicable,not applicable,not applicable,not applicable,Complete genome sequence of Mycobacterium tuberculosis in Vietnam,,,,,,,,,,,,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.8653,Mycobacterium tuberculosis strain HN-506,HN-506,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00076258,1773,,,,,,,,2017-05-11T00:00:00Z,,PRJDB5607,GCA_002357975.1,AP018036,,"Department of International Health, Institute of Tropical Medicine, Nagasaki University",PacBio SMRT,167.09X,Hierarchical Genome Assembly Process v. 3,1,,1,4413362,65.61,4297,4064,sputum,isolated from Vietnamese tuberculosis patients in Hanoi,2009-03-24,Viet Nam,Viet Nam: Hanoi,env_biome:not applicable,,,Pulmonary tuberculosis,,,Susceptible;Resistant,Computational Prediction,Positive,Bacilli,No,Mesophilic,37,Aerobic,HostAssociated,tuberculosis,"The complete genome sequences of Mycobacterium tuberculosis clinical strains, HN-205, HN-321, and HN-506. These strains were isolated from Vietnamese tuberculosis patients in Hanoi. Their genotypes were those of three major clusters in a surveillance study, which means that they might be prevalent in the area.",,not applicable,not applicable,not applicable,not applicable,Complete genome sequence of Mycobacterium tuberculosis in Vietnam,,,,,,,,,,,,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.8657,Mycobacterium tuberculosis strain CSV4519,CSV4519,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664823,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446875.1,CP023573,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411288,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8658,Mycobacterium tuberculosis strain CSV4644,CSV4644,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664824,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446895.1,CP023574,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411271,65.61,4289,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8659,Mycobacterium tuberculosis strain CSV5769,CSV5769,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664825,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446915.1,CP023575,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411312,65.61,4297,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8660,Mycobacterium tuberculosis strain CSV10399,CSV10399,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664826,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446935.1,CP023576,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411180,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8661,Mycobacterium tuberculosis strain CSV11678,CSV11678,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664827,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446955.1,CP023577,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411382,65.61,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8662,Mycobacterium tuberculosis strain LE486,LE486,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664828,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446975.1,CP023578,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411180,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8663,Mycobacterium tuberculosis strain LE492,LE492,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664829,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002446995.1,CP023579,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411208,65.61,4309,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8664,Mycobacterium tuberculosis strain LN180,LN180,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664830,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447015.1,CP023580,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411436,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8665,Mycobacterium tuberculosis strain LN2358,LN2358,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664831,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447035.1,CP023581,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411353,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8666,Mycobacterium tuberculosis strain LN3756,LN3756,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664832,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447055.1,CP023582,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411315,65.61,4303,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8667,Mycobacterium tuberculosis strain MDRDM260,MDRDM260,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664833,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447075.1,CP023583,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411280,65.61,4310,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8668,Mycobacterium tuberculosis strain MDRDM627,MDRDM627,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664834,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447095.1,CP023584,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411215,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,2.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8669,Mycobacterium tuberculosis strain MDRDM1098,MDRDM1098,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664835,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447115.1,CP023585,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411148,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8670,Mycobacterium tuberculosis strain MDRMA2491,MDRMA2491,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664836,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447135.1,CP023586,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411121,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8671,Mycobacterium tuberculosis strain ME1473,ME1473,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664837,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447155.1,CP023587,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411217,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8672,Mycobacterium tuberculosis strain TBDM425,TBDM425,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664838,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447175.1,CP023588,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411143,65.61,4297,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru:Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8673,Mycobacterium tuberculosis strain TBV5000,TBV5000,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664839,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447195.1,CP023589,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411318,65.61,4305,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8674,Mycobacterium tuberculosis strain TBV5362,TBV5362,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664840,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447215.1,CP023590,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411331,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8675,Mycobacterium tuberculosis strain TBV5365,TBV5365,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664841,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447235.1,CP023591,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411398,65.6,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,2.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8676,Mycobacterium tuberculosis strain SLM036,SLM036,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664842,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447255.1,CP023592,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411342,65.61,4308,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8677,Mycobacterium tuberculosis strain SLM040,SLM040,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664843,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447275.1,CP023593,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411408,65.61,4296,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8678,Mycobacterium tuberculosis strain SLM060,SLM060,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664845,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447315.1,CP023595,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411134,65.61,4306,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8679,Mycobacterium tuberculosis strain SLM056,SLM056,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664844,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447295.1,CP023594,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411306,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8680,Mycobacterium tuberculosis strain SLM063,SLM063,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664846,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447335.1,CP023596,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411337,65.61,4293,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8681,Mycobacterium tuberculosis strain SLM088,SLM088,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664847,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447355.1,CP023597,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411385,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8682,Mycobacterium tuberculosis strain SLM100,SLM100,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664848,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447375.1,CP023598,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411394,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8683,Mycobacterium tuberculosis strain CSV383,CSV383,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664849,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447395.1,CP023599,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411115,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8684,Mycobacterium tuberculosis strain CSV3611,CSV3611,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664850,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447415.1,CP023600,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411439,65.61,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8685,Mycobacterium tuberculosis strain LE63,LE63,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664853,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447475.1,CP023603,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411415,65.61,4297,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8686,Mycobacterium tuberculosis strain LE13,LE13,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664852,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447455.1,CP023602,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411412,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8687,Mycobacterium tuberculosis strain LE76,LE76,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664854,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447495.1,CP023604,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411211,65.61,4308,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8688,Mycobacterium tuberculosis strain LE79,LE79,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664855,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447515.1,CP023605,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411475,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8689,Mycobacterium tuberculosis strain LE103,LE103,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664856,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447535.1,CP023606,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411243,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8690,Mycobacterium tuberculosis strain LE371,LE371,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664857,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447555.1,CP023607,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411137,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8691,Mycobacterium tuberculosis strain CSV9577,CSV9577,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664851,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447435.1,CP023601,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411230,65.61,4305,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8692,Mycobacterium tuberculosis strain LE410,LE410,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664858,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447575.1,CP023608,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411365,65.61,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8693,Mycobacterium tuberculosis strain LN55,LN55,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664859,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447595.1,CP023609,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411186,65.61,4303,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8694,Mycobacterium tuberculosis strain LN317,LN317,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664860,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447615.1,CP023610,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411340,65.6,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8695,Mycobacterium tuberculosis strain LN763,LN763,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664861,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447635.1,CP023611,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411321,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8696,Mycobacterium tuberculosis strain LN2978,LN2978,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664862,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447655.1,CP023612,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411331,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8697,Mycobacterium tuberculosis strain LN3584,LN3584,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664863,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447675.1,CP023613,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411326,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8698,Mycobacterium tuberculosis strain LN3588,LN3588,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664864,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447695.1,CP023614,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411379,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8699,Mycobacterium tuberculosis strain LN3589,LN3589,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664865,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447715.1,CP023615,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411392,65.61,4305,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8700,Mycobacterium tuberculosis strain LN3672,LN3672,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664867,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447755.1,CP023617,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411335,65.61,4307,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8701,Mycobacterium tuberculosis strain LN3668,LN3668,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664866,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447735.1,CP023616,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411494,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8702,Mycobacterium tuberculosis strain LN3695,LN3695,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664868,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447775.1,CP023618,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411449,65.61,4294,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8703,Mycobacterium tuberculosis strain LN1100,LN1100,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664869,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447795.1,CP023619,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411392,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8704,Mycobacterium tuberculosis strain LN1856,LN1856,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664870,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447815.1,CP023620,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411299,65.61,4300,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8705,Mycobacterium tuberculosis strain MDRDM827,MDRDM827,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664872,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447855.1,CP023622,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411315,65.61,4303,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8706,Mycobacterium tuberculosis strain LN2900,LN2900,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664871,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447835.1,CP023621,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411327,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8707,Mycobacterium tuberculosis strain MDRMA203,MDRMA203,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664873,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447875.1,CP023623,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411290,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8708,Mycobacterium tuberculosis strain MDRMA701,MDRMA701,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664874,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447895.1,CP023624,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411338,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8709,Mycobacterium tuberculosis strain MDRMA863,MDRMA863,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664875,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447915.1,CP023625,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411432,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8710,Mycobacterium tuberculosis strain MDRMA1565,MDRMA1565,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664876,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447935.1,CP023626,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411159,65.61,4313,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8711,Mycobacterium tuberculosis strain MDRMA2019,MDRMA2019,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664877,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447955.1,CP023627,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411229,65.61,4304,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8712,Mycobacterium tuberculosis strain MDRMA2260,MDRMA2260,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664879,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447995.1,CP023629,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411352,65.61,4287,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8713,Mycobacterium tuberculosis strain MDRMA2082,MDRMA2082,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664878,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002447975.1,CP023628,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411479,65.61,4301,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8714,Mycobacterium tuberculosis strain MDRMA2441,MDRMA2441,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664880,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448015.1,CP023630,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411454,65.61,4298,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8715,Mycobacterium tuberculosis strain TBDM1506,TBDM1506,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664881,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448035.1,CP023631,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411157,65.61,4307,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8716,Mycobacterium tuberculosis strain TBDM2189,TBDM2189,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664882,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448055.1,CP023632,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411316,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8717,Mycobacterium tuberculosis strain TBDM2487,TBDM2487,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664884,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448095.1,CP023634,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411314,65.61,4313,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8718,Mycobacterium tuberculosis strain TBDM2444,TBDM2444,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664883,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448075.1,CP023633,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411284,65.61,4309,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8719,Mycobacterium tuberculosis strain TBDM2489,TBDM2489,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664885,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448115.1,CP023635,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411369,65.61,4297,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8720,Mycobacterium tuberculosis strain TBDM2699,TBDM2699,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664886,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448135.1,CP023636,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411457,65.61,4299,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8721,Mycobacterium tuberculosis strain TBDM2717,TBDM2717,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664887,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448155.1,CP023637,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411442,65.61,4302,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8722,Mycobacterium tuberculosis strain TBV4766,TBV4766,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664888,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448175.1,CP023638,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411310,65.61,4293,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8723,Mycobacterium tuberculosis strain TBV4768,TBV4768,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664889,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448195.1,CP023639,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411173,65.61,4294,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.8724,Mycobacterium tuberculosis strain TBV4952,TBV4952,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07664890,1773,,,,,,,,2017-10-05T00:00:00Z,,PRJNA407834,GCA_002448215.1,CP023640,,Universidad Peruana Cayetano Heredia,Illumina HiSeq,362x,De Bruijn v. 2012,1,,1,4411414,65.61,4294,,sputum,isolated from unrelated TB patients in Peru,2008-07-01,Peru,Peru: Lima,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We genotyped and sequenced the complete genomes of 68 M. tuberculosisstrains isolated from unrelated TB patients in Peru. No clustering pattern of the strainswas verified based on spoligotyping. We analyzed the association between PZAresistance with non-synonymous mutations mutations and specific genes.,collected_by:Patricia Sheen,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9499,Mycobacterium tuberculosis strain GG-111-10,111-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199254,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886145.1,CP025593,,Duke University,Illumina HiSeq,539.0x,bwa Reference alignment v. 0.7.1,1,,1,4411563,65.61568,4387,4244,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9500,Mycobacterium tuberculosis strain GG-5-10,5-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199260,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886165.1,CP025594,,Duke University,Illumina HiSeq,496.0x,bwa Reference alignment v. 0.7.1,1,,1,4411442,65.61512,4393,4244,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9501,Mycobacterium tuberculosis strain GG-20-11,20-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199302,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886195.1,CP025595,,Duke University,Illumina HiSeq,430.0x,bwa Reference alignment v. 0.7.1,1,,1,4411504,65.61508,4396,4242,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9502,Mycobacterium tuberculosis strain 77-11,77-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199276,1773,,,,,,,,2018-01-17T00:00:00Z,,PRJNA422870,GCA_002886225.1,CP025600,,Duke University,Illumina HiSeq,627.0x,bwa Reference alignment v. 0.7.1,1,,1,4411508,65.6155,4399,4244,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9503,Mycobacterium tuberculosis strain GG-90-10,90-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199305,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886335.1,CP025601,,Duke University,Illumina HiSeq,522.0x,bwa Reference alignment v. 0.7.1,1,,1,4411602,65.615486,4402,4249,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9504,Mycobacterium tuberculosis strain GG-129-11,129-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199301,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886405.1,CP025604,,Duke University,Illumina HiSeq,525.0x,bwa Reference alignment v. 0.7.1,1,,1,4411413,65.614555,4404,4243,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9505,Mycobacterium tuberculosis strain GG-134-11,134-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199277,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886505.1,CP025605,,Duke University,Illumina HiSeq,550.0x,bwa Reference alignment v. 0.7.1,1,,1,4411399,65.61454,4386,4243,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9506,Mycobacterium tuberculosis strain GG-229-10,229-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199266,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886585.1,CP025608,,Duke University,Illumina HiSeq,557.0x,bwa Reference alignment v. 0.7.1,1,,1,4411519,65.615,4396,4243,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9507,Mycobacterium tuberculosis strain GG-37-11,37-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199347,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886685.1,CP025598,,Duke University,Illumina HiSeq,530.0x,bwa Reference alignment v. 0.7.1,1,,1,4411526,65.615524,4390,4247,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9508,Mycobacterium tuberculosis strain GG-121-10,121-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199271,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886775.1,CP025603,,Duke University,Illumina HiSeq,526.0x,bwa Reference alignment v. 0.7.1,1,,1,4411510,65.61568,4398,4242,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9509,Mycobacterium tuberculosis strain GG-186-10,186-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199268,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886865.1,CP025607,,Duke University,Illumina HiSeq,327.0x,bwa Reference alignment v. 0.7.1,1,,1,4411478,65.61488,4385,4246,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9510,Mycobacterium tuberculosis strain GG-27-11,27-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199265,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002886945.1,CP025596,,Duke University,Illumina HiSeq,565.0x,bwa Reference alignment v. 0.7.1,1,,1,4411443,65.61484,4393,4247,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9511,Mycobacterium tuberculosis strain GG-36-11,36-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199267,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002887065.1,CP025597,,Duke University,Illumina HiSeq,557.0x,bwa Reference alignment v. 0.7.1,1,,1,4411469,65.61485,4400,4244,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9512,Mycobacterium tuberculosis strain GG-45-11,45-11,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199303,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002887145.1,CP025599,,Duke University,Illumina HiSeq,464.0x,bwa Reference alignment v. 0.7.1,1,,1,4411469,65.61651,4392,4242,human patient,,2011,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9513,Mycobacterium tuberculosis strain GG-109-10,109-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199306,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002887255.1,CP025602,,Duke University,Illumina HiSeq,550.0x,bwa Reference alignment v. 0.7.1,1,,1,4411463,65.61501,4407,4244,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9514,Mycobacterium tuberculosis strain GG-137-10,137-10,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08199348,1773,,,,,,,,2018-02-02T00:00:00Z,,PRJNA422870,GCA_002887335.1,CP025606,,Duke University,Illumina HiSeq,475.0x,bwa Reference alignment v. 0.7.1,1,,1,4411446,65.61529,4402,4243,human patient,,2010,Guatemala,Guatemala,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequence data of Guatemalan isolates of Mycobacterium tuberculosis to identify endemic strains in Guatemala City,collected_by:Blanca Samayoa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1773.9516,Mycobacterium tuberculosis strain Beijing/MYC004,MYC004,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06854786,1773,,,,,,,,2018-01-22T00:00:00Z,,PRJNA384962,GCA_002895065.1,CP024614,,UNIVERSIDAD MICHOACANA DE SAN NICOLAS DE HIDALGO,SOLiD,17.48x,SOLiD BioScope v. 1.3,1,,1,4411530,64.7351,4877,4151,cerebrospinal fluid,,2009,Mexico,Mexico: Michoacan,,,,Tuberculosis,,,Susceptible,Computational Prediction,,,,,,,,,The projects aims to describe genomic variations in M. tuberculosis isolates known by causing meningeal tuberculosis in order to improve the knowledge about mycobacterial determinants of virulence.;high contig L50;low contig N50,collected_by:LABORATORIO ESTATAL DE SALUD PUBLICA,,,,,,,Tuberculosis,,,,,,,,,,,,,,96.7,3.8,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1773.9528,Mycobacterium tuberculosis strain LJ319,LJ319,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08462824,1773,,,,,,,,2018-02-19T00:00:00Z,,PRJNA432837,GCA_002946495.1,CP026742,,"Dr. D. Y. Patil Medical College, (DPU)",Illumina MiSeq,100.0x,SPAdes v. 3.11,1,,1,4399460,65.55304,4392,4235,csf,,2016-06-04,India,India,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Epidemiological study and drug resistance from MDR and XDR TUBERCULOSIS,collected_by:Swarupa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1773.9529,Mycobacterium tuberculosis strain WC059,WC059,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07414820,1773,,,,,,,,2018-03-16T00:00:00Z,29188195,PRJNA395787,GCA_003006115.1,CP022578,,University of Hong Kong,PacBio,307.0x,Hierarchical Genome Assembly Process v.,1,,1,4413669,65.61527,4382,4243,sputum,,2012-02,Hong Kong,Hong Kong,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"This is a de novo assembled genome of a multidrug-resistant Mycobacterium tuberculosis (MDR-TB) clinical isolate retrieved from a patient before initiation of anti-TB therapy. Subsequent MDR-TB clinical isolate four months after initiation of anti-TB therapy showed that the strain has improved in vitro growth fitness with elevated resistance towards rifabutin, isoniazid and ethambutol.","collected_by:Department of Microbiology, the University of Hong Kong",,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9530,Mycobacterium tuberculosis strain WC078,WC078,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07414819,1773,,,,,,,,2018-03-16T00:00:00Z,29188195,PRJNA395786,GCA_003006135.1,CP022577,,University of Hong Kong,PacBio,241.0x,Hierarchical Genome Assembly Process v.,1,,1,4413712,65.61538,4385,4242,sputum,,2012-06,Hong Kong,Hong Kong,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"This is a de novo assembled genome of a multi-drug resistant Mycobacterium tuberculosis (MDR-TB) clinical isolate retrieved from a patient four months after initiation of anti-TB treatment. This strain exhibited improved growth fitness and 4- to 16-fold elevation in rifabutin, isoniazid and ethambutol resistance when compared to its parent strain.","collected_by:Department of Microbiology, the University of Hong Kong",,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9536,Mycobacterium tuberculosis strain LJ338,LJ338,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08765497,1773,,,,,,,,2018-05-16T00:00:00Z,,PRJNA439387,GCA_003129545.1,CP029326,,"Dr. D. Y. Patil Medical College, (DPU)",Illumina MiSeq,100.0x,SPAdes v. 3.11,1,,1,4408432,65.58462,4409,4236,sputum,,2014-11-21,India,India,,,,Tuberculosis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Epidemiological study and drug resistance from MDR and XDR TUBERCULOSIS,collected_by:Swarupa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9549,Mycobacterium tuberculosis strain CAS,CAS,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08794918,1773,,,,,,,,2018-04-08T00:00:00Z,,PRJNA445659,GCA_003044235.1,CP028428,,"Dr. D. Y. Patil Medical College, (DPU)",Illumina MiSeq,100.0x,SPAdes 3.11 v. 3.11,1,,1,4394577,65.55276,4433,4258,csf,,2016-08-06,India,India,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Epidemiological study and drug resistance from MDR and XDR TUBERCULOSIS,collected_by:Swarupa,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1773.9607,Mycobacterium tuberculosis strain RUS_B0,RUS_B0,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN09453176,1773,,,,,genotype:Beijing,,,2018-06-26T00:00:00Z,,PRJNA476697,GCA_003265005.1,CP030093,,Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA,Illumina,470.0x,SPAdes v. 3.5.0,1,,1,4418559,65.60981,4394,4252,sputum,,2008,Russia,Russia: Saint-Petersburg,,,,tuberculosis,,,Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of the Mycobacterium tuberculosis Beijing B0 strain from Russia.,collected_by:Research Institute of Phtisiopulmonology,,,,,,,tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9608,Mycobacterium tuberculosis strain H54,H54,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06292592,1773,,,,,,,,2018-07-03T00:00:00Z,,PRJNA369711,GCA_003287125.1,CP019610,,The Hong Kong Polytechnic University,PacBio,150.0x,HGAP v. 2,1,,1,4416938,65.607056,4378,4259,sputum,,2008,Hong Kong,Hong Kong,,,,homo sapiens,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Comparative genomics between hypervirulent and hypovirulent strains of Mycobacterium tuberculosis.,collected_by:Gilman,,,,,,,homo sapiens,,,,,,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1773.9609,Mycobacterium tuberculosis strain H83,H83,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06292590,1773,,,,,,,,2018-07-03T00:00:00Z,,PRJNA369711,GCA_003287145.1,CP019611,,The Hong Kong Polytechnic University,PacBio,150.0x,HGAP v. 2,1,,1,4413214,65.63437,4372,4240,sputum,,2008,Hong Kong,Hong Kong,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Comparative genomics between hypervirulent and hypovirulent strains of Mycobacterium tuberculosis.,collected_by:Gilman,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,1773.9610,Mycobacterium tuberculosis strain H107,H107,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06292065,1773,,,,,,,,2018-07-03T00:00:00Z,,PRJNA369711,GCA_003287165.1,CP019612,,The Hong Kong Polytechnic University,PacBio,150.0x,HGAP v. 2,1,,1,4418796,65.61425,4394,4246,csf,,2008,Hong Kong,Hong Kong,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Comparative genomics between hypervirulent and hypovirulent strains of Mycobacterium tuberculosis.,collected_by:Gilman,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1773.9611,Mycobacterium tuberculosis strain H112,H112,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06292067,1773,,,,,,,,2018-07-03T00:00:00Z,,PRJNA369711,GCA_003287185.1,CP019613,,The Hong Kong Polytechnic University,PacBio,150.0x,HGAP v. 2,1,,1,4406346,65.623215,4362,4247,csf,,2008,Hong Kong,Hong Kong,,,,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Comparative genomics between hypervirulent and hypovirulent strains of Mycobacterium tuberculosis.,collected_by:Gilman,,,,,,,Tuberculosis,,,,,,,,,,,,,,100,1.1,Respiratory Diseases,Tuberculosis,Central Nervous System,Respiratory Diseases-Tuberculosis HP,1773.9612,Mycobacterium tuberculosis strain TBMENG-03,TBMENG-03,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08973501,1773,,,,,,,,2018-07-09T00:00:00Z,,PRJNA453104,GCA_003293655.1,CP029065,,National JALMA Institute for Leprosy and Other Mycobacterial Diseases,Illumina NextSeq,1.0x,SPAdes v. V3.9.0,1,,1,4359659,65.55878,4396,4218,sputum,,2016-04-12,India,India,,male,36,Tuberculous meningitis,,host_disease_stage:Accute,Susceptible,Computational Prediction,,,,,,,,,To study the genetic variations between bacilli causing Tuberculous meningitis &\; Pulmonary tuberculosis,collected_by:NRL-National JALMA Institute for Leprosy & Other Mycobacterial Diseases,,,,,,,Tuberculous meningitis,,,,Accute,,,,,,,,,,98.9,2.1,Neurological Diseases,Meningitis,Respiratory Tract,Neurological Diseases-Meningitis HP,1774.107,Mycobacteroides chelonae strain Myco3b,Myco3b,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13542596,1774,not applicable,,not applicable,,genotype:not applicable,not applicable,,2020-12-30T00:00:00Z,33166284,PRJNA594977,GCA_016446355.1,CP050146,,University of Pennsylvania,Illumina HiSeq & Oxford Nanopore,"50x, 90x",Unicycler v. v0.4.8-beta,1,0,1,5061074,64.01568,4987,4890,not applicable; patient,,2017,USA,USA:Philadelphia,,not applicable,61,infection,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:Myco3,,,,,,,,,,,Mycobacterium chelonae isolates from patients at the Hospital of the University of Pennsylvania,collected_by:HUP;passage_history:not applicable;specimen_voucher:not applicable,,,,,,,infection,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,99.5,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1774.108,Mycobacteroides chelonae strain Myco1,Myco1,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13542593,1774,not applicable,,not applicable,,genotype:not applicable,not applicable,,2020-12-30T00:00:00Z,33166284,PRJNA594977,GCA_016446375.1,CP050223,,University of Pennsylvania,Illumina HiSeq & Oxford Nanopore,"50x, 90x",Unicycler v. v0.4.8-beta,1,0,1,4958937,64.09975,4930,4775,not applicable; patient,,2017,USA,USA:Philadelphia,,not applicable,45,infection,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:Myco1,,,,,,,,,,,Mycobacterium chelonae isolates from patients at the Hospital of the University of Pennsylvania,collected_by:HUP;passage_history:not applicable;specimen_voucher:not applicable,,,,,,,infection,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,99.29,0.03,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1774.109,Mycobacteroides chelonae strain Myco3a,Myco3a,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13542597,1774,not applicable,,not applicable,,genotype:not applicable,not applicable,,2021-01-28T00:00:00Z,33166284,PRJNA594977,GCA_016767715.1,CP050145,,University of Pennsylvania,Illumina HiSeq & Oxford Nanopore,"50x, 90x",Unicycler v. v0.4.8-beta,1,0,1,5061177,64.016174,4987,4890,not applicable; patient,,2017,USA,USA:Philadelphia,,not applicable,61,infection,,host_description:not applicable;host_disease_outcome:not applicable;host_disease_stage:not applicable;host_health_state:not applicable;host_subject_id:Myco3,,,,,,,,,,,Mycobacterium chelonae isolates from patients at the Hospital of the University of Pennsylvania,collected_by:HUP;passage_history:not applicable;specimen_voucher:not applicable,,,,,,,infection,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,99.5,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1774.124,Mycobacteroides chelonae MCHE08,MCHE08,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15422980,1774,,,,,,,,2022-01-31T00:00:00Z,,PRJNA643662,GCA_021729805.1,CP058976,,,Illumina MiSeq; Oxford Nanopore,268x,SPAdes v. 3.13; Other v. Unicycler,1,0,1,5040728,64.08503,4981,4873,wound,,2019-10,Switzerland,Switzerland: Bern,,,,skin and soft tissue infections,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases,,,,,,,skin and soft tissue infections,,,,,,,,,,,,,,99.5,0.03,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1774.130,Mycobacteroides chelonae MCHL-2034,MCHL-2034,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN33426568,1774,,,,,,,,2023-03-08T00:00:00Z,,PRJNA938130,,CP118920,,,Illumina MiSeq; Oxford Nanopore MinION,152.1x,Trycycler v. 0.5.3; Flye v. 2.9; miniasm,1,0,1,5143578,64.032875,5067,4965,respiratory specimen,,2016-12-23,USA,"USA:Tyler, Texas",,,,Respiratory infection,,,,,,,,,,,,,,collected_by:University of Texas at Tyler,,,,,,,Respiratory infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1774.131,Mycobacteroides chelonae MCHL-2035,MCHL-2035,Mycobacteroides chelonae,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN33426364,1774,,,,,,,,2023-03-08T00:00:00Z,,PRJNA938130,,"CP118919,CP118918",,,Illumina MiSeq; Oxford Nanopore MinION,55.7x,Trycycler v. 0.5.3; Flye v. 2.9-b1768;,1,1,2,5281102,64.028755,5197,5095,respiratory specimen,,2016-12-23,USA,"USA: Tyler, Texas",,,,Respiratory infection,,,,,,,,,,,,,,collected_by:University of Texas at Tyler,,,,,,,Respiratory infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,1778.48,Mycobacterium gordonae strain 24T,24T,Mycobacterium gordonae,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15540336,1778,,,,,,,,2020-07-22T00:00:00Z,,PRJNA646334,GCA_013466425.1,CP059165,,"Beijing Chest Hospital, Capital Medical University",PacBio Sequel,100.0x,SMRT Link v. v5.0.1,1,0,1,6266765,65.3523,5817,5587,sputum of a chinese patient with pulmonary infection,isolated from sputum of a Chinese patient with pulmonary infection,2008,China,China:Guangdong,,,,pulmonary infection,,,,,,,,,,,,,"A slowly growing, scotochromogenic mycobacterial strain (24T) was isolated from sputum of a Chinese patient with pulmonary infection. The phylogenetic analysis based on 16S rRNA gene assigned 24T into Mycobacterium gordonae complex, which composing of Mycobacterium gordonae and Mycobacterium paragordonae. The phenotypic characteristics, unique mycolic acid profile, and the phylogenetic analysis based on hsp65 and rpoB sequences strongly supported the taxonomic status of the strain 24T as a representative of a species distinct from other members of M. gordonae complex.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.94,0.9,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1781.90,Mycobacterium marinum strain MMA1,MMA1,Mycobacterium marinum,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN14832045,1781,,,,,,,,2021-01-22T00:00:00Z,33336253,PRJNA630296,GCA_016745295.1,CP058277,,NIH,PacBio Sequel,260.0x,HGAP v. 6.0,1,0,1,6321947,65.798386,5595,5228,elbow skin biopsy from patient with disseminated infection,,2018-04-27,USA,USA:Maryland,,,,Disseminated Mycobacterium marinum infection,,,,,,,,,,,,,Whole genome sequencing of serial M. marinum isolates from a single patient with disseminated disease,collected_by:NIAID,,,,,,,Disseminated Mycobacterium marinum infection,,,,,,,,,,,,,,99.88,0.68,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,1796635.16,Longicatena caecimuris strain 3BBH23,3BBH23,Longicatena caecimuris,Longicatena,Erysipelotrichaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMD00283801,1796635,,,,,,,,2021-05-22T00:00:00Z,34016676,PRJDB11313,GCA_018406465.1,AP024510,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,773x,Unicycler v. 0.4.6,1,0,1,3103757,38.31505,3021,2866,feces of healthy japanese,,,Japan,Japan,,,,,,,,,,,,,,,,,"Complete genome sequence of Longicatena caecimuris strain 3BBH23 isolated from healthy Japanese, composed a circular chromosome",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,100,0,,,Gastrointestinal,- HP,1802.10,Mycolicibacterium farcinogenes strain BKK/CU-MFGLA-001,BKK/CU-MFGLA-001,Mycolicibacterium farcinogenes,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN20463125,1802,,,,,,,,2021-08-24T00:00:00Z,,PRJNA749947,GCA_019739095.1,CP080510,,Chulalongkorn University,Oxford Nanopore MiniION,22x,Flye v. 2.8.3,1,0,1,6276329,66.40089,6060,5919,liver,,2019,Thailand,Thailand: Bangkok,,,,Liver abscessus,,,,,,,,,,,,,Mycobacterium app isolated from patients in Thailand,collected_by:King Chulalongkorn Memorial Hospital,,,,,,,Liver abscessus,,,,,,,,,,,,,,99.78,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,1802.11,Mycolicibacterium farcinogenes strain BKK/CU-MFGFA-001,BKK/CU-MFGFA-001,Mycolicibacterium farcinogenes,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN20463126,1802,,,,,,,,2021-08-24T00:00:00Z,,PRJNA749947,GCA_019739075.1,"CP081673,CP081674,CP081675,CP081676",,Chulalongkorn University,Oxford Nanopore MiniION,77x,Flye v. 2.8.3,1,3,4,6607534,66.37084,6372,6253,skin,,2020,Thailand,Thailand: Bangkok,,,,Facial abscessus,,,,,,,,,,,,,Mycobacterium app isolated from patients in Thailand,collected_by:King Chulalongkorn Memorial Hospital,,,,,,,Facial abscessus,,,,,,,,,,,,,,99.69,0.38,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,180434.14,Morganella morganii subsp. morganii strain 171229813,171229813,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12769847,180434,,,,,,,,2020-03-19T00:00:00Z,,PRJNA565832,GCA_011465095.1,CP043955,,Institude of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,0,1,3982591,51.07878,4067,3786,blood,,2017,China,China: Nanjing,,,,Severe pancreatitis,,,,,,,,,,,,,Complete sequence of chromosome of strain 171229813,,,,,,,,Severe pancreatitis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Pancreatic Disorders,Blood and Circulatory System,Gastrointestinal Diseases-Pancreatic Disorders NHP,1805478.3,Olsenella sp. Marseille-P2300,Marseille-P2300,Olsenella timonensis,Olsenella,Atopobiaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMEA4554851,1805478,,,,,,,,2016-11-23T00:00:00Z,,PRJEB16351,GCF_900119915.1,LT635455,NZ_LT635455.1,URMITE,,,,1,,1,2176737,68.08,2017,,stool,isolated from stool in a healthy patient as part of a culturomics study aiming at cultivating all bacteria in human stool,,,,,,,,,,,,,,,,,,,,Olsenella timonensis was isolated from stool in a healthy patient as part of a culturomics study aiming at cultivating all bacteria in human stool.,,,,,,,,,,,,,,,,,,,,,,100,0.8,,,Gastrointestinal,- HP,1806.23,Mycobacterium tuberculosis variant microti strain Mycobacterium microti Maus III,Mycobacterium microti Maus III,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA7336317,1806,,,,,,ATCC 35782,,2021-01-25T00:00:00Z,,PRJEB40500,GCA_904810345.1,LR882498,,IP,,,,1,0,1,4382575,65.62021,4247,,human clinical isolate,isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M,2000,Germany,Germany,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We performed whole-genome sequencing of the five following Mycobacterium microti strains: (1) Mycobacterium microti OV254, which was originally isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston\; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M.P. Prague]), which was purchased from the American Type Culture Collection\; (3) Mycobacterium microti 94-2272, which was isolated in 1988 from the perfusion fluid of a 41-year-old dialysis patient and was kindly provided by L. M. Parsons\; (4) Mycobacterium microti Maus III (also known as strain 6740/00), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany\; and (5) Mycobacterium microti Maus IV (also known as strain 1479/99), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany. On one hand, genomic DNA of M. microti strain were prepared using the SMRTbell Template library preparation kit and sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using the PacBio SMRT long-read sequencing technology (Chemistry v2.1\; Sequel ICS v5.0.1\; SMRT Link v5.0.1). On the other hand, genomic DNA of M. microti strains were sequenced using the Illumina paired-end short-read sequencing technology. Strains OV254, ATCC 35782, 94-2272 and Maus IV were sequenced at the Wellcome Trust Sanger Institute (Hinxton, UK) using a Genome Analyzer IIx device, while strain Maus III was sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. First, Raw PacBio subreads were assembled using Canu and generated supercontigs were then organized as compared to the genome of M. bovis BCG Pasteur 1173P2 using MeDuSa. Second, Illumina read pairs were trimmed using Trimmomatic. Complete read pairs were then assembled using SPAdes and providing either raw PacBio subreads or the scaffolds of PacBio supercontigs. Illumina contigs thus generated were then compared to the PacBio scaffolds using BLASTN to correct erroneous arrangements and to fill undefined gaps. Third, Illumina read pairs were mapped against the resulting assembled genome using BWA-MEM. Variants were then called using VarScan to detect and correct sequencing errors within whole-genome assemblies.",,,,,,,,,diseased,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1806.24,Mycobacterium tuberculosis variant microti strain Mycobacterium microti 94-2272,Mycobacterium microti 94-2272,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA7336316,1806,,,,,,ATCC 35782,,2021-01-25T00:00:00Z,,PRJEB40500,GCA_904810365.1,LR882500,,IP,,,,1,0,1,4384561,65.62093,4264,,human clinical isolate,isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M,1988,Netherlands,Netherlands,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We performed whole-genome sequencing of the five following Mycobacterium microti strains: (1) Mycobacterium microti OV254, which was originally isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston\; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M.P. Prague]), which was purchased from the American Type Culture Collection\; (3) Mycobacterium microti 94-2272, which was isolated in 1988 from the perfusion fluid of a 41-year-old dialysis patient and was kindly provided by L. M. Parsons\; (4) Mycobacterium microti Maus III (also known as strain 6740/00), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany\; and (5) Mycobacterium microti Maus IV (also known as strain 1479/99), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany. On one hand, genomic DNA of M. microti strain were prepared using the SMRTbell Template library preparation kit and sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using the PacBio SMRT long-read sequencing technology (Chemistry v2.1\; Sequel ICS v5.0.1\; SMRT Link v5.0.1). On the other hand, genomic DNA of M. microti strains were sequenced using the Illumina paired-end short-read sequencing technology. Strains OV254, ATCC 35782, 94-2272 and Maus IV were sequenced at the Wellcome Trust Sanger Institute (Hinxton, UK) using a Genome Analyzer IIx device, while strain Maus III was sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. First, Raw PacBio subreads were assembled using Canu and generated supercontigs were then organized as compared to the genome of M. bovis BCG Pasteur 1173P2 using MeDuSa. Second, Illumina read pairs were trimmed using Trimmomatic. Complete read pairs were then assembled using SPAdes and providing either raw PacBio subreads or the scaffolds of PacBio supercontigs. Illumina contigs thus generated were then compared to the PacBio scaffolds using BLASTN to correct erroneous arrangements and to fill undefined gaps. Third, Illumina read pairs were mapped against the resulting assembled genome using BWA-MEM. Variants were then called using VarScan to detect and correct sequencing errors within whole-genome assemblies.",,,,,,,,,diseased,,,,,,,,,,,,,99.61,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1806.25,Mycobacterium tuberculosis variant microti strain Mycobacterium microti Maus IV,Mycobacterium microti Maus IV,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA7336318,1806,,,,,,ATCC 35782,,2021-01-25T00:00:00Z,,PRJEB40500,GCA_904810355.1,LR882497,,IP,,,,1,0,1,4385022,65.61625,4260,,human clinical isolate,isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M,1999,Germany,Germany,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We performed whole-genome sequencing of the five following Mycobacterium microti strains: (1) Mycobacterium microti OV254, which was originally isolated from voles in the UK in the 1930's and was kindly supplied by M. J. Colston\; (2) Mycobacterium microti ATCC 35782 (also designated as TMC 1608 [M.P. Prague]), which was purchased from the American Type Culture Collection\; (3) Mycobacterium microti 94-2272, which was isolated in 1988 from the perfusion fluid of a 41-year-old dialysis patient and was kindly provided by L. M. Parsons\; (4) Mycobacterium microti Maus III (also known as strain 6740/00), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany\; and (5) Mycobacterium microti Maus IV (also known as strain 1479/99), which was obtained from the collection of the National Reference Center for Mycobacteria, Forschungszentrum Borstel, Germany. On one hand, genomic DNA of M. microti strain were prepared using the SMRTbell Template library preparation kit and sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using the PacBio SMRT long-read sequencing technology (Chemistry v2.1\; Sequel ICS v5.0.1\; SMRT Link v5.0.1). On the other hand, genomic DNA of M. microti strains were sequenced using the Illumina paired-end short-read sequencing technology. Strains OV254, ATCC 35782, 94-2272 and Maus IV were sequenced at the Wellcome Trust Sanger Institute (Hinxton, UK) using a Genome Analyzer IIx device, while strain Maus III was sequenced at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. First, Raw PacBio subreads were assembled using Canu and generated supercontigs were then organized as compared to the genome of M. bovis BCG Pasteur 1173P2 using MeDuSa. Second, Illumina read pairs were trimmed using Trimmomatic. Complete read pairs were then assembled using SPAdes and providing either raw PacBio subreads or the scaffolds of PacBio supercontigs. Illumina contigs thus generated were then compared to the PacBio scaffolds using BLASTN to correct erroneous arrangements and to fill undefined gaps. Third, Illumina read pairs were mapped against the resulting assembled genome using BWA-MEM. Variants were then called using VarScan to detect and correct sequencing errors within whole-genome assemblies.",,,,,,,,,diseased,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1806053.106,Corynebacterium diphtheriae bv. mitis strain 2633/22,2633/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508179,1806053,,,non-toxigenic,,genotype:ST-819,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968185.1,CP103876,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,212 x,CLC NGS Cell v. 22,1,0,1,2362553,53.544407,2366,2122,wound,isolated in Poland in 2017-2022,2022,,Poland,,,90,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.67,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.107,Corynebacterium diphtheriae bv. mitis strain 1781/22,1781/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508177,1806053,,,non-toxigenic,,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968305.1,CP103878,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,208 x,CLC NGS Cell v. 22,1,0,1,2446415,53.612366,2560,2285,unk,isolated in Poland in 2017-2022,2022,,Poland,,,58,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,97.83,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1806053.108,Corynebacterium diphtheriae bv. mitis strain 2102/22,2102/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508178,1806053,,,NTTB,MLST.Corynebacterium_diphtheriae.40,genotype:ST-40,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968345.1,CP103877,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,198 x,CLC NGS Cell v. 22,1,0,1,2507117,53.58282,2695,2365,blood,isolated in Poland in 2017-2022,2022,,Poland,,,51,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,NTTB,,,,,,,,,98.4,0.44,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1806053.109,Corynebacterium diphtheriae bv. mitis strain 641/21,641/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508168,1806053,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968385.1,CP103886,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,98 x,CLC NGS Cell v. 22,1,0,1,2444807,53.609222,2550,2274,respiratory tracks,isolated in Poland in 2017-2022,2021,,Poland,,,39,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.72,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1806053.110,Corynebacterium diphtheriae bv. mitis strain 824/20,824/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508163,1806053,,,non-toxigenic,,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968525.1,CP103891,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,1022 x,Unicycler v. not specified,1,0,1,2442362,53.60172,2426,2264,blood,isolated in Poland in 2017-2022,2020,,Poland,,,35,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1806053.111,Corynebacterium diphtheriae bv. mitis strain 38009/20,38009/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508164,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968705.1,CP103890,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,213 x,Unicycler v. not specified,1,0,1,2444487,53.60961,2423,2271,eye,isolated in Poland in 2017-2022,2020,,Poland,,,62,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,1806053.112,Corynebacterium diphtheriae bv. mitis strain 1251/22,1251/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508176,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968865.1,CP103879,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION,203 x,CLC NGS Cell v. 22,1,0,1,2448688,53.60797,2542,2285,wound,isolated in Poland in 2017-2022,2022,,Poland,,,35,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,98.66,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.113,Corynebacterium diphtheriae bv. mitis strain 6272/17,6272/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508152,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969445.1,CP103902,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,195 x,Unicycler v. not specified,1,0,1,2444489,53.61002,2425,2271,wound,isolated in Poland in 2017-2022,2017,,Poland,,,57,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.114,Corynebacterium diphtheriae bv. mitis strain 230/19,230/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508159,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969505.1,CP103895,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,74 x,Unicycler v. not specified,1,0,1,2444495,53.609764,2426,2272,wound,isolated in Poland in 2017-2022,2019,,Poland,,,53,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.45,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.115,Corynebacterium diphtheriae bv. mitis strain 632/19,632/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508160,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969545.1,CP103894,,National Institute of Public Health NIH - NRI,Oxford Nanopore GridION; MiSeq,155 x,Unicycler v. not specified,1,0,1,2444491,53.609894,2425,2272,respiratory tracks,isolated in Poland in 2017-2022,2019,,Poland,,,66,,,,,,,,,,,,,,Complete sequenced genomes of 30 non-toxigenic Corynebacterium diphtheriae strains isolated in Poland in 2017-2022.,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1806053.117,Corynebacterium diphtheriae bv. mitis 1781/22,1781/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508177,1806053,,,non-toxigenic,,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968305.1,CP103878,,,Oxford Nanopore GridION,208 x,CLC NGS Cell v. 22,1,0,1,2446415,53.612366,2560,2285,unk,,2022,Poland,Poland,,,58,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.9,4.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1806053.118,Corynebacterium diphtheriae bv. mitis 2102/22,2102/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508178,1806053,,,NTTB,MLST.Corynebacterium_diphtheriae.40,genotype:ST-40,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968345.1,CP103877,,,Oxford Nanopore GridION,198 x,CLC NGS Cell v. 22,1,0,1,2507117,53.58282,2695,2365,blood,,2022,Poland,Poland,,,51,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,NTTB,,,,,,,,,99.7,4.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1806053.119,Corynebacterium diphtheriae bv. mitis 641/21,641/21,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508168,1806053,,,non-toxigenic,,genotype:ST-8,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968385.1,CP103886,,,Oxford Nanopore GridION,98 x,CLC NGS Cell v. 22,1,0,1,2444807,53.609222,2550,2274,respiratory tracks,,2021,Poland,Poland,,,39,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.7,4.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1806053.120,Corynebacterium diphtheriae bv. mitis 824/20,824/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508163,1806053,,,non-toxigenic,,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968525.1,CP103891,,,Oxford Nanopore GridION; MiSeq,1022 x,Unicycler v. not specified,1,0,1,2442362,53.60172,2426,2264,blood,,2020,Poland,Poland,,,35,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1806053.121,Corynebacterium diphtheriae bv. mitis 38009/20,38009/20,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508164,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968705.1,CP103890,,,Oxford Nanopore GridION; MiSeq,213 x,Unicycler v. not specified,1,0,1,2444487,53.60961,2423,2271,eye,,2020,Poland,Poland,,,62,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,1806053.122,Corynebacterium diphtheriae bv. mitis 1251/22,1251/22,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508176,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024968865.1,CP103879,,,Oxford Nanopore GridION,203 x,CLC NGS Cell v. 22,1,0,1,2448688,53.60797,2542,2285,wound,,2022,Poland,Poland,,,35,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,99.9,3.8,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.123,Corynebacterium diphtheriae bv. mitis 6272/17,6272/17,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508152,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969445.1,CP103902,,,Oxford Nanopore GridION; MiSeq,195 x,Unicycler v. not specified,1,0,1,2444489,53.61002,2425,2271,wound,,2017,Poland,Poland,,,57,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.124,Corynebacterium diphtheriae bv. mitis 230/19,230/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508159,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969505.1,CP103895,,,Oxford Nanopore GridION; MiSeq,74 x,Unicycler v. not specified,1,0,1,2444495,53.609764,2426,2272,wound,,2019,Poland,Poland,,,53,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,1806053.125,Corynebacterium diphtheriae bv. mitis 632/19,632/19,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN30508160,1806053,,,non-toxigenic,MLST.Corynebacterium_diphtheriae.67,genotype:ST-439,,,2022-09-06T00:00:00Z,,PRJNA873913,GCA_024969545.1,CP103894,,,Oxford Nanopore GridION; MiSeq,155 x,Unicycler v. not specified,1,0,1,2444491,53.609894,2425,2272,respiratory tracks,,2019,Poland,Poland,,,66,,,,,,,,,,,,,,,collected_by:National Institute of Public Health NIH - NRI,,,,,,,not provided,,,,,non-toxigenic,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,1806053.29,Corynebacterium diphtheriae bv. mitis strain PC0646,PC0646,Corynebacterium diphtheriae,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11811052,1806053,,,,,,,,2020-09-30T00:00:00Z,,PRJNA541849,GCA_014826095.1,CP040557,,"Divison of Bacterial Diseases, Centers for Disease Control",PacBio RSII; Illumina MiSeq,316x,HGAP v. 3,1,0,1,2386265,53.513,2386,2242,wound,"recovered from clinical specimens, most notably C. diphtheriae from human respiratory, blood, or cutaneous infection",2018,USA,USA: WA,,,,diphtheria,,,,,,,,,,,,,"The Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention characterizes isolates of Corynebacterium species recovered from clinical specimens, most notably C. diphtheriae from human respiratory, blood, or cutaneous infection. However, collection does include some isolates from other sources. Isolates of C. diphtheriae and C. ulcerans have been tested for the presence and expression of diphtheria toxin. These data are made available to facilitate genomic study of these pathogens.",,,,,,,,diphtheria,,,,,,,,,,,,,,99.4,0.44,Respiratory Diseases,Other Respiratory Diseases,Skin and Soft Tissue,Respiratory Diseases-Other Respiratory Diseases HP,1809.14,Mycobacterium ulcerans strain SGL03,SGL03,Mycobacterium ulcerans,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA5169402,1809,,,,,,,,2019-01-03T00:00:00Z,,PRJEB30333,GCA_900638745.1,LR135168,,UNIVERSITY OF MELBOURNE,,,,1,,1,5625184,65.463585,5611,,biopsy,"isolated from all Buruli ulcer foci in DRC, The Republic of Congo, and Angola that have ever yielded positive M. ulcerans cultures",2003,Democratic Republic of the Congo,Democratic Republic of the Congo,,,,,,host_health_state:diseased,,,,,,,,,,,"Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Mycobacterium ulcerans. We used genomics to reconstruct in detail the evolutionary trajectory and dynamics of M. ulcerans populations at the central African scale, and at smaller geographical village scales. WGS data were analyzed from 179 M. ulcerans strains isolated from all Buruli ulcer foci in DRC, The Republic of Congo, and Angola that have ever yielded positive M. ulcerans cultures.",,,,,,,,,diseased,,,,,,,,,,,,,98.71,0.51,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1809.26,Mycobacterium ulcerans strain JKD8049,JKD8049,Mycobacterium ulcerans,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN22253492,1809,,,,,,,,2021-10-26T00:00:00Z,,PRJNA771185,GCA_020616615.1,"CP085200,CP085201",,University of Melbourne,Oxford Nanopore,240.0x,FLYE v. 2021,1,1,2,5789332,65.41058,5720,5159,missing,,2004,Australia,"Australia: Point Lonsdale, Victoria",,male,,Buruli ulcer,,,,,,,,,,,,,Complete genome of Mycobacterium ulcerans strain JKD8049,collected_by:Victorian Infectious Diseases Reference Laboratory,,,,,,,Buruli ulcer,,,,,,,,,,,,,,99.04,0.51,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,1812935.133,Enterobacter roggenkampii strain OIPH-N260,OIPH-N260,Enterobacter roggenkampii,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00235761,1812935,,,,,genotype:ST1059,,,2021-01-05T00:00:00Z,33385587,PRJDB10185,GCA_016756655.1,"AP023447,AP023448,AP023449,AP023450,AP023451",,Osaka Institute of Public Health,Illumina MiSeq; Oxford Nanopore,1117X,Flye v. 2.6,1,4,5,5487998,55.249184,5528,5376,human bile,,2019,Japan,Japan:Osaka,,,,,,,,,Negative,Bacilli,Yes,Mesophilic,37,Aerobic,HostAssociated,AMR infection,"The complete genome sequence of Enterobacter roggenkampii clinical isolate, OIPH-N260. This strain belongs to ST1059 and possesses 4 plasmids including the IncP6 plasmid carrying blaIMP-1 and blaGES-5, and the IncHI2 plasmid carrying mcr-9 gene.",,not applicable,not applicable,not applicable,not applicable,"The complete genome sequence of blaIMP-1, blaGES-5 and mcr-9 positive Enterobacter roggenkampii, OIPH-N260.",,,,,,,,,,,,not applicable,,,,99.07,1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,1812935.134,Enterobacter roggenkampii strain 339389L,339389L,Enterobacter roggenkampii,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999968,1812935,,,,MLST.Enterobacter_cloacae.232,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864055.1,CP045317,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,77.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,4825268,55.895477,4643,,,,2017,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:rectum,,,,,,,,,,,,,,,,,,,,,96.4,0.05,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1812935.33,Enterobacter roggenkampii strain ECY546,ECY546,Enterobacter roggenkampii,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10188240,1812935,,,,MLST.Enterobacter_cloacae.466,,,,2019-02-05T00:00:00Z,30671441,PRJNA494999,GCA_004138605.1,"CP032916,CP032915",,Wenzhou Medical University,PacBio RSII,100.0x,canus v. 1.6,1,1,2,4996659,55.88276,4888,4761,"human clinical specimens, and e","isolated from human clinical specimens, and E. cloacae is among the Enterobacter sp",2008-10-30,China,China:Wenzhou,,,,,,,,,,,,,,,,,"Currently, E. cloacae and E. hormaechei are most frequently isolated from human clinical specimens, and E. cloacae is among the Enterobacter sp. that have most commonly caused nosocomial infections in the last decade. Furthermore, E. cloacae has assumed clinical importance and has emerged as a major human pathogen.",sample_type:single culture,,,,,,,,,,,,,hospital isolate,,,,,,,,98.88,0.38,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1812935.34,Enterobacter roggenkampii strain BP10374,BP10374,Enterobacter roggenkampii,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11283933,1812935,,,,,,,,2019-04-07T00:00:00Z,,PRJNA529775,GCA_004684365.1,CP038471,,"Christian Medical college, Vellore",IonTorrent; Oxford Nanopore MiniION,59.0x,Canu v. 1.7; Unicycler v. 0.4.6,1,,1,4851717,56.111683,4879,4603,blood,,2018,India,India,,,,Bacteremia,,,,,,,,,,,,,"Colistin resistant Enterobacter roggenkampii strain BP10374 chromosome, complete genome",collected_by:Christian Medical college,,,,,,,Bacteremia,,,,,,,,,,,,,,98.59,0.51,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,1812935.384,Enterobacter roggenkampii Ek140,Ek140,Enterobacter roggenkampii,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27363776,1812935,,,,,,,,2022-05-16T00:00:00Z,,PRJNA823881,GCA_023375625.1,"CP095180,CP095181",,,PacBio,100.0x,Unicycler v. v0.4.8,1,1,2,5160484,55.755295,5057,4841,pus,,2019,China,China: Jilin,,,,,,,,,,,,,,,,,,collected_by:Jilin university,,,,,,,not available,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,1817405.5,Abyssicoccus albus S31,S31,Abyssicoccus albus,Abyssicoccus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06196447,1817405,,,,,,,,2017-02-07T00:00:00Z,28086066,PRJNA359636,GCA_001989575.1,CP019573,,,PacBio,629.0x,HGAP v. 2.0,1,0,1,1745789,34.06437,1766,1722,healthy human skin surface,,2012,India,India: New Delhi,,,,,,,,,,,,,,,,,,,,,,"Isolated from healthy human skin and grows on LB, pH 7.2 at 30oC",,,,,,,,,,,,,Human skin,,,,100,0,,,Skin and Soft Tissue,- NHP,1841863.3,Gordonibacter sp. Marseille-P2775 strain Marseille-P2775,Marseille-P2775,Gordonibacter massiliensis (ex Traore et al. 2017),Gordonibacter,Eggerthellaceae,Eggerthellales,Coriobacteriia,Actinomycetota,SAMEA103910952,1841863,,,,,,,,2017-03-21T00:00:00Z,,PRJEB19975,GCA_900170005.1,LT827128,,URMITE,,,,1,,1,3948172,65.06,3531,,stool,isolated from stool in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina,,,,,,,,,,,,,,,,,,,,Gordonibacter massiliensis was isolated from stool in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina.,,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,184246.7,Streptococcus constellatus subsp. constellatus CCUG 24889,CCUG 24889,Streptococcus constellatus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00019675,184246,,,,,,,,2022-04-02T00:00:00Z,,PRJDB3105,GCA_023167545.1,AP014647,,,PacBio,,The SMRT Analysis HGAP v. 2.1.1,1,0,1,1901581,38.073425,1901,1864,,,1994-06-03,,unkown,,,,,,,,,,,,,,,,,,,Human,clinical,Human dental plaque,16333101,Whole genome sequencing of Streptococcus constellatus,,,,,,,,,,,,Human,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1851514.13,Scandinavium goeteborgense CCUG 66741,CCUG 66741,Scandinavium goeteborgense,Scandinavium,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05150228,1851514,,,,,,CCUG:66741,,2020-06-10T00:00:00Z,31781055,PRJNA305687,GCA_003935895.2,LYLP00000000,,,Illumina NovaSeq 6000; Oxford Nanopore,1000.0x,SPAdes v. 3.13.1; Canu v. 1.8,1,1,2,4713964,54.31743,4565,4392,wound,,2014-12-20,Sweden,"Sweden: Vastra Gotaland, Gothenburg",,,,,,,,,,,,,,,,,,"sample_type:Wound;collected_by:Bacteriology Laboratory, Department of Clinical Bacteriology, Sahlgrenska University Hospital",,,,,,,,,,,,,,,,,,,,,99.3,0.8,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,185332.6,Vibrio cholerae O37 strain ATCC 25872,ATCC 25872,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13736322,185332,O37,,,MLST.Vibrio_cholerae.68,,ATCC:25872,,2021-05-11T00:00:00Z,,PRJNA599000,GCA_018336415.1,"CP047305,CP047306",,EPFL,PacBio Sequel,1796.0x,HGAP v. 4,2,0,2,4018449,47.5633,3720,3576,missing,,1965,Czechoslovakia,Czechoslovakia,,,,gastroenteritis/cholera,,,,,,,,,,,,,The goal of this study was understand the regulatory circuit of the type VI secretion system (T6SS) in non-pandemic but toxigenic V. cholerae.,passage_history:E. Aldova->O. Felsenfeld->ATTC->M. Blokesch,,,,,,,gastroenteritis/cholera,,,,,,,,,,,,,,100,0.05,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,1855823.16,Macrococcus canis strain LI021,LI021,Macrococcus canis,Macrococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13496966,1855823,,,,,,,,2021-05-05T00:00:00Z,,PRJNA593968,GCA_018278985.1,CP046590,,University of Bern,Oxford Nanopore MiniION; Illumina NovaSeq,100.0x,Unicycler v. 0.4.4,1,0,1,2216765,36.85587,2287,2221,skin,,2019-07,Switzerland,Switzerland,,,,skin infection,,,,,,,,,,,,,Macrococcus canis from human infection,collected_by:Nadia Liassine;sample_type:bacterial culture,,,,,,,skin infection,,,,,,,,,,,,,,96.13,1.29,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,1867846.3,Legionella clemsonensis strain CDC-D5610,CDC-D5610,Legionella clemsonensis,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN05254214,1867846,,,,,,,,2017-08-02T00:00:00Z,,PRJNA326348,GCA_002240035.1,CP016397,,Clemson University,PacBio,133.73,Prokka v. v1.11,1,,1,3272100,39.36,3056,2932,bronchial wash,,2007-01-09,USA,USA: Ohio,,male,89,Legionnaires' Disease,,,,,,,,,,,,,Characterization of a novel clinical isolate.,,,,,,,,Legionnaires' Disease,,,,,,,,,,,,,,97.8,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- NHP,1870984.4,Anaerococcus sp. Marseille-P2765,Marseille-P2765T,Anaerococcus mediterraneensis,Anaerococcus,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMEA4555797,1870984,,,,,,,,2016-11-25T00:00:00Z,,PRJEB15655,GCF_900128415.1,LT635772,NZ_LT635772.1,URMITE,,,,1,,1,2080215,34.58,2035,,vaginal,isolated from vaginal in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina,,,,,,,,,,,,,,,,,,,,Anaerococcus mediterraneensis was isolated from vaginal in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina.,,,,,,,,,,,,,,,,,,,,,,99.3,0,,,Genitourinary,- NHP,187327.396,Acidaminococcus intestini strain D21,D21,Acidaminococcus intestini,Acidaminococcus,Acidaminococcaceae,Acidaminococcales,Negativicutes,Bacillota,SAMN20222632,187327,,,,,,,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025144545.1,CP102249,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2305309,50.04739,2291,2105,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:BEI,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,1891914.162,Streptococcus oralis subsp. oralis strain ATCC 10557,ATCC 10557,Streptococcus oralis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN15049614,1891914,,,,MLST.Streptococcus_oralis.75,,ATCC:10557,,2020-07-23T00:00:00Z,,PRJNA635656,GCA_013488065.1,CP054135,,Abigail Wexner Research Institute at NCH,PacBio,100.0x,Celera Assembler v. 1.8,1,0,1,1995690,41.417076,1907,1855,blood,,,,,,,,Infective endocarditis,,,,,,,,,,,,,"These strains bind sialic acid but some lack SRRPs, so we sequenced them to elucidate the SRRP-independent mechanism to bind sialic acid",,,,,,,,Infective endocarditis,,,,,,,,,,,,,,99.47,0.2,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,192955.739,Salmonella enterica subsp. enterica serovar Kentucky strain Sal-FJ2064,Sal-FJ2064,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30448801,192955,Kentucky,,,MLST.Salmonella_enterica.198,genotype:ST198,,,2022-09-13T00:00:00Z,,PRJNA872212,GCA_025159055.1,CP104049,,Fujian Provincial Center for Disease Control and Prevention,PacBio; Illumina HiSeq,100.0x,SOAPdenovo v. 2.04,1,0,1,4888433,52.219883,4958,4636,,,2020-09-10,China,"China: Fujian, Fu'an",,,,,,,,,,,,,,,,,Genomic characteristion of a multidrug-resistant Salmonella Kentucky ST198 isolated from clinical patient,sample_type:whole orfanism,,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1935181.3,Shigella flexneri 1c strain Y394,Y394,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06706581,1935181,1c,,,,,,,2017-10-04T00:00:00Z,28899344,PRJNA382451,GCA_002442995.1,CP020753,,Australian National University,PacBio; Illumina MiSeq,203.0x,HGAP3.3 SMRT Pipeline v. 2.3.0; Pilon v.,1,,1,4584634,50.91,5175,4822,human stool sample,,1988,Bangladesh,Bangladesh: Matlab,,,,Shigellosis,,,,,,,,,,,,,"Shigella species cause bacillary dysentery – a severe form of diarrhoea, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps and bloody mucoid stools. Out of four species of Shigella, S. flexneri is the most prevalent enteric pathogen in developing countries. Shigella is transmitted through faecal-oral route and can cause gastrointestinal infection via an exceptionally low infectious dose (as many as 10 bacteria). S. flexneri is classified into different serotypes based on the O-antigen structure of its lipopolysaccharide. The serotype conversion is mediated by bacteriophages and plasmids carrying genes that modify the O-antigen. The S. flexneri serotype 1c is a novel serotype, which has now been found to be prevalent in many developing countries. However, little is known about its virulence signatures and evolution. Here, we provide the unique features of this serotype through the whole genome sequencing and bioinformatics tools. We also identified it as a highly adaptive pathogen with unique O-antigen modification possibly mediated by three different bacteriophages during its evolution. Furthermore, this serotype possesses several hypothetical genes and putative bacteriophage regions that will guide future investigation to identify novel genes involved in pathogen’s virulence and its survival in the host environment.;many frameshifted proteins",collected_by:Nils I. A. Carlin,,,,,,,Shigellosis,,,,,,,,,,,,,,99.6,0,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,1940789.6,Lactococcus petauri strain CF11,CF11,Lactococcus petauri,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13196990,1940789,,,,,,,,2019-11-14T00:00:00Z,,PRJNA587631,GCA_009662295.1,CP045924,,Southern Medical University,Illumina,12.0x,SPAdes v. 3.8.2,1,,1,1997720,38.210762,2012,,feces of woman,,2018-06-10,China,"China: Baiyun district, Guangzhou city, Guangdong province",,,,,,,,,,,,,,,,,High-yielding SCFAs strains were obtained by screening the bacteria producing SCFAs in the intestinal tract through various media.Exploring its potential application value has important clinical and practical significance.,sample_type:tissue sample,,,,,,,,,,,,,,,,,,,,,99.62,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,1944646.3,Phoenicibacter massiliensis strain Marseille-P3241,Marseille-P3241,Phoenicibacter congonensis,Phoenicibacter,Eggerthellaceae,Eggerthellales,Coriobacteriia,Actinomycetota,SAMEA103910411,1944646,,,,,,,,2017-03-14T00:00:00Z,,PRJEB19959,GCA_900169485.1,LT821227,,URMITE,,,,1,,1,1447956,43.44,1320,,stool,isolated from stool in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina,,,,,,,,,,,,,,,,,,,,Phoenicibacter massiliensis was isolated from stool in a healthy patient as part of a culturomics study aimaing at cultivating all bacteria in human vagina.,,,,,,,,,,,,,,,,,,,,,,94.9,0,,,Gastrointestinal,- HP,195.4521,Campylobacter coli 10-02932,10-02932,Campylobacter coli,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN31167590,195,,,,,,,,2022-10-30T00:00:00Z,,PRJNA887425,GCA_025908295.1,"CP109654,CP109655",,,Oxford Nanopore MinION,7394.0x,flye v. 2.9.1,1,1,2,1740532,31.377361,1807,,majorca stay with severe diarrhea bloody,,2010-06-22,Germany,Germany,,,,Diarrhoea,,,,,,,,,,,,,,collected_by:Robert Koch-Institute,,,,,,,Diarrhoea,,,,,,,,,,,,,,100,0.1,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,196024.107,Aeromonas dhakensis strain 71453,71453,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168051,196024,,,,MLST.Aeromonas_spp.356,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,GCA_020405305.1,CP084349,,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,0,1,4907981,61.254433,4552,4316,bile,,2020-10-14,China,China:Ningbo,,male,76,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,196024.108,Aeromonas dhakensis strain 71431,71431,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168049,196024,,,,,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,GCA_020405345.1,CP084351,,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,0,1,4771925,61.730118,4380,4212,bile,,2020-08-06,China,China:Ningbo,,female,56,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,99.97,0,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,196024.165,Aeromonas dhakensis DAMIAN 12594,DAMIAN 12594,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901112,196024,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121795,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4697715,61.803387,4326,,plasma,,2019-06-20,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,196024.166,Aeromonas dhakensis DAMIAN 19342,DAMIAN 19342,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901111,196024,,,,MLST.Aeromonas_spp.351,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121800,CP121799",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,5008282,61.221394,4659,,plasma,,2021-11-11,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,196024.167,Aeromonas dhakensis BOND 19077,BOND 19077,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901110,196024,,,,MLST.Aeromonas_spp.111,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121801,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4770244,61.76877,4355,,plasma,,2021-10-06,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,196024.168,Aeromonas dhakensis BOND 14504,BOND 14504,Aeromonas dhakensis,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901109,196024,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121802,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4848532,61.721817,4439,,plasma,,2020-02-27,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,1962118.361,Mycobacterium abscessus subsp. massiliense strain 381,381,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07281091,1962118,,,,,,,,2019-05-07T00:00:00Z,,PRJNA392077,GCA_005222645.1,"CP022230,CP022231,CP022232,CP022233,CP022234,CP022235",,Instituto de Quimica,IonTorrent,50.0x,MIRA v. 4.9.5; Medusa v. 1.6,1,5,6,4819065,64.2412,4954,4801,clinical sample,,2009-12-22,Brazil,Brazil: Campos do Jordao,,,,Mycobacteriosis,,,,,,,,,,,,,Study of Mycobacterium abcessus resistance genes,collected_by:Adolfo Lutz Institute,,,,,,,Mycobacteriosis,,,,,,,,,,,,,,98.71,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1962118.397,Mycobacteroides abscessus subsp. massiliense strain GD53,GD53,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16581384,1962118,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183855.1,CP065033,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,73x,Unicycler v. 0.4.8,1,0,1,4642874,64.21578,4804,4654,clinical patient,isolated from patients around the world,2019,USA,"USA: Lebanon, NH",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Dartmouth-Hitchcock Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,95.33,0.08,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1962118.398,Mycobacteroides abscessus subsp. massiliense strain GD68B,GD68B,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828766,1962118,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183975.1,CP065272,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,62x,Unicycler v. 0.4.8,1,0,1,5119711,64.13466,5192,5046,clinical patient,isolated from patients around the world,2019,USA,"USA: Long Beach, CA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Long Beach Memorial Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.08,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1962118.399,Mycobacteroides abscessus subsp. massiliense strain GD68A,GD68A,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828765,1962118,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017190535.1,CP065273,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,92x,Unicycler v. 0.4.8,1,0,1,5119772,64.13454,5196,5045,clinical patient,isolated from patients around the world,2019,USA,"USA: Long Beach, CA",,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Long Beach Memorial Medical Center,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.08,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,1962641.4,Salmonella enterica subsp. enterica serovar Birkenhead strain AUSMDU00010532,AUSMDU00010532,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191642,1962641,Birkenhead,,,MLST.Salmonella_enterica.424,mlst:ST424,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664615.1,"CP045958,CP045959",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,288x,de novo,1,1,2,5021303,52.148357,5122,4718,missing,,2015,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.43,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,197.11692,Campylobacter jejuni strain FORC_046,Not reported,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN05411282,197,,,,MLST.Campylobacter_jejuni.22,,,,2017-07-05T00:00:00Z,,PRJNA329382,GCA_002214785.1,"CP017229,CP017230,CP017231",,Seoul National University,PacBio,590x,HGAP v. 2.0,1,2,3,1709747,30.48,1784,1751,human stool,isolated from the stool of food-poisoned patient in Korea,2016,South Korea,South Korea: Seoul,,,,Not reported,,,,,,,,,,,,,Campylobacter jejuni is one of prevalent food-borne pathogens with acute symptoms. This sample was isolated from the stool of food-poisoned patient in Korea.,collected_by:Korea Center for Disease Control and Prevention,,,,,,,Not reported,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,197.11720,Campylobacter jejuni strain RM1246-ERRC,RM1246-ERRC,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN07304762,197,serovar HS,,,MLST.Campylobacter_jejuni.45,,,,2017-07-27T00:00:00Z,15956396,PRJNA392692,GCA_002234455.1,"CP022470,CP022471",,U.S. Department of Agriculture,PacBio,20.0x,Celera Assembler v. 2014-05-21,1,1,2,1704891,30.52,1748,1733,human,derived from a case of human disease by the California State Public Health Lab in Berkeley California (Sharon L. Abbott) and exhibited Penner serotype HS:7,,USA,USA: Berkeley California,,,,,,,,,,,,,,,,,"Campylobacter jejuni strain RM1246-ERRC was a kind gift from the laboratory collection of Dr Robert Mandrell (USDA-WRRC, Albany, CA) and previously labeled as RM1246. This strain originally designated 92A3120 was a clinical isolate derived from a case of human disease by the California State Public Health Lab in Berkeley California (Sharon L. Abbott) and exhibited Penner serotype HS:7. This strain has been utilized in multiple antimicrobial challenge studies. In a recent study the strain exhibited resistance to quaternary ammonium compounds (QACs) in excess of other Campylobacter jejuni strains used in the same study. The genetic material of the strain consists of a chromosome of 1.66 MB and a single plasmid of 45.20 KB in size. The chromosome of the strain possess four separate genes that code for membrane transporters of cationic drugs belonging to the SMR family of proteins. Orthologues of these genes in other species have been shown to be capable of the efflux of QACs.",collected_by:Dr. Robert Mandrell,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,197.17929,Campylobacter jejuni strain 15AR1555,15AR1555,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10873096,197,,,,,,,,2020-01-29T00:00:00Z,31742539,PRJNA520992,GCA_009939645.1,CP035891,,Massey University,PacBio RSII,409x,HGAP v. 3,1,0,1,1709614,30.595537,1863,,stool,,2014-12-22,New Zealand,New Zealand,,,,diarrhea,,,,,,,,,,,,,Rapid and concurrent emergence of fluoroquinolone and tetracycline-resistant Campylobacter jejuni in humans and poultry in New Zealand,collected_by:The New Zealand Food Safety Science & Research Centre (NZFSSRC),,,,,,,diarrhea,,,,,,,,,,,,,,99.5,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,197.17930,Campylobacter jejuni strain 15AR0984,15AR0984,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10873095,197,,,,,,,,2020-01-29T00:00:00Z,31742539,PRJNA520992,GCA_009939665.1,"CP035892,CP035893",,Massey University,PacBio RSII,490x,HGAP v. 3,1,1,2,1790913,30.467503,1943,,stool,,2015-04-30,New Zealand,New Zealand,,,,diarrhea,,,,,,,,,,,,,Rapid and concurrent emergence of fluoroquinolone and tetracycline-resistant Campylobacter jejuni in humans and poultry in New Zealand,collected_by:The New Zealand Food Safety Science & Research Centre (NZFSSRC),,,,,,,diarrhea,,,,,,,,,,,,,,99.53,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,197.17931,Campylobacter jejuni strain 15AR0919,15AR0919,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10873094,197,,,,,,,,2020-01-29T00:00:00Z,31742539,PRJNA520992,GCA_009939705.1,CP035894,,Massey University,PacBio RSII,467x,HGAP v. 3,1,0,1,1747687,30.541311,1892,,stool,,2015-04-23,New Zealand,New Zealand,,,,diarrhea,,,,,,,,,,,,,Rapid and concurrent emergence of fluoroquinolone and tetracycline-resistant Campylobacter jejuni in humans and poultry in New Zealand,collected_by:The New Zealand Food Safety Science & Research Centre (NZFSSRC),,,,,,,diarrhea,,,,,,,,,,,,,,99.53,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,197.17932,Campylobacter jejuni strain 15AR0917,15AR0917,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10873093,197,,,,,,,,2020-01-29T00:00:00Z,31742539,PRJNA520992,GCA_009939725.1,"CP035895,CP035896",,Massey University,PacBio RSII,600x,HGAP v. 3,1,1,2,1720482,30.51834,1832,,stool,,2015-04-20,New Zealand,New Zealand,,,,diarrhea,,,,,,,,,,,,,Rapid and concurrent emergence of fluoroquinolone and tetracycline-resistant Campylobacter jejuni in humans and poultry in New Zealand,collected_by:The New Zealand Food Safety Science & Research Centre (NZFSSRC),,,,,,,diarrhea,,,,,,,,,,,,,,99.53,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,197.18038,Campylobacter jejuni strain 129108,129108,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN14988370,197,,,,,,,,2020-06-02T00:00:00Z,,PRJNA634324,GCA_013205685.1,CP053854,,University Utrecht,454,12.0x,Velvet v. 2,1,0,1,1792949,30.185219,1940,1789,feces,,1988,Netherlands,Netherlands,,,,campylobacyteriosis,,,,,,,,,,,,,This is a human pathogenic Campylobacter jejuni strain,collected_by:Hubert endtz,,,,,,,campylobacyteriosis,,,,,,,,,,,,,,99.46,0.18,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,197.20760,Campylobacter jejuni strain R12,R12,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN15004781,197,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2021-03-16T00:00:00Z,,PRJNA634604,GCA_017356785.1,CP071576,,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,294.0x,Geneious Reference Assembly v. 2020.2.2;,1,0,1,1664509,30.4956,1713,1663,not collected,,2002,Netherlands,Netherlands,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,Campylobacter jejuni HS:19 clinical isolates from enteritis and GBS patients,collected_by:Erasmus MC,,,,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,,99.85,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,197.20761,Campylobacter jejuni strain R31,R31,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN15004783,197,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2021-03-16T00:00:00Z,,PRJNA634604,GCA_017356845.1,CP071581,,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,94.0x,Newbler v. 2.3; Geneious Reference,1,0,1,1627412,30.563189,1665,1611,not collected,,2002,Netherlands,Netherlands,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,Campylobacter jejuni HS:19 clinical isolates from enteritis and GBS patients,collected_by:Erasmus MC,,,,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,,99.85,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,197.20762,Campylobacter jejuni strain R23,R23,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN15004782,197,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2021-03-16T00:00:00Z,,PRJNA634604,GCA_017356825.1,CP071580,,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,95.0x,Newbler v. 2.3; Geneious Reference,1,0,1,1627008,30.5583,1664,1615,not collected,,2002,Netherlands,Netherlands,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,Campylobacter jejuni HS:19 clinical isolates from enteritis and GBS patients,collected_by:Erasmus MC,,,,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,,99.85,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,197.20765,Campylobacter jejuni strain R73,R73,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN15004785,197,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2021-03-16T00:00:00Z,,PRJNA634604,GCA_017356905.1,CP071584,,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,55.0x,Newbler v. 2.3; Geneious Reference,1,0,1,1625802,30.558702,1665,1613,not collected,,2002,Netherlands,Netherlands,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,Campylobacter jejuni HS:19 clinical isolates from enteritis and GBS patients,collected_by:Erasmus MC,,,,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,,99.85,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,197.20767,Campylobacter jejuni strain R72,R72,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN15004784,197,HS:19,,,MLST.Campylobacter_jejuni.22,,,,2021-03-16T00:00:00Z,,PRJNA634604,GCA_017356965.1,CP071578,,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,96.0x,Newbler v. 2.3; Geneious Reference,1,0,1,1637100,30.583715,1672,1625,not collected,,2002,Netherlands,Netherlands,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,Campylobacter jejuni HS:19 clinical isolates from enteritis and GBS patients,collected_by:Erasmus MC,,,,,,,Campylobacter gastroenteritis,,,,,,,,,,,,,,99.85,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases NHP,1981510.4,Monoglobus pectinilyticus strain 14,14,Monoglobus pectinilyticus,Monoglobus,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN06817956,1981510,,,,,,DSM 104782,,2018-01-11T00:00:00Z,,PRJNA383867,GCA_002874775.1,CP020991,,Plant and Food Research,Illumina HiSeq,4000.0x,SPAdes v. 3.7.1,1,,1,2759678,37.42572,2438,2263,faecal sample from a 27 year old healthy female,isolated from human faeces,2015-06-30,New Zealand,New Zealand,env_biome:Human,,,,,,,,,,,,,,,,Draft genome of Fructococcus pectinolyticus strain 14 (JCM 31914 = DSM 104782). This strain is a pectinolytic strict anaerobe isolated from human faeces.,,,,,Strict anaerobic and mesophilic,,,,,,,,,,,,,Human,,,,98.4,0.7,,,Ear,- NHP,1982626.4,Faecalibacillus intestinalis strain 14EGH31,14EGH31,Faecalibacillus intestinalis,Faecalibacillus,Erysipelotrichaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMD00238634,1982626,,,,,,JCM:34082,,2020-10-01T00:00:00Z,,PRJDB10321,GCA_015097455.1,AP024085,,National Institute of Genetics,PacBio Sequel; Illumina HiSeq2500,4018x,Canu v. 2.0; Pilon v. 1.23,1,0,1,2869982,29.795414,2987,2948,fecal sample of a healthy japanese,isolated from a fecal sample of a healthy Japanese,,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of Faecalibacillus intestinalis strain 14EGH31 isolated from a fecal sample of a healthy Japanese.,,human-associated habitat,Intestinal,feces,not applicable,Complete genome sequencing of Faecalibacillus intestinalis strain 14EGH31,,,,,,,,,,,,human-associated habitat,,,,99.06,0,,,Gastrointestinal,- HP,1986146.3,Desulfobulbus sp. ORNL,ORNL,Desulfobulbus oralis,Desulfobulbus,Desulfobulbaceae,Desulfobulbales,Desulfobulbia,Thermodesulfobacteriota,SAMN06909033,1986146,,,,,,,,2018-02-14T00:00:00Z,,PRJNA385722,GCA_002952055.1,CP021255,,Oak Ridge National Laboratory,PacBio,700.0x,RS_HGAP Assembly v. 2,1,,1,2774417,59.75994,2817,2395,oral subgingival,,2015-10-01,USA,USA: Columbus Ohio,,,,,,,,,,,,,,,,,"Isolation and characterization of Desulfobulbus oralis, a human oral delta proteobacterium associated with periodontitis",sample_type:pure isolate culture,,,,,,,,,,,,,,,,,,,,,97.7,2.3,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,199.2265,Campylobacter concisus strain P15UCO-S2,P15UCO-S2,Campylobacter concisus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN05908162,199,,,,,,,,2020-11-24T00:00:00Z,33111662,PRJNA348396,GCA_015679945.1,"CP049234,CP049236,CP049235",,University of New South Wales,Oxford Nanopore MiniION,421x,Canu v. 1.7.1,1,2,3,1946644,39.455135,1952,1873,oral,,2015-01-08,Australia,Australia,,,,Ulcerative colitis,,,,,,,,,,,,,Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis,collected_by:UNSW,,,,,,,Ulcerative colitis,,,,,,,,,,,,,,99.51,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,199.2267,Campylobacter concisus strain P3UCB1,P3UCB1,Campylobacter concisus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN05908158,199,,,,,,,,2020-11-24T00:00:00Z,33111662,PRJNA348396,GCA_015680005.1,CP049238,,University of New South Wales,Oxford Nanopore MiniION,18x,Canu v. 1.7.1,1,0,1,1831655,37.605225,1901,1835,intestinal biopsy,,2009-01-02,Australia,Australia,,,,Ulcerative colitis,,,,,,,,,,,,,Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis,collected_by:UNSW,,,,,,,Ulcerative colitis,,,,,,,,,,,,,,99.88,0.37,Gastrointestinal Diseases,Gastritis and Ulcers,Genitourinary,Gastrointestinal Diseases-Gastritis and Ulcers HP,199.2268,Campylobacter concisus strain P3UCO1,P3UCO1,Campylobacter concisus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN05908159,199,,,,,,,,2020-11-24T00:00:00Z,33111662,PRJNA348396,GCA_015679985.1,CP049239,,University of New South Wales,Oxford Nanopore MiniION,57x,Canu v. 1.7.1,1,0,1,1800519,37.69113,1855,1794,oral,,2009-01-02,Australia,Australia,,,,Ulcerative colitis,,,,,,,,,,,,,Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis,collected_by:UNSW,,,,,,,Ulcerative colitis,,,,,,,,,,,,,,99.88,0.37,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,1993.11,Actinomadura madurae MRC008,MRC008,Actinomadura madurae,Actinomadura,Thermomonosporaceae,Streptosporangiales,Actinomycetes,Actinomycetota,SAMN23388486,1993,,,,,,,,2022-05-31T00:00:00Z,,PRJNA782605,GCA_023614255.1,CP094265,,,Oxford Nanopore MinION; Illumina iSeq,86x,Flye v. 2.8.2; Medaka v. 1.2.1; pilon v.,1,0,1,10230156,72.11752,10067,9564,mycetoma lesion,,2018-11-25,Sudan,Sudan,,,,Actinomycetoma,,,,,,,,,,,,,,collected_by:Mycetoma Research Centre,,,,,,,Actinomycetoma,,,,,,,,,,,,,,98,4.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2003188.3,Parolsenella catena strain JCM 31932,JCM 31932,Parolsenella catena,Parolsenella,Atopobiaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMD00152193,2003188,,,,,,,,2018-12-01T00:00:00Z,,PRJDB7698,GCA_003966955.1,AP019367,,National Institute of Genetics,PacBio RSII; Illumina MiSeq,537X,HGAP v. 3.0; SPAdes v. 3.8.1,1,,1,1796691,65.604324,1600,1585,fecal sample from a healthy japanese man,isolated from a fecal sample from a healthy Japanese man,,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of Parolsenella catena strain JCM 31932 isolated from a fecal sample from a healthy Japanese man.,,human-associated habitat,Intestinal,feces,10.1099/ijsem.0.002645,Complete genome sequencing of Parolsenella catena strain JCM 31932,,,,,,,,,,,,human-associated habitat,,,,99.19,0.81,,,Gastrointestinal,- HP,2014.4,Nocardiopsis dassonvillei strain HZNU_N_1,HZNU_N_1,Nocardiopsis dassonvillei,Nocardiopsis,Nocardiopsaceae,Streptosporangiales,Actinomycetes,Actinomycetota,SAMN07347491,2014,,,,,,,,2017-08-21T00:00:00Z,,PRJNA394048,GCA_002260685.1,CP022434,,Hangzhou Normal University,PacBio,183.0x,other v. 3.0,1,,1,6641645,72.62,5924,5509,pleural effusion,"isolated in pleural effusion, which secreted from a patient suffered coughing and shortness of breath",2016-08-09,China,China: Hangzhou,,,,pneumonia,,,,,,,,,,,,,"Complete genome sequence analysis of Nocardiopsis dassonvillei reveals a unique human pathogenesis charactersA Nocardiopsis strain was isolated in pleural effusion, which secreted from a patient suffered coughing and shortness of breath. We determined the complete genomic nucleotide sequence of the bacteria. According to our data, the genome is a circular chromosome bp long with % G+C content that encodes proteins. It will provided new genomic evidence of Nocardiopsis infection for human pathogenesis.","collected_by:Xiao-Fei, Zhao",,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2026186.17,Bacillus paranthracis strain NCCP 14796,NCCP 14796,Bacillus paranthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN12302793,2026186,,,,,,,,2020-01-14T00:00:00Z,,PRJNA555180,GCA_009873395.1,"CP041750,CP041751,CP041752",,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,241.0x,SPAdes v. 3.1,1,2,3,5114935,35.526787,5727,5254,stool,,2008-01-01,South Korea,South Korea: Ulsan,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Bacillus,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,92.52,0.71,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2026186.18,Bacillus paranthracis strain NCCP 15910,NCCP 15910,Bacillus paranthracis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN12340779,2026186,,,,MLST.Bacillus_cereus.994,,NCCP:15910,,2020-01-15T00:00:00Z,,PRJNA556101,GCA_009884335.1,"CP041981,CP041980",,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,207.0x,SPAdes v. 3.1,1,1,2,5507895,35.40349,6090,5589,stool,,2013-05-20,South Korea,South Korea: Seoul,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Bacillus,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,99.1,0.59,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2026187.8,Bacillus pacificus strain NCCP 15909,NCCP 15909,Bacillus pacificus,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN12340734,2026187,,,,MLST.Bacillus_cereus.1032,,NCCP:15909,,2020-01-15T00:00:00Z,,PRJNA556100,GCA_009884315.1,"CP041979,CP041978,CP041977",,Korea Centers for Disease Control & Prevention (KCDC),PacBio; IonTorrent,243.0x,SPAdes v. 3.1,1,2,3,5463271,35.450447,6078,5558,stool,,2013-03-13,South Korea,South Korea: Seoul,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Bacillus,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,97.63,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2026240.29,Klebsiella quasivariicola strain 08A119,08A119,Klebsiella quasivariicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024810,2026240,,,,MLST.Klebsiella_pneumoniae.1214,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525665.1,"CP084768,CP084769",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5869016,56.822468,5862,5570,blood,,1997,,Germany,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,1.01,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2026240.3,Klebsiella sp. KPN1705,KPN1705,Klebsiella quasivariicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06438648,2026240,,,,MLST.Klebsiella_pneumoniae.1155,genotype:STNF*\; Capsule locus KL153,,,2017-08-24T00:00:00Z,,PRJNA376414,GCA_002269255.1,"CP022823,CP022824,CP022825,CP022826",,Houston Methodist Hospital,Illumina NextSeq; Oxford Nanopore MinION,88.0x,Unicycler v. 0.4.0; SPAdes v. 3.10.0,1,3,4,5946706,56.66,6151,5940,wound,,2014-08-26,USA,USA: Houston,,,,Klebsiella Infections,,host_description:HMH:KPN:1705,,,,,,,,,,,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",collected_by:Houston Methodist Hospital,,,,,,,Klebsiella Infections,,,HMH:KPN:1705,,,,,,,,,,,99.1,0.6,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,204.123,Campylobacter showae strain B91_SC,B91_SC,Campylobacter showae,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMEA4535847,204,,,,,,,,2019-03-04T00:00:00Z,,PRJEB17707,GCA_900699785.1,LR535679,,Univeristy of Aberdeen,,,,1,,1,2160580,45.998344,2349,,biopsy,,2011,United Kingdom,United Kingdom,,,,,,host_health_state:diseased,,,,,,,,,,,"In this study the genomes of eight C. showae strains were sequenced, assembled and annotated including four strains from paediatric Crohn’s disease patients, three strains from colonic adenomas and one from a gastroenteritis patient.",,,,,,,,,diseased,,,,,,,,,,,,,99.88,1.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2048778.3,Escherichia coli O178:H19 strain 2012C-4431,2012C-4431,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04851096,2048778,O178:H19,,STEC,MLST.Escherichia_coli_2.537,,,,2017-11-02T00:00:00Z,,PRJNA218110,GCA_002741595.1,"CP024289,CP024290,CP024291,CP024292",,CDC,PacBio,430.0x,HGAP v. 3,1,3,4,5307783,50.76,5316,,stool,,2012-10-18,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:EDLB-CDC,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,2058152.48,Klebsiella grimontii strain 2481359,2481359,Klebsiella grimontii,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17215155,2058152,,,,,,,,2021-04-08T00:00:00Z,,PRJNA689715,GCA_017863855.1,"CP067380,CP067381,CP067382,CP067383",,University of Bern,Illumina NovaSeq; Oxford Nanopore MinION,250.98x,Unicycler v. 0.4.8,1,3,4,6316653,55.284103,6218,5854,urine,,2015-10,Switzerland,Switzerland,,,,Urinary Tract Infection,,,,,,,,,,,,,"Whole genome sequencing and characterization of two multidrug-resistant K. grimontii strains possessing blaVIM-1 and blaVIM-1 together with mcr-9, respectively.","collected_by:Institute for Infectious Diseases, University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,100,0.18,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,2058152.49,Klebsiella grimontii strain 5512.56,5512.56,Klebsiella grimontii,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17215154,2058152,,,,MLST.Klebsiella_oxytoca.16,,,,2021-04-08T00:00:00Z,,PRJNA689715,GCA_017863935.1,"CP067391,CP067390,CP067389,CP067384,CP067388,CP067387,CP067386,CP067385",,University of Bern,Illumina NovaSeq; Oxford Nanopore MinION,262.28x,Unicycler v. 0.4.8,1,7,8,6193468,55.697018,6101,5770,not defined,,2014-09,Switzerland,Switzerland,,,,Not defined,,,,,,,,,,,,,"Whole genome sequencing and characterization of two multidrug-resistant K. grimontii strains possessing blaVIM-1 and blaVIM-1 together with mcr-9, respectively.","collected_by:Institute for Infectious Diseases, University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,Not defined,,,,,,,,,,,,,,100,0.72,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,206506.9,Kerstersia gyiorum strain SWMUKG01,SWMUKG01,Kerstersia gyiorum,Kerstersia,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10273024,206506,,,,,,,,2019-04-01T00:00:00Z,,PRJNA497911,GCA_004551665.1,CP033936,,Southwest Medical University,PacBio RSII; Illumina HiSeq,128.0x,canu v. v1.5,1,,1,3945801,62.431683,3705,3392,a patient with respiratory infection,,2018-05,China,China:Luzhou,,,,,,,,,,,,,,,,,Kerstersia gyiorum SWMUKG01 chromosome，complete genome.,sample_type:genomic DNA,,,,,,,,,,,,,,,,,,,,,99.29,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,2072463.10,Escherichia coli O78 strain 3,3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21542538,2072463,O78,,,MLST.Escherichia_coli_1.57,,,,2021-10-03T00:00:00Z,,PRJNA765063,GCA_020217445.1,"CP084096,CP084097",,The First Hospital of Jilin University,Illumina HiSeq 4000 platform,99.92x,SOAPdenovo v. July-2020,1,1,2,5360188,50.65537,5341,5021,sputum,,2016-05-05,China,China:Jilin Province,,,,pneumonia,,,,,,,,,,,,,To find the relevant gene for biofilms information,collected_by:Zhimin Guo,,,,,,,pneumonia,,,,,,,,,,,,,,99.97,0.04,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,208224.408,Enterobacter kobei S18_CRE18,S18_CRE18,Enterobacter kobei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387637,208224,,,,MLST.Enterobacter_cloacae.191,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP075345,CP075346,CP075347",,,Illumina NextSeq; PacBio Sequel,554x,Unicycler v. v0.4.7,1,2,3,4952602,54.8274,4795,4639,"urine, clean catch",,2017-07-29,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,208224.79,Enterobacter kobei strain C16,C16,Enterobacter kobei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289356,208224,,,,MLST.Enterobacter_cloacae.191,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931545.1,"CP042578,CP042579,CP042580,CP042581",,University of Oxford,Oxford Nanopore MiniION,1557x,Unicycler v. SEP-2017,1,3,4,5366747,54.398296,5423,5232,clinical sample,,2009-03-12,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,99.7,0.78,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,208962.68,Escherichia albertii strain 1551-2,1551-2,Escherichia albertii,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08159313,208962,,,,MLST.Escherichia_coli_1.984,,,,2018-01-22T00:00:00Z,,PRJNA421872,GCA_002895205.1,CP025317,,Federal University of Sao Paulo,PacBio,139.18x,SMRT Link v. v4.0.0,1,,1,4730877,49.864326,4878,4695,,,1989,Brazil,Brazil: Sao Paulo state,,,,,,,,,,,,,,,,,"The sequenced escherichia albertii strain was previously classified as atypical enteropathogenic Escherichia coli. Because of its invasive ability and potential intracellular persistence in vitro, knowledge about its genome could help identify potential effectors or pathogenic islands that could be involved in the pathogenicity of this strain",sample_type:Single cell,,,,,,,,,,,,,,,,,,,,,97.8,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2098.65,Mycoplasma hominis strain 4788,4788,Metamycoplasma hominis,Metamycoplasma,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN10839205,2098,,,,,genotype:MLVA type 10,,,2019-11-15T00:00:00Z,31681239,PRJNA493181,GCA_009664265.1,CP035542,,USC EA3671 IHMC,Oxford Nanopore GridION,250.0x,CANU v. 1.7,1,,1,712385,26.98288,634,,vaginal secretion,,2008,France,France:Bordeaux,,female,,vaginosis,,,,,,,,,,,,,Sequencing of 14 clinical isolates of Mycoplasma hominis,collected_by:Bordeaux University Hospital,,,,,,,vaginosis,,,,,,,,,,,,,,100,0.38,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,210.10420,Helicobacter pylori oh1,oh1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN14967316,210,,,,MLST.Helicobacter_pylori.31,,,,2022-11-17T00:00:00Z,,PRJNA633596,,CP109885,,,Illumina HiSeq,1599923.0x,De novo assembly v. QUAST version 2.30,1,0,1,1600023,39.028316,1584,1487,gut tissue,,2018-04-27,South Korea,South Korea,,not applicable,30,Gastroenteritis,,host_disease_outcome:chronic disease;host_disease_stage:secondary stage;host_health_state:stomach pain,,,,,,,,,,,,collected_by:Deog-Hwan Oh,,,,,,,Gastroenteritis,stomach pain,chronic disease,,secondary stage,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,210.10520,Helicobacter pylori 444A6,444A6,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN32959140,210,,,,,,,,2023-02-17T00:00:00Z,,PRJNA929472,,"CP117024,CP117023",,,Illumina MiSeq; Oxford Nanopore MinION,129.0x,Flye v. 2.9; Circulator v. 1.5.5; Medaka,1,1,2,1627316,38.984806,1618,,gastric antrum,,2009-09-03,,not applicable,,,,gastritis,,,,,,,,,,,,,,collected_by:Daniel Wilkinson,,,,,,,gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.10656,Helicobacter pylori GCT85,GCT85,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18296287,210,,,,,,,,2023-05-22T00:00:00Z,,PRJNA604073,,CP071937,,,Illumina NovaSeq,102x,SPAdes v. 3.15.1,1,0,1,1623483,39.189198,1630,,tolima,,2019-07-17,Colombia,Colombia: Tolima,,female,62,Non-atrophic gastritis,,host_disease_stage:Non-atrophic gastritis,,,,,,,,,,,,"collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Non-atrophic gastritis,,,,Non-atrophic gastritis,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.10657,Helicobacter pylori GCT56,GCT56,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18296284,210,,,,,,,,2023-05-22T00:00:00Z,,PRJNA604073,,CP071938,,,Illumina NovaSeq,102x,SPAdes v. 3.15.1,1,0,1,1624702,38.98731,1640,,caldas,,2018-10-05,Colombia,Colombia: Tolima,,female,40,Non-atrophic gastritis,,host_disease_stage:Non-atrophic gastritis,,,,,,,,,,,,"collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Non-atrophic gastritis,,,,Non-atrophic gastritis,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.10658,Helicobacter pylori GCT55,GCT55,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18296283,210,,,,,,,,2023-05-22T00:00:00Z,,PRJNA604073,,CP071939,,,Illumina NovaSeq,100x,SPAdes v. 3.15.1,1,0,1,1596494,39.01362,1623,,boyaca,,2018-10-05,Colombia,Colombia: Tolima,,female,28,Non-atrophic gastritis,,host_disease_stage:Non-atrophic gastritis,,,,,,,,,,,,"collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Non-atrophic gastritis,,,,Non-atrophic gastritis,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.10659,Helicobacter pylori GCT17,GCT17,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18296282,210,,,,,,,,2023-05-22T00:00:00Z,,PRJNA604073,,CP071940,,,Illumina NovaSeq,102x,SPAdes v. 3.15.1,1,0,1,1635188,39.027153,1631,,tolima,,2017-11-01,Colombia,Colombia: Tolima,,female,46,Non-atrophic gastritis,,host_disease_stage:Non-atrophic gastritis,,,,,,,,,,,,"collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Non-atrophic gastritis,,,,Non-atrophic gastritis,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.2712,Helicobacter pylori strain G272,G272,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN07338981,210,,,,,,,,2017-07-20T00:00:00Z,,PRJNA393647,GCA_002222575.1,"CP022409,CP022410",,Guizhou Medical University,Illumina Hiseq,300.0x,SMRT portal v. 3.2.0,1,1,2,1584869,38.84,1643,1522,gastric mucasa,,2016-07-18,China,China:Guizhou,,,,Gastritis,,,,,,,,,,,,,to characterize the geographic diversity of Helicabacter pylori strains isolated from the Han people of Guiyang city and from the Buyi andthe Miao people of Qiannan autonomous prefecture,"collected_by:CHEN Zhenghong, WANG Qiong,YIN Lin",,,,,,,Gastritis,,,,,,,,,,,,,,100,2.1,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.4150,Helicobacter pylori strain FDAARGOS_300,FDAARGOS_300,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN06173313,210,,,,MLST.Helicobacter_pylori.199,genotype:cagA+ vacA+,FDA:FDAARGOS_300,,2018-03-09T00:00:00Z,,PRJNA231221,GCA_002983705.1,CP027404,,US Food and Drug Administration,PacBio; Illumina,16.4410831120036x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,1645738,39.182484,1650,1555,gastric antral biopsy; duodenal ulcer from patient in tennessee,,1994,USA,USA:VA,,male,48Y,Duodenitis,,"host_disease_outcome:2nd upper endoscopy was completed 6 yrs later (2000);host_health_state:Refused antimicrobial therapy;host_description:Caucasian, no family history of peptic ulceration;host_disease_stage:Persistent dyspepsia",,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC < MJ Jones < M.J. Blaser,,,,,,,Duodenitis,Refused antimicrobial therapy,2nd upper endoscopy was completed 6 yrs later (2000),"Caucasian, no family history of peptic ulceration",Persistent dyspepsia,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,210.4220,Helicobacter pylori strain FDAARGOS_298,FDAARGOS_298,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN06173311,210,,,,MLST.Helicobacter_pylori.3327,,FDA:FDAARGOS_298,,2018-04-13T00:00:00Z,,PRJNA231221,GCA_003050665.1,CP028325,,US Food and Drug Administration,PacBio; Illumina,24.67x,CA v. 8.2,1,,1,1680898,38.825912,1722,1634,"endoscropic biopsy specimens of human gastric mucosa; human gastric antrum from royal perth hospital, australia",,1983,USA,USA:VA,,,,Gastritis,,host_disease_outcome:Cleared infection;host_description:Elderly Russian patient,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC < NCTC < CS Goodwin and DI Annear < H Royce,,,,,,,Gastritis,Missing,Cleared infection,Elderly Russian patient,Missing,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5180,Helicobacter pylori strain GD63,GD63,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09809602,210,,,,MLST.Helicobacter_pylori.3170,,,,2018-10-12T00:00:00Z,,PRJNA485550,GCA_003640585.1,"CP031558,CP031559",,"University of Science, VNU-HCM",Illumina MiSeq; Oxford Nanopore MiniION,180.0x,Unicycler v. v0.4.4,1,1,2,1590969,38.782215,1682,1524,gastric antrum,,2017,Viet Nam,Viet Nam: Ho Chi Minh City,,,,Gastric ulcer,,,,,,,,,,,,,The goal of this project is the genomic characterization of the Helicobacter pylori strains isolated from Vietnamese patients,"collected_by:Department of Genetics, University of Science, HCM-VNU",,,,,,,Gastric ulcer,,,,,,,,,,,,,,99.58,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5250,Helicobacter pylori strain Hpbs1,Hpbs1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10461767,210,,,,,,,,2018-12-02T00:00:00Z,,PRJNA506489,GCA_003855475.1,CP034071,,BGI,Illumina,995.0x,Newbler v. NOV22-2018,1,,1,1563701,38.90955,1581,,"patients with gastritis or gastric ulcer examined with a gastroscope at people's hospital, bama county",,2015-11-30,China,China: Baise,,,,Gastritis or gastric ulcer,,,,,,,,,,,,,"Helicobacter pylori CompleteGenome Sequencing， the strain is resistant to claymycin, metronidazole, levofloxacin.",collected_by:yanqiang huang,,,,,,,Gastritis or gastric ulcer,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5255,Helicobacter pylori strain HP42K,HP42K,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10181238,210,,,,,,,,2018-12-12T00:00:00Z,,PRJNA494842,GCA_003939085.1,"CP034314,CP034313,CP034312",,Gomel state medical universitate,IonTorrent,40.0x,SPAdes v. 3.13,1,2,3,1658454,38.849434,1685,1560,1751; stomach biopsy,,2018-08-15,Belarus,Belarus,,female,48,Gastritis and duodenitis,,host_disease_outcome:chronic disease;host_subject_id:42,,,,,,,,,,,Complete genome Helicobacter pylori in Belarus,collected_by:Evgenii Voropaev,,,,,,,Gastritis and duodenitis,,chronic disease,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5625,Helicobacter pylori strain Hpbs3,Hpbs3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10663175,210,,,,,,,,2019-01-21T00:00:00Z,,PRJNA512257,GCA_004088075.1,CP035106,,BGI,Illumina,996.0x,Newbler v. DEC31-2018,1,,1,1514674,38.960857,1532,,"patients with gastritis or gastric ulcer examined with a gastroscope at people's hospital, bama county",,2015-11-28,China,China: Baise,,,,Gastritis,,,,,,,,,,,,,"Helicobacter pylori CompleteGenome Sequencing. The Hpbs3 strain comes from the gastric mucosa of patients with chronic gastritis, it is Helicobacter pylori with resistant to claymycin.",collected_by:yanqiang huang,,,,,,,Gastritis,,,,,,,,,,,,,,99.62,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5627,Helicobacter pylori strain Hpbs2,Hpbs2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10663081,210,,,,,,,,2019-01-21T00:00:00Z,,PRJNA512253,GCA_004088155.1,CP035105,,BGI,Illumina,998.0x,Newbler v. DEC31-2018,1,,1,1535248,38.90616,1559,,"patients with gastritis or gastric ulcer examined with a gastroscope at people's hospital, bama county",,2015-11-28,China,China: Baise,,,,Gastritis,,,,,,,,,,,,,"Helicobacter pylori CompleteGenome Sequencing. The Hpbs2 strain comes from the gastric mucosa of patients with chronic gastritis, it is Helicobacter pylori with resistant to claymycin, metronidazole, levofloxacin.",collected_by:yanqiang huang,,,,,,,Gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5906,Helicobacter pylori strain 479-A2-EK4,479-A2-EK4,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053852,210,,,,MLST.Helicobacter_pylori.1611,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337265.1,CP032472,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1636444,38.866714,1620,,gastric antrum patient479,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-25,Germany,Germany: Magdeburg,,male,69,atrophic gastritis,,host_subject_id:#479,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5907,Helicobacter pylori strain 476-A2-EK2,476-A2-EK2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053800,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337285.1,CP032473,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1649543,38.91084,1649,,gastric antrum patient476,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-24,Germany,Germany: Magdeburg,,male,34,gastritis,,host_subject_id:#476,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0.28,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5908,Helicobacter pylori strain 381-F-EK9,381-F-EK9,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053787,210,,,,MLST.Helicobacter_pylori.1557,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337305.1,CP032475,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1580965,39.10833,1602,,gastric fundus patient381,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2013-11-26,Germany,Germany: Magdeburg,,female,42,atrophic gastritis,,host_subject_id:#381,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0.14,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5909,Helicobacter pylori strain 381-C-EK1,381-C-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053769,210,,,,MLST.Helicobacter_pylori.1557,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337325.1,CP032476,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1588985,39.10641,1613,,gastric corpus patient381,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2013-11-26,Germany,Germany: Magdeburg,,female,42,atrophic gastritis,,host_subject_id:#381,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0.14,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5910,Helicobacter pylori strain 169-C-EK8,169-C-EK8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053716,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337345.1,CP032477,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1611628,38.99504,1616,,gastric corpus patient169,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2012-03-05,Germany,Germany: Magdeburg,,female,50,gastritis,,host_subject_id:#169,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5911,Helicobacter pylori strain 25-A-EK9,25-A-EK9,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053600,210,,,,MLST.Helicobacter_pylori.1717,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337365.1,CP032478,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1540135,39.154816,1534,,gastric antrum patient25,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-11-16,Germany,Germany: Magdeburg,,male,56,gastritis,,host_subject_id:#25,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0.1,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5912,Helicobacter pylori strain 21-F-EK1,21-F-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053522,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337385.1,CP032479,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1583343,39.04795,1580,,gastric fundus patient21,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-18,Germany,Germany: Magdeburg,,male,58,gastritis,,host_subject_id:#21,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.57,0.24,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5913,Helicobacter pylori strain 19-C-EK1,19-C-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053452,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337405.1,CP032480,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1709363,38.72378,1707,,gastric corpus patient19,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-14,Germany,Germany: Magdeburg,,female,32,gastritis,,host_subject_id:#19,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.3,0.1,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5914,Helicobacter pylori strain 476-A-EK5,476-A-EK5,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053793,210,,,,MLST.Helicobacter_pylori.103,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337425.1,CP032900,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1634797,38.93994,1652,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-24,Germany,Germany: Magdeburg,,male,34,gastritis,,host_subject_id:#476,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5915,Helicobacter pylori strain 381-A-EK4,381-A-EK4,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053762,210,,,,MLST.Helicobacter_pylori.1557,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337445.1,CP032901,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1579431,39.11516,1601,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2013-11-26,Germany,Germany: Magdeburg,,female,42,atrophic gastritis,,host_subject_id:#381,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0.14,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5916,Helicobacter pylori strain 280-A-EK1,280-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053739,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337465.1,CP032902,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1609437,38.953934,1634,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2013-01-22,Germany,Germany: Magdeburg,,female,76,gastritis,,host_subject_id:#280,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.42,0.14,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5917,Helicobacter pylori strain 173-A-EK1,173-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053719,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337485.1,CP032903,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1690720,38.76313,1680,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2012-03-15,Germany,Germany: Magdeburg,,female,44,gastritis,,host_subject_id:#173,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5918,Helicobacter pylori strain 169-A-EK5,169-A-EK5,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053703,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337625.1,CP032904,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1610187,39.0005,1616,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2012-03-05,Germany,Germany: Magdeburg,,female,50,gastritis,,host_subject_id:#169,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5919,Helicobacter pylori strain 26-A-EK1,26-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053622,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337745.1,CP032905,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1643421,38.91979,1679,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-11-22,Germany,Germany: Magdeburg,,female,47,atrophic gastritis,,host_subject_id:#26,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5920,Helicobacter pylori strain 24-A-EK1,24-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053562,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006337875.1,CP032907,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1659500,38.85339,1638,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-11-11,Germany,Germany: Magdeburg,,male,33,gastritis,,host_subject_id:#24,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5921,Helicobacter pylori strain 23-A-EK1,23-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053532,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338045.1,CP032908,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1679162,38.77303,1649,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-11-08,Germany,Germany: Magdeburg,,male,30,gastritis,,host_subject_id:#23,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5922,Helicobacter pylori strain 21-A-EK1,21-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053502,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338145.1,CP032909,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1582133,39.047916,1576,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-18,Germany,Germany: Magdeburg,,male,58,gastritis,,host_subject_id:#21,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.57,0.24,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5923,Helicobacter pylori strain 20-A-EK1,20-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053472,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338285.1,CP032910,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1599658,39.1148,1615,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-14,Germany,Germany: Magdeburg,,female,55,gastritis,,host_subject_id:#20,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5924,Helicobacter pylori strain 19-A-EK3,19-A-EK3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053444,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338415.1,CP032911,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1706376,38.727512,1702,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-14,Germany,Germany: Magdeburg,,female,32,gastritis,,host_subject_id:#19,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0.1,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5925,Helicobacter pylori strain 13-A-EK8,13-A-EK8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053419,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338545.1,CP032912,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1619300,39.07003,1636,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-07-06,Germany,Germany: Magdeburg,,female,54,gastritis,,host_subject_id:#13,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.57,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5926,Helicobacter pylori strain 479-C2-EK2,479-C2-EK2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053865,210,,,,MLST.Helicobacter_pylori.1611,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338685.1,CP032471,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1637783,38.85637,1618,,gastric corpus patient479,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-25,Germany,Germany: Magdeburg,,male,69,atrophic gastritis,,host_subject_id:#479,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5927,Helicobacter pylori strain 476-C-EK5,476-C-EK5,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053808,210,,,,MLST.Helicobacter_pylori.103,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006338815.1,CP032474,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1601381,38.996468,1613,,gastric corpus patient476,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-24,Germany,Germany: Magdeburg,,male,34,gastritis,,host_subject_id:#476,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5928,Helicobacter pylori strain 479-C-EK2,479-C-EK2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053855,210,,,,MLST.Helicobacter_pylori.1611,,,,2019-06-13T00:00:00Z,,PRJNA490474,GCA_006338945.1,CP032898,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1638022,38.86877,1620,,gastric corpus,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-25,Germany,Germany: Magdeburg,,male,69,atrophic gastritis,,host_subject_id:#479,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.36,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5929,Helicobacter pylori strain 478-A-EK1,478-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053819,210,,,,,,,,2019-06-13T00:00:00Z,,PRJNA490474,GCA_006339065.1,CP032899,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1628623,38.923313,1622,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2014-11-25,Germany,Germany: Magdeburg,,male,70,atrophic gastritis,,host_subject_id:#478,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,atrophic gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5930,Helicobacter pylori strain 25-A-EK1,25-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053592,210,,,,MLST.Helicobacter_pylori.1717,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006339235.1,CP032906,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1540214,39.14969,1531,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-11-16,Germany,Germany: Magdeburg,,male,56,gastritis,,host_subject_id:#25,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.36,0.1,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.5931,Helicobacter pylori strain 5-A-EK1,5-A-EK1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10053382,210,,,,,,,,2019-06-13T00:00:00Z,31118420,PRJNA490474,GCA_006339365.1,CP032913,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,,1,1596986,38.96947,1601,,gastric antrum,"isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology)",2016-06-10,Germany,Germany: Magdeburg,,female,49,gastritis,,host_subject_id:#5,,,,,,,,,,,"Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.","collected_by:Otto von Guericke University, Dept. of Gastroenterology, Hepatology and Infectious Diseases, Magdeburg, Germany",,,,,,,gastritis,,,,,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6117,Helicobacter pylori strain G-Mx-2011-147,G-Mx-2011-147,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935054,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032475.1,CP032037,,University of California at Davis,PacBio RSII,274x,HGAP v. 15-May,1,,1,1667329,38.8814,1701,1586,not collected,,2011-09-19,Mexico,Mexico: Mexico City,,male,39,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Irma Ramos,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.36,0.81,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6118,Helicobacter pylori strain G-Mx-2011-124,G-Mx-2011-124,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935053,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032615.1,CP032038,,University of California at Davis,PacBio RSII,370x,HGAP v. 15-Jun,1,,1,1661266,38.96221,1733,1586,not collected,,2008-05-31,Mexico,Mexico: Mexico City,,male,45,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Irma Ramos,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,98.96,0.06,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6120,Helicobacter pylori strain G-Mx-2006-583,G-Mx-2006-583,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935052,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032935.1,CP032039,,University of California at Davis,PacBio RSII,306x,HGAP v. 15-May,1,,1,1645512,39.06681,1823,1577,not collected,,2006-06-20,Mexico,Mexico: Mexico City,,female,47,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Irma Ramos,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,98.82,0.57,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6121,Helicobacter pylori strain G-Mx-2006-46,G-Mx-2006-46,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935046,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032955.1,"CP032046,CP032047",,University of California at Davis,PacBio RSII,355x,HGAP v. 15-May,1,1,2,1636468,39.01745,1780,1559,not collected,,1999-10-19,Mexico,Mexico: Mexico City,,female,45,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr. Fernando Bernal,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.09,0.54,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6122,Helicobacter pylori strain G-Mx-2006-152,G-Mx-2006-152,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935051,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032975.1,CP032040,,University of California at Davis,PacBio RSII,340x,HGAP v. 15-May,1,,1,1613306,39.143356,1645,1531,not collected,,1999-12-09,Mexico,Mexico: Mexico City,,female,40,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr. Fernando Bernal,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.3,0.41,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6123,Helicobacter pylori strain G-Mx-2005-337,G-Mx-2005-337,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935050,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008032995.1,CP032041,,University of California at Davis,PacBio RSII,354x,HGAP v. 15-Apr,1,,1,1697806,38.87852,1782,1636,not collected,,2000-07-25,Mexico,Mexico: Mexico City,,male,41,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr Juan Miguel Abdo,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,98.96,0.81,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6124,Helicobacter pylori strain G-Mx-2005-108,G-Mx-2005-108,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935049,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008033015.1,CP032042,,University of California at Davis,PacBio RSII,354x,HGAP v. 15-May,1,,1,1654849,38.95787,1683,1571,not collected,,2000-09-21,Mexico,Mexico: Mexico City,,male,34,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr. Fernando Bernal,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.36,0.41,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6125,Helicobacter pylori strain G-Mx-2003-93,G-Mx-2003-93,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935048,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008033035.1,CP032043,,University of California at Davis,PacBio RSII,52x,HGAP v. 15-Apr,1,,1,1632682,39.0539,1851,1551,not collected,,1999-10-13,Mexico,Mexico: Mexico City,,female,45,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr Juan Miguel Abdo,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,98.76,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6126,Helicobacter pylori strain G-Mx-2003-250,G-Mx-2003-250,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935045,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008033055.1,CP032048,,University of California at Davis,PacBio RSII,408x,HGAP v. 15-May,1,,1,1672280,38.93307,1689,1569,not collected,,2001-03-22,Mexico,Mexico: Mexico City,,male,40,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr. Fernando Bernal,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.55,0.41,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6127,Helicobacter pylori strain G-Mx-2003-108,G-Mx-2003-108,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN09935047,210,,,,,,,,2019-08-20T00:00:00Z,,PRJNA203445,GCA_008033075.1,"CP032044,CP032045",,University of California at Davis,PacBio RSII,363x,HGAP v. 15-May,1,1,2,1686171,38.895626,1737,1606,not collected,,1999-10-14,Mexico,Mexico: Mexico City,,female,42,Non-Atrophic Gastritis,,,,,,,,,,,,,"University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.",collected_by:Dr. Fernando Bernal,,,,,,,Non-Atrophic Gastritis,,,,,,,,,,,,,,99.42,0.1,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6129,Helicobacter pylori strain TN2wt,TN2wt,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN02724990,210,,,,MLST.Helicobacter_pylori.1436,,,,2019-08-23T00:00:00Z,,PRJNA244276,GCA_008326525.1,AP019730,,Oita University,PacBio,567x,HGAP v. 2.0,1,,1,1604952,38.731564,1654,1545,"oita, japan",,2010-04-01,Japan,Japan: Oita,,,,Gastroduodenal disease,,,,,Negative,Spirilla,Yes,Mesophilic,,Microaerophilic,HostAssociated,Gastroduodenal disease,Constructing a high quality complete genome sequence of Helicobacter pylori TN2wt to perform comparative genomic analyses in a high resolution manner.,collected_by:Yoshio Yamaoka,,,,,,,Gastroduodenal disease,,,,,,,,,,,,,,99.42,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,210.6638,Helicobacter pylori strain GCT 27,GCT 27,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN13950472,210,,,,MLST.Helicobacter_pylori.2001,,,,2020-02-21T00:00:00Z,,PRJNA604073,GCA_010917155.1,CP048601,,"Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",Illumina NovaSeq,102x,SPAdes v. 3.13.0,1,0,1,1643850,38.986538,1655,1505,gastric biopsy specimen,"isolated from Colombian residents of Tolima, diagnosed with chronic gastritis",2017-11-14,Colombia,Colombia: Valle del Cauca,,female,38,Chronic active gastritis,,host_disease_stage:Chronic active gastritis,,,,,,,,,,,"We present here the complete genome sequence of three Helicobacter pylori strains, isolated from Colombian residents of Tolima, diagnosed with chronic gastritis. These genomes allow to the scientific community to expand knowledge about the strains that infect the Tolimense population to identify genetic factors in H. pylori that may be involved in the development of gastric diseases.","collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Chronic active gastritis,,,,Chronic active gastritis,,,,,,,,,,99.57,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6639,Helicobacter pylori strain GCT 43,GCT 43,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN13950473,210,,,,,,,,2020-02-21T00:00:00Z,,PRJNA604073,GCA_010917555.1,CP048600,,"Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",Illumina NovaSeq,102x,SPAdes v. 3.13.0,1,0,1,1642466,39.020264,1653,1513,gastric biopsy specimen,"isolated from Colombian residents of Tolima, diagnosed with chronic gastritis",2018-08-02,Colombia,Colombia: Risaralda,,male,37,Chronic active gastritis,,host_disease_stage:Chronic active gastritis,,,,,,,,,,,"We present here the complete genome sequence of three Helicobacter pylori strains, isolated from Colombian residents of Tolima, diagnosed with chronic gastritis. These genomes allow to the scientific community to expand knowledge about the strains that infect the Tolimense population to identify genetic factors in H. pylori that may be involved in the development of gastric diseases.","collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Chronic active gastritis,,,,Chronic active gastritis,,,,,,,,,,99.61,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.6640,Helicobacter pylori strain GCT 97,GCT 97,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN13950474,210,,,,,,,,2020-02-21T00:00:00Z,,PRJNA604073,GCA_010917675.1,CP048599,,"Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",Illumina NovaSeq,103x,SPAdes v. 3.13.0,1,0,1,1656646,38.986385,1670,1518,gastric biopsy specimen,"isolated from Colombian residents of Tolima, diagnosed with chronic gastritis",2017-03-14,Colombia,Colombia: Tolima,,male,61,Chronic active gastritis,,host_disease_stage:Chronic active gastritis,,,,,,,,,,,"We present here the complete genome sequence of three Helicobacter pylori strains, isolated from Colombian residents of Tolima, diagnosed with chronic gastritis. These genomes allow to the scientific community to expand knowledge about the strains that infect the Tolimense population to identify genetic factors in H. pylori that may be involved in the development of gastric diseases.","collected_by:Group of Cytogenetics, Phylogeny and Population Evolution, University of Tolima",,,,,,,Chronic active gastritis,,,,Chronic active gastritis,,,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7407,Helicobacter pylori strain H1,H1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961649,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456275.1,CP036379,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563305,38.950363,1558,,missing,,1998,USA,USA: Houston,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Veterans Affairs Medical Center, Houston, USA",,,,,,,gastritis,,,,,,isolated from person innoculated with strain BCS 100,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7408,Helicobacter pylori strain 125C7,125C7,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961648,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456295.1,CP036380,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563239,38.95041,1555,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 125,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7409,Helicobacter pylori strain 125A3,125A3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961647,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456315.1,CP036381,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563276,38.950447,1556,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 125,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7410,Helicobacter pylori strain 119C10,119C10,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961646,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456475.1,CP036382,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563317,38.950512,1558,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 119,,,,,,,,99.01,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7411,Helicobacter pylori strain 119A2,119A2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961645,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456665.1,CP036383,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563232,38.95052,1563,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 119,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7412,Helicobacter pylori strain 103C8,103C8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961644,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011456895.1,CP036384,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1566721,38.95269,1559,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 103,,,,,,,,99.42,0.41,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7413,Helicobacter pylori strain 103A4,103A4,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961643,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011457115.1,CP036385,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563266,38.950504,1556,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 103,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7414,Helicobacter pylori strain 87C7,87C7,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961642,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011457355.1,CP036386,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563411,38.950348,1561,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 87,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7415,Helicobacter pylori strain 81C9,81C9,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961640,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011457815.1,CP036388,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563438,38.950123,1558,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 81,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7416,Helicobacter pylori strain 87A3,87A3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961641,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011457615.1,CP036387,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563302,38.95012,1557,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 87,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7417,Helicobacter pylori strain 81A1,81A1,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961639,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011458015.1,CP036389,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563405,38.95024,1555,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 81,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7418,Helicobacter pylori strain 78C8,78C8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961638,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011458095.1,CP036390,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563292,38.950306,1568,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 78,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7419,Helicobacter pylori strain 78A3,78A3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961637,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011458315.1,CP036391,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563274,38.95069,1563,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 78,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7420,Helicobacter pylori strain 48A2,48A2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961635,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011462375.1,CP036393,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563280,38.950413,1560,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 48,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7421,Helicobacter pylori strain 48C8,48C8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961636,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011462215.1,CP036392,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563290,38.95029,1555,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 48,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7422,Helicobacter pylori strain 29C8,29C8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961634,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011462575.1,CP036394,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1562072,38.950638,1559,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 29,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7423,Helicobacter pylori strain 29A2,29A2,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961633,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011462735.1,CP036395,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563333,38.949795,1560,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 29,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7424,Helicobacter pylori strain 12C8,12C8,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961632,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011462915.1,CP036396,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563409,38.950397,1558,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 12,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7425,Helicobacter pylori strain 12A3,12A3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961631,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011463035.1,CP036397,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563420,38.950504,1559,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 12,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7426,Helicobacter pylori strain 8C10,8C10,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961630,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011463055.1,CP036398,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563260,38.950336,1559,,gastric corpus,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 8,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.7427,Helicobacter pylori strain 8A3,8A3,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN10961629,210,,,,MLST.Helicobacter_pylori.1759,,,,2020-03-19T00:00:00Z,,PRJNA522954,GCA_011463175.1,CP036399,,Max von Pettenkofer-Institut,PacBio RSII,300x,HGAP v. 3,1,0,1,1563267,38.950607,1556,,gastric antrum,,2003,Germany,Germany: Berlin,,,,gastritis,,,,,,,,,,,,,"Using SMRT� sequencing technology, we investigated the degree of genome and methylome evolution of H. pylori re-isolates from the antrum and corpus of 10 infected human volunteers who participated in an experimental human infection study.In addition, Illumina sequencing was performed to examine the variability within 16 colonies from the challenge strain (BCS 100).","collected_by:Medical Clinic I, Charite, Campus Benjamin Franklin, Berlin",,,,,,,gastritis,,,,,,isolated from patient 8,,,,,,,,99.42,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.8997,Helicobacter pylori J99 derivative,J99 derivative,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN23610989,210,,,,MLST.Helicobacter_pylori.199,,,,2021-12-15T00:00:00Z,,PRJNA786001,GCA_021184145.1,CP089283,,,PacBio Sequel,397x,Microbial Assembler v. DEC-2020,1,0,1,1685094,39.039604,1672,1538,duodenum biopsy,,2000,USA,USA: Nashville,,male,54 years,"duodenal ulcer, gastritis",,host_description:Caucasian,,,,,,,,,,,,collected_by:Richard Peek Jr.,,,,,,,"duodenal ulcer, gastritis",,,Caucasian,,,,,,,,,,,98.68,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9073,Helicobacter pylori Hpfe125,Hpfe125,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675609,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921215.1,"CP094054,CP094055",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1557058,38.93728,1577,1450,gastric biopsy,,2021-11-23,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9074,Helicobacter pylori Hpfe127,Hpfe127,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675611,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921175.1,CP094051,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1577655,38.837894,1598,1492,gastric biopsy,,2021-11-23,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9075,Helicobacter pylori Hpfe126,Hpfe126,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675610,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921195.1,"CP094052,CP094053",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1627588,38.64301,1671,1524,gastric biopsy,,2021-11-23,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9076,Helicobacter pylori Hpfe124,Hpfe124,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675608,210,,,,MLST.Helicobacter_pylori.2248,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921235.1,"CP094056,CP094057",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1552368,38.93561,1585,1459,gastric biopsy,,2021-11-20,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9077,Helicobacter pylori Hpfe123,Hpfe123,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675607,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921255.1,CP094058,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1615068,38.711372,1640,1507,gastric biopsy,,2021-11-18,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9078,Helicobacter pylori Hpfe122,Hpfe122,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675606,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921275.1,"CP094059,CP094060",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1563646,38.815243,1586,1462,gastric biopsy,,2021-11-18,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9079,Helicobacter pylori Hpfe120,Hpfe120,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675605,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921295.1,CP094061,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1609748,38.67444,1633,1494,gastric biopsy,,2021-11-16,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9080,Helicobacter pylori Hpfe118,Hpfe118,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675604,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921315.1,CP094062,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1637345,38.71255,1670,1520,gastric biopsy,,2021-11-13,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9082,Helicobacter pylori Hpfe114,Hpfe114,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675602,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921355.1,CP094064,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1557498,38.914593,1585,1467,gastric biopsy,,2021-11-12,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9083,Helicobacter pylori Hpfe112,Hpfe112,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675600,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921575.1,CP094065,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1644007,38.68122,1677,1535,gastric biopsy,,2021-11-10,China,China: Hengyang,,,,Duodenal ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Duodenal ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9084,Helicobacter pylori Hpfe113,Hpfe113,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675601,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921455.1,CP094174,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1570128,38.833447,1602,1452,gastric biopsy,,2021-11-10,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9085,Helicobacter pylori Hpfe110,Hpfe110,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675599,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921695.1,CP094066,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1664142,38.589016,1707,1574,gastric biopsy,,2021-11-09,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9086,Helicobacter pylori Hpfe108,Hpfe108,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675597,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921755.1,"CP094067,CP094068,CP094069",,,illumina,100x,Unicycler v. 0.4.8,1,2,3,1581972,38.74778,1633,1495,gastric biopsy,,2021-11-04,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9087,Helicobacter pylori Hpfe106,Hpfe106,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675595,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921795.1,"CP094071,CP094072",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1594453,38.717606,1624,1487,gastric biopsy,,2021-11-03,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9088,Helicobacter pylori Hpfe107,Hpfe107,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675596,210,,,,MLST.Helicobacter_pylori.2158,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921775.1,CP094070,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1620835,38.701473,1659,1512,gastric biopsy,,2021-11-04,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9089,Helicobacter pylori Hpfe104,Hpfe104,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675593,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921815.1,CP094073,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1574424,38.834583,1585,1456,gastric biopsy,,2021-10-28,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9090,Helicobacter pylori Hpfe103,Hpfe103,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675592,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921835.1,"CP094074,CP094075",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1602592,38.778492,1610,1495,gastric biopsy,,2021-10-27,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9091,Helicobacter pylori Hpfe102,Hpfe102,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675591,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921855.1,"CP094076,CP094077",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1616207,38.707664,1638,1495,gastric biopsy,,2021-10-27,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9092,Helicobacter pylori Hpfe100,Hpfe100,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675589,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921895.1,CP094079,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1555854,38.89703,1573,1450,gastric biopsy,,2021-10-22,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9093,Helicobacter pylori Hpfe101,Hpfe101,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675590,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921875.1,CP094078,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1572519,38.849705,1600,1473,gastric biopsy,,2021-10-25,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9094,Helicobacter pylori Hpfe099,Hpfe099,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675588,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921915.1,"CP094080,CP094081",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1649450,38.63791,1675,1548,gastric biopsy,,2021-10-16,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9095,Helicobacter pylori Hpfe097,Hpfe097,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675586,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921935.1,CP094082,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1640211,38.5287,1638,1520,gastric biopsy,,2021-10-15,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9096,Helicobacter pylori Hpfe096,Hpfe096,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675585,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921955.1,"CP094083,CP094084",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1564753,38.88863,1610,1479,gastric biopsy,,2021-10-15,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9097,Helicobacter pylori Hpfe093,Hpfe093,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675582,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921995.1,CP094087,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1604124,38.733166,1636,1499,gastric biopsy,,2021-10-12,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9098,Helicobacter pylori Hpfe095,Hpfe095,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675584,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022921975.1,"CP094085,CP094086",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1603559,38.713387,1616,1489,gastric biopsy,,2021-10-13,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9099,Helicobacter pylori Hpfe092,Hpfe092,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675581,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922015.1,"CP094088,CP094089",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1624101,38.675243,1640,1521,gastric biopsy,,2021-10-12,China,China: Hengyang,,,,Duodenal ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Duodenal ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9100,Helicobacter pylori Hpfe089,Hpfe089,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675579,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922035.1,CP094090,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1625567,38.74242,1636,1516,gastric biopsy,,2021-10-09,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9101,Helicobacter pylori Hpfe086,Hpfe086,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675576,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922175.1,CP094092,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1588502,38.774895,1608,1484,gastric biopsy,,2021-10-09,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9102,Helicobacter pylori Hpfe088,Hpfe088,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675578,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922055.1,CP094091,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1558458,38.876827,1581,1456,gastric biopsy,,2021-10-09,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9103,Helicobacter pylori Hpfe085,Hpfe085,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675575,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922295.1,CP094093,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1574428,38.8785,1583,1463,gastric biopsy,,2021-09-27,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9104,Helicobacter pylori Hpfe084,Hpfe084,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675574,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922415.1,CP094094,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1629886,38.60503,1687,1535,gastric biopsy,,2021-09-20,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9105,Helicobacter pylori Hpfe082,Hpfe082,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675572,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922655.1,"CP094096,CP094097",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1617045,38.63034,1635,1498,gastric biopsy,,2021-09-19,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9106,Helicobacter pylori Hpfe083,Hpfe083,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675573,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922515.1,CP094095,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1577172,38.842117,1581,1467,gastric biopsy,,2021-09-20,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9107,Helicobacter pylori Hpfe081,Hpfe081,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675571,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922775.1,CP094098,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1573286,38.86407,1607,1466,gastric biopsy,,2021-09-19,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9108,Helicobacter pylori Hpfe080,Hpfe080,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675570,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922915.1,"CP094099,CP094100",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1566531,38.86173,1586,1455,gastric biopsy,,2021-09-18,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9109,Helicobacter pylori Hpfe079,Hpfe079,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675569,210,,,,MLST.Helicobacter_pylori.2158,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922955.1,CP094101,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1622213,38.67821,1673,1511,gastric biopsy,,2021-09-17,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9110,Helicobacter pylori Hpfe077,Hpfe077,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675567,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922995.1,"CP094103,CP094104",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1634695,38.68887,1672,1526,gastric biopsy,,2021-09-07,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9111,Helicobacter pylori Hpfe078,Hpfe078,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675568,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022922975.1,CP094102,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1609466,38.692337,1643,1500,gastric biopsy,,2021-09-16,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9112,Helicobacter pylori Hpfe076,Hpfe076,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675566,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923015.1,CP094105,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1573039,38.843346,1571,1450,gastric biopsy,,2021-09-07,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9113,Helicobacter pylori Hpfe075,Hpfe075,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675565,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923035.1,CP094106,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1652404,38.654167,1665,1528,gastric biopsy,,2021-08-30,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9114,Helicobacter pylori Hpfe074,Hpfe074,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675564,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923055.1,CP094107,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1602783,38.732815,1629,1482,gastric biopsy,,2021-08-30,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9115,Helicobacter pylori Hpfe073,Hpfe073,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675563,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923075.1,CP094108,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1607927,38.70493,1637,1503,gastric biopsy,,2021-08-27,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9116,Helicobacter pylori Hpfe071,Hpfe071,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675561,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923115.1,CP094110,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1618643,38.65596,1624,1499,gastric biopsy,,2021-08-16,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9117,Helicobacter pylori Hpfe072,Hpfe072,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675562,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923095.1,CP094109,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1610658,38.735287,1617,1477,gastric biopsy,,2021-08-19,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9118,Helicobacter pylori Hpfe070,Hpfe070,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675560,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923135.1,"CP094111,CP094112",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1583533,38.798748,1584,1480,gastric biopsy,,2021-08-15,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9119,Helicobacter pylori Hpfe069,Hpfe069,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675559,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923155.1,"CP094113,CP094114",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1583621,38.799244,1583,1479,gastric biopsy,,2021-08-05,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9120,Helicobacter pylori Hpfe068,Hpfe068,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675558,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923275.1,CP094115,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1566753,38.90122,1562,1449,gastric biopsy,,2021-08-05,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9121,Helicobacter pylori Hpfe066,Hpfe066,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675556,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923395.1,CP094116,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1586299,38.83177,1617,1486,gastric biopsy,,2021-08-04,China,China: Hengyang,,,,Duodenal ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Duodenal ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9122,Helicobacter pylori Hpfe065,Hpfe065,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675555,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923515.1,"CP094117,CP094118",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1575278,38.866283,1585,1459,gastric biopsy,,2021-08-03,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9123,Helicobacter pylori Hpfe064,Hpfe064,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675554,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923555.1,CP094119,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1615760,38.67808,1656,1503,gastric biopsy,,2021-08-02,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9124,Helicobacter pylori Hpfe063,Hpfe063,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675553,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923575.1,"CP094175,CP094176",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1608340,38.70239,1633,1504,gastric biopsy,,2021-08-02,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9125,Helicobacter pylori Hpfe062,Hpfe062,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675552,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923595.1,CP094177,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1560534,38.880344,1589,1460,gastric biopsy,,2021-07-28,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9126,Helicobacter pylori Hpfe059,Hpfe059,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675549,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923655.1,CP094121,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1588133,38.859215,1607,1472,gastric biopsy,,2021-07-22,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9127,Helicobacter pylori Hpfe061,Hpfe061,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675551,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923615.1,CP094120,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1613185,38.7242,1615,1502,gastric biopsy,,2021-07-28,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9128,Helicobacter pylori Hpfe058,Hpfe058,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675548,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923675.1,"CP094122,CP094123",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1625426,38.672325,1645,1526,gastric biopsy,,2021-07-13,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9129,Helicobacter pylori Hpfe060,Hpfe060,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675550,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923635.1,CP094178,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1576166,38.826176,1619,1490,gastric biopsy,,2021-07-22,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9130,Helicobacter pylori Hpfe056,Hpfe056,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675546,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923775.1,"CP094126,CP094127",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1659860,38.605667,1682,1544,gastric biopsy,,2021-07-05,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9131,Helicobacter pylori Hpfe057,Hpfe057,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675547,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923695.1,"CP094124,CP094125",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1580664,38.772945,1615,1478,gastric biopsy,,2021-07-05,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9132,Helicobacter pylori Hpfe055,Hpfe055,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675545,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022923915.1,CP094128,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1572908,38.861523,1587,1467,gastric biopsy,,2021-07-01,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9133,Helicobacter pylori Hpfe054,Hpfe054,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675544,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924035.1,CP094129,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1563078,38.91879,1564,1463,gastric biopsy,,2021-06-24,China,China: Hengyang,,,,Atrophic gastic,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastic,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,210.9134,Helicobacter pylori Hpfe053,Hpfe053,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675543,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924175.1,CP094130,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1617070,38.745445,1681,1518,gastric biopsy,,2021-06-22,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9135,Helicobacter pylori Hpfe052,Hpfe052,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675542,210,,,,MLST.Helicobacter_pylori.2152,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924275.1,CP094131,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1560058,38.901566,1562,1447,gastric biopsy,,2021-04-26,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9136,Helicobacter pylori Hpfe051,Hpfe051,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675541,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924355.1,CP094132,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1616176,38.717564,1630,1506,gastric biopsy,,2021-04-25,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9137,Helicobacter pylori Hpfe049,Hpfe049,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675540,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924375.1,CP094133,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1613080,38.671547,1634,1503,gastric biopsy,,2021-04-23,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9138,Helicobacter pylori Hpfe048,Hpfe048,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675539,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924395.1,CP094134,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1613194,38.742767,1623,1500,gastric biopsy,,2021-04-23,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9139,Helicobacter pylori Hpfe040,Hpfe040,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675538,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924415.1,CP094135,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1566721,38.845524,1577,1472,gastric biopsy,,2021-04-23,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9140,Helicobacter pylori Hpfe039,Hpfe039,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675537,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924435.1,CP094136,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1626226,38.67359,1650,1510,gastric biopsy,,2021-04-23,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9141,Helicobacter pylori Hpfe038,Hpfe038,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675536,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924455.1,CP094137,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1576312,38.935566,1604,1475,gastric biopsy,,2021-04-20,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9142,Helicobacter pylori Hpfe037,Hpfe037,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675535,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924475.1,CP094138,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1596715,38.7892,1615,1486,gastric biopsy,,2021-04-20,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9143,Helicobacter pylori Hpfe036,Hpfe036,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675534,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924495.1,CP094139,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1561930,38.89739,1569,1463,gastric biopsy,,2021-04-15,China,China: Hengyang,,,,Duodenal ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Duodenal ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9144,Helicobacter pylori Hpfe035,Hpfe035,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675533,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924515.1,"CP094140,CP094141",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1597939,38.72601,1612,1477,gastric biopsy,,2021-04-15,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9145,Helicobacter pylori Hpfe033,Hpfe033,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675532,210,,,,MLST.Helicobacter_pylori.2271,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924535.1,CP094142,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1559352,38.92553,1578,1459,gastric biopsy,,2021-04-15,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9146,Helicobacter pylori Hpfe032,Hpfe032,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675531,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924555.1,CP094143,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1626209,38.673565,1637,1491,gastric biopsy,,2021-04-01,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9147,Helicobacter pylori Hpfe029,Hpfe029,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675530,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924575.1,CP094144,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1569933,38.82172,1600,1465,gastric biopsy,,2021-04-01,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9148,Helicobacter pylori Hpfe028,Hpfe028,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675529,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924655.1,"CP094145,CP094146",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1568827,38.839973,1560,1449,gastric biopsy,,2021-04-01,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9149,Helicobacter pylori Hpfe024,Hpfe024,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675527,210,,,,MLST.Helicobacter_pylori.75,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924875.1,CP094148,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1595545,38.74325,1620,1491,gastric biopsy,,2021-03-09,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9150,Helicobacter pylori Hpfe022,Hpfe022,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675525,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925175.1,CP094150,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1617425,38.68309,1635,1496,gastric biopsy,,2021-01-26,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9151,Helicobacter pylori Hpfe027,Hpfe027,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675528,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924735.1,CP094147,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1581642,38.81523,1610,1470,gastric biopsy,,2021-03-15,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9152,Helicobacter pylori Hpfe023,Hpfe023,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675526,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022924995.1,CP094149,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1608056,38.719982,1620,1497,gastric biopsy,,2021-01-26,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9153,Helicobacter pylori Hpfe019,Hpfe019,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675524,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925215.1,"CP094151,CP094152",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1662094,38.561596,1683,1534,gastric biopsy,,2021-01-26,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9154,Helicobacter pylori Hpfe010,Hpfe010,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675523,210,,,,MLST.Helicobacter_pylori.2103,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925255.1,"CP094153,CP094154,CP094155",,,illumina,100x,Unicycler v. 0.4.8,1,2,3,1586095,38.768547,1625,1494,gastric biopsy,,2021-01-26,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9155,Helicobacter pylori Hpfe0016,Hpfe0016,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675518,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925575.1,CP094160,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1564699,38.888695,1591,1469,gastric biopsy,,2021-01-04,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9156,Helicobacter pylori Hpfe005,Hpfe005,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675521,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925275.1,CP094156,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1595694,38.78933,1603,1488,gastric biopsy,,2021-01-11,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9157,Helicobacter pylori Hpfe0020,Hpfe0020,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675519,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925415.1,CP094159,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1576980,38.8237,1589,1465,gastric biopsy,,2021-01-04,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9158,Helicobacter pylori Hpfe0021,Hpfe0021,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675520,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925295.1,"CP094157,CP094158",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1620723,38.867035,1609,1496,gastric biopsy,,2021-01-11,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9159,Helicobacter pylori Hpfe0013,Hpfe0013,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675516,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925755.1,CP094163,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1613739,38.700497,1646,1509,gastric biopsy,,2020-12-29,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9160,Helicobacter pylori Hpfe0015,Hpfe0015,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675517,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925675.1,"CP094161,CP094162",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1569162,38.881264,1590,1455,gastric biopsy,,2021-01-04,China,China: Hengyang,,,,Gastric ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Gastric ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9161,Helicobacter pylori Hpfe0011,Hpfe0011,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675514,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925795.1,"CP094165,CP094166",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1628951,38.672558,1653,1518,gastric biopsy,,2020-12-10,China,China: Hengyang,,,,Duodenal ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Duodenal ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9162,Helicobacter pylori Hpfe0012,Hpfe0012,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675515,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925775.1,CP094164,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1627796,38.696003,1646,1508,gastric biopsy,,2020-12-29,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9163,Helicobacter pylori Hpfe0008,Hpfe0008,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675513,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925815.1,CP094179,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1607782,38.722336,1619,1490,gastric biopsy,,2020-12-10,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9164,Helicobacter pylori Hpfe0006,Hpfe0006,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675511,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925855.1,"CP094168,CP094169",,,illumina,100x,Unicycler v. 0.4.8,1,1,2,1563148,38.864265,1592,1452,gastric biopsy,,2020-12-02,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9165,Helicobacter pylori Hpfe0007,Hpfe0007,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675512,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925835.1,CP094167,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1562288,38.925537,1578,1460,gastric biopsy,,2020-12-02,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9166,Helicobacter pylori Hpfe0004,Hpfe0004,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675510,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925875.1,CP094170,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1560176,38.88869,1578,1446,gastric biopsy,,2020-11-30,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9167,Helicobacter pylori Hpfe0003,Hpfe0003,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675509,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925905.1,CP094171,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1564612,38.852634,1560,1454,gastric biopsy,,2020-11-16,China,China: Hengyang,,,,Compound ulcer,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Compound ulcer,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9168,Helicobacter pylori Hpfe0002,Hpfe0002,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675508,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925925.1,CP094172,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1615483,38.724083,1634,1499,gastric biopsy,,2020-09-19,China,China: Hengyang,,,,Atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,210.9169,Helicobacter pylori Hpfe0001,Hpfe0001,Helicobacter pylori,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN26675507,210,,,,,,,,2022-04-12T00:00:00Z,,PRJNA816422,GCA_022925945.1,CP094173,,,illumina,100x,Unicycler v. 0.4.8,1,0,1,1649959,38.579563,1676,1545,gastric biopsy,,2020-09-11,China,China: Hengyang,,,,Non-atrophic gastritis,,,,,,,,,,,,,,collected_by:Hu Limiao,,,,,,,Non-atrophic gastritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Other,Gastrointestinal Diseases-Gastritis and Ulcers HP,2104.162,Mycoplasma pneumoniae strain S63-tet-R,S63-tet-R,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN06699082,2104,,,,MLST.Mycoplasma_pneumoniae.1,,,,2017-04-13T00:00:00Z,,PRJNA382063,GCA_002090215.1,CP020689,,Affiliated Hospital of Academy of Military Medical Science,Illumina MiSeq,40.0x,Newbler v. 2.9,1,,1,816435,40.01,794,749,throat swab,,2016-07,China,China: Beijing,,,,pneumoniae,,,,,,,,,,,,,mycoplasma pneumoniae with tetracylcine-resistance developed in vitro,collected_by:affliated hospital of accademy of military medical science,,,,,,,pneumoniae,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,2104.189,Mycoplasma pneumoniae strain KCH-402,KCH-402,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMD00044317,2104,,,,MLST.Mycoplasma_pneumoniae.2,,,,2017-07-28T00:00:00Z,28619800,PRJDB4434,GCA_002355695.1,AP017318,,National Institute of Infectious Diseases,Illumina HiSeq 4000; ABI 3130xl,2285x,CLC Genomics Workbench v. 8.0.2,1,,1,817074,39.98,785,735,throat swab,,2012-10-22,Japan,Japan,env_biome:human body,,,,,,,,,,,,,,,,"Mycoplasma pneumoniae is one of the simplest self-replicating bacteria known and is an etiological agent of pneumoniae and bronchitis in humans. M. pneumoniae strains can be classified into two distinct lineages (subtype 1 and 2) based on their p1 gene sequence that encode a major cytadhesin protein of this bacterium. The reference strains, M129-B7 (GenBank: CP003913) and FH (GenBank: CP010546) carry subtype 1 and 2 p1 genes, respectively. In addition, several variants of p1 gene sequences are also known. The strain 309 (GenBank: AP012303) carries variant 2a (subtype 2 variant) p1 gene sequence. In this study, we have sequenced complete genome of M. pneumoniae KCH-402 strain that has variant 2b p1 gene.",,human body,respratory tract,throat swab,missing,Genome sequencing of Mycoplasma pneumoniae KCH-402,,,Pneumonia,,,,,,,,,human body,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,2104.190,Mycoplasma pneumoniae strain KCH-405,KCH-405,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMD00044318,2104,,,,MLST.Mycoplasma_pneumoniae.14,,,,2017-07-28T00:00:00Z,28619800,PRJDB4435,GCA_002355715.1,AP017319,,"Department of Bacteriology II, National Institute of Infectious Diseases",Illumina HiSeq 4000; ABI 3130xl,2169x,CLC Genomics Workbench v. 8.0.2,1,,1,817099,39.97,792,742,throat swab,,2012-10-22,Japan,Japan,env_biome:human body,,,,,,,,,,,,,,,,"Mycoplasma pneumoniae is one of the simplest self-replicating bacteria known and is an etiological agent of pneumoniae and bronchitis in humans. M. pneumoniae strains can be classified into two distinct lineages (subtype 1 and 2) based on their p1 gene sequence that encode a major cytadhesin protein of this bacterium. The reference strains, M129-B7 (GenBank: CP003913) and FH (GenBank: CP010546) carry subtype 1 and 2 p1 genes, respectively. In addition, several variants of p1 gene sequences are also known. The strain 309 (GenBank: AP012303) carries variant 2a (subtype 2 variant) p1 gene sequence. In this study, we have sequenced complete genome of M. pneumoniae KCH-405 strain that has variant 2c p1 gene.",,human body,respratory tract,throat swab,missing,Genome sequencing of Mycoplasma pneumoniae KCH-405,,,Pneumonia,,,,,,,,,human body,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,2104.435,Mycoplasma pneumoniae strain 16-734,16-734,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472224,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939745.1,CP039761,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,818445,39.968353,793,744,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.436,Mycoplasma pneumoniae strain 16-710,16-710,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472223,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939765.1,CP039762,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816537,40.00529,783,742,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.437,Mycoplasma pneumoniae strain 16-462,16-462,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472222,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939785.1,CP039763,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816525,40.00453,785,740,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.46,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.438,Mycoplasma pneumoniae strain 16-032,16-032,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472220,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939825.1,CP039765,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816471,40.0035,783,740,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.46,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.439,Mycoplasma pneumoniae strain 16-118,16-118,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472221,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939805.1,CP039764,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816467,40.00321,785,740,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.46,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.440,Mycoplasma pneumoniae strain 16-004,16-004,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472219,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939845.1,CP039766,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816561,40.00595,786,742,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.441,Mycoplasma pneumoniae strain 16-002,16-002,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472218,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009939975.1,CP039767,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816530,40.008083,784,741,nasophraynx,,2016,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.25,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.442,Mycoplasma pneumoniae strain 15-982,15-982,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472217,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009940325.1,CP039768,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816495,40.003307,780,743,nasophraynx,,2015,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.443,Mycoplasma pneumoniae strain 15-969,15-969,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472216,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009940965.1,CP039769,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816389,40.001884,790,743,nasophraynx,,2015,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.444,Mycoplasma pneumoniae strain 15-885,15-885,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472215,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009941325.1,CP039770,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816420,40.00086,785,743,nasophraynx,,2015,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.445,Mycoplasma pneumoniae strain 15-215,15-215,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472214,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009941705.1,CP039771,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816388,40.001934,786,740,nasophraynx,,2015,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.446,Mycoplasma pneumoniae strain 14-637,14-637,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472213,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009942155.1,CP039772,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,818560,39.972145,800,746,nasophraynx,,2014,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.447,Mycoplasma pneumoniae strain 12-060,12-060,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472211,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009942655.1,CP039774,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816506,40.003014,785,739,nasophraynx,,2012,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.448,Mycoplasma pneumoniae strain 11-1384,11-1384,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472210,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009942915.1,CP039775,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,818669,39.97171,798,746,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.449,Mycoplasma pneumoniae strain 12-091,12-091,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472212,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009942395.1,CP039773,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816510,40.004898,788,744,nasophraynx,,2012,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.450,Mycoplasma pneumoniae strain 11-994,11-994,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472209,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009943205.1,CP039776,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816304,40.005196,786,741,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.451,Mycoplasma pneumoniae strain 11-634,11-634,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472207,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009943805.1,CP039778,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816551,40.00497,784,740,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.452,Mycoplasma pneumoniae strain 11-949,11-949,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472208,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009943505.1,CP039777,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,817102,39.976036,793,741,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.453,Mycoplasma pneumoniae strain 11-473,11-473,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472206,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009944075.1,CP039779,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816518,40.00524,787,741,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.454,Mycoplasma pneumoniae strain 11-212,11-212,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472205,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009944335.1,CP039780,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816503,40.004875,787,739,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.46,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.455,Mycoplasma pneumoniae strain 11-174,11-174,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472204,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009944725.1,CP039781,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,815686,39.98708,785,739,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.456,Mycoplasma pneumoniae strain 11-129,11-129,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472203,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009945165.1,CP039782,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816432,40.007862,786,741,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.25,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.457,Mycoplasma pneumoniae strain 11-107,11-107,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472202,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009945535.1,CP039783,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816346,40.00473,782,741,nasophraynx,,2011,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.25,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.458,Mycoplasma pneumoniae strain 10-1385,10-1385,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472201,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009945865.1,CP039784,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,817191,39.98086,789,741,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.459,Mycoplasma pneumoniae strain 10-1257,10-1257,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472200,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009946285.1,CP039785,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816333,40.004265,786,739,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.5,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.460,Mycoplasma pneumoniae strain 10-1213,10-1213,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472199,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009946845.1,CP039786,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816521,40.005096,782,740,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.25,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.461,Mycoplasma pneumoniae strain 10-1110,10-1110,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472198,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009947205.1,CP039787,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816522,40.010067,786,742,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,98.46,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.462,Mycoplasma pneumoniae strain 10-1059,10-1059,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472197,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009947575.1,CP039788,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816681,40.00999,785,741,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.463,Mycoplasma pneumoniae strain 10-1048,10-1048,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472196,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009947985.1,CP039789,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816465,40.006615,786,740,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.22,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,2104.464,Mycoplasma pneumoniae strain 10-980,10-980,Mycoplasmoides pneumoniae,Mycoplasmoides,Metamycoplasmataceae,Mycoplasmoidales,-,Mycoplasmatota,SAMN11472195,2104,,,,,,,,2020-01-29T00:00:00Z,31783732,PRJNA533936,GCA_009948395.1,CP039790,,Chungbuk National University Hospital,Illumina MiSeq,1x,SPAdes v. 3.13.0,1,0,1,816424,40.00997,786,742,nasophraynx,,2010,South Korea,South Korea: Seoul,,,,Pneumonia,,,,,,,,,,,,,30 Korean Mycoplasma pneumoniae,collected_by:Eun Hwa Choi,,,,,,,Pneumonia,,,,,,,,,,,,,,99.25,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,211880.19,Leptospira interrogans serovar Canicola strain 611,611,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN12871448,211880,Canicola,,,"MLST.Leptospira_spp_2.3,MLST.Leptospira_spp_3.34,MLST.Leptospira_spp.37",,,,2019-10-07T00:00:00Z,,PRJNA574874,GCA_008831465.1,"CP044513,CP044514,CP044515,CP044516",,Chinese National Human Genome Center at Shanghai,PacBio RSII,100.0x,HGAP v. 3.0,2,2,4,4755342,35.02219,4654,,,,1950-01-01,China,China:JiangXi,,,,Leptospirosis,,,,,,,,,,,,,We sequenced the genome of Leptospira interrogans serogroup Canicola vaccine strain and circulating isolate,collected_by:YH XU,,,,,,,Leptospirosis,,,,,,,,,,,,,,96.47,0,Specific Bacterial Infections,Leptospirosis,Other,Specific Bacterial Infections-Leptospirosis HP,2126982.6,Escherichia coli O18:H1 strain CFSAN067215,CFSAN067215,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08737532,2126982,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,,,2019-04-11T00:00:00Z,,PRJNA230969,GCA_004771135.1,"CP028320,CP028321,CP028322,CP028323",,FDA/CFSAN,PacBio,405.0x,HGAP v. 3.0,1,3,4,5242835,50.63415,5484,5362,missing,,2000,USA,USA:CA,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,collected_by:Dudley Lab/Penn State,,,,,,,missing,,,,,,,,,,,,,,99.97,0.06,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,213.51,Helicobacter cinaedi strain MRY08-1234,MRY08-1234,Helicobacter cinaedi,Helicobacter,Helicobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMD00047012,213,,,,MLST.Helicobacter_cinaedi.10,,,,2017-11-23T00:00:00Z,,PRJDB4571,GCA_003574195.1,AP017374,,National Institute of Infectious Diseases,PacBio RSII; Illumina Miseq,32x; 127x,DDBJ Read Annotation Pipeline v. 2.2.0;,1,,1,2199263,38.22826,2361,2361,"human blood, which caused nosocomial infection","isolated from human blood, which caused nosocomial infection in a hospital in Japan",2008,Japan,Japan,,,,,,,,,,,,,,,,,"Complete genome sequence of Helicobacter cinaedi MRY08-1234 isolated from human blood, which caused nosocomial infection in a hospital in Japan.",,missing,missing,missing,missing,Helicobacter cinaedi MRY08-1234 genome sequencing project,,,,,,,,,,,,missing,,,,100,1.6,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2130.41,Ureaplasma urealyticum strain 315,315,Ureaplasma urealyticum,Ureaplasma,Mycoplasmataceae,Mycoplasmatales,Mollicutes,Mycoplasmatota,SAMN10716289,2130,,,,,,,,2019-07-09T00:00:00Z,,PRJNA513930,GCA_006777105.1,CP039963,,"Sir Run Run Shaw Hospital, Zhejiang University School of Medicine",Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.7,1,,1,853955,25.740232,679,660,male semen,,2016-06,China,China,,,,infertility,,,,,,,,,,,,,A clinical Ureaplasma urealyticum isolated from infertile male,collected_by:Department of Clinical Laboratory Sir Run Run Shaw Hospital Zhejiang University School of Medicine,,,,,,,infertility,,,,,,,,,,,,,,99.05,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2130.45,Ureaplasma urealyticum UU_WJSL,UU_WJSL,Ureaplasma urealyticum,Ureaplasma,Mycoplasmataceae,Mycoplasmatales,Mollicutes,Mycoplasmatota,SAMN16253843,2130,,,,,,,,2022-03-28T00:00:00Z,,PRJNA665455,GCA_022700735.1,CP062067,,,Illumina NextSeq; Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.8,1,0,1,827615,25.79569,652,640,cerebrospinal fluid,,2020-01-05,China,China: Hangzhou,,,,Intracranial infection,,,,,,,,,,,,,,collected_by:Long Sun,,,,,,,Intracranial infection,,,,,,,,,,,,,,97,2.5,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- NHP,214851.67,Subdoligranulum variabile strain DSM 15176,DSM 15176,Subdoligranulum variabile,Subdoligranulum,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222717,214851,,,,,,DSM:15176,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025152575.1,CP102293,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3244954,57.91478,3185,2999,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,97.96,0,,,Other,- HP,216804.7,Salmonella enterica subsp. enterica serovar Liverpool Liv11,Liv11,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21399560,216804,Liverpool,,,MLST.Salmonella_enterica.1959,,,,2022-10-17T00:00:00Z,36095868,PRJNA762632,GCA_025723045.1,CP083758,,,Oxford Nanopore,40x,SPAdes v. 3.12.0,1,0,1,4802405,52.262444,4744,,egg farm cage shed,,2019-07-19,Australia,Australia,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:CSIRO,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases NHP,216816.1974,Bifidobacterium longum strain 51A,51A,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN08457432,216816,,,,,,,,2019-04-30T00:00:00Z,,PRJNA432691,GCA_004936435.1,CP026999,,UFMG,Illumina HiSeq,1239.0x,SPAdes v. 3.6,1,,1,2365873,60.1616,2020,1814,fecal sample,isolated in 1899 and exhibits some probiotic characteristics such as immunomodulation and fighting intestinal infections,2017,Brazil,Brazil,,,,,,,,,,,,,,,,,"The genus Bifidobacterium is represented by gram positive and anaerobic bacteria that normally colonize the human gastrointestinal tract (GIT), with some species also being found in the oral and vaginal cavities. The B. longum species is commonly associated with the maintenance of homeostasis in the GIT aiding in the digestion of food. It was first isolated in 1899 and exhibits some probiotic characteristics such as immunomodulation and fighting intestinal infections.",,,,,Missing,,,,,,,,,,,,,,,,,100,0.46,,,Gastrointestinal,- NHP,216816.2033,Bifidobacterium longum strain BAMA-B05,BAMA-B05,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN12569298,216816,,,,,,,,2019-08-26T00:00:00Z,,PRJNA560141,GCA_008086305.1,CP043002,,Haerbin Meihua Biotechnology,Illumina HiSeq,200.0x,SOAPdenovo v. 2.04,1,,1,2268110,59.883163,1955,,feces of healthy centenarian,,2010-10,China,China: guangxi province,,,,,,,,,,,,,,,,,The complete genome sequence of Bifidobacterium longum B05,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,216816.2087,Bifidobacterium longum strain LTBL16,LTBL16,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN10473362,216816,,,,,,,,2019-12-04T00:00:00Z,,PRJNA506747,GCA_009728915.1,CP034089,,GuangXi University,Illumina HiSeq; Oxford Nanopore MiniION,279.0x,Unicycler v. 0.4.6,1,0,1,2430682,60.26757,2091,,feces,,2013-05,China,China: GuangXi,,,,,,,,,,,,,,,,,Complete genome sequence of Bifidobacterium longum LTBL16 from healthy centenarians,,Gut microbiota,Healthy centenarians,feces,anaerobic culture,,,,,,,,,,,,,Gut microbiota,,,,100,0.23,,,Gastrointestinal,- NHP,216816.2457,Bifidobacterium longum strain NBRC 114370,NBRC 114370,Bifidobacterium longum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21163585,216816,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181415.1,"CP084012,CP084013",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,297.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,1,2,2594022,60.13723,2320,2200,human feces,,2019,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,221027.35,Treponema putidum OMZ 847,OMZ 847,Treponema putidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253851,221027,,,,,,,,2022-07-25T00:00:00Z,,PRJNA284866,GCA_024400855.1,CP038802,,,Oxford Nanopore MiniION and illumina,1278x,"Celera Assembler v. Canu 1.8,",1,0,1,2951713,37.18888,2890,2765,subgingival plaque,,2000-06,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,221027.36,Treponema putidum OMZ 846,OMZ 846,Treponema putidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253850,221027,,,,,,,,2022-07-25T00:00:00Z,,PRJNA284866,GCA_024401005.1,CP038803,,,Oxford Nanopore MiniION and illumina,845x,"Celera Assembler v. Canu 1.8,",1,0,1,2915271,37.17346,2984,2736,subgingival plaque,,1998-05,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,221027.37,Treponema putidum OMZ 835,OMZ 835,Treponema putidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253849,221027,,,,,,,,2022-07-25T00:00:00Z,,PRJNA284866,GCA_024401155.1,CP038804,,,Oxford Nanopore MiniION and illumina,469x,"Celera Assembler v. Canu 1.8,",1,0,1,2762635,37.28477,2687,2563,subgingival plaque,,1998-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,221027.38,Treponema putidum OMZ 758,OMZ 758,Treponema putidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN02980915,221027,,,,,,ATCC:700334,,2014-10-30T00:00:00Z,25342686,PRJNA257943,GCA_000755145.1,"CP009228,CP009229",,,454,54x,454 Newbler v. 2.7,1,1,2,2800562,37.294254,2773,2225,periodontitis lesion,,1993,Switzerland,Switzerland,,,,periodontitis,,,,,,,,,,,,,,collected_by:C. Wyss,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,222805.80,Mycobacterium chimaera strain AUSMDU00007395,AUSMDU00007395,Mycobacterium intracellulare,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13191638,222805,,,,,mlst:ST81,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664715.1,"CP045963,CP045964,CP045965,CP045966,CP045967,CP045968",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,154x,de novo,1,5,6,6384143,67.500854,6243,5915,missing,,2016,Australia,Australia,,,,,,,,,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.94,1.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,224729.58,Salmonella enterica subsp. enterica serovar Java strain P7704,P7704,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16674985,224729,Java,,,MLST.Salmonella_enterica.86,,,,2021-07-07T00:00:00Z,,PRJNA674772,GCA_019163295.1,"CP065185,CP065186,CP065187,CP065188",,IHU Mediterranee Infection,Illumina MiSeq; Oxford Nanopore MinION,27.0x,SPAdes v. 3.12.0,1,3,4,4772484,52.183945,4821,4510,blood,,2019,France,France,,,,bacteremia,,,,,,,,,,,,,oxa-48 producing Salmonella paratyphi B variant Java,collected_by:IHU Mediterranee infection,,,,,,,bacteremia,,,,,,,,,,,,,,99.95,0.33,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia NHP,2259134.3,Sutterella sp. 6FBBBH3,6FBBBH3,Sutterella megalosphaeroides,Sutterella,Sutterellaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMD00129657,2494234,,,,,,JCM:32470,,2018-10-10T00:00:00Z,,PRJDB7182,GCA_003609995.1,AP018786,,"Microbe Division/ Japan Collection of Microorganisms, RIKEN BioResource Research Center",PacBio RSII,Unknown,HGAP v. 3.0,1,,1,2725161,62.83915,2363,2113,fecal sample of a healthy japanese man,isolated from a fecal sample of a healthy Japanese man,2017-02-28,,,,,,,,,,,,,,,,,,,"Strain 6FBBBH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative cocci, was isolated from a fecal sample of a healthy Japanese man. Strain 6FBBBH3 was affiliated to the genus Sutterella, with highest similarity to S. stercoricanis CCUG 47620T (97.1 %), followed by S. parvirubra YIT 11816T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). We analyzed the draft genome sequence of strain 6FBBBH3.",,not applicable,not applicable,not applicable,missing,Complete genome sequence of Sutterella megasphaeroides,,,,,,,,,,,,not applicable,,,,96.27,0.62,,,Gastrointestinal,- HP,225992.5,Comamonas kerstersii strain 8943,8943,Comamonas kerstersii,Comamonas,Comamonadaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06562982,225992,,,,,,,,2017-03-21T00:00:00Z,,PRJNA378865,GCA_002056725.1,CP020121,,Zhejiang University,PacBio,672.0x,SmrtPipe v. 1.87,1,,1,3547915,59.63,3461,3233,,,2014,China,China:Hangzhou,,,,,,,,,,,,,,,,,We describe the first whole genome sequencing (WGS) of Comamonas kerstersii to offer enhanced resolution for precise diagnosis of infectious diseases.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,2.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,226665.7,Rickettsia conorii subsp. heilongjiangensis B8,B8,Rickettsia conorii,Rickettsia,Rickettsiaceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN31806548,226665,,,,,,,,2022-11-27T00:00:00Z,,PRJNA903496,,CP112971,,,Illumina,6.0x,SPAdes v. 3.12.0,1,0,1,1275045,32.35815,1589,1396,serum,,2020-09-12,China,"China: Hanshan county, Anhui province",,,,rickettsiosis,,,,,,,,,,,,,,collected_by:Yan Liu,,,,,,,rickettsiosis,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2339227.6,"Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) strain 14-SA00836-0",14-SA00836-0,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15099378,2339227,"61:k:1,5,(7)",,,MLST.Salmonella_enterica.432,,,,2020-06-11T00:00:00Z,,PRJNA637259,GCA_013328855.1,"CP054422,CP054423",,The German Federal Institute for Risk Assessment (BfR),Illumina NextSeq; Oxford Nanopore MiniION,100.0x,Unicycler v. v0.4.4,1,1,2,4875020,51.406372,4937,4535,urine,isolated from human urine,2012,Germany,Germany,,,,urinary tract infection,,,,,,,,,,,,,"Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) is a serovar commonly associated with sheep. Occasionally, the serovar has been found to also infect humans. Here, we report the complete genome sequence of strain 14-SA00836-0, isolated from human urine.",collected_by:Robert Koch Institute,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0.6,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,235.183,Brucella abortus strain IVRI/95,IVRI/95,Brucella abortus,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN10484931,235,,,,MLST.Brucella_spp.1,,,,2019-01-05T00:00:00Z,,PRJNA507115,GCA_003994435.1,"CP034695,CP034696",,IVRI,Illumina,99.0x,Edena v. 3.13; CLC Genomics workbench v.,2,,2,3295536,57.24654,3493,3307,blood,,1995,India,"India: Bijapur, Karnataka",,,,Brucellosis,,,,,,,,,,,,,"Brucella abortus is a Gram-negative bacteria in the family Brucellaceae and is one of the causative agents of brucellosis. It causes abortions in cattle and undulantfever, endocarditis, arthritis and osteomyelitis in humans.",collected_by:B G Mantur,,,,,,,Brucellosis,,,,,,,,,,,,,,99.5,0.76,Specific Bacterial Infections,Brucellosis,Blood and Circulatory System,Specific Bacterial Infections-Brucellosis NHP,2364647.33,Kalamiella piersonii GABEKP28,GABEKP28,Kalamiella piersonii,Kalamiella,Erwiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30885900,2364647,,,,,,,,2023-01-04T00:00:00Z,36586465,PRJNA881082,,"CP104758,CP104759,CP104760,CP104761",,,Oxford Nanopore MinION; MGI tech,219.0x,Unicycler v. 0.5.0,1,3,4,4762926,57.17647,4638,4364,unstimulated saliva,,2022-05-09,Ireland,Ireland: Galway,,,,,,,,,,,,,,,,,,sample_type:Cell culture;collected_by:University of Galway,Salivary microbiome,,,,,,,,,,,,,,,,Salivary microbiome,,,,100,0.3,,,Genitourinary,- HP,2364647.34,Kalamiella piersonii URMC-2103A041,URMC-2103A041,Kalamiella piersonii,Kalamiella,Erwiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32512754,2364647,,,,,,,,2023-01-19T00:00:00Z,,PRJNA916888,,"CP115895,CP115899,CP115898,CP115897,CP115896",,,Illumina MiSeq; Oxford Nanopore MinION,58.0x,SPAdes v. v3.13.0; Unicycler v. v05.50,1,4,5,4990348,57.023056,4907,4616,blood,,2021-03,USA,USA: New York,,,,Bacteremia,,,Susceptible;Resistant,AMR Panel,,,,,,,,,,collected_by:UR Medicine Labs,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,2382163.3,Streptococcus sp. JS71 strain KCOM 2890 (=JS71),KCOM 2890 (=JS71),Streptococcus koreensis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10135881,2382163,,,,,,KCOM:2890,,2018-10-07T00:00:00Z,,PRJNA493533,GCA_003627135.1,CP032620,,Korean Collection for Oral Microbiology,PacBio; Illumina HiSeq,1260.0x,RS HGAP v. 3.0; SPAdes v. 3.8.2,1,,1,2009598,42.0814,1994,1942,subgingival plaque,,2014-11-29,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Streptococcus sp. KCOM 2890 (=JS71),collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,99.83,0.18,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases NHP,239935.2075,Akkermansia muciniphila strain H2,H2,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMN03278370,239935,,,,,,,,2019-01-22T00:00:00Z,,PRJNA270907,GCA_004101765.1,CP010553,,Wageningen UR,PAcBio RS2 & Illumina MiSeq,100X,PacBio HGAP SMRT v. 2.2 and Ray assembler,1,,1,2819944,55.31832,2789,2043,feces,,2010-11-12,Belgium,Belgium: Ghent,temperature:37,male,32,,,host_subject_id:#2,,,,,,,,,,,Akkermansia muciniphila isolation and genome sequencing,,,,,15388697,,,,healthy,,,,,,,,symbiont,enviromental material,,,,97.05,0.68,,,Gastrointestinal,- NHP,239935.2189,Akkermansia muciniphila strain JCM 30893,JCM 30893,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMD00192834,239935,,,,,,JCM:30893,,2019-11-29T00:00:00Z,,PRJDB8988,GCA_009731575.1,"AP021898,AP021899",,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,402x,Unicycler v. 0.4.6,1,1,2,2878459,55.637306,2821,2375,human feces,,,Japan,Japan,,,,,,,,,,,,,,,,,The complete genome sequence of Akkermansia muciniphila JCM30893 with its novel phage or prophage which isolated from healthy Japanese feces,,missing,missing,missing,missing,A_muchiniphila_JCM30893,,,,,,,,,,,,missing,,,,97.96,0.68,,,Gastrointestinal,- NHP,239935.2356,Akkermansia muciniphila strain KGMB01990,KGMB01990,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMN18309826,239935,,,,,,,,2021-03-23T00:00:00Z,,PRJDB7416,GCA_017570505.1,CP071886,,"Korean Collection for Type Culture, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology",PacBio RSII,344.0x,HGAP v. 3,1,0,1,2844062,55.23009,2811,2327,feces,,2017-05-18,South Korea,"South Korea:Gyeonggi-do, Seongnam-si",,,,,,,,,,,,,,,,,"The human gastrointestinal tract (GIT) contains a diverse microbial community such as bacteria, archaea and eukarya. Therefore, we will development the standard bank and support of Korean gut microbiome.",,human,gut,feces,TSA supplemented with blood,,,,,,,,,,,,,human,,,,97.96,0,,,Gastrointestinal,- NHP,239935.2357,Akkermansia muciniphila strain KGMB02009,KGMB02009,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMN18309827,239935,,,,,,,,2021-03-23T00:00:00Z,,PRJDB7416,GCA_017570425.1,CP071885,,"Korean Collection for Type Culture, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology",PacBio RSII,317.0x,HGAP v. 3,1,0,1,2844059,55.23008,2803,2331,feces,,2017-05-18,South Korea,"South Korea:Gyeonggi-do, Seongnam-si",,,,,,,,,,,,,,,,,"The human gastrointestinal tract (GIT) contains a diverse microbial community such as bacteria, archaea and eukarya. Therefore, we will development the standard bank and support of Korean gut microbiome.",,human,gut,feces,TSA supplemented with blood,,,,,,,,,,,,,human,,,,97.96,0,,,Gastrointestinal,- NHP,239935.2358,Akkermansia muciniphila strain KGMB01988,KGMB01988,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMN18309824,239935,,,,,,,,2021-03-23T00:00:00Z,,PRJDB7416,GCA_017570525.1,CP071888,,"Korean Collection for Type Culture, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology",PacBio RSII,318.0x,HGAP v. 3,1,0,1,2844056,55.229923,2798,2329,feces,,2017-05-18,South Korea,"South Korea:Gyeonggi-do, Seongnam-si",,,,,,,,,,,,,,,,,"The human gastrointestinal tract (GIT) contains a diverse microbial community such as bacteria, archaea and eukarya. Therefore, we will development the standard bank and support of Korean gut microbiome.",,human,gut,feces,TSA supplemented with blood,,,,,,,,,,,,,human,,,,97.96,0,,,Gastrointestinal,- NHP,239935.2359,Akkermansia muciniphila strain KGMB01989,KGMB01989,Akkermansia muciniphila,Akkermansia,Akkermansiaceae,Verrucomicrobiales,Verrucomicrobiae,Verrucomicrobiota,SAMN18309825,239935,,,,,,,,2021-03-23T00:00:00Z,,PRJDB7416,GCA_017570485.1,CP071887,,"Korean Collection for Type Culture, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology",PacBio RSII,321.0x,HGAP v. 3,1,0,1,2844036,55.230034,2791,2328,feces,,2017-05-18,South Korea,"South Korea:Gyeonggi-do, Seongnam-si",,,,,,,,,,,,,,,,,"The human gastrointestinal tract (GIT) contains a diverse microbial community such as bacteria, archaea and eukarya. Therefore, we will development the standard bank and support of Korean gut microbiome.",,human,gut,feces,TSA supplemented with blood,,,,,,,,,,,,,human,,,,97.96,0,,,Gastrointestinal,- HP,244319.350,Escherichia coli O26:H11 strain FWSEC0001,FWSEC0001,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768102,244319,O26:H11,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037725.2,NELP00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,66.48x;325.05x,Unicycler;Canu v. 0.4.4.0;1.7,1,3,4,5803315,50.620842,6391,6195,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2002,Canada,"Canada:British Columbia,Vancouver",,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.97,0.38,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,244366.382,Klebsiella variicola strain AJ055,AJ055,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128435,244366,,,,MLST.Klebsiella_pneumoniae.695,,102.100.100.25725,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622585.1,"LR130539,LR130540",,Bioplatforms Australia,,,,1,1,2,5669009,57.235188,5488,,urine,,2001-12-05,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,244366.383,Klebsiella variicola strain AJ292,AJ292,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128436,244366,,,,,,102.100.100.25727,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622595.1,LR130538,,Bioplatforms Australia,,,,1,,1,5445132,57.621487,5211,,blood,,2002-10-23,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,0.95,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,244366.384,Klebsiella variicola strain 04153260899A,04153260899A,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128440,244366,,,,MLST.Klebsiella_pneumoniae.355,,102.100.100.25730,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622615.1,LR130543,,Bioplatforms Australia,,,,1,,1,5368944,57.54482,5148,,,,,,,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,244366.385,Klebsiella variicola strain 03-311-0071,03-311-0071,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128439,244366,,,,,,102.100.100.25729,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622625.1,LR130544,,Bioplatforms Australia,,,,1,,1,5425242,57.636066,5166,,,,,,,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,244366.569,Klebsiella variicola strain KPN029,KPN029,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16685814,244366,,,,MLST.Klebsiella_pneumoniae.347,,,,2020-11-29T00:00:00Z,,PRJNA674961,GCA_015694045.1,"CP065162,CP065163,CP065164,CP065165,CP065166",,Monash University,Oxford Nanopore MinION,101x,Unicycler v. 0.4.7,1,4,5,6187617,56.521355,6286,5994,urine,,2017-03-28,Australia,Australia: Melbourne,,,,urinary tract infection,,,,,,,,,,,,,"Whole-genome sequencing of Klebsiella pneumoniae species complex isolates collected from hospital patients in Melbourne, Australia.","collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,99.85,0.96,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,244366.656,Klebsiella variicola strain JNQH579,JNQH579,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20064304,244366,,,,MLST.Klebsiella_pneumoniae.2013,,,,2021-07-15T00:00:00Z,,PRJNA702614,GCA_019222805.1,"CP078146,CP078147,CP078148",,The First Affiliated Hospital of Shandong First Medical University,IonTorrent,129.0x,Flye v. 2.8.3,1,2,3,6149961,56.655514,6215,5865,sputum,isolated from China,2021-03-21,China,China: Shandong,,,,pneumoniae,,,,,,,,,,,,,"The studies are aimed at determining the characteristics of epidemiology, antimicrobial resistance and pathogenicity for carbapenem resistant enterobacteriaceae, especially for strains isolated from China.",collected_by:Mingju Hao,,,,,,,pneumoniae,,,,,,,,,,,,,,100,1.51,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia NHP,246787.511,Bacteroides cellulosilyticus strain CL06T03C01,CL06T03C01,Bacteroides cellulosilyticus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451184,246787,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292125.1,"CP072251,CP072252,CP072253",,Brigham & Women's Hospital,PacBio Sequel,171x,FALCON-Unzip v. 1.2.0,1,2,3,7271073,42.829292,5952,5516,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.07,0,,,Gastrointestinal,- HP,246787.523,Bacteroides cellulosilyticus strain BFG-250,BFG-250,Bacteroides cellulosilyticus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546934,246787,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091405.1,CP081903,,National Institute of Allergy and Infectious Disease,PacBio Sequel,267x,Canu v. v. 1.6,1,0,1,6935738,43.22454,5655,5226,biopsy,,1987,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.25,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2489010.4,Klebsiella africana strain 200023,200023,Klebsiella africana,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024779,2489010,,,,,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020526085.1,"CP084874,CP084875",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5443802,56.696957,5334,5120,feces,,2016,,Senegal,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,99.82,0.48,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,2490633.3,Streptococcus sp. KCOM 2412,KCOM 2412,Streptococcus periodonticum,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN10465145,2490633,,,,,,KCOM:2412,,2018-12-23T00:00:00Z,,PRJNA506614,GCA_003963555.1,CP034543,,Korean Collection for Oral Microbiology,Illumina HiSeq; PacBio,1538.3x,SPAdes v. 3.8.2; RS HGAP Assembly v. v3.0,1,,1,1903815,38.94848,1893,1797,subgingival dental plaque,,2003-02-13,South Korea,South Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Streptococcus sp. KCOM 2412 (=ChDC F135),collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,99.88,0.71,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,2494701.30,Enterobacter chengduensis WCHECl-C4 = WCHECh050004,WCHECl-C4 = WCHECh050004,Enterobacter chengduensis,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06249239,2494701,,,,MLST.Enterobacter_cloacae.414,,,,2019-09-03T00:00:00Z,30302649,PRJNA415108,GCA_001984825.2,MTSO00000000,,,Illumina HiSeq; Oxford Nanopore MiniION,200.0x,Unicycler v. 0.4.7,1,1,2,5218125,55.736935,5144,4929,blood,,2015-02-01,China,"China: Chengdu, Sichuan",,,,"liver cirrhosis, cholecystitis",,,,,,,,,,,,,,collected_by:WCH,,,,,,,"liver cirrhosis, cholecystitis",,,,,,,,,,,,,,99.8,0.2,Urinary Tract Diseases,Lower UTI,Blood and Circulatory System,Urinary Tract Diseases-Lower UTI HP,2497989.77,Candidatus Ornithobacterium hominis MSHR-COH1,MSHR-COH1,Candidatus Ornithobacterium hominis,Ornithobacterium,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA113386633,2497989,,,,,,ATCC:ATCC:TSD-185,,2023-05-10T00:00:00Z,,PRJEB61795,,OX579588,,,,,,1,0,1,2036909,35.72359,1953,1873,nasopharynx,,2009,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,250.33,Chryseobacterium gleum strain 110146,110146,Chryseobacterium gleum,Chryseobacterium,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN08972773,250,,,,,,,,2019-03-06T00:00:00Z,,PRJNA451538,GCA_004328965.1,CP031676,,"The First Affiliated Hospital of Medical College, Zhejiang University",PacBio RSII,246.0x,Celera Assembler v. PBcR-MHAP,1,,1,4715692,36.93691,4359,4175,sputum,,2012-11-05,China,China: Quanzhou,,male,63,pulmonary infection,,,,,,,,,,,,,We performed genomic sequencing and comparative genomic analysis of Chryseobacterium gleum to clarify the bacteria resistance and pathogenicity mechanisms with aim to promote the development of better management strategy.,collected_by:Desong Ming,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,2508289.5,Pandoraea commovens LB-19-202-79,LB-19-202-79,Pandoraea commovens,Pandoraea,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN30015177,2508289,,,,,,,,2022-08-16T00:00:00Z,,PRJNA849608,GCA_024704525.1,"CP102780,CP102779",,,Oxford Nanopore GridION; Illumina MiSeq,80.0x,Flye v. 2.9; Racon v. 1.4.20; Medaka v.,1,1,2,6056872,62.665516,5549,5292,tracheobronchial secretion,,2019-08-09,Germany,Germany: Berlin,,,,"Infection, Burkholderia",,,,,,,,,,,,,,collected_by:Labor Berlin - Charite Vivantes GmbH,,,,,,,"Infection, Burkholderia",,,,,,,,,,,,,,98.4,3.9,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,2561898.4,Campylobacter sp. CGEMS strain 19S00001,19S00001,Candidatus Campylobacter infans,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN14120449,2561898,,,,,,,,2020-07-15T00:00:00Z,,PRJNA607035,GCA_013416015.1,"CP049075,CP049076",,Utrecht University,Illumina NextSeq; Oxford Nanopore MiniION,100.0x,SPAdes v. 3.10.1; Unicycler v. 0.4.7,1,1,2,1760367,35.85542,1875,1673,feces,,2019-01-20,Netherlands,Netherlands: Utrecht,,male,,gastroenteritis,,,,,,,,,,,,,Full genome candidates campylobacter infans,"collected_by:Jaap Wagenaar, Birgitta Duim",,,,,,,gastroenteritis,,,,,,,,,,,,,,98.46,0.12,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2572075.3,Campylobacter sp. CFSAN093257,CFSAN093257,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487379,197,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012889875.1,CP040616,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",76x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1720666,30.4689,1817,1754,,,2018-01-03,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.38,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2582419.3,Dialister sp. 5BBH33,5BBH33,Dialister hominis,Dialister,Veillonellaceae,Veillonellales,Negativicutes,Bacillota,SAMD00172296,2582419,,,,,,JCM:33369,,2019-07-11T00:00:00Z,,PRJDB8335,GCA_007164725.1,AP019697,,National Institute of Genetics,PacBio Sequel,1681x,HGAP v. 4,1,,1,2407548,48.175903,2353,2191,fecal sample of a healthy japanese,isolated from a fecal sample of a healthy Japanese,2016-12-05,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of Dialister sp. strain 5BBH33 isolated from a fecal sample of a healthy Japanese.,biomaterial_provider:JCM 33369,human-associated habitat,Intestinal,feces,not applicable,Complete genome sequencing of Dialister sp. strain 5BBH33,,,healthy,,,,,,,,,human-associated habitat,,,,98.1,0.02,,,Gastrointestinal,- NHP,2583452.3,Absiella sp. 9CBEGH2,9CBEGH2,Amedibacterium intestinale,Amedibacterium,Erysipelotrichaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMD00172920,2583452,,,,,,,,2020-01-28T00:00:00Z,,PRJDB8364,GCA_010537335.1,AP019711,,National Institute of Genetics,PacBio Sequel,1279x,HGAP v. 4,1,0,1,2488096,33.93,2473,2414,fecal sample of a healthy japanese,isolated from a fecal sample of a healthy Japanese,2018-02-09,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of Absiella sp. strain 9CBEGH2 isolated from a fecal sample of a healthy Japanese.,,human-associated habitat,Intestinal,feces,not applicable,Complete genome sequencing of Absiella sp. strain 9CBEGH2,,,,,,,,,,,,human-associated habitat,,,,100,0,,,Gastrointestinal,- NHP,2584944.3,Sutterella sp. KGMB03119,KGMB03119,Sutterella faecalis,Sutterella,Sutterellaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11897248,2584944,,,,,,,,2019-06-13T00:00:00Z,,PRJNA545582,GCA_006337085.1,CP040882,,korea research institute of bioscience and biotechnology,PacBio Sequel,133.0x,HGAP v. 4.0,1,,1,2987884,58.298916,2666,2415,feces,,2017-09-01,South Korea,South Korea,,,,,,,,,,,,,,,,,Korean gut microbiome bank,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,2585117.3,Alistipes sp. 3BBH6,3BBH6,Alistipes onderdonkii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166230,2585117,,,,,,JCM:32839,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542645.1,AP019734,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,550x,Unicycler v. 0.4.6,1,,1,3507492,58.002785,3161,2923,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,99.28,0.64,,,Gastrointestinal,- NHP,2585118.3,Alistipes sp. 5CBH24,5CBH24,Alistipes communis,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166231,2585118,,,,,,JCM:32850,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542665.1,AP019735,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,450x,Unicycler v. 0.4.6,1,,1,3301347,58.46044,3064,2675,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,100,0.48,,,Gastrointestinal,- NHP,2585119.3,Alistipes sp. 5CPEGH6,5CPEGH6,Alistipes dispar,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166232,2585119,,,,,,JCM:32848,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542685.1,AP019736,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,800x,Unicycler v. 0.4.6,1,,1,2962376,61.291985,2645,2414,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,99.52,0.48,,,Gastrointestinal,- NHP,2585754.3,Alistipes sp. 5CPYCFAH4,5CPYCFAH4,Alistipes onderdonkii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166233,2585117,,,,,,JCM:32845,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542705.1,AP019737,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,900x,Unicycler v. 0.4.6,1,,1,3312673,57.974148,3026,2791,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,98.8,0.48,,,Gastrointestinal,- NHP,2585755.3,Alistipes sp. 5NYCFAH2,5NYCFAH2,Alistipes onderdonkii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166234,2585117,,,,,,JCM:32847,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542725.1,AP019738,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,470x,Unicycler v. 0.4.6,1,,1,3312682,57.974205,3034,2794,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,98.8,0.48,,,Gastrointestinal,- NHP,2585756.3,Alistipes sp. 6CPBBH3,6CPBBH3,Alistipes communis,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00166235,2585118,,,,,,JCM:32851,,2019-06-15T00:00:00Z,,PRJDB8150,GCA_006542745.1,AP019739,,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,500x,Unicycler v. 0.4.6,1,,1,3302129,58.37219,3126,2755,feces,,2018-09-27,Japan,Japan,,,,,,,,,,,,,,,,,"The complete genome of 6 Alistipes sp. strains (3BBH6, 5CBH24, 5CPEGH6, 5CPYCFAH4, 5NYCFA2, 6CPBBH3) which from healthy Japanese",,missing,missing,feces,missing,missing,,,,,,,,,,,,missing,,,,100,0.48,,,Gastrointestinal,- HP,2590157.11,Klebsiella variicola subsp. variicola strain 01A065,01A065,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024812,2590157,,,,,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525605.1,CP084766,,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,0,1,5467687,57.56573,5332,5162,blood,,1997,,Austria,,,,,,,,,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2590157.28,Klebsiella variicola subsp. variicola KPN692,KPN692,Klebsiella variicola,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286210,2590157,,,,MLST.Klebsiella_pneumoniae.1737,,,,2021-12-19T00:00:00Z,,PRJNA674961,GCA_021228835.1,"CP089385,CP089386,CP089387,CP089388,CP089389,CP089390",,,Illumina HiSeq; Oxford Nanopore MinION,5x,Unicycler v. v0.4.8,1,5,6,5811039,57.261086,5720,5484,blood,,2018-03-26,Australia,Australia: Melbourne,,,,blood infection,,,,,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,blood infection,,,,,,,,,,,,,,100,0.87,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,2592065.4,Escherichia coli O1:H42 strain CLSC36,CLSC36,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12158196,2592065,O1:H42,,UPEC,MLST.Escherichia_coli_1.648,,,,2019-07-09T00:00:00Z,,PRJNA551561,GCA_006777045.1,"CP041300,CP041299",,McGill University,PacBio,138.0x,HGAP v. May-2015; Celera Assembler v.,1,1,2,5278774,50.42186,5293,4992,urine from healthy adult with cystitis,,2005-09-26,Canada,Canada: Montreal,,,,cystitis,,,,,,,,,,,,,This strain was sequenced as part of a study that investigated the activity of the outer membrane protease OmpT among uropathogenic Escherichia coli clinical isolates. Healthy adult with cystitis,collected_by:Student health services McGill University,,,,,,,cystitis,,,,,UPEC,,,,,,,,,99.97,0.36,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,2598458.3,Cohnella sp. KS 22,KS 22,Cohnella cholangitidis,Cohnella,Paenibacillaceae,Bacillales,Bacilli,Bacillota,SAMN12340927,2598458,,,,,,,,2020-08-07T00:00:00Z,,PRJNA556120,GCA_014107495.1,CP041969,,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,240.0x,SPAdes v. 3.1,1,0,1,6408853,51.23641,6228,5772,blood,,2016-05,South Korea,South Korea,,,,cholangitis,,,,,,,,,,,,,A novel speices of the genus Cohnella,collected_by:Gyeongsang National University,,,,,,,cholangitis,,,,,,,,,,,,,,99.46,0.18,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,2599927.4,Francisella salimarina strain CHUGA-F75 strain Not applicable,Not applicable,Francisella salimarina,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN19689720,2599927,,,,,,,,2021-06-21T00:00:00Z,,PRJNA737314,GCA_018972105.1,CP076680,,CHU Grenoble Alpes,Illumina MiSeq; Oxford Nanopore MinION,1.0x,Unicycler v. january-2021,1,0,1,1940863,33.011913,1857,1838,blood,,2017-07-31,France,France,,,,bacteremia,,,,,,,,,,,,,We describe the first case of human infection caused by Francisella salimarina. This Francisella species was previously isoleted from seawater and fishes.,collected_by:CHU de Poitiers,,,,,,,bacteremia,,,,,,,,,,,,,,99.69,0.13,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,260678.68,Salmonella enterica subsp. enterica serovar Goldcoast 5ASAL05,5ASAL05,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24108481,260678,Goldcoast,,,MLST.Salmonella_enterica.358,,,,2022-01-10T00:00:00Z,,PRJNA478278,GCA_021397625.1,"CP090137,CP090138,CP090139,CP090140",,,Illumina MiSeq; Oxford Nanopore MinION,140.0x,unicycler v. 0.8.4,1,3,4,5008388,51.982994,5100,4738,stool,,2021-01-23,Taiwan,Taiwan: Taichung,,female,92,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Tungs' Taichung MetroHarbor Hospital (TTMHH),,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,260678.69,Salmonella enterica subsp. enterica serovar Goldcoast 5ASAL09,5ASAL09,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24108485,260678,Goldcoast,,,MLST.Salmonella_enterica.358,,,,2022-01-10T00:00:00Z,,PRJNA478278,GCA_021397645.1,"CP090141,CP090142,CP090144,CP090143",,,Illumina MiSeq; Oxford Nanopore MinION,319.0x,unicycler v. 0.8.4,1,3,4,4999641,51.98397,5091,4724,stool,,2021-01-24,Taiwan,Taiwan: Taichung,,female,90,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Tungs' Taichung MetroHarbor Hospital (TTMHH),,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,260678.7,Salmonella enterica subsp. enterica serovar Goldcoast strain Sal-5364,Sal-5364,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11353131,260678,Goldcoast,,,MLST.Salmonella_enterica.358,,,,2019-06-11T00:00:00Z,,PRJNA531216,GCA_006228345.1,"CP039169,CP039170",,Zhejiang University School of Medicine,Oxford Nanopore GridION,300.0x,Unicycler v. 0.4.7,1,1,2,4923922,51.981674,5047,4779,stool,,2018-06-03,Taiwan,Taiwan: Taoyuan,,,,gestroenteritis,,,,,,,,,,,,,to investigate multi-resistant Salmonella in Taiwan,collected_by:CGMH,,,,,,,gestroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,260678.70,Salmonella enterica subsp. enterica serovar Goldcoast 5ASAL07,5ASAL07,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24108483,260678,Goldcoast,,,MLST.Salmonella_enterica.358,,,,2022-01-10T00:00:00Z,,PRJNA478278,GCA_021397675.1,"CP090133,CP090134,CP090136,CP090135",,,Illumina MiSeq; Oxford Nanopore MinION,139.0x,Unicycler v. 0.4.8,1,3,4,4999530,51.984165,5092,4724,stool,,2021-01-24,Taiwan,Taiwan: Taichung,,male,84,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Tungs' Taichung MetroHarbor Hospital (TTMHH),,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2607663.3,Yersinia sp. NCTC 14382,NCTC 14382,Yersinia canariae,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12676035,2607663,,,,,,NCTC:14382,,2020-01-06T00:00:00Z,,PRJNA563543,GCA_009831415.1,CP043727,,University College Dublin,Oxford Nanopore MiniION; Illumina HiSeq,993.0x,Flye v. v2.5,1,0,1,4710154,47.173447,4564,4261,,,2018,United Kingdom,United Kingdom,,,,yersiniosis,,,,,,,,,,,,,Whole genome sequencing of Yersinia canariae,collected_by:PHE,,,,,,,yersiniosis,,,,,,,,,,,,,,99.84,0.1,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases NHP,261299.117,Intestinibacter bartlettii strain DSM 16795,DSM 16795,Intestinibacter bartlettii,Intestinibacter,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN20222675,261299,,,,,,DSM:16795,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148965.1,CP102273,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3006269,29.072348,2707,2664,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,263.138,Francisella tularensis strain Schu4 F. tul Mut-127,Schu4 F. tul Mut-127,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN04378279,263,,,,,,,,2017-01-05T00:00:00Z,,PRJNA307317,GCF_001936015.1,CP013853,,USAMRIID,PacBio,275,HGAP v. 2.1,,,1,1877932,32.31,2071,1793,,,2009-01-01,,,,,,Tularemia,,,,,,,,,C,,,,Ciprofloxacin resistant Schu4 F tularensis,collected_by:Henry S. Heine III Collection,,,,,,,Tularemia,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,263.679,Francisella tularensis strain 2017317779,2017317779,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737169,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019134735.1,CP073122,,USAMRIID,"PacBio, Illumina",200x,Unicycler v. 0.4.4,1,0,1,1885192,32.221756,2087,1842,lung tissue,,2017,USA,USA: MN,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:Minnesota Public Health,,,,,,,Tularemia,,,,,,,,,,,,,,99.62,0.27,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,263.681,Francisella tularensis strain 2014313438,2014313438,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737168,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019134755.1,CP073123,,USAMRIID,"PacBio, Illumina",200x,Unicycler v. 0.4.4,1,0,1,1890979,32.262653,2086,1842,broncheoalveolar lavage,,2014,USA,USA: IL,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:Minnesota Public Health,,,,,,,Tularemia,,,,,,,,,,,,,,99.62,0.27,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,263.682,Francisella tularensis strain 2015315990,2015315990,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737167,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019134815.1,CP073124,,USAMRIID,PacBio,200x,HGAP v. 4,1,0,1,1892232,32.28267,2154,1844,csf,,2015,USA,USA: MT,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:Minnesota Public Health,,,,,,,Tularemia,,,,,,,,,,,,,,99.19,0.1,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,263.683,Francisella tularensis strain COLL,COLL,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737165,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019134835.1,CP073126,,USAMRIID,PacBio,200x,HGAP v. 4,1,0,1,1892723,32.260822,2095,1848,digital ulcer,,1955,USA,USA: OH,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,,,,,,,,Tularemia,,,,,,,,,,,,,,99.21,0.27,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,263.684,Francisella tularensis strain Schu S4,Schu S4,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737163,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019137555.1,CP073128,,USAMRIID,"PacBio, Illumina",200x,Unicycler v. 0.4.4,1,0,1,1892599,32.260433,2083,1841,patient,,1951,USA,USA: MD,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:USAMRIID,,,,,,,Tularemia,,,,,,,,,,,,,,99.62,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,263.685,Francisella tularensis strain Schu S4_249,Schu S4_249,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737162,263,,,,,,,,2021-07-06T00:00:00Z,,PRJNA721727,GCA_019137575.1,CP073129,,USAMRIID,PacBio,200x,HGAP v. 4,1,0,1,1892778,32.259304,2085,1849,patient,,1951,USA,USA: MD,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,collected_by:USAMRIID,,,,,,,Tularemia,,,,,,,,,,,,,,99.62,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,263.687,Francisella tularensis strain Scherm,Scherm,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN18737164,263,,,,,,,,2021-07-07T00:00:00Z,,PRJNA721727,GCA_019182265.1,CP073127,,USAMRIID,PacBio,200x,HGAP v. 4,1,0,1,1857929,32.284443,2076,1827,digital lesion,,1944,USA,USA: OH,,,,Tularemia,,,,,,,,,,,,,Complete sequencing and characterization of 10 Francisella tularensis strains to be used for vaccine and treatment testing,,,,,,,,Tularemia,,,,,,,,,,,,,,99.51,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,264.23,Francisella tularensis subsp. novicida strain AZ06-7470,AZ06-7470,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN03107514,264,,,,,,,,2016-11-17T00:00:00Z,,PRJNA260086,GCF_001880245.1,"CP009682,CP009683","NZ_CP009682.1,NZ_CP009683.1",Los Alamos National Laboratory,Illumina; PacBio,366.7x; 338.9x,Velvet v. 1.2.08; IDBA-UD 1.1.0; Phrap v.,1,1,2,1925251,32.47,1853,1828,human clinical,,2006,USA,USA: AZ,,,,,,,,,Negative,Coccobacilli,No,,,Aerobic,,,Genome sequence assembly of Francisella novicida AZ06-7470,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,264.27,Francisella tularensis subsp. novicida strain TCH2015,TCH2015,Francisella tularensis,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN06481648,264,,,,,,,,2018-02-12T00:00:00Z,,PRJNA378245,GCA_002952075.1,CP021490,,BCM,PacBio,260.51x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2000087,32.354744,1932,1879,patient believed to have been infected in guatemala,isolated from the lymph node of a 6-year-old boy from Guatemala and isolated in Texas,2015-12,USA,"USA: Houston, TX",env_biome:lymph node,,6 years,,,,,,,,,,,,,,"TCH2015 was isolated from the lymph node of a 6-year-old boy from Guatemala and isolated in Texas. Source of infection is unknown, but may potentially have ben acquired from contaminated ocean, canal, or shower water.",,,,,https://lrn.hr.state.or.us/home/bt/docs/tularemia/levelaprocedures.pdf,,,,,,,,,,,,,lymph node,,,,100,0.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2666100.4,Neisseria brasiliensis strain N.177.16,N.177.16,Neisseria brasiliensis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13243042,2666100,,,,,genotype:Capsule group B,,,2019-11-19T00:00:00Z,,PRJNA588397,GCA_009671065.1,CP046027,,University of Pittsburgh,Oxford Nanopore MiniION,80x,SPAdes v. 3.6,1,0,1,2617510,49.228695,2828,2532,ulcer exudate,,2016-02,Brazil,Brazil: Parana State.,,female,74,Wound infection,,host_description:Leprosy (Hansen's disease);host_health_state:poor,,,,,,,,,,,Isolates from two human cases of Neisseria brasiliensis carrying N. meningitidis capsule genes,"collected_by:Claudio Sacchi Institute Adolfo Lutz, Brazil",,,,,,,Wound infection,poor,unknown,Leprosy (Hansen's disease),,,,,,,,,,,99.25,0.45,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,2666183.42,Pseudomonas juntendi PP_2463,PP_2463,Pseudomonas juntendi,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN24966705,2666183,,,,,,,,2022-01-24T00:00:00Z,,PRJNA796941,GCA_021560075.1,"CP091088,CP091089,CP091090",,,Illumina NovaSeq; Oxford Nanopore,100.0x,Unicycler v. 0.4.8,1,2,3,5630196,62.406548,5301,5129,urine,,2021-03-25,China,China: Sanmen,,,,Urinary tract infection,,,,,,,,,,,,,,collected_by:Danni Bao,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.61,1.27,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,2682456.3,Veillonella sp. T1-7,T1-7,Veillonella nakazawae,Veillonella,Veillonellaceae,Veillonellales,Negativicutes,Bacillota,SAMD00199103,2682456,,,,,,,,2020-06-26T00:00:00Z,,PRJDB3830,GCA_013393365.1,AP022321,,Health Sciences University of Hokkaido,Illumina MiSeq; GridION X5,250x,Unicycler v. 0.4.8,1,0,1,2097818,38.640198,1937,1925,,,2017-01-17,Japan,Japan:Hokkaido,,,,,,,,,Negative,Cocci,No,,,,,,It is already reported that Veillonella has important roles to form oral biofilms at early stage. The goal of this study is set as the development of novel method to control the biofilm formation at early stage to clarify the roles of Veillonella. Whole genome sequence has important parts of this project.,,not applicable,not applicable,not applicable,29458564,"Whole genome sequences of oral Veillonella, Analyzing roles of Veillonella in oral biofilm.",,,,,,,,,,,,not applicable,,,,99.8,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2697517.3,Escherichia coli O84:H7 strain Trh52,Trh52,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13782172,2697517,O84:H7,,EPEC/ExPEC,MLST.Escherichia_coli_1.28,genotype:ST28,,,2021-02-03T00:00:00Z,,PRJNA593384,GCA_016803935.1,"CP047600,CP047601",,Norwegian University of Life Sciences,Oxford Nanopore MiniION; Illumina MiSeq,27.7x,Unicycler v. 0.4.7.0,1,1,2,4926859,50.58391,4863,4617,feces,,2002,Norway,Norway: Trondelag,,,<5,Diarrhea,,,,,,,,,,,,,Sequencing of enteropathogenic Escherichia coli clinical isolates,"collected_by:Department of Medical Microbiology, St. Olavs Hospital",,,,,,,Diarrhea,,,,,EPEC/ExPEC,,,,,,,,,99.97,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2702.108,Gardnerella vaginalis strain GV37,GV37,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN06199463,2702,,,,,,,,2017-01-17T00:00:00Z,,PRJNA360037,GCF_001953155.1,CP019058,NZ_CP019058.1,"Institute of Biotechnology, Vilnius University",Illumina,116x,Meraculous2 v. 2.0.3,1,,1,1746718,41.76,1514,1416,blood culture,isolated from blood cultures of the patient,2011,France,France: Paris,,female,19,Gardnerella vaginalis bacteremia,,host_disease_outcome:recovery;host_health_state:bacteremia associated with severe acute encephalopathy,,,,,,,,,,,"The female patient experienced an episode of acute toxic-type encephalopathy associated with a concomitant Gardnerella vaginalis bacteremia, which was preceded by abnormal vaginal discharge. G.vaginalis was isolated from blood cultures of the patient. The isolate was susceptible to amoxicillin and amoxicillin clavuanate, therefore encephalopathy quickly resolved after initiation of adequate antibiotic treatment. The complete genome sequence of this highly virulent G.vaginalis isolate was performed.",collected_by:Jacques Tankovic,,,,,,,Gardnerella vaginalis bacteremia,bacteremia associated with severe acute encephalopathy,recovery,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia NHP,2702.157,Gardnerella vaginalis strain UGent 06.41,UGent 06.41,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN09373173,2702,,,,,,,,2018-07-09T00:00:00Z,,PRJNA474758,GCA_003293675.1,CP029984,,Ghent University,Illumina MiSeq,785x,SPAdes v. 3.11.1,1,,1,1563545,42.098274,1250,,vagina,,2008,Belgium,Belgium: Ghent,,,,commensal/bacterial vaginosis,,,,,,,,,,,,,"The goal of this study is to clarify the taxonomy of Gardnerella vaginalis, an important bacteria associated with bacterial vaginosis",collected_by:Mario Vaneechoutte,,,,,,,commensal/bacterial vaginosis,,,,,,,,,,,,,,100,0,,,Genitourinary,- HP,2702.434,Gardnerella vaginalis JNFY13,JNFY13,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246405,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277625.1,CP083172,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1682566,41.64205,1351,1294,vaginal secretion,,2019-05,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.435,Gardnerella vaginalis JNFY14,JNFY14,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246406,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277605.1,CP083171,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1680963,41.671173,1345,1285,vaginal secretion,,2019-05,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.436,Gardnerella vaginalis JNFY17,JNFY17,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246408,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277565.1,CP083169,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1595814,42.735683,1321,1226,vaginal secretion,,2019-06,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.438,Gardnerella vaginalis JNFY9,JNFY9,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246403,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277665.1,CP083174,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1640523,41.410942,1304,1237,vaginal secretion,,2019-04,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.439,Gardnerella vaginalis JNFY11,JNFY11,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246404,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277645.1,CP083173,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1743456,41.81895,1439,1349,vaginal secretion,,2019-04,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.440,Gardnerella vaginalis JNFY4,JNFY4,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246402,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277685.1,CP083175,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1742450,41.557175,1424,1356,vaginal secretion,,2019-03,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.7,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2702.441,Gardnerella vaginalis JNFY1,JNFY1,Gardnerella vaginalis,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246400,2702,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277725.1,CP083177,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1711437,41.611874,1398,1310,vaginal secretion,,2019-03,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0.9,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis NHP,2742601.6,Limosilactobacillus portuensis LV1276_C155,LV1276_C155,Limosilactobacillus portuensis,Limosilactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN33053616,2742601,,,,,,,,2023-02-13T00:00:00Z,,PRJNA930673,,"CP117296,CP117297",,,Illumina; Oxford Nanopore MinION,1x,unicycler v. v0.4.8,1,1,2,1990713,40.26653,1996,1934,urine,,2020-06-03,,not applicable,,,,,,,,,,,,,,,,,,,urogenital microbiome,urine sample,urine,CDC Anaerobe Blood Agar,,,,,,,,,,,,,urogenital microbiome,,,,99.7,0,,,Urinary Tract,- NHP,2751153.3,Coprobacter sp. 2CBH44,2CBH44,Coprobacter secundus,Coprobacter,Barnesiellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00236451,2751153,,,,,,,,2020-09-24T00:00:00Z,,PRJDB10247,GCA_015097275.1,AP023322,,National Institute of Genetics,PacBio Sequel,1076x,HGAP v. 4,1,0,1,4171466,38.438118,3543,3277,fecal sample of a healthy japanese,isolated from a fecal sample of a healthy Japanese,,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of Coprobacter sp. strain 2CBH44 isolated from a fecal sample of a healthy Japanese.,,human-associated habitat,Intestinal,feces,not applicable,Complete genome sequencing of Coprobacter sp. strain 2CBH44,,,,,,,,,,,,human-associated habitat,,,,99.5,0,,,Gastrointestinal,- NHP,2751154.3,Clostridia bacterium 12CBH8,12CBH8,Solibaculum mannosilyticum,Solibaculum,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMD00236452,2780922,,,,,,,,2020-10-21T00:00:00Z,,PRJDB10248,GCA_015140235.1,AP023321,,National Institute of Genetics,PacBio Sequel,1619x,HGAP v. 4,1,0,1,2541474,50.565067,2488,2286,fecal sample of a healthy japanese,isolated from a fecal sample of a healthy Japanese,,Japan,Japan,,,,,,,,,,,,,,,,,We report the complete genome sequence of unidentified Clostridia bacterium strain 12CBH8 isolated from a fecal sample of a healthy Japanese.,,human-associated habitat,Intestinal,feces,not applicable,Complete genome sequencing of unidentified Clostridia bacterium strain 12CBH8,,,,,,,,,,,,human-associated habitat,,,,97.32,0,,,Gastrointestinal,- NHP,2754044.3,Selenomonas sp. Marseille-Q3039,Marseille-Q3039,Selenomonas timonae,Selenomonas,Selenomonadaceae,Selenomonadales,Negativicutes,Bacillota,SAMN15581671,2754044,,,,,,,,2020-08-19T00:00:00Z,,PRJNA647307,GCA_014250475.1,CP060204,,IHU - Mediterranee Infection,Nanopore; Illumina,33.891x,SPAdes v. 3.10,1,0,1,2351879,57.177185,2247,2184,,,2020,France,France:Marseille,,,,,,,,,,,,,,,,,Selenomonas timonensis strain Marseille-Q3039 was isolated from a dental plaque as part of a culturomics study aiming at cultivating all the bacteria on human oral microbiota,sample_type:dental plaque,,,,,,,,,,,,,,,,,,,,,99.65,0.22,,,Other,- NHP,2754694.3,Chryseobacterium sp. Marseille-Q2069,Marseille-Q2069,Chryseobacterium manosquense,Chryseobacterium,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN15543002,2754694,,,,,,,,2020-09-16T00:00:00Z,,PRJNA646415,GCA_014623485.1,CP060203,,IHU - Mediterranee Infection,Nanopore; Illumina,61.0566x,SPAdes v. 3.10,1,0,1,2944264,36.921318,3006,2750,,,2019,France,France:Marseille,,,,,,,,,,,,,,,,,Chryseobacterium manosquense strain Marseille-Q2069 was isolated from a healthy skin swab as part of a cultuxromics study aiming at cultivating all the bacteria on human healthy skin,sample_type:skin swab,,,,,,,,,,,,,,,,,,,,,100,1.1,,,Other,- HP,2754725.3,Corynebacterium sp. Marseille-Q3630,Marseille-Q3630,Corynebacterium incognita,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15548381,2754725,,,,,,,,2020-08-17T00:00:00Z,,PRJNA646619,GCA_014217255.1,CP059404,,IHU - Mediterannee Infection,Illumina; Oxford Nanopore GridION,22.017x,SPAdes v. 3.10,1,0,1,2348705,62.435318,2167,2115,,,2020,France,France:Marseille,,,,,,,,,,,,,,,,,Corynebacterium incognita strain Marseille-Q3630 is a new bacteria isolated in IHU Mediteranee Infection,sample_type:organic fluid,,,,,,,,,,,,,,,,,,,,,97.8,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2755382.4,Nocardia huaxiensis BCHNH01,BCHNH01,Nocardia huaxiensis,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN23376436,2755382,,,,,,,,2021-12-05T00:00:00Z,,PRJNA778436,GCA_021044705.1,CP088007,,,Oxford Nanopore; Illumina NovaSeq,35.0x,unicycler v. 0.4.8,1,0,1,8314373,67.83689,7761,7520,eye,,2021-06-27,China,China,,,,endophthalmitis,,,,,,,,,,,,,,collected_by:Beijing Children Hospital,,,,,,,endophthalmitis,,,,,,,,,,,,,,99.94,2.01,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,2760407.3,"Salmonella enterica subsp. diarizonae serovar b,50:-:- strain XXB1403",XXB1403,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15683642,2760407,"b,50:-:-",,,MLST.Salmonella_enterica.430,,,,2020-08-10T00:00:00Z,,PRJNA649845,GCA_014123145.1,"CP059886,CP059887",,"Institute of Microbiology, Chinese Academy of Sciences",Illumina HiSeq; Oxford Nanopore GridION,312.0x,Unicycler v. March-2020,1,1,2,5196399,51.22349,5366,4868,urine sample,,2017-05-23,China,China:Shanghai,,male,,Urinary tract infection,,,,,,,,,,,,,Genome sequence of Salmonella enterica subsp. diarizonae XXB1403,collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.9,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases NHP,2787628.3,Treponema sp. RCC2812,RCC2812,Treponema peruense,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN16746786,2787628,,,,,,,,2020-12-18T00:00:00Z,,PRJNA676019,GCA_016117655.1,CP064936,,VIB-KU LEUVEN,PacBio Sequel,424.0x,SMRT portal v. Version 3.2.0,1,0,1,2738066,41.242615,2519,2438,feaces,,2015-06-11,Peru,Peru: Remoyacu,,,,,,,,,,,,,,,,,"This Treponema is the first commensal Treponema isolated from the human fecal flora, which may shed light on their impact on human health",,ENVO:00000109,village near amazon river,feaces,"Treponema peruensis sp. nov., a commensal spirochaete from human faeces",,,,,,,,,,,,,ENVO:00000109,,,,99.3,0,,,Other,- HP,2792977.4,Gardnerella piotii JNFY15,JNFY15,Gardnerella piotii,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246407,2792977,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277585.1,CP083170,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1541442,42.545616,1256,1164,vaginal secretion,,2019-06,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis HP,2792979.8,Gardnerella swidsinskii JNFY3,JNFY3,Gardnerella swidsinskii,Gardnerella,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN21246401,2792979,,,,,,,,2022-05-09T00:00:00Z,,PRJNA761238,GCA_023277705.1,CP083176,,,Oxford Nanopore PromethION,1x,Celera Assembler v. canu,1,0,1,1602355,42.01784,1332,1227,vaginal secretion,,2019-03,China,China: Shandong,,,,bacterial vaginosis,,,,,,,,,,,,,,collected_by:Kun Wang,,,,,,,bacterial vaginosis,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Bacterial Vaginosis,Genitourinary,Sexually Transmitted Infections (STIs)-Bacterial Vaginosis NHP,28025.127,Bifidobacterium animalis strain 01,01,Bifidobacterium animalis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN10817706,28025,,,,,,,,2019-02-04T00:00:00Z,,PRJNA516982,GCA_004135895.1,CP035497,,China Agricultural University,Illumina,311.0x,SOAPdenovo v. 2.04,1,,1,1931632,60.492992,1651,1583,feces,,,China,China: Guangxi,,,,,,,,,,,,,,,,,a probiotic bacterium with antioxidant activity,,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,28025.133,Bifidobacterium animalis strain B06,B06,Bifidobacterium animalis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN12569105,28025,,,,,,,,2019-08-21T00:00:00Z,,PRJNA560132,GCA_008041995.1,CP042940,,Haerbin Meihua Biotechnology,Illumina HiSeq,200.0x,SOAPdenovo v. 2.04,1,,1,1944145,60.489162,1662,1593,feces of healthy chinese centenarian,,2010-10,China,China: guangxi province,,,,,,,,,,,,,,,,,The complete genome sequence of Bifidobacterium animalis B06,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,28025.19,Bifidobacterium animalis strain BL3,BL3,Bifidobacterium animalis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN05631165,28025,,,,,,,,2017-07-18T00:00:00Z,28702200,PRJNA340074,GCA_002220485.1,CP017098,,Korea Food Research Institute,PacBio,322x,HGAP v. 3.0,1,,1,1944323,60.48,1651,1546,commercial dietary supplements,,2015-10-21,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,BL3 strain was isolated from Commercial dietary supplements,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.3,,,Other,- NHP,28026.1094,Bifidobacterium pseudocatenulatum strain YIT12820,YIT12820,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN20132667,28026,,,,,,,,2021-10-21T00:00:00Z,,PRJNA745059,GCA_020541825.1,CP079231,,Yakult Central Institute,Illumina MiSeq + Oxford Nanopore MiniION,287.87274435306864x,Unicycler v. 0.4.7,1,0,1,2303552,56.40437,1994,1856,fecal material [envo:00002003],,,,Japan,,,,,,,,,,,,,,,,,"Genomes of Bifidobacterium pseudocatenulatum, transcriptomes of B. pseudocatenulatum utilizing xylan-related carbohydrates, and 16S amplicon reads of feces from subjects in intervention trials of xylan-rich diets.",,bodily fluid material biome [ENVO:02000019],excreta material [ENVO:02000022],fecal material [ENVO:00002003],missing,,,,,,,,,,,,commensal,bodily fluid material biome [ENVO:02000019],,,,100,0.23,,,Gastrointestinal,- NHP,28026.1095,Bifidobacterium pseudocatenulatum strain YIT11956,YIT11956,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN20132666,28026,,,,,,,,2021-10-21T00:00:00Z,,PRJNA745059,GCA_020541865.1,CP079232,,Yakult Central Institute,Illumina MiSeq + Oxford Nanopore MiniION,549.7649242993981x,Unicycler v. 0.4.7,1,0,1,2373495,56.497864,2071,1911,fecal material [envo:00002003],,,,Japan,,,,,,,,,,,,,,,,,"Genomes of Bifidobacterium pseudocatenulatum, transcriptomes of B. pseudocatenulatum utilizing xylan-related carbohydrates, and 16S amplicon reads of feces from subjects in intervention trials of xylan-rich diets.",,bodily fluid material biome [ENVO:02000019],excreta material [ENVO:02000022],fecal material [ENVO:00002003],missing,,,,,,,,,,,,commensal,bodily fluid material biome [ENVO:02000019],,,,100,0.23,,,Gastrointestinal,- NHP,28026.1096,Bifidobacterium pseudocatenulatum strain YIT11952,YIT11952,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN20132664,28026,,,,,,,,2021-10-21T00:00:00Z,,PRJNA745059,GCA_020541905.1,CP079235,,Yakult Central Institute,Illumina MiSeq + PacBio RSII,411.5194597331471x,Unicycler v. 0.4.7,1,0,1,2316707,56.483837,1954,1806,fecal material [envo:00002003],,,,Japan,,,,,,,,,,,,,,,,,"Genomes of Bifidobacterium pseudocatenulatum, transcriptomes of B. pseudocatenulatum utilizing xylan-related carbohydrates, and 16S amplicon reads of feces from subjects in intervention trials of xylan-rich diets.",,bodily fluid material biome [ENVO:02000019],excreta material [ENVO:02000022],fecal material [ENVO:00002003],missing,,,,,,,,,,,,commensal,bodily fluid material biome [ENVO:02000019],,,,100,0.38,,,Gastrointestinal,- NHP,28026.1097,Bifidobacterium pseudocatenulatum strain YIT11953,YIT11953,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN20132665,28026,,,,,,,,2021-10-21T00:00:00Z,,PRJNA745059,GCA_020541885.1,"CP079233,CP079234",,Yakult Central Institute,Illumina MiSeq + PacBio RSII,196.8223093598884x,Unicycler v. 0.4.7,1,1,2,2245999,56.35768,1896,1773,fecal material [envo:00002003],,,,Japan,,,,,,,,,,,,,,,,,"Genomes of Bifidobacterium pseudocatenulatum, transcriptomes of B. pseudocatenulatum utilizing xylan-related carbohydrates, and 16S amplicon reads of feces from subjects in intervention trials of xylan-rich diets.",,bodily fluid material biome [ENVO:02000019],excreta material [ENVO:02000022],fecal material [ENVO:00002003],missing,,,,,,,,,,,,commensal,bodily fluid material biome [ENVO:02000019],,,,100,0.23,,,Gastrointestinal,- NHP,28026.1098,Bifidobacterium pseudocatenulatum strain YIT11027,YIT11027,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN20132663,28026,,,,,,,,2021-10-21T00:00:00Z,,PRJNA745059,GCA_020541925.1,CP079236,,Yakult Central Institute,Illumina MiSeq + Oxford Nanopore MiniION,442.96698121324664x,Unicycler v. 0.4.7,1,0,1,2556908,56.653545,2283,2125,fecal material [envo:00002003],,,,Japan,,,,,,,,,,,,,,,,,"Genomes of Bifidobacterium pseudocatenulatum, transcriptomes of B. pseudocatenulatum utilizing xylan-related carbohydrates, and 16S amplicon reads of feces from subjects in intervention trials of xylan-rich diets.",,bodily fluid material biome [ENVO:02000019],excreta material [ENVO:02000022],fecal material [ENVO:00002003],missing,,,,,,,,,,,,commensal,bodily fluid material biome [ENVO:02000019],,,,100,0.23,,,Gastrointestinal,- NHP,28026.1206,Bifidobacterium pseudocatenulatum JCLA3,JCLA3,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN24730997,28026,,,,,,,,2022-01-16T00:00:00Z,,PRJNA795522,GCA_021484885.1,CP090598,,,PacBio,535.0x,HGAP v. 4.0,1,0,1,2369863,56.60724,2060,1917,newborn[ncit_c16731],,2013-03-01,Mexico,Mexico,,,,,,,,,,,,,,,,,,,excreta material[ENVO_02000022],feces material[ENVO_00002003],Newborn[NCIT_C16731],"Fecal samples were collected from healthy breastfed infants of 2.5 months of age, born by natural birth.",,,,,,,,,,,,,excreta material[ENVO_02000022],,,,99.94,0.45,,,Other,- NHP,28026.1633,Bifidobacterium pseudocatenulatum Bi-OTA128,Bi-OTA128,Bifidobacterium pseudocatenulatum,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN26116972,28026,,,,,,,,2023-04-03T00:00:00Z,,PRJNA808866,,CP092470,,,PacBio,120.0x,HGAP v. 1.3,1,0,1,2296011,56.526165,1953,1812,feces from a 66-year-old healthy woman,,2021-08-01,China,China: Beijing,,,,,,,,,,,,,,,,,,sample_type:fecal sample,,,,,,,,,,,,,,,,,,,,,100,1.3,,,Gastrointestinal,- NHP,28035.168,Staphylococcus lugdunensis strain MBAZ2,MBAZ2,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15783914,28035,,,,,,,,2021-02-03T00:00:00Z,,PRJNA656409,GCA_016804245.1,CP060160,,The BioArte Limited,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Unicycler v. 2020,1,0,1,2606118,33.815468,2498,2425,skin,,2019,Malta,Malta,,,,,,,,,,,,,,,,,This isolate was obtained from the skin of a human healthy volunteer. The strain is capable of survival in 99% and 70% ethanol,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.61,0,,,Skin and Soft Tissue,- HP,28035.20,Staphylococcus lugdunensis strain FDAARGOS_222,FDAARGOS_222,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN04875559,28035,,,,MLST.Staphylococcus_lugdunensis.24,,FDA:FDAARGOS_222,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073395.2,CP020406,,US Food and Drug Administration,PacBio,15.748192964108x,HGAP v. 3,1,,1,2540253,33.85,2436,2335,axillary lymph node,,1988,France,France,,,,Soft tissue infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:USAMRIID,,,,,,,Soft tissue infection,Missing,Missing,Missing,Missing,,,,,,,,,,97.8,2.2,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,28035.271,Staphylococcus lugdunensis CGMH-SL131,CGMH-SL131,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN13870883,28035,,,,,,,,2022-05-19T00:00:00Z,,PRJNA589350,GCA_023508855.1,CP048007,,,PacBio,120X,HGAP v. v4,1,0,1,2646605,33.726868,2502,,blood,,2014-10-01,Taiwan,Taiwan,,,,catheter infection,,,,,,,,,,,,,,sample_type:cell culture,,,,,,,catheter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,28035.272,Staphylococcus lugdunensis CGMH-SL138,CGMH-SL138,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14009864,28035,,,,,,,,2022-05-19T00:00:00Z,,PRJNA589350,GCA_023508875.1,CP048713,,,PacBio,120X,HGAP v. v4,1,0,1,2625330,33.778343,2477,,blood infection,,2012-12-25,Taiwan,Taiwan,,,,,,,,,,,,,,,,,,sample_type:blood,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,28035.29,Staphylococcus lugdunensis strain FDAARGOS_377,FDAARGOS_377,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07312421,28035,,,,MLST.Staphylococcus_lugdunensis.3,,FDA:FDAARGOS_377,,2017-10-02T00:00:00Z,,PRJNA231221,GCA_002407165.1,CP023539,,US Food and Drug Administration,PacBio; Illumina,17.57x,Celera v. 8.2,1,,1,2571633,33.8,2451,2396,abscess,,2015-04-11,USA,USA:DC,,female,6Y,Abscess,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Abscess,Missing,Missing,Missing,Missing,,,,,,,,,,97.8,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,28035.30,Staphylococcus lugdunensis strain FDAARGOS_381,FDAARGOS_381,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07312425,28035,,,,MLST.Staphylococcus_lugdunensis.3,,FDA:FDAARGOS_381,,2017-10-18T00:00:00Z,,PRJNA231221,GCA_002591215.1,"CP023970,CP023971",,US Food and Drug Administration,PacBio; Illumina,18.69x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,2570702,33.81,2467,2399,abscess,,2015-04-23,USA,USA:DC,,male,6Y,Abscess,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Abscess,Missing,Missing,Missing,Missing,,,,,,,,,,97.8,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,28035.66,Staphylococcus lugdunensis strain SL29,SL29,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12283062,28035,,,,,genotype:ST1,,,2019-09-30T00:00:00Z,,PRJNA554757,GCA_008728715.1,CP041723,,EA2656 GRAM,Pacbio RS,367x,HGAP v. 2.3.0,1,,1,2660394,33.88314,2555,2488,vascular prosthesis infection,,,France,France: Rouen,,,,,,,,,,,,,,,,,Whole genome sequencing of 3 pathogenic and 3 carriage strains collected from 4 geographic origins in France and Sweden,sample_type:not collected,,,,,,,,,,,,,,,,,,,,,99.61,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28035.67,Staphylococcus lugdunensis strain SL55,SL55,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12283063,28035,,,,,genotype:ST10,,,2019-09-30T00:00:00Z,,PRJNA554757,GCA_008728735.1,CP041724,,EA2656 GRAM,Pacbio RS,272x,HGAP v. 2.3.0,1,,1,2624231,33.890232,2538,2450,skin and soft tissues infection,,,France,France: Nantes,,,,,,,,,,,,,,,,,Whole genome sequencing of 3 pathogenic and 3 carriage strains collected from 4 geographic origins in France and Sweden,sample_type:not collected,,,,,,,,,,,,,,,,,,,,,99.61,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,28035.71,Staphylococcus lugdunensis strain SL13,SL13,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN12283061,28035,,,,,genotype:ST6,,,2019-09-30T00:00:00Z,,PRJNA554757,GCA_008728815.1,CP041722,,EA2656 GRAM,Pacbio RS,336x,HGAP v. 2.3.0,1,,1,2694981,33.837273,2613,2533,infective endocarditis,,,France,France: Rouen,,,,,,,,,,,,,,,,,Whole genome sequencing of 3 pathogenic and 3 carriage strains collected from 4 geographic origins in France and Sweden,sample_type:not collected,,,,,,,,,,,,,,,,,,,,,99.61,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,28035.73,Staphylococcus lugdunensis strain APC 3758,APC 3758,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11338654,28035,,,,MLST.Staphylococcus_lugdunensis.38,,,,2020-01-27T00:00:00Z,,PRJNA521309,GCA_009931395.1,CP038807,,University College Cork,PacBio,398.0x,Flye v. 2.4.1,1,0,1,2570129,33.792,2472,2401,human milk,,2017-07-14,Ireland,Ireland: Cork,,,,,,,,,,,,,,,,,Mining for novel biological antimicrobials from human milk samples,"sample_type:human milk;biomaterial_provider:Colin Hill, APC Microbiome Ireland;collected_by:Angeliki Angelopoulou, APC Microbiome Ireland",,,,,,,,,,,,,,,,,,,,,99.04,0,,,Other,- HP,28035.86,Staphylococcus lugdunensis strain JICS135,JICS135,Staphylococcus lugdunensis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00184897,28035,,,,,,,,2020-02-05T00:00:00Z,,PRJDB8742,GCA_011403135.1,AP021848,,Department of Microbiology Juntendo University Graduate School of Medicine,PacBio RS II,433x,HGAP v. 2.0,1,0,1,2687768,33.72036,2542,2498,venous blood,isolated from blood culture,2014-01-15,Japan,"Japan:Kanagawa, Yokohama, Tsurumi-ku",,,77,"hepatitis C, chronic kidney disease",,,,,Positive,Cocci,No,Mesophilic,35,Facultative,HostAssociated,Bacteremia,Methicillin-resistant staphylococcus lugdunensis isolated from blood culture. This strain was subjected to complete genome sequencing.,biomaterial_provider:Department of Microbiology Juntendo University Graduate School of Medicine,No available,No available,No available,10.1128/CMR.00036-07,Complete genome sequence of a Methicillin-Resistant Staphylococcus lugdunensis strain,,,"hepatitis C, chronic kidney disease",,,,,,,,,No available,,,,99.61,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,28037.1359,Streptococcus mitis strain S022-V3-A4,S022-V3-A4,Streptococcus mitis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11382546,28037,,,,,,,,2020-06-09T00:00:00Z,,PRJNA208927,GCA_013305725.1,CP047883,,Universita' di Siena,Illumina; Oxford Nanopore,400.0x,Unicycler v. NOV-2018,1,0,1,2086958,39.748714,2015,1938,saliva,,2012,United Kingdom,United Kingdom,,,,,,,,,Positive,Cocci,No,,,,,,"Streptococcus mitis is a human commensal, a minocycline resistant isolate has been sequenced in order to characterize its mobile genetic elements",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.82,0.91,,,Oral,- HP,28037.1388,Streptococcus mitis strain Nm-65,Nm-65,Streptococcus mitis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMD00239187,28037,,,,,,,,2020-08-20T00:00:00Z,,PRJDB10372,GCA_014467095.1,AP023349,,"Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University",Roche 454; Nanopore MinION,300x,Unicycler v. 0.4.8; SPADdes v. 3.13.2,1,0,1,2085837,40.047234,2111,2039,the patient with kawasaki disease,isolated from the patient with Kawasaki disease,,,,,,,Kawasaki disease,,,,,,,,,,,,,This study is to reveal the complete genome sequence of Streptococcus mitis strain Nm-65 isolated from the patient with Kawasaki disease.,,not applicable,not applicable,not applicable,missing,Streptococcus mitis Nm-65 genome,,,,,,,,,,,,not applicable,,,,98.72,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,28037.1407,Streptococcus mitis strain S022-V7-A3,S022-V7-A3,Streptococcus mitis,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN17258151,28037,,,,,,,,2021-01-18T00:00:00Z,,PRJNA690734,GCA_016658865.1,CP067992,,University of Siena,Illumina HiSeq; Oxford Nanopore MinION,250.0x,Unicycler v. 0.4.7,1,0,1,2033396,40.235546,1980,1926,saliva,,2012,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Streptococcus mitis is a human commensal, a minocycline resistant isolate has been sequenced in order to characterize its mobile genetic elements",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.82,0.64,,,Oral,- HP,2810409.4,Escherichia coli H20 strain MIN6,MIN6,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17831481,2810409,H20,,,"MLST.Escherichia_coli_1.533,MLST.Escherichia_coli_2.310",genotype:ST-553,,,2021-03-23T00:00:00Z,,PRJNA700422,GCA_017570685.1,"CP069692,CP069693,CP069694,CP069696,CP069697,CP069698,CP069699,CP069700,CP069695",,Medical University of Bialystok,Illumina MiSeq; Oxford Nanopore MinION,446x,Unicycler hybrid assembly v. v0.4.8-beta,1,8,9,5186956,50.59108,5268,4909,wound,,2017-09-06,Poland,Poland: Bialystok,,,,,,,,,,,,,,,,,Genome and mobilome structures of extraintestinal E. coli strains isolated in Poland,,Human bedsore swab,end-stage renal disease,wound,37 degrees,,,,,,,,,,,,,Human bedsore swab,,,,99.93,0.17,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,28110.68,Francisella philomiragia strain 18844,18844,Francisella philomiragia,Francisella,Francisellaceae,Thiotrichales,Gammaproteobacteria,Pseudomonadota,SAMN16400346,28110,,,,,,,,2021-04-23T00:00:00Z,,PRJNA668170,GCA_018135955.1,"CP063138,CP063139",,University Hospital Muenster,PacBio Sequel,571.0x,HGAP v. SMRT Link V. 9,1,1,2,2017543,32.532986,1933,1901,soft tissue,"isolate from an infection with Francisella philomiragia, a rare opportunistic pathogen in patients with chronic granulomatous disease, that presented with axillar soft tissue infection, corresponding lymphadenitis and bipulmonary granuloma",2020,Germany,Germany,,,,soft tissue infection,,,,,,,,,,,,,"We sequenced the isolate from an infection with Francisella philomiragia, a rare opportunistic pathogen in patients with chronic granulomatous disease, that presented with axillar soft tissue infection, corresponding lymphadenitis and bipulmonary granuloma.","collected_by:Inst. Med. Microbiology, UKM",,,,,,,soft tissue infection,,,,,,,,,,,,,,99.41,0.49,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections NHP,28111.542,Bacteroides eggerthii strain DSM 20697,DSM 20697,Bacteroides eggerthii,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222646,28111,,,,,,DSM:20697,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146565.1,CP102258,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4206509,44.584667,3704,3385,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.26,0,,,Other,- HP,28113.3,Bacteroides heparinolyticus strain F0111,F0111,Bacteroides heparinolyticus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN08439035,28113,,,,,,,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002998535.1,CP027234,,The Forsyth Institute,PacBio,230x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,3608975,47.246185,3172,2853,14 mesial subgingival,,1983-03,USA,"USA: Blacksberg, VA",env_biome:Human oral cavity,male,55,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,Periodontitis moderate,,,,,,,,,Human oral cavity,,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,28116.1605,Bacteroides ovatus strain CL06T03C20,CL06T03C20,Bacteroides ovatus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451186,28116,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292045.1,"CP072244,CP072245",,Brigham & Women's Hospital,PacBio Sequel,224x,FALCON-Unzip v. 1.2.0,1,1,2,6753620,41.908043,5618,5258,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.46,0.36,,,Gastrointestinal,- HP,28116.1661,Bacteroides ovatus strain BFG-107,BFG-107,Bacteroides ovatus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546949,28116,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091525.1,"CP081917,CP081918,CP081919",,National Institute of Allergy and Infectious Disease,PacBio Sequel,362x,Canu (chr)/HGAP/FALCON (plasmids) v. v.,1,2,3,7043773,42.05746,6074,5633,blood,,1985,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.51,0.97,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,28116.1884,Bacteroides ovatus strain ATCC 8483,ATCC 8483,Bacteroides ovatus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222651,28116,,,,,,ATCC:8483,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146775.1,CP102259,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,6472384,41.879112,5081,4824,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.46,0.12,,,Other,- NHP,28116.1918,Bacteroides ovatus KR001_HAM_0001,KR001_HAM_0001,Bacteroides ovatus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100329,28116,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757525.1,CP107192,,,PacBio Sequel II,11x,hifiasm_meta v. 0.2-r040,1,0,1,6770402,41.737965,5318,5027,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.2,,,Gastrointestinal,- NHP,28116.1919,Bacteroides ovatus KR001_HIC_0032,KR001_HIC_0032,Bacteroides ovatus,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100330,28116,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757905.1,CP107193,,,PacBio Sequel II,479x,HiCanu v. 2.1.1,1,0,1,6628096,41.7188,5257,4970,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- HP,28119.4,Bacteroides zoogleoformans strain ATCC 33285,ATCC 33285,Bacteroides zoogleoformans,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN08472433,28119,,,,,,ATCC:33285,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002998435.1,CP027231,,The Forsyth Institute,PacBio,220x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,3361794,47.455822,2997,2743,curette,,1979-08,USA,"USA: Blacksberg, VA",env_biome:Human oral cavity,female,20,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,Periodontitis severe,,,,,,,,,Human oral cavity,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28129.11,Prevotella denticola strain KCOM 1525,KCOM 1525,Prevotella denticola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN09781058,28129,,,,,,,,2018-09-09T00:00:00Z,,PRJNA485030,GCA_003515045.1,"CP032056,CP032057",,Korean Collection for Oral Microbiology,PacBio; Illumina HiSeq,984.8x,RS HGAP v. 3.0; SPAdes v. 3.8.2,2,,2,2893847,50.134544,2730,2319,periapical abscess,,2002-08-09,South Korea,South Korea: Gwangju,,,,Periapical abscess,,,,,,,,,,,,,Genome sequencing of Prevotella denticola KCOM 1525,collected_by:Korean Collection for Oral Microbiology,,,,,,,Periapical abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses NHP,28129.55,Prevotella denticola strain F0119,F0119,Prevotella denticola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352183,28129,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128185.1,CP072373,,The Forsyth Institute,PacBio Sequel,569x,Pacbio MA v. 9.0.0.92188,1,0,1,3038072,49.877357,2836,2327,human oral cavity,,1985-01,USA,"USA: Blacksberg, Virginia",,male,46,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02167;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.32,0,,,Oral,- HP,28129.56,Prevotella denticola strain F0288,F0288,Prevotella denticola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352185,28129,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128165.1,"CP072371,CP072372",,The Forsyth Institute,PacBio Sequel,311x,Pacbio MA v. 9.0.0.92188,2,0,2,2938122,50.35962,2723,2230,human oral cavity,,1979-07,USA,"USA: Blacksberg, Virginia",,male,16,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02168;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,localized juvenile periodontitis,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,28129.57,Prevotella denticola strain F0115,F0115,Prevotella denticola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352182,28129,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128205.1,"CP072374,CP072375,CP072376",,The Forsyth Institute,PacBio Sequel,266x,Pacbio MA v. 9.0.0.92188,2,1,3,3106544,50.10021,2942,2404,human oral cavity,,1993-02,USA,"USA: Blacksberg, Virginia",,female,37,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02166;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.32,0.11,,,Oral,- NHP,28129.60,Prevotella denticola strain F0105,F0105,Prevotella denticola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352179,28129,,,,,,,,2021-04-28T00:00:00Z,,PRJNA282954,GCA_018141825.1,CP073339,,The Forsyth Institute,PacBio Sequel,348x,Pacbio MA v. 9.0.0.92188,1,0,1,3027740,49.960926,2856,2372,human oral cavity,,1988-10,USA,"USA: Blacksberg, Virginia",,male,14,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02165;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,98.65,0,,,Oral,- HP,28131.10,Prevotella intermedia strain OMA14,OMA14,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00017481,28131,,,,,,,,2016-09-28T00:00:00Z,26645327,PRJDB2896,GCA_002355195.1,"AP014597,AP014598",,Nagasaki University,454 GS FLX; ABI 3130x; MiSeq,47x(454 GS FLX); 70x(MiSeq),Newbler version v. 2.6,2,,2,3148117,43.84,3179,2797,periodontal pockets of patients with chronic periodontitis,isolated from periodontal pockets of patients with chronic periodontitis,2000,Japan,Japan,env_biome:animal,,,,,,,,,,,,,,,,"The Gram-negative oral anaerobe is major periodontal pathogens in human, frequently isolated from periodontal pockets of patients with chronic periodontitis. Such periodontal pathogens were identified as red and orange complex bacteria (Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia etc.). Previous studies indicated a number of potent virulence factors of Porphyromonas gingivalis such as cysteine proteinase, gingipains and fimbria. From genomic information of P. gingivalis, we found a novel secretion system (type IX secretion system) that translocate virulence factors to cell surface. It suggested that the genomic information was indispensable to elucidate virulence factors in other periodontal pathogens. This project try to determine the whole genome sequence of periodontal pathogens, then to elucidate there pathogenicity comprehensively.",,animal,Human oral,periodontal pocket plaque,doi: 10.1099/ijs.0.012831-0,Study of oral pathogen,,,disease,,,,,,,,,animal,,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28131.17,Prevotella intermedia strain KCOM 2836,KCOM 2836,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07956007,28131,,,,,,KCOM:2836,,2017-11-13T00:00:00Z,,PRJNA416409,GCA_002763575.1,CP024697,,Korean Collection for Oral Microbiology,PacBio,308.5x,RS HGAP v. 3.0,1,,1,2760702,43.24,2745,2368,subgingival dental plaque,,2014-09-01,South Korea,South Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 2836,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28131.18,Prevotella intermedia strain KCOM 2033,KCOM 2033,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07955957,28131,,,,,,KCOM:2033,,2017-11-13T00:00:00Z,,PRJNA416397,GCA_002763535.1,CP024696,,Korean Collection for Oral Microbiology,PacBio,290.6x,RS HGAP v. 3.0,1,,1,2777805,43.71,2812,2446,subgingival dental plaque,,2005-03-01,South Korea,South Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 2033,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,1.3,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,28131.19,Prevotella intermedia strain KCOM 1949,KCOM 1949,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07955952,28131,,,,,,KCOM:1949,,2017-11-13T00:00:00Z,,PRJNA416391,GCA_002763715.1,"CP024727,CP024728",,Korean Collection for Oral Microbiology,PacBio,416.8x,RS HGAP v. 3.0,2,,2,2764740,43.4,2731,2371,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,periimplantitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 1949,collected_by:Korean Collection for Oral Microbiology,,,,,,,periimplantitis,,,,,,,,,,,,,,100,0,Surgical Site Infections,,Oral,Surgical Site Infections- HP,28131.20,Prevotella intermedia strain KCOM 2837,KCOM 2837,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07956008,28131,,,,,,KCOM:2837,,2017-11-13T00:00:00Z,,PRJNA416410,GCA_002763745.1,"CP024723,CP024724",,Korean Collection for Oral Microbiology,PacBio,395.8x,RS HGAP v. 3.0,2,,2,2890050,43.44,2909,2523,subgingival dental plaque,,2014-09-01,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 2837,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28131.21,Prevotella intermedia strain KCOM 2838,KCOM 2838,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07956010,28131,,,,,,KCOM:2838,,2017-11-13T00:00:00Z,,PRJNA416411,GCA_002763785.1,"CP024725,CP024726",,Korean Collection for Oral Microbiology,PacBio,401.1x,RS HGAP v. 3.0,2,,2,2775833,43.4,2686,2383,subgingival dental plaque,,2014-09-01,South Korea,South Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 2838,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28131.22,Prevotella intermedia strain KCOM 1933,KCOM 1933,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07955950,28131,,,,,,KCOM:1933,,2017-11-13T00:00:00Z,,PRJNA416381,GCA_002763845.1,"CP024729,CP024730",,Korean Collection for Oral Microbiology,PacBio,278.6x,RS HGAP v. 3.0,2,,2,2737112,43.5,2750,2387,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 1933,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,98.7,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28131.24,Prevotella intermedia strain KCOM 1944,KCOM 1944,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07980959,28131,,,,,,KCOM:1944,,2017-11-13T00:00:00Z,,PRJNA417207,GCA_002763975.1,"CP024734,CP024735",,Korean Collection for Oral Microbiology,PacBio,234.2x,RS HGAP v. 3.0,2,,2,2813841,43.53,2829,2462,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 1944,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28131.35,Prevotella intermedia strain KCOM 2734,KCOM 2734,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07955960,28131,,,,,,,,2018-06-26T00:00:00Z,,PRJNA416401,GCA_003265025.1,"CP030094,CP030095",,Korean Collection for Oral Microbiology,PacBio,380.8x,RS HGAP v. 3.0,2,,2,2949063,43.56119,2952,2563,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Prevotella intermedia KCOM 2734,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,4.9,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,28131.7,Prevotella intermedia strain strain 17,17,Prevotella intermedia,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN04529095,28131,,,,,,ATCC 25611,Yes,2017-01-18T00:00:00Z,,PRJNA313956,GCF_001953935.1,"CP019302,CP019303","NZ_CP019302.1,NZ_CP019303.1",The Forsyth Institute,PacBio,200.0x,Celera Assembler v. June 2016; HGAP v.,2,,2,2736315,43.45,2745,2385,periodontal pocket,,1992,Japan,Japan,,,,periodontal disease,,,,,,,,,C,,,,Re-sequencing of the Prevotella intermedia type strain ATCC25611 and clinical isolate Prevotella intermedia strain-17 (January 2016) using using a PacBio RS II system (Pacific Biosciences) on a single-molecule real-time (SMRT) cell using PacBio P6-C4 chemistry.,"collected_by:Fukushima, H, Moroi H, Inoue J, Onoe T, Ezaki T, Yabuuchi E, Leung KP, Walker CB, Clark WB, Sagawa H.",,,,,,,periodontal disease,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,28132.302,Prevotella melaninogenica strain F0692,F0692,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352193,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127905.1,"CP072345,CP072346",,The Forsyth Institute,PacBio Sequel,131x,Flye v. 2.8,2,0,2,3169665,40.916973,2641,2382,human oral cavity,,1992-03,USA,"USA: Blacksberg, Virginia",,male,45,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02180;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,adult periodontitis,,,,,,,,,human oral cavity,,,,98.65,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28132.303,Prevotella melaninogenica strain F0516,F0516,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352191,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127925.1,"CP072348,CP072347",,The Forsyth Institute,PacBio Sequel,142x,Flye v. 2.8,2,0,2,3360806,41.173336,2840,2591,human oral cavity,,2008-07-21,USA,"USA: Boston, Massachusetts",,male,2.33,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02179;collected_by:Anne Tanner, Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,severe early childhood caries,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28132.305,Prevotella melaninogenica strain F0054,F0054,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352174,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128045.1,"CP072361,CP072362",,The Forsyth Institute,PacBio Sequel,325x,Pacbio MA v. 9.0.0.92188,2,0,2,3358299,41.10486,2897,2632,human oral cavity,,1979-02,USA,"USA: Blacksberg, Virginia",,female,20,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02173;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,localized juvenile periodontitis,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28132.306,Prevotella melaninogenica strain F0091,F0091,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352176,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128065.1,"CP072360,CP072359",,The Forsyth Institute,PacBio Sequel,120x,Flye v. 2.8,2,0,2,3342898,41.30503,2932,2593,human oral cavity,,1993-05,USA,"USA: Blacksberg, Virginia",,female,24,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02174;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,juvenile periodontitis,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28132.315,Prevotella melaninogenica strain F0300,F0300,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352187,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127945.1,"CP072351,CP072352,CP072353",,The Forsyth Institute,PacBio Sequel,288x,Pacbio MA v. 9.0.0.92188,2,1,3,3334355,40.839474,2864,2613,human oral cavity,,1979-09,USA,"USA: Blacksberg, Virginia",,male,28,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02177;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,severe periodontitis,,,,,,,,,human oral cavity,,,,99.32,0.17,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,28132.316,Prevotella melaninogenica strain F0695,F0695,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352194,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127885.1,"CP072343,CP072344",,The Forsyth Institute,PacBio Sequel,393x,Pacbio MA v. 9.0.0.92188,2,0,2,3168321,40.91716,2600,2378,human oral cavity,,1988-07,USA,"USA: Blacksberg, Virginia",,male,12,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02181;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.32,0,,,Oral,- NHP,28132.317,Prevotella melaninogenica strain F0301,F0301,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352188,28132,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127965.1,"CP072349,CP072350",,The Forsyth Institute,PacBio Sequel,125x,Flye v. 2.8,2,0,2,3218481,40.86086,2700,2431,human oral cavity,,1988-12,USA,"USA: Blacksberg, Virginia",,male,14,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02178;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.16,0,,,Oral,- HP,28132.5,Prevotella melaninogenica strain GAI 07411,GAI 07411,Prevotella melaninogenica,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00078755,28132,,,,,,,,2017-09-01T00:00:00Z,,PRJDB5703,GCA_003609775.1,"AP018049,AP018050,AP018051",,"Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences",PacBio RSII,246x,HGAP v. 3,2,1,3,3090326,40.773464,2520,2410,vagina,isolated from not only periodontal pockets but also purulent infections,,Japan,Japan,,female,,,,,,,,,,,,,,,"Prevotella melaninogenica is frequently isolated from not only periodontal pockets but also purulent infections. Similar to all species of the genus Prevotella, it is strictly anaerobic, gram-negative bacterium with non-spore forming coccobacilli. We used to the generation sequencing technique (PacBio RS II) to sequence the whole genome of Prevotella melaninogenica GAI 07411 isolated from the vagina. A number of potent virulence factors possessed by bacteria belonging to phylum Bacteroidetes were suggested by analyzing the genomic information. Therefore, the genomic information is indispensable to evaluate the pathogenicity and host interactions. This genomic information may provide insight into the functional activity of this strain.","biomaterial_provider:Life science Research Center, Gifu University",missing,missing,missing,missing,whole genome sequence of Prevotella melaninogenica GAI 07411,,,,,,,,,,,,missing,,,,99.32,0.34,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,28133.89,Prevotella nigrescens strain F0109,F0109,Prevotella nigrescens,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352181,28133,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127825.1,"CP072339,CP072338,CP072337",,The Forsyth Institute,PacBio Sequel,546x,Pacbio MA v. 9.0.0.92188,2,1,3,2887107,42.451664,2756,2365,human oral cavity,,1990-11,USA,"USA: Blacksberg, Virginia",,male,37,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02184;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,adult periodontitis,,,,,,,,,human oral cavity,,,,99.65,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,28133.90,Prevotella nigrescens strain F0630,F0630,Prevotella nigrescens,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352192,28133,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127845.1,"CP072335,CP072336",,The Forsyth Institute,PacBio Sequel,168x,Pacbio MA v. 9.0.0.92188,2,0,2,2928207,42.697666,2814,2394,human oral cavity,,2015-05-07,USA,"USA: Cambridge, Massachusetts",,male,48,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02185;collected_by:Pallavi Murugkar, Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,periodontitis,,,,,,,,,human oral cavity,,,,99.31,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,28137.14,Prevotella veroralis strain F0319,F0319,Prevotella veroralis,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352189,28137,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127765.1,"CP072330,CP072331,CP072332",,The Forsyth Institute,PacBio Sequel,377x,Pacbio MA v. 9.0.0.92188,2,1,3,2990547,41.92387,2755,2384,human oral cavity,,1985-09,USA,"USA: Blacksberg, Virginia",,male,11,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02188;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.32,0,,,Oral,- HP,28141.673,Cronobacter sakazakii strain GZcsf-1,GZcsf-1,Cronobacter sakazakii,Cronobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08928172,28141,O1,,,MLST.Cronobacter_spp.256,genotype:ST256,,,2018-12-19T00:00:00Z,30334728,PRJNA450456,GCA_003955925.1,"CP028974,CP028975,CP028976",,"Guangdong Institute of Microbiology, Guangzhou city, China",PacBio,38.69x,HGAP v. HGAP.3,1,2,3,4908057,56.29564,4895,4676,brain abscess fluid,,2015,China,China,,,,Neonatal purulent meningitis,,,,,,,,,,,,,A retrospective analysis of one C. sakazakii strain causing neonatal meningitis from a hospital of China,"collected_by:Guangdong Institute of Microbiology, China",,,,,,,Neonatal purulent meningitis,,,,,,,,,,,,,,99.99,0.48,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,28141.828,Cronobacter sakazakii strain 5563_17,5563_17,Cronobacter sakazakii,Cronobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15493123,28141,,,,MLST.Cronobacter_spp.1,,,,2020-07-20T00:00:00Z,,PRJNA645121,GCA_013425995.1,CP059045,,National Medicines Institute,Illumina MiSeq; Oxford Nanopore MiniION,50.0x,Unicycler v. 0.4.7,1,0,1,4315383,56.96236,4098,3908,blood,,2017-07-03,Poland,Poland:Wrocaw,,,,brain abscess,,,,,,,,,,,,,Cronobacter sakazakii ST1 infection in premature newborn,"collected_by:Department of Neonatology, Wrocaw Medical University, Poland",,,,,,,brain abscess,,,,,,,,,,,,,,99.69,0.19,Skin and Soft Tissue Infections,Wounds and Abscesses,Blood and Circulatory System,Skin and Soft Tissue Infections-Wounds and Abscesses HP,28141.913,Cronobacter sakazakii strain C767,C767,Cronobacter sakazakii,Cronobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14112905,28141,,,,MLST.Cronobacter_spp.1,,,,2021-06-15T00:00:00Z,,PRJNA399551,GCA_018884085.1,"CP049147,CP049149,CP049148",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)","PacBio Sequel, Illumina HiSeq",281x,unicycler v. 3.11.0,1,2,3,4585350,56.67493,4458,4246,dyalisis liquid,,2006-06-14,Mexico,Mexico:Mexico City,,male,,Chronic renal insufficiency,,,,,,,,,,,,,Genomic characterization of Mexican Cronobacter sakazakii strains,collected_by:INNCMSZ (Clinical Microbiology Laboratory),,,,,,,Chronic renal insufficiency,,,,,,,,,,,,,,99.69,0.32,Renal Diseases,,Other,Renal Diseases- HP,28141.915,Cronobacter sakazakii strain C757,C757,Cronobacter sakazakii,Cronobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14112904,28141,,,,MLST.Cronobacter_spp.1,,,,2021-06-15T00:00:00Z,,PRJNA399551,GCA_018884145.1,"CP049150,CP049153,CP049152,CP049151",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)","PacBio Sequel, Illumina HiSeq",156x,unicycler v. 3.11.0,1,3,4,4591950,56.6688,4467,4252,dyalisis liquid,,2006-06-14,Mexico,Mexico:Mexico City,,male,,Chronic renal insufficiency,,,,,,,,,,,,,Genomic characterization of Mexican Cronobacter sakazakii strains,collected_by:INNCMSZ (Clinical Microbiology Laboratory),,,,,,,Chronic renal insufficiency,,,,,,,,,,,,,,99.69,0.32,Renal Diseases,,Other,Renal Diseases- HP,28152.31,Yersinia kristensenii strain ATCC BAA-2637,ATCC BAA-2637,Yersinia kristensenii,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09765716,28152,,,,MLST.Yersinia_spp.84,,ATCC: BAA-2637,,2018-09-27T00:00:00Z,,PRJNA484516,GCA_003600645.1,"CP032482,CP032483,CP032484",,Mayo Clinic,Illumina MiSeq,200.0x,SPAdes v. JAN-2014,1,2,3,4448883,47.492855,4249,3996,feces,,2011-01,USA,"USA: Rochester, MN",,,,diarrhea,,,Susceptible;Intermediate,AMR Panel,,,,,,,,,Whole genome sequencing of Yersinia kristensenii EPLC-04,collected_by:Mayo Clinic,,,,,,,diarrhea,,,,,,,,,,,,,,99.95,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2815358.3,Leclercia sp. 4-9-1-25,4-9-1-25,Leclercia pneumoniae,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18093163,2815358,,,,,,,,2021-03-13T00:00:00Z,,PRJNA705593,GCA_017348915.1,"CP071383,CP071384",,University Hospital Leipzig,Illumina MiSeq; Oxford Nanopore MinION,80.0x,Unicycler v. 0.4.8,1,1,2,4395246,54.96229,4329,4136,sputum,isolated from an infant with pneumonia and septicemia at the Leipzig University Hospital,2019-08-01,Germany,Germany: Leipzig,,,,pneumonia,,,,,,,,,,,,,Strain 4-9-1-25 was isolated from an infant with pneumonia and septicemia at the Leipzig University Hospital.,collected_by:Mario Hoenemann,,,,,,,pneumonia,,,,,,,,,,,,,,99.37,0.05,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,2815358.4,Leclercia sp. 4-9-1-25,4-9-1-25,Leclercia pneumoniae,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19717142,2815358,,,,,,,,2021-06-23T00:00:00Z,,PRJNA738272,GCA_018987305.1,CP076838,,University Hospital Leipzig,Oxford Nanopore; Illumina,100.0x,SPAdes v. v3.12.0,1,0,1,4392327,54.968655,4316,4136,sputum,,2019-08-01,Germany,Germany: Leipzig,,,,pneumonia,,,,,,,,,,,,,Strain: 4-9-1-25,collected_by:Mario Hoenemann,,,,,,,pneumonia,,,,,,,,,,,,,,99.37,0.05,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,28184.41,Leptospira weilii FMAS_PD2,FMAS_PD2,Leptospira weilii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919580,28184,,,,,,,,2022-02-20T00:00:00Z,,PRJNA528695,GCA_022344045.1,"CP092203,CP092202,CP092201,CP092204,CP092205",,,PacBio Sequel System,1778x,canu v. 2.1,2,3,5,4896793,40.726555,5577,4463,blood,,2017-09-06,Sri Lanka,Sri Lanka:Peradeniya,,male,41 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,0,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,28184.42,Leptospira weilii FMAS_RT1,FMAS_RT1,Leptospira weilii,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919575,28184,,,,,,,,2022-03-01T00:00:00Z,,PRJNA528695,GCA_022453935.2,"CP092206,CP092207,CP092208,CP092209,CP092210",,,PacBio Sequel System,1611x,canu v. 2.1,2,3,5,5153847,40.89225,5916,4819,blood,,2017-08-10,Sri Lanka,Sri Lanka:Rathnapura,,male,43 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,98.82,1.18,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,28188.25,Capnocytophaga canimorsus strain RBWH,RBWH,Capnocytophaga canimorsus,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN10160287,28188,,,,,,,,2018-11-19T00:00:00Z,,PRJNA494285,GCA_003795085.1,CP032681,,The University of Queensland,Oxford Nanopore MiniION; Illumina NextSeq,215.0x,Canu v. 1.7; Miniasm v. JULY-2018; Racon,1,,1,2555606,36.24127,2528,2303,missing,,2018-03-21,Australia,Australia:Queensland,,,,Sepsis,,,,,,,,,,,,,Capnocytophaga canimorsus isolated from dog and human origin,collected_by:Royal Brisbane and Women's Hospital,,,,,,,Sepsis,,,,,,,Clinical isolate,,,,,,,98.57,0,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,28188.26,Capnocytophaga canimorsus strain NCTC11921,NCTC11921,Capnocytophaga canimorsus,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMEA104210801,28188,not available: to be reported later,,,,,NCTC:11921,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638435.1,LR134513,,SC,,,,1,,1,2528270,36.11173,2415,2220,blood,,1900-1986,,,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0.24,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2820673.3,Pseudoclavibacter sp. 125703-2019 strain 125703-19,125703-19,Pseudoclavibacter triregionum,Pseudoclavibacter,Microbacteriaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMEA8951503,2820673,,,,,,,,2021-07-13T00:00:00Z,,PRJEB43861,GCA_910822395.1,OU365335,,University Hospital Basel,,,,1,0,1,2360996,72.74316,2100,2063,clinical sample,,2019-03,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,Taxonomic study of Pseudoclavibacter sp. 125703-2019,,,,,,,,,diseased,,,,,,,,,,,,,98.25,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2823899.4,Corynebacterium sp. CCUG 27540,CCUG 27540,Corynebacterium pseudogenitalium,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18647611,38303,,,,,,CCUG:27540,,2022-07-27T00:00:00Z,,PRJNA305687,GCA_024453815.1,CP072934,,University of Gothenburg - CCUG,"Illumina HiSeq, Oxford Nanopore MiniION",564x,Unicycler v. v0.4.8,1,0,1,2389603,60.66129,2229,2167,healthy human,,1990,,United Kingdom,,,,,,,,,,,,,,,,,Whole genome sequencing of bacterial species of the Culture Collection University of Gothenburg (CCUG),sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.9,0,,,Other,- HP,282402.5,Prevotella multiformis strain F0096,F0096,Prevotella multiformis,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352177,282402,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127985.1,"CP072357,CP072358",,The Forsyth Institute,PacBio Sequel,128x,Flye v. 2.8,2,0,2,3025491,51.84104,2833,2281,human oral cavity,,1982-11,USA,"USA: Blacksberg, Virginia",,male,50,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02182;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,moderate periodontitis,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,283686.18,Kosakonia radicincitans strain DSM 107547,DSM 107547,Kosakonia radicincitans,Kosakonia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11638161,283686,,,,,,DSM:107547,,2019-09-09T00:00:00Z,,PRJNA542777,GCA_008330085.1,"CP040392,CP040393",,University of Tuebingen,PacBio RSII SMRT,110.39x,HGAP.3 v. OCT-2018,1,1,2,5774740,53.951088,5714,5371,blood,,2017-10-30,Austria,Austria: Graz,,,,Kosakonia bacteremia,,,,,,,,,,,,,"There are rare reports of Kosakonia spp. involved in human infections, but there are known species that can act as human pathogens. Identification of Kosakonia spp. is not yet possible when using standard laboratory tools. Sequencing approaches for identification is thus recommended.","collected_by:Institute of Hygiene, Microbiology and Environmental Medicine - Medical University of Graz",,,,,,,Kosakonia bacteremia,,,,,,,,,,,,,,99.57,2.27,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,283734.1700,Staphylococcus pseudintermedius strain 53_88,53_88,Staphylococcus pseudintermedius,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10880486,283734,,,,,,,,2019-02-27T00:00:00Z,,PRJNA521119,GCA_004307335.1,CP035740,,Texas A&M University,Hybrid Assembly: Nanopore MinION &,150-200X,"Canu with Pilon polishing v. Canu v 1.5,",1,,1,2593941,37.69176,2502,2371,blood,,2015,USA,USA: California,,,,Bacteremia,,,,,,,,,,,,,"We sequenced 8 Staphylococcus pseudintermedius isolates (4 from human bacteremia infections, 4 from canine bacteremia infections) with both MinION and MiSeq, in order to create complete whole-genome hybrid assemblies. These will provide information for analysis of virulence genes and potential virulence factors important to these infections in canines and humans.",collected_by:UCLA/RMA,,,,,,,Bacteremia,,,,,,,,,,,,,,99.43,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,283734.1701,Staphylococcus pseudintermedius strain 53_60,53_60,Staphylococcus pseudintermedius,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10880484,283734,,,,,,,,2019-02-27T00:00:00Z,,PRJNA521119,GCA_004307355.1,CP035741,,Texas A&M University,Hybrid Assembly: Nanopore MinION &,150-200X,"Canu with Pilon polishing v. Canu v 1.5,",1,,1,2615959,37.471706,2507,2377,blood,,2015,USA,USA: Georgia,,,,Bacteremia,,,,,,,,,,,,,"We sequenced 8 Staphylococcus pseudintermedius isolates (4 from human bacteremia infections, 4 from canine bacteremia infections) with both MinION and MiSeq, in order to create complete whole-genome hybrid assemblies. These will provide information for analysis of virulence genes and potential virulence factors important to these infections in canines and humans.",collected_by:CDC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.43,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,28450.1836,Burkholderia pseudomallei strain BPs110,BPs110,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10948535,28450,,,,,,,,2019-03-04T00:00:00Z,,PRJNA522658,GCA_004323015.1,"CP036452,CP036451",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,170.0x,SPAdes v. V 3.10.1,2,,2,6962327,68.46934,7332,7184,blood from melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,,,Melioidosis,,,,,,,,,,,,,Goal of the study is to explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo;sample_type:Pure culture",,,,,,,Melioidosis,,,,,,,,,,,,,,99.92,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1837,Burkholderia pseudomallei strain BPs111,BPs111,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10948547,28450,,,,,,,,2019-03-04T00:00:00Z,,PRJNA522663,GCA_004323035.1,"CP036454,CP036453",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,155.0x,SPAdes v. V 3.10.1,2,,2,6966412,68.451965,7333,7183,blood from melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,,,Melioidosis,,,,,,,,,,,,,Explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,,,,,,,,,,,,,,99.92,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1838,Burkholderia pseudomallei strain BPs115,BPs115,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10961208,28450,,,,,genotype:MLST1413,,,2019-03-13T00:00:00Z,,PRJNA522936,GCA_004348055.1,"CP037758,CP037757",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,190.0x,SPAdes v. V 3.10.1,2,,2,6958638,68.407524,7339,7167,blood from melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,,,Melioidosis,,,,,,,,,,,,,Genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,,,,,,,,,,,,,,99.99,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1839,Burkholderia pseudomallei strain BPs116,BPs116,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10961418,28450,,,,,,,,2019-03-13T00:00:00Z,,PRJNA522951,GCA_004348075.1,"CP037760,CP037759",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,179.0x,SPAdes v. V 3.10.1,2,,2,6920216,68.469826,7266,7105,blood from melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,,,Melioidosis,,,,,,,,,,,,,Genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,,,,,,,,,,,,,,99.66,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1846,Burkholderia pseudomallei strain BPs114,BPs114,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11124809,28450,,,,MLST.Burkholderia_pseudomallei.594,genotype:ST594,,,2019-03-23T00:00:00Z,,PRJNA522658,GCA_004367665.1,"CP037974,CP037973",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,253.0x,SPAdes v. V 3.10.1,2,,2,6941499,68.43822,7321,7146,blood from a melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,female,62 yrs,Melioidosis,,host_disease_outcome:Recovery;host_disease_stage:Acute sepsis;host_health_state:Diabetic,,,,,,,,,,,Goal of the study is to explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,Diabetic,Recovery,,Acute sepsis,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1847,Burkholderia pseudomallei strain BPs123,BPs123,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11109762,28450,,,,,genotype:ST594,,,2019-03-23T00:00:00Z,,PRJNA522658,GCA_004367685.1,"CP037970,CP037969",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,165.0x,SPAdes v. V 3.10.1,2,,2,6975017,68.431816,7366,7179,blood and joint fluid of melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloae,,female,28 yrs,Melioidosis,,host_disease_outcome:Death;host_disease_stage:Acute sepsis,,,,,,,,,,,Goal of the study is to explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,,Death,,Acute sepsis,,,,,,,,,,99.92,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1848,Burkholderia pseudomallei strain BPs112 strain Melioidosis patient,Melioidosis patient,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11125344,28450,,,,MLST.Burkholderia_pseudomallei.1138,genotype:ST1442,,,2019-03-23T00:00:00Z,,PRJNA522658,GCA_004367705.1,"CP037976,CP037975",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,143.0x,SPAdes v. V 3.10.1,2,,2,6945494,68.44893,7300,7145,blood,,2015,Sri Lanka,Sri Lanka: Batticaloae,,male,66 yrs,Melioidosis,,host_disease_outcome:Recovery;host_disease_stage:Acute sepsis;host_health_state:Diabetic,,,,,,,,,,,Goal of the study is to explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,Diabetic,Recovery,,Acute sepsis,,,,,,,,,,99.6,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1849,Burkholderia pseudomallei strain BPs133 strain Melioidosis patient,Melioidosis patient,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11110186,28450,,,,MLST.Burkholderia_pseudomallei.594,genotype:ST594,,,2019-03-23T00:00:00Z,,PRJNA522658,GCA_004367725.1,"CP037972,CP037971",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,245.0x,SPAdes v. V 3.10.1,2,,2,6941963,68.43737,7316,7156,blood,,2015,Sri Lanka,Sri Lanka: Batticaloa,,male,46 yrs,Melioidosis,,host_disease_outcome:Recovery;host_disease_stage:Acute sepsis;host_health_state:Diabetic,,,,,,,,,,,Goal of the study is to explore genetic variations among clinical isolates of B. pseudomallei isolated from Sri Lankan Melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,Diabetic,Recovery,,Acute sepsis,,,,,,,,,,99.92,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1850,Burkholderia pseudomallei strain BPs122,BPs122,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11180678,28450,,,,MLST.Burkholderia_pseudomallei.594,genotype:ST594,,,2019-03-31T00:00:00Z,,PRJNA528379,GCA_004526325.1,"CP038195,CP038194",,General Sir John Kotelawala Defence Uinversity,Illumina MiSeq,354.0x,SPAdes v. V 3.10.1,2,,2,6986353,68.43648,7366,7213,blood from melioidosis patient,,2015,Sri Lanka,Sri Lanka: Batticaloa,,female,28 yrs,Melioidosis,,host_disease_outcome:Recovery;host_disease_stage:Acute sepsis;host_health_state:Diabetic,,,,,,,,,,,Genetic diversity of clinical isolates of Burkholderia pseudomallei isolated from Sri Lankan melioidosis patients,"collected_by:Department of Microbiology, Faculty of Medicine, University of Colombo",,,,,,,Melioidosis,Diabetic,Recovery,,Acute sepsis,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1851,Burkholderia pseudomallei strain HNBP001,HNBP001,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09373889,28450,,,,MLST.Burkholderia_pseudomallei.55,,,,2019-04-23T00:00:00Z,,PRJNA474798,GCA_004842085.1,"CP038805,CP038806",,"Key Laboratory of Tropical Biomedicine,and School of Tropical Medicine and Laboratory Medicine",PacBio,99.2x,Celera Assembler v. 8.3,2,,2,7163595,68.17842,7175,,serum,,2018-01-02,China,"China:Hainan,Wenchang",,,,,,,,,,,,,,,,,"Burkholderia pseudomallei (B. pseudomallei), a Gramnegative bacillus, is the agent of melioidosis, a tropical infectious disease, which is endemic to Southeast Asia and Northeast Australia. It is commonly found in soil and water, and it has been isolated from a variety of clinical samples in endemic areas",,,,,PMID,,,,,,,,,,,,,tropic,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28450.1852,Burkholderia pseudomallei strain VB3253,VB3253,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11774884,28450,,,,MLST.Burkholderia_pseudomallei.412,,,,2019-05-27T00:00:00Z,,PRJNA543683,GCA_005853645.1,"CP040531,CP040532",,"Christian Medical college, Vellore",IonTorrent; Oxford Nanopore MiniION,30.0x,Canu v. 1.7; Unicycler v. 0.4.6,2,,2,7180501,68.09895,7747,7369,blood aspirate,,2019,India,India,,,,Blood stream infection,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei strain VB3253,collected_by:Christian Medical College,,,,,,,Blood stream infection,,,,,,,,,,,,,,99.38,0.03,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,28450.1853,Burkholderia pseudomallei strain VB2514,VB2514,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11792775,28450,,,,MLST.Burkholderia_pseudomallei.734,,,,2019-05-28T00:00:00Z,,PRJNA543968,GCA_005862325.1,"CP040551,CP040552",,Christian Medical College,Oxford Nanopore; IonTorrent,40.0x,SPAdes v. v5.0.0.0; Canu v. v1.7;,2,,2,7103279,67.96937,7750,7338,blood aspirate,,2019,India,India: Vellore,,,,Blood stream infection,,,,,,,,,,,,,Complete genome sequence of Burkholderia pseudomallei VB2514,"collected_by:Christian Medical College, Vellore",,,,,,,Blood stream infection,,,,,,,,,,,,,,97.51,0.07,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,28450.1891,Burkholderia pseudomallei strain InDRE_1Son2018,InDRE_1Son2018,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12046668,28450,,,,MLST.Burkholderia_pseudomallei.92,,,,2019-07-02T00:00:00Z,,PRJNA550436,GCA_006542565.1,"CP041218,CP041219",,InDRE,Illumina MiSeq,33.0x,CLC NGS Cell v. 12,2,,2,7319711,68.32875,7418,7236,blood culture,,2018-09-21,Mexico,Mexico: Huasabas,,male,12 years,melioidosis,,,,,,,,,,,,,Bukholderia pseudomallei chr 1 complete genome,,,,,,,,melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.1892,Burkholderia pseudomallei strain InDRE_2Son2018,InDRE_2Son2018,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12047222,28450,,,,MLST.Burkholderia_pseudomallei.92,,,,2019-07-02T00:00:00Z,,PRJNA550439,GCA_006542585.1,"CP041220,CP041221",,InDRE,Illumina MiSeq,24.0x,CLC NGS Cell v. 12,2,,2,7319837,68.33025,7437,7227,blood culture,,2018-09-21,Mexico,Mexico:Huasabas,,female,16 years,Melioidosis,,,,,,,,,,,,,Burkholderia pseudomallei complete genome,,,,,,,,Melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.2164,Burkholderia pseudomallei strain VB29710,VB29710,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN17766538,28450,,,,,,,,2021-02-11T00:00:00Z,,PRJNA699139,GCA_016864355.1,"CP069360,CP069361",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,58.0x,CANU v. v. 1.7; UNICYCLER HYBRID v. v.,2,0,2,7470254,67.9358,7611,6390,blood,,2020,India,India,,,,sepsis,,,,,,,,,,,,,Complete genome of gentamicin susceptible Burkholderia pseudomallei,collected_by:Christian Medical College,,,,,,,sepsis,,,,,,,,,,,,,,99.38,0.08,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2249,Burkholderia pseudomallei strain VBM364,VBM364,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18219106,28450,,,,,,,,2021-03-16T00:00:00Z,,PRJNA707663,GCA_017356705.1,CP071525,,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,58.49x,CANU v. v. 1.7; UNICYCLER HYBRID v. v.,1,0,1,7387439,67.92485,7347,6265,blood,,2020,India,India,,,,sepsis,,,,,,,,,,,,,Complete genome of B. pseudomallei_VBM364,collected_by:Christian Medical College,,,,,,,sepsis,,,,,,,,,,,,,,100,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2250,Burkholderia pseudomallei strain VBM399,VBM399,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18219191,28450,,,,,,,,2021-03-16T00:00:00Z,,PRJNA707835,GCA_017356725.1,CP071526,,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,68.5x,CANU v. V.1.7; UNICYCLER HYBRID v.,1,0,1,7387707,67.92499,7369,6267,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBM399,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.92,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2251,Burkholderia pseudomallei strain VBM21822,VBM21822,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18236381,28450,,,,,,,,2021-03-18T00:00:00Z,,PRJNA711505,GCA_017378155.1,"CP071746,CP071747,CP071748",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,49.04x,CANU v. v.1.7; UNICYCLER HYBRID v.,3,0,3,7378952,67.92787,7397,6276,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBM21822,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2252,Burkholderia pseudomallei strain VBM21885,VBM21885,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18236418,28450,,,,MLST.Burkholderia_pseudomallei.734,,,,2021-03-18T00:00:00Z,,PRJNA711825,GCA_017378195.1,"CP071749,CP071750",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,39.4x,CANU v. v.1.7; UNICYCLER HYBRID v.,2,0,2,7320639,68.050606,7308,6205,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBM21885,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2253,Burkholderia pseudomallei strain VBM23831,VBM23831,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18236557,28450,,,,MLST.Burkholderia_pseudomallei.501,,,,2021-03-18T00:00:00Z,,PRJNA711969,GCA_017378235.1,"CP071751,CP071752,CP071753",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,59.12x,CANU v. v.1.7; UNICYCLER HYBRID v.,3,0,3,7369223,67.82769,7330,6213,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBM23831,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,97.64,0.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2254,Burkholderia pseudomallei strain VBP399,VBP399,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18236780,28450,,,,MLST.Burkholderia_pseudomallei.300,,,,2021-03-18T00:00:00Z,,PRJNA712233,GCA_017378275.1,"CP071757,CP071758",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,55.35x,CANU v. v.1.7; UNICYCLER HYBRID v.,2,0,2,7270936,68.072945,7205,6147,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBP399,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2255,Burkholderia pseudomallei strain VBP364,VBP364,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18236779,28450,,,,,,,,2021-03-18T00:00:00Z,,PRJNA712119,GCA_017378315.1,"CP071754,CP071755,CP071756",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,37.48x,CANU v. v.1.7; UNICYCLER HYBRID v.,3,0,3,7391218,67.926056,7411,6271,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBP364,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.66,0.37,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2256,Burkholderia pseudomallei strain VBP23831,VBP23831,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18237804,28450,,,,MLST.Burkholderia_pseudomallei.734,,,,2021-03-18T00:00:00Z,,PRJNA712960,GCA_017378435.1,"CP071761,CP071762",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,47.54x,CANU v. v.1.7; UNICYCLER HYBRID v.,2,0,2,7299287,67.95221,7292,6216,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBP23831,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2257,Burkholderia pseudomallei strain VBP21885,VBP21885,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18237298,28450,,,,MLST.Burkholderia_pseudomallei.734,,,,2021-03-18T00:00:00Z,,PRJNA712794,GCA_017378355.1,"CP071759,CP071760",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,55.85x,CANU v. v.1.7; UNICYCLER HYBRID v.,2,0,2,7220562,68.0238,7189,6131,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBP21885,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,97.64,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2352,Burkholderia pseudomallei strain VBP21822,VBP21822,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN19473366,28450,,,,,,,,2021-06-08T00:00:00Z,,PRJNA734137,GCA_018771365.1,"CP076297,CP076298,CP076299,CP076300",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,49.0x,CANU v. v.1.7; UNICYCLER HYBRID v.,2,2,4,7377022,67.92696,7412,6280,blood,,2020,India,India,,,,Sepsis,,,,,,,,,,,,,Complete genome of Burkholderia pseudomallei_VBP21822,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.03,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,28450.2525,Burkholderia pseudomallei 14M0960418,14M0960418,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05762138,28450,,,,MLST.Burkholderia_pseudomallei.70,,,,2018-01-04T00:00:00Z,,PRJNA342555,,"CP019042,CP019043",,,PacBio,140.0x,Pacbio v. May-2015,2,0,2,7222235,68.15865,7448,7304,blood culture,,2014-01-01,Hong Kong,Hong Kong,,,,blood,,,,,,,,,,,,,,collected_by:doctor,,,,,,,blood,,,,,,,,,,,,,,100,0.4,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,28450.2526,Burkholderia pseudomallei MSHR7744,MSHR7744,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06473509,28450,,,,MLST.Burkholderia_pseudomallei.131,,,,2022-11-23T00:00:00Z,,PRJNA321854,,"CP111136,CP111137",,,Oxford Nanopore MinION; Illumina MiSeq,112x,Flye v. 2.8.1,2,0,2,7039884,68.02463,7058,6089,sputum,,2013-01-10,Australia,Australia: Northern Territory,,,,melioidosis,,host_description:Patient with chronic infection,,,,,,,,,,,,collected_by:Menzies,,,,,,,melioidosis,,,Patient with chronic infection,,,,,,,,,,,100,0.5,Respiratory Diseases,Melioidosis,Respiratory Tract,Respiratory Diseases-Melioidosis HP,28450.2527,Burkholderia pseudomallei MSHR1713,MSHR1713,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06473477,28450,,,,MLST.Burkholderia_pseudomallei.131,,,,2022-11-23T00:00:00Z,,PRJNA321854,,"CP111138,CP111139",,,Oxford Nanopore MinION; Illumina MiSeq,34.4x,Flye v. 2.8.1,2,0,2,7026608,68.00038,7075,6093,sputum,,2003-09-10,Australia,Australia: Northern Territory,,,,melioidosis,,host_description:Patient with chronic infection,,,,,,,,,,,,collected_by:Menzies,,,,,,,melioidosis,,,Patient with chronic infection,,,,,,,,,,,100,0.4,Respiratory Diseases,Melioidosis,Respiratory Tract,Respiratory Diseases-Melioidosis HP,28450.2528,Burkholderia pseudomallei MSHR1046,MSHR1046,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06473431,28450,,,,MLST.Burkholderia_pseudomallei.131,,,,2022-11-23T00:00:00Z,,PRJNA321854,,"CP111140,CP111141",,,Oxford Nanopore MinION; Illumina MiSeq,238x,Flye v. 2.8.1,2,0,2,7026580,68.00885,7077,6094,sputum,,2000-07-17,Australia,Australia: Northern Territory,,,,melioidosis,,host_description:Patient with chronic infection,,,,,,,,,,,,collected_by:Menzies,,,,,,,melioidosis,,,Patient with chronic infection,,,,,,,,,,,100,0.2,Respiratory Diseases,Melioidosis,Respiratory Tract,Respiratory Diseases-Melioidosis HP,28450.2597,Burkholderia pseudomallei MSHR5087,MSHR5087,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN32784011,28450,,,,MLST.Burkholderia_pseudomallei.881,,,,2023-01-29T00:00:00Z,,PRJNA925200,,"CP116403,CP116404",,,Illumina MiSeq; Oxford Nanopore MinION,77.0x,Unicycler v. v0.4.8,2,0,2,6998733,68.23982,6935,6021,,,2011,Malaysia,Malaysia,,,,melioidosis,,,,,,,,,,,,,,collected_by:Menzies School of Health Research,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.2699,Burkholderia pseudomallei GTC3P0254T,GTC3P0254T,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMD00592127,28450,,,,MLST.Burkholderia_pseudomallei.51,,ATCC:23343,,2023-05-31T00:00:00Z,,PRJDB15627,,"AP028077,AP028078",,,Illumina NovaSeq; Nanopore MiNION,537x,Flye assembler v. 2.7-b1585; Pilon v. 1.23,2,0,2,7081111,68.24843,6998,5894,,,,USA,USA,,,,,,,,,,,,,,,,,,,not applicable,not applicable,not applicable,not applicable,,Human,,,,,,,,,,,not applicable,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28450.2700,Burkholderia pseudomallei Kanagawa,Kanagawa,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMD00592128,28450,,,,MLST.Burkholderia_pseudomallei.821,,,,2023-05-31T00:00:00Z,,PRJDB15627,,"AP028079,AP028080",,,Illumina NovaSeq; Nanopore MiNION,926x,Flye assembler v. 2.7-b1585; Pilon v. 1.23,2,0,2,7134388,68.25627,7107,5969,,,2010,Japan,Japan,,,,,,,,,,,,,,,,,,,not applicable,not applicable,not applicable,not applicable,,Human,,,,,,,,,,,not applicable,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28450.2704,Burkholderia pseudomallei Tokushima,Tokushima,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMD00592129,28450,,,,MLST.Burkholderia_pseudomallei.46,,,,2023-05-31T00:00:00Z,,PRJDB15627,,"AP028081,AP028082",,,Illumina NovaSeq; Nanopore MiNION,963x,Flye assembler v. 2.7-b1585; Pilon v. 1.23,2,0,2,7173407,68.13181,7176,6053,,,2013,Japan,Japan,,,,,,,,,,,,,,,,,,,not applicable,not applicable,not applicable,not applicable,,Human,,,,,,,,,,,not applicable,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28450.377,Burkholderia pseudomallei strain Burk178-Type1,Burk178-Type1,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05571215,28450,,,,MLST.Burkholderia_pseudomallei.553,,,,2016-11-30T00:00:00Z,,PRJNA338800,GCF_001887555.1,"CP016909,CP016910","NZ_CP016909.1,NZ_CP016910.1",USAMRIID,PacBio,missing,HGAP3 v. 2.2.0,2,,2,7290949,68.04,7415,6184,sputum,,2011,Australia,Australia,,,,Melioidosis,,,,,,,,,,,,,Genome sequence and assembly of two different colony morphotypes of Burkholderia pseudomallei,collected_by:Royal Darwin Hospital,,,,,,,Melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Respiratory Tract,Respiratory Diseases-Melioidosis HP,28450.378,Burkholderia pseudomallei strain Burk178-Type2,Burk178-Type2,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05571216,28450,,,,MLST.Burkholderia_pseudomallei.553,,,,2016-11-30T00:00:00Z,,PRJNA338800,GCF_001887575.1,"CP016911,CP016912","NZ_CP016911.1,NZ_CP016912.1",USAMRIID,PacBio,missing,HGAP2 v. 2.2.0,2,,2,7290882,68.04,7429,6188,sputum,,2011,Australia,Australia,,,,Melioidosis,,,,,,,,,,,,,Genome sequence and assembly of two different colony morphotypes of Burkholderia pseudomallei,collected_by:Royal Darwin Hospital,,,,,,,Melioidosis,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Melioidosis,Respiratory Tract,Respiratory Diseases-Melioidosis HP,28450.382,Burkholderia pseudomallei strain MSHR6522,MSHR6522,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05607055,28450,,,,MLST.Burkholderia_pseudomallei.437,genotype:ST-437,,,2017-01-27T00:00:00Z,,PRJNA339871,GCA_001974745.1,"MECZ00000000,CM007659",,Menzies School of Health Research,PacBio; Illumina HiSeq,16.0x,Celera Assembler v. 8.3; MGAP v. 1.0,3,,3,7285806,68.15,7460,6199,blood,,2012,Australia,Australia: Northern Territory,,,,Melioidosis,,,,,,,,,,,,,Comparison of isogenic B. pseudomallei isolates obtained from three patients who had received meropenem for melioidosis treatment.,collected_by:Prof. Bart Currie,,,,,,,Melioidosis,,,,,,,,,,,,,,100,1.3,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.383,Burkholderia pseudomallei strain MSHR7929,MSHR7929,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05607057,28450,,,,MLST.Burkholderia_pseudomallei.437,genotype:ST-437,,,2017-01-30T00:00:00Z,,PRJNA339871,GCF_001975065.1,"CP017044,CP017045","NZ_CP017044.1,NZ_CP017045.1",Menzies School of Health Research,PacBio; Illumina HiSeq,16.0x,Celera Assembler v. 8.3; MGAP v. 1.0,2,,2,7248498,68.15,7399,6166,blood,,2013,Australia,Australia: Northern Territory,,,,Melioidosis,,,,,,,,,,,,,Comparison of isogenic B. pseudomallei isolates obtained from three patients who had received meropenem for melioidosis treatment.,collected_by:Prof. Bart Currie,,,,,,,Melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.384,Burkholderia pseudomallei strain MSHR6755,MSHR6755,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05607056,28450,,,,MLST.Burkholderia_pseudomallei.975,genotype:ST-975,,,2017-01-30T00:00:00Z,,PRJNA339871,GCF_001975085.1,"CP017046,CP017047","NZ_CP017046.1,NZ_CP017047.1",Menzies School of Health Research,PacBio; Illumina HiSeq,19.0x,Celera Assembler v. 8.3; MGAP v. 1.0,2,,2,7300607,68.11,7448,6169,blood,,2012,Australia,Australia: Northern Territory,,,,Melioidosis,,,,,,,,,,,,,Comparison of isogenic B. pseudomallei isolates obtained from three patients who had received meropenem for melioidosis treatment.,collected_by:Prof. Bart Currie,,,,,,,Melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.385,Burkholderia pseudomallei strain MSHR5864,MSHR5864,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05607051,28450,,,,MLST.Burkholderia_pseudomallei.975,genotype:ST-975,,,2017-01-30T00:00:00Z,,PRJNA339871,GCF_001975105.1,"CP017048,CP017049","NZ_CP017048.1,NZ_CP017049.1",Menzies School of Health Research,PacBio; Illumina HiSeq,14.0x,HGAP v. 3; MGAP v. 1.0,2,,2,7317380,68.09,7470,6194,blood,,2011,Australia,Australia: Northern Territory,,,,Melioidosis,,,,,,,,,,,,,Comparison of isogenic B. pseudomallei isolates obtained from three patients who had received meropenem for melioidosis treatment.,collected_by:Prof. Bart Currie,,,,,,,Melioidosis,,,,,,,,,,,,,,100,1.6,Respiratory Diseases,Melioidosis,Blood and Circulatory System,Respiratory Diseases-Melioidosis HP,28450.644,Burkholderia pseudomallei strain 2002721684,2002721684,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007558,28450,,,,MLST.Burkholderia_pseudomallei.297,genotype:ST-297\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002110925.1,"CP018375,CP018376",,Centers for Disease Control and Prevention,PacBio,102.7x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7265000,68.04,7667,7258,clinical,,2004,USA,USA: Texas,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.5,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.645,Burkholderia pseudomallei strain 2008724734,2008724734,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007561,28450,,,,MLST.Burkholderia_pseudomallei.95,genotype:ST-95\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002110945.1,"CP018380,CP018381",,Centers for Disease Control and Prevention,PacBio,60.4x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7482386,67.84,7947,7521,clinical,,2009,USA,USA: California ex Mexico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.646,Burkholderia pseudomallei strain 2011756295,2011756295,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007566,28450,,,,MLST.Burkholderia_pseudomallei.297,genotype:ST-297\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002110965.1,"CP018391,CP018392",,Centers for Disease Control and Prevention,PacBio,56.7x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7498324,67.81,7917,7486,clinical,,2012,USA,USA: Florida ex Trinidad,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.647,Burkholderia pseudomallei strain 2011756296,2011756296,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007567,28450,,,,MLST.Burkholderia_pseudomallei.297,genotype:ST-297\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002110985.1,"CP018393,CP018394",,Centers for Disease Control and Prevention,PacBio,125.1x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7300707,67.97,7700,7304,clinical,,2012,USA,USA: Puerto Rico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.7,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.648,Burkholderia pseudomallei strain 2013746878,2013746878,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007572,28450,,,,MLST.Burkholderia_pseudomallei.1038,genotype:ST-1038\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111005.1,"CP018404,CP018405",,Centers for Disease Control and Prevention,PacBio,87.5x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7330383,67.97,7736,7342,clinical,,2013,USA,USA: Rhode Island ex Guatemala,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.651,Burkholderia pseudomallei strain 2002721100,2002721100,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007554,28450,,,,,genotype:ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111065.1,"CP018367,CP018368",,Centers for Disease Control and Prevention,PacBio,128.7x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7347948,67.95,7682,7295,clinical,,1982,USA,USA: Puerto Rico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.652,Burkholderia pseudomallei strain 2002721184,2002721184,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007557,28450,,,,MLST.Burkholderia_pseudomallei.11,genotype:ST-11\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111085.1,"CP018373,CP018374",,Centers for Disease Control and Prevention,PacBio,88.2x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7382136,67.94,7760,7368,clinical,,1960,Ecuador,Ecuador,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.653,Burkholderia pseudomallei strain 2002734728,2002734728,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007559,28450,,,,MLST.Burkholderia_pseudomallei.518,genotype:ST-518\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111105.1,"CP018418,CP018419",,Centers for Disease Control and Prevention,PacBio,71.2x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7234496,68.08,7618,7202,clinical,,2007,USA,USA: California,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.654,Burkholderia pseudomallei strain 2008724860,2008724860,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007563,28450,,,,MLST.Burkholderia_pseudomallei.698,genotype:ST-698\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111125.1,"CP018384,CP018386,CP018385",,Centers for Disease Control and Prevention,PacBio,49.0x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,1,3,7542656,67.79,8011,7530,clinical,,2010,USA,USA: New York ex Aruba,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,3.1,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.655,Burkholderia pseudomallei strain 2010007509,2010007509,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007564,28450,,,,MLST.Burkholderia_pseudomallei.518,genotype:ST-518\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111145.1,"CP018387,CP018388",,Centers for Disease Control and Prevention,PacBio,78.5x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7186084,68.09,7552,7174,clinical,,2009,USA,USA: Arizona ex Costa Rica,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.656,Burkholderia pseudomallei strain 2011756189,2011756189,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007565,28450,,,,MLST.Burkholderia_pseudomallei.92,genotype:ST-92\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111165.1,"CP018389,CP018390",,Centers for Disease Control and Prevention,PacBio,114.9x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7344971,67.96,7727,7351,clinical,,2010,Switzerland,Switzerland: ex Martinique,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.657,Burkholderia pseudomallei strain 2013746776,2013746776,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007568,28450,,,,MLST.Burkholderia_pseudomallei.297,genotype:ST-297\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111185.1,"CP018395,CP018397,CP018396",,Centers for Disease Control and Prevention,PacBio,83.3x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,1,3,7376039,67.99,7808,7425,clinical,,2013,USA,USA: California ex Mexico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.4,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.659,Burkholderia pseudomallei strain 2013746811,2013746811,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007570,28450,,,,MLST.Burkholderia_pseudomallei.17,genotype:ST-17\; ITS type CE\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111225.1,"CP018400,CP018401",,Centers for Disease Control and Prevention,PacBio,104.4x,SMRT Analysis v. 2.3.0; HGAP v. 3;,2,,2,7200858,68.14,7697,7201,clinical,,2013,USA,USA: Ohio,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.;many frameshifted proteins,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,1.7,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.660,Burkholderia pseudomallei strain 2013746877,2013746877,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007571,28450,,,,MLST.Burkholderia_pseudomallei.1038,genotype:ST-1038\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111245.1,"CP018402,CP018403",,Centers for Disease Control and Prevention,PacBio,66.5x,SMRT Analysis v. 2.3.0; HGAP v. 3;,2,,2,7330290,67.97,7757,7349,clinical,,2013,USA,USA: Rhode Island ex Guatemala,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.7,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.662,Burkholderia pseudomallei strain 3000047530,3000047530,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007578,28450,,,,MLST.Burkholderia_pseudomallei.92,genotype:ST-92\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111285.1,"CP018414,CP018415",,Centers for Disease Control and Prevention,PacBio,173.5x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7436525,67.88,7929,7396,clinical,,2014,USA,USA: Illinois ex Mexico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.;many frameshifted proteins,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,1.6,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.663,Burkholderia pseudomallei strain 3000465972,3000465972,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007579,28450,,,,MLST.Burkholderia_pseudomallei.436,genotype:ST-436\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111305.1,"CP018416,CP018417",,Centers for Disease Control and Prevention,PacBio,108.0x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7428404,67.92,7578,6300,clinical,,2015,USA,USA: Georgia ex Panama and Peru,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.666,Burkholderia pseudomallei strain 2008724758,2008724758,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007562,28450,,,,MLST.Burkholderia_pseudomallei.550,genotype:ST-550\; ITS type C\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111365.1,"CP018382,CP018383",,Centers for Disease Control and Prevention,PacBio,128.1x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7383789,67.92,7804,7412,clinical,,2010,USA,USA: California,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.667,Burkholderia pseudomallei strain 3000015486,3000015486,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007577,28450,,,,MLST.Burkholderia_pseudomallei.92,genotype:ST-92\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111385.1,"CP018412,CP018413",,Centers for Disease Control and Prevention,PacBio,98.9x,SMRT Analysis v. 2.3.0; HGAP v. 3;,2,,2,7447673,67.88,7869,7472,clinical,,2015,USA,USA: Texas ex Mexico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.4,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.711,Burkholderia pseudomallei strain 3000015237,3000015237,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007576,28450,,,,MLST.Burkholderia_pseudomallei.951,genotype:ST-951\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111045.1,"CP018410,CP018411",,Centers for Disease Control and Prevention,PacBio,174.0x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7319687,67.94,7730,7328,clinical,,2014,USA,USA: California ex Mexico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.8,0.7,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.713,Burkholderia pseudomallei strain 2002721123,2002721123,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007555,28450,,,,MLST.Burkholderia_pseudomallei.92,genotype:ST-92\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111325.1,"CP018369,CP018370",,Centers for Disease Control and Prevention,PacBio,80.5x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7235491,68.03,7638,7234,clinical,,1998,USA,USA: Puerto Rico,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,99.7,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.714,Burkholderia pseudomallei strain 2002721171,2002721171,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007556,28450,,,,MLST.Burkholderia_pseudomallei.12,genotype:ST-12\; ITS type G\; YLF-positive,,,2017-04-26T00:00:00Z,,PRJNA352974,GCA_002111345.1,"CP018371,CP018372",,Centers for Disease Control and Prevention,PacBio,174.1x,SMRT Analysis v. 2.3.0; HGAP v. 3,2,,2,7191137,68.11,7540,7208,clinical,,1976,Venezuela,Venezuela,,,,melioidosis,,,,,,,,,,,,,WGS was performed on Burkholderia pseudomallei isolates associated with the Western Hemisphere. The goals are to determine phylogenetic relatedness among strains and to improve molecular analysis and subtyping for better epidemiological attribution to enhance public health responses. The relevance is to improve the ability to recognize and respond to cases of melioidosis in the Western Hemisphere since we believe the disease is underreported in this hemisphere.,collected_by:Centers for Disease Control and Prevention,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.736,Burkholderia pseudomallei strain MSHR1435,MSHR1435,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06473485,28450,,,,MLST.Burkholderia_pseudomallei.131,,,,2017-12-18T00:00:00Z,,PRJNA321854,GCA_002843645.1,"CP025264,CP025265",,Northern Arizona University,PacBio,50.0x,Canu v. 1.3,2,,2,7278330,68.09,7686,7458,environment,,2002-08-08,Australia,Australia: Northern Territory,,,,melioidosis,,,,,,,,,,,,,Sequencing of isolates from a chronic B. pseudomallei infection,collected_by:Menzies,,,,,,,melioidosis,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Melioidosis,Other,Respiratory Diseases-Melioidosis HP,28450.812,Burkholderia pseudomallei strain D286,D286,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08120362,28450,,,,MLST.Burkholderia_pseudomallei.289,,,,2018-09-12T00:00:00Z,,PRJNA420802,GCA_003547035.1,"CP025306,CP025307",,Universiti Kebangsaan Malaysia,PacBio,139.0x,SMRT portal analysis v. v2.1.1 release,2,,2,7102313,68.18518,7143,,clinical,isolated from a patient in Malaysia,1986,Malaysia,Malaysia,,,,,,,,,,,,,,,,,Burkholderia pseudomallei D286 was isolated from a patient in Malaysia.,,,,,,,,Missing,,,,,,,,,,,,,,100,3.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28450.828,Burkholderia pseudomallei strain FDAARGOS_592 strain Not applicable,Not applicable,Burkholderia pseudomallei,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10228572,28450,,,,MLST.Burkholderia_pseudomallei.17,,FDA:FDAARGOS_592,,2018-11-20T00:00:00Z,,PRJNA231221,GCA_003798265.1,"CP033705,CP033706",,US Food and Drug Administration,Pacbio; Illumina,35.90x,Canu v. 1.7,2,,2,7146686,68.1553,7528,7326,ucc isolate,,,Thailand,Thailand: Ubon Ratchathani,,,,Meliodosis,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,,,,,,,Meliodosis,Unknown,Unknown,Not applicable,Unknown,,,clinical isolate,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2848143.3,Escherichia coli O85:H1 strain 03-3638,03-3638,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19011648,2848143,O85:H1,,STEC,MLST.Escherichia_coli_1.706,,,,2021-06-22T00:00:00Z,,PRJNA735700,GCA_018986775.1,"CP076714,CP076715,CP076716,CP076717",,Health Canada,Illumina MiSeq/NextSeq and Oxford,61x (Illumina)/x,Unicycler (normal mode) using PE Illumina,1,3,4,5163097,50.494915,5184,4907,missing,,2003,Canada,Canada,,,,,,,,,,,,,,,,,Characterization of shiga toxin (stx) genes in E. coli including novel stx variants/subtypes,collected_by:Health Canada - Bureau of Microbial Hazards,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.38,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,286783.334,Salmonella enterica subsp. enterica serovar Indiana strain SI102,SI102,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450154,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012052605.1,"CP050771,CP050772,CP050773,CP050774,CP050775,CP050776",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,202x,Unicycler v. 0.4.8,1,5,6,4985118,51.891388,5097,4708,diarrheal patient,,2013-01-31,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.335,Salmonella enterica subsp. enterica serovar Indiana strain SI115,SI115,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450157,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012052805.1,"CP050762,CP050763",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,97x,Unicycler v. 0.4.8,1,1,2,4974085,51.853798,5074,4710,diarrheal patient,,2013-11-05,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.336,Salmonella enterica subsp. enterica serovar Indiana strain SI170,SI170,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450158,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012052965.1,"CP050760,CP050761",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,42x,Unicycler v. 0.4.8,1,1,2,5028693,51.801968,5144,4740,diarrheal patient,,2014-09-02,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.338,Salmonella enterica subsp. enterica serovar Indiana strain SI96,SI96,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450153,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012053525.1,"CP050777,CP050778",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,37x,Unicycler v. 0.4.8,1,1,2,4973648,51.85727,5078,4718,diarrheal patient,,2013-07-08,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.339,Salmonella enterica subsp. enterica serovar Indiana strain SI111,SI111,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450156,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012053145.1,"CP050764,CP050765,CP050766,CP050767,CP050768",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,124x,Unicycler v. 0.4.8,1,4,5,4899773,52.014328,4982,4633,diarrheal patient,,2013-11-13,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,99.71,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.345,Salmonella enterica subsp. enterica serovar Indiana strain SI108,SI108,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450155,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012053325.1,"CP050769,CP050770",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,103x,Unicycler v. 0.4.8,1,1,2,5071476,52.011604,5216,4836,diarrheal patient,,2013-09-22,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,286783.407,Salmonella enterica subsp. enterica serovar Indiana strain S530,S530,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962527,286783,Indiana,,,MLST.Salmonella_enterica.17,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015697765.1,CP061118,,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,0,1,5059260,51.865707,5184,4766,stool,,2017-01,China,China:Hangzhou,,,,"Fracture, diarrhea",,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,"Fracture, diarrhea",,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,287.10161,Pseudomonas aeruginosa strain AG1,AG1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13182580,287,,,,MLST.Pseudomonas_aeruginosa.111,,,,2019-11-14T00:00:00Z,,PRJNA587210,GCA_009662315.1,CP045739,,Universidad de Costa Rica,Illumina HiSeq; Oxford Nanopore GridION,400.0x,Unicycler (hybrid) v. 0.4.7,1,,1,7190208,65.70743,6899,6620,sputum-lungs,isolated from a Costa Rican Hospital during 2010,2010,Costa Rica,Costa Rica,,,,Pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa AG1 was isolated from a Costa Rican Hospital during 2010. This strain displays a resistance phenotype to several antibiotics. The genome was sequenced using short (Illumina) and long (Oxford Nanopore) reads technologies. Genome assembly and annotation were finished to identify molecular determinants associated with possible mechanisms underlying its resistance to multiple antibiotics and other phenotypes.,"collected_by:Toval F., Guzman-Marte A., Madriz V., Somogyi T., Rodriguez C., Molina-Mora J.and Garcia F.",,,,,,,Pneumonia,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.10162,Pseudomonas aeruginosa strain ST773,ST773,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12307670,287,,,,MLST.Pseudomonas_aeruginosa.773,genotype:ST773,,,2019-11-15T00:00:00Z,31658962,PRJNA555326,GCA_009664165.1,CP041945,,The University of Texas Health Science Center at Houston,Oxford Nanopore GridION,40x,Celera Assembler v. 1.8,1,,1,6835731,66.09429,6619,6506,urine,,2017-09-29,USA,USA:Houston,,,,sepsis,,,Resistant,Computational Prediction,,,,,,,,,"Submission of consensus genome assemblies from a critically ill patient with polymicrobial infections due to multi-drug resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa who had traveled to India and was also colonized by Candida auris. A precision medicine approach using whole genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181. This case illustrates the rapidly evolving landscape of resistance and its challenges to clinicians.",collected_by:William R. Miller,,,,,,,sepsis,,,,,,,,,,,,,,99.68,0.16,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,287.10273,Pseudomonas aeruginosa strain 1811-13R031,1811-13R031,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13267614,287,,,,MLST.Pseudomonas_aeruginosa.395,,,,2019-11-20T00:00:00Z,,PRJNA589136,GCA_009676765.1,CP046061,,Center for Disease Prevention and Control of PLA,Illumina MiSeq; Oxford Nanopore MiniION,55.55x,Unicycler v. 0.4.8,1,0,1,7344079,65.76664,7088,,sputum,,2018-11-13,China,China,,,,lung infection,,,Susceptible,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa isolate 1811-13R031,collected_by:Kaiying Wang,,,,,,,lung infection,,,,,,,,,,,,,,99.68,0.78,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,287.10274,Pseudomonas aeruginosa strain 1811-18R001,1811-18R001,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13267615,287,,,,MLST.Pseudomonas_aeruginosa.395,,,,2019-11-20T00:00:00Z,,PRJNA589137,GCA_009676785.1,CP046060,,Center for Disease Prevention and Control of PLA,Illumina MiSeq; Oxford Nanopore MiniION,55.65x,Unicycler v. 0.4.8,1,0,1,7343000,65.76752,7087,,sputum,,2018-11-18,China,China,,,,lung infection,,,Susceptible,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa isolate 1811-18R001,collected_by:Kaiying Wang,,,,,,,lung infection,,,,,,,,,,,,,,99.68,0.78,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,287.10441,Pseudomonas aeruginosa strain INP-43,INP-43,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13611833,287,,,,,,,,2020-01-19T00:00:00Z,26048733,PRJNA596064,GCA_009905195.1,CP047592,,Universidad Nacional Autonoma de Mexico,Illumina,80.0x,Velvet v. JUN-2019,1,0,1,6335031,66.43638,5976,5805,cystic fibrosis pediatric isolate,,1998-05-18,Mexico,Mexico,,,,,,,Resistant,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa INP43 is a clinical strain. This strain is a cystic fibrosis pediatric isolate in Mexico with unusual Quorum sensing system.,sample_type:Tissue sample;collected_by:Rafael Coria-Jimenez,,,,,,,,,,,,,,,,,,,,,99.68,0.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.10563,Pseudomonas aeruginosa strain VIT PC9,VIT PC9,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14054838,287,,,,MLST.Pseudomonas_aeruginosa.2041,,,,2020-02-18T00:00:00Z,,PRJNA605318,GCA_010694505.1,CP048791,,Vellore Institute of Technology,Oxford Nanopore MiniION,60.0x,Flye v. 2.7b,1,0,1,6367369,66.44634,7199,5837,pus,,2017-01-11,India,"India: Tamil Nadu, Vellore",,,,Diabetic Foot Ulcer,,,Susceptible,Computational Prediction,,,,,,,,,Multiple drug resistant Pseudomonas aeruginosa CL9 isolated from pus region of Diabetic Foot Ulcer patient,collected_by:Prakhar Srivastava,,,,,,,Diabetic Foot Ulcer,,,,,,,,,,,,,,95.07,0.22,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,287.10573,Pseudomonas aeruginosa strain PcyII-40,PcyII-40,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA6246861,287,non-typable O11,,,MLST.Pseudomonas_aeruginosa.309,,,,2020-01-25T00:00:00Z,,PRJEB35547,GCA_902703195.1,LR739069,,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,1,0,1,6831274,66.12367,6496,6295,clinical,,2010-03-19,France,France,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,"We investigated the characteristics of three Pseudomonas aeruginosa clinical strains naturally resistant to phages belonging to ten different genera. These strains spontaneously release phages and pyocins, and form colonies with a rough aspect. Their genome was completely sequenced showing the presence of multiple prophages, insertion elements, genomic islands, in sharp contrast with the genomes of two strains highly sensitive to phages.",,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.10574,Pseudomonas aeruginosa strain PcyII-29,PcyII-29,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA6246860,287,non-typable O4,,,MLST.Pseudomonas_aeruginosa.175,,,,2020-01-25T00:00:00Z,,PRJEB35547,GCA_902703185.1,LR739068,,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,1,0,1,6621209,66.25574,6225,6056,clinical,,2010-01-06,France,France,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We investigated the characteristics of three Pseudomonas aeruginosa clinical strains naturally resistant to phages belonging to ten different genera. These strains spontaneously release phages and pyocins, and form colonies with a rough aspect. Their genome was completely sequenced showing the presence of multiple prophages, insertion elements, genomic islands, in sharp contrast with the genomes of two strains highly sensitive to phages.",,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.10575,Pseudomonas aeruginosa strain C7-25,C7-25,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA6246859,287,O6,,,MLST.Pseudomonas_aeruginosa.1710,,,,2020-01-25T00:00:00Z,,PRJEB35547,GCA_902703215.1,LR739071,,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,1,0,1,6479881,66.31617,6058,5869,clinical,,2007-02-27,France,France,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We investigated the characteristics of three Pseudomonas aeruginosa clinical strains naturally resistant to phages belonging to ten different genera. These strains spontaneously release phages and pyocins, and form colonies with a rough aspect. Their genome was completely sequenced showing the presence of multiple prophages, insertion elements, genomic islands, in sharp contrast with the genomes of two strains highly sensitive to phages.",,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.10891,Pseudomonas aeruginosa strain CMC-115,CMC-115,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13451386,287,,,,,,not applicable,,2020-04-13T00:00:00Z,,PRJNA593818,GCA_012276675.1,CP046602,,"Virginia Tech Carilion School of Medicine, Carilion Clinic, Virginia Tech Polytechnic",Illumina NextSeq,1500x,Geneious v. 11.0.4,1,0,1,6375262,66.39427,6006,5850,tracheal aspirate,,2010-12-06,USA,USA:VA,,male,71,HCAP - acute pneumonia,,"host_description:acutely ventilated with fever, leukocytosis, increased sputum production;host_disease_outcome:Survived;host_disease_stage:Acute infection;host_health_state:Acute on chronic SDH and COPD",Susceptible,Computational Prediction,,,,,,,,,"Genome 115, a Pseudomonas strain isolated from tracheal aspirate of a pneumonia patient at Carilion Clinic",collected_by:Carilion Roanoke Memorial Hospital,,,,,,,HCAP - acute pneumonia,Acute on chronic SDH and COPD,Survived,"acutely ventilated with fever, leukocytosis, increased sputum production",Acute infection,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11130,Pseudomonas aeruginosa strain Ps33,Ps33,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12815552,287,,,,,,,,2020-05-19T00:00:00Z,,PRJNA573525,GCA_013122735.1,CP044533,,Center for Genome Sciences,Illumina MiSeq,73.0x,SPAdes v. 3.11.0,1,0,1,6297536,66.50856,5932,5902,sepsis/hemoculture,,2006,Mexico,"Mexico:Mexico City, Instituto Nacional de Pediatria",,,,,,,Susceptible,Computational Prediction,,,,,,,,,This project covers the genome sequencing of Pseduomonas aeruginosa clinical strains from Mexico screened for their susceptibility to phage infection,sample_type:hemoculture,,,,,,,,,,,,,,,,,,,,,99.68,0.14,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,287.11186,Pseudomonas aeruginosa strain SCAID PHRX1-2019,SCAID PHRX1-2019,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14968947,287,,,,,,,,2020-05-31T00:00:00Z,,PRJNA627194,GCA_013200975.1,CP053686,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,64.0x,Bowtie v. 1.2.3; SPAdes v. 3.1.0,1,0,1,6335471,66.43973,6098,5781,pharynx,,2019-07-23,Kazakhstan,Kazakhstan: Almaty,,female,7,Tonsilitis,,host_disease_outcome:Recovery;host_disease_stage:Acute tonsilitis,Susceptible,Computational Prediction,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Tonsilitis,,Recovery,,Acute tonsilitis,,,,,,,,,,99.12,0.11,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,287.11536,Pseudomonas aeruginosa strain PSE6684,PSE6684,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14986373,287,,,,MLST.Pseudomonas_aeruginosa.773,,,,2020-06-03T00:00:00Z,,PRJNA634205,GCA_013255565.1,CP053917,,Yonsei University College of Medicine,PacBio RS,87.0x,HGAP v. 3.0,1,0,1,6924367,66.03259,6624,6401,urine,,2019-02-02,South Korea,South Korea,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,NDM-producing Pseudomonas aerugniosa ST773,collected_by:Jun Sung HONG,,,,,,,pneumonia,,,,,,,,,,,,,,99.68,0.55,Respiratory Diseases,Pneumonia,Urinary Tract,Respiratory Diseases-Pneumonia HP,287.11578,Pseudomonas aeruginosa strain DVT429,DVT429,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271777,287,,,,MLST.Pseudomonas_aeruginosa.1094,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343335.1,CP050323,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6805219,66.214386,6540,6376,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.35,0.15,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11579,Pseudomonas aeruginosa strain DVT729,DVT729,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271780,287,,,,MLST.Pseudomonas_aeruginosa.27,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343315.1,CP050322,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6546693,66.35242,6258,6026,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Resistant,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.52,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11580,Pseudomonas aeruginosa strain DVT425,DVT425,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271773,287,,,,MLST.Pseudomonas_aeruginosa.226,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343375.1,CP050325,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6506945,66.39675,6128,5962,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Resistant,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11581,Pseudomonas aeruginosa strain DVT423,DVT423,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271772,287,,,,MLST.Pseudomonas_aeruginosa.17,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343395.1,CP050326,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6716245,66.23046,6359,6178,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11582,Pseudomonas aeruginosa strain DVT427,DVT427,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271775,287,,,,MLST.Pseudomonas_aeruginosa.439,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343355.1,CP050324,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6414921,66.38074,5995,5850,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,100,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11583,Pseudomonas aeruginosa strain DVT421,DVT421,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271770,287,,,,,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343415.1,CP050327,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6065263,66.46802,5720,5520,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.4,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11584,Pseudomonas aeruginosa strain DVT419,DVT419,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271769,287,,,,MLST.Pseudomonas_aeruginosa.1712,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343435.1,CP050328,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6052044,66.304146,5731,5579,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.35,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11585,Pseudomonas aeruginosa strain DVT779,DVT779,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271766,287,,,,,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343475.1,CP050330,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6386887,66.446144,5998,5850,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11586,Pseudomonas aeruginosa strain DVT417,DVT417,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271767,287,,,,MLST.Pseudomonas_aeruginosa.663,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343455.1,CP050329,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6298009,66.498665,5911,5754,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.19,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11587,Pseudomonas aeruginosa strain DVT413,DVT413,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271763,287,,,,MLST.Pseudomonas_aeruginosa.815,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343515.1,CP050332,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6930600,66.068245,6671,6464,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11588,Pseudomonas aeruginosa strain DVT414,DVT414,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271764,287,,,,,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343495.1,CP050331,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6522476,66.32851,6143,5984,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.43,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11589,Pseudomonas aeruginosa strain DVT410,DVT410,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271760,287,,,,,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343555.1,CP050334,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6229931,66.54748,5796,5647,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Resistant,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,98.84,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11590,Pseudomonas aeruginosa strain DVT412,DVT412,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271762,287,,,,MLST.Pseudomonas_aeruginosa.589,,,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343535.1,CP050333,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6394923,66.42721,5994,5836,lung,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,cystic fibrosis,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,cystic fibrosis,,,,,,,,,,,,,,99.49,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.11591,Pseudomonas aeruginosa strain DVT401,DVT401,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14271758,287,,,,,,ATCC:14210,,2020-06-15T00:00:00Z,,PRJNA610040,GCA_013343575.1,CP050335,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,6557595,66.25372,6178,6020,wound,isolated and molecularly characterized phages are lacking,,USA,"USA: Pennsylvania, Pittsburgh",,,,leg ulcer,,,Susceptible,Computational Prediction,,,,,,,,,"Pseudomonas aeruginosa infections are a problem for which new treatment approaches are needed. Bacteriophage therapy is a promising alternative, but large numbers of isolated and molecularly characterized phages are lacking. We used 23 genetically and phenotypically diverse P. aeruginosa isolates from cystic fibrosis patients and clinical infections to screen for lytic bacteriophages present in hospital wastewater.",collected_by:University of Pittsburgh Medical Center,,,,,,,leg ulcer,,,,,,,,,,,,,,99.68,0.11,Gastrointestinal Diseases,Gastritis and Ulcers,Skin and Soft Tissue,Gastrointestinal Diseases-Gastritis and Ulcers HP,287.11595,Pseudomonas aeruginosa strain PABCH09,PABCH09,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183617,287,O6,,,MLST.Pseudomonas_aeruginosa.262,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375775.1,"CP056095,CP056096,CP056097",,Harvard Medical School,PacBio,50X,HGAP v. 2,1,2,3,7038926,65.647,6783,6552,endotracheal tube (ett) or tracheostomy tube,,2013-02-16,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,1.24,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11596,Pseudomonas aeruginosa strain PABCH13,PABCH13,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183615,287,O4,,,MLST.Pseudomonas_aeruginosa.639,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375795.1,CP056093,,Harvard Medical School,PacBio,50X,HGAP v. 2,1,0,1,6496201,66.33779,6150,5982,endotracheal tube (ett) or tracheostomy tube,,2013-04-01,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11597,Pseudomonas aeruginosa strain PABCH10,PABCH10,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183622,287,O10,,,MLST.Pseudomonas_aeruginosa.667,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375815.1,CP056094,,Harvard Medical School,PacBio,50X,HGAP v. 2,1,0,1,7025666,66.09253,6715,6521,endotracheal tube (ett) or tracheostomy tube,,2013-02-20,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.35,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11598,Pseudomonas aeruginosa strain PABCH01,PABCH01,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183620,287,O6,,,MLST.Pseudomonas_aeruginosa.155,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375915.1,CP056100,,Harvard Medical School,PacBio,50X,HGAP v. 2,1,0,1,7046451,65.95178,6797,6583,endotracheal tube (ett) or tracheostomy tube,,2013-01-11,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.49,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11599,Pseudomonas aeruginosa strain PABCH45,PABCH45,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183618,287,O6,,,MLST.Pseudomonas_aeruginosa.959,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375835.1,"CP056101,CP056102",,Harvard Medical School,PacBio,50X,HGAP v. 2,1,1,2,7093372,66.05759,6818,6620,endotracheal tube (ett) or tracheostomy tube,,2013-09-25,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.22,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11600,Pseudomonas aeruginosa strain PABCH14,PABCH14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183616,287,O6,,,MLST.Pseudomonas_aeruginosa.155,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375855.1,CP056092,,Harvard Medical School,PacBio,50X,HGAP v. 2,1,0,1,7123084,65.91527,6844,6631,endotracheal tube (ett) or tracheostomy tube,,2013-04-08,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.38,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11601,Pseudomonas aeruginosa strain PABCH46,PABCH46,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183621,287,O11,,,MLST.Pseudomonas_aeruginosa.446,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375875.1,CP056089,,Harvard Medical School,PacBio,50X,HGAP v. 2,1,0,1,6866206,65.77057,6445,6232,endotracheal tube (ett) or tracheostomy tube,,2013-10-09,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.45,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11602,Pseudomonas aeruginosa strain PABCH42,PABCH42,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183619,287,O6,,,MLST.Pseudomonas_aeruginosa.179,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375895.1,"CP056090,CP056091",,Harvard Medical School,PacBio,50X,HGAP v. 2,1,1,2,7274920,65.69593,7021,6798,endotracheal tube (ett) or tracheostomy tube,,2013-07-26,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Resistant,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.15,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11738,Pseudomonas aeruginosa strain PABCH05,PABCH05,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15183614,287,O9,,,MLST.Pseudomonas_aeruginosa.2062,,,,2020-06-29T00:00:00Z,,PRJNA638217,GCA_013375755.1,"CP056098,CP056099",,Harvard Medical School,PacBio,50X,HGAP v. 2,1,1,2,6319265,66.45931,5983,5824,endotracheal tube (ett) or tracheostomy tube,,2012-12-13,USA,USA:Boston,,,,Ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,We sampled Pseudomonas aeruginosa isolates from mechanically ventilated patients in the pediatric or cardiac intensive care unit of Boston Children's Hospital who exhibited signs of ventilator-associated pneumonia. Genomes of isolates were sequenced for long-reads on the PacBio platform and assembled.,collected_by:Gregory P. Priebe,,,,,,,Ventilator-associated pneumonia,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11740,Pseudomonas aeruginosa strain SE5331,SE5331,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13419003,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2020-07-08T00:00:00Z,,PRJNA592264,GCA_013393665.1,CP046402,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,7056430,65.89346,6781,6552,respiratory,,2018-03-05,China,China:Suzhou,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain SE5331,collected_by:a teaching hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11741,Pseudomonas aeruginosa strain SE5369,SE5369,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13419538,287,,,,MLST.Pseudomonas_aeruginosa.179,,,,2020-07-08T00:00:00Z,,PRJNA592269,GCA_013393685.1,CP046403,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v 3.0,1,0,1,7153217,65.81547,6870,6647,shunt fluid,,2016-09-14,China,China:Suzhou,,,,peritonitis,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain SE5369,collected_by:a teaching hospital,,,,,,,peritonitis,,,,,,,,,,,,,,99.68,0.15,Gastrointestinal Diseases,Peritoneal Conditions,Other,Gastrointestinal Diseases-Peritoneal Conditions HP,287.11742,Pseudomonas aeruginosa strain SE5416,SE5416,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13419547,287,,,,MLST.Pseudomonas_aeruginosa.697,,,,2020-07-08T00:00:00Z,,PRJNA592271,GCA_013393705.1,CP046404,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6874270,66.06268,6585,6387,sputum,,2013-01-11,China,China:Suzhou,,,,Infection caused by fracture,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain SE5416,collected_by:a teaching hospital,,,,,,,Infection caused by fracture,,,,,,,,,,,,,,99.68,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.11744,Pseudomonas aeruginosa strain SE5458,SE5458,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13419657,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2020-07-08T00:00:00Z,,PRJNA592278,GCA_013394475.1,CP046406,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,7157752,65.95602,6986,6754,respiratory,,2011-01-15,China,China:Suzhou,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain SE5458,collected_by:a teaching hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.68,0.46,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.11748,Pseudomonas aeruginosa strain UAB2PBS,UAB2PBS,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687768,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013414905.1,CP053110,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264519,66.55599,5813,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11749,Pseudomonas aeruginosa strain UAB2CT,UAB2CT,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687767,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013414925.1,CP053111,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264482,66.5559,5811,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11750,Pseudomonas aeruginosa strain PAO1PBS,PAO1PBS,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687766,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013414945.1,CP053112,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264534,66.555954,5811,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11751,Pseudomonas aeruginosa strain PAO1CT,PAO1CT,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687765,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013414965.1,CP053113,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264575,66.55608,5815,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11752,Pseudomonas aeruginosa strain P4PBS,P4PBS,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687764,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013414985.1,CP053114,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264575,66.555984,5815,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11753,Pseudomonas aeruginosa strain P4CT,P4CT,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687763,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013415005.1,CP053115,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264523,66.55596,5811,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11754,Pseudomonas aeruginosa strain P16PBS,P16PBS,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687762,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013415025.1,CP053116,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264523,66.55598,5815,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11755,Pseudomonas aeruginosa strain P16CT,P16CT,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687761,287,,,,MLST.Pseudomonas_aeruginosa.266,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013415045.1,CP053117,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264654,66.56158,5809,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11756,Pseudomonas aeruginosa strain A17CT,A17CT,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687759,287,,,,MLST.Pseudomonas_aeruginosa.511,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013415085.1,CP053119,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264758,66.55771,5811,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Resistant,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.11757,Pseudomonas aeruginosa strain A17PBS,A17PBS,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14687760,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2020-07-14T00:00:00Z,,PRJNA627527,GCA_013415065.1,CP053118,,University of Adelaide,Illumina MiSeq,100x,Other v. bwa 0.7.17-r1188,1,0,1,6264506,66.555885,5814,,respiratory tract,,2017-12-09,Australia,Australia: Adelaide,,,,Chronic rhinosinusitis,,,Susceptible,Computational Prediction,,,,,,,,,"Whole genome sequencing was performed on Pseudomonas aeruginosa human respiratory tract isolates from P. aeruginosa biofilms treated with either a bacteriophage cocktail, or the vehicle control.",collected_by:University of Adelaide,,,,,,,Chronic rhinosinusitis,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Rhinosinusitis,Respiratory Tract,Respiratory Diseases-Rhinosinusitis HP,287.12049,Pseudomonas aeruginosa strain GIMC5034:PA52Ts32,GIMC5034:PA52Ts32,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15501998,287,,,,MLST.Pseudomonas_aeruginosa.357,genotype:ST357,,,2020-08-07T00:00:00Z,,PRJNA625416,GCA_014109785.1,"CP059063,CP059062",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina NextSeq,190.0x,CLC Genomics Workbench v. 20; SPAdes,1,1,2,6824624,65.92645,6383,6419,tracheal aspirate,isolated in intensive care unit,2020-01,Russia,Russia: Moscow,,,,no_data,,,Resistant,Computational Prediction,,,,,,,,,Multidrug-resistant strain isolated in intensive care unit.,collected_by:Kovyrshina A.V.,,,,,,,no_data,,,,,,,,,,,,,,99.35,0.55,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.12055,Pseudomonas aeruginosa strain 401853,401853,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15732853,287,,,,,,,,2020-08-11T00:00:00Z,,PRJNA655354,GCA_014155905.1,CP059995,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,7092673,65.812004,6846,6612,missing,,2015,China,China: Nanjing,,,,pancreatitis,,,Resistant,Computational Prediction,,,,,,,,,To reveal the resistance mechanism of strain 401853,collected_by:Beijing Institute of Microbiology and Epidemiology,,,,,,,pancreatitis,,,,,,,,,,,,,,99.68,0.19,Gastrointestinal Diseases,Pancreatic Disorders,Other,Gastrointestinal Diseases-Pancreatic Disorders HP,287.12057,Pseudomonas aeruginosa strain JNQH-PA57,JNQH-PA57,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15755534,287,,,mucoid type,MLST.Pseudomonas_aeruginosa.1197,,,,2020-08-17T00:00:00Z,,PRJNA655803,GCA_014217315.1,CP060086,,"The First Affiliated Hospital of Shandong First Medical University,",Illumina NovaSeq; Oxford Nanopore,147.0x,unicycler v. 0.4.8,1,0,1,6747067,66.02977,6364,6160,the sputum of a pneumonia patient,,2019-09-18,China,China: Shandong,,male,86,heart failure combined pulmonary infection,,,Susceptible,Computational Prediction,,,,,,,,,"The prevalence of multidrug-resistant (MDR) Pseudomonas aeruginosa is increasingly being implicated worldwide in a variety of infections, and is associated with high mortality rates. Here, we report the complete genome sequence of a mucoid strain P. aeruginosa JNQH-PA57 that exhibits high levels of resistance to cephalosporins and carbapenem. The dataset presented in this study provides essential insights into the underlying mechanisms of the highly antimicrobial-resistant of this mucoid P. aeruginosa strain and assists in the development of effective control strategies.",collected_by:Yujiao Wang,,,,,,,heart failure combined pulmonary infection,,,,,mucoid type,,,,,,,,,99.57,0.26,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.13268,Pseudomonas aeruginosa strain PA179,PA179,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15332912,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2020-09-28T00:00:00Z,,PRJNA640813,GCA_014775635.1,CP058257,,Imam Abdulrahman bin faisal university,Illumina HiSeq,100.0x,SOAPdenovo v. 1.05,1,0,1,6580692,66.113846,6245,6023,blood,,2017,Saudi Arabia,Saudi Arabia: Khobar,,,,sepsis,,,Resistant,Computational Prediction,,,,,,,,,An XDR-Pseudomonas strain was isolated from a sepsis case and a whole genome sequences was carried out to characterize the resistant mechanisms,collected_by:Aisha Alamri,,,,,,,sepsis,,,,,,,,,,,,,,99.68,0.5,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,287.13272,Pseudomonas aeruginosa strain mPA08-31,mPA08-31,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16435645,287,,,,MLST.Pseudomonas_aeruginosa.683,,,,2020-10-28T00:00:00Z,,PRJNA669133,GCA_015034565.1,CP063237,,University of Kansas,Illumina NextSeq,95.0x,Velvet v. Oct-2020,1,0,1,6735669,66.190865,6427,6241,,,2017-06,USA,USA: Alabama,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Genome sequence of Pseudomonas aeruginosa mPA08-31, a mucoid clinical isolate cultured from patients with cystic fibrosis at the University of Alabama at Birmingham. mPA08-31 is currently in use in experiments for developing a vaccine for Pseumonas aeruginosa.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.68,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.13705,Pseudomonas aeruginosa strain C-I-1,C-I-1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15783929,287,,,,,genotype:ST3227,,,2020-12-14T00:00:00Z,,PRJNA656414,GCA_015697605.1,CP060241,,Normandie Univ,PacBio Sequel,150x,smrtlink v. v8,1,0,1,6325392,66.45175,5946,5912,urine,,2016-11-01,France,France: Rouen,,male,82,Urinary Tract Infetion,,,Susceptible,Computational Prediction,,,,,,,,,"We used whole genome sequencing to investigate the sequential urinary isolates of 7 patients colonized and/or infected by P. aeruginosa, and study within-host P. aeruginosa population diversity at a given time and over time, and we then explored the impact of the genetic variations observed on phenotypic characteristics of the isolates such as fitness and biofilm production.",collected_by:Rouen University Hospital,,,,,,,Urinary Tract Infetion,,,,,,,,,,,,,,99.68,0.11,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.13706,Pseudomonas aeruginosa strain G-I-1,G-I-1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15783930,287,,,,MLST.Pseudomonas_aeruginosa.232,genotype:ST232,,,2020-12-14T00:00:00Z,,PRJNA656414,GCA_015697465.1,CP060240,,Normandie Univ,PacBio Sequel,150x,smrtlink v. v8,1,0,1,6480192,66.33556,6169,6118,urine,,2017-11-18,France,France: Rouen,,male,77,Urinary Tract Infetion,,,Susceptible,Computational Prediction,,,,,,,,,"We used whole genome sequencing to investigate the sequential urinary isolates of 7 patients colonized and/or infected by P. aeruginosa, and study within-host P. aeruginosa population diversity at a given time and over time, and we then explored the impact of the genetic variations observed on phenotypic characteristics of the isolates such as fitness and biofilm production.",collected_by:Rouen University Hospital,,,,,,,Urinary Tract Infetion,,,,,,,,,,,,,,99.68,0.14,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.13708,Pseudomonas aeruginosa strain A-I-1,A-I-1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15783927,287,,,,MLST.Pseudomonas_aeruginosa.111,genotype:ST111,,,2020-12-14T00:00:00Z,,PRJNA656414,GCA_015697665.1,CP060243,,Normandie Univ,PacBio Sequel,150x,smrtlink v. v8,1,0,1,7087087,65.834595,6868,6780,urine,,2016-07-18,France,France: Rouen,,female,70,Urinary Tract Infetion,,,Resistant,Computational Prediction,,,,,,,,,"We used whole genome sequencing to investigate the sequential urinary isolates of 7 patients colonized and/or infected by P. aeruginosa, and study within-host P. aeruginosa population diversity at a given time and over time, and we then explored the impact of the genetic variations observed on phenotypic characteristics of the isolates such as fitness and biofilm production.",collected_by:Rouen University Hospital,,,,,,,Urinary Tract Infetion,,,,,,,,,,,,,,99.68,0.11,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.13714,Pseudomonas aeruginosa strain P33,P33,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16965915,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2020-12-08T00:00:00Z,,PRJNA681715,GCA_015832055.1,"CP065412,CP065413,CP065414,CP065415,CP065416",,Sir Run Run Shaw Hospital,Illumina,100.0x,Unicycler v. v. 0.4.7,1,4,5,7117586,65.71876,6816,6598,,,2019-08-27,China,China:Hangzhou,,,,,,,Resistant,Computational Prediction,,,,,,,,,"the epidemic Pseudomonas aeruginosa ST463 in Hangzhou, China",sample_type:metagenomic assembly,,,,,,,,,,,,,,,,,,,,,99.35,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.13715,Pseudomonas aeruginosa strain P23,P23,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16965916,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2020-12-08T00:00:00Z,,PRJNA681716,GCA_015832075.1,"CP065417,CP065418",,Sir Run Run Shaw Hospital,Illumina,100.0x,Unicycler v. v. 0.4.7,1,1,2,6950191,65.824554,6585,6383,,,2019-08-20,China,China:Hangzhou,,,,,,,Resistant,Computational Prediction,,,,,,,,,"the epidemic Pseudomonas aeruginosa ST463 in Hangzhou, China",sample_type:metagenomic assembly,,,,,,,,,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.13729,Pseudomonas aeruginosa strain CMC-097,CMC-097,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15950776,287,,,,MLST.Pseudomonas_aeruginosa.282,,,,2020-12-15T00:00:00Z,,PRJNA660482,GCA_016064595.1,CP065848,,"Virginia Tech Carilion School of Medicine, Carilion Clinic, Virginia Tech Polytechnic",Illumina NextSeq,1487.0x,Geneious v. 11.0.4,1,0,1,7044064,66.0635,6765,6550,tracheal aspirate,isolated from the tracheal aspirate of a ventilator-associated pneumonia patient,2010-10-03,USA,USA:VA,,female,51,Chronic respiratory failure,,"host_description:Chronically ventilated, stable respiratory status, systemic inflammatory response due to PICC line infection;host_disease_outcome:Survived;host_disease_stage:Chronic colonization, health care associated;host_health_state:Chronic respiratory failure due to quadriplegia, PICC line from previous MDR Pseudomonas pneumonia",Resistant,Computational Prediction,,,,,,,,,A clinical strain of Pseudomonas aeruginosa isolated from the tracheal aspirate of a ventilator-associated pneumonia patient.,collected_by:Carilion Roanoke Memorial Hospital,,,,,,,Chronic respiratory failure,"Chronic respiratory failure due to quadriplegia, PICC line from previous MDR Pseudomonas pneumonia",Survived,"Chronically ventilated, stable respiratory status, systemic inflammatory response due to PICC line infection","Chronic colonization, health care associated",,,,,,,,,,99.68,0.43,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.13844,Pseudomonas aeruginosa strain LYSZa7,LYSZa7,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15770402,287,,,,MLST.Pseudomonas_aeruginosa.1445,,,,2021-01-08T00:00:00Z,,PRJNA656096,GCA_016584725.1,CP061699,,Southern University of Science and Technology,PacBio Sequel,376.0x,HGAP v. 4,1,0,1,6534364,66.20526,6165,5961,covid-19 patient who suffered persistent bacterial coinfection and eventually recovered from critical illness,isolated from a COVID-19 patient who suffered persistent bacterial coinfection and eventually recovered from critical illness,2020-02,China,"China:Shenzhen,Guangdong",,,,,,,Susceptible,Computational Prediction,,,,,,,,,This study characterized genetically adapted Pseudomonas aeruginosa small colony variants isolated from a COVID-19 patient who suffered persistent bacterial coinfection and eventually recovered from critical illness.,,Human Biome,respiratory,sputum,Strain was isolated from sputum sample and cultured in lab.,,,,,,,,,,,,,Human Biome,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.13863,Pseudomonas aeruginosa strain 1903031130,1903031130,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15834152,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2021-01-22T00:00:00Z,,PRJNA657641,GCA_016745195.1,CP060392,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,0,1,6905506,66.01244,6541,6351,sputum,,2019,China,China: Henan,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain 1903031130,collected_by:a teaching hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.14047,Pseudomonas aeruginosa strain 152962,152962,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17575725,287,,,,MLST.Pseudomonas_aeruginosa.654,,,,2021-02-07T00:00:00Z,,PRJNA548476,GCA_016811975.1,CP069198,,French National Center for Antibiotics Resistance,Oxford Nanopore MinION,136x,Flye v. 2,1,0,1,6950174,65.95348,6613,6398,blood,,2015-07-01,France,France: Paris,,,,Sepsis,,,Resistant,Computational Prediction,,,,,,,,,Genetic context of CTX-M producing Pseudomonas aeruginosa,collected_by:French NRC,,,,,,,Sepsis,,,,,,,,,,,,,,99.43,0.11,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,287.14070,Pseudomonas aeruginosa strain PARM801,PARM801,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05383898,287,,,,,,,,2021-02-11T00:00:00Z,,PRJNA328898,GCA_016864415.1,CP024024,,Peking university people's hospital,Illumina HiSeq,100.0x,SOAPdenovo v. 2.3.0,1,0,1,7130555,65.7632,6813,,blood,,2016,China,China: Beijing,,,,acute pulmonary infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome sequencing were performed on a Pseudomonas aeruginosa isolate which caused acute pulmonary infection. It is differ from other projects because the genome is larger and more complicate.,sample_type:cell culture;collected_by:Peking university people's hospital,,,,,,,acute pulmonary infection,,,,,,,,,,,,,,99.68,0.6,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases HP,287.14257,Pseudomonas aeruginosa strain B17932,B17932,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17915152,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2021-02-24T00:00:00Z,,PRJNA701857,GCA_016925475.1,"CP070471,CP070472,CP070473",,Christian Medical College,Illumina; Oxford Nanopore,89.0x,Canu v. 1.8,1,2,3,6850198,65.81786,6460,6235,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Pseudomonas aeruginosa B17932,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,99.68,0.54,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,287.14258,Pseudomonas aeruginosa strain B17416,B17416,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17915141,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2021-02-24T00:00:00Z,,PRJNA701855,GCA_016925455.1,"CP070467,CP070468,CP070469,CP070470",,Christian Medical College,Illumina; Oxford Nanopore,84.0x,Canu v. 1.8,1,3,4,6850181,65.81775,6462,6235,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Pseudomonas aeruginosa B17416,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,99.68,0.54,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,287.14277,Pseudomonas aeruginosa strain LYSZa5,LYSZa5,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN18237805,287,,,,,,,,2021-03-18T00:00:00Z,,PRJNA712958,GCA_017378395.1,CP071730,,Southern University of Science and Technology,PacBio RSII,1115.0x,HGAP4 v. v9.0,1,0,1,6638990,66.23619,6287,6097,,,2020-02,China,China:Shenzhen,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"P. aeruginosa isolates, a top coinfecting bacterium in COVID-19 patients,were collected from two critically illed COVID-19 patients and analyzed the adaptation and convergent evolution of nosocomial P. aeruginosa during coinfection in COVID-19 patients. We sequenced and compared the genomes and transcriptomes of P. aeruginosa isolates for the evolutionary traits.",sample_type:respiratory sample,,,,,,,,,,,,,,,,,,,,,99.68,0.48,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14278,Pseudomonas aeruginosa strain LYSZa2,LYSZa2,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN18237922,287,,,,MLST.Pseudomonas_aeruginosa.1074,,,,2021-03-18T00:00:00Z,,PRJNA712961,GCA_017378475.1,CP071731,,Southern University of Science and Technology,PacBio RSII,1252.0x,HGAP4 v. v9.0,1,0,1,6638980,66.23621,6288,6097,,,2020-02,China,China:Shenzhen,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"P. aeruginosa isolates, a top coinfecting bacterium in COVID-19 patients,were collected from two critically illed COVID-19 patients and analyzed the adaptation and convergent evolution of nosocomial P. aeruginosa during coinfection in COVID-19 patients. We sequenced and compared the genomes and transcriptomes of P. aeruginosa isolates for the evolutionary traits.",sample_type:respiratory sample,,,,,,,,,,,,,,,,,,,,,99.68,0.48,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14719,Pseudomonas aeruginosa strain NDTH9845,NDTH9845,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN18738583,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2021-04-24T00:00:00Z,,PRJNA721782,GCA_018138045.1,"CP073080,CP073081",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore MinION; Illumina,70.0x,Unicycler v. 0.4.8,1,1,2,7600543,65.15849,7411,7127,,,2018-11,China,China: Nanjing,,,,,,,Resistant,Computational Prediction,,,,,,,,,Clinical Pseudomonas aeruginosa isolates carring blaAFM,,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.68,1.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14720,Pseudomonas aeruginosa strain WTJH17,WTJH17,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN18738584,287,,,,MLST.Pseudomonas_aeruginosa.260,,,,2021-04-24T00:00:00Z,,PRJNA721782,GCA_018138065.1,"CP073082,CP073083",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Illumina; Oxford Nanopore MinION,153.0x,Unicycler v. 0.4.8,1,1,2,6826424,65.798386,6514,6307,,,2018-02,China,China: Wuhan,,,,,,,Resistant,Computational Prediction,,,,,,,,,Clinical Pseudomonas aeruginosa isolates carring blaAFM,,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.68,1.32,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14732,Pseudomonas aeruginosa strain PAG7,PAG7,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16881673,287,,,,MLST.Pseudomonas_aeruginosa.1639,,,,2021-04-27T00:00:00Z,,PRJNA680489,GCA_018141565.1,CP065374,,College of Life Science,Oxford Nanopore PromethION,105.0x,flye v. 2.7,1,0,1,6715242,66.2025,6423,6210,urine,,2016-07,China,China:Shaanxi,,,,urine infection,,,Resistant,Computational Prediction,,,,,,,,,To gain understanding of the genetic features of opportunistic pathogen,collected_by:Northwest University,,,,,,,urine infection,,,,,,,,,,,,,,99.68,0.43,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.14733,Pseudomonas aeruginosa strain PAS6,PAS6,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17065252,287,,,,MLST.Pseudomonas_aeruginosa.1639,,,,2021-04-27T00:00:00Z,,PRJNA684637,GCA_018141625.1,CP065947,,College of Life Science,Oxford Nanopore PromethION,105.0x,flye v. 2.7,1,0,1,6742928,66.20431,6459,6235,urine,,2016-07,China,China:Shaanxi,,,,urine infection,,,Resistant,Computational Prediction,,,,,,,,,To gain understanding of the genetic features of opportunistic pathogen,collected_by:Northwest University,,,,,,,urine infection,,,,,,,,,,,,,,99.68,0.43,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.14734,Pseudomonas aeruginosa strain PAM68,PAM68,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17065268,287,,,,MLST.Pseudomonas_aeruginosa.1639,,,,2021-04-27T00:00:00Z,,PRJNA684639,GCA_018141645.1,CP065948,,College of Life Science,Oxford Nanopore PromethION,105.0x,flye v. 2.7,1,0,1,6560248,66.15338,6278,6084,urine,,2016-07,China,China:Shaanxi,,,,urine infection,,,Resistant,Computational Prediction,,,,,,,,,To gain understanding of the genetic features of opportunistic pathogen,collected_by:Northwest University,,,,,,,urine infection,,,,,,,,,,,,,,99.68,0.43,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.14742,Pseudomonas aeruginosa strain ZBX-P23,ZBX-P23,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16132411,287,,,,MLST.Pseudomonas_aeruginosa.233,,,,2021-05-05T00:00:00Z,,PRJNA663432,GCA_018279245.1,CP061777,,Lebanese American University,PacBio Sequel,30X,HGAP v. 4,1,0,1,7168136,65.861626,6854,6632,dta,,2018-02-16,Lebanon,Lebanon: Beirut,,,,Pseudomonas infection,,,Resistant,Computational Prediction,,,,,,,,,Mechanisms of Resistance Against Ceftolozane/Tazobactam in Pseudomonas aeruginosa Clinical Isolates in Lebanon,collected_by:George F. Araj,,,,,,,Pseudomonas infection,,,,,,,,,,,,,,99.35,0.49,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14743,Pseudomonas aeruginosa strain ZBX-P13,ZBX-P13,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16132401,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2021-05-05T00:00:00Z,,PRJNA663432,GCA_018279265.1,CP061778,,Lebanese American University,PacBio Sequel,30X,HGAP v. 4,1,0,1,6878937,65.82877,6519,6277,dta,,2018-04-30,Lebanon,Lebanon: Beirut,,,,Pseudomonas infection,,,Resistant,Computational Prediction,,,,,,,,,Mechanisms of Resistance Against Ceftolozane/Tazobactam in Pseudomonas aeruginosa Clinical Isolates in Lebanon,collected_by:George F. Araj,,,,,,,Pseudomonas infection,,,,,,,,,,,,,,99.68,0.55,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14744,Pseudomonas aeruginosa strain ZBX-P12,ZBX-P12,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16132400,287,,,,MLST.Pseudomonas_aeruginosa.233,,,,2021-05-05T00:00:00Z,,PRJNA663432,GCA_018279285.1,CP061779,,Lebanese American University,PacBio Sequel,30X,HGAP v. 4,1,0,1,7080089,65.883934,6768,6546,urine,,2018-07-30,Lebanon,Lebanon: Beirut,,,,Pseudomonas infection,,,Resistant,Computational Prediction,,,,,,,,,Mechanisms of Resistance Against Ceftolozane/Tazobactam in Pseudomonas aeruginosa Clinical Isolates in Lebanon,collected_by:George F. Araj,,,,,,,Pseudomonas infection,,,,,,,,,,,,,,99.35,0.11,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.14745,Pseudomonas aeruginosa strain ZBX-P11,ZBX-P11,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN16132399,287,,,,MLST.Pseudomonas_aeruginosa.316,,,,2021-05-05T00:00:00Z,,PRJNA663432,GCA_018279305.1,CP061780,,Lebanese American University,PacBio Sequel,30X,HGAP v. 4,1,0,1,6734601,66.15412,6348,6169,dta,,2018-09-21,Lebanon,Lebanon: Beirut,,,,Pseudomonas infection,,,Susceptible,Computational Prediction,,,,,,,,,Mechanisms of Resistance Against Ceftolozane/Tazobactam in Pseudomonas aeruginosa Clinical Isolates in Lebanon,collected_by:George F. Araj,,,,,,,Pseudomonas infection,,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.14821,Pseudomonas aeruginosa strain PA790,PA790,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN19136540,287,,,,MLST.Pseudomonas_aeruginosa.773,,,,2021-05-23T00:00:00Z,,PRJNA729627,GCA_018448985.1,CP075176,,Sanjay Gandhi Post Graduate Institute of Medical Sciences,Illumina HiSeq; Oxford Nanopore MinION,114.01x,Unicycler v. 0.4.8,1,0,1,6932250,66.025185,6664,6451,urine,"isolated at Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India",2019-01-16,India,India: Lucknow,,,,Urinary Tract Infection,,,Resistant,Computational Prediction,,,,,,,,,"The Pseudomonas aeruginosa PA790 was isolated at Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India. Whole Genome Sequencing was performed to understand its phylogeny and study the presence of AMR genes.","collected_by:Department of Microbiology, SGPGIMS",,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,99.68,0.16,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.15252,Pseudomonas aeruginosa strain TL1285,TL1285,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN14884364,287,,,,,,,,2021-06-22T00:00:00Z,,PRJNA631587,GCA_018986715.1,CP053390,,wenzhou medical university,PacBio RSII,80.0x,canu v. 1.7,1,0,1,6609407,66.06024,6373,6074,,,2008,China,China: Wenzhou,,,,,,,Resistant,Computational Prediction,,,,,,,,,clinical isolates drug resistance monitoring,sample_type:blood,,,,,,,,,,,,,,,,,,,,,99.1,0.78,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.15852,Pseudomonas aeruginosa strain TL3773,TL3773,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20342957,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2021-07-28T00:00:00Z,,PRJNA748735,GCA_019379355.1,"CP080011,CP080012",,First affiliated hospital of Wenzhou medical university,Oxford Nanopore,248.0x,HGAP v. FEB-2021,1,1,2,6760516,65.73201,6430,6223,blood,,2018-05-23,China,China,,,,"severe sepsis, urinary tract infection and lung infection",,,Resistant,Computational Prediction,,,,,,,,,TL3773:KPC-2-producing multidrug-resistant clinical Pseudomonas aeruginosa carrying two crpP-like genes,"collected_by:Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University",,,,,,,"severe sepsis, urinary tract infection and lung infection",,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Lung Diseases,Blood and Circulatory System,Respiratory Diseases-Lung Diseases HP,287.15907,Pseudomonas aeruginosa strain UNC_PaerCF14,UNC_PaerCF14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362537,287,,,,,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434155.1,CP080285,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,246x,Flye v. 2.8.3-b1705,1,0,1,6110239,66.58055,5756,5545,sputum,,2018-11-15,USA,"USA: Chapel Hill, North Carolina",,,,,,,Resistant,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.69,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15908,Pseudomonas aeruginosa strain UNC_PaerCF05,UNC_PaerCF05,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362534,287,,,,,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434175.1,CP080288,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,265x,Flye v. 2.8.3-b1705,1,0,1,6140089,66.56392,5794,5595,sputum,,2018-04-19,USA,"USA: Chapel Hill, North Carolina",,,,,,,Resistant,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.63,0.16,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15909,Pseudomonas aeruginosa strain UNC_PaerCF17,UNC_PaerCF17,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362539,287,,,,MLST.Pseudomonas_aeruginosa.882,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434095.1,CP080281,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,233x,Flye v. 2.8.3-b1705,1,0,1,6347079,66.47866,6000,5793,sputum,,2012-08-02,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.29,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15911,Pseudomonas aeruginosa strain UNC_PaerCF16,UNC_PaerCF16,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362538,287,,,,MLST.Pseudomonas_aeruginosa.483,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434115.1,"CP080282,CP080283,CP080284",,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,261x,Flye v. 2.8.3-b1705,1,2,3,6471169,66.34695,6309,5916,sputum,,2010-10-28,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,97.85,0.27,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15912,Pseudomonas aeruginosa strain UNC_PaerCF20,UNC_PaerCF20,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362540,287,,,,MLST.Pseudomonas_aeruginosa.179,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434075.1,CP080280,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,87x,Flye v. 2.8.3-b1705,1,0,1,6792133,66.17079,6391,6199,sputum,,2011-09-23,USA,"USA: Chapel Hill, North Carolina",,,,,,,Resistant,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.59,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15913,Pseudomonas aeruginosa strain UNC_PaerCF12,UNC_PaerCF12,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362536,287,,,,MLST.Pseudomonas_aeruginosa.1720,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434135.1,CP080286,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,5x,Flye v. 2.8.3-b1705,1,0,1,6300755,66.4974,5932,5763,sputum,,2018-11-08,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.81,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.15914,Pseudomonas aeruginosa strain UNC_PaerCF11,UNC_PaerCF11,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20362535,287,,,,MLST.Pseudomonas_aeruginosa.2106,,,,2021-08-02T00:00:00Z,,PRJNA749299,GCA_019434195.1,CP080287,,University of North Carolina at Chapel Hill,Oxford Nanopore GridION,31x,Flye v. 2.8.3-b1705,1,0,1,6520583,66.34396,6259,5953,sputum,,2018-10-08,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24) which seeks to characterize clinical isolates of P. aeruginosa to identify strains with increased likelihood of establishing chronic lung infections.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,98.09,0.22,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.16517,Pseudomonas aeruginosa strain P8W,P8W,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20703519,287,,,,MLST.Pseudomonas_aeruginosa.664,,,,2021-08-24T00:00:00Z,,PRJNA753640,GCA_019738995.1,"CP081477,CP081478,CP081479",,Nankai University,Oxford Nanopore MinION,92.11x,Canu v. v1.5,1,2,3,7472793,65.56779,7469,7151,burn wound,isolated Pseudomonas aeruginosa strain P9W,2018-03-10,China,"China:Tianjin,Affiliated Hospital of Nankai University",,,,,,,Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing(WGS) of clinical isolated Pseudomonas aeruginosa strain P9W.,sample_type:burn wound,,,,,,,,,,,,,,,,,,,,,99.68,1.63,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.16551,Pseudomonas aeruginosa strain SCAID WND1-2021 (9/195) strain SCAID WND1-2021 (9/195) strain SCAID WND1-2021 (9/195),SCAID WND1-2021 (9/195),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20982451,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915445.1,CP082822,,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,210x,Canu v. 2.0,1,0,1,7093992,65.89944,6926,6675,swab from wound,,2021-03-10,Kazakhstan,Kazakhstan: Almaty,,,,wound discharge,,,Resistant;Susceptible;Intermediate,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,wound discharge,,,,,,,,,,,,,,99.68,0.51,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,287.16552,Pseudomonas aeruginosa strain SCAID TST-2021 (7/157) strain SCAID TST-2021 (7/157) strain SCAID TST-2021 (7/157),SCAID TST-2021 (7/157),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20982450,287,,,,MLST.Pseudomonas_aeruginosa.308,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915465.1,CP082823,,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,82x,Canu v. 2.0,1,0,1,7173620,65.81309,7049,6796,swab from tracheostomic tube,,2021-03-10,Kazakhstan,Kazakhstan: Almaty,,,,"Surgical Procedures, Operative",,,Resistant;Intermediate;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,"Surgical Procedures, Operative",,,,,,,,,,,,,,99.68,1.72,Surgical Site Infections,,Other,Surgical Site Infections- HP,287.16553,Pseudomonas aeruginosa strain SCAID PLC1-2021 (16/222) strain SCAID PLC1-2021 (16/222) strain SCAID PLC1-2021 (16/222),SCAID PLC1-2021 (16/222),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20982452,287,,,,MLST.Pseudomonas_aeruginosa.308,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915485.1,CP082821,,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,116x,Canu v. 2.0,1,0,1,7124329,65.852,6981,6754,pleural cavity,,2021-03-18,Kazakhstan,Kazakhstan: Almaty,,,,Surgical Procedures,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Surgical Procedures,,,,,,,,,,,,,,99.68,0.43,Surgical Site Infections,,Other,Surgical Site Infections- HP,287.18077,Pseudomonas aeruginosa strain P96131,P96131,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23245613,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2021-11-27T00:00:00Z,,PRJNA781297,GCA_020990445.1,CP087673,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,7046998,65.780975,6795,6567,urine,,2018,Sierra Leone,Sierra Leone: Freetown,,,,Fever,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain P96131,collected_by:a public hospital,,,,,,,Fever,,,,,,,,,,,,,,99.68,0.43,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.18078,Pseudomonas aeruginosa strain P4970C,P4970C,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23245687,287,,,,MLST.Pseudomonas_aeruginosa.234,,,,2021-11-27T00:00:00Z,,PRJNA781305,GCA_020990465.1,CP087674,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6935768,65.89211,6671,6454,urine,,2018,Sierra Leone,Sierra Leone: Freetown,,,,Fever,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain P4970C,collected_by:a public hospital,,,,,,,Fever,,,,,,,,,,,,,,99.68,0.25,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.18079,Pseudomonas aeruginosa strain P93127,P93127,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23245698,287,,,,MLST.Pseudomonas_aeruginosa.234,,,,2021-11-27T00:00:00Z,,PRJNA781334,GCA_020990485.1,CP087675,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6909349,65.89353,6636,6420,urine,,2018,Sierra Leone,Sierra Leone: Freetown,,,,Fever,,,Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain P93127,collected_by:a public hospital,,,,,,,Fever,,,,,,,,,,,,,,99.68,0.25,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.18131,Pseudomonas aeruginosa strain UNC_PaerCF41,UNC_PaerCF41,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605137,287,,,,MLST.Pseudomonas_aeruginosa.1403,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166255.1,CP089061,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,291x,Flye v. 2.9,1,0,1,6441117,66.41618,5980,5833,bal,,2011-03-08,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18132,Pseudomonas aeruginosa strain UNC_PaerCF38,UNC_PaerCF38,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605136,287,,,,MLST.Pseudomonas_aeruginosa.809,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166275.1,CP089062,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,235x,Flye v. 2.9,1,0,1,6369924,66.50173,5951,5799,sputum,,2011-02-22,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18133,Pseudomonas aeruginosa strain UNC_PaerCF37,UNC_PaerCF37,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605135,287,,,,,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166295.1,CP089063,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,26x,Flye v. 2.9,1,0,1,6724106,66.16469,6895,6247,sputum,,2011-05-19,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,95.98,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18134,Pseudomonas aeruginosa strain UNC_PaerCF35,UNC_PaerCF35,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605134,287,,,,,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166315.1,CP089064,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,481x,Flye v. 2.9,1,0,1,6323929,66.5084,5925,5754,bal,,2011-01-04,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18135,Pseudomonas aeruginosa strain UNC_PaerCF34,UNC_PaerCF34,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605133,287,,,,MLST.Pseudomonas_aeruginosa.782,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166335.1,"CP089065,CP089066",,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,70x,Flye v. 2.9,1,1,2,6668644,66.282036,6355,6158,bal,,2010-11-30,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.65,0.22,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18136,Pseudomonas aeruginosa strain UNC_PaerCF19,UNC_PaerCF19,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605132,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166355.1,CP089067,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,155x,Flye v. 2.9,1,0,1,6851634,65.98305,6586,6372,sputum,,2011-01-04,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.68,0.28,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18137,Pseudomonas aeruginosa strain UNC_PaerCF13,UNC_PaerCF13,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23605131,287,,,,,,,,2021-12-12T00:00:00Z,,PRJNA749299,GCA_021166375.1,CP089068,,University of North Carolina at Chapel Hill,Oxford Nanopore MinION,40x,Flye v. 2.9,1,0,1,6346474,66.498245,5936,5756,sputum,,2018-11-15,USA,"USA: Chapel Hill, North Carolina",,,,,,,Susceptible,Computational Prediction,,,,,,,,,"The generation of a robust and reproducible chronic pulmonary bacterial infection model in mice is a major requirement for the study of infectious airways disease pathogenesis and therapy in cystic fibrosis (CF). These genomes were sequenced as part of an NIH Task Order (A24, A24 Option 3, and A43 Base Period) which seeks to characterize clinical isolates of P. aeruginosa and S. aureus to identify strains with increased likelihood of establishing chronic lung infections.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.66,0.11,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18285,Pseudomonas aeruginosa R06,R06,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234657,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513375.1,CP069323,,,Hybrid (MinION + MiSeq),131.50722407964878x,Unicycler v. 0.4.8,1,0,1,6269726,66.31126,5928,5731,sputum,,2012-08,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18286,Pseudomonas aeruginosa R05,R05,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234656,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513395.1,CP069324,,,Hybrid (MinION + MiSeq),130.41781811473803x,Unicycler v. 0.4.8,1,0,1,6255746,66.33541,5913,5714,sputum,,2013-05,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18287,Pseudomonas aeruginosa R02,R02,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234653,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513415.1,CP069325,,,Hybrid (MinION + MiSeq),158.44364009787188x,Unicycler v. 0.4.8,1,0,1,6270238,66.30898,5945,5733,sputum,,2013-04,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18288,Pseudomonas aeruginosa R11,R11,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234662,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513435.1,CP069326,,,Hybrid (MinION + MiSeq),99.97042546438728x,Unicycler v. 0.4.8,1,0,1,6270090,66.310036,5931,5730,sputum,,2013-04,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18290,Pseudomonas aeruginosa R04,R04,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234655,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513455.1,CP069328,,,Hybrid (MinION + MiSeq),114.72090340460159x,Unicycler v. 0.4.8,1,0,1,6269926,66.31046,5941,5732,sputum,,2012-11,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18291,Pseudomonas aeruginosa R03,R03,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234654,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513475.1,CP069327,,,Hybrid (MinION + MiSeq),111.26414784641874x,Unicycler v. 0.4.8,1,0,1,6269046,66.310165,5931,5732,sputum,,2013-01,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18293,Pseudomonas aeruginosa R10,R10,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234661,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513495.1,CP069329,,,Hybrid (MinION + MiSeq),173.11911799786344x,Unicycler v. 0.4.8,1,0,1,6267105,66.31057,5934,5731,sputum,,2012-11,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18294,Pseudomonas aeruginosa R07,R07,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234658,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513515.1,CP069330,,,Hybrid (MinION + MiSeq),187.087125278231x,Unicycler v. 0.4.8,1,0,1,6270419,66.30995,5931,5732,sputum,,2012-10,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18295,Pseudomonas aeruginosa R09,R09,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234660,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513535.1,CP069331,,,Hybrid (MinION + MiSeq),181.80169148449636x,Unicycler v. 0.4.8,1,0,1,6268813,66.311325,5929,5730,sputum,,2012-10,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18296,Pseudomonas aeruginosa R08,R08,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234659,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513555.1,CP069332,,,Hybrid (MinION + MiSeq),205.8057872248105x,Unicycler v. 0.4.8,1,0,1,6268635,66.31069,5929,5731,sputum,,2012-08,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18297,Pseudomonas aeruginosa E03,E03,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234650,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513595.1,CP069334,,,Hybrid (MinION + MiSeq),189.447276926777x,Unicycler v. 0.4.8,1,0,1,6315897,66.43696,5934,5757,sputum,,1991,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18298,Pseudomonas aeruginosa R01,R01,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234652,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513575.1,CP069333,,,Hybrid (MinION + MiSeq),104.9925033100838x,Unicycler v. 0.4.8,1,0,1,6270234,66.309456,5940,5733,sputum,,2012-08,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.14,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18299,Pseudomonas aeruginosa E02,E02,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234649,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513615.1,CP069335,,,Hybrid (MinION + MiSeq),158.1987147163087x,Unicycler v. 0.4.8,1,0,1,6330120,66.41214,5960,5777,sputum,,1991,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.59,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18300,Pseudomonas aeruginosa E01,E01,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234648,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513635.1,CP069336,,,Hybrid (MinION + MiSeq),181.50643519145976x,Unicycler v. 0.4.8,1,0,1,6315896,66.43708,5930,5756,sputum,,1991,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18302,Pseudomonas aeruginosa E04,E04,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN13234651,287,,,,MLST.Pseudomonas_aeruginosa.110,,,,2022-01-19T00:00:00Z,34826267,PRJNA588274,GCA_021513675.1,CP069337,,,Hybrid (MinION + MiSeq),217.70179127496135x,Unicycler v. 0.4.8,1,0,1,6407559,66.47385,5992,5848,sputum,,1991,New Zealand,New Zealand: Dunedin,,male,,Cystic Fibrosis,,host_disease_outcome:death;host_subject_id:Patient001,Susceptible,Computational Prediction,,,,,,,,,,collected_by:University of Otago,,,,,,,Cystic Fibrosis,,death,,,,,,,,,,,,99.68,0.15,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,287.18647,Pseudomonas aeruginosa JNQH-PA027,JNQH-PA027,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN23672503,287,,,,MLST.Pseudomonas_aeruginosa.244,,,,2021-12-15T00:00:00Z,,PRJNA786423,GCA_021184245.1,"CP089236,CP089237",,,Illumina HiSeq; PacBio,100.0x,SOAPdenovo2 v. Version 2.04; Unicycler v.,1,1,2,7013321,65.721275,6932,6697,sputum,,2019-05-10,China,"China: Jinan, Shandong province",,,,pulmonary infection,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:Yujiao Wang,,,,,,,pulmonary infection,,,,,,,,,,,,,,99.68,0.54,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.18688,Pseudomonas aeruginosa PA0523,PA0523,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN24059709,287,,,,MLST.Pseudomonas_aeruginosa.671,,,,2021-12-22T00:00:00Z,,PRJNA789140,GCA_021266605.1,CP089849,,,Illumina HiSeq; PacBio,100.0x,HGAP v. 4; FALCON v. 0.3,1,0,1,6589770,65.98549,6333,6132,sputum,,2021-09,China,China:Zhuhai,,,,infection,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:Zhuhai Hospital,,,,,,,infection,,,,,,,,,,,,,,99.68,0.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.18697,Pseudomonas aeruginosa PA8329,PA8329,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN24425653,287,,,,MLST.Pseudomonas_aeruginosa.9,,,,2022-01-10T00:00:00Z,,PRJNA792458,GCA_021398755.1,CP090348,,,Illumina HiSeq; PacBio,189.47x,HGAP v. 4; FALCON v. 0.3,1,0,1,6382961,66.375244,6004,5841,broncho alveolar lavage fluid,,2021-09,China,China: Zhuhai,,,,pulmonary infection,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Wei Wang,,,,,,,pulmonary infection,,,,,,,,,,,,,,99.68,0.11,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.19555,Pseudomonas aeruginosa NDM1_2,NDM1_2,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN20669214,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2022-03-14T00:00:00Z,,PRJNA753000,GCA_022559565.1,CP081148,,,Illumina; Oxford Nanopore MinION,100x,Unicycler v. 0.4.8,1,0,1,7039082,65.90981,6671,,urine,,2017-12-14,Serbia,Serbia,,,,,,,Resistant,Computational Prediction,,,,,,,,,,,clinical,urine,human,culture,,,,,,,,,,,,,clinical,,,,99.68,0.49,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.24693,Pseudomonas aeruginosa PA1_NCHU,PA1_NCHU,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN26650298,287,,,,,,,,2022-03-22T00:00:00Z,,PRJNA815903,GCA_022670795.1,CP093395,,,illumina iSeq100; Oxford Nanopore MinION,66.0x,unicycler v. 0.4.8; polypolish v. 0.5.0,1,0,1,6534898,66.30223,6188,6014,blood,,2019,Taiwan,Taiwan,,,,septicemia,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:YS Lin,,,,,,,septicemia,,,,,,,,,,,,,,99.5,2.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,287.24703,Pseudomonas aeruginosa PAD8,PAD8,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15963197,287,,,,MLST.Pseudomonas_aeruginosa.639,,,,2022-03-28T00:00:00Z,,PRJNA660892,GCA_022700635.1,"CP061073,CP061074",,,Oxford Nanopore PromethION,105.0x,flye v. 2.7,1,1,2,6613026,66.09623,6268,6067,urine,,2016-07,China,China:Shaanxi,,,,urine infection,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:Northwest University,,,,,,,urine infection,,,,,,,,,,,,,,99.2,1.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.24981,Pseudomonas aeruginosa 34Pae36,34Pae36,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27570671,287,,,,MLST.Pseudomonas_aeruginosa.111,,,,2022-04-24T00:00:00Z,,PRJNA826526,GCA_023093935.1,"CP095770,CP095771",,,PacBio RSII,185.0x,"HGAP v. 3,0",1,1,2,7583544,65.3387,7430,,collection,,2017-04,Colombia,Colombia: Bogota,,,,Bacterial infectious disease,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:LGMB,,,,,,,Bacterial infectious disease,,,,,,,,,,,,,,99.6,3.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.24982,Pseudomonas aeruginosa 34Pae23,34Pae23,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27570672,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2022-05-04T00:00:00Z,,PRJNA826526,GCA_023093955.2,"CP095772,CP095773",,,PacBio RSII,233.0x,"HGAP v. 3,0",1,1,2,6913444,65.9288,6598,,urine,,2017-05,Colombia,Colombia: Bogota,,,,Bacterial infectious disease,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:LGMB,,,,,,,Bacterial infectious disease,,,,,,,,,,,,,,99.1,2.9,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.24983,Pseudomonas aeruginosa 34Pae8,34Pae8,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27570673,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2022-04-24T00:00:00Z,,PRJNA826526,GCA_023093975.1,"CP095774,CP095775",,,PacBio RSII,150.0x,"HGAP v. 3,0",1,1,2,6910734,65.97314,6531,,blood,,2017-05,Colombia,Colombia: Bogota,,,,Bacterial infectious disease,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:LGMB,,,,,,,Bacterial infectious disease,,,,,,,,,,,,,,99.2,2.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,287.24991,Pseudomonas aeruginosa L00-a,L00-a,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28206123,287,,,,MLST.Pseudomonas_aeruginosa.532,,,,2022-05-23T00:00:00Z,,PRJNA837561,GCA_023520735.1,CP097383,,,Oxford Nanopore MinION; Illumina MiSeq,211.0x,Trycycler v. v0.5.0; Pilon v. v1.23;,1,0,1,7010374,65.80775,6728,6506,bal,,2020-06,USA,USA:Chicago,,,,Pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,,,,,,,,,Pneumonia,,,,,,,,,,,,,,99.5,2.8,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.25766,Pseudomonas aeruginosa PAO1-L,PAO1-L,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27739533,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2022-07-03T00:00:00Z,,PRJNA830884,GCA_024126335.1,CP099798,,,Illumina MiSeq,175x,SPAdes v. Galaxy Version 3.15.3,1,0,1,6276485,66.53563,5861,5711,wound infection,,1955,Australia,Australia: Melbourne,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,99.4,1.1,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.25767,Pseudomonas aeruginosa PAO1-N,PAO1-N,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27739534,287,,,,MLST.Pseudomonas_aeruginosa.549,,,,2022-07-03T00:00:00Z,,PRJNA830884,GCA_024126355.1,CP099797,,,Illumina MiSeq,56x,SPAdes v. Galaxy Version 3.15.3,1,0,1,6217942,66.53608,5819,5672,wound infection,,1955,Australia,Australia: Melbourne,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,98.9,1.1,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.25798,Pseudomonas aeruginosa PA-1,PA-1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28550649,287,,,,MLST.Pseudomonas_aeruginosa.654,,,,2022-07-14T00:00:00Z,,PRJNA839732,GCA_024266915.1,"CP097709,CP097845",,,illumina + GridION,2.0x,TRYCYCLER v. 0.4.3,1,1,2,7100966,65.945366,6788,6594,urine,,2019-02,Chile,Chile,,,,sepsis,,,Resistant,Computational Method,,,,,,,,,,collected_by:Aniela Wozniak,,,,,,,sepsis,,,,,,,,,,,,,,99.5,3,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,287.25799,Pseudomonas aeruginosa PA-2,PA-2,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28550875,287,,,,MLST.Pseudomonas_aeruginosa.654,,,,2022-07-14T00:00:00Z,,PRJNA839735,GCA_024266935.1,"CP097710,CP097844",,,illumina + GridION,2.0x,TRYCYCLER v. 0.4.3,1,1,2,7102090,65.94487,6794,6596,endotracheal aspirate,,2019-02,Chile,Chile,,,,pneumonia,,,Resistant,Computational Method,,,,,,,,,,collected_by:Aniela Wozniak,,,,,,,pneumonia,,,,,,,,,,,,,,99.5,3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.25803,Pseudomonas aeruginosa R20-14,R20-14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN27119722,287,,,,,,,,2022-07-18T00:00:00Z,,PRJNA721782,GCA_024300845.1,"CP094851,CP094852",,,Illumina; Oxford Nanopore,150.0x,Unicycler v. v0.4.8,1,1,2,6403588,66.41833,5991,5823,drainage,,2020-02-24,China,China: Hangzhou,,,,Hip joint infection,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:Qing, Yang",,,,,,,Hip joint infection,,,,,,,,,,,,,,99.3,1.5,Bone and Joint Infections,Other Joint Infections,Other,Bone and Joint Infections-Other Joint Infections HP,287.26038,Pseudomonas aeruginosa PA5083,PA5083,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30074508,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2022-08-08T00:00:00Z,,PRJNA864563,GCA_024584495.1,CP102174,,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,0,1,6902250,66.00898,6547,6359,sputum,,2022-03-14,China,China,,,,respiratory tract infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,respiratory tract infection,,,,,,,,,,,,,,99.2,2.8,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.26096,Pseudomonas aeruginosa SCAID TCT1-2022 (325) strain SCAID TCT1-2022 (325),SCAID TCT1-2022 (325),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30333621,287,,,,,,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734795.1,CP102944,,,PacBio Sequel,126x,Velvet v. 1.2.10,1,0,1,6871852,65.84994,6544,6333,swab from tracheostomy tube,,2022-04,Kazakhstan,Kazakhstan: Almaty,,,,respiratory tube,,,Resistant;Susceptible;Intermediate,Computational Method,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,respiratory tube,,,,,,,,,,,,,,99.3,2.2,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,287.26097,Pseudomonas aeruginosa SCAID WND1-2022 (148) strain SCAID WND1-2022 (148),SCAID WND1-2022 (148),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30333620,287,,,,MLST.Pseudomonas_aeruginosa.439,,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734815.1,CP102946,,,PacBio Sequel,96x,Velvet v. 1.2.10,1,0,1,6515978,66.33532,6118,5967,swab from purulent wound,,2022-03,Kazakhstan,Kazakhstan: Almaty,,,,atherosclerosis,,,Resistant;Intermediate;Susceptible,Computational Method,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,atherosclerosis,,,,,,,,,,,,,,99.6,1.9,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.26400,Pseudomonas aeruginosa NY4593,NY4593,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30863685,287,,,,MLST.Pseudomonas_aeruginosa.1101,,,,2022-09-25T00:00:00Z,,PRJNA880798,GCA_025398835.1,CP104720,,,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6074358,66.45112,5716,5555,phlegm,,2016,China,China:BeiJing,,,,,,,Susceptible,Computational Method,,,,,,,,,,,,,,,,,fever,,,,,,,,,,,,,,95.4,1.7,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.27067,Pseudomonas aeruginosa Pa3,Pa3,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN22773561,287,,,,MLST.Pseudomonas_aeruginosa.111,,,,2022-10-17T00:00:00Z,36175406,PRJNA776240,GCA_025723085.1,CP086213,,,Illumina MiniSeq; Oxford Nanopore MinION,94.0x,Unicycler v. 0.4.8,1,0,1,7223955,65.51853,6971,6745,blood,,2018,Belgium,Belgium,,,,Sepsis,,,Resistant,Computational Method,,,,,,,,,,collected_by:CUSL,,,,,,,Sepsis,,,,,,,,,,,,,,99.4,3.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,287.27709,Pseudomonas aeruginosa BIAI 157,BIAI 157,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN31815321,287,,,,MLST.Pseudomonas_aeruginosa.633,,,,2022-12-04T00:00:00Z,,PRJNA903854,,CP113106,,,Oxford Nanopore GridION; Illumina NextSeq,100.0x,flye v. 2.9,1,0,1,6830555,66.064926,6523,6318,breast,,2019,USA,USA:St. Louis,,,,Breast Implant Associated Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Margaret Olsen,,,,,,,Breast Implant Associated Infection,,,,,,,,,,,,,,99.2,2.2,Surgical Site Infections,,Other,Surgical Site Infections- HP,287.27710,Pseudomonas aeruginosa SMC4386,SMC4386,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN31867617,287,,,,MLST.Pseudomonas_aeruginosa.2012,,,,2022-12-05T00:00:00Z,,PRJNA905210,,CP113246,,,PacBio Sequel,1000.0x,HGAP v. 14/4/2022,1,0,1,6273495,66.5149,5866,5722,clinical,,2009,India,India,,,,Eye infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Senjuti Saha,,,,,,,Eye infection,,,,,,,,,,,,,,99.5,1.1,Eye Conditions,,Other,Eye Conditions- HP,287.27711,Pseudomonas aeruginosa BIAI 160,BIAI 160,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN31815323,287,,,,MLST.Pseudomonas_aeruginosa.633,,,,2022-12-05T00:00:00Z,,PRJNA903855,,CP113230,,,Oxford Nanopore GridION; Illumina NextSeq,100.0x,flye v. 2.9,1,0,1,6830406,66.06499,6522,6322,breast,,2019,USA,USA:St. Louis,,,,Breast Implant Associated Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Margaret Olsen,,,,,,,Breast Implant Associated Infection,,,,,,,,,,,,,,99.1,2,Surgical Site Infections,,Other,Surgical Site Infections- HP,287.27718,Pseudomonas aeruginosa M6A146,M6A146,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN32079354,287,,,,MLST.Pseudomonas_aeruginosa.688,,,,2022-12-13T00:00:00Z,,PRJNA909305,,CP113974,,,PacBio Sequel,87.6x,HGAP v. 2020-01-23,1,0,1,6755766,66.22981,6459,6211,lung,,1998-09-03,Canada,Canada: Calgary,,male,29,Lower respiratory tract disease,,host_description:Cystic fibrosis,Susceptible,Computational Method,,,,,,,,,,collected_by:Michael Parkins,,,,,,,Lower respiratory tract disease,,,Cystic fibrosis,,,,,,,,,,,99.7,2.7,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.27742,Pseudomonas aeruginosa NF143349,NF143349,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN32299599,287,,,,MLST.Pseudomonas_aeruginosa.277,,,,2022-12-27T00:00:00Z,,PRJNA913466,,"CP114761,CP114762",,,Illumina HiSeq; PacBio,106.65x,Hifiasm v. 0.13-r308; Canu v. 1.7,1,1,2,7256240,65.34948,7069,6800,blood,,2022,China,China: Guangzhou,,,,infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:Jing Chen,,,,,,,infection,,,,,,,,,,,,,,99.5,3.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,287.28558,Pseudomonas aeruginosa MF1,MF1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN33193898,287,,,,MLST.Pseudomonas_aeruginosa.309,genotype:ST309,,,2023-02-14T00:00:00Z,,PRJNA932461,,CP117527,,,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Raven v. 1.8.1; Flye v. 2.9.1; Canu v.,1,0,1,7043257,65.99068,6790,6552,blood,,2022-01-01,Chile,Chile,,,,Polymicrobial infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:Laboratory,,,,,,,Polymicrobial infection,,,,,,,,,,,,,,99.2,3.8,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,287.28570,Pseudomonas aeruginosa HS18-89,HS18-89,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN17508957,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2023-02-21T00:00:00Z,,PRJNA694231,,"CP084321,CP084322",,,PacBio Sequel,216x,HGAP v. 4,1,1,2,7542056,65.173965,7329,7061,urine,,2018-07-06,China,China: Shanghai,,,,,,,Resistant,Computational Method,,,,,,,,,,sample_type:clinical sample,,,,,,,,,,,,,,,,,,,,,99.2,3,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.29210,Pseudomonas aeruginosa P23,P23,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN32292837,287,,,,MLST.Pseudomonas_aeruginosa.621,,,,2023-03-16T00:00:00Z,,PRJNA913392,,JAPWKT000000000,,,Oxford Nanopore MinION,1.0x,Flye v. 2.9.1,1,0,1,6931140,65.84389,6545,6348,urinary catheter,,2021-10-26,Egypt,Egypt: Mansoura,,,,Urinary tract infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Mohamed Eladawy,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.4,2.6,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.29212,Pseudomonas aeruginosa P9,P9,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN32292824,287,,,,,,,,2023-03-16T00:00:00Z,,PRJNA913392,,JAPWLG000000000,,,Oxford Nanopore MinION,1.0x,Flye v. 2.9.1,1,2,3,6990601,65.776146,6756,6560,urinary catheter,,2021-10-05,Egypt,Egypt: Mansoura,,,,Urinary tract infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:Mohamed Eladawy,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.4,2.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.29817,Pseudomonas aeruginosa ZY156,ZY156,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN33446047,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2023-05-18T00:00:00Z,,PRJNA938808,,"CP125363,CP125364",,,Oxford Nanopore MinION,100x,SPAdes v. 3.8.2,1,1,2,7045512,65.81028,6692,6499,urine,,2021-02-25,China,China: Hangzhou,,,,Acute toxic encephalopathy,,,Resistant,Computational Method,,,,,,,,,,collected_by:Zhang Piaopiao,,,,,,,Acute toxic encephalopathy,,,,,,,,,,,,,,99.2,2,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.29818,Pseudomonas aeruginosa ZY94,ZY94,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN33446046,287,,,,MLST.Pseudomonas_aeruginosa.463,,,,2023-05-18T00:00:00Z,,PRJNA938808,,"CP125361,CP125362",,,Oxford Nanopore MinION,100x,SPAdes v. 3.8.2,1,1,2,7039758,65.81589,6683,6493,sputum,,2021-02-09,China,China: Hangzhou,,,,Pulmonary infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:Zhang Piaopiao,,,,,,,Pulmonary infection,,,,,,,,,,,,,,99.2,1.9,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.30216,Pseudomonas aeruginosa NY5507,NY5507,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28004167,287,,,,MLST.Pseudomonas_aeruginosa.1976,,,,2023-05-26T00:00:00Z,,PRJNA833554,,"CP096929,CP096930,CP096931",,,PacBio RSII,100.0x,HGAP v. v3.0,1,2,3,6925568,65.91452,6631,6426,broncholveolr lvge fluid,,2019,China,China:HeNan,,,,Pulmonary infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:a public hospital,,,,,,,Pulmonary infection,,,,,,,,,,,,,,99.2,1.7,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.30243,Pseudomonas aeruginosa NY5523,NY5523,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28004302,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2023-05-26T00:00:00Z,,PRJNA833561,,CP096941,,,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6918147,66.00089,6568,6369,phlegm,,2019,China,China:HeNan,,,,pneumonia,,,Resistant,Computational Method,,,,,,,,,,collected_by:a public hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.3,2.9,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.30246,Pseudomonas aeruginosa NY11210,NY11210,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28004767,287,,,,MLST.Pseudomonas_aeruginosa.1976,,,,2023-05-26T00:00:00Z,,PRJNA833577,,"CP096958,CP096959",,,PacBio RSII,100.0x,HGAP v. v3.0,1,1,2,6970081,65.86144,6662,6458,phlegm,,2019,China,China:HeNan,,,,pneumonia,,,Resistant,Computational Method,,,,,,,,,,collected_by:a public hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.4,2,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.30290,Pseudomonas aeruginosa NY5525,NY5525,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN28004304,287,,,,MLST.Pseudomonas_aeruginosa.292,,,,2023-05-26T00:00:00Z,,PRJNA833566,,CP096945,,,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,6740322,65.7862,6571,6346,phlegm,,2019,China,China:HeNan,,,,pneumonia,,,Resistant,Computational Method,,,,,,,,,,collected_by:a public hospital,,,,,,,pneumonia,,,,,,,,,,,,,,96.2,3.4,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.3104,Pseudomonas aeruginosa strain NHmuc,NHmuc,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN03940420,287,,,,MLST.Pseudomonas_aeruginosa.387,,DSM:100776,,2016-12-12T00:00:00Z,,PRJNA291143,GCF_001900265.1,CP013479,NZ_CP013479.1,Leibniz Institute DSMZ,PacBio; Illumina GAIIx,100x,HGAP2 SMRTPortal v. 2.1.1,1,,1,6213276,66.57,5814,5619,,,2013-01-01,Netherlands,Netherlands,,,,,,,,,,,,,C,,,,Large scale genome inversion in P. aeruginosa drives adaptation to chronic infection in cystic fibrosis,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.31132,Pseudomonas aeruginosa strain_87,strain_87,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN35773956,287,,,,MLST.Pseudomonas_aeruginosa.1197,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128445,,,Illumina,25x,SPAdes v. v3.15.5,1,0,1,6276181,66.43813,6144,6012,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,98.3,3.9,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.31138,Pseudomonas aeruginosa strain_9,strain_9,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN35773949,287,,,,,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128438,,,Illumina,45x,SPAdes v. v3.15.5,1,0,1,6303537,66.38525,6128,5964,tip of urine catheter,,2021,Gaza Strip,Gaza Strip,,,,infection,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,97.7,2.8,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,287.3869,Pseudomonas aeruginosa strain E6130952,E6130952,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN06349407,287,O11,,,MLST.Pseudomonas_aeruginosa.235,,,,2017-04-11T00:00:00Z,,PRJNA376024,GCA_002085755.1,"CP020603,CP020602",,Universite Laval,PacBio,73.0x,Celera Assembler v. AUG-2014,1,1,2,7077406,65.83,6888,6586,sputum,,2014,Canada,Canada: Toronto,,,,respiratory failure,,host_disease_outcome:death,,,,,,,,,,,strain resistant to all current antibiotics,collected_by:St. Joseph's Hospital,,,,,,,respiratory failure,,death,,,,,,,,,,,,99.4,0.3,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.3877,Pseudomonas aeruginosa strain PASGNDM345,PASGNDM345,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN06689794,287,,,,MLST.Pseudomonas_aeruginosa.308,,,,2017-04-18T00:00:00Z,,PRJNA381838,GCA_002104615.1,CP020703,,Nanyang Technological University,PacBio,163x,Celera Assembler,1,,1,6893164,66.07,6681,6552,sputum,,2015-05-02,Singapore,Singapore,,,,N.A.,,,,,,,,,,,,,The aim of this study is to elucidate the complete genome map of NDM-1 producing P. aeruginosa clinical isolate. We also aim to understand the transmission of blaNDM-1 into P. aeruginosa.,collected_by:Jeanette WP Teo,,,,,,,N.A.,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.3878,Pseudomonas aeruginosa strain PASGNDM699,PASGNDM699,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN06689795,287,,,,MLST.Pseudomonas_aeruginosa.308,,,,2017-04-18T00:00:00Z,,PRJNA381838,GCA_002104595.1,CP020704,,Nanyang Technological University,PacBio,161x,Celera Assembler,1,,1,6985102,66,6791,6661,sputum,,2015-04-11,Singapore,Singapore,,,,N.A.,,,,,,,,,,,,,The aim of this study is to elucidate the complete genome map of NDM-1 producing P. aeruginosa clinical isolate. We also aim to understand the transmission of blaNDM-1 into P. aeruginosa.,collected_by:Jeanette WP Teo,,,,,,,N.A.,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.4050,Pseudomonas aeruginosa strain 124,124,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020323,287,,,,MLST.Pseudomonas_aeruginosa.309,,,,2017-06-13T00:00:00Z,,PRJNA389181,GCA_002192475.1,CP021774,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,91.0x,other v. HGAP 3,1,,1,7008516,65.84,6785,6617,bronchial washing,,2006-11-01,Mexico,Mexico: Mexico city,,,,ventilator-associated pneumonia,,,Resistant,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.4051,Pseudomonas aeruginosa strain 58,58,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020321,287,,,,MLST.Pseudomonas_aeruginosa.308,,,,2017-06-13T00:00:00Z,,PRJNA389181,GCA_002192495.1,CP021775,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,83.0x,HGAP v. 3,1,,1,7241575,65.8,7146,6927,bronchial washing,,2005-10-25,Mexico,Mexico: Mexico city,,,,ventilator-associated pneumonia,,,Resistant,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,99.4,0.9,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.4090,Pseudomonas aeruginosa strain 84,84,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020322,287,,,,,,,,2017-06-22T00:00:00Z,,PRJNA389181,GCA_002205335.1,CP021999,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,89.0x,HGAP v. 3,1,,1,6566724,66.23,6348,6202,bronchial washing,,2005-07-20,Mexico,Mexico: Mexico city,,,,ventilator-associated pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.4091,Pseudomonas aeruginosa strain 127,127,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020324,287,,,,MLST.Pseudomonas_aeruginosa.309,,,,2017-06-22T00:00:00Z,,PRJNA389181,GCA_002205355.1,CP022000,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,91.0x,HGAP v. 3,1,,1,7148302,65.74,7025,6777,bronchial washing,,2006-11-10,Mexico,Mexico: Mexico city,,,,ventilator-associated pneumonia,,,Resistant,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,100,3.2,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.4092,Pseudomonas aeruginosa strain 1242,1242,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020326,287,,,,MLST.Pseudomonas_aeruginosa.277,,,,2017-06-22T00:00:00Z,,PRJNA389181,GCA_002205375.1,CP022002,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,181.0x,HGAP v. 3,1,,1,7050510,65.83,6967,6654,blood,,2014-05-02,Mexico,Mexico: Mexico city,,female,12 years,Chiari malformation,,,Resistant,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,Chiari malformation,,,,,,,,,,,,,,99.4,2.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,287.4094,Pseudomonas aeruginosa strain 1207,1207,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05020325,287,,,,MLST.Pseudomonas_aeruginosa.155,,,,2017-06-22T00:00:00Z,,PRJNA389181,GCA_002208645.1,CP022001,,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",PacBio,146.0x,HGAP v. 3,1,,1,7411863,65.73,7297,7072,blood,,2012-06-27,Mexico,Mexico: Mexico city,,male,3 years and 3 months,Comunity-adquired pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",collected_by:not applicable,,,,,,,Comunity-adquired pneumonia,,,,,,,,,,,,,,100,3.3,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,287.4621,Pseudomonas aeruginosa strain PB369,PB369,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08101547,287,,,,MLST.Pseudomonas_aeruginosa.319,,,,2017-12-06T00:00:00Z,,PRJNA419916,GCA_002812825.1,CP025049,,New York Medical College,PacBio & Illumina,100x,HGAP & SPAdes v. v2.3.0 & v3.10.0,1,,1,6526814,66.02,6351,6216,abscess,,2014-12-09,USA,USA: New York,,,,,,,Resistant,Computational Prediction,,,,,,,,,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,,,,,,,,,,,,,,,,,,,,97.3,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.4622,Pseudomonas aeruginosa strain PB368,PB368,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08101546,287,,,,MLST.Pseudomonas_aeruginosa.319,,,,2017-12-06T00:00:00Z,,PRJNA419916,GCA_002812845.1,CP025050,,New York Medical College,PacBio & Illumina,100x,HGAP & SPAdes v. v2.3.0 & v3.10.0,1,,1,6638559,65.96,6461,6320,abscess,,2014-11-12,USA,USA: New York,,,,,,,Resistant,Computational Prediction,,,,,,,,,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,,,,,,,,,,,,,,,,,,,,98.2,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.4623,Pseudomonas aeruginosa strain PB350,PB350,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08101543,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2017-12-06T00:00:00Z,,PRJNA419916,GCA_002812905.1,CP025055,,New York Medical College,PacBio & Illumina,100x,HGAP & SPAdes v. v2.3.0 & v3.10.0,1,,1,6752870,66.2,6462,6340,sputum,,2016-04-17,USA,USA: New York,,,,,,,Resistant,Computational Prediction,,,,,,,,,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.4624,Pseudomonas aeruginosa strain PB367,PB367,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08101542,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2017-12-06T00:00:00Z,,PRJNA419916,GCA_002812925.1,CP025056,,New York Medical College,PacBio & Illumina,100x,HGAP & SPAdes v. v2.3.0 & v3.10.0,1,,1,6752906,66.2,6457,6340,tracheal aspirate,,2016-04-03,USA,USA: New York,,,,,,,Resistant,Computational Prediction,,,,,,,,,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.5956,Pseudomonas aeruginosa strain CCUG 70744,CCUG 70744,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN07602569,287,,,,MLST.Pseudomonas_aeruginosa.395,,CCUG:70744,,2018-06-06T00:00:00Z,,PRJNA401330,GCA_003194245.1,CP023255,,Chalmers University of Technology,Illumina MiSeq; PacBio,68.0x,SPAdes v. v3.7.0,1,,1,6859232,66.04034,6683,6535,sputum,,2013-01-08,Sweden,Sweden: Gothenburg,,,,,,,Intermediate;Not defined;Resistant;Susceptible,AMR Panel,,,,,,,,,"In this study, we aimed to characterize the resistome of highly multi-resistant pathogens, all phenotypically resistant to at least one carbapenem antibiotic.","collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,N/A,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.5968,Pseudomonas aeruginosa strain K34-7,K34-7,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08954392,287,,,,MLST.Pseudomonas_aeruginosa.233,,,,2018-06-11T00:00:00Z,,PRJNA450903,GCA_003206535.1,"CP029707,CP029708",,University of Oslo,PacBio; Illumina HiSeq,200.0x,HGAP v. 4,1,1,2,7042452,65.88912,6839,6704,tracheal secretions,,2006,Norway,Norway: Olso,,,,,,,Resistant,Computational Prediction,,,,,,,,,"Carbapenem-resistant Pseudomonas aeruginosa is listed by the World Health Organisation as as a critical threat to public health. Complete, high quality reference genomes facilitate further research into mechanisms of resistance and their dissemination. Furthermore, these data will also aid in the discovery and development of new therapies for multi-drug resistant infections.",collected_by:Ullevaal University Hospital,,,,,,,unknown,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.6364,Pseudomonas aeruginosa strain Y89,Y89,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09469733,287,,,,MLST.Pseudomonas_aeruginosa.245,,,,2018-08-10T00:00:00Z,,PRJNA477434,GCA_003369735.1,"CP030913,CP030914",,Yonsei University College of Medicine,PacBio,119.68x,HGAP v. 2.3.0,1,1,2,6954674,65.97815,6641,6329,sputum,,2009,South Korea,South Korea: Seoul,,male,69,Pneumonia,,host_subject_id:Y89,Resistant,Computational Prediction,,,,,,,,,Genome sequencing project of multidrug resistant pseudomonas aeruginosa Y89,collected_by:Yonsei University Severance Hospital,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.6365,Pseudomonas aeruginosa strain Y82,Y82,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09469732,287,,,,MLST.Pseudomonas_aeruginosa.111,,,,2018-08-10T00:00:00Z,,PRJNA477432,GCA_003369755.1,CP030912,,Yonsei University College of Medicine,PacBio,135.44x,HGAP v. 2.3.0,1,,1,7106857,65.75086,6815,6383,sputum,,2009,South Korea,South Korea: Seoul,,male,58,Pneumonia,,host_subject_id:Y82,Resistant,Computational Prediction,,,,,,,,,Genome sequencing project of pseudomonas aeruginosa Y82,collected_by:Yonsei University Severance Hospital,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.6366,Pseudomonas aeruginosa strain Y31,Y31,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09469677,287,,,,,,,,2018-08-10T00:00:00Z,,PRJNA477422,GCA_003369775.1,CP030910,,Yonsei University College of Medicine,PacBio,131.23x,HGAP v. 2.3.0,1,,1,6831076,66.1532,6442,6190,sputum,,2009,South Korea,South Korea: Seoul,,female,58,Pneumonia,,host_subject_id:Y31,Susceptible,Computational Prediction,,,,,,,,,Genome sequencing project of antibiotic susceptible pseudomonas aeruginosa Y31,collected_by:Yonsei University Severance Hospital,,,,,,,Pneumonia,,,,,,,,,,,,,,100,1.2,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.6376,Pseudomonas aeruginosa strain Y71,Y71,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09469727,287,,,,MLST.Pseudomonas_aeruginosa.245,,,,2018-08-20T00:00:00Z,,PRJNA477430,GCA_003408495.1,CP030911,,Yonsei University College of Medicine,PacBio,119.5x,HGAP v. 2.3.0,1,,1,6940949,65.96863,6664,6334,sputum,,2009,South Korea,South Korea: Seoul,,male,70,Pneumonia,,host_subject_id:Y71,Resistant,Computational Prediction,,,,,,,,,Genome sequencing project of multidrug resistant pseudomonas aeruginosa Y71,collected_by:Yonsei University Severance Hospital,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.6480,Pseudomonas aeruginosa strain PABL012,PABL012,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09831327,287,,,,MLST.Pseudomonas_aeruginosa.708,,,,2018-08-28T00:00:00Z,,PRJNA485889,GCA_003429185.1,CP031659,,Northwestern University Feinberg School of Medicine,PacBio; Illumina HiSeq,185.0x,Celera Assembler v. 8.1; Circlator v.,1,,1,6546467,66.28976,6292,6167,blood,,1999-10,USA,"USA: Chicago, Illinois",,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa isolates collected from patients with bloodstream infections.,,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,287.6481,Pseudomonas aeruginosa strain PABL017,PABL017,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN09831332,287,,,,MLST.Pseudomonas_aeruginosa.2167,,,,2018-08-28T00:00:00Z,,PRJNA485889,GCA_003429205.1,CP031660,,Northwestern University Feinberg School of Medicine,PacBio; Illumina HiSeq,179.0x,Celera Assembler v. 8.1; Circlator v.,1,,1,6503460,66.31253,6192,6091,blood,,2000-01,USA,"USA: Chicago, Illinois",,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa isolates collected from patients with bloodstream infections.,,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,287.6482,Pseudomonas aeruginosa strain 24Pae112,24Pae112,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN07958398,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2018-08-30T00:00:00Z,,PRJNA416504,GCA_003433235.1,CP029605,,El Bosque University,PacBio,147.0x,HGAP v. 2.3,1,,1,7097241,65.989555,6844,6598,blood,isolate from a Intensive Care Unit patient,2015-03-05,Colombia,Colombia,,,,Sepsis,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem resistant clinical isolate from a Intensive Care Unit patient.,collected_by:Bacterial Molecular Genetics Laboratory,,,,,,,Sepsis,,,,,,,,,,,,,,100,1.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,287.6799,Pseudomonas aeruginosa strain BA7823,BA7823,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10135988,287,,,,,,,,2018-10-07T00:00:00Z,,PRJNA493550,GCA_003626935.1,CP032569,,Christian Medical College,Oxford Nanopore MiniION,75.6x,Miniasm v. 0.2,1,,1,6876788,65.758316,7734,6483,blood,,2017-03-16,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,"Complete genome of multi drug resistant, metallo beta lactamase (blaVIM) producing Pseudomonas aeruginosa isolated from bacteraemia;many frameshifted proteins","collected_by:Department of Clinical Microbiology, Christian Medical College",,,,,,,Bacteraemia,,,,,,,,,,,,,,91.12,0.9,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,287.7086,Pseudomonas aeruginosa strain BA15561,BA15561,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10187561,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-11-06T00:00:00Z,,PRJNA494979,GCA_003713085.1,CP033432,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,65.2x,CANU v. 1.7; Unicycler v. 0.4.6,1,,1,6793961,65.838135,6729,6337,blood,,2016-06-14,India,India,,,,Bacteremia,,,Resistant,Computational Prediction,,,,,,,,,"Complete genome of extensive drug resistant, blaNDM producing Pseudomonas aeruginosa;many frameshifted proteins",collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,98.91,0.54,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,287.7087,Pseudomonas aeruginosa strain SP4528,SP4528,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10187562,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-11-07T00:00:00Z,,PRJNA494980,GCA_003716765.1,CP033439,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,70.52x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6877287,65.84826,6681,6421,sputum,,2016,India,India,,,,Respiratory tract infection,,,Resistant,Computational Prediction,,,,,,,,,"Complete genome of extensive drug resistant, blaPME &\; blaNDM producing Pseudomonas aeruginosa",collected_by:Christian Medical College,,,,,,,Respiratory tract infection,,,,,,,,,,,,,,99,0.54,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,287.7092,Pseudomonas aeruginosa strain H26027,H26027,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10374626,287,,,,MLST.Pseudomonas_aeruginosa.17,,,,2018-11-20T00:00:00Z,,PRJNA503802,GCA_003798105.1,CP033684,,Lausanne University Hospital,PacBio RSII; Illumina HiSeq,228x,HGAP3 v. SMRTPortal; Pilon v. v. 2.3.0;,1,,1,7079598,66.07256,6863,6726,skin,,2010-04-06,Switzerland,Switzerland,,,,Burned,,,Susceptible,Computational Prediction,,,,,,,,,Use of whole genome sequencing to study the epidemiology of the nosocomial pathogen Pseudomonas aeruginosa,collected_by:Lausanne University Hospital,,,,,,,Burned,,,,,,,,,,,,,,99.68,0.85,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,287.7093,Pseudomonas aeruginosa strain H25883,H25883,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10374624,287,,,,MLST.Pseudomonas_aeruginosa.1076,,,,2018-11-20T00:00:00Z,,PRJNA503802,GCA_003798125.1,CP033686,,Lausanne University Hospital,PacBio RSII; Illumina HiSeq,223x,HGAP3 v. SMRTPortal; Pilon v. v. 2.3.0;,1,,1,6706800,66.15038,6434,6317,biopsy,,2010-05-25,Switzerland,Switzerland,,,,Burned,,,Susceptible,Computational Prediction,,,,,,,,,Use of whole genome sequencing to study the epidemiology of the nosocomial pathogen Pseudomonas aeruginosa,collected_by:Lausanne University Hospital,,,,,,,Burned,,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.7094,Pseudomonas aeruginosa strain H26023,H26023,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10374625,287,,,,MLST.Pseudomonas_aeruginosa.253,,,,2018-11-20T00:00:00Z,,PRJNA503802,GCA_003798145.1,CP033685,,Lausanne University Hospital,PacBio RSII; Illumina HiSeq,217x,HGAP3 v. SMRTPortal; Pilon v. v. 2.3.0;,1,,1,6729216,66.2119,6450,6333,bronchial aspirate,,2010-01-08,Switzerland,Switzerland,,,,Cardiac arrest,,,Susceptible,Computational Prediction,,,,,,,,,Use of whole genome sequencing to study the epidemiology of the nosocomial pathogen Pseudomonas aeruginosa,collected_by:Lausanne University Hospital,,,,,,,Cardiac arrest,,,,,,,,,,,,,,99.68,0.81,Cardiovascular Diseases,Other Cardiovascular Diseases,Respiratory Tract,Cardiovascular Diseases-Other Cardiovascular Diseases HP,287.7735,Pseudomonas aeruginosa strain IMP-13,IMP-13,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10503341,287,,,,MLST.Pseudomonas_aeruginosa.621,,,,2018-12-15T00:00:00Z,,PRJNA507737,GCA_003950015.1,"CP034354,CP034355",,Universite Paris-Sud,PacBio,60.0x,CLC NGS Cell v. 9.5,1,1,2,7178010,65.62876,6928,6785,urine,,2011,Belgium,Belgium,,,,urinary infection,,,Resistant,Computational Prediction,,,,,,,,,Pseudomonas aeruginosa IMP-13,collected_by:Hopital Bicetre,,,,,,,urinary infection,,,,,,,,,,,,,,99.68,0.81,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.7736,Pseudomonas aeruginosa strain B41226,B41226,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10525951,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-16T00:00:00Z,,PRJNA508613,GCA_003950235.1,CP034368,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,59.4x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6814295,65.870834,6730,6415,blood,,2014-11-21,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of extensive drug resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,99.06,0.54,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,287.7737,Pseudomonas aeruginosa strain SP4371,SP4371,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10526368,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-16T00:00:00Z,,PRJNA508615,GCA_003950255.1,CP034369,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,57.98x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6937609,65.80527,6803,6520,sputum,,2016-09-18,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of extensive drug resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,99.08,0.71,Bloodstream Infections,Other Bloodstream Infections,Respiratory Tract,Bloodstream Infections-Other Bloodstream Infections HP,287.7738,Pseudomonas aeruginosa strain SP2230,SP2230,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10578979,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-18T00:00:00Z,,PRJNA509357,GCA_003952285.1,CP034434,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,46.2x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6976603,65.7357,6896,6564,sputum,,2014-05-04,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of extensive drug resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,98.58,0.82,Bloodstream Infections,Other Bloodstream Infections,Respiratory Tract,Bloodstream Infections-Other Bloodstream Infections HP,287.7739,Pseudomonas aeruginosa strain B14130,B14130,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10579055,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-18T00:00:00Z,,PRJNA509362,GCA_003952305.1,CP034435,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,45.9x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6759594,65.87406,6644,6340,blood,,2014-05-04,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of multiple drug resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,97.87,0.5,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,287.7740,Pseudomonas aeruginosa strain B17932,B17932,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10579150,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-18T00:00:00Z,,PRJNA509363,GCA_003952325.1,CP034436,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,283.0x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,6744658,65.93709,6594,6338,blood,,2014-05-16,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of carbapenem resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,98.79,0.17,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,287.8035,Pseudomonas aeruginosa strain SP4527,SP4527,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10525987,287,,,,MLST.Pseudomonas_aeruginosa.357,,,,2018-12-17T00:00:00Z,,PRJNA508614,GCA_003991465.1,CP034409,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,51.7x,CANU v. 1.7; UNICYCLER v. 0.4.6,1,,1,7005215,65.79297,6903,6567,sputum,,2016-09-27,India,India,,,,Bacteraemia,,,Resistant,Computational Prediction,,,,,,,,,Complete genome of extensive drug resistant Pseudomonas aeruginosa,collected_by:Christian Medical College,,,,,,,Bacteraemia,,,,,,,,,,,,,,99.19,1.68,Bloodstream Infections,Other Bloodstream Infections,Respiratory Tract,Bloodstream Infections-Other Bloodstream Infections HP,287.8037,Pseudomonas aeruginosa strain LW,LW,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN07256503,287,,,,MLST.Pseudomonas_aeruginosa.1182,,,,2019-01-10T00:00:00Z,,PRJNA391028,GCA_004010895.1,CP022478,,Plant protection and Microbiology Research Institute,PacBio,116.78,HGAP v. 2.0,1,,1,6824837,65.97381,6536,6377,sputum,,2012-10-01,China,China: Beijing,,,,infection,,,Resistant,Computational Prediction,,,,,,,,,resistance gene,collected_by:ZAAS,,,,,,,infection,,,,,,,,,,,,,,99.51,0.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,287.8043,Pseudomonas aeruginosa strain paerg000,paerg000,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916038,287,,,,MLST.Pseudomonas_aeruginosa.27,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618245.1,LR130528,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6493562,66.425545,6145,5940,hospital,,2017,Switzerland,Switzerland,,,,,,host_health_state:diseased,Resistant,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.43,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8044,Pseudomonas aeruginosa strain paerg002,paerg002,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916049,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618255.1,LR130527,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6451470,66.40451,6070,5850,hospital,,2015-09-16,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8045,Pseudomonas aeruginosa strain paerg004,paerg004,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916061,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618265.1,LR130531,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6452809,66.40161,6055,5843,hospital,,2015-09-16,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8046,Pseudomonas aeruginosa strain paerg003,paerg003,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916059,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618275.1,LR130530,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6433962,66.3979,6035,5821,hospital,,2015,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.59,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8047,Pseudomonas aeruginosa strain paerg005,paerg005,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916069,287,,,,MLST.Pseudomonas_aeruginosa.309,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618285.1,LR130534,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6931425,65.99554,6573,6319,hospital,,2017,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.57,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8048,Pseudomonas aeruginosa strain paerg009,paerg009,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916107,287,,,,MLST.Pseudomonas_aeruginosa.309,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618305.1,LR130533,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6941287,65.97912,6625,6361,hospital,,2017-04-25,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.27,0.57,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8049,Pseudomonas aeruginosa strain paerg010,paerg010,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916108,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618315.1,LR130536,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6433960,66.39751,6035,5820,hospital,,2015-09-16,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.59,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8050,Pseudomonas aeruginosa strain paerg011,paerg011,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916113,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618325.1,LR130535,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6434133,66.39782,6038,5823,hospital,,2015-09-16,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8051,Pseudomonas aeruginosa strain paerg012,paerg012,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA4916123,287,,,,MLST.Pseudomonas_aeruginosa.262,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618335.1,LR130537,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,6434020,66.3977,6027,5821,hospital,,2015-09-16,Switzerland,Switzerland,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.68,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.8919,Pseudomonas aeruginosa strain 1334/14,1334/14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN10880118,287,,,,MLST.Pseudomonas_aeruginosa.234,genotype:ST234,,,2019-02-13T00:00:00Z,,PRJNA521107,GCA_004193735.1,CP035739,,National Medicines Institute,Illumina MiSeq; Oxford Nanopore MiniION,110.0x,MaSuRCA v. JUL-2016,1,,1,6902135,65.79952,6684,6567,eye,,2014-03-10,Poland,Poland,,,82,conjunctiva infection,,,Resistant,Computational Prediction,,,,,,,,,Sequencing of nosocomial P. aeruginosa isolate genome carrying metallo-beta-lactamase genes blaNDM and blaDIM.,collected_by:National Medicines Institute,,,,,,,conjunctiva infection,,,,,,,,,,,,,,99.68,0.84,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,287.8922,Pseudomonas aeruginosa strain PA-VAP-3,PA-VAP-3,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08706629,287,,,,MLST.Pseudomonas_aeruginosa.253,,,,2019-03-12T00:00:00Z,,PRJNA438112,GCA_004346985.1,CP028330,,EA3826,Illumina MiSeq,130 x,SPAdes v. 3.11,1,,1,6665262,66.22902,6404,6305,bal,,2015-06-06,France,France,,,,VAP,,,Resistant,Computational Prediction,,,,,,,,,"We investigated wether the evolution towards resistance could be associated with virulence changes, in the context of P. aeruginosa acute infections like ventilator-associated pneumonia (VAP).",collected_by:CHU Nantes,,,,,,,VAP,,,,,,,,,,,,,,99.68,0.11,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,287.8923,Pseudomonas aeruginosa strain PA-VAP-1,PA-VAP-1,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08706627,287,,,,MLST.Pseudomonas_aeruginosa.1027,,,,2019-03-12T00:00:00Z,,PRJNA438112,GCA_004347005.1,CP028332,,EA3826,Illumina MiSeq,130 x,SPAdes v. 3.11,1,,1,6382137,66.51928,6105,6026,bal,,2015-07-18,France,France,,,,VAP,,,Susceptible,Computational Prediction,,,,,,,,,"We investigated wether the evolution towards resistance could be associated with virulence changes, in the context of P. aeruginosa acute infections like ventilator-associated pneumonia (VAP).",collected_by:CHU Nantes,,,,,,,VAP,,,,,,,,,,,,,,99.68,0.11,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,287.8924,Pseudomonas aeruginosa strain PA-VAP-2,PA-VAP-2,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08706628,287,,,,,,,,2019-03-12T00:00:00Z,,PRJNA438112,GCA_004347025.1,CP028331,,EA3826,Illumina MiSeq,130 x,SPAdes v. 3.11,1,,1,6283481,66.5525,5989,5908,bal,,2015-04-14,France,France,,,,VAP,,,Susceptible,Computational Prediction,,,,,,,,,"We investigated wether the evolution towards resistance could be associated with virulence changes, in the context of P. aeruginosa acute infections like ventilator-associated pneumonia (VAP).",collected_by:CHU Nantes,,,,,,,VAP,,,,,,,,,,,,,,99.68,0.46,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,287.8925,Pseudomonas aeruginosa strain PA-VAP-4,PA-VAP-4,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN08706630,287,,,,MLST.Pseudomonas_aeruginosa.2042,,,,2019-03-12T00:00:00Z,,PRJNA438112,GCA_004347045.1,CP028368,,EA3826,Illumina MiSeq,130 x,SPAdes v. 3.11,1,,1,6271764,66.583824,6000,5908,bal,,2015-07-18,France,France,,,,VAP,,,Susceptible,Computational Prediction,,,,,,,,,"We investigated wether the evolution towards resistance could be associated with virulence changes, in the context of P. aeruginosa acute infections like ventilator-associated pneumonia (VAP).",collected_by:CHU Nantes,,,,,,,VAP,,,,,,,,,,,,,,99.68,0.43,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,287.9848,Pseudomonas aeruginosa strain 60503,60503,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12306201,287,,,,MLST.Pseudomonas_aeruginosa.773,,,,2019-07-28T00:00:00Z,,PRJNA555258,GCA_007559065.1,CP041774,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,,1,6809062,66.147675,6571,6469,sputum specimen,,2016,China,China: Beijing,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Sequencing and genomic diversity analysis of IncpRBL16 plasmids,collected_by:a public hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.68,0.45,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,287.9851,Pseudomonas aeruginosa strain 243931,243931,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12306121,287,,,,MLST.Pseudomonas_aeruginosa.235,,,,2019-07-28T00:00:00Z,,PRJNA555248,GCA_007559125.1,CP041772,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,,1,6514208,66.33976,6197,6086,sputum specimen,,2016,China,China: Zhejiang,,,,urinary tract infection,,,Susceptible,Computational Prediction,,,,,,,,,Sequencing and genomic diversity analysis of IncpRBL16 plasmids,collected_by:a teaching hospital,,,,,,,urinary tract infection,,,,,,,,,,,,,,98.86,0.14,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Respiratory Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.9852,Pseudomonas aeruginosa strain SCAID WND2-2019 strain Swab from not healing wound,Swab from not healing wound,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12288114,287,,,,MLST.Pseudomonas_aeruginosa.234,,,,2019-07-29T00:00:00Z,,PRJNA554979,GCA_007566955.1,CP041786,,SCAID,IonTorrent,18x,Velvet v. 1.2.10,1,,1,6185611,66.69734,6215,6084,wound,,2019-04-03,Kazakhstan,Kazakhstan: Almaty,,female,47,Purulent wound,,host_disease_outcome:Recovery,Resistant;Intermediate;Susceptible,Computational Prediction,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon.","collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Purulent wound,,Recovery,,,,,,,,,,,,96.8,0.11,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,287.9853,Pseudomonas aeruginosa strain SCAID WND3-2019 strain Swab from not healing wound,Swab from not healing wound,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12288115,287,,,,MLST.Pseudomonas_aeruginosa.1031,,,,2019-07-29T00:00:00Z,,PRJNA554979,GCA_007567125.1,CP041785,,SCAID,IonTorrent,20x,Velvet v. 1.2.10,1,,1,6382154,66.60915,6420,6293,wound,,2019-04-08,Kazakhstan,Kazakhstan: Almaty,,female,,Purulent wound,,host_disease_outcome:Chronic disease,Resistant;Susceptible;Intermediate,Computational Prediction,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon.","collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Purulent wound,,Chronic disease,,,,,,,,,,,,98.24,0.11,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,287.9857,Pseudomonas aeruginosa strain C79,C79,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN11836198,287,,,,MLST.Pseudomonas_aeruginosa.316,,,,2019-08-05T00:00:00Z,,PRJNA544424,GCA_007833895.1,"CP040684,CP040685",,"Zhujiang Hospital, Southern Medical University",PacBio Sequel,250.0x,MECAT v. V1.2,1,1,2,6796334,66.09415,6532,6436,,,2017-09-22,China,China,,,,,,,Resistant,Computational Prediction,,,,,,,,,Emergence of a clinical Pseudomonas aeruginosa isolate carrying blaGES-5 and blaKPC-2,sample_type:Bacterial cell culture,,,,,,,,,,,,,,,,,,,,,99.62,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,287.9877,Pseudomonas aeruginosa strain CCUG 51971,CCUG 51971,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12634799,287,,,,MLST.Pseudomonas_aeruginosa.235,,CCUG:51971,,2019-09-02T00:00:00Z,,PRJNA305687,GCA_008195485.1,CP043328,,University of Gothenburg - CCUG,Illumina; Oxford Nanopore MiniION,1047.0x,Unicycler v. 0.4.7,1,,1,7012798,66.059395,6812,6690,urine sample,,2001-11,Sweden,Sweden:Solna,,,,Urinary tract infection,,host_description:Greek citizen,Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of bacterial species of the Culture Collection University of Gothenburg (CCUG),collected_by:Karolinska University Hospital,,,,,,,Urinary tract infection,,,Greek citizen,,,,,,,,,,,99.68,0.27,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,287.9883,Pseudomonas aeruginosa strain GIMC5001:PAT-23,GIMC5001:PAT-23,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12640651,287,,,,MLST.Pseudomonas_aeruginosa.235,genotype:ST235,,,2019-09-09T00:00:00Z,,PRJNA562421,GCA_008330985.1,"CP043483,CP043482",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,454; Illumina,129,CLC Genomics Workbench v. 12.0,1,1,2,6477693,65.99175,6219,6176,no data,,2006-10,Russia,Russia: Moscow,,,,no data,,,Resistant,Computational Prediction,,,,,,,,,Causative agent of nosocomial infections,collected_by:Gabrielyan N.I.,,,,,,,no data,,,,,,,,,,,,,,98.82,0.43,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28901.13805,Salmonella enterica strain colony_17,colony_17,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713984,28901,,,,MLST.Salmonella_enterica.29,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657125.1,CP067991,,Ministry of Public Health-Thailand,Illumina HiSeq,93.0106x,De Bruijn Graph De Novo Assembler v.,1,0,1,4557079,52.59468,4413,3987,missing,,,Thailand,Thailand: Nongkhai,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,99.12,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28901.13806,Salmonella enterica strain colony_14,colony_14,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713983,28901,,,,MLST.Salmonella_enterica.239,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657265.1,CP067978,,Ministry of Public Health-Thailand,Illumina HiSeq,94.479x,De Bruijn Graph De Novo Assembler v.,1,0,1,4550588,52.541477,4355,,missing,,,Thailand,Thailand: Nongkhai,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.69,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,28901.15677,Salmonella enterica 2017028-SE,2017028-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619906,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474245.1,"CP090545,CP090546",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,1,2,5270631,51.924145,5446,5087,patient,,2017,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15678,Salmonella enterica 2008079-SE,2008079-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619911,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474265.1,"CP090529,CP090531,CP090532,CP090530",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,3,4,5315182,51.83734,5505,5102,patient,,2008,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.18,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15679,Salmonella enterica 2017005-SE,2017005-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619910,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474285.1,"CP090533,CP090534",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,1,2,5311968,51.874447,5511,5133,patient,,2017,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15680,Salmonella enterica 2016089-SE,2016089-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619909,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474305.1,"CP090535,CP090537,CP090538,CP090536",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,3,4,5220260,51.956818,5352,4981,patient,,2016,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15681,Salmonella enterica 2016062-SE,2016062-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619908,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474325.1,"CP090539,CP090540",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,1,2,5224182,51.93502,5384,5023,patient,,2016,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15682,Salmonella enterica 2010112-SE,2010112-SE,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24619907,28901,,,,MLST.Salmonella_enterica.34,,,,2022-01-15T00:00:00Z,,PRJNA794298,GCA_021474345.1,"CP090541,CP090543,CP090544,CP090542",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,Unicycler v. v0.4.4,1,3,4,5113953,51.947937,5241,4878,patient,,2010,China,China: Henan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Pei Zhang,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15845,Salmonella enterica S639,S639,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23671188,28901,,,,MLST.Salmonella_enterica.26,,,,2021-12-14T00:00:00Z,,PRJNA786417,GCA_021183525.1,"CP089207,CP089208",,,Illumina HiSeq; Oxford Nanopore MinION,100x,unicycler v. v0.4.8,1,1,2,5054985,51.97157,5175,4830,stool,,2018,China,"China:Zhejiang province,Hangzhou",,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:the First Peoples Hospital of Hangzhou,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.37,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15847,Salmonella enterica S15,S15,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23671187,28901,,,,MLST.Salmonella_enterica.34,,,,2021-12-14T00:00:00Z,,PRJNA786417,GCA_021183545.1,"CP089209,CP089210",,,Illumina HiSeq; Oxford Nanopore MinION,100x,unicycler v. v0.4.8,1,1,2,5238821,51.869152,5386,5024,stool,,2011,China,"China:Zhejiang province,Hangzhou",,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:the First Peoples Hospital of Hangzhou,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.15960,Salmonella enterica P281972,P281972,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25761580,28901,,,,,,,,2022-02-15T00:00:00Z,,PRJNA804648,GCA_022226915.1,"CP092075,CP092076",,,Oxford Nanopore; Illumina MiniSeq,88.0x,Unicycler v. FEB-2022,1,1,2,4776458,52.104866,4917,4581,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,100,0.09,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.16171,Salmonella enterica P164045,P164045,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26317632,28901,,,,MLST.Salmonella_enterica.3044,,,,2022-03-09T00:00:00Z,,PRJNA811245,GCA_022533545.1,"CP092861,CP092862",,,Oxford Nanopore MinION; Illumina MiniSeq,56.0x,Unicycler v. 0.4.8,1,1,2,5313749,52.09307,5590,5160,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,99.71,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.16172,Salmonella enterica 1505,1505,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941602,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559345.1,"CP060834,CP060836,CP060835",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,2,3,4936085,51.987293,4992,4610,feces,,2015-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16173,Salmonella enterica 852,852,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941601,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559365.1,"CP060837,CP060839,CP060838",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,2,3,4952034,52.036636,5020,4631,feces,,2019-12,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16174,Salmonella enterica 770,770,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941599,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559405.1,"CP060844,CP060845",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,1,2,4662207,52.018475,4697,4340,feces,,2019-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,96.47,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16175,Salmonella enterica 805,805,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941600,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559385.1,"CP060840,CP060842,CP060843,CP060841",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,3,4,4914331,51.994606,4968,4572,feces,,2019-09,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16176,Salmonella enterica 467,467,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941596,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559465.1,"CP060852,CP060854,CP060853",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,2,3,4970901,51.967663,5027,4640,feces,,2018-07,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.22,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16179,Salmonella enterica 733,733,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941598,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559425.1,"CP060846,CP060848,CP060847",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,2,3,4941369,51.995632,4995,4613,feces,,2019-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16180,Salmonella enterica 453,453,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941595,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559485.1,"CP060855,CP060856",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,1,2,4903141,51.97234,4944,4576,feces,,2018-07,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.16182,Salmonella enterica 724,724,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15941597,28901,,,,MLST.Salmonella_enterica.358,,,,2022-03-14T00:00:00Z,,PRJNA660241,GCA_022559445.1,"CP060849,CP060851,CP060850",,,Oxford Nanopore,100x,Unicycler v. 0.4.8,1,2,3,4983946,52.0061,5042,4657,feces,,2019-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17522,Salmonella enterica P048595,P048595,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26662412,28901,,,,,,,,2022-03-21T00:00:00Z,,PRJNA816181,GCA_022655645.1,"CP093386,CP093387,CP093388,CP093389",,,Illumina MiniSeq; Oxford Nanopore MinION,20.0x,Unicycler v. 0.4.8,1,3,4,4957390,52.211807,5062,4716,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.17523,Salmonella enterica P287611,P287611,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26664046,28901,,,,,,,,2022-03-21T00:00:00Z,,PRJNA804648,GCA_022655665.1,CP093391,,,Illumina MiniSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,0,1,4714721,52.232,4811,4505,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.17524,Salmonella enterica P201982,P201982,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26664045,28901,,,,,,,,2022-03-21T00:00:00Z,,PRJNA804648,GCA_022655705.1,"CP093392,CP093393",,,Illumina MiniSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,1,2,4763016,52.1166,4908,4569,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.17525,Salmonella enterica P289597,P289597,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26664047,28901,,,,,,,,2022-03-21T00:00:00Z,,PRJNA804648,GCA_022655685.1,CP093390,,,Illumina MiniSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,0,1,4713600,52.230206,4800,4498,feces,,2021,Australia,Australia: Tasmania,,,,Salmonella,,,,,,,,,,,,,,collected_by:THS,,,,,,,Salmonella,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.17574,Salmonella enterica 1618,1618,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25249355,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330705.1,"CP091544,CP091546,CP091545",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,2,3,5170682,51.962196,5320,4961,stool,,2021-06-29,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17575,Salmonella enterica 751,751,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419723,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330765.1,"CP091554,CP091555",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,1,2,5224450,51.90466,5391,5017,stool,,2019-08-17,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17576,Salmonella enterica 143,143,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419719,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330845.1,"CP091563,CP091565,CP091564",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,2,3,5389798,51.88638,5614,5242,stool,,2017-04-24,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17577,Salmonella enterica 632,632,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419722,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330785.1,"CP091556,CP091557",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,1,2,5131059,51.97241,5311,4949,stool,,2019-05-16,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17578,Salmonella enterica 179,179,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419720,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330825.1,"CP091560,CP091562,CP091561",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,2,3,5208710,51.955936,5375,5011,stool,,2017-06-01,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17579,Salmonella enterica 137,137,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419718,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330865.1,"CP091566,CP091568,CP091567",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,2,3,5015033,52.109867,5138,4800,stool,,2017-04-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17580,Salmonella enterica 418,418,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419721,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330805.1,"CP091558,CP091559",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,1,2,5296145,51.848316,5515,5126,stool,,2018-06-12,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17581,Salmonella enterica 1559,1559,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25249354,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330725.1,"CP091547,CP091549,CP091548",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,2,3,5297217,51.880337,5494,5123,stool,,2021-06-14,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17582,Salmonella enterica 628,628,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419724,28901,,,,MLST.Salmonella_enterica.26,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330745.1,"CP091550,CP091552,CP091553,CP091551",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,3,4,5161746,51.983147,5317,4972,stool,,2019-05-13,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,1.2,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17583,Salmonella enterica 2,2,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419716,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330905.1,"CP091571,CP091572,CP091573,CP091574,CP091576,CP091575",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,5,6,5382329,51.80276,5596,5181,stool,,2016-04-26,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.17584,Salmonella enterica 131,131,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16419717,28901,,,,MLST.Salmonella_enterica.34,,,,2022-05-11T00:00:00Z,,PRJNA660241,GCA_023330885.1,"CP091569,CP091570",,,Oxford Nanopore GridION; Illumina NovaSeq,100X,Unicycler v. 0.4.8,1,1,2,5227029,51.87249,5389,5024,stool,,2017-01-19,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18080,Salmonella enterica SC2014107,SC2014107,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29629757,28901,,,,MLST.Salmonella_enterica.684,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364825.1,"CP101365,CP101366",,,Oxford Nanopore; BGISEQ-50,100.0x,Unicycler v. 3.14.0,1,1,2,4945546,51.98621,5028,4728,human,,2014-08-01,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18081,Salmonella enterica SC2014238,SC2014238,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630085,28901,,,,MLST.Salmonella_enterica.463,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364845.1,"CP101369,CP101368,CP101371,CP101370",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. 3.14.0,1,3,4,5103129,52.048595,5240,4865,missing,,2014-11-07,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18082,Salmonella enterica SC2016025,SC2016025,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630109,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364865.1,CP101372,,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. 3.14.0,1,0,1,5245093,51.90718,5405,5040,missing,,2016-05-23,China,China: Ya'an,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,1.2,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18083,Salmonella enterica SC2016042,SC2016042,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630254,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364885.1,"CP101373,CP101374",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,1,2,4984268,52.12314,5101,4766,missing,,2016-06-12,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18084,Salmonella enterica SC2016090,SC2016090,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630270,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364905.1,CP101375,,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,0,1,5247576,51.898705,5403,5042,missing,,2016-07-15,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18085,Salmonella enterica SC2016091,SC2016091,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630309,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364925.1,"CP101376,CP101377,CP101378",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,2,3,5121969,52.141354,5262,4930,missing,,2016-07-15,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18086,Salmonella enterica SC2016290,SC2016290,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630312,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364945.1,"CP101379,CP101381,CP101380",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,2,3,5150418,52.207355,5315,4986,missing,,2016-11-01,China,China: Ya'an,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18087,Salmonella enterica SC2017030,SC2017030,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630349,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364965.1,"CP101382,CP101385,CP101384,CP101383",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,3,4,5226478,51.909298,5396,5021,missing,,2017-03-29,China,China: Chengdu,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18088,Salmonella enterica SC2017100,SC2017100,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630500,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024364985.1,"CP101386,CP101387",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,1,2,5191692,51.868176,5327,4982,missing,,2017-05-13,China,China: Bazhong,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18089,Salmonella enterica SC2017297,SC2017297,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29631754,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024365025.1,"CP101390,CP101391",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,1,2,5227863,51.89266,5384,5024,missing,,2017-07-31,China,China: Panzhihua,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18090,Salmonella enterica SC2017167,SC2017167,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29630588,28901,,,,MLST.Salmonella_enterica.34,,,,2022-07-21T00:00:00Z,,PRJNA855361,GCA_024365005.1,"CP101388,CP101389",,,Oxford Nanopore MinION; BGISEQ-50,100.0x,Unicycler v. v0.4.8,1,1,2,5258906,51.912205,5407,5052,missing,,2017,China,China: Suining,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18530,Salmonella enterica ZYX,ZYX,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814743,28901,,,,MLST.Salmonella_enterica.2039,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113534,,,Illumina NovaSeq,246x,HGAP v. v4.0,1,0,1,4709424,52.312428,4628,,excrement,,2022-09-13,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18531,Salmonella enterica ZLQ,ZLQ,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814742,28901,,,,MLST.Salmonella_enterica.34,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113535,,,Illumina NovaSeq,204x,HGAP v. v4.0,1,0,1,4972313,52.178032,4983,,excrement,,2022-07-19,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18532,Salmonella enterica XSK,XSK,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814739,28901,,,,MLST.Salmonella_enterica.19,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113538,,,Illumina NovaSeq,282x,HGAP v. v4.0,1,0,1,4850957,52.14602,4806,,excrement,,2022-07-13,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18533,Salmonella enterica YZY,YZY,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814740,28901,,,,MLST.Salmonella_enterica.2529,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113537,,,Illumina NovaSeq,248x,HGAP v. v4.0,1,0,1,4677491,52.23063,4558,,excrement,,2022-07-05,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18534,Salmonella enterica FFL,FFL,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814738,28901,,,,MLST.Salmonella_enterica.155,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113539,,,Illumina NovaSeq,232x,HGAP v. v4.0,1,0,1,4722848,52.229736,4651,,excrement,,2022-06-26,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18535,Salmonella enterica ZCX,ZCX,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814741,28901,,,,MLST.Salmonella_enterica.19,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113536,,,Illumina NovaSeq,224x,HGAP v. v4.0,1,0,1,4855728,52.200226,4843,,excrement,,2022-08-10,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18536,Salmonella enterica CYX,CYX,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814737,28901,,,,MLST.Salmonella_enterica.11,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113540,,,Illumina NovaSeq,224x,HGAP v. v4.0,1,0,1,4714057,52.165703,4674,,excrement,,2022-08-30,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18537,Salmonella enterica CHC,CHC,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31814736,28901,,,,MLST.Salmonella_enterica.19,,,,2022-12-11T00:00:00Z,,PRJNA903824,,CP113541,,,Illumina NovaSeq,235x,HGAP v. v4.0,1,0,1,4844220,52.131054,4797,,excrement,,2022-07-30,China,China,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:haibing liu,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18538,Salmonella enterica 1902,1902,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270681,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091604,CP091606,CP091605",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,2,3,4944965,52.000427,5015,4653,feces,,2021-09,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18539,Salmonella enterica 1810,1810,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270680,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091607,CP091609,CP091610,CP091608",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4926562,51.98814,4983,4627,feces,,2021-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18540,Salmonella enterica 1795,1795,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270679,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091611,CP091612,CP091613,CP091614",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4696484,52.24349,4705,4395,feces,,2021-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18541,Salmonella enterica 1653,1653,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270678,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091615,CP091617,CP091618,CP091616",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4953107,51.989773,5030,4657,feces,,2021-07,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18542,Salmonella enterica 1419,1419,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270676,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091622,CP091623",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,1,2,4663696,52.24217,4654,4350,feces,,2021-02,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18543,Salmonella enterica 1473,1473,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270677,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091619,CP091621,CP091620",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,2,3,4823296,52.01582,4851,4515,feces,,2021-05,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18544,Salmonella enterica 1382,1382,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270675,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091624,CP091625",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,1,2,4694630,52.245758,4689,4385,feces,,2021-02,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18545,Salmonella enterica 1165,1165,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270674,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091626,CP091628,CP091629,CP091627",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4914347,51.99458,4968,4604,feces,,2020-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18546,Salmonella enterica 1147,1147,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270673,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091630,CP091632,CP091633,CP091631",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4950462,51.98937,5022,4654,feces,,2020-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18547,Salmonella enterica 1116,1116,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270672,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091634,CP091635",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,1,2,4686733,52.244858,4684,4380,feces,,2020-08,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18548,Salmonella enterica 1063,1063,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270671,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091636,CP091638,CP091639,CP091637",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,3,4,4986976,51.87003,5069,4704,feces,,2020-07,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.18549,Salmonella enterica 965,965,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25270670,28901,,,,MLST.Salmonella_enterica.358,,,,2022-12-13T00:00:00Z,,PRJNA660241,,"CP091640,CP091642,CP091641",,,Oxford Nanopore; Illumina NovaSeq,100x,Unicycler v. 0.4.8,1,2,3,4925254,51.986538,4990,4631,feces,,2020-06,China,China: Hangzhou,,,,enteritis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,enteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.19064,Salmonella enterica SC2020597,SC2020597,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33818803,28901,,,,MLST.Salmonella_enterica.26,,,,2023-04-02T00:00:00Z,,PRJNA946266,,"CP120671,CP120672,CP120673",,,Oxford Nanopore MinION; Illumina HiSeq,100.0x,Unicycler v. v0.4.8,1,2,3,5089659,51.904007,5189,4827,feces,,2020-11-25,China,China: Guangyuan,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Center for Disease Control and Prevention of Sichuan Province,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,1.2,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.19091,Salmonella enterica CRIN525628,CRIN525628,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33715203,28901,,,,MLST.Salmonella_enterica.32,,,,2023-04-12T00:00:00Z,,PRJNA912184,,"CP119980,CP119981",,,Illumina; Oxford Nanopore MinION,100X,Unicycler v. 0.4.8,1,1,2,5021166,52.15406,5147,4762,human feces,,2018,Costa Rica,Costa Rica,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:INCIENSA,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.19410,Salmonella enterica BC01,BC01,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35713968,28901,,,,MLST.Salmonella_enterica.1,,,,2023-07-11T00:00:00Z,,PRJNA982791,,CP129108,,,Oxford Nanopore MinION,590.0x,Unicycler v. October-2022,1,0,1,4806952,52.0813,5065,4620,blood,,2015-09-18,Tanzania,Tanzania,,,,typhoid fever,,,,,,,,,,,,,,collected_by:Annette Onken,,,,,,,typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,28901.2334,Salmonella enterica strain FORC_030,FORC_030,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04550937,28901,,,,,,,,2017-04-05T00:00:00Z,,PRJNA315190,GCA_002079245.1,"CP015598,CP015599",,Ajou University,PacBio,119x,SMRT v. 2.3.0,1,1,2,5037523,52.14,5330,4976,stool,isolated from stool of foodborne poisoning patient in South Korea,2009-12-09,South Korea,South Korea: Gangwon,,,,Not reported,,,,,,,,,,,,,Salmonella is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,collected_by:Korea Center for Disease Control and Prevention,,,,,,,Not reported,,,,,,,,,,,,,,100,4.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.2706,Salmonella enterica strain FORC_051,FORC_051,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05756207,28901,,,,MLST.Salmonella_enterica.11,,,,2017-09-19T00:00:00Z,,PRJNA342395,GCA_002313085.1,"CP017232,CP017233",,Seoul National University,PacBio,134.36x,SMRT Analysis v. 2.3.0,1,1,2,4776636,52.12,4896,4902,blood,"isolated from the blood of a food-poisoned patient in Seoul, Korea",2016,Korea,Korea: Seoul,,,,Not reported,,,,,,,,,,,,,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activities with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",collected_by:Samsung Seoul Hospital,,,,,,,Not reported,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,28901.3875,Salmonella enterica strain 201001922,201001922,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08784247,28901,Kentucky,,,MLST.Salmonella_enterica.198,,,,2018-04-03T00:00:00Z,,PRJNA445436,GCA_003030965.1,CP028357,,The University of Melbourne,454; Illumina HiSeq,27.0x,Celera Assembler v. 6.1,1,,1,4858671,52.237206,5010,4835,human,,,,,,,,gastroenteritis,,,,,,,,,,,,,"Investigation of the global population structure of S. Kentucky ST198, spanning several different geographical locations",collected_by:not applicable,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,28901.3934,Salmonella enterica strain DA34821,DA34821,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245755,28901,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003177235.1,CP029567,,Uppsala University,PacBio; Illumina HiSeq 2000,100.0x,CLC Genomics workbench v. 11.0.1,1,,1,4900176,52.196186,5054,4901,feces,,,Germany,Germany,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.3935,Salmonella enterica strain DA34837,DA34837,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245760,28901,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003177255.1,CP029568,,Uppsala University,PacBio; Illumina MiSeq,30.0x,CLC Genomics workbench v. 11.0.1,1,,1,5070296,52.118595,5307,5154,urine,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,28901.3936,Salmonella enterica strain DA34827,DA34827,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245756,28901,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181075.1,"CP029593,CP029594",,Uppsala University,PacBio; Illumina HiSeq 2000,60.0x,CLC Genomics workbench v. 11.0.1,1,1,2,5027611,52.132355,5295,5102,feces,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.3937,Salmonella enterica strain DA34833,DA34833,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245758,28901,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181155.1,"CP029595,CP029596",,Uppsala University,PacBio; Illumina HiSeq 2000,100.0x,CLC Genomics workbench v. 11.0.1,1,1,2,5027523,52.13235,5303,5103,feces,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,28901.4306,Salmonella enterica strain FORC_074,FORC_074,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07604329,28901,,,,MLST.Salmonella_enterica.11,,NCCP:14545,,2018-09-10T00:00:00Z,,PRJNA401394,GCA_003515965.1,"CP023436,CP023437,CP023438",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,193 x,PacBio SMRT Analysis v. 2.3.0,1,2,3,4795266,52.11636,4857,4576,human stool,isolated from human stool in South Korea,2002-08-08,South Korea,South Korea,,,,food poisoning,,,,,,,,,,,,,Salmonella Enteritidis FORC_074 Complete genome sequencing.Salmonella Enteritidis is one of the well-known food-borne pathogen. It was isolated from human stool in South Korea.,collected_by:NCCP,,,,,,,food poisoning,,,,,,,,,,,,,,100,0.4,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,28901.6957,Salmonella enterica strain FORC_079,FORC_079,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08277293,28901,Typhimurium,,,MLST.Salmonella_enterica.328,,,,2019-01-08T00:00:00Z,,PRJNA427944,GCA_003999215.1,"CP025736,CP025737",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,140x,PacBio SMRT Analysis v. 2.3.0,1,1,2,4966497,52.170856,5031,4751,human stool,isolated from the human stool in South Korea,2017-08-31,South Korea,South Korea,,,,Salmonellosis,,,,,,,,,,,,,Salmonella enterica subsp. enterica serovar Typhimurium is one of the well-known food-borne pathogen. It was isolated from the human stool in South Korea.,collected_by:National Culture Collection for Pathogen,,,,,,,Salmonellosis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,28901.9635,Salmonella enterica strain FORC_078,FORC_078,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08449845,28901,,,,MLST.Salmonella_enterica.11,,,,2019-02-04T00:00:00Z,,PRJNA432476,GCA_004135835.1,"CP026713,CP026714",,"Food-borne Pathogen Omics Research Center,FORC",PacBio,195X,Pacbio SMRT v. 2.3.0,1,1,2,4745355,52.163918,4790,4458,stool,isolated from human stool in South Korea,2002-08-08,South Korea,South Korea,,,,food poisoning,,,,,,,,,,,,,Salmonella Enteritidis FORC_078 Complete genome sequencingSalmonella Enteritidis is one of the well-known food-borne pathogen. It was isolated from human stool in South Korea.,collected_by:NCCP,,,,,,,food poisoning,,,,,,,,,,,,,,99.99,0.13,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,28901.9825,Salmonella enterica strain S61394,S61394,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10914546,28901,serovar Typhimurium,,,MLST.Salmonella_enterica.34,,,,2019-10-09T00:00:00Z,31580437,PRJNA521810,GCA_008931225.1,"CP035915,CP035916",,Zhejiang University,PacBio,210.0x,SMRT v. 2.3.0,1,1,2,5210346,51.84773,5288,,blood culture,,2017,China,China,,,,bacteremia,,,,,,,,,,,,,Multidrug-resistant Salmonella enterica serovar Typhimurium ST34 carrying mcr-1 isolated from bloodstream and intestinal infection children in China,collected_by:Zhejiang University,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.11,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,28901.9826,Salmonella enterica strain S44712,S44712,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10914547,28901,serovar Typhimurium,,,MLST.Salmonella_enterica.34,,,,2019-10-09T00:00:00Z,31580437,PRJNA521810,GCA_008931245.1,"CP035917,CP035918",,Zhejiang University,PacBio,210.0x,SMRT v. 2.3.0,1,1,2,5226840,51.87218,5317,,stool,,2017,China,China: Hangzhou,,,,acute gastroenteritis,,,,,,,,,,,,,Multidrug-resistant Salmonella enterica serovar Typhimurium ST34 carrying mcr-1 isolated from bloodstream and intestinal infection children in China,collected_by:Zhejiang University,,,,,,,acute gastroenteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,2893020.3,Nocardia sp. BCHNH01,BCHNH01,Nocardia huaxiensis,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN23376436,2755382,,,,,,,,2021-12-05T00:00:00Z,,PRJNA778436,GCA_021044705.1,CP088007,,"Beijing Institute of Microbiology and Epidemiology, Beijing",Oxford Nanopore; Illumina NovaSeq,35.0x,unicycler v. 0.4.8,1,0,1,8314373,67.83689,7761,7520,eye,,2021-06-27,,China,,,,endophthalmitis,,,,,,,,,,,,,A case of bacteria endophthalmitis caused by an emerging pathogen: Nocardia huaxiensis,collected_by:Beijing Children Hospital,,,,,,,endophthalmitis,,,,,,,,,,,,,,99.23,0.34,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,290434.9,Borreliella bavariensis PBi,PBi,Borreliella bavariensis,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN08918524,290434,,,,,genotype:ST84,,,2018-11-23T00:00:00Z,,PRJNA449844,GCA_003814425.1,"CP028872,CP028877,CP028880,CP028881,CP028876,CP028874,CP028882,CP028875,CP028878,CP028879,CP028883,CP028873",,,PacBio; Illumina MiSeq,443.5x,HGAP v. v2.3.0; other v. 9.5.3,1,11,12,1279859,27.831503,1383,1263,missing,,1984,Germany,Germany,,,,Lyme borreliosis,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme borreliosis,,,,,,,species normally has rodents as reservoir host and ticks of the genus Ixodes as vectors,,,,,,,99.19,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease NHP,291644.194,Bacteroides salyersiae strain CL06T03C19,CL06T03C19,Bacteroides salyersiae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451187,291644,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018291945.1,CP072243,,Brigham & Women's Hospital,PacBio Sequel,464x,FALCON-Unzip v. 1.2.0,1,0,1,5546719,42.09377,4887,4448,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.13,0.87,,,Gastrointestinal,- HP,291644.201,Bacteroides salyersiae strain BFG-288,BFG-288,Bacteroides salyersiae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546909,291644,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091345.1,"CP081899,CP081900",,National Institute of Allergy and Infectious Disease,PacBio Sequel,472x,HGAP/FALCON v. v. 6.0,1,1,2,5307048,41.94524,4392,3998,abscess,,1991,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.26,0.42,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,291644.202,Bacteroides salyersiae strain BFG-256,BFG-256,Bacteroides salyersiae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547012,291644,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091385.1,CP081902,,National Institute of Allergy and Infectious Disease,PacBio Sequel,370x,HGAP/FALCON v. v. 6.0,1,0,1,5374479,41.85628,4514,4099,drainage,,2001,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.26,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,291644.253,Bacteroides salyersiae WAL9166,WAL9166,Bacteroides salyersiae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663856,291644,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914135.1,CP083674,,,Illumina HiSeq,286x,A5ud v. v1,1,0,1,5482387,42.00954,4654,4244,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,291644.254,Bacteroides salyersiae WAL7960,WAL7960,Bacteroides salyersiae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663855,291644,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914155.1,CP083675,,,Illumina HiSeq,381x,A5ud v. v1,1,0,1,5338186,41.897114,4532,4107,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,95.7,3.3,,,Gastrointestinal,- NHP,291645.91,Bacteroides nordii WAL7935,WAL7935,Bacteroides nordii,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663853,291645,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914175.1,CP083676,,,Illumina HiSeq,317x,A5ud v. v1,1,0,1,5453739,40.401844,4355,4045,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,99.8,0.7,,,Gastrointestinal,- HP,292.297,Burkholderia cepacia strain 39628,39628,Burkholderia cepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08724754,292,,,,,,,,2020-10-06T00:00:00Z,,PRJNA438725,GCA_014854795.1,"CP032009,CP032011,CP032010",,"University of Nevada, Reno",PacBio,16.04X,"SMRT v. 2.3.0, HGAP v. 3",3,0,3,8403907,66.80368,8278,8437,sputum,,2014-04-08,Laos,Laos,,,,,,,,,,,,,,,,,Identification of Burkholderia cepacia strains expressing a unique capsular polysaccharide antigen.,sample_type:bactera,,,,,,,,,,,,,clinical sample,,,,,,,,99.87,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- NHP,292800.569,Flavonifractor plautii strain NBRC 113805,NBRC 113805,Flavonifractor plautii,Flavonifractor,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN21163592,292800,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181555.1,CP084007,,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore GridION,389.0x,Flye v. 2.8.3; Racon v. 1.4.20; Pilon v.,1,0,1,4277038,60.34973,4548,4155,human feces,,2017,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.33,0.81,,,Gastrointestinal,- NHP,292800.696,Flavonifractor plautii KR001_HAM_0036,KR001_HAM_0036,Flavonifractor plautii,Flavonifractor,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100335,292800,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025758085.1,CP107198,,,PacBio Sequel II,5x,hifiasm_meta v. 0.2-r040,1,0,1,4477720,59.956406,4836,4383,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- HP,29318.3,Winkia neuii subsp. anitrata NY0527,NY0527,Winkia neuii,Winkia,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMN32781369,29318,,,,,,,,2023-01-29T00:00:00Z,,PRJNA925112,,"CP116394,CP116395",,,Illumina NovaSeq; Oxford Nanopore MinION,100.0x,Unicycler v. 0.49,1,1,2,2293926,56.61133,2132,2058,hip abscess fluids,,2022-05-27,China,China: Shenzhen,,,,hip abscess,,,,,,,,,,,,,,collected_by:Xunchao Cai,,,,,,,hip abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,29380.12,Staphylococcus caprae strain JMUB145,JMUB145,Staphylococcus caprae,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00115877,29380,,,,,,,,2018-10-24T00:00:00Z,,PRJDB6943,GCA_003966585.1,AP018585,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MiSeq;ABI 3730,112.46X,Velvet de novo Assembly v. 1.0.0,1,,1,2618380,33.66177,2487,2489,humans,isolated from humans,2015,Japan,Japan,,,,,,,,,Positive,Cocci,,,,,,,We determined the complete genome sequences of three methicillin-resistant S. caprae strains isolated from humans.,,missing,missing,blood,23901096,Complete genome sequencing of three human clinical isolates of Staphylococcus caprae,,,,,,,,,,,,missing,,,,99.81,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29380.13,Staphylococcus caprae strain JMUB590,JMUB590,Staphylococcus caprae,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00115876,29380,,,,,,,,2018-10-24T00:00:00Z,,PRJDB6943,GCA_003966605.1,AP018586,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MiSeq;ABI 3730,179.3X,Velvet de novo Assembly v. 1.0.0,1,,1,2629173,33.610455,2509,2510,humans,isolated from humans,2015,Japan,Japan,,,,,,,,,Positive,Cocci,,,,,,,We determined the complete genome sequences of three methicillin-resistant S. caprae strains isolated from humans.,,missing,missing,nasal cavity,23901096,Complete genome sequencing of three human clinical isolates of Staphylococcus caprae,,,,,,,,,,,,missing,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29380.14,Staphylococcus caprae strain JMUB898,JMUB898,Staphylococcus caprae,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00115875,29380,,,,,,,,2018-10-24T00:00:00Z,,PRJDB6943,GCA_003966625.1,AP018587,,"Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University",MiSeq;ABI 3730,150.6X,Velvet de novo Assembly v. 1.0.0,1,,1,2598513,33.619728,2473,2476,humans,isolated from humans,2015,Japan,Japan,,,,,,,,,Positive,Cocci,,,,,,,We determined the complete genome sequences of three methicillin-resistant S. caprae strains isolated from humans.,,missing,missing,graft infection,23901096,Complete genome sequencing of three human clinical isolates of Staphylococcus caprae,,,,,,,,,,,,missing,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29380.70,Staphylococcus caprae strain SY333,SY333,Staphylococcus caprae,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14639260,29380,,,,,,,,2020-04-27T00:00:00Z,,PRJNA626385,GCA_012851115.1,"CP051643,CP051647,CP051645,CP051648,CP051646,CP051644",,Wenzhou Medical University,PacBio RSII; Oxford Nanopore MiniION;,100.0x,Canu v. 1.8,1,5,6,2764332,33.48024,2731,2647,puncture fluid,,2018-09-01,China,China: Lishui,,,,fever of unknown origin,,,,,,,,,,,,,"Staphylococcus caprae SY333 genome, complete sequence",collected_by:Junwan Lu,,,,,,,fever of unknown origin,,,,,,,,,,,,,,99.7,0.51,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29385.174,Staphylococcus saprophyticus strain FDAARGOS_336,FDAARGOS_336,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06173349,29385,,,,,,FDA:FDAARGOS_336,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002208905.2,"CP022056,CP022055,CP022057",,US Food and Drug Administration,PacBio,16.0057786948174x,"SMRT v. 2.3.0, HGAP v. 3.0",1,2,3,2635575,33.11,2677,2508,urine clean catch,,2015-02-25,USA,USA:DC,,female,18Y,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,99.6,4.8,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,29385.175,Staphylococcus saprophyticus strain FDAARGOS_355,FDAARGOS_355,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06173368,29385,,,,,,FDA:FDAARGOS_355,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002209265.2,"CP022093,CP022091,CP022092,CP022094",,US Food and Drug Administration,PacBio,18.7876891512697x,"SMRT v. 2.3.0, HGAP v. 3.0",1,3,4,2639009,33.14,2699,2525,urine,,1935,United Kingdom,United Kingdom: Manchester University,,,,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < ATCC < NCTC-UK,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,99.6,4.8,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,29385.319,Staphylococcus saprophyticus strain UTI-035,UTI-035,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089825,29385,,,,,,,,2020-06-14T00:00:00Z,,PRJNA636387,GCA_013341395.1,"CP054434,CP054435,CP054436,CP054437",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",201.0x,Unicycler v. 0.4.8,1,3,4,2644333,33.069736,2607,2520,urine specimens,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29385.320,Staphylococcus saprophyticus strain UTI-042y,UTI-042y,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089827,29385,,,,,,,,2020-06-14T00:00:00Z,,PRJNA636387,GCA_013341415.1,"CP054438,CP054439",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",146.0x,Unicycler v. 0.4.8,1,1,2,2647442,33.180405,2639,2516,urine specimens,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29385.321,Staphylococcus saprophyticus strain UTI-056,UTI-056,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089852,29385,,,,,,,,2020-06-14T00:00:00Z,,PRJNA636387,GCA_013341435.1,"CP054444,CP054445,CP054446,CP054447,CP054448",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",234.0x,Unicycler v. 0.4.8,1,4,5,2636688,33.140896,2615,2535,urine specimens,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29385.322,Staphylococcus saprophyticus strain UTI-058y,UTI-058y,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089863,29385,,,,,,,,2020-06-14T00:00:00Z,,PRJNA636387,GCA_013341455.1,"CP054440,CP054441,CP054442,CP054443",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",211.0x,Unicycler v. 0.4.8,1,3,4,2632236,33.136505,2610,2525,urine specimens,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,0.56,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29385.323,Staphylococcus saprophyticus strain UTI-050,UTI-050,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089828,29385,,,,,,,,2020-06-15T00:00:00Z,,PRJNA636387,GCA_013343055.1,"CP054575,CP054576,CP054577,CP054578,CP054579",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",181.0x,Unicycler v. 0.4.8,1,4,5,2703096,33.1663,2724,2610,urine specimens,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,1.11,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29385.324,Staphylococcus saprophyticus strain UTI-045,UTI-045,Staphylococcus saprophyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15089826,29385,,,,,,,,2020-06-18T00:00:00Z,,PRJNA636387,GCA_013358365.1,"CP054831,CP054832,CP054833,CP054834,CP054835",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",189.0x,Unicycler v. 0.4.8,1,4,5,2744227,33.14314,2730,2637,urine,"isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections",2019,USA,USA: California,,female,,,,,,,,,,,,,,,"Several species of bacteria have been identified as major causes of urinary tract infection, but the prevalence of different bacteria can vary significantly, depending on location, timing, and demographics of the population being studied. This study is directed at identifying shared genomic and phenotypic traits in bacteria isolated from urine specimens provided by female patients presenting at a college health clinic, who were experiencing symptoms of urinary tract infections.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.44,0.56,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29388.315,Staphylococcus capitis strain XZ03,XZ03,Staphylococcus capitis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN23019561,29388,,,,,,,,2021-11-18T00:00:00Z,,PRJNA779231,GCA_020883475.1,CP086659,,Affiliated Hospital of Xuzhou Medical University,PacBio RSII,230.0x,FALCON v. v0.3.0; Celera Assembler v. 8.3,1,0,1,2565475,32.927353,2458,,blood,,2019-09-01,,China,,,,bacteremia,,,,,,,,,,,,,Phenotypic and genotypic characterization of linezolid resistance coagulase-negative Staphylococci,collected_by:Fei Jiang,,,,,,,bacteremia,,,,,,,,,,,,,,99.81,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,29388.68,Staphylococcus capitis strain TW2795,TW2795,Staphylococcus capitis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00041516,29388,,,,,,,,2017-02-02T00:00:00Z,,PRJDB4225,GCA_002356175.1,"AP014956,AP017298",,"Department of Bacteriology, Jichi medical University",454 GS FLX;ABI 3730,Unknown,GS De Novo Assembler v. 2.0,1,1,2,2486776,33.05,2381,2326,,,1997-12-22,Japan,Japan:Tokyo,env_biome:not applicable,,,,,,,,,,,,,,,,Whole genome sequence of Staphylococcus capitis and relationship of its genome and antibiotics resistance,,not applicable,missing,missing,missing,JMUB staphylococcus project,,,Pacemaker-related endocarditis,,,,,,,,,not applicable,,,,98.6,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29430.66,Acinetobacter haemolyticus strain sz1652,sz1652,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09767503,29430,,,,,,,,2018-12-18T00:00:00Z,,PRJNA484667,GCA_003952705.1,"CP032135,CP032136,CP032137",,Guangdong Medical University,PacBio RS; Illumina,130.0x,SOAPdenovo v. 2.04; HGAP v. 2.3.0,1,2,3,3588183,39.59224,3866,3394,urinary tract,isolated strains,2017,China,China: Shenzhen,,,,,,,,,,,,,,,,,This study aimed to analyze the drug resistance determinants and related pathogenic system in carbapenem-resistant Acinetobacter haemolyticus strain SZ1652 in an attempt to better understand the resistance and pathogenic mechanisms of the isolated strains.,sample_type:single cell(Pathogenic microorganism),,,,,,,,,,,,,,,,,,,,,99.41,0.55,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,29430.69,Acinetobacter haemolyticus strain TJR01,TJR01,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11157875,29430,,,,,,,,2019-03-26T00:00:00Z,,PRJNA527688,GCA_004379355.1,"CP038009,CP038010,CP038011",,Tianjin University,PacBio,,Canu v.1.3,1,2,3,3734602,39.784935,3646,3446,respiratory patient,isolated from a respiratory patient in china,2012,China,China: Tianjin,,,,Acinetobacter infections,,,,,,,,,,,,,Acinetobacter haemolyticus strain TJR01 was isolated from a respiratory patient in china.,collected_by:He Huang,,,,,,,Acinetobacter infections,,,,,,,,,,,,,,99.73,0.72,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,29430.72,Acinetobacter haemolyticus strain AN4,AN4,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09927973,29430,,,,MLST.Acinetobacter_baumannii_2.86,,,,2020-01-16T00:00:00Z,,PRJNA311558,GCA_009892285.1,"CP031979,CP031983,CP031982,CP031981,CP031980",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio Sequel,104x,Unicycler v. 0.4.1,1,4,5,3674400,39.72605,3736,3524,ulcer by decubitus,,2010-11-26,Mexico,Mexico: Puebla,,male,13 years,Acinetobacter infection,,host_description:Infectology patitent,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital para el Nino Poblano,,,,,,,Acinetobacter infection,,,Infectology patitent,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,29430.74,Acinetobacter haemolyticus strain AN3,AN3,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09927972,29430,,,,,,,,2020-01-16T00:00:00Z,,PRJNA311558,GCA_009892325.1,"CP031984,CP031987,CP031986,CP031985",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio Sequel,95x,Unicycler v. 0.4.1,1,3,4,3396816,39.64557,3245,3142,peritoneal dialysis liquid,,2010-04-05,Mexico,Mexico: Puebla,,female,13 years,Acinetobacter infection,,host_description:Patient was at the Emergency services,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital para el Nino Poblano,,,,,,,Acinetobacter infection,,,Patient was at the Emergency services,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,29430.75,Acinetobacter haemolyticus strain AN43,AN43,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09927974,29430,,,,MLST.Acinetobacter_baumannii_2.86,,,,2020-01-16T00:00:00Z,,PRJNA311558,GCA_009892265.1,"CP031976,CP031978,CP031977",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,220x,Unicycler v. 0.4.1,1,2,3,3669945,39.549583,3593,3430,peritoneal dialysis liquid,,2015-04-24,Mexico,Mexico: Puebla,,male,10 years,Acinetobacter infection,,host_description:Internal medicine services,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital para el Nino Poblano,,,,,,,Acinetobacter infection,,,Internal medicine services,,,,,,,,,,,100,0.59,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,29430.76,Acinetobacter haemolyticus strain INNSZ174,INNSZ174,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09927969,29430,,,,,,,,2020-01-16T00:00:00Z,,PRJNA311558,GCA_009892365.1,"CP031998,CP032001,CP032000,CP031999",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,259x,Unicycler v. 0.4.1,1,3,4,3558578,39.70451,3529,3357,unknown,,1998-05-21,Mexico,Mexico: Mexico City,,,,Acinetobacter infection,,,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29430.79,Acinetobacter haemolyticus strain AN59,AN59,Acinetobacter haemolyticus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09927975,29430,,,,MLST.Acinetobacter_baumannii_2.86,,,,2020-01-16T00:00:00Z,,PRJNA311558,GCA_009892245.1,"CP031972,CP031975,CP031974,CP031973",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,296x,Unicycler v. 0.4.1,1,3,4,3694983,39.536716,3637,3467,peritoneal dialysis liquid,,2016-04-06,Mexico,Mexico: Puebla,,male,13 years,Acinetobacter infection,,host_description:Patient was at the Emergency services,,,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital para el Nino Poblano,,,,,,,Acinetobacter infection,,,Patient was at the Emergency services,,,,,,,,,,,100,0.73,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,29459.332,Brucella melitensis strain BwIM_AFG_63,BwIM_AFG_63,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932969,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191235.1,"CP018478,CP018479",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,139.9,SPAdes v. 3.9.0,2,,2,3311054,57.22,3523,3349,,,2016,Afghanistan,Afghanistan,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.333,Brucella melitensis strain BwIM_ALB_46,BwIM_ALB_46,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932954,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191255.1,"CP018480,CP018481",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,158.6,SPAdes v. 3.9.0,2,,2,3313147,57.22,3528,3352,,,2015,Albania,Albania,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.334,Brucella melitensis strain BwIM_IRN_28,BwIM_IRN_28,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932957,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191275.1,"CP018484,CP018485",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,89.8,SPAdes v. 3.9.0,2,,2,3311132,57.22,3516,3348,,,2015,Iran,Iran,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.335,Brucella melitensis strain BwIM_IRN_37,BwIM_IRN_37,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932947,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191295.1,"CP018486,CP018487",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,128.2,SPAdes v. 3.9.0,2,,2,3313492,57.22,3521,3352,,,2015,Iran,Iran,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.336,Brucella melitensis strain BwIM_IRQ_11,BwIM_IRQ_11,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932931,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191315.1,"CP018488,CP018489",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,82.6,SPAdes v. 3.9.0,2,,2,3312286,57.22,3522,3348,,,2014,Iraq,Iraq,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.337,Brucella melitensis strain BwIM_IRQ_32,BwIM_IRQ_32,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932974,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191335.1,"CP018490,CP018491",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,71.2,SPAdes v. 3.9.0,2,,2,3311923,57.22,3515,3348,,,2014,Iraq,Iraq,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.338,Brucella melitensis strain BwIM_ITA_45,BwIM_ITA_45,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932955,29459,,,,MLST.Brucella_spp.43,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191355.1,"CP018494,CP018495",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,105.1,SPAdes v. 3.9.0,2,,2,3310467,57.22,3513,3349,,,2015,Italy,Italy,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.339,Brucella melitensis strain BwIM_ITA_55,BwIM_ITA_55,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932987,29459,,,,MLST.Brucella_spp.11,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191375.1,"CP018496,CP018497",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,68.9,SPAdes v. 3.9.0,2,,2,3309727,57.22,3517,3349,,,2016,Italy,Italy,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.340,Brucella melitensis strain BwIM_JOR_13,BwIM_JOR_13,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932952,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191395.1,"CP018498,CP018499",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,56.4,SPAdes v. 3.9.0,2,,2,3312622,57.21,3520,3349,,,2015,Jordan,Jordan,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0.6,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.341,Brucella melitensis strain BwIM_MAR_25,BwIM_MAR_25,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932985,29459,,,,MLST.Brucella_spp.11,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191415.1,"CP018502,CP018503",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,69.8,SPAdes v. 3.9.0,2,,2,3310615,57.21,3523,3351,,,2016,Morocco,Morocco,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.342,Brucella melitensis strain BwIM_SOM_36a,BwIM_SOM_36a,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932921,29459,,,,MLST.Brucella_spp.12,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191435.1,"CP018506,CP018507",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,87.4,SPAdes v. 3.9.0,2,,2,3303199,57.22,3504,3346,,,2014,Somalia,Somalia,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.343,Brucella melitensis strain BwIM_SYR_04,BwIM_SYR_04,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932948,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191455.1,"CP018512,CP018513",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,150.4,SPAdes v. 3.9.0,2,,2,3312670,57.22,3525,3349,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.344,Brucella melitensis strain BwIM_SYR_05,BwIM_SYR_05,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932956,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191475.1,"CP018514,CP018515",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,96.7,SPAdes v. 3.9.0,2,,2,3311691,57.21,3518,3345,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.345,Brucella melitensis strain BwIM_SYR_07,BwIM_SYR_07,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932963,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191495.1,"CP018516,CP018517",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,58.0,SPAdes v. 3.9.0,2,,2,3312780,57.22,3514,3350,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.346,Brucella melitensis strain BwIM_SYR_34,BwIM_SYR_34,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932960,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191515.1,"CP018530,CP018531",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,69.4,SPAdes v. 3.9.0,2,,2,3312548,57.22,3513,3348,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.347,Brucella melitensis strain BwIM_SYR_41,BwIM_SYR_41,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932970,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191535.1,"CP018532,CP018533",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,118.5,SPAdes v. 3.9.0,2,,2,3312631,57.22,3517,3351,,,2016,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.348,Brucella melitensis strain BwIM_TKM_56,BwIM_TKM_56,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932951,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191575.1,"CP018536,CP018537",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,119.2,SPAdes v. 3.9.0,2,,2,3311409,57.22,3517,3348,,,2015,Turkmenistan,Turkmenistan,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.349,Brucella melitensis strain BwIM_SYR_53,BwIM_SYR_53,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932962,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191555.1,"CP018534,CP018535",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,46.5,SPAdes v. 3.9.0,2,,2,3313072,57.21,3525,3351,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.350,Brucella melitensis strain BwIM_TUR_02,BwIM_TUR_02,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932989,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191595.1,"CP018538,CP018539",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,70.2,SPAdes v. 3.9.0,2,,2,3313533,57.22,3520,3351,,,2016,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.351,Brucella melitensis strain BwIM_TUR_03,BwIM_TUR_03,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932920,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191615.1,"CP018540,CP018541",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,134.7,SPAdes v. 3.9.0,2,,2,3312739,57.22,3520,3349,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.352,Brucella melitensis strain BwIM_TUR_15,BwIM_TUR_15,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932916,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191635.1,"CP018542,CP018543",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,107.4,SPAdes v. 3.9.0,2,,2,3312547,57.22,3521,3349,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.353,Brucella melitensis strain BwIM_TUR_17,BwIM_TUR_17,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932930,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191655.1,"CP018544,CP018545",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,99.3,SPAdes v. 3.9.0,2,,2,3312719,57.22,3523,3349,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.354,Brucella melitensis strain BwIM_TUR_19,BwIM_TUR_19,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932975,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191675.1,"CP018546,CP018547",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,70.8,SPAdes v. 3.9.0,2,,2,3312621,57.22,3520,3349,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.355,Brucella melitensis strain BwIM_TUR_27,BwIM_TUR_27,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932961,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191695.1,"CP018550,CP018551",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,69.9,SPAdes v. 3.9.0,2,,2,3314625,57.21,3533,3359,,,2015,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0.6,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.356,Brucella melitensis strain BwIM_TUR_38,BwIM_TUR_38,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932978,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191715.1,"CP018552,CP018553",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,59.7,SPAdes v. 3.9.0,2,,2,3311118,57.21,3521,3345,,,2015,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.357,Brucella melitensis strain BwIM_TUR_40,BwIM_TUR_40,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932971,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191735.1,"CP018556,CP018557",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,68.8,SPAdes v. 3.9.0,2,,2,3314720,57.22,3525,3353,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.358,Brucella melitensis strain BwIM_TUR_59,BwIM_TUR_59,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932973,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191755.1,"CP018560,CP018561",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,68.5,SPAdes v. 3.9.0,2,,2,3312616,57.22,3518,3351,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.359,Brucella melitensis strain BwIM_TUR_60,BwIM_TUR_60,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932972,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191775.1,"CP018562,CP018563",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,70.2,SPAdes v. 3.9.0,2,,2,3312594,57.22,3522,3351,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.360,Brucella melitensis strain BwIM_XXX_12,BwIM_XXX_12,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932965,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191795.1,"CP018564,CP018565",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,104.7,SPAdes v. 3.9.0,2,,2,3312757,57.22,3526,3352,,,2015,,,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.361,Brucella melitensis strain BwIM_XXX_22,BwIM_XXX_22,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932950,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191815.1,"CP018566,CP018567",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,107.7,SPAdes v. 3.9.0,2,,2,3313536,57.22,3516,3349,,,2015,,,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.362,Brucella melitensis strain BwIM_XXX_54,BwIM_XXX_54,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932980,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191835.1,"CP018568,CP018569",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,55.3,SPAdes v. 3.9.0,2,,2,3312633,57.22,3518,3351,,,2015,,,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.363,Brucella melitensis strain BwIM_BGR_21,BwIM_BGR_21,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932986,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191855.1,"CP018482,CP018483",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,57.6,SPAdes v. 3.9.0,2,,2,3312294,57.22,3522,3350,,,2016,Bulgaria,Bulgaria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.364,Brucella melitensis strain BwIM_IRQ_43,BwIM_IRQ_43,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932959,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191875.1,"CP018492,CP018493",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,75.3,SPAdes v. 3.9.0,2,,2,3312703,57.22,3523,3350,,,2015,Iraq,Iraq,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.365,Brucella melitensis strain BwIM_KWT_42,BwIM_KWT_42,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932984,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191895.1,"CP018500,CP018501",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,61.0,SPAdes v. 3.9.0,2,,2,3311497,57.22,3524,3348,,,2016,Kuwait,Kuwait,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.366,Brucella melitensis strain BwIM_SAU_09,BwIM_SAU_09,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932949,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191915.1,"CP018504,CP018505",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,86.2,SPAdes v. 3.9.0,2,,2,3311334,57.22,3525,3348,,,2015,Saudi Arabia,Saudi Arabia,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.367,Brucella melitensis strain BwIM_SOM_36b,BwIM_SOM_36b,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932922,29459,,,,MLST.Brucella_spp.12,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191935.1,"CP018508,CP018509",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,99.5,SPAdes v. 3.9.0,2,,2,3303645,57.21,3504,3346,,,2014,Somalia,Somalia,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.368,Brucella melitensis strain BwIM_SYR_01,BwIM_SYR_01,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932958,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002191995.1,"CP018510,CP018511",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,110.0,SPAdes v. 3.9.0,2,,2,3311385,57.21,3512,3346,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.369,Brucella melitensis strain BwIM_SYR_08,BwIM_SYR_08,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932967,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192015.1,"CP018518,CP018519",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,126.6,SPAdes v. 3.9.0,2,,2,3313634,57.22,3514,3349,,,2016,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.370,Brucella melitensis strain BwIM_SYR_10,BwIM_SYR_10,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932968,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192035.1,"CP018520,CP018521",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,157.2,SPAdes v. 3.9.0,2,,2,3313251,57.22,3521,3350,,,2016,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.371,Brucella melitensis strain BwIM_SYR_14,BwIM_SYR_14,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932964,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192055.1,"CP018522,CP018523",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,51.0,SPAdes v. 3.9.0,2,,2,3312579,57.22,3522,3351,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.372,Brucella melitensis strain BwIM_SYR_23,BwIM_SYR_23,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932966,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192075.1,"CP018524,CP018525",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,116.2,SPAdes v. 3.9.0,2,,2,3312952,57.22,3524,3352,,,2016,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.373,Brucella melitensis strain BwIM_SYR_26,BwIM_SYR_26,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932953,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192095.1,"CP018526,CP018527",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,107.7,SPAdes v. 3.9.0,2,,2,3312779,57.22,3515,3347,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.374,Brucella melitensis strain BwIM_SYR_31,BwIM_SYR_31,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932979,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192115.1,"CP018528,CP018529",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,70.5,SPAdes v. 3.9.0,2,,2,3312673,57.22,3523,3350,,,2015,Syria,Syria,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.375,Brucella melitensis strain BwIM_TUR_24,BwIM_TUR_24,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932983,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192135.1,"CP018548,CP018549",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,65.2,SPAdes v. 3.9.0,2,,2,3312503,57.22,3519,3352,,,2015,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.376,Brucella melitensis strain BwIM_TUR_39,BwIM_TUR_39,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932976,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192155.1,"CP018554,CP018555",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,68.7,SPAdes v. 3.9.0,2,,2,3312521,57.22,3513,3349,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.377,Brucella melitensis strain BwIM_TUR_51,BwIM_TUR_51,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932917,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192175.1,"CP018558,CP018559",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,65.8,SPAdes v. 3.9.0,2,,2,3311587,57.22,3526,3348,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.378,Brucella melitensis strain BwIM_TUR_30,BwIM_TUR_30,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN05932932,29459,,,,,,,,2017-06-13T00:00:00Z,28388689,PRJNA347914,GCA_002192195.1,"CP018570,CP018571",,"Bundeswehr, Institute of Microbiology",Illumina MiSeq,80.3,SPAdes v. 3.9.0,2,,2,3314350,57.21,3519,3353,,,2014,Turkey,Turkey,env_biome:not applicable,,,Brucellosis,,,,,,,,,,,,,Brucella melitensis strains isolated from various sources for epidemiological purposes,,,,,missing,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29459.399,Brucella melitensis strain 2007BM/1,2007BM/1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN07580939,29459,,,,MLST.Brucella_spp.8,,,,2017-09-12T00:00:00Z,,PRJNA400844,GCA_002290125.1,"CP023171,CP023172",,IVRI,Illumina,50.0x,CLC NGS Cell v. 6.0; Edena v. 3.13;,2,,2,3302684,56.26,3473,3253,blood,,2007-11-11,India,India:Karnataka,,female,60 years,Fever,,host_description:not applicable;host_disease_outcome:not applicable;host_health_state:not applicable;host_subject_id:not applicable,,,,,,,,,,,Indian field isolate Brucella melitensis;missing ribosomal protein genes;missing tRNA genes,collected_by:Dr. B. G. Mantur;passage_history:not applicable;specimen_voucher:not applicable,,,,,,,Fever,not applicable,not applicable,not applicable,missing,missing,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,29459.407,Brucella melitensis strain CIIMS-BH-2,CIIMS-BH-2,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN08176517,29459,,,,,,,,2018-01-22T00:00:00Z,,PRJNA422344,GCA_002895105.1,"CP025680,CP025681",,"Dr. G.M. Taori, Central India Institute of Medical Sciences",Illumina HiSeq,295.0x,SPAdes v. 3.10.1,2,,2,3311210,57.220985,3515,3297,blood,,2016-02-24,India,"India: Vijayapura, Karnataka",,,,Brucellosis,,,,,,,,,,,,,Brucellosis is an infectious disease caused by Brucella spp. It is transmitted from animal to human. To study virulent gene responsible for infection in human is objective of study.,collected_by:Vijayapura,,,,,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Blood and Circulatory System,Specific Bacterial Infections-Brucellosis HP,29459.408,Brucella melitensis strain B3 strain CIIMS-PH-3,CIIMS-PH-3,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN08242171,29459,,,,MLST.Brucella_spp.8,,,,2018-01-22T00:00:00Z,,PRJNA427646,GCA_002895125.1,"CP026005,CP026006",,"Dr. G.M. Taori, Central India Institute of Medical Sciences",Illumina HiSeq,615.0x,SPAdes v. 3.10.1,2,,2,3310711,57.218735,3524,3303,blood,,2016-02-28,India,India:Chandigarh,,,,Brucellosis,,,,,,,,,,,,,Brucellosis is a bacterial infection that affects thousands of people world wide. The goal of study is to identify virulent proteins responsible for pathogenesis in our isolate.,"collected_by:PGIMER, Chandigarh",,,,,,,Brucellosis,,,,,,,,,,,,,,100,0.6,Specific Bacterial Infections,Brucellosis,Blood and Circulatory System,Specific Bacterial Infections-Brucellosis HP,29459.410,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369531,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236335.1,"LT962928,LT962929",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295083,57.225605,3355,,human,,2002,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.411,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369548,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236345.1,"LT963350,LT963351",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3294929,57.22485,3355,,human,,2016,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.412,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369537,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236355.1,"LT962945,LT962946",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295079,57.224583,3354,,human,,2011,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.413,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369542,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236365.1,"LT962940,LT962941",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295230,57.22442,3357,,human,,2014,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.414,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369533,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236375.1,"LT962947,LT962948",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295073,57.222893,3344,,human,,2003,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.415,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369541,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236385.1,"LT962910,LT962911",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295156,57.224274,3352,,human,,2013,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.416,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369543,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236395.1,"LT962943,LT962944",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295219,57.22464,3355,,human,,2014,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.417,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369536,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236405.1,"LT962914,LT962915",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295161,57.22425,3349,,human,,2010,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.418,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369549,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236415.1,"LT962926,LT962927",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295221,57.224453,3351,,human,,2016,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.419,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369535,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236425.1,"LT962922,LT962923",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295104,57.222237,3344,,human,,2010,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.420,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369538,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236435.1,"LT962916,LT962917",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295145,57.22447,3351,,human,,2012,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.421,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369527,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236445.1,"LT962924,LT962925",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295128,57.225067,3357,,human,,2006,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.422,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369545,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236455.1,"LT962912,LT962913",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295212,57.224335,3348,,human,,2015,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.423,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369546,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236465.1,"LT962920,LT962921",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295087,57.22526,3351,,human,,2016,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.424,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369539,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236485.1,"LT962918,LT962919",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295085,57.222565,3337,,human,,2012,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.425,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369547,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236495.1,"LT963348,LT963349",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295056,57.22237,3340,,human,,2016,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.426,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369544,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236515.1,"LT962930,LT962931",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295070,57.224678,3356,,human,,2015,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.427,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369530,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236525.1,"LT962932,LT962933",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295083,57.22454,3350,,human,,1999,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.428,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369528,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236535.1,"LT962938,LT962939",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295033,57.222404,3345,,human,,2006,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.429,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369540,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236545.1,"LT962934,LT962935",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295203,57.224247,3350,,human,,2013,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.430,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369529,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236555.1,"LT962936,LT962937",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295047,57.224136,3350,,human,,1999,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.431,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369532,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236565.1,"LT962953,LT962954",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295107,57.225277,3353,,human,,2003,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.432,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369534,29459,,,,MLST.Brucella_spp.8,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236575.1,"LT962951,LT962952",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3294987,57.224346,3365,,human,,2009,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.433,Brucella melitensis strain 1,1,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMEA104369526,29459,,,,MLST.Brucella_spp.12,,,,2017-12-01T00:00:00Z,,PRJEB23353,GCA_900236585.1,"LT962949,LT962950",,NORWEGIAN INSTITUTE OF PUBLIC HEALTH,,,,2,,2,3295066,57.22323,3346,,human,,2005,Norway,Norway,,,,,,,,,,,,,,,,,"Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection. A total of 24 isolates was analysed by whole genome sequencing. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa.",,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,29459.480,Brucella melitensis strain B29,B29,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN10829700,29459,,,,,,,,2019-02-17T00:00:00Z,,PRJNA517393,GCA_004208655.1,"CP035793,CP035794",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,100X,HGAP v. 2,2,,2,3311869,57.220287,3512,3305,blood,,2018-06,China,China:Hulunbuir,,,,bloodstream infection,,,,,,,,,,,,,Complete genome sequencing of Brucella melitensis strains isolated from human Brucellosis,collected_by:Xiuwen Liang,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.45,0.76,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,29459.481,Brucella melitensis strain B15,B15,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN10829699,29459,,,,,,,,2019-02-17T00:00:00Z,,PRJNA517393,GCA_004208675.1,"CP035795,CP035796",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,100X,HGAP v. 2,2,,2,3311846,57.21972,3514,3305,blood,,2018-05,China,China:Hulunbuir,,,,bloodstream infection,,,,,,,,,,,,,Complete genome sequencing of Brucella melitensis strains isolated from human Brucellosis,collected_by:Xiuwen Liang,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.45,0.76,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,29459.482,Brucella melitensis strain B9,B9,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN10829698,29459,,,,,,,,2019-02-17T00:00:00Z,,PRJNA517393,GCA_004208695.1,"CP035797,CP035798",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,100X,HGAP v. 2,2,,2,3311825,57.218964,3522,3304,blood,,2018-02,China,China:Hulunbuir,,,,bloodstream infection,,,,,,,,,,,,,Complete genome sequencing of Brucella melitensis strains isolated from human Brucellosis,collected_by:Xiuwen Liang,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.45,0.76,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,29459.642,Brucella melitensis strain VB700,VB700,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN12917484,29459,,,,,,,,2019-10-13T00:00:00Z,,PRJNA575949,GCA_009017355.1,"CP044983,CP044984",,Christian Medical College and Hospital,Oxford Nanopore MiniION; IonTorrent,200.0x,Canu v. 1.8; Unicycler v. 0.4.7,2,,2,3311614,57.217537,3615,3307,blood,,2019-06-14,India,India,,,,Bacterimia,,,,,,,,,,,,,Brucella melitensis complete genome,collected_by:Christian Medical College and Hospital Vellore,,,,,,,Bacterimia,,,,,,,,,,,,,,99.17,0.76,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,29459.643,Brucella melitensis strain VB12455,VB12455,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN12917575,29459,,,,,,,,2019-10-13T00:00:00Z,,PRJNA575951,GCA_009017395.1,"CP044985,CP044986",,Christian Medical College and Hospital,Oxford Nanopore MiniION; IonTorrent,200.0x,Canu v. 1.8; Unicycler v. 0.4.7,2,,2,3311723,57.21747,3594,3301,blood,,2019-04-28,India,India,,,,Bacterimia,,,,,,,,,,,,,Brucella melitensis complete genome,collected_by:Christian Medical College and Hospital Vellore,,,,,,,Bacterimia,,,,,,,,,,,,,,99.28,0.76,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,29459.889,Brucella melitensis strain PB150210,PB150210,Brucella melitensis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN30248435,29459,,,,,,,,2022-08-31T00:00:00Z,,PRJNA868508,GCA_024802385.1,"CP103417,CP103418",,Xinjiang Medical University,PacBio RSII,168.0x,HGAP v. April-2015,2,0,2,3310616,57.221676,3379,3146,patient,isolated from the blood of patient with heart valve dissolvedBrucellosis is a major bacterial zoonosis mammalianal animals and humans around the globe,2015,China,China:Xinjiang,,,,heart valve dissolved,,,,,,,,,,,,,"omplete genome sequence of Brucella melitensis isolated from the blood of patient with heart valve dissolvedBrucellosis is a major bacterial zoonosis mammalianal animals and humans around the globe. The complete genome sequence of B. melitensis in size of 16M(Rajashekara, Glasner et al. 2004). Four genome sequences including virulent strain B. melitensis M28-12 and vaccine strains B. melitensis M5 and M111 and B. suis S2 have been finished, showing different virulences and pathogenicities(Ding, Pan et al. 2011). Ten species of Brucellosis are clustered into four clades as Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact beta-ketoadipate pathway, responsible for utilization of plant-derived compounds (Wattam, Williams et al. 2009). A comparison of three genomes of Brucellosis published in Plos One (Crasta, Folkerts et al. 2008) showed 24 genes which may be associated with virulences of Brucellosis abourtus virulent strains. Four genes have an inserts of 60 bp fragment, which is likely associated with the virulence.",collected_by:Wenbao Zhang,,,,,,,heart valve dissolved,,,,,,,,,,,,,,99.45,0.76,Cardiovascular Diseases,Other Cardiovascular Diseases,Other,Cardiovascular Diseases-Other Cardiovascular Diseases HP,29461.115,Brucella suis strain 7121680725,7121680725,Brucella suis,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN21183180,29461,,,,,,,,2021-09-15T00:00:00Z,,PRJNA759654,GCA_019998625.1,"CP083232,CP083233",,"Faculty of Medicne, University Malaya",Illumina HiSeq,466.4x,Geneious Prime 2020 v. 2020.1.2,2,0,2,3297225,57.24079,3268,,"kuala lumpur, malaysia",,2017-12-07,Malaysia,Malaysia,,,,brucellosis,,,,,,,,,,,,,Brucella suis from blood culture of a Malaysian patient,collected_by:University Malaya Medical Centre,,,,,,,brucellosis,,,,,,,,,,,,,,99.44,0.91,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,29495.53,Vibrio navarrensis strain 20-VB00237,20-VB00237,Vibrio navarrensis,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN16880831,29495,,biovar pommerensis,,,,,,2020-12-06T00:00:00Z,,PRJNA680459,GCA_015767675.1,"CP065217,CP065218,CP065219",,German Federal Institute for Risk Assessment,Illumina MiSeq; Oxford Nanopore MinION,36.0x,Unicycler v. v0.4.8,2,1,3,5109806,47.903072,5110,4662,not provided,,2020,Germany,Germany,,,,wound infection,,,,,,,,,,,,,Vibrio navarrensis biotype pommerensis strain 20-VB00237 genome sequencing,"collected_by:Institut fuer Medizinische Diagnostik (IMD), Greifswald",,,,,,,wound infection,,,,,,,,,,,,,,100,1.44,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,29507.9,Leptospira kirschneri FMAS_PN5,FMAS_PN5,Leptospira kirschneri,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN11919596,29507,,,,"MLST.Leptospira_spp_3.99,MLST.Leptospira_spp.68",,,,2022-03-10T00:00:00Z,,PRJNA528695,GCA_024526015.1,"CP092660,CP092657,CP092658,CP092659,CP092661",,,PacBio Sequel System,1116x,canu v. 2.1,2,3,5,4902417,36.31127,5101,4167,blood,,Not collected,Sri Lanka,Sri Lanka:Polonnaruwa,,male,40 yrs,Leptospirosis,,host_disease_outcome:recovery;host_disease_stage:acute,,,,,,,,,,,,"collected_by:Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka",,,,,,,Leptospirosis,,recovery,,acute,,,,,,,,,,100,0.9,Specific Bacterial Infections,Leptospirosis,Blood and Circulatory System,Specific Bacterial Infections-Leptospirosis HP,29518.255,Borreliella afzelii PBabu,PBabu,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328436,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075440,,,Illumina MiSeq,335x,SPAdes v. 3.13.0,1,0,1,903559,28.306396,826,,missing,,2001,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.256,Borreliella afzelii PBec,PBec,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328437,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075441,,,Illumina MiSeq,31x,SPAdes v. 3.13.0,1,0,1,899896,28.266256,825,,missing,,1988,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.257,Borreliella afzelii PFes,PFes,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328438,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075442,,,Illumina MiSeq,56x,SPAdes v. 3.13.0,1,0,1,899763,28.271793,820,,missing,,1988,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.258,Borreliella afzelii PHam,PHam,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328439,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075443,,,Illumina MiSeq,410x,SPAdes v. 3.13.0,1,0,1,900162,28.252485,823,,missing,,1987,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.259,Borreliella afzelii PSto,PSto,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328444,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075449,,,Illumina MiSeq,363x,SPAdes v. 3.13.0,1,0,1,900022,28.253532,825,,missing,,1986,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.260,Borreliella afzelii PMel,PMel,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328442,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075447,,,Illumina MiSeq,172x,SPAdes v. 3.13.0,1,0,1,900173,28.250792,820,,missing,,1990,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.261,Borreliella afzelii PObf,PObf,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328443,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075448,,,Illumina MiSeq,159x,SPAdes v. 3.13.0,1,0,1,903227,28.30486,825,,missing,,1998,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.262,Borreliella afzelii PWat,PWat,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18917948,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075450,,,Illumina MiSeq,319x,SPAdes v. 3.13.0,1,0,1,901903,28.258083,826,,missing,,1994,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.263,Borreliella afzelii PJe,PJe,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328440,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075444,,,Illumina MiSeq,8x,SPAdes v. 3.13.0,1,0,1,825708,28.624132,925,,missing,,1992,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,95.8,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.264,Borreliella afzelii PKL,PKL,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18917949,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075445,,,Illumina MiSeq,41x,SPAdes v. 3.13.0,1,0,1,867990,28.61613,835,,missing,,1993,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29518.265,Borreliella afzelii PKr,PKr,Borreliella afzelii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328441,29518,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075446,,,Illumina MiSeq,28x,SPAdes v. 3.13.0,1,0,1,887504,28.327261,825,,missing,,1992,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.452,Borreliella garinii PKie,PKie,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18917947,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075403,,,Illumina MiSeq,59x,SPAdes v. 3.13.0,1,0,1,901425,28.281887,829,,missing,,1993,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.454,Borreliella garinii J21,J21,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328481,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075407,,,Illumina MiSeq,135x,SPAdes v. 3.13.0,1,0,1,905112,28.386763,824,,missing,,1996,Japan,Japan,,,,Lyme disease,,,,,,,,,,,,,,"collected_by:NIH Tokyo, japan",,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.455,Borreliella garinii Konnai20_clone1,Konnai20_clone1,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328483,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075405,,,Illumina MiSeq,55x,SPAdes v. 3.13.0,1,0,1,902468,28.401814,884,,missing,,2011,Japan,Japan,,,,Lyme disease,,,,,,,,,,,,,,"collected_by:NIH Tokyo, japan",,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.462,Borreliella garinii Malouvrh,Malouvrh,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328487,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075414,,,Illumina MiSeq,436x,SPAdes v. 3.13.0,1,0,1,901906,28.283436,826,,missing,,,Slovenia,Slovenia,,,,Lyme disease,,,,,,,,,,,,,,collected_by:Slovenia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.464,Borreliella garinii PMa,PMa,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328486,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075415,,,Illumina MiSeq,41x,SPAdes v. 3.13.0,1,0,1,902648,28.292202,834,,missing,,1989,,,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.465,Borreliella garinii PNov,PNov,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328491,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075416,,,Illumina MiSeq,229x,SPAdes v. 3.13.0,1,0,1,904672,28.341684,832,,missing,,1990,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.472,Borreliella garinii PStg,PStg,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328495,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075424,,,Illumina MiSeq,59x,SPAdes v. 3.13.0,1,0,1,901672,28.290554,833,,missing,,1996,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.473,Borreliella garinii PSoR,PSoR,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328494,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075425,,,Illumina MiSeq,330x,SPAdes v. 3.13.0,1,0,1,901711,28.280901,831,,missing,,1989,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.475,Borreliella garinii POhm,POhm,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328493,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075426,,,Illumina MiSeq,39x,SPAdes v. 3.13.0,1,0,1,901534,28.282856,828,,missing,,1991,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.476,Borreliella garinii PUl,PUl,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328496,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075423,,,Illumina MiSeq,341x,SPAdes v. 3.13.0,1,0,1,902716,28.306133,833,,missing,,1999,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.477,Borreliella garinii PLa,PLa,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328484,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075431,,,Illumina MiSeq,25x,SPAdes v. 3.13.0,1,0,1,888870,28.43059,850,,missing,,1988,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.478,Borreliella garinii PLi,PLi,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328485,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075430,,,Illumina MiSeq,38x,SPAdes v. 3.13.0,1,0,1,902415,28.312693,835,,missing,,1988,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.479,Borreliella garinii PMit,PMit,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328490,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075428,,,Illumina MiSeq,52x,SPAdes v. 3.13.0,1,0,1,902082,28.295052,835,,missing,,1997,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.480,Borreliella garinii PKi,PKi,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328482,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075432,,,Illumina MiSeq,41x,SPAdes v. 3.13.0,1,0,1,901814,28.283659,834,,missing,,1992,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.481,Borreliella garinii PFr,PFr,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328477,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075435,,,Illumina MiSeq,14x,SPAdes v. 3.13.0,1,0,1,898477,28.404392,863,,missing,,1995,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.482,Borreliella garinii PHez,PHez,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328479,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075433,,,Illumina MiSeq,69x,SPAdes v. 3.13.0,1,0,1,901662,28.28033,829,,missing,,1994,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.483,Borreliella garinii PHc,PHc,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328478,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075434,,,Illumina MiSeq,47x,SPAdes v. 3.13.0,1,0,1,901601,28.281025,832,,missing,,1996,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.484,Borreliella garinii PMek,PMek,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328489,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075427,,,Illumina MiSeq,61x,SPAdes v. 3.13.0,1,0,1,902752,28.310244,833,,missing,,1998,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.485,Borreliella garinii PMe,PMe,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328488,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075429,,,Illumina MiSeq,16x,SPAdes v. 3.13.0,1,0,1,896387,28.434702,845,,missing,,1988,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.486,Borreliella garinii Mek,Mek,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18917943,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075438,,,Illumina MiSeq,16x,SPAdes v. 3.13.0,1,0,1,895431,28.427942,837,,missing,,1992,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.487,Borreliella garinii Phei,Phei,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN18917942,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075437,,,Illumina MiSeq,96x,SPAdes v. 3.13.0,1,0,1,906155,28.35409,827,,missing,,1987,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,29519.488,Borreliella garinii PBes,PBes,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328475,29519,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075436,,,Illumina MiSeq,57x,SPAdes v. 3.13.0,1,0,1,901835,28.29531,835,,missing,,1989,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,2969654.4,Escherichia coli O7:H15 strain ST70,ST70,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30077658,2969654,O7:H15,,,MLST.Escherichia_coli_1.70,,,,2022-08-09T00:00:00Z,,PRJNA864658,GCA_024599975.1,"CP102244,CP102245",,Policlinico Sant'Orsola-Malpighi,Illumina iSeq; Oxford Nanopore MinION,190.0x,Unicycler v. 0.5.0,1,1,2,5229956,50.537117,5142,4862,blood,,2020-09-30,Italy,Italy: Bologna,,male,,Escherichia coli infection,,,,,,,,,,,,,This Escherichia coli isolate was cultured from a blood sample of an adult patient. The genome was sequenced using both Illumina iSeq 100 and Oxford Nanopore MinION platforms. Genome assembly was performed using Unicycler 0.5.0 with hybrid approach.,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,Escherichia coli infection,,,,,,,,,,,,,,99.56,1.41,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2986278.3,Nocardia sp. Y13_IFM12275,IFM12275,Nocardia sputorum,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00548744,2986278,,,,,,,,2022-11-16T00:00:00Z,,PRJDB14512,,"AP026976,AP026977",,,MGISEQ; GridION,54.7x,Unicycler v. 0.4.8,1,1,2,7610579,68.76017,7396,6947,sputum of a patient suspected with respiratory tract infection; clinical sample of a patient suspected with bacterial infection,,2008,Japan,Japan,,,,,,,,,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.7,1.4,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,299766.187,Enterobacter hormaechei subsp. steigerwaltii strain colR,colR,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30695413,299766,,,,MLST.Enterobacter_cloacae.89,,,,2022-09-20T00:00:00Z,,PRJNA877279,GCA_025311535.1,"CP104401,CP104402",,Medical University of Bialystok,Hybrid: Illumina NovaSeq and Oxford,727x,Unicycler v. v0.4.9,1,1,2,4987708,55.416496,4842,4726,not collected,,2019,,Poland,,,,not applicable,,,,,,,,,,,,,The rapid spread of antibiotic resistance is a serious problem owing to the limited treatment options. The aim of the work reported here was to better understand the response mechanisms following prolonged adaptation to synthetic mimics of antimicrobial peptides such as ceragenins and the last-line antibiotic colistin in an E.hormaechei clinical isolate.,collected_by:Medical University of Bialystok,,,,,,,not applicable,,,,,,derived from strain 4236,,,,,,,,99.17,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,299766.188,Enterobacter hormaechei subsp. steigerwaltii strain csa13R,csa13R,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30695412,299766,,,,MLST.Enterobacter_cloacae.89,,,,2022-09-20T00:00:00Z,,PRJNA877279,GCA_025311555.1,"CP104403,CP104404",,Medical University of Bialystok,Hybrid: Illumina NovaSeq and Oxford,556x,Unicycler v. v0.4.9,1,1,2,4964002,55.456463,4820,4705,not collected,,2019,,Poland,,,,not applicable,,,,,,,,,,,,,The rapid spread of antibiotic resistance is a serious problem owing to the limited treatment options. The aim of the work reported here was to better understand the response mechanisms following prolonged adaptation to synthetic mimics of antimicrobial peptides such as ceragenins and the last-line antibiotic colistin in an E.hormaechei clinical isolate.,collected_by:Medical University of Bialystok,,,,,,,not applicable,,,,,,derived from 4236,,,,,,,,99.47,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,299766.189,Enterobacter hormaechei subsp. steigerwaltii strain 4236,4236,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30695411,299766,,,,MLST.Enterobacter_cloacae.89,,,,2022-09-20T00:00:00Z,,PRJNA877279,GCA_025311595.1,"CP104405,CP104406",,Medical University of Bialystok,Hybrid: Illumina NovaSeq and Oxford,415x,Unicycler v. v0.4.9,1,1,2,4960175,55.4303,4805,4689,not collected,,2019,,Poland,,,,not applicable,,,,,,,,,,,,,The rapid spread of antibiotic resistance is a serious problem owing to the limited treatment options. The aim of the work reported here was to better understand the response mechanisms following prolonged adaptation to synthetic mimics of antimicrobial peptides such as ceragenins and the last-line antibiotic colistin in an E.hormaechei clinical isolate.,collected_by:Medical University of Bialystok,,,,,,,not applicable,,,,,,,,,,,,,,99.47,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,299766.91,Enterobacter hormaechei subsp. steigerwaltii strain C309,C309,Enterobacter hormaechei,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104700146,299766,,,,MLST.Enterobacter_cloacae.110,,,,2018-03-22T00:00:00Z,,PRJEB25613,GCA_900322715.1,"LT991954,LT991955,LT991956",,CHU Clermont-ferrand,,,,1,2,3,5200769,54.956104,5002,,hospital,isolated over a one-year period and originating from hospital environment,2015,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,"We investigated nosocomial infections involving unusual carbapenemase-producing Enterobacter cloacae complex (ECC) strains isolated over a one-year period and originating from hospital environment. Whole-genome sequence typing revealed the predominance of epidemic isolates belonging to the novel sequence type ST873 , which produced the carbapenemase VIM-4. The mechanism underlying the one-year outbreak involved the emergence of a new phylogenetic lineage within the ECC, which should be closely monitored in the context of nosocomial infections",,,,,,,,,diseased,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,302911.167,Bifidobacterium animalis subsp. lactis strain H1,H1,Bifidobacterium animalis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN16477311,302911,,,,,,,,2021-02-08T00:00:00Z,,PRJNA263203,GCA_016835115.1,CP069248,,"Institute of Microbiology, Belarus National Academy of Sciences",Oxford Nanopore MinION; Illumina MiSeq,1000.0x,Barapost v. 2020-12-28 edition; Flye v.,1,0,1,1944352,60.48797,1632,1548,human gut,,2008-03-09,Belarus,Belarus,,,,,,,,,Positive,Bacilli,No,Mesophilic,37C,Anaerobic,HostAssociated,,Comparative analysis of genomes of two potentially probiotic strains of B. animalis subsp. lactis,sample_type:bacterial culture;collected_by:Anastasiya V Sidarenka,,,,,,,,,,,,,,,,,,,,,100,0,,,Other,- NHP,302911.168,Bifidobacterium animalis subsp. lactis strain H3,H3,Bifidobacterium animalis,Bifidobacterium,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN03098186,302911,,,,,,,,2021-02-08T00:00:00Z,,PRJNA263288,GCA_016835135.1,CP069249,,"Institute of Microbiology, Belarus National Academy of Sciences",Illumina MiSeq,250.0x,SPAdes v. 3.14.1; A5-miseq v. 20160825,1,0,1,1944351,60.487946,1630,1548,,,2008-03-09,,not applicable,,female,28,,,,,,Positive,Bacilli,No,Mesophilic,37C,Anaerobic,HostAssociated,,Comparison of genome sequences of two potentially probiotic strains of bifidobacteria,,,,,"37 degrees, TPY broth or agar",,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,303.397,Pseudomonas putida strain PP112420,PP112420,Pseudomonas putida,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN05715224,303,,,,,,,,2016-11-28T00:00:00Z,,PRJNA340924,GCF_001886975.1,CP017073,NZ_CP017073.1,South China University of Technology,Illumina; PacBio,138,HGAP v. 2013,1,,1,6031212,62.01,5496,5314,urine,,2011-10-11,China,China: Guangzhou,,,,Urinary tract infection,,,,,,,,,,,,,Whole genome sequencing of multidrug resistant strain Pseudomonas putida PP112420,collected_by:First Affiliated Hospital of Guangzhou Medical University,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,303.750,Pseudomonas putida strain GIMC5401:PPKH-115,GIMC5401:PPKH-115,Pseudomonas putida,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15892526,303,,,,,,,,2020-09-24T00:00:00Z,,PRJNA658886,GCA_014726755.1,CP060529,,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq,430.0x,clc genomics workbench v. 20,1,0,1,5793382,61.905922,5357,5301,purulent synovial fluid,,2018-10-14,Russia,Russia: Moscow,,male,,septic joint,,,,,,,,,,,,,rare case of Pseudomonas putida infection of joint,collected_by:Zhukhovitsky V.G.,,,,,,,septic joint,,,,,,,,,,,,,,100,0.89,Bloodstream Infections,Sepsis,Bone and Joint,Bloodstream Infections-Sepsis HP,315405.161,Streptococcus gallolyticus XH2168,XH2168,Streptococcus gallolyticus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN31395130,315405,,,,MLST.Streptococcus_gallolyticus.90,,,,2022-12-28T00:00:00Z,,PRJNA892746,,CP113954,,,Illumina; Oxford Nanopore MinION,286.0x,Raven v. v. 1.5.0,1,0,1,2392629,37.686913,2375,2302,blood,,2020-11-16,China,China: Hangzhou,,,,infective endocarditis,,,,,,,,,,,,,,collected_by:Sir Run Run Shaw Hospital,,,,,,,infective endocarditis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,316.449,Pseudomonas stutzeri strain NCTC10450,NCTC10450,Stutzerimonas stutzeri,Stutzerimonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA3881056,316,not available: to be reported later,,,,,NCTC:10450,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900636845.1,LR134319,,SC,,,,1,,1,4438731,64.13371,4184,4078,leg ulcer,,1965,United Kingdom,United Kingdom: Preston,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0.14,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,316435.29,Escherichia coli Nissle 1917,Nissle 1917,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07451663,316435,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,,,2018-09-12T00:00:00Z,,PRJNA397210,GCA_003546975.1,"CP022686,CP023342,CP022687",,University of California,PacBio,299.1x,HGAP v. V2,1,2,3,5072329,50.56338,5162,5071,feces; stool,,1917,Germany,Germany: Freiburg,,,,,,,,,,,,,,,,,Nissle 1917 is a strain with probiotic and medical applications and a tool in gut microbiome research,sample_type:cell culture;collected_by:Nissle,,,,,,,,,,,,,,,,,,,,,100,0.4,,,Gastrointestinal,- NHP,316435.58,Escherichia coli Nissle 1917,Nissle 1917,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18749717,316435,,,,"MLST.Escherichia_coli_2.4,MLST.Escherichia_coli_1.73",,,,2021-09-14T00:00:00Z,,PRJNA722272,GCA_019967895.1,"CP082949,CP082950,CP082951",,Skolkovo Institute of Science and Technology,Illumina NextSeq,217.0x,SPAdes v. v3.13.1,1,2,3,5064230,50.573406,5001,4717,stool,,2020,Germany,Germany:Herdecke,,,,,,,,,,,,,,,,,Genome sequencing of a probiotic Escherichia coli strain Nissle 1917.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,99.67,0.12,,,Gastrointestinal,- HP,319705.146,Mycobacteroides abscessus subsp. bolletii strain GD91,GD91,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN16828769,319705,,,,,,,,2021-03-05T00:00:00Z,,PRJNA669041,GCA_017183915.1,CP065265,,University of Pittsburgh,Illumina MiSeq; Oxford Nanopore MinION,99x,Unicycler v. 0.4.8,1,0,1,5312857,63.936916,5405,5230,clinical patient,isolated from patients around the world,2020,France,France: Bordeaux,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,These are genomic sequences from a number of NTM strains isolated from patients around the world. The strains were sent to the University of Pittsburgh in the hope that the patients might be treated with phage therapy.,collected_by:Centre Hospitalier Universitaire de Bordeaux,,,,,,,Non-tuberculosis mycobacteria (NTM) infection,,,,,,,,,,,,,,100,0.44,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,32019.100,Campylobacter fetus subsp. fetus strain CITCf01,CITCf01,Campylobacter fetus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18438628,32019,,,,MLST.Campylobacter_fetus.3,,,,2021-04-10T00:00:00Z,,PRJNA716560,GCA_017896385.1,CP072664,,Munster Technological University,Nanopore; Illumina,100.0x,SPAdes v. 3.11.1,1,0,1,1781331,33.30145,1778,,blood,,2017,Ireland,Ireland,,,,endocarditis,,,,,,,,,,,,,Genomic comparison of Campylobacter fetus strains isolated from a case of recurrent prosthetic valve endocarditis,collected_by:Caoimhe Lynch@,,,,,,,endocarditis,,,,,,,,,,,,,,99.69,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,32019.101,Campylobacter fetus subsp. fetus strain CITCf02,CITCf02,Campylobacter fetus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN18438775,32019,,,,MLST.Campylobacter_fetus.3,,,,2021-04-10T00:00:00Z,,PRJNA716563,GCA_017896405.1,CP072665,,Munster Technological University,Nanopore; Illumina,100.0x,SPAdes v. 3.11.1,1,0,1,1766884,33.290527,1781,,blood,,2019,Ireland,Ireland,,,,endocarditis,,,,,,,,,,,,,Genomic comparison of Campylobacter fetus strains isolated from a case of recurrent prosthetic valve endocarditis,collected_by:Caoimhe Lynch,,,,,,,endocarditis,,,,,,,,,,,,,,99.69,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,32022.293,Campylobacter jejuni subsp. jejuni strain FDAARGOS_263,FDAARGOS_263,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN04875589,32022,O2,,,MLST.Campylobacter_jejuni.43,,FDA:FDAARGOS_263,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002209025.1,CP022077,,US Food and Drug Administration,PacBio,17.23531761x,HGAP v. 3,1,,1,1641468,30.55,1696,1658,feces,,1977,USA,USA:VA,,,,Human campylobacteriosis,,host_description:Diarrhoea,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC < NCTC;passage_history:Minimally passaged,,,,,,,Human campylobacteriosis,Missing,Missing,Diarrhea,Missing,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,32022.685,Campylobacter jejuni subsp. jejuni strain huA17,huA17,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN08687180,32022,,,,,,,,2018-12-27T00:00:00Z,30200886,PRJNA437928,GCA_003971585.1,"CP028372,CP028373",,University Medical Center Goettingen,PacBio; Illumina,382x,HGAP SMRTPortal v. 2.3.0,1,1,2,1817819,30.14871,1912,1812,stool,,2000,Germany,Germany: Goettingen,,,,diarrhea,,,,,,,,,,,,,Analysis auf Campylobacter type 6 secetion system and chemoreceptor genes,collected_by:Andreas Erich Zautner,,,,,,,diarrhea,,,,,,,,,,,,,,99.57,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,32022.688,Campylobacter jejuni subsp. jejuni strain NCTC10983,NCTC10983,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMEA104210759,32022,not available: to be reported later,,,MLST.Campylobacter_jejuni.43,,NCTC:10983,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638365.1,LR134511,,SC,,,,1,,1,1641302,30.54642,1693,1663,blood,,1974,,,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.38,0.15,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,32022.874,Campylobacter jejuni subsp. jejuni strain LDG17f,LDG17f,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11415929,32022,,,,,,,,2020-07-08T00:00:00Z,,PRJNA532555,GCA_013393785.1,CP040015,,Veterinary Research Institute,Illumina NextSeq,199x,SPAdes v. v3.10.1,1,0,1,1765444,30.297194,1855,1772,feces,,2016,Czech Republic,Czech Republic: Brno,,,,Campylobacter enteritis,,,,,,,,,,,,,We determined and compared genome sequences of C. jejuni isolates originating from water sources and human beings.,collected_by:Veterinary Research Institute Brno,,,,,,,Campylobacter enteritis,,,,,,,,,,,,,,99.52,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,32022.875,Campylobacter jejuni subsp. jejuni strain 9090,9090,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11415912,32022,,,,,,,,2020-07-08T00:00:00Z,,PRJNA532555,GCA_013393805.1,CP040016,,Veterinary Research Institute,Illumina NextSeq,580x,SPAdes v. v3.10.1,1,0,1,1710461,30.568953,1819,1768,feces,,2009,Slovenia,Slovenia,,,,Campylobacter enteritis,,,,,,,,,,,,,We determined and compared genome sequences of C. jejuni isolates originating from water sources and human beings.,collected_by:University of Ljubljana,,,,,,,Campylobacter enteritis,,,,,,,,,,,,,,99.53,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,32022.893,Campylobacter jejuni subsp. jejuni strain BP18682,BP18682,Campylobacter jejuni,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN14451476,32022,,,,,,,,2020-12-26T00:00:00Z,,PRJNA615343,GCA_016403125.1,"CP050683,CP050684",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,31.43x,Canu v. 1.7; Unicycler v. 0.4.6,1,1,2,1728842,30.465769,1885,1735,blood,,2019,India,India: Vellore,,,,Bacteremia,,,,,,,,,,,,,The complete genome sequence of Campylobacter jejuni isolated from blood stream infection,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,98.57,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,326522.8,Neisseria animaloris strain NCTC12227,NCTC12227,Neisseria animaloris,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMEA104210758,326522,not available: to be reported later,,,,,NCTC:12227,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638345.1,LR134516,,SC,,,,1,,1,2283939,49.45535,2383,2063,abscess following dog bite,,1900-1980,France,France: Montreal,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,328812.163,Parabacteroides goldsteinii strain BFG-241,BFG-241,Parabacteroides goldsteinii,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547026,328812,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091425.1,"CP081906,CP081904,CP081905",,National Institute of Allergy and Infectious Disease,PacBio Sequel,280x,HGAP/FALCON v. v. 6.0,1,2,3,7053599,43.624184,6014,5572,left flank,,1988,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.62,0.38,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,328813.144,Alistipes onderdonkii strain DSM 19147,DSM 19147,Alistipes onderdonkii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222635,328813,,,,,,DSM:19147,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025145285.1,CP102251,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3869542,57.81046,3445,3142,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.28,0.48,,,Other,- NHP,328813.146,Alistipes onderdonkii KR001_HAM_0061,KR001_HAM_0061,Alistipes onderdonkii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100351,328813,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757545.1,CP107205,,,PacBio Sequel II,10x,hifiasm_meta v. 0.2-r040,1,0,1,3395839,57.648228,3131,2844,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.2,,,Gastrointestinal,- HP,329.112,Ralstonia pickettii strain K-288,K-288,Ralstonia pickettii,Ralstonia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN17126705,329,,,,,,DSM 6297,,2021-01-04T00:00:00Z,,PRJNA686860,GCA_016466415.1,"CP066771,CP066772,CP066773",,University of Southampton,Illumina HiSeq; PacBio RS,125.72x,ABySS v. v1.5.1,2,1,3,4831423,63.90611,4618,4464,missing,,1973,USA,USA,,,,,,,,,,,,,,,,,"The complete genome of Ralstonia pickettii DSM 6297 was determined by Illumina and PacBio sequencing, revealing two circular chromosomes and a novel conjugative plasmid in this strain. The presence of type II and IV secretion system components in the plasmid suggest a relevant role in the pathogenesis of R. pickettii.",sample_type:single cell;biomaterial_provider:DSMZ,,,,,,,,,,,,,,,,,,,,,99.94,0.01,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,329854.496,Bacteroides intestinalis strain APC919/174,APC919/174,Bacteroides intestinalis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16802558,329854,,,,,,,,2021-10-07T00:00:00Z,34407825,PRJNA678472,GCA_020341695.1,CP064941,,University College Cork,Oxford Nanopore MinION; Illumina HiSeq,55x,SPAdes v. 3.13.0,1,0,1,5785768,42.543015,4704,4344,fastidious anaerobe broth,,2020,Ireland,Ireland:Cork,,,,,,,,,,,,,,,,,"The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we employ a combination of genomic and transcriptomic approaches to investigate persistence mechanisms of phage crAss001 in cultures of its host Bacteroides intestinalis both in vitro and in vivo.",,culturing environment [ENVO:01000312],in vitro anaerobic culture,Fastidious Anaerobe Broth,PMID: 30429469,,,,,,,,,,,,,culturing environment [ENVO:01000312],,,,99.25,0,,,Genitourinary,- NHP,329854.497,Bacteroides intestinalis strain APC919/174,APC919/174,Bacteroides intestinalis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16802559,329854,,,,,,,,2021-10-07T00:00:00Z,34407825,PRJNA678472,GCA_020341675.1,CP064940,,University College Cork,Oxford Nanopore MinION; Illumina HiSeq,80x,SPAdes v. 3.13.0,1,0,1,5785766,42.544086,4711,4349,fastidious anaerobe broth,,2020,Ireland,Ireland:Cork,,,,,,,,,,,,,,,,,"The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we employ a combination of genomic and transcriptomic approaches to investigate persistence mechanisms of phage crAss001 in cultures of its host Bacteroides intestinalis both in vitro and in vivo.",,culturing environment [ENVO:01000312],in vitro anaerobic culture,Fastidious Anaerobe Broth,PMID: 30429469,,,,,,,,,,,,,culturing environment [ENVO:01000312],,,,99.25,0,,,Genitourinary,- NHP,33010.102,Cutibacterium avidum strain KGMB09337,KGMB09337,Cutibacterium avidum,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN17320317,33010,,,,,,,,2021-01-28T00:00:00Z,,PRJNA545582,GCA_016766755.1,CP068550,,korea research institute of bioscience and biotechnology,PacBio RSII,252.0x,HGAP v. 3,1,0,1,2812988,63.492413,2683,2507,,,2020-01-15,South Korea,South Korea: Seongnam-si,,,,,,,,,,,,,,,,,Korean gut microbiome bank,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,0.66,,,Other,- NHP,33010.103,Cutibacterium avidum strain KGMB02810,KGMB02810,Cutibacterium avidum,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN17320314,33010,,,,,,,,2021-01-28T00:00:00Z,,PRJNA545582,GCA_016766735.1,CP068549,,korea research institute of bioscience and biotechnology,PacBio RSII,404.0x,HGAP v. 3,1,0,1,2609136,63.408806,2495,2328,feces,,2017-09-11,South Korea,South Korea: Seongnam-si,,,,,,,,,,,,,,,,,Korean gut microbiome bank,sample_type:Whole genome sequence,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,33010.104,Cutibacterium avidum strain KCTC 5339,KCTC 5339,Cutibacterium avidum,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN17320327,33010,,,,,,KCTC:5339,,2021-02-08T00:00:00Z,,PRJNA545582,GCA_016834535.1,CP069240,,korea research institute of bioscience and biotechnology,PacBio RSII,318.0x,HGAP v. 3,1,0,1,2554716,63.397263,2418,2268,,,2020-01-15,South Korea,South Korea: Jeongeup-si,,,,,,,,,,,,,,,,,Korean gut microbiome bank,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,0,,,Other,- HP,33010.142,Cutibacterium avidum TP-CV302,TP-CV302,Cutibacterium avidum,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMD00577072,33010,,,,,,,,2023-03-10T00:00:00Z,,PRJDB15193,,AP027369,,,Sequel IIe,120x,Flye v. 2.9.1-b1780,1,0,1,2575722,63.165977,2438,2323,acne pustule,,2016,Japan,Japan,,,,,,,,,,,,,,,,,,sample_type:acne pustule,,,,,,,,,,,,,,,,,,,,,95.9,2.2,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,33011.99,Cutibacterium granulosum TP-CG7,TP-CG7,Cutibacterium granulosum,Cutibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMD00517775,33011,,,,,,,,2023-02-02T00:00:00Z,,PRJDB14093,,"AP026710,AP026711",,,DNBSEQ-G400; GridION,1633x,Unicycler v. 0.4.7,1,1,2,2179712,64.15967,2071,1852,acne pustule from patient with acne vulgaris; acne pustule,,2014-11-21,Japan,Japan:Tokyo,,,,Acne vulgaris,,,,,,,,,,,,,,,,,,,,,Acne vulgaris,,,,,,,,,,,,,,99.9,0.1,Skin and Soft Tissue Infections,Acne,Skin and Soft Tissue,Skin and Soft Tissue Infections-Acne HP,33028.46,Staphylococcus saccharolyticus 13T0028,13T0028,Staphylococcus saccharolyticus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09259155,33028,,,,,,,,2021-02-09T00:00:00Z,30915059,PRJNA473062,GCA_004291115.2,QHKF00000000,,,Oxford Nanopore MinION; Illumina MiSeq,205.0x,Unicycler v. v0.4.6,1,1,2,2352566,32.17678,2757,2221,implant-asscoiated infection,,2017,Sweden,Sweden: Oerebro,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,33033.16,Parvimonas micra strain KCOM 1037,KCOM 1037,Parvimonas micra,Parvimonas,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMN09781070,33033,,,,,,KCOM:1037,,2018-09-05T00:00:00Z,,PRJNA485032,GCA_003454775.1,CP031971,,Korean Collection for Oral Microbiology,PacBio; Illumina HiSeq,1407.4x,RS HGAP v. 3.0; SPAdes v. 3.8.2,1,,1,1661863,28.904247,1553,1540,postoperative maxillary cyst,,2002-02-21,South Korea,South Korea: Gwangju,,,,maxillary sinusitis,,,,,,,,,,,,,Genome sequencing of Parvimonas micra KCOM 1037,collected_by:Korean Collection for Oral Microbiology,,,,,,,maxillary sinusitis,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,33038.1234,[Ruminococcus] gnavus CC55_001C,CC55_001C,[Ruminococcus] gnavus,Mediterraneibacter,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN27589614,33038,,,,,,,,2023-06-05T00:00:00Z,,PRJNA821229,,CP096671,,,PacBio Sequel,830x,PacBio SMRT Link v. pbcommand version,1,0,1,3195566,43.086266,3132,2999,feces,,not applicable,,,,not applicable,,not applicable,,,,,,,,,,,,,,,Human gut,human gut microbiome,feces,TSBA or BHI plates,,,not applicable,,,,,,,,,,Human gut,,,,100,0.3,,,Gastrointestinal,- NHP,33038.863,[Ruminococcus] gnavus strain NBRC 114413,NBRC 114413,[Ruminococcus] gnavus,Mediterraneibacter,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN21163587,33038,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,,"CP084014,CP084015",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,334.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,1,2,3757469,42.49142,3843,3635,human feces,,2019,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.42,0.39,,,Gastrointestinal,- NHP,33043.1679,Coprococcus eutactus strain ATCC 27759,ATCC 27759,Coprococcus eutactus,Coprococcus,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222687,33043,,,,,,ATCC:27759,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149915.1,CP102278,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3112919,43.095436,2781,2677,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.33,0,,,Other,- HP,333965.11,Providencia vermicola strain P8538,P8538,Providencia vermicola,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14083272,333965,,,,,,,,2020-02-19T00:00:00Z,,PRJNA606029,GCA_010748935.1,"CP048796,CP048797",,"MEPHI, IRD, APHM, IHU-Mediterranee Infection, Marseille, France",Oxford Nanopore,35.0x,Canu v. 1.8,1,1,2,4432495,41.18299,4257,3982,blood,,2016-02,Democratic Republic of the Congo,Democratic Republic of the Congo: Kinshasa,,,,Bacteremia,,,,,,,,,,,,,First complete genome sequence of clinical MDR Providencia vermicola isolate,collected_by:David Lupande Mwenebitu,,,,,,,Bacteremia,,,,,,,,,,,,,,100,1.62,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,33892.41,Mycobacterium tuberculosis variant bovis BCG strain BCG-S48,BCG-S48,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN10279424,33892,,,,,,,,2018-10-31T00:00:00Z,,PRJNA498011,GCA_003703995.1,CP033310,,University of Pretoria,Illumina MiSeq,100.0x,CLC NGS Cell v. 7,1,,1,4294448,65.46515,4362,4186,superficial abscess,,2015-09-29,South Africa,South Africa: Pretoria,,,4 months,Tuberculosis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Clinical BCG isolates were sequenced and compared to reference BCG genome to identify genetic variations,collected_by:Lesedi Modipane,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.06,0,Respiratory Diseases,Tuberculosis,Skin and Soft Tissue,Respiratory Diseases-Tuberculosis HP,33892.42,Mycobacterium tuberculosis variant bovis BCG strain BCG_S49,BCG_S49,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN10278076,33892,,,,,,,,2018-10-31T00:00:00Z,,PRJNA498011,GCA_003704015.1,CP033311,,University of Pretoria,Illumina MiSeq,100.0x,CLC NGS Cell v. 7,1,,1,4294423,65.41946,4402,4232,superficial swab,,2014-08-05,South Africa,South Africa,,male,8 months 1o days,Tuberculosis,,host_description:infant,Susceptible,Computational Prediction,,,,,,,,,Clinical BCG isolates were sequenced and compared to reference BCG genome to identify genetic variations,collected_by:Lesedi Modipane,,,,,,,Tuberculosis,,,infant,,,,,,,,,,,98.62,0,Respiratory Diseases,Tuberculosis,Other,Respiratory Diseases-Tuberculosis HP,33894.95,Mycobacterium tuberculosis variant africanum strain Various,Various,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA104679304,33894,,,,,,,,2021-01-25T00:00:00Z,,PRJEB42445,GCA_905183025.1,LR993210,,Institut Pasteur,,,,1,0,1,4366809,65.59074,4262,,human,,2007,France,France,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We performed whole-genome assembly of the two following strains of the mycobacterium tuberculosis complex: (1) Mycobacterium africanum 01 (lineage L6)\; and (2) Mycobacterium africanum 65 (lineage L5.1). Genome sequencing was performed at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 28\; TRAILING 28\; SLIDINGWINDOW windowSize 5, requiredQuality 28\; MINLEN 50\; AVGQUAL 28). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful\; -k 21,33,55\; --phred-offset 33). Generated contigs were finally organized as compared to the reference genome of Mycobacterium africanum GM041182 using MeDuSa v1.6 (default parameters).",,,,,,,,,diseased,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,33894.96,Mycobacterium tuberculosis variant africanum strain Various,Various,Mycobacterium tuberculosis,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA104679305,33894,,,,,,,,2021-01-25T00:00:00Z,,PRJEB42445,GCA_905183075.1,LR993208,,Institut Pasteur,,,,1,0,1,4374993,65.596016,4271,,human,,2007,France,France,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,"We performed whole-genome assembly of the two following strains of the mycobacterium tuberculosis complex: (1) Mycobacterium africanum 01 (lineage L6)\; and (2) Mycobacterium africanum 65 (lineage L5.1). Genome sequencing was performed at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 28\; TRAILING 28\; SLIDINGWINDOW windowSize 5, requiredQuality 28\; MINLEN 50\; AVGQUAL 28). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful\; -k 21,33,55\; --phred-offset 33). Generated contigs were finally organized as compared to the reference genome of Mycobacterium africanum GM041182 using MeDuSa v1.6 (default parameters).",,,,,,,,,diseased,,,,,,,,,,,,,99.94,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,34105.36,Streptobacillus moniliformis strain FDAARGOS_310,FDAARGOS_310,Streptobacillus moniliformis,Streptobacillus,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN06173323,34105,,,,,,FDA:FDAARGOS_310,,2018-03-09T00:00:00Z,,PRJNA231221,GCA_002983685.1,"CP027400,CP027399",,US Food and Drug Administration,PacBio; Illumina,19.2623542581892x,"SMRT v. 2.3.0, HGAP v. 3.0",1,1,2,1685928,26.25628,1577,1486,blood culture from a patient in france,,1925-03,France,France,,male,,Rat-bite fever/bite wound,,"host_disease_outcome:Recovered;host_description:Muscular pain, fever, nervous symptoms, lymphangitis, rash",,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC < CH Pierce-Chase < L Dienes 9901,,,,,,,Rat-bite fever/bite wound,Missing,Recovered,"Muscular pain, fever, nervous symptoms, lymphangitis, rash",,,,,,,,,,,100,2.5,Skin and Soft Tissue Infections,Wounds and Abscesses,Blood and Circulatory System,Skin and Soft Tissue Infections-Wounds and Abscesses HP,34105.52,Streptobacillus moniliformis strain BK14232,BK14232,Streptobacillus moniliformis,Streptobacillus,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN20239707,34105,,,,,,,,2021-07-25T00:00:00Z,,PRJNA746743,GCA_019334605.1,CP079714,,Jena University Hospital,Oxford Nanopore GridION,24.0x,flye v. 2.8,1,0,1,1655770,26.184494,1744,1585,putrid secret,,2021-06,Germany,Germany,,,,left-sided periprosthetic infection,,,,,,,,,,,,,Streptobacillus moniliformis clinical isolate,collected_by:UKJ,,,,,,,left-sided periprosthetic infection,,,,,,,,,,,,,,93.82,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,342617.7,Streptococcus agalactiae CJB111,CJB111,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN16191206,342617,,,,MLST.Streptococcus_agalactiae.1,,,,2020-11-03T00:00:00Z,,PRJNA663970,GCA_015221735.1,CP063198,,University of Colorado-Anschutz Medical Campus,Illumina NextSeq; Oxford Nanopore; Sanger,472x; 310x,Unicycler v. JULY-2020,1,0,1,2093987,35.52104,2078,2009,blood,isolated from a neonate with bacteremia in 1990,1990-07-18,USA,USA,,female,55 days,bacteremia without focus,,,,,,,,,,,,,CJB111 is a Group B streptococcal strain isolated from a neonate with bacteremia in 1990.,collected_by:Carol J Baker,,,,,,,bacteremia without focus,,,,,,,,,,,,,,100,0.18,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,345072.24,Vibrio cholerae MO10,MO10,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN15756141,345072,O139,,,MLST.Vibrio_cholerae.69,,,,2020-08-17T00:00:00Z,,PRJNA598947,GCA_014217395.1,"CP060094,CP060095",,EPFL,PacBio Sequel,174.0x,SMRT Link Version v. 8,2,0,2,4138926,47.562378,3841,3676,missing,,1992,India,India: Madras,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:Blokesch strain collection,,,,,,,cholera,,,,,,,,,,,,,,100,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera NHP,357276.1035,Bacteroides dorei strain DSM 17855,DSM 17855,Phocaeicola dorei,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN13293921,357276,,,,,,DSM:17855,,2020-05-11T00:00:00Z,,PRJNA589910,GCA_013009555.1,CP046176,,University of Florida,Oxford Nanopore GridION,139.0x,Flye v. 2.6,1,0,1,5625488,42.109966,4963,4550,biological product [envo:02000043],,2004-07,Japan,Japan,,male,,,,,,,,,,,,,,,Genome sequencing and assembly of Bacteroides dorei isolates from the DIPP cohort,,terrestrial biome [ENVO:00000446],human-associated habitat [ENVO:00009003],biological product [ENVO:02000043],https://www.dsmz.de/collection/catalogue/details/culture/DSM-17855,,,,,,,,,,,,commensal,terrestrial biome [ENVO:00000446],,,,99.25,0,,,Other,- NHP,357276.1234,Phocaeicola dorei strain CL06T03C03,CL06T03C03,Phocaeicola dorei,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451185,357276,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292105.1,"CP072246,CP072247,CP072248,CP072249,CP072250",,Brigham & Women's Hospital,PacBio Sequel,370x,FALCON-Unzip v. 1.2.0,1,4,5,5809409,42.01768,5228,4751,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.25,0,,,Gastrointestinal,- NHP,357276.1436,Phocaeicola dorei strain DSM 17855,DSM 17855,Phocaeicola dorei,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222645,357276,,,,,,DSM:17855,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146415.1,CP102257,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,5625379,42.11041,4958,4526,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.25,0,,,Other,- NHP,357276.1448,Phocaeicola dorei DH3716Y,DH3716Y,Phocaeicola dorei,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663830,357276,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916455.1,CP083689,,,Illumina HiSeq,224x,A5ud v. v1,1,0,1,5301996,41.817795,4608,4193,feces,,not collected,USA,USA: Maywood,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,12902247,,,,,,,,,,,,,human gut microbiome,,,,100,0.2,,,Gastrointestinal,- HP,35814.79,Bordetella holmesii strain J862,J862,Bordetella holmesii,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09288611,35814,,,,MLST.Bordetella_spp.80,,,,2020-05-05T00:00:00Z,,PRJNA287884,GCA_012974165.1,CP052852,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,530x,HGAP v. 3,1,0,1,3699764,62.687405,3780,3590,nasopharyngeal swab,,2017,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to characterize genomes of Bordetella species other than B. pertussis. Members of the genus Bordetella cause respiratory and opportunistic infection in a variety of hosts. These data are being made available to facilitate comparative analyses for the study of this important group of bacterial pathogens.,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,35814.81,Bordetella holmesii strain CIDM-BH3,CIDM-BH3,Bordetella holmesii,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18200434,35814,,,,MLST.Bordetella_spp.80,,,,2021-03-16T00:00:00Z,,PRJNA695314,GCA_017357145.1,CP071603,,Centre for Infectious Diseases and Microbiology - Public Health,Oxford Nanopore; Illumina,107x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,0,1,3696713,62.68934,3740,3479,blood,,2016,Australia,Australia,,,,,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,,,,,,,unknown,,,,,,,Unknown,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,364106.45,Escherichia coli UTI89,UTI89,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16339622,364106,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2020-10-25T00:00:00Z,,PRJNA666979,GCA_014930875.1,CP062985,,SASTRA University,Illumina MiSeq,10.0x,BRESEQ v. 0.33.1,1,0,1,5065741,50.604206,4941,,urine,,2018-09-20,India,India: Thanjavur,,,,,,,,,,,,,,,,,From uropathogenic E.coli UTI89 strain we are able to get variant matrix producing colonies. In our study we are trying to understand the interactions between these variants in vivo and in vitro conditions. These sequence will help to understand the variants between ancestral strain and variant strain.,sample_type:Bacterial culture,,,,,,,,,,,,,Colony variants,,,,,,,,99.97,0.12,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,364410.3,Granulibacter bethesdensis strain NIH7.1,NIH7.1,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05879420,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA347348,GCF_001889445.1,CP018193,NZ_CP018193.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",454,"CANU v. 1.0, Bowtie2 2.2.4, pilon v. 1.16,",1,,1,2708311,58.76,2514,2516,male patient with chronic granulomatous disease,,2014-02,USA,United States,,male,36,Granulibacter bethesdensis Infection,,host_health_state:Still receiving treatment as of 2015;host_subject_id:#5,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:NIH,,,,,,,Granulibacter bethesdensis Infection,Still receiving treatment as of 2015,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,364410.4,Granulibacter bethesdensis strain NIH9.1,NIH9.1,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05991787,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA352742,GCF_001889505.1,CP018191,NZ_CP018191.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",503,"CANU v. 1.0, Bowtie 2 2.2.4, pilon 1.16,",1,,1,2738876,59.17,2580,2549,host,,2006-08,Spain,Spain: Cordoba,,male,10,Chronic Granulomatous Disease,,,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:Hospital Universitario Reina Sofia,,,,,,,Chronic Granulomatous Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,364410.5,Granulibacter bethesdensis strain NIH6.1,NIH6.1,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05879404,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA347345,GCF_001889525.1,CP018192,NZ_CP018192.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",525,"CANU v. 1.0, Bowtie2 2.2.4, pilon v. 1.16,",1,,1,2690741,58.55,2529,2511,male patient with chronic granulomatous disease,,2011-11,USA,United States,,male,19,Granulibacter bethesdensis Infection,,host_subject_id:#2,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:NIH Clinical Center,,,,,,,Granulibacter bethesdensis Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,364410.6,Granulibacter bethesdensis strain NIH8.1,NIH8.1,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05879666,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA347349,GCF_001889545.1,CP018194,NZ_CP018194.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",694,"CANU v. 1.0, Bowtie2 2.2.4, pilon v. 1.16,",1,,1,2738877,59.17,2579,2558,cerebrospinal fluid; male patient with chronic granulomatous disease,,2012,Portugal,Portugal,,male,16,Granulibacter bethesdensis Infection,,host_subject_id:#3,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:Centro Hospitalar de Lisboa Central,,,,,,,Granulibacter bethesdensis Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,364410.7,Granulibacter bethesdensis strain NIH5.1,NIH5.1,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05878969,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA347332,GCF_001889485.1,CP018190,NZ_CP018190.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",441,"CANU v. 1.0, Bowtie2 2.2.4, pilon v. 1.16,",1,,1,2709750,59.07,2561,2560,host lymph node biopsy,,2009-05,USA,United States,,male,37,Granulibacter bethesdensis infection,,host_subject_id:#5,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:NIH Clinical Center,,,,,,,Granulibacter bethesdensis infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,364410.8,Granulibacter bethesdensis strain NIH1.4,NIH1.4,Granulibacter bethesdensis,Granulibacter,Acetobacteraceae,Rhodospirillales,Alphaproteobacteria,Pseudomonadota,SAMN05992017,364410,,,,,,,,2016-12-06T00:00:00Z,,PRJNA352786,GCF_001889465.1,CP018195,NZ_CP018195.1,"Igenbio, Inc","Illumina MiSeq, PacBio RSII",514,"CANU v. 1.0, Bowtie2 2.2.4, pilon v. 1.16,",1,,1,2708447,59.07,2557,2554,cervical lymph nodes; host,,2005-11,USA,USA: Bethesda,,male,39,Chronic Granulomatous Disease,,host_disease_outcome:recovery,,,,,,,,,,,Comparative genomic and phenotypic analysis of Granulibacter bethesdensis clinical isolates from patients with chronic granulomatous disease,collected_by:National Institutes of Health (NIH) Clinical Center,,,,,,,Chronic Granulomatous Disease,,recovery,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,36809.429,Mycobacterium abscessus strain G153,G153,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08931137,36809,,,,,,,,2018-05-02T00:00:00Z,,PRJNA448987,GCA_003076875.1,CP029074,,"Shanghai Pulmonary Hospital, Tongji University School of Medicine",Illumina HiSeq,100X,SPAdes v. 3.11.1,1,,1,4886609,64.174095,4925,4848,sputum,,2017,China,China: Shanghai,,,,M. abscessus lung disease,,,,,,,,,,,,,This study aimed to determine the antibiotic susceptibility and resistance related genotypes of Mycobacterium abscessus.,collected_by:Shanghai Pulmonary Hospital,,,,,,,M. abscessus lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,36809.430,Mycobacterium abscessus strain G141,G141,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08931136,36809,,,,,,,,2018-05-02T00:00:00Z,,PRJNA448987,GCA_003076855.1,CP029075,,"Shanghai Pulmonary Hospital, Tongji University School of Medicine",Illumina HiSeq,100X,SPAdes v. 3.11.1,1,,1,4876254,64.225815,4923,4848,sputum,,2017,China,China: Shanghai,,,,M. abscessus lung disease,,,,,,,,,,,,,This study aimed to determine the antibiotic susceptibility and resistance related genotypes of Mycobacterium abscessus.,collected_by:Shanghai Pulmonary Hospital,,,,,,,M. abscessus lung disease,,,,,,,,,,,,,,100,4.8,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,36809.431,Mycobacterium abscessus strain 199,199,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08931120,36809,,,,MLST.Mycobacterium_abscessus.19,,,,2018-05-02T00:00:00Z,,PRJNA448987,GCA_003076835.1,CP029076,,"Shanghai Pulmonary Hospital, Tongji University School of Medicine",Illumina HiSeq,100X,SPAdes v. 3.11.1,1,,1,5094861,64.0224,5080,4992,sputum,,2017,China,China: Shanghai,,,,M. abscessus lung disease,,,,,,,,,,,,,This study aimed to determine the antibiotic susceptibility and resistance related genotypes of Mycobacterium abscessus.,collected_by:Shanghai Pulmonary Hospital,,,,,,,M. abscessus lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,36809.432,Mycobacterium abscessus strain G122,G122,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08931144,36809,,,,,,,,2018-05-02T00:00:00Z,,PRJNA448987,GCA_003076815.1,CP029073,,"Shanghai Pulmonary Hospital, Tongji University School of Medicine",Illumina HiSeq,100X,SPAdes v. 3.11.1,1,,1,4933836,64.20223,4977,4905,sputum,,2017,China,China: Anhui,,,,M. abscessus lung disease,,,,,,,,,,,,,This study aimed to determine the antibiotic susceptibility and resistance related genotypes of Mycobacterium abscessus.,collected_by:Shanghai Pulmonary Hospital,,,,,,,M. abscessus lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,36809.433,Mycobacterium abscessus strain G220,G220,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN08931148,36809,,,,,,,,2018-05-02T00:00:00Z,,PRJNA448987,GCA_003076795.1,CP029072,,"Shanghai Pulmonary Hospital, Tongji University School of Medicine",Illumina HiSeq,100X,SPAdes v. 3.11.1,1,,1,4800506,64.18226,4813,4739,sputum,,2017,China,China: Hubei,,,,M. abscessus lung disease,,,,,,,,,,,,,This study aimed to determine the antibiotic susceptibility and resistance related genotypes of Mycobacterium abscessus.,collected_by:Shanghai Pulmonary Hospital,,,,,,,M. abscessus lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,36809.582,Mycobacteroides abscessus strain GZ002 (R) strain GZ002 (R) strain GZ0 1,GZ0 1,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN10188242,36809,,,,,,not applicable,,2019-01-16T00:00:00Z,,PRJNA495001,GCA_004027995.1,CP034191,,"Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences (CAS)",PacBio,100.0x,GS De Novo Assembler v. 7/06/2018,1,,1,5075529,64.18509,5078,,not applicable,isolate from the patient have the pulmonary infection in south China,2015-04-16,China,China,,,,pulmonary,,,,,,,,,,,,,"Mycobacterium abscessus is a nontuberculous mycobacteria (NTM) causes pulmonary infection in human. The treatment of this emerging pathogen is a major challenge because it is resistant to most of the antituberculous drugs and most of the antimicrobial agents. We obtained a Mycobacterium abscessus clinical isolate from the patient have the pulmonary infection in south China. This clinical isolate showed rough morphology. In our study, we sequenced the genome of rough phenotype variants using SMRT sequencing technology. The significance of this study will facilitate to understand pathonenicity of this emerging pathogen at genome level.",collected_by:Guangzhou chest hospital,,,,,,,pulmonary,,,,,,,,,,,,,,99.64,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,36809.583,Mycobacteroides abscessus strain GZ002-S,GZ002,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN10391661,36809,,,,,,,,2019-01-16T00:00:00Z,,PRJNA504433,GCA_004028015.1,"CP034181,CP034180",,"Guangzhou Institutes of Biomedicine and Health , Chinese Academy of Sciences (CAS)",PacBio,100.0x,HGAP v. version 4.0,1,1,2,5082434,64.144485,5081,5033,not applicable,,2015-04-16,China,China,,,,pulmonary,,,,,,,,,,,,,"Mycobacterium abscessus causes pulmonary infections in human. The treatment of this emerging pathogen is a major challenge because it is resistant to most of the effective drugs along with disinfectants. It is very important to study the genetic composition of this emerging pathogen. Therefore, we have sequenced the whole genome of Mycobacterium abscessus clinical isolate showing smooth colony morphology.",collected_by:Guangzhou chest hospital,,,,,,,pulmonary,,,,,,,Smooth phenotype),,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,36809.765,Mycobacteroides abscessus strain W7,W7,Mycobacteroides abscessus,Mycobacteroides,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15806907,36809,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,GCA_020227595.1,CP060408,,University of Wisconsin-Madison,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,0,1,4802793,64.278046,4799,4698,urine,,,,USA,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),,,,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,99.67,0,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,371142.3,Sphingobacterium daejeonense strain NCTC13534,NCTC13534,Sphingobacterium daejeonense,Sphingobacterium,Sphingobacteriaceae,Sphingobacteriales,Sphingobacteriia,Bacteroidota,SAMEA3121329,371142,,,,,,NCTC:13534,,2019-05-10T00:00:00Z,,PRJEB6403,GCA_901472535.1,LR590470,,SC,,,,1,,1,4732363,37.342064,5873,5557,clinical material,,1800-2017,,,,,,,,host_health_state:not available: not collected,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,not available: not collected,,,91.47,0.48,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,371601.1171,Bacteroides xylanisolvens KR001_HAM_0012,KR001_HAM_0012,Bacteroides xylanisolvens,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100332,371601,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757585.1,CP107195,,,PacBio Sequel II,6x,hifiasm_meta v. 0.2-r040,1,0,1,6165932,42.024857,5216,4900,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.4,,,Gastrointestinal,- HP,371601.675,Bacteroides xylanisolvens strain funn3,funn3,Bacteroides xylanisolvens,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN13118627,371601,,,,,,,,2021-02-11T00:00:00Z,,PRJNA579769,GCA_016864215.1,"CP045612,CP045613,CP045614,CP045615,CP045616",,Odense University Hospital,Illumina MiSeq; Oxford Nanopore MiniION,100.0x,Unicycler v. Unicycler 0.4.7; manual,1,4,5,6644928,42.215553,5760,5399,abscess,,2013,Norway,Norway:Oslo,,,,Abscess,,,,,,,,,,,,,Complete genome sequencing of the metronidazole resistant Bacteroides xylanisolvens strain Funn3.,collected_by:Nina Handal and Truls Michael Leegaard,,,,,,,Abscess,,,,,,,,,,,,,,99.14,0.16,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses NHP,371601.814,Bacteroides xylanisolvens strain CL11T00C41,CL11T00C41,Bacteroides xylanisolvens,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451199,371601,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289035.1,"CP072212,CP072213,CP072214,CP072215",,Brigham & Women's Hospital,PacBio Sequel,185x,FALCON-Unzip v. 1.2.0,1,3,4,6827031,42.039856,5825,5427,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.46,0.33,,,Gastrointestinal,- NHP,371601.815,Bacteroides xylanisolvens strain CL11T00C03,CL11T00C03,Bacteroides xylanisolvens,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451198,371601,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289135.1,"CP072216,CP072217,CP072218,CP072219",,Brigham & Women's Hospital,PacBio Sequel,287x,FALCON-Unzip v. 1.2.0,1,3,4,6558523,42.0751,5641,5255,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.46,0.08,,,Gastrointestinal,- HP,373045.6,Escherichia coli O111:NM strain FWSEC0005,FWSEC0005,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768106,373045,O111:NM,,,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037805.2,NJGR00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,108.41x;252.38x,Unicycler;Canu v. 0.4.4.0;1.7,1,,1,5132754,50.64242,5466,5279,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2000,Canada,Canada:Saskatchewan,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.06,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,37326.9,Nocardia brasiliensis strain FDAARGOS_352,FDAARGOS_352,Nocardia brasiliensis,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06173365,37326,,,,,,FDA:FDAARGOS_352,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002209125.2,CP022088,,US Food and Drug Administration,PacBio,14.5210323611477x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,8934655,68.24,8661,8052,"mycetomatous lesion of the thigh, leg, and foot",,1909,Brazil,Brazil,,,,Nocardiosis (actinomycosis),,host_description:Limited motion of the knee,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < Inst. Pasteur,,,,,,,Nocardiosis (actinomycosis),Missing,Missing,Limited motion of the knee,Missing,,,,,,,,,,99.6,2.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,37329.12,Nocardia farcinica strain W6977,W6977,Nocardia farcinica,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN09723209,37329,,,,,,,,2018-08-08T00:00:00Z,,PRJNA482969,GCA_003367415.1,"CP031418,CP031419,CP031420",,Bacterial Special Pathogens Branch (CDC),PacBio RSII; Illumina MiSeq,313.0x,Unicycler v. 0.4.6,1,2,3,6429634,70.66112,6343,5991,madura foot,,,,,,,,Mycetoma pedis,,,,,,,,,,,,,clinical Nocardia spp. were sequenced,,,,,,,,Mycetoma pedis,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,376725.3,Escherichia coli O103:H2 strain FWSEC0007,FWSEC0007,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768108,376725,O103:H2,,,MLST.Escherichia_coli_1.17,,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037795.2,NJGQ00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,103.12x;58.53x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5470829,50.687874,5856,5741,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2004,Canada,"Canada:Manitoba,Winnipeg",,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.93,0.28,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,37734.111,Enterococcus casseliflavus strain EC291,EC291,Enterococcus casseliflavus,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN13152475,37734,,,,,,,,2019-11-24T00:00:00Z,,PRJNA580195,GCA_009707345.1,"CP046123,CP046124,CP046125,CP046126",,Center for Diagnosis and Treatment of Infectious Diseases,PacBio RSII,200x,SPAdes v. 3.10.2,1,3,4,3786868,41.97968,3896,3625,blood,,2018-12-16,China,"China: Zhengzhou, Henan",,,,bloodstream infection,,,,,,,,,,,,,"Detection and genome characteristic of a blood enterococcus casselifavus isolate from Zhengzhou,china",collected_by:PeiPei Wen,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.25,0.77,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,37734.92,Enterococcus casseliflavus strain 4928STDY7387870,4928STDY7387870,Enterococcus casseliflavus,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA4623294,37734,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166785.1,LR607377,,SC,,,,1,,1,3744746,43.36827,3173,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.62,0.38,,,Other,- HP,379893.15,Trabulsiella odontotermitis TBY01,TBY01,Trabulsiella odontotermitis,Trabulsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35035477,379893,,,,,,,,2023-05-21T00:00:00Z,,PRJNA971482,,"CP125781,CP125782",,,PacBio,120.0x,Canu v. v2.0; Racon v. v1.4.13,1,1,2,4702252,54.664616,4521,4363,blood,,2022-10-22,China,China: Zhengzhou,,,,bloodstream infection,,,,,,,,,,,,,,collected_by:Jing Yu,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.3,0.7,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,38303.38,Corynebacterium pseudogenitalium CCUG 27540,CCUG 27540,Corynebacterium pseudogenitalium,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN18647611,38303,,,,,,CCUG:27540,,2022-07-27T00:00:00Z,,PRJNA305687,GCA_024453815.1,CP072934,,,"Illumina HiSeq, Oxford Nanopore MiniION",564x,Unicycler v. v0.4.8,1,0,1,2389603,60.66129,2229,2167,healthy human,,1990,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Other,- HP,38313.141,Shewanella algae strain CCU4051,CCU4051,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN18876193,38313,,,,,,,,2021-07-18T00:00:00Z,,PRJNA725326,GCA_019264685.1,"CP078513,CP078514",,National Chung Cheng University,PacBio,340.0x,canu v. 1.4,1,1,2,4919537,53.043694,4853,4368,,,2016-08-20,Taiwan,Taiwan,,,,biliary tract disease,,,,,,,,,,,,,Study of Antibiotic Resistance in Shewanella Haliotis during treatment,collected_by:Taichung Veteran General Hospital,,,,,,,biliary tract disease,,,,,,,,,,,,,,99.55,0.54,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,38313.142,Shewanella algae strain CCU4053,CCU4053,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN18876195,38313,,,,,,,,2021-07-18T00:00:00Z,,PRJNA725326,GCA_019265025.1,"CP078518,CP078517",,National Chung Cheng University,PacBio,331.0x,canu v. 1.4,1,1,2,4919868,53.04675,4653,4330,,,2016-09-01,Taiwan,Taiwan,,,,biliary tract disease,,,,,,,,,,,,,Study of Antibiotic Resistance in Shewanella Haliotis during treatment,collected_by:Taichung Veteran General Hospital,,,,,,,biliary tract disease,,,,,,,,,,,,,,99.28,0.54,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,38313.143,Shewanella algae strain CCU4054,CCU4054,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN18876196,38313,,,,,,,,2021-07-18T00:00:00Z,,PRJNA725326,GCA_019265045.1,"CP078519,CP078520",,National Chung Cheng University,PacBio,346.0x,canu v. 1.4,1,1,2,4919717,53.045288,4713,4350,,,2016-10-07,Taiwan,Taiwan,,,,biliary tract disease,,,,,,,,,,,,,Study of Antibiotic Resistance in Shewanella Haliotis during treatment,collected_by:Taichung Veteran General Hospital,,,,,,,biliary tract disease,,,,,,,,,,,,,,99.46,0.54,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,38313.144,Shewanella algae strain CCU4052,CCU4052,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN18876194,38313,,,,,,,,2021-07-18T00:00:00Z,,PRJNA725326,GCA_019265005.1,"CP078515,CP078516",,National Chung Cheng University,PacBio,302.0x,canu v. 1.4,1,1,2,4919930,53.04734,4633,4335,,,2016-08-25,Taiwan,Taiwan,,,,biliary tract disease,,,,,,,,,,,,,Study of Antibiotic Resistance in Shewanella Haliotis during treatment,collected_by:Taichung Veteran General Hospital,,,,,,,biliary tract disease,,,,,,,,,,,,,,99.73,0.54,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,38313.196,Shewanella algae VGH117,VGH117,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN09988152,38313,,,,,,,,2022-10-11T00:00:00Z,30809393,PRJNA490065,GCA_025643615.1,"CP032415,CP032414",,,PacBio,102.89x,Canu v. 1.5,1,1,2,4919668,53.04675,4672,4365,blood,,2015,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,,collected_by:Ching-Lin Shy,,,,,,,infection,,,,,,,,,,,,,,99.1,4.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,38313.197,Shewanella algae B2215466,B2215466,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN31456038,38313,,,,,,,,2022-11-06T00:00:00Z,,PRJNA894467,GCA_026013945.1,CP110338,,,Oxford Nanopore MinION; Illumina iSeq,398.0x,Flye v. 2.9.1; NextPolish v. 1.4.1;,1,0,1,4946841,52.943363,4525,4298,patient blood,,2022-09-02,Germany,Germany: Marburg,,,,Sepsis,,,,,,,,,,,,,,collected_by:Institute of Microbiology,,,,,,,Sepsis,,,,,,,,,,,,,,99.8,1.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,38313.98,Shewanella algae strain VGH117,VGH117,Shewanella algae,Shewanella,Shewanellaceae,Alteromonadales,Gammaproteobacteria,Pseudomonadota,SAMN08166472,38313,,,,,,,,2020-09-22T00:00:00Z,,PRJNA507868,GCA_014702225.1,CP034246,,National Chung Cheng University,Oxford Nanopore; Illumina,100.0x,Unicycler v. 0.4.7,1,0,1,4796801,53.148506,4347,4149,tissue,,2015,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,Analysis of the genome in order to understand the genetic factors leading to virulence and antibiotic resistance,collected_by:Ching-Lin Shy,,,,,,,infection,,,,,,,,,,,,,,99.64,0.54,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,38323.51,Bartonella henselae Berlin-I,Berlin-I,Bartonella henselae,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN18647579,38323,,,,,genotype:1,,,2022-01-24T00:00:00Z,,PRJNA720375,GCA_021560465.1,CP072901,,,PacBio Sequel,652x,HGAP v. 4,1,0,1,1931655,38.24953,1988,1584,skin biopsy specimen; -,,1993,Germany,Germany: Berlin,,,,Bacillary angiomatosis; Cat Scratch Disease,,,,,,,,,,,,,,"collected_by:Institut fur Infektionsmedizin, Universitatsklinikum Benjamin Franklin, Freie Universitat Berlin",,,,,,,Bacillary angiomatosis; Cat Scratch Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,38323.52,Bartonella henselae G-5436,G-5436,Bartonella henselae,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN18647580,38323,,,,,genotype:1,,,2022-01-24T00:00:00Z,,PRJNA720375,GCA_021560445.1,CP072900,,,PacBio Sequel,629x,HGAP v. 4,1,0,1,1963796,38.268486,1999,1577,-,,1995,USA,USA: Houston,,,,Cat Scratch Disease,,,,,,,,,,,,,,collected_by:Centers for Disease Control and Prevention,,,,,,,Cat Scratch Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,38323.53,Bartonella henselae ATCC49882T var-2/ Houston-I,ATCC49882T var-2/ Houston-I,Bartonella henselae,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN18647578,38323,,,,,genotype:1,,,2022-01-24T00:00:00Z,,PRJNA720375,GCA_021560485.1,CP072902,,,PacBio Sequel,651x,HGAP v. 4,1,0,1,1931585,38.248848,1983,1579,-,,1996,Germany,Germany: Frankfurt,,,,Cat Scratch Disease,,,,,,,,,,,,,,"collected_by:Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University",,,,,,,Cat Scratch Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,38323.54,Bartonella henselae ATCC49882T var-1/ Houston-I,ATCC49882T var-1/ Houston-I,Bartonella henselae,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN18647577,38323,,,,,genotype:1,,,2022-01-24T00:00:00Z,,PRJNA720375,GCA_021560505.1,CP072903,,,PacBio Sequel,1113x,HGAP v. 4,1,0,1,1955459,38.26943,1988,1574,-,,2004,Switzerland,Switzerland: Basel,,,,Cat Scratch Disease,,,,,,,,,,,,,,"collected_by:Division of Molecular Microbiology, Biozentrum, University of Basel",,,,,,,Cat Scratch Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,38323.55,Bartonella henselae Marseille/ URLLY-8,Marseille/ URLLY-8,Bartonella henselae,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN18647576,38323,,,,,genotype:2,,,2022-01-24T00:00:00Z,,PRJNA720375,GCA_021560525.1,CP072904,,,PacBio Sequel,802x,HGAP v. 4,1,0,1,1906759,38.107647,2020,1566,serum; -,,1996,France,France: Marseille,,,,Cat Scratch Disease,,,,,,,,,,,,,,collected_by:Unite des Rickettsies et des pathogenes emergents,,,,,,,Cat Scratch Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,384638.11,[Bacteroides] pectinophilus strain ATCC 43243,ATCC 43243,[Bacteroides] pectinophilus,-,-,Eubacteriales,Clostridia,Bacillota,SAMN20222652,384638,,,,,,ATCC:43243,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146925.1,CP102260,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3078488,41.973106,2959,2851,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.33,0,,,Other,- HP,38504.9,Ureaplasma parvum serovar 3 strain OMC-P162,OMC-P162,Ureaplasma parvum,Ureaplasma,Mycoplasmataceae,Mycoplasmatales,Mollicutes,Mycoplasmatota,SAMD00111973,38504,3,,,MLST.Ureaplasma_spp.1,,,,2018-10-18T00:00:00Z,30325937,PRJDB6718,GCA_003953005.1,AP018561,,"Department of Developmental Medicine, Research Institute, Osaka Women’s and Children’s Hospital",PacBio RSII,996x,HGAP v. 2,1,,1,732031,25.466818,956,582,,,2007,Japan,Japan,,,,,,,,,,,,,,,,,"Here we present the complete genome sequence of Ureaplasma parvum serovar 3, clinical strain OMC-P162, derived from human placenta of a preterm delivery at 26 weeks’ gestation",,not applicable,not applicable,placenta,10.1203/PDR.0b013e3181c6e58e,whole genome sequence of ureaplasma parvum,,,,,,,,,,,,not applicable,,,,98.87,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,386585.154,Escherichia coli O157:H7 str. Sakai,Sakai,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01911278,386585,E. coli O157:H7,,"EHEC, STEC","MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.296",,ATCC:BAA-460,,2018-06-07T00:00:00Z,"10734605,11108008,11111050,11258796",PRJNA226,GCA_000008865.2,"BA000007,AB011548,AB011549",,,,,,1,2,3,5594605,50.484154,5725,5289,human intestinal microflora,,1996,Japan,"Japan: Sakai City, Osaka prefecture",,,,"Hemorrhagic colitis, HUS",,host_description:typical patient during the Sakai outbreak,,,,,,,,,,,,"collected_by:M Yoh, T Honda",,,,,,,"Hemorrhagic colitis, HUS",,,typical patient during the Sakai outbreak,,"EHEC, STEC",,,,,,,,,100,0,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Genitourinary,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,392021.14,Rickettsia rickettsii str. 'Sheila Smith',Sheila Smith,Rickettsia rickettsii,Rickettsia,Rickettsiaceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN34104445,392021,,,,,,,,2023-05-01T00:00:00Z,,PRJNA846795,,CP121767,,,PacBio Sequel; Illumina MiSeq,450.0x,Canu v. v2.1.1; Pilon v. v1.22,1,0,1,1257745,32.46588,1608,1390,,,,,,,,,rocky mountain spotted fever,,,,,,,,,,,,,,,,,,,,,rocky mountain spotted fever,,,,,,,,,,,,,,100,0.9,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,39486.544,Dorea formicigenerans strain ATCC 27755,ATCC 27755,Dorea formicigenerans,Dorea,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222688,39486,,,,,,ATCC:27755,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150245.1,CP102279,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3188304,40.97812,3169,3040,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.42,0,,,Other,- NHP,39492.622,[Eubacterium] siraeum strain DSM 15702,DSM 15702,[Eubacterium] siraeum,-,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222691,39492,,,,,,DSM:15702,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150425.1,CP102281,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2694742,44.987423,2543,2361,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,98.32,0,,,Other,- NHP,39496.427,Eubacterium ventriosum strain ATCC 27560,ATCC 27560,Eubacterium ventriosum,Eubacterium,Eubacteriaceae,Eubacteriales,Clostridia,Bacillota,SAMN20222692,39496,,,,,,ATCC:27560,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150745.1,CP102282,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2856089,34.920166,2615,2545,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.33,0,,,Other,- HP,39831.29,Klebsiella pneumoniae subsp. rhinoscleromatis KP4831,KP4831,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26900494,39831,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-04-03T00:00:00Z,,PRJNA819173,GCA_022809675.1,"CP094451,CP094452,CP094453,CP094454",,,Illumina HiSeq; PacBio,377.02x,HGAP v. 4; FALCON v. 0.3,1,3,4,6023598,57.011524,6135,5900,hospital,,2022,China,China:Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Jie Wei,,,,,,,infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,40041.383,Streptococcus equi subsp. zooepidemicus strain B630793,B630793,Streptococcus equi,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN20691904,40041,,,,,,,,2021-08-17T00:00:00Z,,PRJNA753239,GCA_019645895.1,CP080959,,Sygehus Lillebaelt,Oxford Nanopore MinION,500.0x,Flye assembler v. 2.8.3,1,0,1,2085367,41.747425,2265,1858,blood,,2021-02-21,Denmark,Denmark: Vejle,,,,Endocarditis,,,,,,,,,,,,,Complete Genome Sequences of a Streptococcus equi subsp. zooepidemics isolated from isolated from blood of a patient with endocarditis,collected_by:Charlotte Agergaard Nielsen,,,,,,,Endocarditis,,,,,,,,,,,,,,99.72,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,40041.56,Streptococcus equi subsp. zooepidemicus strain NCTC12090,NCTC12090,Streptococcus equi,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3542451,40041,not available: to be reported later,,,MLST.Streptococcus_zooepidemicus.5,,NCTC:12090,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900474875.1,LS483328,,SC,,,,1,,1,2128266,41.564587,2153,1952,blood culture,,1987,United Kingdom,United Kingdom: Northallerton,,,,,,host_health_state:Port-Streptococcal Glomerulonephritis (Fatal Case),,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Port-Streptococcal Glomerulonephritis (Fatal Case),,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,40041.57,Streptococcus equi subsp. zooepidemicus strain NCTC11606,NCTC11606,Streptococcus equi,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3597586,40041,not available: to be reported later,,,MLST.Streptococcus_zooepidemicus.72,,NCTC:11606,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900475125.1,LS483354,,SC,,,,1,,1,2071453,41.855404,2072,1854,throat swab,,1983,United Kingdom,United Kingdom: North Yorkshire,,,,,,host_health_state:Nephritis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Nephritis,,,100,1.6,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,40091.19,Helcococcus kunzii strain H13,H13,Helcococcus kunzii,Helcococcus,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMN13819011,40091,,,,,,,,2021-05-11T00:00:00Z,,PRJNA600407,GCA_018336595.1,CP048105,,INSERM U1047,Illumina HiSeq,750.0x,SPAdes v. 3.10.0,1,0,1,2062793,29.32873,1920,1852,ncit:c17627,,2015,France,France:Cahors,,,,,,,,,,,,,,,,,Decrease of Staphylococcus aureus virulence by Helcococcus kunzii H13 in a Caenorhabditis elegans model,,ENVO:2100003,NCIT:C84415,NCIT:C17627,Anaerobiosis,,,,,,,,,,,,,ENVO:2100003,,,,93.9,1.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,40215.119,Acinetobacter junii strain CAM121,CAM121,Acinetobacter junii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17266783,40215,,,,,,KCTC:72438,,2021-01-22T00:00:00Z,,PRJNA690869,GCA_016743155.1,CP068253,,Daegu Catholic University School of Medicine,PacBio RS II with P6-C4 chemistry,97.31x,SMRT Analysis v. 2.3.0,1,0,1,3361061,38.797985,3353,3071,mouth,,2016-01-13,Cambodia,Cambodia: Battambang,,,5 year,healthy,,,,,,,,,,,,,"Complete genome sequence of bacterial pathogen, Acinetobacter junii strain CAM121",collected_by:Yong-Hak Kim,,,,,,,healthy,,,,,,,,,,,,,,99.04,0.55,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,40216.95,Acinetobacter radioresistens strain FDAARGOS_731,FDAARGOS_731,Acinetobacter radioresistens,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11056446,40216,,,,,,FDA:FDAARGOS_731,,2020-08-05T00:00:00Z,,PRJNA231221,GCA_014069095.1,"CP059684,CP059685,CP059686,CP059688,CP059689,CP059687",,US Food and Drug Administration,Pacbio; Illumina,1015.66x,"SMRT v. 2.3.0, HGAP v. 3",1,5,6,3377444,41.51613,3300,3146,normal skin of the right arm,,,USA,USA:VA,,male,57Y,,,host_health_state:Not applicable;host_description:Not applicable;host_disease_stage:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Not applicable,Unknown,Not applicable,Not applicable,,,,,,,,,,100,0.27,,,Skin and Soft Tissue,- HP,40324.1593,Stenotrophomonas maltophilia strain CF13,CF13,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN12500624,40324,,,,,,,,2020-05-04T00:00:00Z,,PRJNA558844,GCA_012971765.1,CP052863,,University of Technology Sydney,Illumina MiSeq; Oxford Nanopore MiniION,30.0x,Hybrid assembly v. 4.0,1,0,1,4591696,66.45869,4269,4128,sputum,,2011,Australia,Australia:Sydney,,,,cystic fibrosis,,,,,,,,,,,,,analysis of antibiotic resistance in nosocomial pathogens,,,,,,,,cystic fibrosis,,,,,,,,,,,,,,100,0.34,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,40324.1713,Stenotrophomonas maltophilia strain UHH_PEG 13-68-68,UHH_PEG 13-68-68,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577962,40324,,,,,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236005.1,CP060021,,Uni Hamburg,Illumina Next Seq,216x,SPAdes v. v.3.7.1,1,0,1,4483650,66.645256,4126,3992,respiratory tract,,2013-11,Germany,Germany: Bochum,,,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,40324.1714,Stenotrophomonas maltophilia strain UHH_PC240,UHH_PC240,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577961,40324,,,,MLST.Stenotrophomonas_maltophilia.77,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236025.1,CP060022,,Uni Hamburg,Illumina Next Seq,144x,SPAdes v. v.3.7.1,1,0,1,4854229,66.68801,4592,4459,perineum,,2012,Germany,Germany: Berlin,,,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:Charite clinic, Berlin",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,40324.1715,Stenotrophomonas maltophilia strain UHH_PC239,UHH_PC239,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577960,40324,,,,MLST.Stenotrophomonas_maltophilia.77,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236045.1,CP060023,,Uni Hamburg,Illumina Next Seq,180x,SPAdes v. v.3.7.1,1,0,1,4855254,66.68863,4599,4459,perineum,,2012,Germany,Germany: Berlin,,,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:Charite clinic, Berlin",,,,,,,,,,,,,,,,,,,,,99.66,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,40324.1716,Stenotrophomonas maltophilia strain UHH_677,UHH_677,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577959,40324,,,,MLST.Stenotrophomonas_maltophilia.1,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236065.1,CP060024,,Uni Hamburg,Illumina Next Seq,54x,SPAdes v. v.3.7.1,1,0,1,4785831,66.399506,4517,4336,respiratory tract,,,Germany,Germany: Karlsruhe,,,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:Institute of technology, Karlsruhe",,,,,,,,,,,,,,,,,,,,,99.62,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,40324.1718,Stenotrophomonas maltophilia strain UHH_ICU331,UHH_ICU331,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577957,40324,,,,MLST.Stenotrophomonas_maltophilia.26,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236105.1,CP060026,,Uni Hamburg,Illumina Next Seq,68x,SPAdes v. v.3.7.1,1,0,1,5062159,66.305435,4800,4603,intensive care uit,,,Germany,Germany: Essen,,female,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:University hospital, Essen",,,,,,,,,,,,,,,,,,,,,99.66,2.81,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,40324.1719,Stenotrophomonas maltophilia strain UHH_454,UHH_454,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577956,40324,,,,,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236125.1,CP060027,,Uni Hamburg,Illumina Next Seq,66x,SPAdes v. v.3.7.1,1,0,1,4652546,66.37578,4355,4170,sputum,,,Germany,Germany: Essen,,female,,Cystic fibrosis,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:University hospital, Essen",,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.66,0.05,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,40324.1728,Stenotrophomonas maltophilia strain UHH_SKK55,UHH_SKK55,Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN15577958,40324,,,,,,,,2020-08-18T00:00:00Z,,PRJNA647802,GCA_014236085.1,CP060025,,Uni Hamburg,Illumina Next Seq,58x,SPAdes v. v.3.7.1,1,0,1,4666115,66.304756,4350,4193,respiratory tract,,,Germany,Germany: Karlsruhe,,,,,,,,,,,,,,,,,The main objective of this study was to analyze the biofilm Phenotype of S.maltophilia clinical isolates and identify key genes and processes involved in the biofilm formation of this organism. This will aid the combat of S.maltophilia infections in clinical settings.,"collected_by:Institute of technology, Karlsruhe",,,,,,,,,,,,,,,,,,,,,99.2,1.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,40324.2327,Stenotrophomonas maltophilia SCAID WND1-2022 (370) strain SCAID WND1-2022 (370),SCAID WND1-2022 (370),Stenotrophomonas maltophilia,Stenotrophomonas,Xanthomonadaceae,Xanthomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30333624,40324,,,,MLST.Stenotrophomonas_maltophilia.162,,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734725.1,"CP102942,CP102943",,,PacBio Sequel,167x,Velvet v. 1.2.10,1,1,2,4919031,66.16588,4597,4433,swab from purulent wound,,2022-04,Kazakhstan,Kazakhstan: Almaty,,,,bacterial sepsis,,,Resistant;Susceptible,AMR Panel,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,bacterial sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Skin and Soft Tissue,Bloodstream Infections-Sepsis HP,405416.50,Acinetobacter baumannii ACICU,ACICU,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09302593,405416,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-05-20T00:00:00Z,,PRJNA474045,GCA_005519135.1,"CP031380,CP031381,CP031382",,University of Sydney,Illumina MiSeq; MinION (Nanopore),243.0x,Unicycler v. 1.00,1,2,3,4013643,38.962933,3814,3729,cerebrospinal fluid,,2005,Italy,Italy: Rome,,,,bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,"Project for the whole genome sequence of ACICU, a multiply resistant clinical isolate. ACICU has been extensively used as a reference isolate. This new genome entry uses Oxford Nanopore long-read sequencing to guide the assembly of Illumina MiSeq short reads.","collected_by:ICU, Hospital S. Giovanni-Addolorata",,,,,,,bacteremia,,,,,,,,,,,,,,99.98,0.61,Bloodstream Infections,Bacteremia,Central Nervous System,Bloodstream Infections-Bacteremia HP,408139.4,Leptospira kmetyi strain LS 001/16,LS 001/16,Leptospira kmetyi,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN10390430,408139,,,,MLST.Leptospira_spp_2.203,,,,2018-11-13T00:00:00Z,,PRJNA504370,GCA_003722295.1,"CP033614,CP033615",,Universiti Sains Malaysia,PacBio,162.28x,HGAP v. 3.0,2,,2,4416922,44.83011,4381,4115,soil,"isolated from a residential area of a patient with leptospirosis in Kelantan, Malaysia",2016-03-29,Malaysia,Malaysia,,,,leptospirosis,,,,,,,,,,,,,"Leptospira kmetyi LS 001/16 is a bacterial pathogen that was isolated from a residential area of a patient with leptospirosis in Kelantan, Malaysia.",collected_by:Muhamad Nuramin Ahmad and Farhana Muhammad Yusoff,,,,,,,,,,,,,,,,,,,,,97.65,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,411459.40,Blautia obeum ATCC 29174,ATCC 29174,Blautia obeum,Blautia,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222666,411459,,,,,,ATCC:29174,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147765.1,CP102265,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3649956,41.625267,3584,3426,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.37,0,,,Other,- NHP,411470.52,[Ruminococcus] gnavus ATCC 29149,ATCC 29149,[Ruminococcus] gnavus,Mediterraneibacter,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222710,411470,,,,,,ATCC:29149,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025152275.1,CP102291,,Stanford University,Illumina HiSeq; PacBio,100x,Unicycler v. 0.4.8,1,0,1,3196943,43.084877,3131,3011,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:BEI,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.42,0,,,Other,- NHP,411477.87,Parabacteroides merdae ATCC 43184,ATCC 43184,Parabacteroides merdae,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222701,411477,,,,,,ATCC:43184,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025151215.1,CP102286,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4377447,45.317898,3832,3464,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.62,0,,,Other,- NHP,411490.43,Anaerostipes caccae L1-92 strain DSM 14662,DSM 14662,Anaerostipes caccae,Anaerostipes,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222639,411490,,,,,,DSM:14662,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146005.1,CP102254,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3590728,44.30113,3621,3443,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.33,4.03,,,Other,- HP,41434.7,Shigella flexneri 1b A-6817,A-6817,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35361133,41434,,,,,,,,2023-07-19T00:00:00Z,,PRJNA780545,,"CP130061,CP130062",,,Illumina MiSeq; Oxford Nanopore MinION,100.0x,Unicycler v. 0.4.8,1,1,2,4725688,50.92996,5298,4712,not applicable,,,,not applicable,,,,shigellosis,,host_description:homo sapiens,,,,,,,,,,,,collected_by:PHO,,,,,,,shigellosis,,,homo sapiens,,,,,,,,,,,99.7,0.2,Specific Bacterial Infections,Shigellosis,Other,Specific Bacterial Infections-Shigellosis HP,41434.8,Shigella flexneri 1b A-10383,A-10383,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35361130,41434,,,,,,,,2023-07-19T00:00:00Z,,PRJNA780545,,"CP130063,CP130065,CP130064,CP130066,CP130067,CP130068,CP130069",,,Illumina MiSeq; Oxford Nanopore MinION,100.0x,Unicycler v. 0.4.8,1,6,7,4901496,50.69342,5554,4907,not applicable,,,,not applicable,,,,shigellosis,,host_description:homo sapiens,,,,,,,,,,,,collected_by:PHO,,,,,,,shigellosis,,,homo sapiens,,,,,,,,,,,99.7,0.2,Specific Bacterial Infections,Shigellosis,Other,Specific Bacterial Infections-Shigellosis HP,423477.9,Veillonella rogosae KCOM 3468,KCOM 3468,Veillonella rogosae,Veillonella,Veillonellaceae,Veillonellales,Negativicutes,Bacillota,SAMN31432570,423477,,,,,,,,2022-11-08T00:00:00Z,,PRJNA893812,GCA_026057735.1,"CP110418,CP110419",,,PacBio Sequel,436.7x,Microbial Assembly Application v.,1,1,2,2205714,38.8855,2027,1993,subgingival plaque of chronic periodontitis lesion,,2018-04-18,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,100,0.8,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,424717.5,Shigella flexneri 3a strain 888048,888048,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17152196,424717,,,,,,,,2021-01-10T00:00:00Z,,PRJNA687663,GCA_016598675.1,CP066809,,University of Bath,Oxford Nanopore MinION; Illumina HiSeq,28.0x,Flye v. 2.7.1,1,0,1,4519004,50.90664,5146,4401,stool,,2020-01,United Kingdom,United Kingdom: London,,male,,shigellosis,,,,,,,,,,,,,Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. This study aimed to look at the location of AMR determinants in CTX-M-27-positive Shigella isolates spread through MSM in England and their relation to known plasmids in Shigella,collected_by:Public Health England,,,,,,,shigellosis,,,,,,,,,,,,,,99.41,0.21,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,424720.8,Shigella flexneri Y strain PE577,PE577,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12588114,424720,Y,,,,,,,2019-09-12T00:00:00Z,,PRJNA533747,GCA_008370775.1,"CP042980,CP042979,CP042978",,Michigan State University,Illumina HiSeq,30.0x,A5 pipeline v. v. 20160825,1,2,3,4598750,50.962784,5076,4559,missing,"isolated in Adelaide, Australia and has been the laboratory host of numerous phages, including SfI, SfII, SfV, Sf6, etc",1990,Australia,Australia: Adelaide,,,,,,,,,,,,,,,,,"Shigella flexneri serotype Y is a common host to many bacteriophages. Strain PE577 was initially isolated in Adelaide, Australia and has been the laboratory host of numerous phages, including SfI, SfII, SfV, Sf6, etc. This strain has also been used to isolate many Shigella phages from the environment. The goal of this study was to sequence the entire genome of this strain for general characterization and future genetic inquiries.",sample_type:monoisolate;biomaterial_provider:C. Murray -> R. Morona -> K. Parent,,,,,,,,,,,,,clinical sample,clinical sample,,,,,,,99.64,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,426430.24,Staphylococcus aureus subsp. aureus str. Newman,NYU,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07629846,426430,,,,MLST.Staphylococcus_aureus.254,mlst:8,,,2017-09-18T00:00:00Z,29487865,PRJNA406184,GCA_002310435.1,CP023390,,NYU Langone Health,Illumina Miseq,200.0x,R studio v. 1.0.136,1,,1,2878897,32.89,2940,2964,genomic dna; osteomyelitis,,2007-07,Japan,Tokyo,,,,invasive_infection,,,Resistant,AMR Panel,,,,,,,,,A single nucleotide polymorphism in the Staphylococcus aureus virulence regulator SaeR abolishes pathogenesis,collected_by:Victor J. Torres,,,,,,,invasive_infection,,,,,,after culture by NYU,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- NHP,428126.20,[Clostridium] spiroforme DSM 1552,DSM 1552,Thomasclavelia spiroformis,Thomasclavelia,Coprobacillaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMN20222683,428126,,,,,,DSM:1552,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149465.1,CP102275,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2528470,28.771946,2400,2331,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,42897.100,Shigella flexneri 2a strain AUSMDU00010535,AUSMDU00010535,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191650,42897,2a,,,,mlst:ST245,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664535.1,"CP045941,CP045942,CP045943,CP045944",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,105x,de novo,1,3,4,5045617,50.72464,5640,4988,missing,,2017,Australia,Australia,,,,,,,Resistant,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.7,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,42897.163,Shigella flexneri 2a Sflex 21-42,Sflex 21-42,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33861938,42897,2a,,,,,,,2023-04-09T00:00:00Z,,PRJNA947612,,"CP121223,CP121218,CP121219,CP121220,CP121221,CP121222",,,Oxford Nanopore GridION,70.0x,metaFlye v. SEP-2021,1,5,6,4980722,50.668358,5586,4955,fecal sample,,2021-03-23,Canada,Canada: Vancouver,,,,Shigellosis,,,,,,,,,,,,,,collected_by:St. Paul's Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,431947.23,Porphyromonas gingivalis ATCC 33277,ATCC 33277,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07315160,431947,,,,MLST.Porphyromonas_gingivalis.96,,ATCC:33277,,2018-01-19T00:00:00Z,29338683,PRJNA393092,GCA_002892575.1,CP025930,,CNRS - Universite de Rennes 1,PacBio,29.9x,canu v. 1.3,1,,1,2379874,48.360123,2245,1796,human gingival sulcus,,,,,,,,Periodontitis,,,,,,,,,,,,,"Resequencing, Reassembly and Reannotation of Porphyromonas gingivalis strains ATCC 33277, TDC60 and W83.",collected_by:ATCC collection;passage_history:less than 20,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0.7,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,436397.4,Streptomyces sudanensis SD 504,SD 504,Streptomyces sudanensis,Streptomyces,Streptomycetaceae,Kitasatosporales,Actinomycetes,Actinomycetota,SAMN27412228,436397,,,,,,DSM:41923,,2022-05-31T00:00:00Z,,PRJNA824685,GCA_023614315.1,CP095474,,,Oxford Nanopore MinION,58x,Canu v. 1.7.1,1,0,1,5259510,73.934654,5202,4782,from patients with mycetoma infections,,1999,Sudan,Sudan,,,,,,,,,,,,,,,,,,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,96.3,1.9,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,43770.574,Corynebacterium striatum strain 215,215,Corynebacterium striatum,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05374476,43770,,,,,,,,2017-12-04T00:00:00Z,,PRJNA278886,GCA_002803965.1,CP024931,,Brigham & Women's Hospital,PacBio,500.0x,HGAP v. v.4,1,,1,2993983,59.2,2897,2746,sputum,,2016,USA,USA:Boston,,male,75,,,host_subject_id:CORYNE-1,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,Missing,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,43770.575,Corynebacterium striatum strain 216,216,Corynebacterium striatum,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05178544,43770,,,,,,,,2017-12-04T00:00:00Z,,PRJNA278886,GCA_002804085.1,CP024932,,Brigham & Women's Hospital,PacBio,500.0x,HGAP v. v.4,1,,1,3031488,59.02,2955,2790,tracheal aspirate,,2016,USA,USA:Boston,,male,62,,,host_subject_id:CORYNE-2,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,Missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- NHP,437897.508,Megamonas funiformis strain NBRC 114415,NBRC 114415,Megamonas funiformis,Megamonas,Selenomonadaceae,Selenomonadales,Negativicutes,Bacillota,SAMN21163590,437897,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181475.1,CP084018,,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore MinION,356.0x,Flye v. 2.8.3; Racon v. 1.4.20; Medaka v.,1,0,1,2464533,31.44892,2453,2412,human feces,,2019,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,1.27,,,Gastrointestinal,- NHP,438033.9,Ruminococcus gauvreauii strain DSM 19829,DSM 19829,Ruminococcus gauvreauii,Ruminococcus,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222709,438033,,,,,,DSM:19829,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025151995.1,CP102290,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4145839,47.634773,3953,3793,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.37,1.27,,,Other,- HP,439334.332,Mycobacterium avium subsp. hominissuis strain HP17,HP17,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05506874,439334,,,,,,,,2017-10-25T00:00:00Z,28957464,PRJNA336241,GCA_002716905.1,CP016818,,Kobe Institute of Health,PacBio,125.8x,HGAP v. 3,1,,1,5100725,69.2,4919,4738,sputum,,2012-06-29,Japan,Japan:Sapporo,,,,MAC lung disease,,,,,,,,,,,,,Comparative genomic analysis of MAH,collected_by:Hokkaido University,,,,,,,MAC lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,439334.333,Mycobacterium avium subsp. hominissuis strain OCU901s_S2_2s,OCU901s_S2_2s,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05862128,439334,,,,,,,,2017-10-25T00:00:00Z,28957464,PRJNA345418,GCA_002716925.1,CP018014,,Kobe Institute of Health,PacBio,unspecified,HGAP2 v. 20161107,1,,1,5186756,69.09,4962,4677,sputum,,2007-03-01,Japan,Japan:Osaka,,,,MAC lung disease,,,,,,,,,,,,,Complete Genome Analysis,collected_by:Osaka City Univ,,,,,,,MAC lung disease,,,,,,,,,,,,,,100,0.7,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,439334.334,Mycobacterium avium subsp. hominissuis strain OCU873s_P7_4s,OCU873s_P7_4s,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05862070,439334,,,,,,,,2017-10-25T00:00:00Z,28957464,PRJNA345414,GCA_002716965.1,CP018020,,Kobe Institute of Health,PacBio,missing,HGAP2 v. 20161107,1,,1,5027510,69.21,4837,4660,sputum,,2007-05-02,Japan,Japan:Osaka,,,,MAC lung disease,,,,,,,,,,,,,Complete Genome Analysis,collected_by:Osaka City Univ,,,,,,,MAC lung disease,,,,,,,,,,,,,,100,1.4,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,439334.461,Mycobacterium avium subsp. hominissuis strain 101174,101174,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11403589,439334,,,,,,,,2019-05-20T00:00:00Z,,PRJNA532547,GCA_005518015.1,"CP040250,CP040248,CP040249",,Children's Hospital of Philadelphia,Oxford Nanopore MiniION; Illumina HiSeq,75.7176x,Unicycler v. v0.4.8-beta; Circlator v.,1,2,3,5167741,69.138954,5048,4855,sputum,isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF,2016-08-24,USA,USA,,male,19,cystic fibrosis,,host_description:cystic fibrosis;host_disease_outcome:chronic disease;host_subject_id:101,,,,,,,,,,,The NTM Project is a study designed to identify in-host adaptation over time during chronic NTM lung infection in patients with cystic fibrosis (CF) by completing whole genome sequencing on longitudinal isolates. The project houses a biobank of nontuberculous mycobacteria (NTM) that have been longitudinally collected and stocked at the Children's Hospital of Philadelphia from 2011-present. Isolates include NTM isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF.,collected_by:Jennifer Bouso,,,,,,,cystic fibrosis,,chronic disease,cystic fibrosis,,,,,,,,,,,99.44,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,439334.462,Mycobacterium avium subsp. hominissuis strain 101034,101034,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11403486,439334,,,,,,,,2019-05-20T00:00:00Z,,PRJNA532547,GCA_005518035.1,"CP040247,CP040246,CP040245",,Children's Hospital of Philadelphia,Oxford Nanopore MiniION,83.1074x,Unicycler v. v0.4.8-beta; Circlator v.,1,2,3,5368111,68.930725,5287,5047,sputum,isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF,2017-02-13,USA,USA,,male,19,cystic fibrosis,,host_disease_outcome:chronic disease;host_subject_id:101,,,,,,,,,,,The NTM Project is a study designed to identify in-host adaptation over time during chronic NTM lung infection in patients with cystic fibrosis (CF) by completing whole genome sequencing on longitudinal isolates. The project houses a biobank of nontuberculous mycobacteria (NTM) that have been longitudinally collected and stocked at the Children's Hospital of Philadelphia from 2011-present. Isolates include NTM isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF.,collected_by:Jennifer M Bouso;passage_history:1,,,,,,,cystic fibrosis,,chronic disease,,,,,,,,,,,,99.94,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,439334.463,Mycobacterium avium subsp. hominissuis strain 101115,101115,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN11403599,439334,,,,,,,,2019-05-20T00:00:00Z,,PRJNA532547,GCA_005518055.1,"CP040255,CP040254,CP040253,CP040251,CP040252",,Children's Hospital of Philadelphia,Oxford Nanopore MiniION; Illumina HiSeq,97.3114x,Unicycler v. v0.4.8-beta; Circlator v.,1,4,5,5393712,68.93579,5302,5050,sputum,isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF,2017-08-01,USA,USA,,male,19,cystic fibrosis,,host_disease_outcome:chronic disease;host_subject_id:101,,,,,,,,,,,The NTM Project is a study designed to identify in-host adaptation over time during chronic NTM lung infection in patients with cystic fibrosis (CF) by completing whole genome sequencing on longitudinal isolates. The project houses a biobank of nontuberculous mycobacteria (NTM) that have been longitudinally collected and stocked at the Children's Hospital of Philadelphia from 2011-present. Isolates include NTM isolated from the lungs of patients with cystic fibrosis (CF) and from patients without CF.,collected_by:Jennifer Bouso,,,,,,,cystic fibrosis,,chronic disease,,,,,,,,,,,,99.39,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,439334.547,Mycobacterium avium subsp. hominissuis strain W9,W9,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15806900,439334,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,GCA_020227555.1,CP060405,,University of Wisconsin-Madison,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,0,1,5052589,69.22911,4941,4754,sputum,,,,USA,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),,,,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,99.74,0.07,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,439334.548,Mycobacterium avium subsp. hominissuis strain w14,w14,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN15806906,439334,,,,,,,,2021-10-04T00:00:00Z,33162087,PRJNA656902,GCA_020227575.1,CP060407,,University of Wisconsin-Madison,Illumina MiSeq,100x,SPAdes v. 3.14.1,1,0,1,5098287,69.22348,4918,4755,sputum,,,,USA,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,Genotypic analysis of NTM isolates from human and milk samples in Wisconsin,collected_by:Wisconsin state lab of hygiene (WSLH),,,,,,,Mycobacterium avium complex disease,,,,,,,,,,,,,,99.94,1.33,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,439334.678,Mycobacterium avium subsp. hominissuis OCU889s_P11_4s,OCU889s_P11_4s,Mycobacterium avium,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN05862091,439334,,,,,,,,2022-02-10T00:00:00Z,,PRJNA345416,GCA_022175585.1,CP018019,,,PacBio,149,HGAP3 v. 20111107,1,0,1,5118245,69.035225,4914,4656,sputum,,2006-12-18,Japan,Japan:Osaka,,,,MAC lung disease,,,,,,,,,,,,,,collected_by:Osaka City Univ,,,,,,,MAC lung disease,,,,,,,,,,,,,,99.61,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,440524.124,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain L-3835",L-3835,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00097512,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2021-05-26T00:00:00Z,,PRJDB6430,GCA_019670145.1,AP023288,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Sequel; NextSeq500,123x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,0,1,4995025,52.146965,5035,4698,homo sapiens,,2007,Japan,Japan,,,,,,,,,,,,,,,,,"Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and the monophasic variant (Salmonella 4,[5],12:i:-) are the major cause of gastroenteritis for both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods of this pathogens in the molecular epidemiological analyses, however the results do not reflect the phylogenetic information precisely. In this study, we performed phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine clades to be discriminated each other as genotypes.",,missing,missing,missing,missing,Whole genome sequencing of Salmonella enterica serovar Typhimurium and its monophasic variant isolated from food animals in Japan,,,,,,,,,,,,missing,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,440524.74,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain PNCS014875",PNCS014875,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10953956,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.2379,,,,2019-12-16T00:00:00Z,,PRJNA522746,GCA_009756475.1,CP037882,,Public Health Agency of Canada,Illumina MiSeq; Oxford Nanopore MiniION,61.0x,SPAdes v. DEC-2018; Unicycler v. DEC-2018,1,0,1,4996832,52.17362,5143,4931,stool,,2014-12-06,Canada,Canada: Britsh Columbia,,male,59 Years,salmonellosis,,,,,,,,,,,,,"Part of TBD paper : Distribution of heavy metal elements in Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype",collected_by:BCCDC Public Health Laboratory,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.11,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,440524.76,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain PNCS009991",PNCS009991,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10953955,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2019-12-16T00:00:00Z,,PRJNA522746,GCA_009756605.1,"CP037881,CP037880",,Public Health Agency of Canada,Illumina MiSeq,139.0x,SPAdes v. DEC-2016,1,1,2,5076935,52.084713,5267,5038,stool,,2012-06-22,Canada,Canada: Quebec,,male,22 Years,salmonellosis,,,,,,,,,,,,,"Part of TBD paper : Distribution of heavy metal elements in Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype",collected_by:Institut national de sante publique du Quebec,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.11,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,440524.77,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain PNCS015054",PNCS015054,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10953953,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.19,,,,2019-12-16T00:00:00Z,,PRJNA522746,GCA_009756555.1,"CP037877,CP037875,CP037876",,Public Health Agency of Canada,Illumina MiSeq; Oxford Nanopore MiniION,106.0x,SPAdes v. DEC-2017; unicycler v. DEC-2017,1,2,3,5130533,51.958267,5329,5049,stool,,2010-12-23,Canada,Canada: Manitoba,,female,1 Year,salmonellosis,,,,,,,,,,,,,"Part of TBD paper : Distribution of heavy metal elements in Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype",collected_by:Cadham Provincial Laboratory,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,440524.78,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain PNCS014863",PNCS014863,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10953954,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2019-12-16T00:00:00Z,,PRJNA522746,GCA_009756585.1,"CP037879,CP037878",,Public Health Agency of Canada,Illumina MiSeq; Oxford Nanopore MiniION,58.0x,SPAdes v. FEB-2018; Unicycler v. FEB-2018,1,1,2,4991151,52.15436,5141,4913,stool,,2011-01-27,Canada,Canada: Britsh Columbia,,male,47 Years,salmonellosis,,,,,,,,,,,,,"Part of TBD paper : Distribution of heavy metal elements in Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype",collected_by:BCCDC Public Health Laboratory,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,440524.79,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain PNCS014854",PNCS014854,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10953952,440524,"4,[5],12:i:-",,,MLST.Salmonella_enterica.19,,,,2019-12-16T00:00:00Z,,PRJNA522746,GCA_009756515.1,"CP037874,CP037873",,Public Health Agency of Canada,Illumina MiSeq; Oxford Nanopore MiniION,60.0x,SPAdes v. DEC-2017; unicycler v. DEC-2017,1,1,2,4911078,52.250748,5049,4811,stool,,2009-08-20,Canada,Canada: Manitoba,,,,salmonellosis,,,,,,,,,,,,,"Part of TBD paper : Distribution of heavy metal elements in Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype",collected_by:Cadham Provincial Laboratory,,,,,,,salmonellosis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,44275.5,Leptospira interrogans serovar Copenhageni strain FDAARGOS_203,FDAARGOS_203,Leptospira interrogans,Leptospira,Leptospiraceae,Leptospirales,Spirochaetia,Spirochaetota,SAMN04875540,44275,Copenhageni,,,"MLST.Leptospira_spp.17,MLST.Leptospira_spp_2.47,MLST.Leptospira_spp_3.2",,FDA:FDAARGOS_203,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073495.2,"CP020414,CP020413",,US Food and Drug Administration,PacBio,15.3569892514686x,HGAP v. 3,1,1,2,4630574,35.05,4780,4087,human clinical sample; human,,1996,Brazil,Brazil,,,,Leptospirosis,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.","collected_by:ATCC < D Haake, A Ko",,,,,,,Leptospirosis,Missing,Missing,Missing,Missing,,,,,,,,,,100,0.4,Specific Bacterial Infections,Leptospirosis,Other,Specific Bacterial Infections-Leptospirosis HP,446.1005,Legionella pneumophila strain 80-045,80-045,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMD00393827,446,,,,,,,,2021-08-13T00:00:00Z,,PRJDB12006,GCA_019974095.1,AP024961,,"Department of Bacteriology I, National Institute of Infectious Diseases",Illumina MiSeq; ONT MinION,91x,Unicycler v. 0.4.8,1,0,1,3438257,38.24708,3216,2994,lung,,1980,,Japan,,,,,,,,,,,,,,,,,Whole-genome sequencing of Legionella pneumophila strain 80-045 that caused the first case of Legionnaires' disease in Japan,,not applicable,not applicable,not applicable,missing,Whole-genome sequencing of Legionella pneumophila strain 80-045,,,,,,,,,,,,not applicable,,,,100,0.19,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,446.637,Legionella pneumophila strain ST23,ST23,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMEA4535097,446,,,,,,,,2016-11-18T00:00:00Z,,PRJEB17630,GCF_900119755.1,LT632615,NZ_LT632615.1,WTSI,,,,1,,1,3509586,38.37,3310,3125,clinical,,1994-01-01,,,,,,,,host_health_state:diseased,,,,,,,,,,,Evaluation of whole genome sequencing for the epidemiological typing of Legionella pneumophila,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,446.638,Legionella pneumophila strain ST62,ST62,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMEA4535100,446,,,,,,,,2016-11-18T00:00:00Z,,PRJEB17630,GCF_900119765.1,LT632614,NZ_LT632614.1,WTSI,,,,1,,1,3530817,38.38,3323,3156,clinical,,2004-10-01,,,,,,,,host_health_state:diseased,,,,,,,,,,,Evaluation of whole genome sequencing for the epidemiological typing of Legionella pneumophila,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,446.639,Legionella pneumophila strain ST37,ST37,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMEA4535098,446,,,,,,,,2016-11-18T00:00:00Z,,PRJEB17630,GCF_900119775.1,LT632616,NZ_LT632616.1,WTSI,,,,1,,1,3474638,38.38,3266,3082,clinical,,2003-11-01,,,,,,,,host_health_state:diseased,,,,,,,,,,,Evaluation of whole genome sequencing for the epidemiological typing of Legionella pneumophila,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,446.640,Legionella pneumophila strain ST42,ST42,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMEA4535099,446,,,,,,,,2016-11-18T00:00:00Z,,PRJEB17630,GCF_900119785.1,LT632617,NZ_LT632617.1,WTSI,,,,1,,1,3430562,38.44,3206,3040,clinical,,1999-01-01,,,,,,,,host_health_state:diseased,,,,,,,,,,,Evaluation of whole genome sequencing for the epidemiological typing of Legionella pneumophila,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,446.641,Legionella pneumophila strain Philadelphia-1,Philadelphia-1,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN03988484,446,,,,,,,,2017-01-10T00:00:00Z,,PRJNA292755,GCF_001941585.1,CP013742,NZ_CP013742.1,Public Health Agency of Canada,PacBio,106.0x,Validated_PacBio v. 2015-12-09,1,,1,3409143,38.33,3178,2963,missing,,1976,USA,"USA: Philadelphia, Pennsylvania",,,,Legionnaire's,,,,,,,,,C,,,,Legionella pneumophila strain Philadelphia-1 Reannotation Project,collected_by:Horowitz,,,,,,,Legionnaire's,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,446.948,Legionella pneumophila strain AUSMDU00010536 strain SBT211,AUSMDU00010536,Legionella pneumophila,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN13191634,446,SBT211,,,,,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664815.1,CP045974,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,460x,de novo,1,0,1,3453356,38.36923,3241,3048,missing,,2016,Australia,Australia,,,,,,,,,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,44750.3,Corynebacterium auris DSM 44122,DSM 44122,Corynebacterium auris,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN06041730,44750,,,,,,DSM:44122,,2023-07-05T00:00:00Z,,PRJNA354155,,CP047047,,,Illumina MiSeq,97.7x,Newbler v. 2.8,1,0,1,2439611,66.983,2288,2213,ear infection,,1994,Switzerland,Switzerland: Zurich University Hospital,,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 44122,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- NHP,449673.71,Bacteroides stercoris ATCC 43183,ATCC 43183,Bacteroides stercoris,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222659,449673,,,,,,ATCC:43183,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147325.1,CP102262,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4007931,45.855156,3611,3309,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,98.88,0.19,,,Other,- HP,450.24,Legionella longbeachae strain FDAARGOS_201,FDAARGOS_201,Legionella longbeachae,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN04875538,450,,,,,,FDA:FDAARGOS_201,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073455.2,CP020412,,US Food and Drug Administration,PacBio,14.69x,CA v. 8.2,1,,1,4162717,37.06,3921,3575,transtracheal aspirate; lung,,1981,USA,USA:CA,,male,59Y,Pneumonia,,host_description:Fever;host_disease_outcome:Death,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:ATCC < RM McKinney,,,,,,,Pneumonia,Missing,Death,Fever,Missing,,,,,,,,,,100,2.1,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,450.89,Legionella longbeachae strain B1445CHC,B1445CHC,Legionella longbeachae,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN13037436,450,1,,,,,,,2020-03-19T00:00:00Z,,PRJNA577762,GCA_011465255.1,"CP045306,CP045305,CP045304",,Canterbury Health Laboratories,Oxford Nanopore GridION; Illumina MiSeq,118.0x,Flye v. 2.4.2; Unicycler v. 0.4.7,1,2,3,4224775,37.20203,3980,3627,sputum sample,"derived from patients hospitalized with LD in Christchurch, New Zealand",2007-01-18,New Zealand,New Zealand: Christchurch,,,,Pneumonia,,,,,,,,,,,,,"Legionella longbeachae serogroup 1, predominantly found in soil and composted plant material, causes the majority of cases of Legionnaires’ disease (LD) in New Zealand. The goal of this study is to produce complete genome sequence of L. longbeachae serogroup 1 isolates derived from patients hospitalized with LD in Christchurch, New Zealand.",collected_by:Cantebury Health Laboratories,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.19,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,450.90,Legionella longbeachae strain B41211CHC,B41211CHC,Legionella longbeachae,Legionella,Legionellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN13042258,450,1,,,,,,,2020-03-19T00:00:00Z,,PRJNA577762,GCA_011465395.1,"CP045308,CP045307",,Canterbury Health Laboratories,Oxford Nanopore GridION; Illumina MiSeq,250.0x,Flye v. 2.4.2; Unicycler v. 0.4.7,1,1,2,4077247,37.14406,3827,3469,sputum sample,"derived from patients hospitalized with LD in Christchurch, New Zealand",2009-09-19,New Zealand,New Zealand: Christchurch,,,,Pneumonia,,,,,,,,,,,,,"Legionella longbeachae serogroup 1, predominantly found in soil and composted plant material, causes the majority of cases of Legionnaires’ disease (LD) in New Zealand. The goal of this study is to produce complete genome sequence of L. longbeachae serogroup 1 isolates derived from patients hospitalized with LD in Christchurch, New Zealand.",collected_by:Cantebury Health Laboratories,,,,,,,Pneumonia,,,,,,,,,,,,,,99.62,0.19,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,455432.5,Nocardia terpenica strain NC_YFY_NT001,NC_YFY_NT001,Nocardia terpenica,Nocardia,Nocardiaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN07764296,455432,,,,,,,,2017-10-17T00:00:00Z,,PRJNA413720,GCA_002568625.1,"CP023778,CP023779",,The first affiliated hospital of NanChang university,PacBio,147.0x,smrt hgap3 v. smrt v2.3 HGAP3,1,1,2,8918539,68.47,8610,7926,cerebrospinal fluid,,2017-06-15,China,China: Nanchang,,,,The central nervous system infection,,,,,,,,,,,,,Nocardia terpenica from human Cerebrospinal fluid,collected_by:Lingbing Zeng,,,,,,,The central nervous system infection,,,,,,,,,,,,,,99.6,0.6,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- NHP,45851.818,Butyrivibrio crossotus strain DSM 2876,DSM 2876,Butyrivibrio crossotus,Butyrivibrio,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222671,45851,,,,,,DSM:2876,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148445.1,CP102270,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2521323,37.908787,2530,2455,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.33,0.67,,,Other,- HP,459472.19,Planomicrobium glaciei strain NRL-ATB46093,NRL-ATB46093,Planococcus glaciei,Planococcus,Planococcaceae,Bacillales,Bacilli,Bacillota,SAMN14558179,459472,,,,,,,,2020-06-23T00:00:00Z,,PRJNA623713,GCA_013368775.1,"CP051177,CP051178,CP051179",,"NIPH, Prague",Oxford Nanopore; Illumina MiSeq,40.0x,CANU v. DEC-2018; Pilon v. APR-2020,1,2,3,4091551,46.847248,4170,3914,acute appendicitis,,2018,Czech Republic,Czech Republic,,,,NRL-ATB46093,,,,,,,,,,,,,Identification of bacteria,collected_by:NIPH Prague,,,,,,,acute appendicitis,,,,,,,,,,,,,,99.34,4.86,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,46170.1081,Staphylococcus aureus subsp. aureus strain HL20709,HL20709,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14667806,1280,,,,MLST.Staphylococcus_aureus.59,,,,2020-05-10T00:00:00Z,,PRJNA627323,GCA_013003945.1,CP053070,,Hallym University College of Medicine,Oxford Nanopore; Illumina MiSeq,800.0x,SPAdes v. 3.14.0,1,0,1,2860303,32.93172,2801,2772,blood,,2017,South Korea,South Korea,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequence of Staphylococcus aureus SCCmec type V isolated from Korea,collected_by:Kangdong Sacred Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,46170.1082,Staphylococcus aureus subsp. aureus strain EDCC5398,EDCC5398,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14830786,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-05-11T00:00:00Z,,PRJNA630284,GCA_013008375.1,CP053101,,University of Regensburg,Illumina,98.0x,HGAP v. 3.1,1,0,1,2843534,32.822536,2787,2739,tissue,,2009-06-09,Germany,Germany,,,,Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Here, we report the high-quality and complete genome sequence of Staphylococcus aureus EDCC5938. Whole genome sequencing of this clinical strain revealed the complete genome sequence with 2,843,534 base pairs. This strain belongs to sequence type 22 (ST22) and contains mecA gene.",collected_by:Eugen Domann,,,,,,,Infection,,,,,,,,,,,,,,99.51,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,46170.1083,Staphylococcus aureus subsp. aureus strain Dresden-275757,Dresden-275757,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN14910682,1280,,,pathovar L-positive,MLST.Staphylococcus_aureus.80,"genotype:Sequence type 80, RIDOM spa t 1849",,,2020-06-21T00:00:00Z,,PRJNA632494,GCA_013363895.1,CP054876,,Leibniz Institute of Photonic Technology (IPHT),Illumina MiSeq; Oxford Nanopore MiniION,139.0x,SPAdes v. 2018-03-13,1,0,1,2789663,32.978104,2735,2694,"clinical sample, pus",,2015,Germany,Germany: Dresden,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"This project describes the seuquence of PVL-positive Staphylococcus aureus strain that bears evidence of large-scale recombination events introducing large fragment of core-genomic DNA of from other strains. One of the donor strains was identified and it is demonstrated that this strain, in turn, also originated from another such recombination.",sample_type:Bacteriological culture,,,,,,,,,,,,,,,,,,,,,99.23,0.11,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,46170.1187,Staphylococcus aureus subsp. aureus strain SA H27,SA H27,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10023130,1280,,,,MLST.Staphylococcus_aureus.22,,,,2020-09-29T00:00:00Z,,PRJNA489991,GCA_014792825.1,CP032161,,University of Pecs,IonTorrent,45.0x,SPAdes v. 3.7.1,1,0,1,2788632,32.727905,2854,2827,skin,"isolated methicillin-resistant Staphylococcus aureus in term of pathogenicity, niche-adaptation, and the emergence of hypervirulent strains",2016-02-25,Hungary,Hungary,,,,Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Comparative genomes analysis of clinically isolated methicillin-resistant Staphylococcus aureus in term of pathogenicity, niche-adaptation, and the emergence of hypervirulent strains.",collected_by:University of Pecs,,,,,,,Infection,,,,,,,,,,,,,,99.46,0.22,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,46170.1188,Staphylococcus aureus subsp. aureus strain SA H29,SA H29,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10080438,1280,,,,MLST.Staphylococcus_aureus.8,,,,2020-09-29T00:00:00Z,,PRJNA491536,GCA_014792845.1,"CP032468,CP032469,CP032470",,University of Pecs,IonTorrent,17.0x,SPAdes v. 3.7.1,1,2,3,2834624,32.654987,3052,2940,nostril,"isolated methicillin-resistant Staphylococcusaureus in term of pathogenicity, niche-adaptation, and the emergence of hypervirulent strains",2016-02-25,Hungary,Hungary,,,,Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Comparative genomes analysis of clinically isolated methicillin-resistant Staphylococcusaureus in term of pathogenicity, niche-adaptation, and the emergence of hypervirulent strains.",collected_by:University of Pecs,,,,,,,Infection,,,,,,,,,,,,,,99.35,0.17,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,46170.1192,Staphylococcus aureus subsp. aureus strain SA G5,SA G5,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN09988922,1280,,,,MLST.Staphylococcus_aureus.45,,,,2020-10-02T00:00:00Z,32864286,PRJNA489767,GCA_014838785.1,CP032160,,University of Pecs,IonTorrent,20.0x,SPAdes v. 3.7.1,1,0,1,2760385,32.77196,2855,2787,infection,,2016-02-25,Germany,Germany,,,,Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Comparative genomes analysis of clinically isolated methicillin-resistant Staphylococcusaureus in term of pathogenicity, niche-adaptation, and the emergence of a hypervirulent strain",collected_by:University of Pecs,,,,,,,Infection,,,,,,,,,,,,,,99.41,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,46170.1193,Staphylococcus aureus subsp. aureus strain CC1153-MRSA,CC1153-MRSA,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN16824906,1280,,,,MLST.Staphylococcus_aureus.1153,"genotype:CC1153, RIDOM spa t504",,,2020-12-15T00:00:00Z,,PRJNA679156,GCA_016065215.1,CP065857,,Leibniz Institute of Photonic Technology (IPHT),Oxford Nanopore MinION,694.0x,Flye v. v2.8.1,1,0,1,2827195,32.752888,2759,2705,wound swab,,2018,United Arab Emirates,United Arab Emirates: Dubai,,male,30,wound infection / SSTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This is a clonal complex 1153 MRSA with a novel SCCmec/SCCfus composite element.,collected_by:Professor A. Senok,,,,,,,wound infection / SSTI,,,,,,,,,,,,,,99.48,0.1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,46170.290,Staphylococcus aureus subsp. aureus strain Clinical isolate,Clinical isolate,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMEA17757418,1280,,,,MLST.Staphylococcus_aureus.8,,,,2016-12-14T00:00:00Z,,PRJEB18112,GCF_900129335.1,"LT671859,LT671860","NZ_LT671859.1,NZ_LT671860.1",JUSTUS LIEBIG UNIVERSITAT,,,,1,1,2,2821874,32.76,2638,2577,wound infection,,1995-03-10,,,,,,,,host_health_state:diseased,,,,,,,,,,,"Here, we report the high-quality complete genome sequence of Staphylococcus aureus EDCC5055. Whole genome sequencing of this clinical strain revealed the complete genome sequence (2,794,437 ) along with one plasmid (27,437bp).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,46170.338,Staphylococcus aureus subsp. aureus strain ATCC,ATCC,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07629847,1280,,,,MLST.Staphylococcus_aureus.254,,,,2017-09-18T00:00:00Z,,PRJNA406184,GCA_002310395.1,CP023391,,NYU Langone Health,Illumina HiSeq,200.0x,R studio v. 1.0.136,1,,1,2878897,32.89,2940,2964,osteomyelitis,,1970,,,,,,invasive_infection,,,Susceptible,Computational Prediction,,,,,,,,,A single nucleotide polymorphism in the Staphylococcus aureus virulence regulator SaeR abolishes pathogenesis,collected_by:Hawiger,,,,,,,invasive_infection,,,,,,from ATCC,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,46170.369,Staphylococcus aureus subsp. aureus UAMS-1,UAMS-1,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,,1280,,,,MLST.Staphylococcus_aureus.30,,,,2017-10-22T04:00:00Z,,,,,,,"Illumina GaIIx, Oxford Nanopore MinION, Sanger","Short Read 1922x, Long Read 34x",Unicycler v. 0.3.0,,,1,2794133,32.79,2635,,debridement from an osteomyelitis patient ,,,USA,"Little Rock, AR",,,,,,Osteomyelitis Patient,Susceptible;Resistant,Computational Prediction,,,,,,,,,,First described by Gillaspy et al in Role of the accessory gene regulator (agr) in pathogenesis of staphylococcal osteomyelitis. 1995. Infect Immun. 63(9):3373–3380.,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,46170.460,Staphylococcus aureus subsp. aureus strain EDCC5464,EDCC5464,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07310553,1280,,,,MLST.Staphylococcus_aureus.22,,,,2017-11-20T00:00:00Z,,PRJNA392815,GCA_002786535.1,CP022291,,Justus Liebig University,PacBio,126.0x,HGAP v. HGAP 3.1,1,,1,2762859,32.84,2739,2736,bone,,2015-04-09,Germany,Germany,,,,implant associated bone infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequence of staphylococcus aureus subsp. aureus EDCC 5464,collected_by:Eugen Domann,,,,,,,implant associated bone infection,,,,,,,,,,,,,,99.4,0,Surgical Site Infections,,Bone and Joint,Surgical Site Infections- HP,46170.461,Staphylococcus aureus subsp. aureus strain EDCC5458,EDCC5458,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07310520,1280,,,,MLST.Staphylococcus_aureus.8,,,,2017-11-20T00:00:00Z,,PRJNA392813,GCA_002786465.1,CP022290,,Justus Liebig University,PacBio,57.0x,HGAP v. HGAP 3.1,1,,1,2848525,32.86,2882,2900,bone,,2014-07-30,Germany,Germany,,,,Implant associated bone infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,staphylococcus aureus subsp. aureus EDCC 5458 complete genome sequence,collected_by:Eugen Domann,,,,,,,Implant associated bone infection,,,,,,,,,,,,,,100,0,Surgical Site Infections,,Bone and Joint,Surgical Site Infections- HP,46170.805,Staphylococcus aureus subsp. aureus strain VB9352,VB9352,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10868410,1280,,,,MLST.Staphylococcus_aureus.772,,,,2019-02-11T00:00:00Z,,PRJNA520811,GCA_004153345.1,CP035670,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,194.9x,CANU v. 1.7; UNICYCLER HYBRID v. 0.4.6,1,,1,2866554,32.853592,3001,2878,blood,,2016,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Heteroresistant vancomycin intermediate Staphylococcus aureus_VB9352_Hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,99.28,0.08,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,46170.806,Staphylococcus aureus subsp. aureus strain VB31683,VB31683,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10868425,1280,,,,MLST.Staphylococcus_aureus.22,,,,2019-02-11T00:00:00Z,,PRJNA520817,GCA_004153365.1,CP035671,,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,194.9x,CANU v. 1.7; UNICYCLER HYBRID v. 0.4.6,1,,1,2841049,32.81862,2926,2855,blood,,2015,India,India,,,,Bloodstream infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Teicoplanin resistant MRSA_VB31683_Hybrid assembly,collected_by:Christian Medical College,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.51,0.22,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,46170.807,Staphylococcus aureus subsp. aureus strain WCUH29,WCUH29,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN11360115,1280,,,,MLST.Staphylococcus_aureus.5,,,,2019-04-12T00:00:00Z,,PRJNA531521,GCA_004785995.1,CP039156,,UNIVERSITY OF MINNESOTA,PacBio RSII,400.0x,HGAP v. 2.3,1,,1,2909934,32.92385,2971,2982,childrens hosptial,,2004,Poland,Poland,,,,Osteomyelitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The goal of this study is to provide genome information of a specific clinical MRSA isolate WCUH29, which has been widely used in antibacterial drug discovery.",collected_by:Yinduo Ji,,,,,,,Osteomyelitis,,,,,,,,,,,,,,99.51,0.08,Bone and Joint Infections,Osteomyelitis,Other,Bone and Joint Infections-Osteomyelitis NHP,46503.2259,Parabacteroides merdae strain CL06T03C08,CL06T03C08,Parabacteroides merdae,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451193,46503,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289315.1,"CP072229,CP072230",,Brigham & Women's Hospital,PacBio Sequel,266x,FALCON-Unzip v. 1.2.0,1,1,2,4799513,45.432358,4315,3955,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.62,0.38,,,Gastrointestinal,- HP,46503.2290,Parabacteroides merdae strain BFG-280,BFG-280,Parabacteroides merdae,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546958,46503,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091365.1,CP081901,,National Institute of Allergy and Infectious Disease,PacBio Sequel,375x,HGAP/FALCON v. v. 6.0,1,0,1,4559639,45.413727,4023,3621,blood,,1989,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.62,0.13,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,46506.2050,Bacteroides stercoris strain BFG-121,BFG-121,Bacteroides stercoris,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547175,46506,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091485.1,CP081913,,National Institute of Allergy and Infectious Disease,PacBio Sequel,457x,Canu v. v. 1.6,1,0,1,3883826,45.835884,3469,3142,missing,,,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.26,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.11103,Acinetobacter baumannii strain ATCC 17978,ATCC 17978,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14217790,470,,,,"MLST.Acinetobacter_baumannii_1.357,MLST.Acinetobacter_baumannii_2.2",,ATCC:17978,,2020-03-07T00:00:00Z,,PRJNA609015,GCA_011067065.1,"CP049363,CP049364,CP049365",,Korea university,PacBio,231.08x,Pacbio v. 20K,1,2,3,3884786,39.03309,3693,,urine,,2011-01-01,South Korea,South Korea: Seoul,,,,,,,Susceptible,Computational Prediction,,,,,,,,,pathogen,collected_by:National Culture Collection,,,,,,,None,,,,,,,,,,,,,,99.54,0.71,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,470.11367,Acinetobacter baumannii strain DT-Ab022,DT-Ab022,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14308866,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-11T00:00:00Z,,PRJNA612123,GCA_012272735.1,"CP050907,CP050908,CP050909,CP050910",,"Beijing Ditan Hospital, Capital Medical University",nanopore,100X,Unicycler v. v0.4.8,1,3,4,4229508,39.113842,4112,4013,sputum,,2017,China,China: Beijing,,,,infection,,,Resistant,Computational Prediction,,,,,,,,,This research is to study the genomic variations associated with the virulence of Acinetobacter baumannii.,"collected_by:Beijing Ditan Hospital, Capital Medical University",,,,,,,infection,,,,,,,,,,,,,,99.98,0.61,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11368,Acinetobacter baumannii strain DT-Ab007,DT-Ab007,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14308853,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-11T00:00:00Z,,PRJNA612123,GCA_012272775.1,"CP050914,CP050915",,"Beijing Ditan Hospital, Capital Medical University",nanopore,100X,Unicycler v. v0.4.8,1,1,2,4050436,38.99259,3889,3801,sputum,,2017,China,China: Beijing,,,,infection,,,Resistant,Computational Prediction,,,,,,,,,This research is to study the genomic variations associated with the virulence of Acinetobacter baumannii.,"collected_by:Beijing Ditan Hospital, Capital Medical University",,,,,,,infection,,,,,,,,,,,,,,99.59,0.61,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11369,Acinetobacter baumannii strain DT-Ab020,DT-Ab020,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14308864,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-11T00:00:00Z,,PRJNA612123,GCA_012272755.1,"CP050911,CP050912,CP050913",,"Beijing Ditan Hospital, Capital Medical University",nanopore,100X,Unicycler v. v0.4.8,1,2,3,4147490,39.038647,4019,3920,sputum,,2018,China,China: Beijing,,,,infection,,,Resistant,Computational Prediction,,,,,,,,,This research is to study the genomic variations associated with the virulence of Acinetobacter baumannii.,"collected_by:Beijing Ditan Hospital, Capital Medical University",,,,,,,infection,,,,,,,,,,,,,,99.98,0.63,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11370,Acinetobacter baumannii strain DT-Ab003,DT-Ab003,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14308849,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-11T00:00:00Z,,PRJNA612123,GCA_012272795.1,"CP050916,CP050917,CP050918",,"Beijing Ditan Hospital, Capital Medical University",nanopore,100X,Unicycler v. v0.4.8,1,2,3,4095067,39.02271,3941,3853,stethoscope,,2017,China,China: Beijing,,,,infection,,,Susceptible,Computational Prediction,,,,,,,,,This research is to study the genomic variations associated with the virulence of Acinetobacter baumannii.,"collected_by:Beijing Ditan Hospital, Capital Medical University",,,,,,,infection,,,,,,,,,,,,,,99.98,0.63,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.11474,Acinetobacter baumannii strain DT-Ab057,DT-Ab057,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14308892,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-11T00:00:00Z,,PRJNA612123,GCA_012272715.1,"CP050904,CP050905,CP050906",,"Beijing Ditan Hospital, Capital Medical University",nanopore,100X,Unicycler v. v0.4.8,1,2,3,4118119,39.11827,3978,3878,bronchoalveolar lavage fluid,,2019,China,China: Beijing,,,,infection,,,Susceptible,Computational Prediction,,,,,,,,,This research is to study the genomic variations associated with the virulence of Acinetobacter baumannii.,"collected_by:Beijing Ditan Hospital, Capital Medical University",,,,,,,infection,,,,,,,,,,,,,,99.98,0.61,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11476,Acinetobacter baumannii strain Ab-B004d-c,Ab-B004d-c,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14667515,470,,,,MLST.Acinetobacter_baumannii_2.103,,,,2020-05-05T00:00:00Z,,PRJNA473419,GCA_012931645.1,"CP051875,CP051876,CP051877,CP051878,CP051879",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; MGI DNBSEQ,1570x,Unicycler v. V 0.4.8,1,4,5,4159123,39.051212,4026,3950,sputum,,2016-01,Ghana,Ghana: Sekondi-Takoradi,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11477,Acinetobacter baumannii strain Ab-D10a-a,Ab-D10a-a,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14667516,470,,,,MLST.Acinetobacter_baumannii_2.103,,,,2020-05-05T00:00:00Z,,PRJNA473419,GCA_012931625.1,"CP051869,CP051870,CP051871,CP051872,CP051873,CP051874",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; MGI DNBSEQ,1469x,Unicycler v. V 0.4.8; Flye v. V 2.6,1,5,6,4174734,39.042286,4069,3971,cerebrospinal fluid,,2016-03,Ghana,Ghana: Sekondi-Takoradi,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,470.11478,Acinetobacter baumannii strain Ab-C102,Ab-C102,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14667518,470,,,,,,,,2020-05-05T00:00:00Z,,PRJNA473419,GCA_012931605.1,"CP051862,CP051863,CP051864,CP051865",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; MGI DNBSEQ,1339x,Unicycler v. V 0.4.8; Flye v. V 2.6,1,3,4,3940086,39.128586,3818,3660,blood,,2016-01,Ghana,Ghana: Sekondi-Takoradi,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.11479,Acinetobacter baumannii strain Ab-C63,Ab-C63,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14667517,470,,,,"MLST.Acinetobacter_baumannii_1.339,MLST.Acinetobacter_baumannii_2.107",,,,2020-05-05T00:00:00Z,,PRJNA473419,GCA_012931665.1,"CP051866,CP051867,CP051868",,Tokyo Medical and Dental University,Illumina MiSeq; Oxford Nanopore MiniION,531x,Unicycler v. V 0.4.8,1,2,3,3965881,39.048977,3794,3709,sputum,,2016-02,Ghana,Ghana: Sekondi-Takoradi,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.11480,Acinetobacter baumannii strain VB82,VB82,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14409516,470,,,,"MLST.Acinetobacter_baumannii_1.691,MLST.Acinetobacter_baumannii_2.25",,,,2020-04-30T00:00:00Z,,PRJNA613562,GCA_012934905.1,"CP050385,CP050386,CP050387",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,144.972x,Canu v. 1.7; Unicycler v. 0.4.6,1,2,3,4433724,39.08739,4337,4224,blood,,2019,India,India,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.11482,Acinetobacter baumannii strain VB11737,VB11737,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14410107,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.369",,,,2020-04-30T00:00:00Z,,PRJNA613587,GCA_012934965.1,"CP050400,CP050392,CP050393,CP050394,CP050395,CP050396,CP050397,CP050398,CP050399",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,72.7314339x,Canu v. 1.7; Unicycler v. 0.4.6,1,8,9,4071841,38.888798,3935,3828,blood,,2019,India,India,,,,Blood stream,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,Blood stream,,,,,,,,,,,,,,99.98,0.63,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.11483,Acinetobacter baumannii strain VB2181,VB2181,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14410138,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2020-04-30T00:00:00Z,,PRJNA613593,GCA_012934985.1,"CP050401,CP050402",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,298.2667525x,Canu v. 1.7; Unicycler v. 0.4.6,1,1,2,3952539,39.09669,3799,3703,sputum,,2019,India,India,,,,Pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,Pneumonia,,,,,,,,,,,,,,99.98,0.65,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11484,Acinetobacter baumannii strain VB723,VB723,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14409813,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-30T00:00:00Z,,PRJNA613583,GCA_012934945.1,"CP050390,CP050391",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,153.2519685x,Canu v. 1.7; Unicycler v. 0.4.6,1,1,2,3928362,39.07168,3777,3680,blood,,2019,India,India,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii Carbapenem Resistant,collected_by:Christian Medical College,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,0.63,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.11485,Acinetobacter baumannii strain VB2486,VB2486,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14414761,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2020-04-30T00:00:00Z,,PRJNA613679,GCA_012935005.1,"CP050403,CP050404,CP050405,CP050406,CP050407,CP050408,CP050409",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,143.3824081x,Canu v. 1.7; Unicycler v. 0.4.6,1,6,7,4277869,39.18465,4179,4061,sputum,,2019,India,India,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.14,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11486,Acinetobacter baumannii strain VB2200,VB2200,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14415334,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-30T00:00:00Z,,PRJNA613683,GCA_012935025.1,"CP050421,CP050422,CP050423",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,116.2229039x,Canu v. 1.7; Unicycler v. 0.4.6,1,2,3,4015124,38.968758,3862,3762,sputum,,2019,India,India,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,pneumonia,,,,,,,,,,,,,,99.98,0.63,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11487,Acinetobacter baumannii strain PM1912235,PM1912235,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14420246,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-30T00:00:00Z,,PRJNA613820,GCA_012935045.1,"CP050410,CP050411",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,190.0930695x,Canu v. 1.7; Unicycler v. 0.4.6,1,1,2,3935172,39.03212,3745,3657,pus,,2019,India,India,,,,Wound infection,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:AIIMS Jai Prakash Narayan Apex Trauma Center,,,,,,,Wound infection,,,,,,,,,,,,,,99.98,0.63,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,470.11488,Acinetobacter baumannii strain PM192696,PM192696,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14420253,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2020-04-30T00:00:00Z,,PRJNA613821,GCA_012935065.1,"CP050412,CP050413,CP050414",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,208.9182034x,Canu v. 1.7; Unicycler v. 0.4.6,1,2,3,4045545,38.909492,3908,3804,sputum,,2019,India,India,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:AIIMS Jai Prakash Narayan Apex Trauma Center,,,,,,,pneumonia,,,,,,,,,,,,,,99.98,0.63,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11489,Acinetobacter baumannii strain PM193665,PM193665,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14420254,470,,,,MLST.Acinetobacter_baumannii_2.10,,,,2020-04-30T00:00:00Z,,PRJNA613824,GCA_012935085.1,"CP050415,CP050416,CP050417,CP050418,CP050419,CP050420",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,180.6371398x,Canu v. 1.7; Unicycler v. 0.4.6,1,5,6,4180241,39.03519,4107,4013,pus,,2019,India,India,,,,Wound infection,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:AIIMS Jai Prakash Narayan Apex Trauma Center,,,,,,,Wound infection,,,,,,,,,,,,,,100,0.68,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,470.11490,Acinetobacter baumannii strain PM194188,PM194188,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14420255,470,,,,MLST.Acinetobacter_baumannii_2.10,,,,2020-04-30T00:00:00Z,,PRJNA613825,GCA_012935105.1,"CP050425,CP050426,CP050427,CP050428,CP050429,CP050430,CP050431",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,157.1399209x,Canu v. 1.7; Unicycler v. 0.4.6,1,6,7,4192382,39.03411,4125,4027,bal,,2019,India,India,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:AIIMS Jai Prakash Narayan Apex Trauma Center,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.68,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11491,Acinetobacter baumannii strain VB2139,VB2139,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14414747,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-30T00:00:00Z,,PRJNA613675,GCA_012935165.1,"CP050526,CP050527,CP050528,CP050529",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,116.6082566x,Canu v. 1.7; Unicycler v. 0.4.6,1,3,4,4017923,38.98126,3863,3762,sputum,,2019,India,India,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,pneumonia,,,,,,,,,,,,,,99.98,0.63,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11492,Acinetobacter baumannii strain PM194229,PM194229,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14422682,470,,,,"MLST.Acinetobacter_baumannii_2.10,MLST.Acinetobacter_baumannii_1.447",,,,2020-04-30T00:00:00Z,,PRJNA613957,GCA_012935125.1,"CP050432,CP050433,CP050434,CP050435",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,185.349194x,Canu v. 1.7; Unicycler v. 0.4.6,1,3,4,4133398,39.066742,4019,3933,bal,,2019,India,India,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:AIIMS Jai Prakash Narayan Apex Trauma Center,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.55,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11493,Acinetobacter baumannii strain VB7036,VB7036,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14410111,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-04-30T00:00:00Z,,PRJNA613590,GCA_012935145.1,"CP050523,CP050524,CP050525",,Christian Medical College,Illumina HiSeq; Oxford Nanopore GridION,114.7808656x,Canu v. 1.7; Unicycler v. 0.4.6,1,2,3,4062974,39.119003,3928,3829,blood,,2019,India,India,,,,Bloodstream infection,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,1.53,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.11494,Acinetobacter baumannii strain VB2107,VB2107,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14414778,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2020-04-30T00:00:00Z,,PRJNA613681,GCA_012935185.1,"CP051474,CP051475,CP051476,CP051477",,Christian Medical College,Oxford Nanopore GridION; Illumina HiSeq,115.39842x,Canu v. 1.7; Unicycler v. 0.4.6,1,3,4,4020539,39.042824,3920,3822,sputum,,2019,India,India,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Carbapenem and colistin Resistant Acinetobacter baumannii,collected_by:Christian Medical College,,,,,,,pneumonia,,,,,,,,,,,,,,99.93,0.63,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11567,Acinetobacter baumannii strain ATCC 19606,ATCC 19606,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12389466,470,,,,"MLST.Acinetobacter_baumannii_1.931,MLST.Acinetobacter_baumannii_2.52",,ATCC:19606,,2019-10-16T00:00:00Z,,PRJNA557095,GCA_009035845.1,"CP045110,CP045108,CP045109",,University of Technology Sydney,Illumina MiSeq; Oxford Nanopore MiniION,100.0x,Hybrid assembly v. July-31,1,2,3,3999136,39.148457,3802,3731,urine,,1948,USA,"USA:Georgia, Atlanta",,,,UTI,,,Susceptible,Computational Prediction,,,,,,,,,This project involves analysis of antibiotic resistance in Acinetobacter baumannii,,,,,,,,UTI,,,,,,,,,,,,,,99.63,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,470.11568,Acinetobacter baumannii strain MS14413,MS14413,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14859482,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-06-09T00:00:00Z,,PRJNA631347,GCA_013305465.1,CP054302,,The University of Queensland,PacBio RSII,219.0x,CANU v. 1.3,1,0,1,4082498,39.035095,3914,3846,urine (catheter),,2016,Australia,Australia: Brisbane,,,,,,,Susceptible,Computational Prediction,,,,,,,,,This project contains the complete Acinetobacter baumannii genome MS14413 relating to the study of an outbreak of carbapenem-resistant Acinetobacter baumannii (CR-Ab) and other associated gram-negative bacilli in a Brisbane ICU and burns ward between 2016-2018.,,,,,,,,N/A,,,,,,,,,,,,,,99.78,2.53,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,470.11610,Acinetobacter baumannii strain TP1,TP1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15344688,470,,,,MLST.Acinetobacter_baumannii_2.570,,,,2020-07-17T00:00:00Z,28807909,PRJNA641163,GCA_013376855.2,"CP056784,CP056785",,Texas A&M University,Illumina MiSeq; Oxford Nanopore,92.0x,Unicycler v. 0.4.7,1,1,2,3873271,39.0486,3660,3566,human clinical sample,,2016,USA,USA,,,,bacterial infectious disease,,,Susceptible,Computational Prediction,,,,,,,,,"This is the complete genome sequence of Acinetobacter baumannii strain TP1, which is a pan-resistant clinical isolate",collected_by:Sharon L. Reed,,,,,,,bacterial infectious disease,,,,,,,,,,,,,,99.98,0.45,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.11611,Acinetobacter baumannii strain A1429,A1429,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13565236,470,,,,MLST.Acinetobacter_baumannii_2.108,,,,2020-06-30T00:00:00Z,,PRJNA595709,GCA_013377175.1,"CP046898,CP046901,CP046900,CP046899",,"Sir Run Run Shaw Hospital, College of medicine,Zhejiang University",Oxford Nanopore; Illumina,200.0x,CLC NGS Cell v. 12,1,3,4,4161887,38.98919,4039,3911,secretion,,2010-10,China,China:Guangdong,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,complete genome of OXA-24-producing Acinetobacter baumannii A1429,collected_by:Yan Chen,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.11617,Acinetobacter baumannii strain ATCC BAA1605,ATCC BAA1605,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15437745,470,,,,MLST.Acinetobacter_baumannii_2.1,,ATCC:BAA1605,,2020-07-13T00:00:00Z,,PRJNA643902,GCA_013403505.1,"CP058625,CP058626",,Monash University Malaysia,Oxford Nanopore; Illumina MiSeq,45.0x,Flye v. 2.7; Pilon v. 1.23,1,1,2,4047902,39.228348,4058,3807,sputum,,2006-06-30,Canada,Canada,,,,Pneumoniae,,,Susceptible,Computational Prediction,,,,,,,,,A multidrug-resistant (MDR) strain A. baumannii (A. baumannii ATCC BAA1605) used as a model organism to investigate the antimicrobial resistance determinants and bacterial defence systems.,collected_by:American Type Culture Collection,,,,,,,Pneumoniae,,,,,,,,,,,,,,99.73,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.11618,Acinetobacter baumannii strain DT0544C,DT0544C,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14833494,470,,,,MLST.Acinetobacter_baumannii_2.374,,,,2020-07-15T00:00:00Z,,PRJNA630392,GCA_013416255.1,"CP053215,CP053216,CP053217",,University of Bergen,Oxford Nanopore; Illumina HiSeq,259.3x,unicycler v. April-2020,1,2,3,3971708,39.105316,3837,3762,missing,,2017-10,Tanzania,Tanzania: Dar es Salaam,,,neonate,Blood stream infection,,,Susceptible,Computational Prediction,,,,,,,,,Molecular characterization of NDM-1 from Acinetobacter baumannii,collected_by:Dr Joel Manyahi,,,,,,,Blood stream infection,,,,,,clinical sample,,,,,,,,100,0.55,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,470.11619,Acinetobacter baumannii strain DT01139C,DT01139C,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14833556,470,,,,MLST.Acinetobacter_baumannii_2.239,,,,2020-07-15T00:00:00Z,,PRJNA630397,GCA_013416275.1,"CP053218,CP053219,CP053220,CP053221",,University of Bergen,Oxford Nanopore; Illumina HiSeq,65.15x,unicycler v. April-2020,1,3,4,3869649,39.02191,3773,3675,missing,,2017-11,Tanzania,Tanzania: Dar es Salaam,,,,Blood stream infection,,,Susceptible,Computational Prediction,,,,,,,,,moleculra characterisation of NDM-1 from Acinetobacter baumannii,collected_by:Dr Joel Manyahi,,,,,,,Blood stream infection,,,,,,clinical sample,,,,,,,,100,0.14,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,470.12061,Acinetobacter baumannii strain B2 strain DETAB-P2,DETAB-P2,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13884837,470,,,,MLST.Acinetobacter_baumannii_2.138,,,,2020-08-27T00:00:00Z,,PRJNA602169,GCA_014322245.1,"CP047973,CP047974,CP047975,CP047976",,Zhejiang University,Oxford Nanopore MiniION; Illumina HiSeq,200.0x,Unicycler v. 0.4.8,1,3,4,4105826,39.208603,4004,3846,rectal swab,,2019-08-06,China,China:Hangzhou,,,,cholecystitis,,,Susceptible,Computational Prediction,,,,,,,,,The complete genome sequence of Acinetobacter baumannii B2,collected_by:Yunsong Yu,,,,,,,cholecystitis,,,,,,,,,,,,,,100,0.14,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,470.12194,Acinetobacter baumannii strain CFSAN093710,CFSAN093710,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12391854,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-09-23T00:00:00Z,,PRJNA300270,GCA_014705805.1,"CP061514,CP061515,CP061516",,Walter Reed Army Institute of Research,PacBio,945x,HGAP v. 4,1,2,3,4179318,39.1606,4088,3970,sterile body site,,2005,USA,USA:DC,,,,,,,Susceptible,Computational Prediction,,,,,C,,,,Acinetobacter baumannii clinical isolates collected within the United States military healthcare system,collected_by:United States Army,,,,,,,missing,,,,,,,,,,,,,,99.98,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12196,Acinetobacter baumannii strain CFSAN093706,CFSAN093706,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12391535,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-09-23T00:00:00Z,,PRJNA300270,GCA_014705845.1,"CP061523,CP061524",,Walter Reed Army Institute of Research,PacBio,293x,HGAP v. 4,1,1,2,4095679,39.280983,3972,3861,blood,,2005,USA,USA:DC,,,,,,,Susceptible,Computational Prediction,,,,,C,,,,Acinetobacter baumannii clinical isolates collected within the United States military healthcare system,collected_by:United States Army,,,,,,,missing,,,,,,,,,,,,,,99.98,0.62,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.12197,Acinetobacter baumannii strain CFSAN093707,CFSAN093707,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12391534,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-09-23T00:00:00Z,,PRJNA300270,GCA_014705865.1,"CP061521,CP061522",,Walter Reed Army Institute of Research,PacBio,307x,HGAP v. 4,1,1,2,4049006,39.248844,3903,3801,sterile body site,,2004,USA,USA:DC,,,,,,,Susceptible,Computational Prediction,,,,,C,,,,Acinetobacter baumannii clinical isolates collected within the United States military healthcare system,collected_by:United States Army,,,,,,,missing,,,,,,,,,,,,,,99.98,0.61,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12198,Acinetobacter baumannii strain CFSAN093708,CFSAN093708,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12391536,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-09-23T00:00:00Z,,PRJNA300270,GCA_014705885.1,"CP061519,CP061520",,Walter Reed Army Institute of Research,PacBio,326x,HGAP v. 4,1,1,2,4148158,39.282112,4040,3931,wound,,2004,USA,USA:DC,,,,,,,Resistant,Computational Prediction,,,,,C,,,,Acinetobacter baumannii clinical isolates collected within the United States military healthcare system,collected_by:United States Army,,,,,,,missing,,,,,,,,,,,,,,99.98,0.62,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.12207,Acinetobacter baumannii strain AC1633,AC1633,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15574350,470,,,,MLST.Acinetobacter_baumannii_2.126,,,,2020-10-09T00:00:00Z,,PRJNA647049,GCA_014874575.1,"CP059300,CP059301,CP059303,CP059304,CP059302",,Universiti Sultan Zainal Abidin,Illumina HiSeq; PacBio RSII,256.0x,SPAdes v. 3.11.1,1,4,5,4566577,38.88545,4431,4315,blood,,2016,Malaysia,Malaysia: Kuala Terengganu,,female,60,hospital-acquired pneumonia,,host_disease_outcome:death,Susceptible,Computational Prediction,,,,,,,,,"Complete genome sequence of NDM-1-producing multidrug-resistant Acinetobacter baumannii AC1633 from Terengganu, Malaysia",collected_by:Hospital Sultanah Nur Zahirah (HSNZ),,,,,,,hospital-acquired pneumonia,,death,,,,,,,,,,,,100,0.41,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,470.12233,Acinetobacter baumannii strain SD,SD,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN16574826,470,,,,,,,,2020-11-12T00:00:00Z,,PRJNA672694,GCA_015356075.1,"CP064292,CP064293,CP064294",,NASA,Oxford Nanopore MinION,13x,Flye v. 2.6; Racon v. 1.4.7; Medaka v.,1,2,3,3943569,38.97173,5524,,clinical isolate,,2018-07-06,USA,USA: San Diego,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"A rapid assembly protocol was leveraged to quickly generate genome assemblies of prokaryotes using minimal computational resources. These assemblies were passed to a pipeline to assemble genome-scale metabolic network reconstructions of these microorganisms. The genomes include a validation reference (E. coli K12 MG1655 BOP27) and three (3) clinical isolates of pathogenic bacteria (Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus faecium).",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,95.44,0.02,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12445,Acinetobacter baumannii strain abA1,abA1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15778733,470,,,,,,,,2020-12-03T00:00:00Z,,PRJNA640471,GCA_015732435.1,CP060732,,Peking University People's Hospital,Illumina NextSeq; PacBio,130x,SPAdes v. 3.13.0,1,0,1,4103762,39.04281,3956,,bronchial,,2018-04-23,China,China:Beijing,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Evolution mechanism of Acinetobacter baumannii,collected_by:Henan Li,,,,,,,Bacteremia,,,,,,,,,,,,,,99.98,0.63,Bloodstream Infections,Bacteremia,Respiratory Tract,Bloodstream Infections-Bacteremia HP,470.12446,Acinetobacter baumannii strain AbBAS-1,AbBAS-1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15676490,470,,,,"MLST.Acinetobacter_baumannii_1.957,MLST.Acinetobacter_baumannii_2.85",,,,2020-12-08T00:00:00Z,,PRJNA649662,GCA_015832155.1,"CP065392,CP065393,CP065394",,University of Cologne,Oxford Nanopore MinION; Illumina MiSeq,26.0x,ONT assembly and Illumina polishing,1,2,3,4086434,38.963898,4271,3837,clinical,,2019,Spain,Spain: Bilbao,,,,dysouria,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii strain AbBAS-1,collected_by:Lucia Gallego,,,,,,,dysouria,,,,,,,,,,,,,,99.68,2.42,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12447,Acinetobacter baumannii strain TP2,TP2,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15735522,470,,,,MLST.Acinetobacter_baumannii_2.570,,,,2020-12-09T00:00:00Z,28807909,PRJNA641163,GCA_015870765.1,"CP060011,CP060012",,Texas A&M University,Illumina MiSeq; Oxford Nanopore,104.0x,Unicycler v. v. 0.4.7,1,1,2,3879291,39.0724,3676,3572,human clinical sample,,2016,USA,USA,,,,bacterial infectious disease,,,Susceptible,Computational Prediction,,,,,,,,,"This is the complete genome sequence of Acinetobacter baumannii strain TP1, which is a pan-resistant clinical isolate",collected_by:Sharon L. Reed,,,,,,,bacterial infectious disease,,,,,,,,,,,,,,99.98,0.45,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12448,Acinetobacter baumannii strain TP3,TP3,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15738014,470,,,,MLST.Acinetobacter_baumannii_2.570,,,,2020-12-09T00:00:00Z,28807909,PRJNA641163,GCA_015870965.1,"CP060013,CP060014",,Texas A&M University,Illumina MiSeq; Oxford Nanopore,96.0x,Unicycler v. v. 0.4.7,1,1,2,3880463,39.071625,3666,3571,human clinical sample,,2016,USA,USA,,,,bacterial infectious disease,,,Susceptible,Computational Prediction,,,,,,,,,"This is the complete genome sequence of Acinetobacter baumannii strain TP1, which is a pan-resistant clinical isolate",collected_by:Sharon L. Reed,,,,,,,bacterial infectious disease,,,,,,,,,,,,,,99.59,0.06,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.12449,Acinetobacter baumannii strain ATCC 17961 strain not applicable,not applicable,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN08687991,470,,,,MLST.Acinetobacter_baumannii_2.438,,ATCC:17961,,2020-12-10T00:00:00Z,,PRJNA437968,GCA_015910475.1,"CP065432,CP065433,CP065434",,East Carolina University,Illumina MiSeq; Oxford Nanopore MinION,188.0x,Unicycler v. v0.4.3,1,2,3,4032448,39.05422,3873,3783,blood,,2016-05,USA,USA,,,,Acinetobacter infections,,,Susceptible,Computational Prediction,,,,,,,,,"Acinetobacter baumannii is an opportunistic bacterial pathogen that can become a persistent contaminant in the healthcare environment. However, after extended culture in the laboratory some strains of A. baumannii lose the ability to survive on dry surfaces. The goal of this project is to identify the genetic changes that occur in these drying-sensitive variants, which will provide a greater understanding of how these bacteria can survive in the clinical setting.",collected_by:ATCC,,,,,,,Acinetobacter infections,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.12473,Acinetobacter baumannii strain G20AB007,G20AB007,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17073615,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-12-24T00:00:00Z,,PRJNA684975,GCA_016350085.1,"CP066237,CP066238,CP066239,CP066240",,Yonsei University College of medicine,PacBio Sequel,236x,other: SMRTLink v. v9.0,1,3,4,4090092,38.964672,3983,3864,blood,recovered from ICU patients within two months,2020-04-11,South Korea,South Korea: Hwaseong-si,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome of the colistin-resistant A. bauamanii blood isolates recovered from ICU patients within two months.,collected_by:Hallym University Dongtan Sacred Heart Hospital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,0.66,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.12474,Acinetobacter baumannii strain G20AB011,G20AB011,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17073618,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-12-24T00:00:00Z,,PRJNA684975,GCA_016350005.1,"CP066229,CP066230,CP066231",,Yonsei University College of medicine,PacBio Sequel,172x,other: SMRTLink v. v9.0,1,2,3,4073824,38.953007,3959,3858,blood,recovered from ICU patients within two months,2020-05-16,South Korea,South Korea: Hwaseong-si,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome of the colistin-resistant A. bauamanii blood isolates recovered from ICU patients within two months.,collected_by:Hallym University Dongtan Sacred Heart Hospital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,0.61,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.12475,Acinetobacter baumannii strain G20AB010,G20AB010,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17073617,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.191",,,,2020-12-24T00:00:00Z,,PRJNA684975,GCA_016350065.1,"CP066232,CP066233,CP066234",,Yonsei University College of medicine,PacBio Sequel,152x,other: SMRTLink v. v9.0,1,2,3,4088238,38.96867,4001,3872,blood,recovered from ICU patients within two months,2020-05-08,South Korea,South Korea: Hwaseong-si,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome of the colistin-resistant A. bauamanii blood isolates recovered from ICU patients within two months.,collected_by:Hallym University Dongtan Sacred Heart Hospital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,0.61,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.12476,Acinetobacter baumannii strain G20AB009,G20AB009,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17073616,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2020-12-24T00:00:00Z,,PRJNA684975,GCA_016350105.1,"CP066235,CP066236",,Yonsei University College of medicine,PacBio Sequel,168x,other: SMRTLink v. v9.0,1,1,2,4076358,38.96331,3957,3855,blood,recovered from ICU patients within two months,2020-05-07,South Korea,South Korea: Hwaseong-si,,,,Bloodstream infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome of the colistin-resistant A. bauamanii blood isolates recovered from ICU patients within two months.,collected_by:Hallym University Dongtan Sacred Heart Hospital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.98,0.61,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.12896,Acinetobacter baumannii strain AbCTX13,AbCTX13,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15501316,470,,,,"MLST.Acinetobacter_baumannii_2.78,MLST.Acinetobacter_baumannii_1.1104",,,,2021-02-11T00:00:00Z,,PRJNA644570,GCA_016864915.1,"CP059729,CP059731,CP059730",,CHRU Besancon,Oxford Nanopore MiniION,100.0x,Flye v. 2.7.1,1,2,3,4092873,39.09899,4085,3831,peritoneal fluid,,2017-08,France,France: Nice,,,,Peritoneal fluid infection,,,Susceptible,Computational Prediction,,,,,,,,,Genetic environment of blaCTX-M-115,collected_by:French NRC,,,,,,,Peritoneal fluid infection,,,,,,,,,,,,,,99.86,0.27,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,470.13017,Acinetobacter baumannii strain AB5075-VUB-itrA::ISAba13,AB5075-VUB-itrA::ISAba13,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17898088,470,,,,"MLST.Acinetobacter_baumannii_2.1,MLST.Acinetobacter_baumannii_1.945",,,,2021-02-23T00:00:00Z,,PRJNA701627,GCA_016919525.1,"CP070358,CP070359,CP070360,CP070361",,Vrije Universiteit Brussel,Oxford Nanopore MinION; Illumina,400x,Flye v. 2.8.2,1,3,4,4119488,39.00298,4124,3889,,,2008,Belgium,Belgium,,,,,,,Susceptible,Computational Prediction,,,,,,,,,A new mechanism that controls the virulence and resistance of A. baumannii.,sample_type:single cell,,,,,,,,,,,,,derived from AB5075,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13018,Acinetobacter baumannii strain AB5075-VUB,AB5075-VUB,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17898087,470,,,,"MLST.Acinetobacter_baumannii_2.1,MLST.Acinetobacter_baumannii_1.945",,,,2021-02-23T00:00:00Z,,PRJNA701627,GCA_016919505.1,"CP070362,CP070363,CP070364,CP070365",,Vrije Universiteit Brussel,Oxford Nanopore MinION; Illumina,400x,Flye v. 2.8.2,1,3,4,4097902,38.98424,4041,3862,,,2008,Belgium,Belgium,,,,,,,Susceptible,Computational Prediction,,,,,,,,,A new mechanism that controls the virulence and resistance of A. baumannii.,sample_type:single cell,,,,,,,,,,,,,derived from AB5075,,,,,,,,99.73,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13030,Acinetobacter baumannii strain 2018HLJAB1,2018HLJAB1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15538696,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-03-01T00:00:00Z,,PRJNA646312,GCA_017098265.1,CP059358,,Peking University People's Hospital,PacBio RSII,280.6457x,HGAP v. 4,1,0,1,3939099,38.96863,3773,3651,pus,,2018-06-26,China,"China: Ha'erbin, Heilongjiang",,,,not collected,,,Resistant,Computational Prediction,,,,,,,,,whole genome sequencing and assembly of Acinetobacter baumannii,collected_by:not collected,,,,,,,not collected,,,,,,,,,,,,,,99.9,0.63,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.13072,Acinetobacter baumannii strain A73,A73,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13831468,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-03-16T00:00:00Z,,PRJNA600804,GCA_017357845.1,CP047930,,Gumushane University,Illumina NovaSeq,0.736032370549x,CLC NGS Cell v. 23.12.2019,1,0,1,4335699,39.304085,3926,,sputum,,2017-12-07,Turkey,Turkey,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,"The whole genome sequencing for antibiotic resistant bacteria offers the potential to provide fast, consistent and accurate estimates of resistance phenotype for a strain.",collected_by:FDH,,,,,,,pneumonia,,,,,,,,,,,,,,99.73,0.61,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.13079,Acinetobacter baumannii strain GIMC5510:ABT-897-17,GIMC5510:ABT-897-17,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18276099,470,,,,MLST.Acinetobacter_baumannii_2.45,,,,2021-03-25T00:00:00Z,,PRJNA561493,GCA_017584105.1,"CP071919,CP071920",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq,36.0x,CLC Genomics Workbench v. 20; SPAdes,1,1,2,3801155,39.12764,3641,3546,blood,,2017,Russia,Russia:Moscow,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,Main pathogens causing nosocomial infections in intensive care units.,collected_by:Zhukhovitsky VG,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.13236,Acinetobacter baumannii strain KSK1,KSK1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18396008,470,,,,"MLST.Acinetobacter_baumannii_2.622,MLST.Acinetobacter_baumannii_1.865",,,,2021-03-30T00:00:00Z,,PRJNA716155,GCA_017639875.1,"CP072122,CP072123,CP072124,CP072125,CP072126",,Christian Medical College,Illumina; Oxford Nanopore,100.09x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,4357638,38.95576,4227,4113,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,99.45,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13237,Acinetobacter baumannii strain KSK6,KSK6,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452234,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716781,GCA_017723975.1,"CP072270,CP072271,CP072272,CP072273,CP072274",,Christian Medical College,Illumina GAII; Oxford Nanopore,134.84x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4390748,38.972584,4258,4137,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13238,Acinetobacter baumannii strain KSK7,KSK7,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452334,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716782,GCA_017724115.1,"CP072275,CP072276,CP072277,CP072278,CP072279",,Christian Medical College,Illumina; Oxford Nanopore,104.97x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4395318,38.97008,4261,4139,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13239,Acinetobacter baumannii strain KSK10,KSK10,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452342,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716785,GCA_017724155.1,"CP072280,CP072281,CP072282,CP072283,CP072284",,Christian Medical College,Illumina; Oxford Nanopore,167.89x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4415810,38.95503,4288,4161,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13240,Acinetobacter baumannii strain KSK11,KSK11,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452659,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716790,GCA_017724195.1,"CP072285,CP072286,CP072287,CP072288,CP072289",,Christian Medical College,Illumina; Oxford Nanopore,202.38x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4398999,38.96543,4266,4145,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13241,Acinetobacter baumannii strain KSK20,KSK20,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452712,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716802,GCA_017726555.1,"CP072300,CP072301,CP072302,CP072303,CP072304",,Christian Medical College,Illumina; Oxford Nanopore,168.41x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4395402,38.96877,4266,4138,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13242,Acinetobacter baumannii strain KSK19,KSK19,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452699,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716795,GCA_017726495.1,"CP072295,CP072296,CP072297,CP072298,CP072299",,Christian Medical College,Illumina; Oxford Nanopore,237.27x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4414631,38.955894,4281,4160,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13243,Acinetobacter baumannii strain KSK18,KSK18,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452698,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-03T00:00:00Z,,PRJNA716794,GCA_017724215.1,"CP072290,CP072291,CP072292,CP072293,CP072294",,Christian Medical College,Illumina; Oxford Nanopore,190.93x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4395318,38.96999,4262,4139,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13244,Acinetobacter baumannii strain KSK Sensitive,KSK Sensitive,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18452713,470,,,,MLST.Acinetobacter_baumannii_2.374,,,,2021-04-03T00:00:00Z,,PRJNA716803,GCA_017726575.1,"CP072305,CP072306,CP072307",,Christian Medical College,Illumina; Oxford Nanopore,187.09x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,2,3,3903094,39.022556,3731,3648,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Susceptible,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13245,Acinetobacter baumannii strain KSK2,KSK2,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18451305,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2021-04-04T00:00:00Z,,PRJNA716762,GCA_017742855.1,"CP072398,CP072399,CP072400,CP072401,CP072402",,Christian Medical College,Illumina; Oxford Nanopore,133.14x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,4400277,38.965206,4270,4146,respiratory specimen,,2020,India,India: New Delhi,,,,Respiratory Infection,,,Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Acinetobacter baumannii,collected_by:Jawaharlal Nehru University,,,,,,,Respiratory Infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.13246,Acinetobacter baumannii strain DETAB-E227,DETAB-E227,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18498586,470,,,,,,,,2021-04-05T00:00:00Z,,PRJNA716893,GCA_017753625.1,"CP072526,CP072527,CP072528,CP072529",,Zhejiang University School of Medicine,Illumina; Oxford Nanopore,150x,Unicycler v. v. 0.4.8,1,3,4,3966915,39.200386,3805,3703,environmental swab and another susceptible a,"isolated from environmental swab and another susceptible A. baumannii from patient's swab in the intensive care unit of a hospital in Hangzhou, China",2019-09-24,China,China:Hangzhou,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"To describe the characterisation of a carbapenem-resistant A. baumannii isolated from environmental swab and another susceptible A. baumannii from patient's swab in the intensive care unit of a hospital in Hangzhou, China.",sample_type:environment swab,,,,,,,,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13377,Acinetobacter baumannii strain DETAB-P39,DETAB-P39,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18498587,470,,,,"MLST.Acinetobacter_baumannii_2.221,MLST.Acinetobacter_baumannii_1.351",,,,2021-04-23T00:00:00Z,,PRJNA716893,GCA_018135585.1,"CP073060,CP073061",,Zhejiang University School of Medicine,Illumina; Oxford Nanopore,150x,Unicycler v. v. 0.4.8,1,1,2,3968176,38.89064,3766,3663,patient,"isolated from environmental swab and another susceptible A. baumannii from patient's swab in the intensive care unit of a hospital in Hangzhou, China",2019-08-27,China,China:Hangzhou,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"To describe the characterisation of a carbapenem-resistant A. baumannii isolated from environmental swab and another susceptible A. baumannii from patient's swab in the intensive care unit of a hospital in Hangzhou, China.",sample_type:Nasogastric tube,,,,,,,,,,,,,,,,,,,,,99.86,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13448,Acinetobacter baumannii strain DD520,DD520,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19073634,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-05-24T00:00:00Z,,PRJNA728250,GCA_018454385.1,"CP075321,CP075322",,Hohai University,Illumina HiSeq; Oxford Nanopore,120x,SMRT Link v. 5.1.0; Unicycle v. 1.0,1,1,2,4084562,39.202488,3921,3820,hospital,,2021-01-12,China,"China: Lushi County, Sanmenxia City, Henan Provience",,male,66 years old,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,"Acinetobacter baumannii and Klebsiella pneumoniae were isolated, and the two strains are both multidrug resistant, incuding carbopenems. Therefore, their genomes were sequenced to characterize the drug resistance genes.",collected_by:Dao-Feng Zhang,,,,,,,pneumonia,,,,,,,,,,,,,,99.59,0.61,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,470.13450,Acinetobacter baumannii strain A24,A24,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14572873,470,,,,"MLST.Acinetobacter_baumannii_1.218,MLST.Acinetobacter_baumannii_2.2",,,,2021-05-26T00:00:00Z,,PRJNA624262,GCA_018502545.1,CP051262,,Artvin Coruh University,Illumina NovaSeq; Illumina NovaSeq,338.0x,CLC NGS Cell v. 18.03.2020,1,0,1,4335682,39.312157,3937,,missing,,2017-07-27,Turkey,Turkey,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Acinetobacter baumannii often causes hospital infections and outbreaks. Strains resistant to antibiotics cause difficulties in treatment. It is a promising technique for whole genome sequencing (WGS), strain typing and outbreak research.",collected_by:Trabzon Fatih State Hospital Micobiology Laboratory,,,,,,,missing,,,,,,,,,,,,,,99.71,0.61,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13567,Acinetobacter baumannii strain Cl415,Cl415,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN18202092,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-06-04T00:00:00Z,,PRJNA607827,GCA_018604365.1,"CP071763,CP071764,CP071765",,University of Technology Sydney,Illumina; Oxford Nanopore MinION,100.0x,Hybrid v. 1.0,1,2,3,3976267,38.98921,3807,3746,blood,,2017,Lebanon,Lebanon,,,,Blood infection,,,Resistant,Computational Prediction,,,,,,,,,Environmental Acinetobacter baumannii genome sequencing and assembly,collected_by:Marwan Osman,,,,,,,Blood infection,,,,,,,,,,,,,,98.8,0.63,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.13609,Acinetobacter baumannii strain D4,D4,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13874777,470,,,,"MLST.Acinetobacter_baumannii_2.25,MLST.Acinetobacter_baumannii_1.364",,,,2021-06-09T00:00:00Z,,PRJNA602058,GCA_018808925.1,"CP048849,CP048851,CP048850",,University of Technology Sydney,Illumina; Oxford Nanopore MiniION,100.0x,Hybrid assembly v. 4.0,1,2,3,4308668,39.281956,4133,4071,wound,,2006,Australia,Australia: Sydney,,,,wound infection,,,Susceptible,Computational Prediction,,,,,,,,,"Complete genome sequence an Australian Acinetobacter baumannii ST25 isolate, strain D4",collected_by:Peter Huntington,,,,,,,wound infection,,,,,,,,,,,,,,100,0.41,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,470.13610,Acinetobacter baumannii strain D46,D46,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN13874778,470,,,,"MLST.Acinetobacter_baumannii_1.229,MLST.Acinetobacter_baumannii_2.25",,,,2021-06-10T00:00:00Z,,PRJNA602058,GCA_018831125.1,"CP048131,CP048132,CP048133,CP048134,CP048135",,University of Technology Sydney,Illumina; Oxford Nanopore MiniION,100.0x,Hybrid assembly v. 4.0,1,4,5,4324770,38.908913,4160,4102,mid stream urine,,2010,Australia,Australia: Sydney,,,,UTI,,,Resistant,Computational Prediction,,,,,,,,,"Complete genome sequence an Australian Acinetobacter baumannii ST25 isolate, strain D4",collected_by:Peter Huntington,,,,,,,UTI,,,,,,,,,,,,,,100,0.14,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,470.13809,Acinetobacter baumannii strain Ab17978VU,Ab17978VU,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN20011940,470,,,,"MLST.Acinetobacter_baumannii_2.437,MLST.Acinetobacter_baumannii_1.112",,,,2021-07-22T00:00:00Z,,PRJNA743285,GCA_019316885.1,CP079213,,Vanderbilt University Medical Center,PacBio,271x,Flye v. 2.4.2,1,0,1,3524474,38.977818,3351,,,,2018,USA,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Two variants of A. baumannii 17978 differ based on the presence of a 44 kb accessory locus. This locus is present in one variant (Ab 17978 UN) but absent in the other (Ab 17978 VU). The two variants exhibit differential pathogenicity in vivo and in vitro.,sample_type:laboratory stock;collected_by:VUMC,,,,,,,,,,,,,variant of ATCC:17978,,,,,,,,90.41,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13810,Acinetobacter baumannii strain Ab17978UN,Ab17978UN,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN20011941,470,,,,"MLST.Acinetobacter_baumannii_1.112,MLST.Acinetobacter_baumannii_2.437",,,,2021-07-22T00:00:00Z,,PRJNA743285,GCA_019316825.1,CP079212,,Vanderbilt University Medical Center,PacBio,219x,Flye v. 2.4.2,1,0,1,3914414,38.9679,3698,,,,2018,USA,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Two variants of A. baumannii 17978 differ based on the presence of a 44 kb accessory locus. This locus is present in one variant (Ab 17978 UN) but absent in the other (Ab 17978 VU). The two variants exhibit differential pathogenicity in vivo and in vitro.,sample_type:laboratory stock;collected_by:University of Nebraska,,,,,,,,,,,,,variant of ATCC:17978,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13903,Acinetobacter baumannii strain K7-3RD,K7-3RD,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN20295817,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-07-27T00:00:00Z,,PRJNA747803,GCA_019356095.1,CP079945,,Peking University People's Hospital,PacBio RSII,190.0x,HGAP v. 4,1,0,1,3941155,38.989685,3753,3653,blood,,2019-02-22,China,China:Beijing,,,,Bacteremia,,,Resistant,Computational Prediction,,,,,,,,,Multiple A. baumannii strains consecutively from K patient diagnosed with A. baumannii infection and treated with tigecycline to observe and analyze the progression of tigecycline resistance within the host.,collected_by:not collected,,,,,,,Bacteremia,,,,,,,,,,,,,,99.98,0.63,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.13904,Acinetobacter baumannii strain B10,B10,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN20295790,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2021-07-27T00:00:00Z,,PRJNA747802,GCA_019356075.1,CP079942,,Peking University People's Hospital,PacBio RSII,202.0x,HGAP v. 4,1,0,1,4010274,39.066658,3877,3753,sputum,,2018-12-13,China,China: Beijing,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Multiple A. baumannii strains consecutively from B patient diagnosed with A. baumannii infection and treated with tigecycline to observe and analyze the progression of tigecycline resistance within the host.,collected_by:not collected,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0.63,Bloodstream Infections,Bacteremia,Respiratory Tract,Bloodstream Infections-Bacteremia HP,470.13908,Acinetobacter baumannii strain CNRAB1,CNRAB1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19988021,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.1114",,,,2021-08-06T00:00:00Z,,PRJNA741866,GCA_019457735.1,"CP078099,CP078100",,Inserm,Illumina; Oxford Nanopore MinION,100.0x,Unicycler v. v0.4.8-beta,1,1,2,4099987,39.194763,3949,3846,unknown,,2012-02,France,France,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Extensive genetic exchanges through horizontal gene transfers (HGT) are one of the driving forces behind the spread of antibiotic resistance among Acinetobacter isolates. In this work, we aimed to evaluate the contribution of natural transformation, a mechanism of HGT commonly found in A. baumannii clinical isolates, in the spread of the carbapenems resistance. An effective and rapid transfer of the carbapenems resistance genetic determinants was possible between different Acinetobacter spp. in experimental conditions that mimic a bacterial community. Furthermore, the naturally transformable A. nosocomialis strain M2 was able to acquire the carbapenems resistance in only a few hours at a high frequency, through natural transformation of a high-quality DNA released by a donor strain. Genetic analyses of transformants showed that natural transformation fostered the acquisition of large DNA fragment containing mobile genetic elements such as the Tn2006 or even a large resistance island named AbaR4 that carry the blaOXA-23 gene conferring the resistance to carbapenems.",collected_by:CNR Antibioresistance,,,,,,,Unknown,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.13909,Acinetobacter baumannii strain MRSN 56,MRSN 56,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19955388,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2021-08-08T00:00:00Z,,PRJNA742487,GCA_019458485.1,"CP080452,CP080453,CP080454,CP080455,CP080456",,The University of Sydney,Illumina MiSeq; Oxford Nanopore MinION,60.0x,Unicycler v. 0.4.0,1,4,5,4053664,39.171104,3912,3798,hip,recovered from human tissue of a U.S,2010-06,USA,USA,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,MRSN 56 was recovered from human tissue of a U.S. service member following a serious injury in Afghanistan. Isolates uploaded as part of the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) - a department within the Bacterial Diseases Branch at the Walter Reed Army Institute of Research (WRAIR) - surveillance of human pathogens within the U.S. military healthcare system. Sequential passage under tobramycin selective pressure to examine the mechanism of tobramycin resistance.,,,,,,,,Infection,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,470.13910,Acinetobacter baumannii strain OCU_Ac18 strain OCU Ac18,OCU Ac18,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMD00330123,470,,,,,,,,2021-07-07T00:00:00Z,,PRJDB11827,GCA_019703285.1,"AP024802,AP024803,AP024812,AP024813,AP024804,AP024805,AP024806,AP024807,AP024808,AP024809,AP024810,AP024811",,"Department of Bacteriology, Graduate School of Medicine, Osaka City University",Illumina Novaseq; ONT Flongle,100x,Unicycler v. 0.4.8,1,11,12,4071981,39.214523,4013,3869,,,2016-07-16,Japan,Japan,,,,,,,Susceptible,Computational Prediction,Negative,Coccobacilli,No,Mesophilic,37,Aerobic,Multiple,,"We study to understand antibiotic resistance mechanisms of Acinetobacter species. This genus shows drug-resistance to various kinds of antibiotics. To acquire some biochemical findings, we attempt to perform whole genome sequencing of Acinetobacter clinical isolates, and compare the sequences to those of related species.",biomaterial_provider:Osaka City University Hospital,human,blood vessels,venous blood,https://www.atcc.org/Products/All/19606.aspx#culturemethod,Comparison of clinical isolates sequences .,,,,,,,,,,,free living,human,,,,100,0.37,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.14055,Acinetobacter baumannii strain AB43,AB43,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21028540,470,,,,MLST.Acinetobacter_baumannii_2.132,,,,2021-09-15T00:00:00Z,,PRJNA732167,GCA_019997865.1,"CP083181,CP083182",,Yangzhou University,Illumina,20x,SOAPdenovo v. 3.0,1,1,2,3959115,39.132103,3901,3750,sputum,isolated from sputum,2017-07-05,China,China:Yangzhou,,,,Bacterial Pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,The strain was isolated from sputum. It has complete I-Fb CRISPR-Cas system and it belongs to sensitive group.,collected_by:Affiliated Hospital of Yangzhou University,,,,,,,Bacterial Pneumonia,,,,,,,,,,,,,,100,0.27,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.14058,Acinetobacter baumannii strain Cl300,Cl300,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21240079,470,,,,"MLST.Acinetobacter_baumannii_1.1089,MLST.Acinetobacter_baumannii_2.85",,,,2021-09-24T00:00:00Z,,PRJNA607827,GCA_020132105.1,"CP082952,CP082953",,University of Technology Sydney,Illumina; Oxford Nanopore,100.0x,Unicycler v. 1.0,1,1,2,4016584,38.894344,3861,3749,tracheal aspirate,,2015,Lebanon,Lebanon,,,,Lung infection,,,Susceptible,Computational Prediction,,,,,,,,,Environmental Acinetobacter baumannii genome sequencing and assembly,collected_by:Ahmad Al Atrouni,,,,,,,Lung infection,,,,,,,,,,,,,,100,0.41,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,470.15463,Acinetobacter baumannii MRSN 58,MRSN 58,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN23416908,470,,,,"MLST.Acinetobacter_baumannii_2.1,MLST.Acinetobacter_baumannii_1.231",,,,2022-01-16T00:00:00Z,,PRJNA742487,GCA_021484905.1,CP090607,,,Illumina MiSeq; Oxford Nanopore MinION,88.0x,Unicycler v. 0.4.0,1,0,1,4264976,39.747494,4282,4168,hip,,2010-06,USA,USA,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,,,,,,,,,Infection,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,470.15825,Acinetobacter baumannii AB1343,AB1343,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN24425237,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-01-10T00:00:00Z,,PRJNA792449,GCA_021398135.1,"CP090182,CP090183",,,Illumina HiSeq; PacBio,309.54x,HGAP v. 4; FALCON v. 0.3,1,1,2,3921614,39.057617,3791,3691,sputum,,2021-10,China,China: Zhuhai,,,,severe pulmonary infection,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Yi Zhang,,,,,,,severe pulmonary infection,,,,,,,,,,,,,,99.98,0.63,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.15875,Acinetobacter baumannii AB329,AB329,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN22170067,470,,,,MLST.Acinetobacter_baumannii_2.98,,,,2022-02-01T00:00:00Z,,PRJNA769700,GCA_021730415.1,"CP091452,CP091453,CP091454",,,Illumina MiSeq; PacBio RS,57.0x,Unicycler v. 0.4.8,3,0,3,4038879,38.882473,3928,,sputum,,2015,Thailand,Thailand:Eastern region hospital,,,,Nosocomial infection,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:Eastern region hospital,,,,,,,Nosocomial infection,,,,,,,,,,,,,,99.98,0.66,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,470.15886,Acinetobacter baumannii AB79,AB79,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN15097904,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-01-24T00:00:00Z,,PRJNA637186,GCA_021559695.1,"CP054416,CP054417",,,Oxford Nanopore MiniION; Illumina NovaSeq,569.0x,Unicycler v. v0.4.8,1,1,2,4072472,39.053185,3948,3850,eye secretion,,2018-11,China,China,,,,fever,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Chen Qiong,,,,,,,fever,,,,,,,,,,,,,,99.98,0.63,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,470.15984,Acinetobacter baumannii MRSN57,MRSN57,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN23416895,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2022-01-26T00:00:00Z,,PRJNA742487,GCA_021609965.1,CP091172,,,Illumina HiSeq; Oxford Nanopore MinION,44.0x,Unicycler v. 0.4.0,1,0,1,4125503,39.54907,4051,3945,hip,,2010-06,USA,USA,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,,,,,,,,,Infection,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,470.16135,Acinetobacter baumannii AB2877,AB2877,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN26082895,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-03-01T00:00:00Z,,PRJNA808263,GCA_022429585.1,"CP092485,CP092486",,,Illumina HiSeq; PacBio,373.7x,HGAP v. 4; FALCON v. 0.3,1,1,2,3895757,39.049305,3726,3621,sputum,,2021-10-12,China,China: Zhuhai,,,,pnuemonia,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Wei Wang,,,,,,,pnuemonia,,,,,,,,,,,,,,99.98,0.63,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.16193,Acinetobacter baumannii AB5116,AB5116,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN25087978,470,,,,"MLST.Acinetobacter_baumannii_2.40,MLST.Acinetobacter_baumannii_1.373",,,,2022-03-17T00:00:00Z,,PRJNA798598,GCA_022605145.1,CP091173,,,PacBio,118.0x,HGAP v. Assembly.3,1,0,1,3907300,38.99808,3794,3663,sputum,,2013,China,China: Xi'an,,,,"Pneumonia, Bacterial",,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Lei Han,,,,,,,"Pneumonia, Bacterial",,,,,,,,,,,,,,99.86,0.18,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.17303,Acinetobacter baumannii NY5301,NY5301,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN26814682,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-03-30T00:00:00Z,,PRJNA818046,GCA_022759565.1,"CP094283,CP094284,CP094285,CP094286,CP094287",,,PacBio RSII,100.0x,HGAP v. V3.0,1,4,5,4230647,38.980515,4176,4070,ascites,,2018,China,China:Hebei,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:a teaching hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Abdominal,Respiratory Diseases-Pneumonia HP,470.17369,Acinetobacter baumannii AB4451,AB4451,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27303889,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-04-12T00:00:00Z,,PRJNA823506,GCA_022921035.1,"CP095091,CP095092",,,Illumina HiSeq; PacBio,157.55x,HGAP v. 4; FALCON v. 0.3,1,1,2,3932611,39.057995,3799,3702,sputum,,2022-01,China,China:Zhuhai,,,,infection,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.17906,Acinetobacter baumannii F46,F46,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27770840,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.423",,,,2022-05-03T00:00:00Z,,PRJNA812061,GCA_023221535.1,CP096575,,,Illumina MiSeq; PacBio RS,45.0x,Unicycler v. 0.4.0,1,0,1,3878974,39.167625,3744,3629,clinical,,1999,Australia,Australia: Brisbane,,,,,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Royal Brisbane Hospital,,,,,,,Unknown,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.18121,Acinetobacter baumannii 280820,280820,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN28980502,470,,,,"MLST.Acinetobacter_baumannii_1.955,MLST.Acinetobacter_baumannii_2.126",,,,2022-06-20T00:00:00Z,,PRJNA848080,GCA_023809625.1,"CP098791,CP098792,CP098793,CP098794",,,Illumina HiSeq; Oxford Nanopore,107.65x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,3,4,4302277,39.045628,4130,4019,blood,,2020,India,India:Mumbai,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:P. D. Hinduja National Hospital & Medical Research Centre,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.18122,Acinetobacter baumannii VB280821,VB280821,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN28981486,470,,,,MLST.Acinetobacter_baumannii_2.126,,,,2022-06-20T00:00:00Z,,PRJNA848083,GCA_023809705.1,"CP098795,CP098796,CP098797,CP098798,CP098799,CP098800",,,Illumina HiSeq; Oxford Nanopore,80.56x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,5,6,4340713,39.050682,4181,4066,blood,,2020,India,India:Mumbai,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:P. D. Hinduja National Hospital & Medical Research Centre,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.18288,Acinetobacter baumannii UC24371,UC24371,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356554,470,,,,"MLST.Acinetobacter_baumannii_1.235,MLST.Acinetobacter_baumannii_2.162",,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024138435.1,"CP076804,CP076805,CP076806",,,Oxford Nanopore; Illumina HiSeq,44x,Unicycler v. 1.0,1,2,3,4103459,38.896282,3948,3855,endotracheal aspirate,,2011,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.18289,Acinetobacter baumannii UC20804,UC20804,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356540,470,,,,MLST.Acinetobacter_baumannii_2.109,,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024139015.1,"CP076807,CP076808,CP076809,CP076810,CP076811",,,Oxford Nanopore; Illumina HiSeq,48x,Unicycler v. 1.0,1,4,5,4045532,39.119453,3971,3832,peritoneal abcess,,2010,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,470.18290,Acinetobacter baumannii UC23022,UC23022,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356535,470,,,,MLST.Acinetobacter_baumannii_2.79,,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024139035.1,"CP076812,CP076813",,,Oxford Nanopore; Illumina HiSeq,47x,Unicycler v. 1.0,1,1,2,4215060,38.993206,4144,4016,blood culture,,2011,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.18291,Acinetobacter baumannii UC21460,UC21460,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356533,470,,,,MLST.Acinetobacter_baumannii_2.318,,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024139055.1,"CP076814,CP076815,CP076816",,,Oxford Nanopore; Illumina HiSeq,63x,Unicycler v. 1.0,1,2,3,3983183,39.208744,3809,3726,tissue,,2010,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.18292,Acinetobacter baumannii UC24137,UC24137,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356530,470,,,,"MLST.Acinetobacter_baumannii_2.15,MLST.Acinetobacter_baumannii_1.225",,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024139075.1,"CP076817,CP076818,CP076819,CP076820",,,Oxford Nanopore; Illumina HiSeq,49x,Unicycler v. 1.0,1,3,4,4093548,39.13825,3952,3847,sacrum ulcer,,2011,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.18293,Acinetobacter baumannii UC22850,UC22850,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356522,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024139095.1,"CP076821,CP076822",,,Oxford Nanopore; Illumina HiSeq,40x,Unicycler v. 1.0,1,1,2,4144160,39.24822,4063,3971,catheter tip,,2011,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,470.18364,Acinetobacter baumannii UC25604,UC25604,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN19356555,470,,,,"MLST.Acinetobacter_baumannii_2.162,MLST.Acinetobacter_baumannii_1.235",,,,2022-07-05T00:00:00Z,,PRJNA731249,GCA_024271825.1,"CP076801,CP076802,CP076803",,,Oxford Nanopore; Illumina HiSeq,48x,Unicycler v. 1.0,1,2,3,3951013,38.978687,3772,3699,peritoneal liquid,,2012,Chile,Chile:Santiago,,,,A. baumannii infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:not known,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,470.18408,Acinetobacter baumannii Cl107,Cl107,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN28871714,470,,,,MLST.Acinetobacter_baumannii_2.25,genotype:ST25,,,2022-07-25T00:00:00Z,,PRJNA846279,GCA_024426665.1,"CP098521,CP098522",,,Illumina MiSeq; Oxford Nanopore MinION,50.0x,Unicycler v. v0.4.7,1,1,2,4254951,39.058712,4093,3993,urine,,2012,Lebanon,Lebanon,,male,80,urine infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:LMSE - Lebanese University,,,,,,,urine infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,470.18518,Acinetobacter baumannii CCBH31270,CCBH31270,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN29981016,470,,,,,genotype:ST374,,,2022-08-02T00:00:00Z,,PRJNA677881,GCA_024505645.1,"CP101887,CP101886",,,Illumina MiniSeq,81.0x,bcftools v. 1.7,1,1,2,4048886,38.99065,3868,3768,tracheal secretion,,2021-03-31,Brazil,Brazil,,female,,Nosocomial infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:LAPIH,,,,,,,Nosocomial infection,,,,,,,,,,,,,,100,0,Nosocomial Infections,Other Nosocomial Infections,Respiratory Tract,Nosocomial Infections-Other Nosocomial Infections HP,470.18563,Acinetobacter baumannii AB3927,AB3927,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN30308647,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-08-22T00:00:00Z,,PRJNA869490,GCA_024730805.1,"CP102831,CP102832",,,Illumina HiSeq; PacBio,90.25x,FALCON v. 0.3; HGAP v. 4; Canu v. 0.7,1,1,2,3996011,39.046566,3889,3793,bronchoalveolar lavage fluid,,2022-03,China,China: Zhuhai,,,,infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.18676,Acinetobacter baumannii strain AB2369,AB2369,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN30472217,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-08-31T00:00:00Z,,PRJNA872864,GCA_024800505.1,"CP103413,CP103414,CP103415",,Jinan University,Illumina HiSeq; PacBio,689.66x,HGAP v. 4; FALCON v. 0.3,1,2,3,3943705,39.045288,3811,3717,sputum,,2022-03,China,China:Zhuhai,,,,pulmonary infection,,,Susceptible,Computational Prediction,,,,,,,,,"Acinetobacter baumannii strain AB2369 chromosome, complete sequence",collected_by:Yongcong Zhan,,,,,,,pulmonary infection,,,,,,,,,,,,,,99.98,0.63,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.18709,Acinetobacter baumannii strain 2021CK-01409,2021CK-01409,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21924071,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258745.1,"CP104340,CP104341,CP104339",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,Flye v. 2.9; Medaka v. 1.6.1,1,2,3,4471416,39.103966,4487,4338,wound/abscess,,2021-08-30,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.18710,Acinetobacter baumannii strain 2021CK-01408,2021CK-01408,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21924070,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258705.1,"CP104335,CP104338,CP104334,CP104337,CP104336",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,Flye v. 2.9; Medaka v. 1.6.1,1,4,5,4473711,39.088577,4508,4337,blood,,2021-08-30,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.18711,Acinetobacter baumannii strain 2021CK-01332,2021CK-01332,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21493859,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258785.1,"CP104347,CP104346,CP104345",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,Flye v. 2.9; Medaka v. 1.6.1,1,2,3,4484114,39.10699,4496,4351,wound/abscess,,2021-08-09,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.18712,Acinetobacter baumannii strain 2021CK-01300,2021CK-01300,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21493827,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258765.1,"CP104342,CP104343,CP104344",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,Unicycler v. 0.5.0,1,2,3,4437104,39.08011,4400,4273,wound/abscess,,2021-08-02,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.18713,Acinetobacter baumannii strain 2021CK-01335,2021CK-01335,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21493862,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258845.1,"CP104351,CP104352,CP104353",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,unicycler v. 0.5.0,1,2,3,4438104,39.07878,4398,4276,wound/abscess,,2021-08-09,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.18714,Acinetobacter baumannii strain 2021CK-01333,2021CK-01333,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21493860,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025258805.1,"CP104350,CP104349,CP104348",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,flye v. 2.9; medaka v. 1.6.1,1,2,3,4477086,39.094112,4481,4340,sputum,,2021-08-10,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,99.86,0.13,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.18719,Acinetobacter baumannii strain 2021CK-01407,2021CK-01407,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN21924069,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2022-09-22T00:00:00Z,,PRJNA812595,GCA_025369955.1,"CP104449,CP104448,CP104447",,Utah Public Health Laboratory Infectious Disease submission group,Oxford Nanopore GridION,20.0x,Flye v. 2.9; Medaka v. 1.6.1,1,2,3,4478641,39.088776,4487,4346,sputum,,2021-08-23,,USA,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.18809,Acinetobacter baumannii 37662,37662,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11997569,470,,,,"MLST.Acinetobacter_baumannii_1.381,MLST.Acinetobacter_baumannii_2.2",,,,2022-09-26T00:00:00Z,,PRJNA548006,GCA_025402915.1,"CP104751,CP104752",,,Illumina HiSeq; Oxford Nanopore MinION,50.0x,Unicycler v. v0.4.8,1,1,2,4048081,39.123352,3904,3809,sputum of an intensive care unit patient at meizhou people's hospital,,2012-05,China,China: Meizhou,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.18847,Acinetobacter baumannii AB2369,AB2369,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN30472217,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-08-31T00:00:00Z,,PRJNA872864,GCA_024800505.1,"CP103413,CP103414,CP103415",,,Illumina HiSeq; PacBio,689.66x,HGAP v. 4; FALCON v. 0.3,1,2,3,3943705,39.045288,3811,3717,sputum,,2022-03,China,China:Zhuhai,,,,pulmonary infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Yongcong Zhan,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,470.19159,Acinetobacter baumannii ARC6851,ARC6851,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31037892,470,,,,"MLST.Acinetobacter_baumannii_1.441,MLST.Acinetobacter_baumannii_2.1",,,,2022-10-13T00:00:00Z,,PRJNA884703,GCA_025677625.1,"CP106943,CP106944,CP106945,CP106946",,,Illumina NextSeq; Oxford Nanopore,216.0x,Unicycler v. MAR-2022,1,3,4,4053623,38.970444,3941,3842,urine,,2017,Greece,Greece,,,,UTI,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Entasis Therapeutic Inc.,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,470.19164,Acinetobacter baumannii GIMC5507:ABT-52Ts18,GIMC5507:ABT-52Ts18,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31029727,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-10-18T00:00:00Z,,PRJNA561493,GCA_025732095.1,"CP107032,CP107033",,,Illumina,98.0x,SPAdes v. 3.13.0; CLC genomic,1,1,2,3987693,39.09585,3875,3787,upper respiratory tract,,2019,Russia,Russia:Moscow,,,,Sepsis and the multiorgan failure,,,Resistant,Computational Method,,,,,,,,,,collected_by:Dolzhikova IV,,,,,,,Sepsis and the multiorgan failure,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.19165,Acinetobacter baumannii GIMC5509:ABT-52Ts19,GIMC5509:ABT-52Ts19,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31029726,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2022-10-18T00:00:00Z,,PRJNA561493,GCA_025732115.1,"CP107034,CP107035",,,Illumina,151.0x,SPAdes v. 3.13.0; CLC genomic,1,1,2,3905337,39.002064,3763,3678,upper respiratory tract,,2019,Russia,Russia:Moscow,,,,Sepsis and the multiorgan failure,,,Resistant,Computational Method,,,,,,,,,,collected_by:Dolzhikova IV,,,,,,,Sepsis and the multiorgan failure,,,,,,,,,,,,,,99.8,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.19232,Acinetobacter baumannii RBH2,RBH2,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31494247,470,,,,MLST.Acinetobacter_baumannii_2.111,,,,2022-11-08T00:00:00Z,,PRJNA893697,GCA_026062515.1,"CP110462,CP110463,CP110464,CP110465,CP110466,CP110467,CP110468",,,Oxford Nanopore MinION; Illumina HiSeq,100.0x,Unicycler v. 0.4.0,1,6,7,4422798,38.86146,4296,4165,unknown,,1999,Australia,Australia: Brisbane,,,,Unknown infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Unknow,,,,,,,Unknown infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.19662,Acinetobacter baumannii AOR07-BL,AOR07-BL,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN30248452,470,,,,MLST.Acinetobacter_baumannii_2.40,,,,2022-12-22T00:00:00Z,,PRJNA868510,,"CP102762,CP102763,CP102764,CP102765",,,PacBio Sequel,1146.0x,HGAP v. 4,1,3,4,4081411,39.05843,3893,,blood,,2020-07,China,China:Beijing,,,,bloodstream infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Henan Li,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,470.19696,Acinetobacter baumannii WU_164,WU_164,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10411726,470,,,,MLST.Acinetobacter_baumannii_2.499,,,,2023-01-03T00:00:00Z,,PRJNA505177,,CP033876,,,PacBio RS,247.0x,HGAP v. 2018-11-08,1,0,1,3977231,38.906643,3863,3768,urine,,08-Aug-2018,USA,USA,,,,UTI,,,Resistant,Computational Method,,,,,,,,,,collected_by:Juan Calix,,,,,,,UTI,,,,,,,,,,,,,,100,1.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,470.19955,Acinetobacter baumannii OCU-Ac19,OCU-Ac19,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMD00258369,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-01-14T00:00:00Z,,PRJDB10765,,"AP025531,AP025532,AP025533,AP025534",,,Illumina NovaSeq; ONT MinION,1075x,"unicycler v. 0.4.8, Pilon v. 1.24",1,3,4,4030153,38.9112,3869,3790,,,2016-08-20,Japan,Japan:Osaka,,,,,,,Susceptible,Computational Method,,,,,,,,,,biomaterial_provider:Osaka City University Hospital,not applicable,Pharyngeal secretions,not applicable,https://www.atcc.org/Products/All/19606.aspx#culturemethod,Whole genome sequence of clinical-isolate Acinetobacter baumannii,,,,,,,,,,,free living,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20024,Acinetobacter baumannii WM98,WM98,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN32770956,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2023-01-29T00:00:00Z,,PRJNA812075,,"CP116387,CP116389,CP116388",,,Illumina MiSeq; Oxford Nanopore MinION,73.0x,Unicycler v. 0.4.0,1,2,3,4129776,39.17283,3994,3904,wound,,1998,Australia,Australia: Sydney,,,,Disease,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Jon Iredell,,,,,,,Disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.20488,Acinetobacter baumannii AB322,AB322,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN33446574,470,,,,"MLST.Acinetobacter_baumannii_1.231,MLST.Acinetobacter_baumannii_2.1",,,,2023-03-13T00:00:00Z,,PRJNA938819,,"CP119232,CP119235,CP119234,CP119233",,,Oxford Nanopore MinION,85.0x,Flye v. Oct 2022,1,3,4,4182912,39.21952,4715,4067,blood,,2001,Taiwan,Taiwan,,,,Bacteremia,,,Resistant,Computational Method,,,,,,,,,,collected_by:Jiunn-Jong Wu,,,,,,,Bacteremia,,,,,,,,,,,,,,100,4,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.20765,Acinetobacter baumannii AB5075,AB5075,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31681936,470,,,,"MLST.Acinetobacter_baumannii_1.945,MLST.Acinetobacter_baumannii_2.1",,,,2023-02-10T00:00:00Z,,PRJNA900181,,"CP113078,CP113079",,,PacBio RSII,529.45x,HGAP v. 3.0,1,1,2,4078713,39.0113,3984,3894,"tibia, osteotomy elitis",,2008,USA,USA,,,,,,,Susceptible,Computational Method,,,,,,,,,,,,,,,,,unknown,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20810,Acinetobacter baumannii GIMC5508:ABT-3Ts65,GIMC5508:ABT-3Ts65,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12618963,470,,,,MLST.Acinetobacter_baumannii_2.2,genotype:ST348,,,2023-04-04T00:00:00Z,,PRJNA561493,,"CP120894,CP120895,CP120896",,,Illumina,169.0x,SPAdes v. 3.13.0; CLC Genomics,1,2,3,3923869,38.969032,3750,3671,sputum,,2016-02-11,Russia,Russia:Moscow,,,,Polysegmental community acquired pneumonia,,,Resistant,Computational Method,,,,,,,,,,collected_by:Fedosova NF,,,,,,,Polysegmental community acquired pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,470.20941,Acinetobacter baumannii MAB25,MAB25,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010264,470,,,,"MLST.Acinetobacter_baumannii_1.499,MLST.Acinetobacter_baumannii_2.158",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121591,CP121592,CP121594,CP121593",,,Illumina MiSeq; Oxford Nanopore MiniION,126x,EToKi v. 1.2,1,3,4,4049593,38.880917,3881,3800,not collected,,2019,Saudi Arabia,Saudi Arabia:Medina,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20942,Acinetobacter baumannii RAB9,RAB9,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010269,470,,,,MLST.Acinetobacter_baumannii_1.218,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121557,CP121558,CP121559",,,Illumina MiSeq; Oxford Nanopore MiniION,213x,EToKi v. 1.2,1,2,3,3875126,39.026783,3741,3627,not collected,,2018,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20943,Acinetobacter baumannii RAB55,RAB55,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010278,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121577,CP121578",,,Illumina MiSeq; Oxford Nanopore MiniION,369x,EToKi v. 1.2,1,1,2,3990945,39.047718,3878,3775,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20944,Acinetobacter baumannii RAB94,RAB94,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010289,470,,,,"MLST.Acinetobacter_baumannii_1.684,MLST.Acinetobacter_baumannii_2.570",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121563,CP121564,CP121566,CP121565",,,Illumina MiSeq; Oxford Nanopore MiniION,142x,EToKi v. 1.2,1,3,4,4069304,38.912796,3945,3831,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20945,Acinetobacter baumannii RAB57,RAB57,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010279,470,,,,"MLST.Acinetobacter_baumannii_1.234,MLST.Acinetobacter_baumannii_2.164",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121570,CP121571,CP121572,CP121573,CP121574,CP121575,CP121576",,,Illumina MiSeq; Oxford Nanopore MiniION,192x,EToKi v. 1.2,1,6,7,4045430,38.874702,4044,3883,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20946,Acinetobacter baumannii RAB97,RAB97,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010291,470,,,,,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121560,CP121561,CP121562",,,Illumina MiSeq; Oxford Nanopore MiniION,462x,EToKi v. 1.2,1,2,3,4081823,38.952545,4048,3929,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20947,Acinetobacter baumannii RAB30,RAB30,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010274,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.557",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121581,CP121582",,,Illumina MiSeq; Oxford Nanopore MiniION,91x,EToKi v. 1.2,1,1,2,4039319,38.961937,3920,3816,not collected,,2018,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20948,Acinetobacter baumannii RAB53,RAB53,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010277,470,,,,MLST.Acinetobacter_baumannii_1.451,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121579,CP121580",,,Illumina MiSeq; Oxford Nanopore MiniION,207x,EToKi v. 1.2,1,1,2,4005937,39.012222,3884,3770,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20949,Acinetobacter baumannii JAB186,JAB186,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010238,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121609,CP121611,CP121610",,,Illumina MiSeq; Oxford Nanopore MiniION,179x,EToKi v. 1.2,1,2,3,4166040,39.043602,4051,3946,not collected,,2019,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20950,Acinetobacter baumannii RAB11,RAB11,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010270,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121586,CP121587",,,Illumina MiSeq; Oxford Nanopore MiniION,172x,EToKi v. 1.2,1,1,2,4004900,39.03803,3902,3791,not collected,,2018,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20951,Acinetobacter baumannii JAB144,JAB144,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010231,470,,,,"MLST.Acinetobacter_baumannii_1.195,MLST.Acinetobacter_baumannii_2.2",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121625,CP121628,CP121627,CP121626",,,Illumina MiSeq; Oxford Nanopore MiniION,190x,EToKi v. 1.2,1,3,4,4192037,39.05025,4124,4003,not collected,,2019,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20952,Acinetobacter baumannii MAB17,MAB17,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010258,470,,,,"MLST.Acinetobacter_baumannii_2.570,MLST.Acinetobacter_baumannii_1.684",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121595,CP121596,CP121597",,,Illumina MiSeq; Oxford Nanopore MiniION,434x,EToKi v. 1.2,1,2,3,4041635,38.9119,3903,3795,not collected,,2019,Saudi Arabia,Saudi Arabia:Medina,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20953,Acinetobacter baumannii MAB16,MAB16,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010257,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121604,CP121605,CP121606,CP121607,CP121608",,,Illumina MiSeq; Oxford Nanopore MiniION,110x,EToKi v. 1.2,1,4,5,4163054,38.967976,4089,3953,not collected,,2019,Saudi Arabia,Saudi Arabia:Medina,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20954,Acinetobacter baumannii JAB77,JAB77,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010219,470,,,,"MLST.Acinetobacter_baumannii_1.218,MLST.Acinetobacter_baumannii_2.2",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121598,CP121599,CP121600",,,Illumina MiSeq; Oxford Nanopore MiniION,131x,EToKi v. 1.2,1,2,3,4113458,38.910934,4017,3897,not collected,,2018,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20955,Acinetobacter baumannii JAB117,JAB117,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010226,470,,,,,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121612,CP121613,CP121614",,,Illumina MiSeq; Oxford Nanopore MiniION,68x,EToKi v. 1.2,1,2,3,4012910,38.995094,3901,3776,not collected,,2018,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20956,Acinetobacter baumannii JAB34,JAB34,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010211,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121601,CP121602,CP121603",,,Illumina MiSeq; Oxford Nanopore MiniION,198x,EToKi v. 1.2,1,2,3,4102389,38.9231,4005,3870,not collected,,2018,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20957,Acinetobacter baumannii JAB116,JAB116,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010225,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121621,CP121622,CP121623,CP121624",,,Illumina MiSeq; Oxford Nanopore MiniION,125x,EToKi v. 1.2,1,3,4,3986917,38.982224,3831,3730,not collected,,2018,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20958,Acinetobacter baumannii JAB270,JAB270,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010253,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.546",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121629,CP121630,CP121631",,,Illumina MiSeq; Oxford Nanopore MiniION,200x,EToKi v. 1.2,1,2,3,4006979,39.01131,3869,3765,not collected,,2019,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20959,Acinetobacter baumannii RAB73,RAB73,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010284,470,,,,,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121567,CP121569,CP121568",,,Illumina MiSeq; Oxford Nanopore MiniION,96x,EToKi v. 1.2,1,2,3,4029797,38.949604,3909,3799,not collected,,2019,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20960,Acinetobacter baumannii JAB108,JAB108,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010224,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121615,CP121618,CP121617,CP121620,CP121619,CP121616",,,Illumina MiSeq; Oxford Nanopore MiniION,93x,EToKi v. 1.2,1,5,6,4223469,38.9302,4146,4020,not collected,,2018,Saudi Arabia,Saudi Arabia:Jeddah,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20961,Acinetobacter baumannii HAB11,HAB11,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010192,470,,,,"MLST.Acinetobacter_baumannii_1.195,MLST.Acinetobacter_baumannii_2.2",,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121632,CP121633",,,Illumina MiSeq; Oxford Nanopore MiniION,195x,EToKi v. 1.2,1,1,2,3975514,39.020866,3850,3745,not collected,,2018,Saudi Arabia,Saudi Arabia:Al-Ahsa,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20962,Acinetobacter baumannii MAB9,MAB9,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010256,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121588,CP121589,CP121590",,,Illumina MiSeq; Oxford Nanopore MiniION,139x,EToKi v. 1.2,1,2,3,4109113,38.94456,4039,3923,not collected,,2019,Saudi Arabia,Saudi Arabia:Medina,,,,Infection,,,Resistant,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20964,Acinetobacter baumannii RAB14,RAB14,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27010271,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-13T00:00:00Z,,PRJNA819214,,"CP121583,CP121584,CP121585",,,Illumina MiSeq; Oxford Nanopore MiniION,102x,EToKi v. 1.2,1,2,3,3967996,39.016346,3808,3708,not collected,,2018,Saudi Arabia,Saudi Arabia:Riyadh,,,,Infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:KAIMRC AMR WGS_Based Surveillance Program,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.20974,Acinetobacter baumannii SCCH66:Ab99738,SCCH66:Ab99738,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN31178858,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-04-18T00:00:00Z,,PRJNA561493,,"CP122365,CP122366,CP122367",,,Illumina,462.0x,SPAdes v. 3.13.0; CLC Genomics,1,2,3,4056817,39.017563,3937,3842,blood,,2019-07-29,Russia,Russia:Moscow,,,,Severe concomitant injury,,host_description:P20\; 2012 year of birth,Resistant,Computational Method,,,,,,,,,,collected_by:Sadeeva Z.Z.,,,,,,,Severe concomitant injury,,,P20; 2012 year of birth,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.20975,Acinetobacter baumannii GIMC5506:ABT-3Ts52,GIMC5506:ABT-3Ts52,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12618962,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.558",genotype:ST558,,,2023-04-18T00:00:00Z,,PRJNA561493,,"CP122363,CP122364",,,Illumina,156.0x,CLC Genomics workbench v. 21; SPAdes,1,1,2,4035462,39.148956,3889,3803,sputum,,2016-01-28,Russia,Russia:Moscow,,,,Sepsis and the multiorgan failure,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Fedosova NF,,,,,,,Sepsis and the multiorgan failure,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.21491,Acinetobacter baumannii Mu1984,Mu1984,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27957725,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2023-06-05T00:00:00Z,,PRJNA833057,,"CP096818,CP096819,CP096820",,,Illumina NextSeq; Oxford Nanopore,100.0x,unicycler v. 0.4.8,1,2,3,4012149,39.111534,3898,3799,blood,,2012/2015,USA,"USA:Georga, Atlanta",,,,,,,Resistant,Computational Method,,,,,,,,,,collected_by:Georgia Emerging Infections Program,,,,,,,N/A,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.21492,Acinetobacter baumannii Mu1956,Mu1956,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN27988045,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.208",,,,2023-06-05T00:00:00Z,,PRJNA833420,,"CP096894,CP096895,CP096896,CP096897,CP096898,CP096899,CP096900,CP096901",,,Oxford Nanopore; Illumina NextSeq,100.0x,unicycler v. 0.4.8,1,7,8,4308180,39.217464,4242,4119,respiratory,,2012/2015,USA,"USA:Georgia,Atlanta",,,,,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Georgia Emerging Infections Program,,,,,,,N/A,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.2908,Acinetobacter baumannii strain HRAB-85,HRAB-85,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN06046790,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2016-11-29T00:00:00Z,,PRJNA348168,GCF_001887305.1,"CP018143,CP018144","NZ_CP018143.1,NZ_CP018144.1",307th Hospital of PLA,PacBio,12.0x,SOAPdenovo v. 05-2016,1,1,2,4098585,38.97,3975,3855,sputum,,2014-09,China,China: Beijing,,,,Infection,,,,,,,,,,,,,The complete genome sequence of An Imipenem Heteroresistant Acinetobacter baumannii Clinical Isolate AB85,collected_by:307th Hospital of PLA,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.2928,Acinetobacter baumannii strain CMC-CR-MDR-Ab4,CMC-CR-MDR-Ab4,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04096368,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2016-12-27T00:00:00Z,,PRJNA296424,GCF_001922205.1,"CP016295,CP016296,CP016297","NZ_CP016295.1,NZ_CP016296.1,NZ_CP016297.1",Virginia Tech,PacBio RS II,165x,SMRT v. 2.2 HGAP.3,1,2,3,4156005,39.01,4018,3900,bal,,,USA,USA:VA,,female,32,Pneumococcal septicemia,,"host_description:Human;host_disease_outcome:Rehab;host_health_state:septicemia, necrosis of liver, acute kidney failure, acute respiratory failure, chronic pulmonary heart disease, pulmonary collapse, DVT",,,,,,Mesophilic,37 C,Aerobic,HostAssociated,Nosocomial,"A genomics investigation that helped to identify the genetic basis for MDR-Ab and provide a supportive summary of demographic and clinical features of patients infected and colonized by Ab, based upon genomic analysis of sporadic Ab isolates collected from a tertiary care teaching hospital in Southwestern Virginia, USA.",collected_by:Carilion Roanoke Memorial Hospital,,,,,,,Pneumococcal septicemia,"septicemia, necrosis of liver, acute kidney failure, acute respiratory failure, chronic pulmonary heart disease, pulmonary collapse, DVT",Rehab,Human,Not available,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.2929,Acinetobacter baumannii strain CMC-MDR-Ab59,CMC-MDR-Ab59,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04096369,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2016-12-27T00:00:00Z,,PRJNA296424,GCF_001922225.1,"CP016298,CP016299","NZ_CP016298.1,NZ_CP016299.1",Virginia Tech,PacBio RS II,161x,SMRT v. 2.2 HGAP.3,1,1,2,4076357,39.08,3895,3794,sputum,,,USA,USA:VA,,male,51,Septicemia,,"host_description:Human;host_disease_outcome:Transfer;host_health_state:Septicemia, acute & chronic respiratory failure, pancreatitis, heart failure, end stage renal disease, coma, morbid obesity, C. diff, chronic pulmonary heart disease",,,,,,Mesophilic,37 C,Aerobic,HostAssociated,Nosocomial,"A genomics investigation that helped to identify the genetic basis for MDR-Ab and provide a supportive summary of demographic and clinical features of patients infected and colonized by Ab, based upon genomic analysis of sporadic Ab isolates collected from a tertiary care teaching hospital in Southwestern Virginia, USA.",collected_by:Carilion Roanoke Memorial Hospital,,,,,,,Septicemia,"Septicemia, acute & chronic respiratory failure, pancreatitis, heart failure, end stage renal disease, coma, morbid obesity, C. diff, chronic pulmonary heart disease",Transfer,Human,Not available,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.3106,Acinetobacter baumannii strain AB34299,AB34299,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04457967,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2017-03-02T00:00:00Z,,PRJNA311034,GCA_002009115.1,"CP014291,CP014292,CP014293",,USAMRIID,PacBio,150,HGAP v. 2.3,1,2,3,3983044,38.87,3955,3710,not collected,,2015-12-01,,,,,,Nosocomial infection,,,Susceptible,Computational Prediction,,,,,,,,,Whole genome long-read sequencing of isolates of Klebsiella and Acinetobacter,collected_by:USAMRIID,,,,,,,Nosocomial infection,,,,,,,,,,,,,,100,2.3,Nosocomial Infections,Other Nosocomial Infections,Other,Nosocomial Infections-Other Nosocomial Infections HP,470.3362,Acinetobacter baumannii strain ab736,ab736,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04621185,470,,,,MLST.Acinetobacter_baumannii_2.52,,,,2017-05-02T00:00:00Z,,PRJNA317553,GCA_002116925.1,"CP015121,CP015122",,USAMRIID,PacBio,516,HGAP v. 2.3,1,1,2,3990425,39.16,3795,3690,,,2015,USA,United States,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Genomic investigation of drug resistance in Acinetobacter baumannii,collected_by:USAMRIID,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,470.3774,Acinetobacter baumannii strain A85,A85,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07125723,470,,,,MLST.Acinetobacter_baumannii_2.1,genotype:global clone 1,,,2017-06-28T00:00:00Z,,PRJNA269083,GCA_002210065.1,"CP021782,CP021783,CP021784,CP021785,CP021786,CP021787",,University of Melbourne,Illumina HiSeq; PacBio,369.0x,Unicycler v. JAN-2017,1,5,6,4144615,39.13,3988,3914,sputum,,2003,Australia,Australia: Sydney,,,,disease,,,Susceptible,Computational Prediction,Negative,,,,,,,,Sequencing of A. baumannii global clone 1 (GC1) isolates,collected_by:Ian Carter,,,,,,,disease,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.4287,Acinetobacter baumannii strain Ab4977,Ab4977,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07943355,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2017-11-08T00:00:00Z,,PRJNA416164,GCA_002762095.1,CP024611,,State Key Laboratory of Pathogen and Biosecurity,PacBio,300x,SPAdes v. v3.10.1,1,,1,3966912,39.09,3836,3744,sputum,,2011-07-07,China,China: Beijing,,,,Infection,,,Resistant,Computational Prediction,,,,,,,,,Acinetobacter baumannii Genome sequencing,collected_by:Institute of Microbiology and Epidemiology Beijing,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.4288,Acinetobacter baumannii strain Ab4568,Ab4568,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07943353,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2017-11-08T00:00:00Z,,PRJNA416164,GCA_002762115.1,CP024613,,State Key Laboratory of Pathogen and Biosecurity,PacBio,300x,SPAdes v. v3.10.1,1,,1,4000452,39.08,3878,3789,sputum,,2011-02-09,China,China: Beijing,,,,Infection,,,Resistant,Computational Prediction,,,,,,,,,Acinetobacter baumannii Genome sequencing,collected_by:Institute of Microbiology and Epidemiology Beijing,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.4289,Acinetobacter baumannii strain Ab4653,Ab4653,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07943354,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2017-11-08T00:00:00Z,,PRJNA416164,GCA_002762155.1,CP024612,,State Key Laboratory of Pathogen and Biosecurity,PacBio,300x,SPAdes v. v3.10.1,1,,1,3913931,39.18,3772,3696,sputum,,2011-03-21,China,China: Beijing,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii Genome sequencing,collected_by:Institute of Microbiology and Epidemiology Beijing,,,,,,,Infection,,,,,,,,,,,,,,99.5,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.4476,Acinetobacter baumannii strain SMC_Paed_Ab_BL01,SMC_Paed_Ab_BL01,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN08054861,470,,,,MLST.Acinetobacter_baumannii_2.2,genotype:ST191,,,2017-12-18T00:00:00Z,,PRJNA419431,GCA_002843665.1,"CP025266,CP025267",,Sungkyunkwan University School of Medicine,PacBio,200,HGAP v. 3.0,1,1,2,4058089,39.02,3950,3864,"blood, central line",,2012-04-12,South Korea,South Korea: Seoul,,female,15,haemophagocytic lymphohistiocytosis,,host_disease_outcome:death,Resistant,Computational Prediction,,,,,,,,,In vivo eveolution of mutlidrug-resistant A. baumannii isolated from a deceased haemophagocytic lymphohistiocytosis patient,"collected_by:Yae-Jean Kim, Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine",,,,,,,haemophagocytic lymphohistiocytosis,,death,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.4703,"Acinetobacter baumannii strain S1; AB1A2 strain S1, AB1A2","S1, AB1A2",Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07977762,470,,,,MLST.Acinetobacter_baumannii_2.2,"genotype:ST208 (Oxford), ST2 (Pasteur)",,,2018-02-21T00:00:00Z,,PRJNA417158,GCA_002948475.1,"CP026943,CP026944,CP026945,CP026946",,University of Pittsburgh,PacBio,100.0x,HGAP v. 4.0,1,3,4,4253577,39.07879,4178,4076,bal,,2007-01-09,USA,USA: Pittsburgh,,,,Acinetobacter Infections,,,Susceptible,Computational Prediction,,,,,,,,,"Phylogenomics of Colistin-Susceptible and Resistant, Extensively Drug-Resistant Acinetobacter baumannii Clinical Strains","collected_by:Yohei Doi, MD, University of Pittsburgh",,,,,,,Acinetobacter Infections,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.5036,Acinetobacter baumannii strain DA33098,DA33098,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09241862,470,ST350,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181015.1,"CP029569,CP029570,CP029571,CP029573,CP029572",,Uppsala University,PacBio; Illumina HiSeq 2000,150.0x,CLC Genomics workbench v. 11.0.1,1,4,5,4173004,39.0731,4155,4045,,,,Spain,Spain,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.5052,Acinetobacter baumannii strain Aba,Aba,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09389171,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-07-05T00:00:00Z,,PRJNA475448,GCA_003288775.1,"CP030083,CP030084",,Chinese PLA General Hospital,PacBio,120.0x,HGAP v. 3,1,1,2,3920467,39.03275,3710,,,,2016-08-30,China,China: Beijing,,,,,,,Susceptible,Computational Prediction,,,,,,,,,These results provide insights into the environmental adaptation of this widespread pathogen.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.5053,Acinetobacter baumannii strain DA33382,DA33382,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09460321,470,ST1567,,,MLST.Acinetobacter_baumannii_2.1,,,,2018-07-09T00:00:00Z,,PRJNA472712,GCA_003296225.1,"CP030106,CP030108,CP030107,CP030109",,Uppsala University,PacBio; Illumina MiSeq,145.0x,CLC Genomics workbench v. 11.0.1,1,3,4,4036816,39.028408,3951,3866,tracheal secretion,,,Germany,Germany,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,99.5,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.5279,Acinetobacter baumannii strain CA-17,CA-17,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04018777,470,,,,,,,,2016-09-08T00:00:00Z,,PRJNA294251,GCA_001721705.1,CP012587,,Monash University,PacBio,120x,HGAP v. v 1.1,1,,1,3719282,39.04552,3449,3356,,,2010,Australia,Australia,,,,Pneamonia,,,Susceptible,Computational Prediction,,,,,C,,,,Genome comparison of community-acquired and hospital-acquired A. baumannii,collected_by:Anton Peleg,,,,,,,Pneamonia,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.5409,Acinetobacter baumannii strain 7804,7804,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07289440,470,,,,MLST.Acinetobacter_baumannii_2.25,,,,2017-07-28T00:00:00Z,,PRJNA311558,GCA_003431385.1,"CP022283,CP022284,CP022285",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",PacBio RSII,98.0x,HGAP in SMRT analysis (Pacific,1,2,3,4342018,38.92036,4323,4127,bronchoalveolar lavage fluid,,2006-07-05,Mexico,"Mexico: Monterrey, Nuevo Leon",,male,25,A. baumannii infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital Universitario de Nuevo Leon,,,,,,,A. baumannii infection,,,,,,,,,,,,,,100,4.5,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.5414,Acinetobacter baumannii strain 7847,7847,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07284119,470,,,,,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003516005.1,"CP023031,CP023032,CP023033",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,337.396x,SPAdes hybrid assembly v. 3.7.1,1,2,3,4080593,38.90653,3966,3869,blood,,2008-04-28,Mexico,"Mexico: Monterrey, Nuevo Leon",,female,,A. baumannii bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital Universitario de Nuevo Leon,,,,,,,A. baumannii bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.5415,Acinetobacter baumannii strain 9201,9201,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520236,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003522665.1,"CP023020,CP023021",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,502.299x,SPAdes hybrid assembly v. 3.7.1,1,1,2,4128152,39.12092,4127,4042,blood,,2013-08,Mexico,Mexico: Guadalajara,,male,37,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital Central de Guadalajara,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,470.5416,Acinetobacter baumannii strain 10324,10324,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520237,470,,,,MLST.Acinetobacter_baumannii_2.10,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003522705.1,"CP023022,CP023023,CP023024,CP023025",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,263.223x,SPAdes hybrid assembly v. 3.7.1,1,3,4,3862444,39.03381,3795,3704,bronchial fluid,,2012-08,Mexico,"Mexico: Acapulco, Guerrero",,male,31,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital General de Acapulco,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.5417,Acinetobacter baumannii strain 10042,10042,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520233,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003522785.1,"CP023026,CP023027,CP023028",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,277.297x,SPAdes hybrid assembly v. 3.7.1,1,2,3,4151876,38.92385,4070,3962,secretion,,2011-04-10,Mexico,"Mexico: Torreon, Coahuila",,female,51,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital de Torreon,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.5418,Acinetobacter baumannii strain 9102,9102,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520232,470,,,,MLST.Acinetobacter_baumannii_2.1,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003522845.1,"CP023029,CP023030",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,279.661x,SPAdes hybrid assembly v. 3.7.1,1,1,2,4066829,38.96043,3955,3849,bronchial fluid,,2010-06-04,Mexico,Mexico: Baja California,,female,46,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital General de Tijuana,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,470.5419,Acinetobacter baumannii strain 5845,5845,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520231,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-09-10T00:00:00Z,,PRJNA311558,GCA_003522885.1,"CP023034,CP023035",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,161.914x,SPAdes hybrid assembly v. 3.7.1,1,1,2,3989947,39.048664,3850,3768,wound,,2009-12-31,Mexico,Mexico: San Luis Potosi,,male,57,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital Ignacio Morones Prieto,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.5836,Acinetobacter baumannii strain MRSN15313,MRSN15313,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10411605,470,,,,"MLST.Acinetobacter_baumannii_1.233,MLST.Acinetobacter_baumannii_2.79",,,,2018-11-21T00:00:00Z,,PRJNA505170,GCA_003812485.1,"CP033869,CP033871,CP033870,CP033872",,Walter Reed Army Institute of Research,PacBio RSII; Illumina MiSeq,300.0x,HGAP v. 3.0,1,3,4,4250823,39.03769,4204,4097,cerebrospinal fluid,,2008,Brazil,Brazil: Salvador,,,,meningitis,,,Susceptible,Computational Prediction,,,,,,,,,Complete genome sequence of a single Acinetobacter baumannii isolate carrying mcr-4.,collected_by:MRSN,,,,,,,meningitis,,,,,,,,,,,,,,100,1.23,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,470.6167,Acinetobacter baumannii strain 09A16CRGN0014,09A16CRGN0014,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258640,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-12-09T00:00:00Z,30312401,PRJNA390934,GCA_003931755.1,CP034242,,Public Health Agency of Canada,Illumina MiSeq; MinION,100x,Unicylcer v. 0.4.6.0,1,,1,3943275,39.018253,3830,3737,not applicable,,2016,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.59,1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.6168,Acinetobacter baumannii strain 09A16CRGN003B,09A16CRGN003B,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258642,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2018-12-09T00:00:00Z,30312401,PRJNA390934,GCA_003931775.1,CP034243,,Public Health Agency of Canada,Illumina MiSeq; MinION,100x,Unicylcer v. 0.4.6.0,1,,1,3943105,39.01664,3827,3738,not applicable,,2016,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.59,1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.6368,Acinetobacter baumannii strain A52,A52,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10441121,470,,,,MLST.Acinetobacter_baumannii_2.77,,,,2019-01-17T00:00:00Z,,PRJNA506023,GCA_004028375.1,"CP034092,CP034093,CP034094,CP034095,CP034096,CP034097",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. 0.4.7,1,5,6,4023316,38.95755,3872,3795,sputum,,2015-08-02,China,China: Hangzhou,,male,66,Septic shock,,,Susceptible,Computational Prediction,,,,,,,,,Whole genome sequencing and comparative genomic analysis of Acinetobacter baumannii,collected_by:Huiqiong Jia,,,,,,,Septic shock,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,470.8348,Acinetobacter baumannii strain 11A1314CRGN088,11A1314CRGN088,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258672,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-01-22T00:00:00Z,30312401,PRJNA390934,GCA_004101685.1,CP035184,,Public Health Agency of Canada,Oxford Nanopore MiniION,100X,Unicycler v. 0.4.2,1,,1,3937511,39.047714,3797,3716,not applicable,,2013,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,2.97,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.8349,Acinetobacter baumannii strain 11A14CRGN003,11A14CRGN003,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258689,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-01-22T00:00:00Z,30312401,PRJNA390934,GCA_004101705.1,CP035183,,Public Health Agency of Canada,Oxford Nanopore MiniION,96X,Unicycler v. 0.4.2,1,,1,3940649,39.04456,3805,3722,not applicable,,2014,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,3.37,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.8350,Acinetobacter baumannii strain 11A1213CRGN055,11A1213CRGN055,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258647,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-01-22T00:00:00Z,30312401,PRJNA390934,GCA_004101725.1,CP035185,,Public Health Agency of Canada,Oxford Nanopore MiniION,95X,Unicycler v. 0.4.2,1,,1,3934099,39.048687,3791,3706,not applicable,,2012,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,2.97,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.8351,Acinetobacter baumannii strain 11A1213CRGN008,11A1213CRGN008,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258645,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-01-22T00:00:00Z,30312401,PRJNA390934,GCA_004101745.1,CP035186,,Public Health Agency of Canada,Oxford Nanopore MiniION,101X,Unicycler v. 0.4.2,1,,1,3944921,39.030895,3801,3720,not applicable,,2012,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.12,2.58,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.8355,Acinetobacter baumannii strain MDR-UNC,MDR-UNC,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09769497,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-02-04T00:00:00Z,,PRJNA484790,GCA_004136355.1,"CP031444,CP031446,CP031445",,National Biodefense Analysis and Countermeasures Center (NBACC),PacBio RSII,380.0x,PBcR v. JAN-2015,1,2,3,4058498,39.141403,3996,3927,"right leg muscle, right leg fascia, central venous catheter, dialysis catheter, surface of the left leg ulcer, and left lower leg",,2012-08-22,USA,"USA: North Carolina, Chapel Hill",,,,necrotizing fasciitis,,,Resistant,Computational Prediction,,,,,,,,,Sequencing of Multidrug resistant Acinetobacter baumannii,collected_by:UNC,,,,,,,necrotizing fasciitis,,,,,,,,,,,,,,99.98,0.61,Skin and Soft Tissue Infections,Necrotizing fasciitis,Skin and Soft Tissue,Skin and Soft Tissue Infections-Necrotizing fasciitis HP,470.8385,Acinetobacter baumannii strain AB053,AB053,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11077519,470,,,,,,,,2019-03-18T00:00:00Z,27917170,PRJNA525860,GCA_004354125.1,CP037869,,University of Manitoba,PacBio RSII,214x,HGAP v. 2.3.0,1,,1,3975250,39.03606,3776,3684,drainage basin water,,2013,Canada,Canada: Ontario,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii environmental isolates Genome sequencing and assembly,collected_by:Kumar lab,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.64,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,470.8386,Acinetobacter baumannii strain AB046,AB046,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11077515,470,,,,,,,,2019-03-18T00:00:00Z,27917170,PRJNA525860,GCA_004354145.1,CP037872,,University of Manitoba,PacBio RSII,78x,HGAP v. 2.3.0,1,,1,3954288,39.042656,3738,3651,drainage basin water,,2013,Canada,Canada: Ontario,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii environmental isolates Genome sequencing and assembly,collected_by:Kumar lab,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,470.8387,Acinetobacter baumannii strain AB047,AB047,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11077516,470,,,,,,,,2019-03-18T00:00:00Z,27917170,PRJNA525860,GCA_004354165.1,CP037871,,University of Manitoba,PacBio RSII,100x,HGAP v. 2.3.0,1,,1,3783653,39.110565,3555,3493,drainage basin water,,2013,Canada,Canada: Ontario,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii environmental isolates Genome sequencing and assembly,collected_by:Kumar lab,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,470.8388,Acinetobacter baumannii strain AB048,AB048,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11077517,470,,,,,,,,2019-03-18T00:00:00Z,27917170,PRJNA525860,GCA_004354185.1,CP037870,,University of Manitoba,PacBio RSII,64x,HGAP v. 2.3.0,1,,1,3975069,39.037285,3805,3697,drainage basin water,,2013,Canada,Canada: Ontario,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii environmental isolates Genome sequencing and assembly,collected_by:Kumar lab,,,,,,,pneumonia,,,,,,,,,,,,,,99.96,1.1,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,470.8415,Acinetobacter baumannii strain CIAT758,CIAT758,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11298775,470,,,,"MLST.Acinetobacter_baumannii_2.10,MLST.Acinetobacter_baumannii_1.585",,,,2019-04-09T00:00:00Z,,PRJNA530138,GCA_004758865.1,"CP038500,CP038501,CP038502,CP038503",,Christian Medical College,Oxford Nanopore MiniION; IonTorrent,56.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,3,4,4172366,39.03917,4263,4040,blood,,2018,India,India,,,,Bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acinetobacter baumannii_CIAT758_hybrid assembly,collected_by:Tata Medical Centre,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.55,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,470.8425,Acinetobacter baumannii strain VB958,VB958,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11554497,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-05-11T00:00:00Z,,PRJNA540743,GCA_005280355.1,"CP040040,CP040041,CP040042,CP040043,CP040044,CP040045,CP040046",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,132.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,6,7,4207397,38.975784,4354,4048,blood,,2019,India,India,,,,Sepsis,,,Resistant,Computational Prediction,,,,,,,,,Colistin resistant Acinetobacter baumannii_VB958_hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,99.96,1.79,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.8426,Acinetobacter baumannii strain VB1190,VB1190,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11554995,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-05-11T00:00:00Z,,PRJNA540755,GCA_005280375.1,"CP040047,CP040048,CP040049",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,82.28x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,2,3,3968665,39.04144,3933,3738,blood,,2019,India,India,,,,Sepsis,,,Resistant,Computational Prediction,,,,,,,,,Colistin resistant Acinetobacter baumannii_VB1190_hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,99.91,1.6,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.8427,Acinetobacter baumannii strain VB35179,VB35179,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11557490,470,,,,,,,,2019-05-11T00:00:00Z,,PRJNA540771,GCA_005280395.1,"CP040053,CP040054,CP040055",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,40.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,2,3,4371075,39.10976,4611,4186,blood,,2018,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acinetobacter baumannii_VB35179_hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,99.82,1.21,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.8428,Acinetobacter baumannii strain VB35435,VB35435,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11557585,470,,,,MLST.Acinetobacter_baumannii_2.575,,,,2019-05-11T00:00:00Z,,PRJNA540773,GCA_005280415.1,"CP040056,CP040057",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,28.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,1,2,4057956,38.931572,4196,3911,blood,,2018,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acinetobacter baumannii_VB35435_hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,99.45,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.8429,Acinetobacter baumannii strain VB16141,VB16141,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11557458,470,,,,MLST.Acinetobacter_baumannii_2.622,,,,2019-05-11T00:00:00Z,,PRJNA540767,GCA_005280435.1,"CP040050,CP040051,CP040052",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,85.6x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,2,3,4277985,39.083305,4222,4090,blood,,2019,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,Colistin resistant Acinetobacter baumannii_VB16141_hybrid assembly,collected_by:Christian Medical College,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,470.8435,Acinetobacter baumannii strain P7774,P7774,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11621520,470,,,,MLST.Acinetobacter_baumannii_2.25,,,,2019-05-20T00:00:00Z,,PRJNA542432,GCA_005518095.1,"CP040259,CP040260,CP040261,CP040262",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,51.31x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,3,4,4366589,39.024166,4343,4178,pus,,2018,India,India,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acinetobacter baumannii_P7774_hybrid assembly,collected_by:Post Graduate Institute of Medical Education and Research,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,470.8436,Acinetobacter baumannii strain PB364,PB364,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11660471,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-05-23T00:00:00Z,,PRJNA543307,GCA_005671375.1,"CP040425,CP040426,CP040427",,New York Medical College,Illumina; PacBio,not specified,SPAdes v. 3.9.0; HGAP v. 2.0,1,2,3,4136467,39.34713,4068,3962,missing,,2016,USA,USA:Valhalla,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Acinetobacter baumannii PB364 is a clinical isolate with multidrug resistance,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.98,0.61,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9122,Acinetobacter baumannii strain UPAB1,UPAB1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09906510,470,,,,MLST.Acinetobacter_baumannii_2.25,,,,2019-05-17T00:00:00Z,,PRJNA487603,GCA_006843645.1,"CP032215,CP032216,CP032218,CP032219,CP032217,CP032220",,Washington University School of Medicine,PacBio RS,349.0x,HGAP v. 2017-04-25,1,5,6,4136114,39.060215,4014,3928,urine,,2016,Argentina,"Argentina: Buenos Aires, San Andres, Hospital Zonal General de Agudos General Manuel Belgrano, Zip B1604BSB",,,,Urinary tract infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome sequencing of an Acinetobacter baumannii urine isolate.,collected_by:Laura Alcaraz,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,470.9148,Acinetobacter baumannii strain MDR-CQ,MDR-CQ,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN06211572,470,,,,"MLST.Acinetobacter_baumannii_1.195,MLST.Acinetobacter_baumannii_2.2",,,,2019-07-30T00:00:00Z,,PRJNA360504,GCA_007647215.1,"CP019114,CP019115",,Chongqing People's Hospital,PacBio RSII,260x,SMRT v. 2.3.0,1,1,2,4002648,38.938225,3873,3803,missing,,2016-07-25,China,China:Chongqing,,,,,,,Resistant,Computational Prediction,,,,,,,,,The complete genome sequence of an acinetobacter baumannii clinical isolate MDR-CQ,collected_by:Miao He,,,,,,,,,,,,,,,,,,,,,99.98,0.65,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9235,Acinetobacter baumannii strain 11A1213CRGN064,11A1213CRGN064,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258648,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-09-03T00:00:00Z,30312401,PRJNA390934,GCA_008244865.1,CP043419,,Public Health Agency of Canada,"Illumina MiSeq, Oxford Nanopore MinION",90X,Unicycler v. 0.4.2,1,,1,3935331,39.045483,3799,3709,not applicable,,2012,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,2.97,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9236,Acinetobacter baumannii strain N13-03449,N13-03449,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258679,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-09-03T00:00:00Z,30312401,PRJNA390934,GCA_008244885.1,CP043417,,Public Health Agency of Canada,"Illumina MiSeq, Oxford Nanopore MinION",85X,Unicycler v. 0.4.2,1,,1,3936362,39.045013,3797,3711,not applicable,,2013,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,2.97,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9237,Acinetobacter baumannii strain 11A1314CRGN089,11A1314CRGN089,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07258673,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-09-03T00:00:00Z,30312401,PRJNA390934,GCA_008244905.1,CP043418,,Public Health Agency of Canada,"Illumina MiSeq, Oxford Nanopore MinION",89X,Unicycler v. 0.4.2,1,,1,3935083,39.05051,3796,3708,not applicable,,2013,Canada,Canada,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Carbapenem resistant Acientobacter sp. in Canada as part of the Canadian Nosocomial Infection Surveillance Program (CNISP) 2010-2016,collected_by:National Microbiology Laboratory (NML),,,,,,,Not applicable,,,,,,,,,,,,,,99.98,2.97,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9351,Acinetobacter baumannii strain CAM180-1,CAM180-1,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12825295,470,,,,"MLST.Acinetobacter_baumannii_2.203,MLST.Acinetobacter_baumannii_1.714",,KCTC:72439,,2019-10-02T00:00:00Z,,PRJNA573751,GCA_008802935.1,"CP044356,CP044357,CP044358",,Daegu Catholic University School of Medicine,PacBio RS II with P6-C4 chemistry,97.31x,SMRT Analysis v. 2.3.0,1,2,3,3923146,39.000946,3903,3578,oral cavity,,2016-01-13,Cambodia,Cambodia: Battambang,,,4,early childhood caries,,,Susceptible,Computational Prediction,,,,,,,,,"Complete genome sequence of bacterial pathogen, Acinetobacter baumannii strain CAM180-1",collected_by:Yong-Hak Kim,,,,,,,early childhood caries,,,,,,,,,,,,,,99.63,0,Oral and Dental Diseases,Dental Caries,Oral,Oral and Dental Diseases-Dental Caries HP,470.9358,Acinetobacter baumannii strain C25,C25,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10135127,470,,,,"MLST.Acinetobacter_baumannii_2.2,MLST.Acinetobacter_baumannii_1.195",,,,2019-10-03T00:00:00Z,,PRJNA493508,GCA_008807055.1,"CP032743,CP032741,CP032742",,Zhejiang university school of medicine,PacBio RSII,190.0x,canu v. 1.5,1,2,3,4029386,38.90434,3978,3827,cerebral-spinal fluid,,2015-06-04,China,China: Shanghai,,,,meningitis,,,Resistant,Computational Prediction,,,,,,,,,to investigate the genetic basis of the Acinetobacter baumannii isolated from cerebral spinal fluid,collected_by:Shanghai Huashan Hospital,,,,,,,meningitis,,,,,,,,,,,,,,99.98,0.63,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,470.9411,Acinetobacter baumannii strain 5457,5457,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09244198,470,,,,MLST.Acinetobacter_baumannii_2.623,,,,2019-10-31T00:00:00Z,,PRJNA472798,GCA_009428985.1,CP045541,,JCVI,PacBio,100x,Canu v. v 1.6,1,,1,4250546,39.139328,4204,4108,,,,India,India,,,,,,,Intermediate;Resistant;Not defined;Susceptible,Computational Prediction,,,,,,,,,"As described in the ARLG research plan for neonatal A. baumannii infections in India, strains will be exchanged between ARGL labs and Indian hospitals, facilitated by the ICMR under the auspices of the Vaccine Action Program (VAP). Initial phenotypic and strain type classification will be performed by the ARLG and approximately 20 DNA samples representing geographic and clinical diversity will be provided to JCVI for sequencing (10 from ARLG and 10 from ICMR). The analysis plan will comprise assembly and annotation, followed by phylogenetic analysis to determine whether the Indian strains represent multiple distinct groups (sporadic infections) or clonal groups that suggest that the strains are endemic in each hospital. Data analysis will be performed in collaboration with ARLG and ICRM scientists.",,,,,,,,,,,,,,,,,,,,,,100,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9416,Acinetobacter baumannii strain 6507,6507,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN09244200,470,,,,MLST.Acinetobacter_baumannii_2.2,,,,2019-11-01T00:00:00Z,,PRJNA472798,GCA_009455505.1,CP045528,,JCVI,PacBio,100x,Canu v. v 1.6,1,,1,4092125,39.035954,3979,3832,,,,India,India,,,,,,,Resistant;Intermediate;Not defined;Susceptible,Computational Prediction,,,,,,,,,"As described in the ARLG research plan for neonatal A. baumannii infections in India, strains will be exchanged between ARGL labs and Indian hospitals, facilitated by the ICMR under the auspices of the Vaccine Action Program (VAP). Initial phenotypic and strain type classification will be performed by the ARLG and approximately 20 DNA samples representing geographic and clinical diversity will be provided to JCVI for sequencing (10 from ARLG and 10 from ICMR). The analysis plan will comprise assembly and annotation, followed by phylogenetic analysis to determine whether the Indian strains represent multiple distinct groups (sporadic infections) or clonal groups that suggest that the strains are endemic in each hospital. Data analysis will be performed in collaboration with ARLG and ICRM scientists.",,,,,,,,,,,,,,,,,,,,,,99.54,1.02,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9425,Acinetobacter baumannii strain 7835,7835,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07520235,470,,,,MLST.Acinetobacter_baumannii_2.422,,,,2019-11-04T00:00:00Z,,PRJNA311558,GCA_009497995.1,"CP033243,CP033244,CP033245",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio RSII,413.295x,SPAdes hybrid assembly v. 3.7.1,1,2,3,4095749,39.004345,4050,3952,tissue,,2007-07-16,Mexico,"Mexico: Monterrey, Nuevo Leon",,male,,Acinetobacter infection,,,Susceptible,Computational Prediction,,,,,,,,,Analysis of the genomic diversity of Acinetobacter isolates,collected_by:Hospital Universitario de Nuevo Leon,,,,,,,Acinetobacter infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,470.9821,Acinetobacter baumannii strain AbCAN2,AbCAN2,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12912378,470,,,,,,,,2020-01-07T00:00:00Z,,PRJNA575861,GCA_009833005.1,CP045428,,Washington University School of Medicine,PacBio,311.0x,HGAP v. 2016-02-25,1,0,1,3809822,39.038544,3729,3559,coccygeal isolate,,2015,Canada,Canada: Edmonton,,,,Infection,,,Susceptible,Computational Prediction,,,,,,,,,Genome annotation of Acinetobacter baumannii pathogenic isolate,collected_by:University of Alberta Hospital,,,,,,,Infection,,,,,,,,,,,,,,100,0.82,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,470146.24,Coprococcus comes ATCC 27758,ATCC 27758,Coprococcus comes,Coprococcus,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222686,470146,,,,,,ATCC:27758,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149785.1,CP102277,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3373066,42.52256,3392,3195,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.42,0,,,Other,- HP,470565.129,Prevotella histicola strain F0411,F0411,Prevotella histicola,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352190,470565,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128125.1,"CP072367,CP072368",,The Forsyth Institute,PacBio Sequel,550x,Pacbio MA v. 9.0.0.92188,2,0,2,2999514,41.246048,2600,2312,human oral cavity,,2007-01-27,USA,"USA: Boston, Massachusetts",,female,3.75,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02170;collected_by:Anne Tanner, Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,severe early childhood caries,,,,,,,,,human oral cavity,,,,99.32,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,471875.138,[Ruminococcus] lactaris ATCC 29176,ATCC 29176,[Ruminococcus] lactaris,Mediterraneibacter,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222711,471875,,,,,,ATCC:29176,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025152405.1,CP102292,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2733858,42.724895,2653,2505,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.42,0,,,Other,- HP,47466.169,Borrelia miyamotoi 1995,1995,Borrelia miyamotoi,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32260475,47466,,,,,,,,2022-12-26T00:00:00Z,,PRJNA912871,,"CP114663,CP114672,CP114670,CP114669,CP114668,CP114675,CP114674,CP114673,CP114671,CP114667,CP114666,CP114665",,,Illumina NovaSeq; PacBio Sequel,1700.0x,Canu v.,1,12,13,1332630,28.627525,1434,1332,"blood of patient with fever after tick-bite innoculated in scid mouse, and isolated in mkp-f culture",,2017,USA,USA: Rhode Island,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,collected_by:Sam Telford,,,,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,100,0,Hard Tick-Borne Relapsing Fever,,Blood and Circulatory System,Hard Tick-Borne Relapsing Fever- HP,47466.170,Borrelia miyamotoi 410,410,Borrelia miyamotoi,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32260473,47466,,,,,,,,2022-12-26T00:00:00Z,,PRJNA912871,,"CP114637,CP114646,CP114644,CP114643,CP114642,CP114649,CP114648,CP114647,CP114645,CP114641,CP114640,CP114639",,,Illumina NovaSeq; PacBio Sequel,1400.0x,Canu v.,1,12,13,1337417,28.64701,1436,1334,"blood of patient with fever after tick-bite innoculated in scid mouse, and isolated in mkp-f culture",,2016,USA,USA: Rhode Island,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,collected_by:Sam Telford,,,,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,100,0,Hard Tick-Borne Relapsing Fever,,Blood and Circulatory System,Hard Tick-Borne Relapsing Fever- HP,47466.173,Borrelia miyamotoi 1938,1938,Borrelia miyamotoi,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32260474,47466,,,,,,,,2022-12-26T00:00:00Z,,PRJNA912871,,"CP114650,CP114659,CP114657,CP114656,CP114655,CP114662,CP114661,CP114660,CP114658,CP114654,CP114653,CP114652",,,Illumina NovaSeq; PacBio Sequel,1300.0x,Canu v.,1,12,13,1335541,28.631544,1434,1341,"blood of patient with fever after tick-bite innoculated in scid mouse, and isolated in mkp-f culture",,2016,USA,USA: Rhode Island,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,collected_by:Sam Telford,,,,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,100,0,Hard Tick-Borne Relapsing Fever,,Blood and Circulatory System,Hard Tick-Borne Relapsing Fever- HP,47466.176,Borrelia miyamotoi 1999,1999,Borrelia miyamotoi,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32260476,47466,,,,,,,,2022-12-26T00:00:00Z,,PRJNA912871,,"CP114676,CP114685,CP114683,CP114682,CP114681,CP114689,CP114688,CP114687,CP114686,CP114684,CP114680,CP114679",,,Illumina NovaSeq; PacBio Sequel,1000.0x,Canu v.,1,13,14,1357715,28.593409,1461,1347,"blood of patient with fever after tick-bite innoculated in scid mouse, and isolated in mkp-f culture",,2016,USA,USA: Rhode Island,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,collected_by:Sam Telford,,,,,,,febrile ilness after I. scapularis tick-bite,,,,,,,,,,,,,,100,0,Hard Tick-Borne Relapsing Fever,,Blood and Circulatory System,Hard Tick-Borne Relapsing Fever- HP,47466.177,Borrelia miyamotoi CT14D4,CT14D4,Borrelia miyamotoi,Borrelia,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN32260480,47466,,,,,,,,2022-12-26T00:00:00Z,,PRJNA912871,,"CP114738,CP114747,CP114745,CP114744,CP114743,CP114752,CP114750,CP114751,CP114749,CP114748,CP114746,CP114742",,,Illumina NovaSeq; PacBio Sequel,800.0x,Canu v.,1,14,15,1383961,28.617353,1492,1377,"blood of patient with lyme disease (erythema migrans) after tick-bite innoculated in rag knock out mouse, and isolated in bsk culture",,2014,USA,USA: Connecticut,,,,Lyme disease with erythema migrans,,,,,,,,,,,,,,collected_by:Linda Bockenstedt (Yale),,,,,,,Lyme disease with erythema migrans,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Lyme Disease,Blood and Circulatory System,Specific Bacterial Infections-Lyme Disease HP,47678.1127,Bacteroides caccae strain BFG-100,BFG-100,Bacteroides caccae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547129,47678,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091545.1,CP081920,,National Institute of Allergy and Infectious Disease,PacBio Sequel,443x,HGAP/FALCON v. v. 6.0,1,0,1,5022820,42.504448,4422,4035,missing,,1985,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.19,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,47678.1222,Bacteroides caccae strain ATCC 43185,ATCC 43185,Bacteroides caccae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222641,47678,,,,,,ATCC:43185,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025146315.1,CP102256,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4570799,41.90471,3863,3601,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.3,0.08,,,Other,- NHP,47715.277,Lactobacillus rhamnosus strain Pen,Pen,Lacticaseibacillus rhamnosus,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN06196449,47715,,,,,,,,2017-04-03T00:00:00Z,,PRJNA359638,GCA_002076955.1,CP020464,,University of Life Sciences in Lublin,Illumina HiSeq,679.0x,SPAdes v. 3.1.1.,1,,1,2884966,46.78,2949,2830,gastrointestinal tract,,2005,Poland,Poland,,,,,,,,,,,,,,,,,Complete genome sequence of Lactobacillus rhamnosus Pen – a probiotic component of medicine preventing of antibiotic-associated diarrhoea in children.,sample_type:cell culture,,,,,,,,,,,,,"used to make the probiotic medicine Lakcid, Biomed-Lublin, Poland",,,,,,,,100,0,,,Genitourinary,- NHP,47715.310,Lactobacillus rhamnosus strain LR5,LR5,Lacticaseibacillus rhamnosus,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN05631078,47715,,,,,,,,2017-09-05T00:00:00Z,,PRJNA340067,GCA_002286235.1,CP017063,,Korea Food Research Institute,PacBio,232x,HGAP v. 3.0,1,,1,2972590,46.7,2950,2695,commercial dietary supplements; feces,,2015-08-24,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,LR5 strain was isolated from Commercial dietary supplements,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,47715.500,Lactobacillus rhamnosus strain LR-B1,LR-B1,Lacticaseibacillus rhamnosus,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN08176627,47715,,,,,,,,2019-01-10T00:00:00Z,,PRJNA422361,GCA_004010975.1,CP025428,,Zhejiang University School of Medicine,PacBio,300.0x,PacBio RS_HGAP v. 3,1,,1,3007503,46.69096,3113,2987,blood,,2017-03,Taiwan,Taiwan: Taoyuan,,,,bacterimia,,,,,,,,,,,,,Genome comparison of multiple isolates collected from an infant who suffered bacterimia,collected_by:Ming-Chou Chiang,,,,,,,bacterimia,,,,,,,,,,,,,,99.46,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,47715.630,Lactobacillus rhamnosus strain BIO6870,BIO6870,Lacticaseibacillus rhamnosus,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN12856534,47715,,,,,,,,2019-10-07T00:00:00Z,,PRJNA574342,GCA_008831425.1,CP044506,,Bioprox,"Illumina Miseq, Oxford Nanopore MinION",100x,Unicycler v. v0.4.5,1,,1,3006715,46.694347,3114,2983,feces,,,,,,,,,,,,,,,,,,,,,Investigation of probiotic properties of different lactic acid bacteria,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.46,0,,,Gastrointestinal,- NHP,47715.656,Lactobacillus rhamnosus strain BIO5326,BIO5326,Lacticaseibacillus rhamnosus,Lacticaseibacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN13344000,47715,,,,,,,,2019-11-30T00:00:00Z,,PRJNA574342,GCA_009720565.1,CP046267,,Bioprox,Illumina MiSeq; Oxford Nanopore GridION,300.0x,Unicycler v. 0.4.5,1,0,1,2989570,46.76435,2986,2808,feces,,,,,,,,,,,,,,,,,,,,,Investigation of probiotic properties of different lactic acid bacteria,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.46,0,,,Gastrointestinal,- HP,47770.266,Lactobacillus crispatus strain AB70,AB70,Lactobacillus crispatus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN08409124,47770,,,,,,,,2018-12-27T00:00:00Z,,PRJNA431864,GCA_003971565.1,"CP026503,CP026504",,KRIBB,PacBio,406.6x,Canu (followed by Circlator and Quiver),1,1,2,2367925,37.264904,2457,2352,korean vaginal fluid,isolated from Korean vaginal fluids and it has strong antimicrobial activity against vaginal pathogens,2014-11-01,South Korea,South Korea,temperature:37 degree celsius,,,,,,,,,,,,,,,,Lactobacillus crispatus AB70 starin was newly isolated from Korean vaginal fluids and it has strong antimicrobial activity against vaginal pathogens. L. crispauts AB70 seems to be related with low risk pregancies and have preventive roles against preterm birth or abortion.,"sample_type:vaginal fluids;biomaterial_provider:Keonyang hospital, Daejeon, Korea;collected_by:Daejeon;identified_by:Dong-Ho Chang;lab_host:Byoung-Chan Kim",,,,,,,,,,,,,,,,,,,,,99.03,0.09,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- NHP,47770.612,Lactobacillus crispatus strain FDAARGOS_743 strain Not applicable,Not applicable,Lactobacillus crispatus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN11056458,47770,,,,,,FDA:FDAARGOS_743,,2019-12-05T00:00:00Z,,PRJNA231221,GCA_009730275.1,"CP046311,CP046312",,US Food and Drug Administration,Pacbio; Illumina,1952.63x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,2386960,37.119892,2453,2316,mid-vaginal wall,,,USA,USA:VA,,female,,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,98.7,0.09,,,Genitourinary,- NHP,47770.918,Lactobacillus crispatus strain Lc1226,Lc1226,Lactobacillus crispatus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN21367958,47770,,,,,,,,2021-09-20T00:00:00Z,,PRJNA761982,GCA_020042125.1,CP083392,,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","382x, 240x",Unicycler v. v.0.4.8,1,0,1,2526154,37.115154,2638,2511,urine,isolated from the urine of postmenopausal women with different histories of rUTI,2019-04,USA,"USA: Dallas, Texas",,,,,,,,,,,,,,,,,"Lactobacilli are commonly found in the urine of healthy women, hinting at a possible protective role in the female urinary tract. Recurrent urinary tract infections (rUTIs) are often associated with microbial dysbiosis in the bladder, involving depletion of lactobacilli. Here, we report the complete genome sequences of several Lactobacillus spp. isolated from the urine of postmenopausal women with different histories of rUTI.",sample_type:Whole organism;collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,,,,,,,,,,,,,,,99.03,0.09,,,Urinary Tract,- NHP,47770.919,Lactobacillus crispatus strain Lc116,Lc116,Lactobacillus crispatus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMN21367957,47770,,,,,,,,2021-09-20T00:00:00Z,,PRJNA761982,GCA_020042225.1,"CP083393,CP083394",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","330x, 352x",Unicycler v. v.0.4.8,1,1,2,2447242,37.164204,2520,2393,urine,isolated from the urine of postmenopausal women with different histories of rUTI,2018-12,USA,"USA: Dallas, Texas",,,,,,,,,,,,,,,,,"Lactobacilli are commonly found in the urine of healthy women, hinting at a possible protective role in the female urinary tract. Recurrent urinary tract infections (rUTIs) are often associated with microbial dysbiosis in the bladder, involving depletion of lactobacilli. Here, we report the complete genome sequences of several Lactobacillus spp. isolated from the urine of postmenopausal women with different histories of rUTI.",sample_type:Whole organism;collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,,,,,,,,,,,,,,,99.03,0.09,,,Urinary Tract,- NHP,47770.934,Lactobacillus crispatus strain KT-11,KT-11,Lactobacillus crispatus,Lactobacillus,Lactobacillaceae,Lactobacillales,Bacilli,Bacillota,SAMD00404900,47770,,,,,,,,2021-10-01T00:00:00Z,,PRJDB12298,GCA_020887095.1,"AP025162,AP025163",,KITII Corporation,Pacbio Sequel,3107x,Canu v. 1.6,1,1,2,2397766,36.698242,2433,,feaces,,,,Japan,,,,,,,,,,,,,,,,,The purpose of this project is to determine the whole genome sequence of the commercial strain Lactobacillus crispatus KT-11 and to analyze its function based on the genome sequence information.,,human-associated habitat,Human feces,feces,19469537,Complete genome project of Lactobacillus crispatus strain KT-11.,,,Health,,,,,,,,,human-associated habitat,,,,98.96,0,,,Other,- NHP,478749.17,Marvinbryantia formatexigens DSM 14469,DSM 14469,Marvinbryantia formatexigens,Marvinbryantia,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222669,478749,,,,,,DSM:14469,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148285.1,CP102268,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4577574,49.534077,4725,4202,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,98.73,0,,,Other,- NHP,480.268,Moraxella catarrhalis strain FDAARGOS_213,FDAARGOS_213,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN04875550,480,Serotype A,,,MLST.Moraxella_catarrhalis.54,,FDA:FDAARGOS_213,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073215.2,CP020400,,US Food and Drug Administration,PacBio,13.8641796063406x,HGAP v. 3,1,,1,1907923,41.59,2009,1702,resident flora of the nasopharynx,,1972,USA,USA:NY,,,,Normal flora,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:USAMRIID,,,,,,,Normal flora,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,,,Respiratory Tract,- HP,480.269,Moraxella catarrhalis strain CCRI-195ME,CCRI-195ME,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN05949222,480,,,,MLST.Moraxella_catarrhalis.70,,,,2017-04-05T00:00:00Z,,PRJNA350869,GCA_002080125.1,"CP018059,CP018060",,Griffith University,PacBio,missing,HGAP v. July 2014,1,1,2,1994386,41.56,2114,1842,middle ear,,2009-02-06,USA,USA:Ohio,,,,otitis media,,,,,,,,,,,,,"Genome sequence of a Moraxella catarrhalis strain isolated from the middle ear of a child, with modM3 methyltransferase allele",collected_by:The Research Institute at Nationwide Children's,,,,,,,otitis media,,,,,,,,,,,,,,100,0,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,480.341,Moraxella catarrhalis strain 74P50B1,74P50B1,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10536191,480,,,,MLST.Moraxella_catarrhalis.371,,,,2018-12-26T00:00:00Z,,PRJNA509208,GCA_003971285.1,CP034664,,"Institute for Genome Sciences, University of Maryland, Baltimore",PacBio Sequel,30x,canu v. 1.4,1,,1,1832216,41.753536,1874,1892,sputum,,2001-08-27,USA,"USA: Buffalo, NY",,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,99.73,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,480.342,Moraxella catarrhalis strain 142P87B1,142P87B1,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10536190,480,,,,MLST.Moraxella_catarrhalis.224,,,,2018-12-26T00:00:00Z,,PRJNA509208,GCA_003971305.1,CP034665,,"Institute for Genome Sciences, University of Maryland, Baltimore",PacBio Sequel,26x,canu v. 1.4,1,,1,1909077,41.60398,1981,1995,sputum,,2010-09-08,USA,"USA: Buffalo, NY",,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,99.73,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,480.343,Moraxella catarrhalis strain 46P58B1,46P58B1,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10536193,480,,,,MLST.Moraxella_catarrhalis.156,,,,2018-12-26T00:00:00Z,,PRJNA509208,GCA_003971325.1,CP034662,,"Institute for Genome Sciences, University of Maryland, Baltimore",PacBio Sequel,24x,canu v. 1.4,1,,1,2045324,41.54613,2143,2165,sputum,,2000-01-03,USA,"USA: Buffalo, NY",,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,99.73,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,480.344,Moraxella catarrhalis strain 74P58B1,74P58B1,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10536192,480,,,,MLST.Moraxella_catarrhalis.371,,,,2018-12-26T00:00:00Z,,PRJNA509208,GCA_003971345.1,CP034663,,"Institute for Genome Sciences, University of Maryland, Baltimore",PacBio Sequel,31x,canu v. 1.4,1,,1,1832141,41.753174,1873,1890,sputum,,2002-05-06,USA,"USA: Buffalo, NY",,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,99.73,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,480.345,Moraxella catarrhalis strain 5P47B2,5P47B2,Moraxella catarrhalis,Moraxella,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10536188,480,,,,MLST.Moraxella_catarrhalis.544,,,,2018-12-26T00:00:00Z,,PRJNA509208,GCA_003971365.1,CP034666,,"Institute for Genome Sciences, University of Maryland, Baltimore",PacBio Sequel,29x,canu v. 1.4,1,,1,1933669,41.50043,1989,2002,sputum,,1999-01-07,USA,"USA: Buffalo, NY",,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,"Moraxella catarrhalis persists in COPD with profound clinical and pathogenetic consequences. Most strains express the major surface antigen Hag/MID on acquisition and then shut off expression, suggesting that Hag/MID is critical for initial colonization and cessation of expression facilitates persistence. Genomes sequences are used to analyze changes in DNA associated with adhesin expression.","collected_by:Univerty at Buffalo, T. Murphy",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,99.45,0.27,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,482957.39,Burkholderia lata strain A05,A05,Burkholderia lata,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08042342,482957,,,,MLST.Burkholderia_cepacia_complex.103,,,,2018-11-05T00:00:00Z,,PRJNA419071,GCA_003711145.1,"CP024943,CP024944,CP024945",,SAHMRI,PacBio,1.0x,HGAP v. 3,3,,3,8787009,66.185,8913,8272,blood,,2016-05-07,Australia,Australia: Adelaide,,,,cepacia syndrome,,,,,,,,,,,,,Burkholderia lata strain A05 from Australasian sublineage,collected_by:SA Pathology,,,,,,,cepacia syndrome,,,,,,,,,,,,,,100,1.58,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,48296.173,Acinetobacter pittii strain YMC2010/8/T346,YMC2010/8/T346,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN05827444,48296,,,,MLST.Acinetobacter_baumannii_1.1031,,,,2017-03-03T00:00:00Z,,PRJNA352745,GCF_002012285.1,"CP017938,CP017939","NZ_CP017938.1,NZ_CP017939.1",Yonsei university college of medicine,PacBio SMRT,242.14x,HGAP v. 2,1,1,2,4045824,38.85,3847,3690,peritoneal catheter tip,,2010-08,South Korea,South Korea: Seoul,,,,,,,,,,,,,,,,,"We identified the carbapenemase gene blaOXA-499, novel variant of blaOXA-143 from clinical isolate of Acinetobacter pittii for the first time. blaOXA-499 gene was cloned into pWH1266 and transformed into susceptible A. baumannii and A. pittii, which resulted in carbapenem resistance.","collected_by:Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine",,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,48296.217,Acinetobacter pittii strain HUMV-6483,HUMV-6483,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN07160582,48296,,,,,,,,2017-05-30T00:00:00Z,,PRJNA387671,GCA_002158945.1,"CP021428,CP021429",,IDIVAL Research Institute,PacBio,6.0x,GS De Novo Assembler v. MAY-2017,1,1,2,4182874,38.96,4025,,urine,,2008-10,Spain,Spain: Santander,,male,,infection,,,,,,,,,,,,,Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 isolated from human urine,collected_by:Microbiology Service,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,48296.362,Acinetobacter pittii strain AP007,AP007,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN11963641,48296,,,,MLST.Acinetobacter_baumannii_2.655,,,,2019-06-16T00:00:00Z,24421787,PRJNA547354,GCA_006351765.1,CP040903,,University of Manitoba,Illumina MiSeq,69.0x,A5_MiSeq assembler v. 20160825,1,,1,3919498,38.619923,3789,3741,hospital,,2009,Canada,Canada:Vancouver,,,,Blood infection,,,,,,,,,,,,,Genome sequencing and assembly of A. pittii AP007,collected_by:CANWARD,,,,,,,Blood infection,,,,,,,,,,,,,,100,0.27,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,48296.366,Acinetobacter pittii strain C54,C54,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12289369,48296,,,,,,,,2019-08-11T00:00:00Z,,PRJNA550014,GCA_007954485.1,"CP042364,CP042365,CP042366,CP042367,CP042368,CP042369,CP042370",,University of Oxford,Oxford Nanopore MiniION,1492x,Unicycler v. SEP-2017,1,6,7,4265778,38.876495,4203,4085,clinical sample,,2014-07-14,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,0.41,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,48296.370,Acinetobacter pittii strain AB17H194,AB17H194,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN10448663,48296,,,,,,,,2019-09-25T00:00:00Z,,PRJNA532848,GCA_008694085.1,"CP040911,CP040912,CP040913",,Peking University First Hospital,PacBio,234.3x,SOAPdenovo v. 2018.09,1,2,3,4009633,39.03906,3861,,excretion; wound secretion,,2013,China,China:Jilin province,,,,infectious diseases,,,,,,,,,,,,,Mechanisms of drug resistance in acinetobacter baumannii,"collected_by:Institute of Clinical Pharmacology, Peking University First Hospital",,,,,,,infectious diseases,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,48296.386,Acinetobacter pittii strain A1254,A1254,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN14278654,48296,,,,MLST.Acinetobacter_baumannii_1.1032,,,,2020-04-03T00:00:00Z,,PRJNA610163,GCA_011996285.1,"CP049806,CP049807,CP049808,CP049809,CP049810",,"Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University",Illumina; Oxford Nanopore,300.0x,SPAdes v. v3.13.0; Unicycler v. v0.4.0,1,4,5,4161573,38.66389,3950,3870,missing,,2010,China,China:Zhejiang province,,male,92,"Pulmonary Disease, Chronic Obstructive",,,,,,,,,,,,,Sequencing of Acinetobacter pittii isolate/populations for investigation of carbapenem resistance mechanism,collected_by:Yunsong Yu,,,,,,,"Pulmonary Disease, Chronic Obstructive",,,,,,,,,,,,,,100,0.68,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,48296.510,Acinetobacter pittii strain OCU_Ac17 strain OCU Ac17,OCU Ac17,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMD00330122,48296,,,,MLST.Acinetobacter_baumannii_2.248,,,,2021-07-07T00:00:00Z,,PRJDB11826,GCA_019703265.1,"AP024798,AP024799,AP024800,AP024801",,"Department of Bacteriology, Graduate School of Medicine, Osaka City University",Illumina Miniseq; ONT Flongle,101x,Unicycler v. 0.4.8,1,3,4,4108536,38.79438,3906,3835,,isolated in the hospital environment spread rapidly within the patient and cause nosocomial infections,,Japan,Japan:Osaka,,,,,,,,,Negative,Coccobacilli,,Mesophilic,37,Aerobic,,,"Strains isolated in the hospital environment spread rapidly within the patient and cause nosocomial infections. Also, resistance to some antibiotics is often easy to appear. Acinetobacter baumannii has been widely studied due to its high mortality rate. On the other hand, although A. pittii is isolated from blood, it has not been well studied compared to A. baumannii. In addition, the emergence of carbapenem-resistant A. pittii strains with carbapenem-hydrolyzed b-lactamases such as NDM-1 has received a great deal of attention. Here, we announce the complete genome sequence of A. pittii OCU Ac17. Our goal is attempting to perform whole genome sequencing of Acinetobacter pittii OCU Ac17, and compare the sequences to those of related species.",biomaterial_provider:Osaka City University Hospital,human,blood vessels,venous blood,https://www.atcc.org/Products/All/19606.aspx#culturemethod,Comparison of clinical isolates sequences.,,,,,,,,,,,free living,human,,,,99.91,0.27,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,48296.674,Acinetobacter pittii XJ88,XJ88,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN06187701,48296,,,,MLST.Acinetobacter_baumannii_2.485,,,,2018-01-05T00:00:00Z,,PRJNA359166,,"CP018909,CP018910",,,Illumina; Pacbio,161x; 235x,HGAP v. 3,1,1,2,4099621,38.749874,3923,3859,sputum,,2013-10-11,China,China: Chengdu,,female,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,"collected_by:The First Affiliated Hospital, Chengdu Medical College",,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,48296.735,Acinetobacter pittii AP8900,AP8900,Acinetobacter pittii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN34258005,48296,,,,MLST.Acinetobacter_baumannii_1.724,,,,2023-04-30T00:00:00Z,,PRJNA957585,,"CP123765,CP123766,CP123767,CP123768,CP123769",,,Illumina NovaSeq; PacBio,160.53x,Hifiasm v. 0.13-r308; Canu v. 0.7; Pilon,1,4,5,4120080,38.96808,4040,3965,sputum,,2022,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,48409.19,Salmonella enterica subsp. enterica serovar Virchow strain FORC_080,FORC_080,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08098100,48409,,,,MLST.Salmonella_enterica.16,,,,2018-12-03T00:00:00Z,,PRJNA419792,GCA_003856755.1,CP025094,,"Food-borne Pathogen Omics Research Center, FORC",PacBio,162 x,PacBio SMRT Analysis v. 2.3.0,1,,1,4828397,52.112038,4901,4606,human stool,isolated from human stool in South Korea,2017,South Korea,South Korea,,,,food poisoning,,,,,,,,,,,,,Salmonella Virchow FORC_080 Complete genome sequencing.Salmonella Virchow is one of the well-known food-borne pathogen. It was isolated from human stool in South Korea.,collected_by:NCCP,,,,,,,food poisoning,,,,,,,,,,,,,,99.96,0.04,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,48409.29,Salmonella enterica subsp. enterica serovar Virchow strain AUSMDU00010533,AUSMDU00010533,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191649,48409,Virchow,,,MLST.Salmonella_enterica.16,mlst:ST16,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664555.1,"CP045945,CP045946",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,305x,de novo,1,1,2,4708729,52.2455,4727,4435,missing,,2016,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.1347,Neisseria gonorrhoeae strain RIVM0610,RIVM0610,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN06251593,485,,,,,,,,2017-08-02T00:00:00Z,,PRJNA362986,GCA_003571445.1,CP019466,,RIVM,Illumina; PacBio,not specified,CLC Genomics Workbench v. 9.5.3,1,,1,2229240,52.355198,2804,2560,,,2008,Netherlands,Netherlands: Bilthoven,,,,gonorrhoeae,,,,,,,,,,,,,submission of RIVM0610 and RIVM0640,collected_by:Dutch National Institute for Public Health and the Environment (RIVM),,,,,,,gonorrhoeae,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.1348,Neisseria gonorrhoeae strain RIVM0640,RIVM0640,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN06251594,485,,,,,,,,2017-08-02T00:00:00Z,,PRJNA362986,GCA_003571465.1,CP019467,,RIVM,Illumina; PacBio,not specified,CLC Genomics Workbench v. 9.5.3,1,,1,2230041,52.355045,2792,2564,unavailable,,2008,Netherlands,Netherlands: Bilthoven,,,,gonorrhoeae,,,,,,,,,,,,,submission of RIVM0610 and RIVM0640,collected_by:Dutch National Institute for Public Health and the Environment (RIVM),,,,,,,gonorrhoeae,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17939,Neisseria gonorrhoeae NG211,NG211,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13151448,485,,,,MLST.Neisseria_spp.1903,genotype:ST1903,,,2022-05-02T00:00:00Z,,PRJNA609416,GCA_023205595.1,"CP050930,CP050931,CP050932,CP050933",,,Illumina MiSeq,10.0x,unicycler v. v0.4.8,1,3,4,2269988,52.31944,2733,2310,urethral discharge,,2009-12-25,Thailand,Thailand: Bangkok,,male,15,Gonorrhea,,,,,,,,,,,,,,"collected_by:Faculty of Medicine Siriraj Hospital, Mahidol University",,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.17940,Neisseria gonorrhoeae 351961,351961,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28094312,485,,,,,,,,2022-05-25T00:00:00Z,,PRJNA835124,GCA_023546945.1,CP097460,,,Illumina HiSeq,50X,SPAdes v. v3.13.0,1,0,1,2242106,52.433796,2573,2125,urethral discharge,,2018,Colombia,Colombia,,,,Gonococcal Urethritis,,,,,,,,,,,,,,collected_by:Universidad de Antioquia,,,,,,,Gonococcal Urethritis,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.17941,Neisseria gonorrhoeae 2312,2312,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28093654,485,,,,,,,,2022-05-25T00:00:00Z,,PRJNA835124,GCA_023546965.1,CP097461,,,Illumina HiSeq,50X,SPAdes v. v3.13.0,1,0,1,2210720,52.521866,2536,2101,urethral discharge,,2018,Colombia,Colombia,,male,,Gonococcal Urethritis,,,,,,,,,,,,,,collected_by:Universidad de Antioquia,,,,,,,Gonococcal Urethritis,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.17942,Neisseria gonorrhoeae 942021,942021,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28094314,485,,,,,,,,2022-05-25T00:00:00Z,,PRJNA835124,GCA_023546925.1,CP097458,,,Illumina HiSeq,50X,SPAdes v. v3.13.0,1,0,1,2177753,52.67151,2524,2085,urethral discharge,,2018,Colombia,Colombia,,,,Gonococcal Urethritis,,,,,,,,,,,,,,collected_by:Universidad de Antioquia,,,,,,,Gonococcal Urethritis,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.17943,Neisseria gonorrhoeae 652,652,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28094313,485,,,,,,,,2022-05-25T00:00:00Z,,PRJNA835124,GCA_023546905.1,CP097459,,,Illumina HiSeq,50X,SPAdes v. v3.13.0,1,0,1,2174453,52.675613,2500,2059,urethral discharge,,2018,Colombia,Colombia,,,,Gonococcal Urethritis,,,,,,,,,,,,,,collected_by:Universidad de Antioquia,,,,,,,Gonococcal Urethritis,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.17944,Neisseria gonorrhoeae CT602,CT602,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13812696,485,,,,,,,,2022-05-31T00:00:00Z,,PRJNA600334,GCA_023611705.1,"CP048246,CP048247,CP048248,CP048249",,,Illumina NovaSeq and Oxford Nanopore,1302.709617x,Unicycler v. 0.4.4,1,3,4,2211092,52.55851,2662,2195,urethra,,2017-07-04,Thailand,Thailand: Bangkok,,male,31,gonorrhea,,,Resistant;Intermediate;Not defined;Susceptible,AMR Panel,,,,,,,,,,collected_by:Natakorn Nokchan,,,,,,,gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.17945,Neisseria gonorrhoeae CT532,CT532,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13812695,485,,,,,,,,2022-05-31T00:00:00Z,,PRJNA600334,GCA_023611765.1,"CP048250,CP048251,CP048252,CP048253",,,Illumina NovaSeq and Oxford Nanopore,882.6201132x,Unicycler v. 0.4.4,1,3,4,2216438,52.535194,2677,2209,urethra,,2015-12-22,Thailand,Thailand: Bangkok,,male,50,gonorrhea,,,Resistant;Not defined;Susceptible,AMR Panel,,,,,,,,,,collected_by:Natakorn Nokchan,,,,,,,gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.17946,Neisseria gonorrhoeae CT530,CT530,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13812694,485,,,,,,,,2022-05-31T00:00:00Z,,PRJNA600334,GCA_023611785.1,"CP048254,CP048255,CP048256,CP048257",,,Illumina NovaSeq and Oxford Nanopore,925.3211491x,Unicycler v. 0.4.4,1,3,4,2220590,52.497578,2700,2208,urethra,,2015-12-19,Thailand,Thailand: Bangkok,,female,25,gonorrhea,,,Resistant;Not defined;Susceptible,AMR Panel,,,,,,,,,,collected_by:Natakorn Nokchan,,,,,,,gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.17985,Neisseria gonorrhoeae strain 10814,10814,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28834904,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169475.1,"CP098460,CP098461",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,303.0x,Unicycler v. 0.4.9,1,1,2,2216522,52.448654,2668,2251,urethal swab,,2019,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17987,Neisseria gonorrhoeae strain 9460,9460,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835168,485,,,,MLST.Neisseria_spp.11177,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169585.1,"CP098462,CP098463",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,306.0x,Unicycler v. 0.4.9,1,1,2,2232723,52.44175,2704,2281,urethal swab,,2016,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.51,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17992,Neisseria gonorrhoeae strain 9458,9458,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835169,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169785.1,"CP098476,CP098477",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,390.0x,Unicycler v. 0.4.9,1,1,2,2237257,52.45848,2699,2293,urethal swab,,2016,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.51,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17994,Neisseria gonorrhoeae strain 10720,10720,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835880,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170155.1,"CP098466,CP098467",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,312.0x,Unicycler v. 0.4.9,1,1,2,2223705,52.41635,2676,2263,urethal swab,,2019,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17995,Neisseria gonorrhoeae strain 10328,10328,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835919,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170325.1,"CP098468,CP098469",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,249.0x,Unicycler v. 0.4.9,1,1,2,2218145,52.4463,2675,2247,urethal swab,,2017,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17996,Neisseria gonorrhoeae strain 10269,10269,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835821,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169995.1,"CP098464,CP098465",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,296.0x,Unicycler v. 0.4.9,1,1,2,2217599,52.43901,2674,2261,urethal swab,,2017,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17997,Neisseria gonorrhoeae strain 10792,10792,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28836998,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170505.1,"CP098470,CP098471",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,287.0x,Unicycler v. 0.4.9,1,1,2,2218601,52.441875,2668,2254,urethal swab,,2019,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17998,Neisseria gonorrhoeae strain 10612,10612,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28837864,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170665.1,"CP098472,CP098473",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,323.0x,Unicycler v. 0.4.9,1,1,2,2220895,52.420353,2698,2265,urethal swab,,2018,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.37,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.17999,Neisseria gonorrhoeae strain 10536,10536,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28859049,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170705.1,"CP098505,CP098506",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,277.0x,Unicycler v. 0.4.9,1,1,2,2232626,52.325825,2737,2295,urethal swab,,2018,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.61,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18000,Neisseria gonorrhoeae strain 10537,10537,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869552,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170725.1,"CP098532,CP098533",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,319.0x,Unicycler v. 0.4.9,1,1,2,2233025,52.364887,2710,2290,urethal swab,,2018,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.61,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18001,Neisseria gonorrhoeae strain 10268,10268,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28858863,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170685.1,"CP098503,CP098504",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,284.0x,Unicycler v. 0.4.9,1,1,2,2218611,52.42172,2673,2265,urethal swab,,2017,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18002,Neisseria gonorrhoeae strain 10525,10525,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869554,485,,,,MLST.Neisseria_spp.6809,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170885.1,"CP098534,CP098535",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,298.0x,Unicycler v. 0.4.9,1,1,2,2215739,52.382072,2706,2263,urethal swab,,2018,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.61,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18003,Neisseria gonorrhoeae strain 10771,10771,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869592,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171075.1,"CP098536,CP098537",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,295.0x,Unicycler v. 0.4.9,1,1,2,2214409,52.445553,2651,2247,urethal swab,,2019,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18004,Neisseria gonorrhoeae strain ATCC 49226,ATCC 49226,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28870224,485,,,,MLST.Neisseria_spp.11075,,ATCC:49226,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171215.1,"CP098538,CP098539",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,198.0x,Unicycler v. 0.4.9,1,1,2,2166844,52.597557,2633,2211,,,2020,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.82,0.42,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18005,Neisseria gonorrhoeae strain 10577,10577,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28870232,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171235.1,"CP098540,CP098541",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,261.0x,Unicycler v. 0.4.9,1,1,2,2218676,52.427032,2675,2270,urethal swab,,2018,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18006,Neisseria gonorrhoeae strain 10704,10704,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871626,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171255.1,"CP098542,CP098543",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,273.0x,Unicycler v. 0.4.9,1,1,2,2222702,52.415035,2706,2262,urethal swab,,2019,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.12,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18007,Neisseria gonorrhoeae strain 9126,9126,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871698,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171295.1,"CP098546,CP098547",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,266.0x,Unicycler v. 0.4.9,1,1,2,2224948,52.406258,2695,2277,urethal swab,,2015,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18008,Neisseria gonorrhoeae strain 10296,10296,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871644,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171275.1,"CP098544,CP098545",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,279.0x,Unicycler v. 0.4.9,1,1,2,2220393,52.437386,2683,2255,urethal swab,,2017,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18009,Neisseria gonorrhoeae strain 9343,9343,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871700,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171315.1,"CP098548,CP098549",,"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,",Illumina MiniSeq; Oxford Nanopore MinION,291.0x,Unicycler v. 0.4.9,1,1,2,2218188,52.41481,2688,2270,urethal swab,,2016,,Russia,,,,gonorrhoea,,,,,,,,,,,,,Isolates from the most common Russian NG-MAST types,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.75,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18013,Neisseria gonorrhoeae 9035,9035,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28859053,485,,,,,,,,2022-10-04T00:00:00Z,,PRJNA768989,GCA_025562635.1,"CP104546,CP104547",,,Illumina MiniSeq; Oxford Nanopore MinION,247.0x,Unicycler v. 0.4.9,1,1,2,2226927,52.392555,2704,2291,urethal swab,,2015,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18014,Neisseria gonorrhoeae 10538,10538,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28859076,485,,,,,,,,2022-10-04T00:00:00Z,,PRJNA768989,GCA_025562675.1,"CP104548,CP104549",,,Illumina MiniSeq; Oxford Nanopore MinION,269.0x,Unicycler v. 0.4.9,1,1,2,2221821,52.417812,2706,2283,urethral swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Urinary Tract,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18015,Neisseria gonorrhoeae 10723,10723,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28858607,485,,,,,,,,2022-10-10T00:00:00Z,,PRJNA768989,GCA_025641865.1,"CP106749,CP106750",,,Illumina MiniSeq; Oxford Nanopore MinION,241.0x,Unicycler v. 0.4.9,1,1,2,2196578,52.51195,2639,2250,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18016,Neisseria gonorrhoeae 10744,10744,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014135,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642335.1,"CP106801,CP106802",,,Illumina MiniSeq; Oxford Nanopore MinION,167.0x,Unicycler v. 0.4.8,1,1,2,2233140,52.448166,2700,2300,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18017,Neisseria gonorrhoeae 10819,10819,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014148,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642355.1,"CP106803,CP106804",,,Illumina MiniSeq; Oxford Nanopore MinION,127.0x,Unicycler v. 0.4.8,1,1,2,2233848,52.450123,2695,2301,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18018,Neisseria gonorrhoeae 10743,10743,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014963,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642375.1,"CP106805,CP106806",,,Illumina MiniSeq; Oxford Nanopore MinION,171.0x,Unicycler v. 0.4.8,1,1,2,2231456,52.445534,2717,2296,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18019,Neisseria gonorrhoeae 10736,10736,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014981,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642395.1,"CP106807,CP106808",,,Illumina MiniSeq; Oxford Nanopore MinION,115.0x,Unicycler v. 0.4.8,1,1,2,2231581,52.442326,2715,2295,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18020,Neisseria gonorrhoeae 10708,10708,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014987,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642415.1,"CP106809,CP106810",,,Illumina MiniSeq; Oxford Nanopore MinION,172.0x,Unicycler v. 0.4.8,1,1,2,2231850,52.447075,2697,2303,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18021,Neisseria gonorrhoeae 9431,9431,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014998,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642475.1,"CP106813,CP106814",,,Illumina MiniSeq; Oxford Nanopore MinION,111.0x,Unicycler v. 0.4.8,1,1,2,2231455,52.44179,2703,2302,urethal swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18022,Neisseria gonorrhoeae 10531,10531,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31014989,485,,,,,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642435.1,"CP106811,CP106812",,,Illumina MiniSeq; Oxford Nanopore MinION,98.0x,Unicycler v. 0.4.8,1,1,2,2219158,52.415737,2680,2278,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18023,Neisseria gonorrhoeae 10562,10562,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31015000,485,,,,,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025642455.1,"CP106815,CP106816",,,Illumina MiniSeq; Oxford Nanopore MinION,133.0x,Unicycler v. 0.4.8,1,1,2,2227383,52.378643,2709,2288,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18024,Neisseria gonorrhoeae 10814,10814,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28834904,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169475.1,"CP098460,CP098461",,,Illumina MiniSeq; Oxford Nanopore MinION,303.0x,Unicycler v. 0.4.9,1,1,2,2216522,52.448654,2668,2251,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18025,Neisseria gonorrhoeae 9399,9399,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28859080,485,,,,,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025169495.2,JANASX000000000,,,Illumina MiniSeq; Oxford Nanopore MinION,287.0x,Unicycler v. 0.4.8,1,1,2,2223359,52.395496,2687,2294,urethral swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Urinary Tract,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18028,Neisseria gonorrhoeae 9460,9460,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835168,485,,,,MLST.Neisseria_spp.11177,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169585.1,"CP098462,CP098463",,,Illumina MiniSeq; Oxford Nanopore MinION,306.0x,Unicycler v. 0.4.9,1,1,2,2232723,52.44175,2704,2281,urethal swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18030,Neisseria gonorrhoeae 10529,10529,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869590,485,,,,,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025169685.2,JAMQMU000000000,,,Illumina MiniSeq; Oxford Nanopore MinION,250.0x,Unicycler v. 0.4.8,1,2,3,2254865,52.348057,2743,2325,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18031,Neisseria gonorrhoeae 9464,9464,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871631,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-11T00:00:00Z,,PRJNA768989,GCA_025169745.2,JAMQRR000000000,,,Illumina MiniSeq; Oxford Nanopore MinION,327.0x,Unicycler v. 0.4.8,1,1,2,2232635,52.445385,2711,2297,urethal swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18032,Neisseria gonorrhoeae 9458,9458,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835169,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169785.1,"CP098476,CP098477",,,Illumina MiniSeq; Oxford Nanopore MinION,390.0x,Unicycler v. 0.4.9,1,1,2,2237257,52.45848,2699,2293,urethal swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18034,Neisseria gonorrhoeae 10269,10269,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835821,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025169995.1,"CP098464,CP098465",,,Illumina MiniSeq; Oxford Nanopore MinION,296.0x,Unicycler v. 0.4.9,1,1,2,2217599,52.43901,2674,2261,urethal swab,,2017,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18035,Neisseria gonorrhoeae 10720,10720,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835880,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170155.2,"CP098466,CP098467",,,Illumina MiniSeq; Oxford Nanopore MinION,312.0x,Unicycler v. 0.4.9,1,1,2,2223705,52.41635,2676,2263,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18036,Neisseria gonorrhoeae 10328,10328,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28835919,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170325.2,"CP098468,CP098469",,,Illumina MiniSeq; Oxford Nanopore MinION,249.0x,Unicycler v. 0.4.9,1,1,2,2218145,52.4463,2675,2247,urethal swab,,2017,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18037,Neisseria gonorrhoeae 10792,10792,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28836998,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170505.2,"CP098470,CP098471",,,Illumina MiniSeq; Oxford Nanopore MinION,287.0x,Unicycler v. 0.4.9,1,1,2,2218601,52.441875,2668,2254,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18038,Neisseria gonorrhoeae 10612,10612,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28837864,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170665.1,"CP098472,CP098473",,,Illumina MiniSeq; Oxford Nanopore MinION,323.0x,Unicycler v. 0.4.9,1,1,2,2220895,52.420353,2698,2265,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,2.2,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18039,Neisseria gonorrhoeae 10268,10268,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28858863,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170685.2,"CP098503,CP098504",,,Illumina MiniSeq; Oxford Nanopore MinION,284.0x,Unicycler v. 0.4.9,1,1,2,2218611,52.42172,2673,2265,urethal swab,,2017,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18040,Neisseria gonorrhoeae 10536,10536,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28859049,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170705.2,"CP098505,CP098506",,,Illumina MiniSeq; Oxford Nanopore MinION,277.0x,Unicycler v. 0.4.9,1,1,2,2232626,52.325825,2737,2295,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18041,Neisseria gonorrhoeae 10537,10537,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869552,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170725.2,"CP098532,CP098533",,,Illumina MiniSeq; Oxford Nanopore MinION,319.0x,Unicycler v. 0.4.9,1,1,2,2233025,52.364887,2710,2290,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18042,Neisseria gonorrhoeae 10525,10525,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869554,485,,,,MLST.Neisseria_spp.6809,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025170885.2,"CP098534,CP098535",,,Illumina MiniSeq; Oxford Nanopore MinION,298.0x,Unicycler v. 0.4.9,1,1,2,2215739,52.382072,2706,2263,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18043,Neisseria gonorrhoeae 10771,10771,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28869592,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171075.1,"CP098536,CP098537",,,Illumina MiniSeq; Oxford Nanopore MinION,295.0x,Unicycler v. 0.4.9,1,1,2,2214409,52.445553,2651,2247,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18044,Neisseria gonorrhoeae ATCC 49226,ATCC 49226,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28870224,485,,,,MLST.Neisseria_spp.11075,,ATCC:49226,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171215.2,"CP098538,CP098539",,,Illumina MiniSeq; Oxford Nanopore MinION,198.0x,Unicycler v. 0.4.9,1,1,2,2166844,52.597557,2633,2211,,,2020,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18045,Neisseria gonorrhoeae 10577,10577,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28870232,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171235.1,"CP098540,CP098541",,,Illumina MiniSeq; Oxford Nanopore MinION,261.0x,Unicycler v. 0.4.9,1,1,2,2218676,52.427032,2675,2270,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18046,Neisseria gonorrhoeae 10704,10704,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871626,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171255.1,"CP098542,CP098543",,,Illumina MiniSeq; Oxford Nanopore MinION,273.0x,Unicycler v. 0.4.9,1,1,2,2222702,52.415035,2706,2262,urethal swab,,2019,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.6,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18047,Neisseria gonorrhoeae 10296,10296,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871644,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171275.1,"CP098544,CP098545",,,Illumina MiniSeq; Oxford Nanopore MinION,279.0x,Unicycler v. 0.4.9,1,1,2,2220393,52.437386,2683,2255,urethal swab,,2017,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18048,Neisseria gonorrhoeae 9126,9126,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871698,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171295.2,"CP098546,CP098547",,,Illumina MiniSeq; Oxford Nanopore MinION,266.0x,Unicycler v. 0.4.9,1,1,2,2224948,52.406258,2695,2277,urethal swab,,2015,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18049,Neisseria gonorrhoeae 9343,9343,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28871700,485,,,,,,,,2022-09-13T00:00:00Z,,PRJNA768989,GCA_025171315.2,"CP098548,CP098549",,,Illumina MiniSeq; Oxford Nanopore MinION,291.0x,Unicycler v. 0.4.9,1,1,2,2218188,52.41481,2688,2270,urethal swab,,2016,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18123,Neisseria gonorrhoeae H035,H035,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31203372,485,,,,,genotype:GyrB_D429V,,,2022-10-21T00:00:00Z,,PRJNA887939,GCA_025758415.1,"CP107223,CP107224",,,Illumina NextSeq,235.0x,Unicycler v. v0.4.7,1,1,2,2172095,52.58716,2613,2225,urethra,,2000,Japan,Japan,,male,33,Gonorrhea,,host_disease_outcome:recovery;host_disease_stage:symptomatic;host_health_state:healthy,Resistant;Intermediate;Susceptible,AMR Panel,,,,,,,,,,collected_by:National Institute of Infectious Diseases,,,,,,,Gonorrhea,healthy,recovery,,symptomatic,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18124,Neisseria gonorrhoeae 10588,10588,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28830140,485,,,,,,,,2022-10-21T00:00:00Z,,PRJNA768989,GCA_025790185.1,"CP098458,CP098459",,,Illumina MiniSeq; Oxford Nanopore MinION,194.0x,Unicycler v. 0.4.9,1,1,2,2225251,52.386856,2691,2261,urethal swab,,2018,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18125,Neisseria gonorrhoeae 10239,10239,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN28833726,485,,,,MLST.Neisseria_spp.11177,,,,2022-10-21T00:00:00Z,,PRJNA768989,GCA_025790205.1,"CP098474,CP098475",,,Illumina MiniSeq; Oxford Nanopore MinION,290.0x,Unicycler v. 0.4.9,1,1,2,2227886,52.45367,2687,2276,urethal swab,,2017,Russia,Russia,,,,gonorrhoea,,,,,,,,,,,,,,collected_by:Alexey Kubanov,,,,,,,gonorrhoea,,,,,,,,,,,,,,100,0.4,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.18126,Neisseria gonorrhoeae 1081168,1081168,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31165854,485,,,,,,ATCC:BAA-3085,,2022-10-22T00:00:00Z,,PRJNA887340,GCA_025790925.1,CP107270,,,Illumina/Oxford Nanopore,374.895x,Unicycler v. v0.4.8,1,0,1,2230282,52.343964,2700,2291,urethra,,2014,Italy,Italy,,male,28,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18127,Neisseria gonorrhoeae 1123850,1123850,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31165853,485,,,,,,ATCC:BAA-3084,,2022-10-22T00:00:00Z,,PRJNA887340,GCA_025790945.1,CP107271,,,Illumina/Oxford Nanopore,521.971x,Unicycler v. v0.4.8,1,0,1,2217711,52.42987,2673,2277,reproductive system,,2014,Taiwan,Taiwan,,male,17,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18128,Neisseria gonorrhoeae 1130991,1130991,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31165852,485,,,,,,ATCC:BAA-3083,,2022-10-22T00:00:00Z,,PRJNA887340,GCA_025790965.1,CP107272,,,Illumina/Oxford Nanopore,494.92x,Unicycler v. v0.4.8,1,0,1,2230471,52.346928,2709,2280,cervix,,2014,Belgium,Belgium,,female,28,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18129,Neisseria gonorrhoeae 1137292,1137292,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31165851,485,,,,,,ATCC:BAA-3082,,2022-10-22T00:00:00Z,,PRJNA887340,GCA_025790985.1,CP107273,,,Illumina/Oxford Nanopore,358.72x,Unicycler v. v0.4.8,1,0,1,2228866,52.359917,2686,2295,urethra,,2014,Israel,Israel,,male,37,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18130,Neisseria gonorrhoeae 1145734,1145734,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31165850,485,,,,,,ATCC:BAA-3081,,2022-10-22T00:00:00Z,,PRJNA887340,GCA_025791005.1,CP107274,,,Illumina/Oxford Nanopore,452.028x,Unicycler v. v0.4.8,1,0,1,2163610,52.65843,2611,2214,urine,,2014,Chile,Chile,,male,30,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18196,Neisseria gonorrhoeae FA1090 N-1-60,FA1090 N-1-60,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31428011,485,,,,,,,,2023-01-17T00:00:00Z,33109763,PRJNA893598,,"CP115654,CP115655",,,Oxford Nanopore MinION; Illumina NextSeq,184.0x,Trycycler v. v0.5.0,1,1,2,2159214,52.689125,2599,2200,genital tract,,,USA,"USA:Durham, North Carolina",,,,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18197,Neisseria gonorrhoeae MS11 HL-1-22,MS11 HL-1-22,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN31428012,485,,,,,,,,2023-01-19T00:00:00Z,,PRJNA893598,,"CP115904,CP115905",,,Oxford Nanopore MinION; Illumina NextSeq,293.0x,Trycycler v. v0.5.0,1,1,2,2263342,52.372154,2762,2338,genital tract,,,USA,"USA: NY, NY",,,,Gonorrhea,,,,,,,,,,,,,,,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0.2,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.18198,Neisseria gonorrhoeae SE690.,SE690.,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN32765978,485,,,,,,,,2023-02-06T00:00:00Z,,PRJNA924675,,"CP116342,CP116343,CP116344,CP116345",,,Illumina MiSeq; Oxford Nanopore MinION,90.0x,Unicycler v. v0.5.0,1,3,4,2218634,52.49221,2694,2262,urethra,,2022,Sweden,Sweden,,,,Gonorrhea,,,Resistant;Susceptible;Not defined,AMR Panel,,,,,,,,,,collected_by:WHO Collaborating Centre for Gonorrhoea and Other STIs,,,,,,,Gonorrhea,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.3183,Neisseria gonorrhoeae strain TFG-A2 strain not applicable,not applicable,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN10035124,485,,,,,,,,2019-03-08T00:00:00Z,,PRJNA451379,GCA_004332535.1,"CP032398,CP032399",,The University of Queensland,PacBio RSII,244.0x,HGAP v. 3.0,1,1,2,2225966,52.399902,2711,2187,clinical sample: throat,,2011-03,Australia,Australia: New South Wales,,male,,gonorrhea,,,,,,,,,,,,,"Antimicrobial resistant Neisseria gonorrhoeae has become a major global public health issue, with particular concern over isolates exhibiting decreased susceptibility to ceftriaxone becoming widespread. Treatment failures have been previously reported with third-generation cephalosporins, with ceftriaxone considered the last remaining empirical monotherapy for gonorrhoea. Here, we report both the pre- and post-treatment isolates from a treatment failure associated with ceftriaxone monotherapy identified in March 2011. This BioProject includes the complete PacBio genome sequence of TFG-A2.",collected_by:not applicable,,,,,,,gonorrhea,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Gonorrhea,Respiratory Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.3184,Neisseria gonorrhoeae strain TFG-B2 strain not applicable,not applicable,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN10031335,485,,,,,,,,2019-03-08T00:00:00Z,,PRJNA451380,GCA_004332555.1,"CP032429,CP032428",,The University of Queensland,PacBio RSII,495.0x,HGAP v. 3.0,1,1,2,2224596,52.40538,2714,2157,clinical sample: throat,,2011-07,Australia,Australia: New South Wales,,male,,gonorrhea,,,,,,,,,,,,,"Antimicrobial resistant Neisseria gonorrhoeae has become a major global public health issue, with particular concern over isolates exhibiting decreased susceptibility to ceftriaxone becoming widespread. Treatment failures have been previously reported with third-generation cephalosporins, with ceftriaxone considered the last remaining empirical monotherapy for gonorrhoea. Here, we report both the pre- and post-treatment isolates from a treatment failure associated with ceftriaxone monotherapy identified in July 2011. This BioProject includes the complete PacBio genome sequence of TFG-B2.",collected_by:not applicable,,,,,,,gonorrhea,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Gonorrhea,Respiratory Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.3283,Neisseria gonorrhoeae strain NJ1711654,NJ1711654,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN12252293,485,,,,MLST.Neisseria_spp.1903,genotype:ST17114,,,2019-07-18T00:00:00Z,,PRJNA553852,GCA_007107165.1,CP041585,,"Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",PacBio RSII,271.0x,HGAP v. 2018,1,,1,2215121,52.412533,2805,2543,urine; urine from a single man with urethral purulent discharge and dysuria,"isolated in Nanjing, China in 2017, revealing the dissemination of FC428 and its subclones",2017-09,China,China:Nanjing,,male,24,urethritis,,host_disease_outcome:recovery,,,,,,,,,,,"Neisseria gonorrhoeae, the etiologic agent of gonorrhea, develops antimicrobial resistance to almost all antibiotic classes used for treatment of gonorrhea, making gonorrhea an untreatable disease in the foreseeable future. A neisseria gonorrhoeae FC428 subclone NJ1711654 with high level resistance to expand-spectrum cephalosporins ceftriaxone and cefixime was isolated in Nanjing, China in 2017, revealing the dissemination of FC428 and its subclones. So it is warrant to enhance surveillance and develop new antimicrobials for the treatment of gonorrhea.","collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,urethritis,,recovery,,,,,,,,,,,,99.79,0.21,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.3284,Neisseria gonorrhoeae strain NJ189125,NJ189125,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN12252303,485,,,,,genotype:ST3435,,,2019-07-18T00:00:00Z,,PRJNA553854,GCA_007107365.1,CP041586,,"Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",PacBio RSII,405.0x,HGAP v. 2019,1,,1,2185626,52.377075,2756,2508,urine a married man with urethral purulent discharge and dysuria,"isolated in Nanjing, China in 2018, revealing the dissemination of FC428 and its subclones",2018-07,China,China:Nanjing,,male,34,urethritis,,host_disease_outcome:recovery,,,,,,,,,,,"Neisseria gonorrhoeae, the etiologic agent of gonorrhea, develops antimicrobial resistance to almost all antibiotic classes used for treatment of gonorrhea, making gonorrhea an untreatable disease in the foreseeable future. A neisseria gonorrhoeae FC428 subclone NJ189125 with high level resistance to expand-spectrum cephalosporins ceftriaxone and cefixime was isolated in Nanjing, China in 2018, revealing the dissemination of FC428 and its subclones. So it is warrant to enhance surveillance and develop new antimicrobials for the treatment of gonorrhea.","collected_by:Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College",,,,,,,urethritis,,recovery,,,,,,,,,,,,98.41,0.21,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,485.3329,Neisseria gonorrhoeae strain AUSMDU00010541,AUSMDU00010541,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN10920452,485,,,,,mlst:ST10899,,,2019-11-12T00:00:00Z,33180013,PRJNA556438,GCA_009650075.1,"CP045832,CP045833,CP045834",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,789x,de novo,1,2,3,2221012,52.487198,2765,2356,missing,,2017,Australia,Australia,,,,Gonorrhea,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.8102,Neisseria gonorrhoeae strain NG290,NG290,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN12676040,485,,,,,genotype:MLST ST1903,,,2020-03-03T00:00:00Z,,PRJNA563548,GCA_011058635.1,"CP043812,CP043813,CP043814,CP043815",,Mahidol University,Illumina; Oxford Nanopore,5.0x,Unicycler v. v0.4.4,1,3,4,2269843,52.29943,2825,2593,vaginal swab,,2011-06-18,Thailand,Thailand: Bangkok,,female,13,Gonorrhea,,,,,,,,,,,,,"Study to sequence Neisseria gonorrhoeae isolates collected at Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand during 2009-2011. These data are part of a pre-publication release.","collected_by:Faculty of Medicine Siriraj Hospital, Mahidol University",,,,,,,Gonorrhea,,,,,,,,,,,,,,99.61,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.8103,Neisseria gonorrhoeae strain NG251,NG251,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN12676039,485,,,,MLST.Neisseria_spp.1903,genotype:MLST ST1903,,,2020-03-03T00:00:00Z,,PRJNA563548,GCA_011058655.1,"CP043816,CP043817,CP043818,CP043819",,Mahidol University,Illumina; Oxford Nanopore,5.0x,unicycler v. v0.4.4,1,3,4,2269994,52.318596,2828,2590,urethral swab,,2010-07-30,Thailand,Thailand: Bangkok,,male,19,Gonorrhea,,,,,,,,,,,,,"Study to sequence Neisseria gonorrhoeae isolates collected at Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand during 2009-2011. These data are part of a pre-publication release.","collected_by:Faculty of Medicine Siriraj Hospital, Mahidol University",,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.8104,Neisseria gonorrhoeae strain NG196,NG196,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN12676038,485,,,,,,,,2020-03-03T00:00:00Z,,PRJNA563548,GCA_011058675.1,"CP043871,CP043872,CP043873,CP043874",,Mahidol University,Illumina; Oxford Nanopore,5.0x,Unicycler v. v0.4.4,1,3,4,2270041,52.311523,2827,2600,urethral discharge,,2009-05-07,Thailand,Thailand: Bangkok,,male,33,Gonorrhea,,,,,,,,,,,,,"Study to sequence Neisseria gonorrhoeae isolates collected at Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand during 2009-2011. These data are part of a pre-publication release.","collected_by:Faculty of Medicine Siriraj Hospital, Mahidol University",,,,,,,Gonorrhea,,,,,,,MLST ST1903,,,,,,,99.71,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.8201,Neisseria gonorrhoeae strain 3648,3648,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN11597889,485,,,,MLST.Neisseria_spp.1926,,,,2020-07-08T00:00:00Z,,PRJNA541586,GCA_013393965.1,CP040394,,University of Saskatchewan,Illumina MiSeq,116x,SPAdes v. 3.10.1,1,0,1,2214431,52.51235,2528,,missing,,1980,Canada,Canada:Ontario,,,,gonorrhea,,,,,,,,,,,,,WGS of Neisseria gonorrhoeae isolates from different Canadian provinces,"collected_by:Laboratory Centre for Disease Control, Health Canada",,,,,,,gonorrhea,,,,,,,,,,,,,,99.24,0.21,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.8202,Neisseria gonorrhoeae strain 4020,4020,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN11597883,485,,,,,,,,2020-07-08T00:00:00Z,,PRJNA541586,GCA_013393985.1,CP040395,,University of Saskatchewan,Illumina MiSeq,83x,SPAdes v. 3.10.1,1,0,1,2203166,52.53001,2538,,missing,,1980,Canada,Canada:Toronto,,,,gonorrhea,,,,,,,,,,,,,WGS of Neisseria gonorrhoeae isolates from different Canadian provinces,"collected_by:Laboratory Centre for Disease Control, Health Canada",,,,,,,gonorrhea,,,,,,,,,,,,,,99.71,0.21,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.879,Neisseria gonorrhoeae strain FDAARGOS_204,FDAARGOS_204,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875541,485,,,,,,FDA:FDAARGOS_204,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073535.2,CP020415,,US Food and Drug Administration,PacBio,13.9046497317419x,HGAP v. 3,1,,1,2212422,52.45,2756,2532,cervix,,,USA,USA:WI,,,,Presumptive gonorrhea,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.","collected_by:ATCC < Enzo Biochem, Inc. < ATCC 27629",,,,,,,Presumptive gonorrhea,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.881,Neisseria gonorrhoeae strain FDAARGOS_207,FDAARGOS_207,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875544,485,,,,MLST.Neisseria_spp.13450,,FDA:FDAARGOS_207,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073655.2,CP020419,,US Food and Drug Administration,PacBio,12.979653063562x,HGAP v. 3,1,,1,2189343,52.36,2721,2505,human,,1983,USA,USA:NC,,,,Probable disseminated gonococcal infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:ATCC < DW Dyer < J Cannon < I Nachamkin,,,,,,,Probable disseminated gonococcal infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0.6,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.938,Neisseria gonorrhoeae strain NCTC13798,NCTC13798,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMEA4076741,485,,,,,,NCTC:13798,,2017-08-15T00:00:00Z,,PRJEB6403,GCA_900186875.1,LT906440,,SC,,,,1,,1,2230241,52.35,2684,2227,throat swab,,2015,United Kingdom,United Kingdom,,male,,,,"host_health_state:Infection, failed treatment",,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,"Infection, failed treatment",,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,485.939,Neisseria gonorrhoeae strain NCTC13800,NCTC13800,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMEA4076768,485,,,,,,NCTC:13800,,2017-08-15T00:00:00Z,,PRJEB6403,GCA_900186915.1,LT906472,,SC,,,,1,,1,2226638,52.36,2690,2217,throat swab,,2015,United Kingdom,United Kingdom,,male,,,,host_health_state:Infection,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Infection,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,485.940,Neisseria gonorrhoeae strain NCTC13799,NCTC13799,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMEA4076765,485,,,,,,NCTC:13799,,2017-08-15T00:00:00Z,,PRJEB6403,GCA_900186935.1,LT906437,,SC,,,,1,,1,2172222,52.56,2605,2157,throat swab,,2015,United Kingdom,United Kingdom,,female,,,,host_health_state:Infection,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Infection,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,485.9831,Neisseria gonorrhoeae strain BJ16148,BJ16148,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14433815,485,,,,,genotype:1903,,,2020-09-22T00:00:00Z,32473014,PRJNA614605,GCA_014700555.1,CP050505,,"National Center for STD Control, China Center for Disease Control and Prevention",PacBio RSII,200X,FALCON v. 0.3,1,0,1,2215157,52.412582,2673,2250,clinical sample,,2016,China,China,,,,Gonorrhea,,,,,,,,,,,,,Ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone isolated from China-GRSP,collected_by:China-GRSP,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9832,Neisseria gonorrhoeae strain SW0274,SW0274,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960555,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844795.1,CP061483,,NCBS,Oxford Nanopore MiniION,220x,BWA v. 0.7.12,1,0,1,2147987,52.590572,2642,2173,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Intermediate,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,98.93,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9833,Neisseria gonorrhoeae strain SW0259,SW0259,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960554,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844815.1,CP061484,,NCBS,Oxford Nanopore MiniION,129x,BWA v. 0.7.12,1,0,1,2150148,52.60191,2610,2165,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Intermediate,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.78,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9834,Neisseria gonorrhoeae strain SW0236,SW0236,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960553,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844835.1,CP061485,,NCBS,Oxford Nanopore MiniION,241x,BWA v. 0.7.12,1,0,1,2148016,52.605007,2644,2169,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,98.64,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9835,Neisseria gonorrhoeae strain SW0223,SW0223,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960552,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844855.1,CP061492,,NCBS,Oxford Nanopore MiniION,86x,BWA v. 0.7.12,1,0,1,2152289,52.582718,2612,2167,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Intermediate,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.56,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9836,Neisseria gonorrhoeae strain SW0015,SW0015,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960551,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844875.1,CP061486,,NCBS,Oxford Nanopore MiniION,848x,BWA v. 0.7.12,1,0,1,2153514,52.631447,2625,2166,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9837,Neisseria gonorrhoeae strain SW0032,SW0032,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960550,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844895.1,CP061487,,NCBS,Oxford Nanopore MiniION,63x,BWA v. 0.7.12,1,0,1,2151426,52.558205,2640,2172,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Resistant,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.23,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9838,Neisseria gonorrhoeae strain SW0018,SW0018,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960548,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844935.1,CP061489,,NCBS,Oxford Nanopore MiniION,272x,BWA v. 0.7.12,1,0,1,2147640,52.520985,2669,2175,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,98.54,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9839,Neisseria gonorrhoeae strain SW0011,SW0011,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960549,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844915.1,CP061488,,NCBS,Oxford Nanopore MiniION,1255x,BWA v. 0.7.12,1,0,1,2153173,52.637447,2616,2173,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Resistant,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.61,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9840,Neisseria gonorrhoeae strain SW0005,SW0005,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960547,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844955.1,CP061490,,NCBS,Oxford Nanopore MiniION,377x,BWA v. 0.7.12,1,0,1,2152607,52.621513,2608,2177,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible;Resistant;Intermediate,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.51,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9841,Neisseria gonorrhoeae strain SW0002,SW0002,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN15960546,485,,,,,,,,2020-10-05T00:00:00Z,,PRJNA660404,GCA_014844975.1,CP061491,,NCBS,Oxford Nanopore MiniION,524x,BWA v. 0.7.12,1,0,1,2153658,52.60857,2619,2177,vaginal discharge,,2012-2017,Kenya,Kenya: Nairobi,,female,,gonorrhoea,,,Susceptible,AMR Panel,,,,,,,,,Genome assembly and analysis to study the basis of anti-microbial resistance and sequence typing,collected_by:Meshack Juma,,,,,,,gonorrhoea,,,,,,,,,,,,,,99.51,0.21,Sexually Transmitted Infections (STIs),Other STIs,Genitourinary,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9863,Neisseria gonorrhoeae strain 20181204,20181204,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN17393045,485,,,,,,,,2021-02-01T00:00:00Z,,PRJNA693638,GCA_016775785.1,"CP068761,CP068762,CP068763,CP068764",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,400.0x,Unicycler v. v0.4.9b,1,3,4,2222653,52.490963,2705,2265,swab,,2018,Australia,Australia,,,,Gonorrhoea,,,,,,,,,,,,,N. gonorrhoeae WGS,collected_by:Queensland Health,,,,,,,Gonorrhoea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9864,Neisseria gonorrhoeae strain SRRSH240,SRRSH240,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14117309,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802315.1,"CP048893,CP048894,CP048895",,Zhejiang University,,,,1,2,3,2257926,52.342327,2686,,urine,,2019-10-04,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9865,Neisseria gonorrhoeae strain SRRSH229,SRRSH229,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116992,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802335.1,"CP048896,CP048897,CP048898",,Zhejiang University,,,,1,2,3,2263203,52.33503,2678,,urine,,2019-07-22,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9866,Neisseria gonorrhoeae strain SRRSH214,SRRSH214,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116991,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802355.1,"CP048899,CP048900,CP048901",,Zhejiang University,,,,1,2,3,2260603,52.346478,2683,,urine,,2019-05-14,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9867,Neisseria gonorrhoeae strain SRRSH207,SRRSH207,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116990,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802385.1,"CP048902,CP048903,CP048904",,Zhejiang University,,,,1,2,3,2257932,52.34232,2677,,urine,,2019-08-20,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9868,Neisseria gonorrhoeae strain SRRSH205,SRRSH205,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116989,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802405.1,"CP048905,CP048906,CP048907",,Zhejiang University,,,,1,2,3,2260643,52.347008,2680,,urine,,2019-08-19,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9869,Neisseria gonorrhoeae strain SRRSH204,SRRSH204,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116988,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802425.1,"CP048911,CP048912,CP048913",,Zhejiang University,Illumina MiniSeq,100.0x,unicycler v. 0.4.7,1,2,3,2260630,52.34669,2686,,urine,,2019-07-25,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9870,Neisseria gonorrhoeae strain SRRSH203,SRRSH203,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14116987,485,,,,,,,,2021-02-02T00:00:00Z,33406237,PRJNA606927,GCA_016802445.1,"CP048908,CP048909,CP048910",,Zhejiang University,,,,1,2,3,2260653,52.346867,2680,,urine,,2019-07-24,China,China:Hangzhou,,,,Gonorrhea,,,,,,,,,,,,,we collected Neisseria gonorrhoeae isolates from patients and identified 7 high level ceftriaxone resistant isolates and did whole genome sequencing and assembly work.,collected_by:Stijn van der Veen,,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9871,Neisseria gonorrhoeae strain ATCC 49226,ATCC 49226,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13008815,485,,,,,,ATCC:49226,Yes,2021-02-03T00:00:00Z,,PRJNA576799,GCA_016803895.1,CP045728,,Zhejiang University,Illumina HiSeq,40.0x,SOAPdenovo v. AUGUST-2016,1,0,1,2069529,52.724323,2512,2204,vagina,,2000-10-30,Germany,Germany: Berlin,,,,gonorrhea,,,,,,,,,,,,,"To obtain more insight in the mechanisms N. gonorrhoeae employs to thrive in the hostile environment of the human host and survive immune attack, the applicant aims to use an unbiased approach. N. gonorrhoeae will be cultured in the presence of fatty acids. By stepwise increasing of the antimicrobial concentrations or by selecting and re-exposing of survivors natural mutants that show enhanced biological fitness can be selected. These mutants will be analyzed by full-genome sequencing and compared with their isogenic wild-type strains to identify beneficial mutations.",collected_by:C. Thornsberry,,,,,,,gonorrhea,,,,,,,,,,,,,,99.82,0.42,Sexually Transmitted Infections (STIs),Gonorrhea,Genitourinary,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9912,Neisseria gonorrhoeae strain NG250,NG250,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13151449,485,,,,,genotype:ST7363,,,2021-06-09T00:00:00Z,,PRJNA609415,GCA_018798905.1,"CP045707,CP045708,CP045709,CP045710",,"Faculty of Science, Mahidol University",Oxford Nanopore MiniION; Illumina HiSeq,5.0x,unicycler v. v0.4.4,1,3,4,2218399,52.483616,2709,2364,penile discharge,,2010-07-20,Thailand,Thailand: Bangkok,,male,15,Gonorrhea,,,,,,,,,,,,,WGS of MLST ST7363 Neisseria gonorrhoeae from Thailand,"collected_by:Faculty of Medicine Siriraj Hospital, Mahidol University",,,,,,,Gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Other,Sexually Transmitted Infections (STIs)-Gonorrhea HP,485.9937,Neisseria gonorrhoeae strain O2D156,O2D156,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998461,485,,,,,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019211805.1,CP078113,,Griffith University,PacBio Sequel,250x,HGAP v. v3,1,0,1,2165933,52.604813,2603,2193,bhi,,2005,Australia,Australia,,,,disseminated infection,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,disseminated infection,,,,,,,,,,,,,,99.82,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.9938,Neisseria gonorrhoeae strain O1G1370,O1G1370,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998459,485,,,,MLST.Neisseria_spp.1584,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019211865.1,CP078115,,Griffith University,PacBio Sequel,167x,HGAP v. v3,1,0,1,2215052,52.452675,2679,2256,bhi,,2005,Australia,Australia,,,,disseminated infection,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,disseminated infection,,,,,,,,,,,,,,99.51,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.9939,Neisseria gonorrhoeae strain 1291,1291,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998455,485,,,,MLST.Neisseria_spp.8422,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019211825.1,CP078119,,Griffith University,PacBio Sequel,275x,HGAP v. v3,1,0,1,2177032,52.561928,2622,2208,bhi,,1970,USA,USA,,,,gonorrhoeae,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,gonorrhoeae,,,,,,,,,,,,,,99.82,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9940,Neisseria gonorrhoeae strain 98D159,98D159,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998460,485,,,,,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019211845.1,CP078114,,Griffith University,PacBio Sequel,168x,HGAP v. v3,1,0,1,2172572,52.596554,2634,2200,bhi,,2005,Australia,Australia,,,,disseminated infection,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,disseminated infection,,,,,,,,,,,,,,99.71,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.9941,Neisseria gonorrhoeae strain MS11,MS11,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998456,485,,,,,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019212165.1,CP078118,,Griffith University,PacBio Sequel,289x,HGAP v. v3,1,0,1,2234079,52.365604,2702,2279,bhi,,1970,USA,USA,,,,gonorrhoeae,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,gonorrhoeae,,,,,,,,,,,,,,99.71,0.21,Sexually Transmitted Infections (STIs),Other STIs,Other,Sexually Transmitted Infections (STIs)-Other STIs HP,485.9942,Neisseria gonorrhoeae strain SK92679,SK92679,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998457,485,,,,MLST.Neisseria_spp.6715,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019212025.1,CP078117,,Griffith University,PacBio Sequel,91x,HGAP v. v3,1,0,1,2173187,52.583878,2620,2194,bhi,,2000,USA,USA,,,,disseminated infection,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,disseminated infection,,,,,,,,,,,,,,99.82,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.9943,Neisseria gonorrhoeae strain 88G285,88G285,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19998458,485,,,,,,,,2021-07-14T00:00:00Z,,PRJNA743132,GCA_019211885.1,CP078116,,Griffith University,PacBio Sequel,127x,HGAP v. v3,1,0,1,2174189,52.597633,2615,2183,bhi,,2005,Australia,Australia,,,,disseminated infection,,,,,,,,,,,,,Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections,,,,,,,,disseminated infection,,,,,,,,,,,,,,99.82,0.42,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,485.9947,Neisseria gonorrhoeae strain CT213,CT213,Neisseria gonorrhoeae,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN14131123,485,,,,,,,,2021-07-28T00:00:00Z,,PRJNA607374,GCA_019380275.1,"CP048929,CP048930,CP048931,CP048932",,"Faculty of Medicine Siriraj Hospital, Mahidol University",Illumina NovaSeq and Oxford Nanopore,1566.400443x,Unicycler v. 0.4.4,1,3,4,2219615,52.50523,2680,2226,urethra,,2010-01-15,Thailand,Thailand: Bangkok,,,15,gonorrhea,,,,,,,,,,,,,To explore the genomic dynamics of co-evolution between Neisseria gonorrhoeae and Schaalia turicensis,collected_by:Natakorn Nokchan,,,,,,,gonorrhea,,,,,,,,,,,,,,99.82,0.31,Sexually Transmitted Infections (STIs),Gonorrhea,Urinary Tract,Sexually Transmitted Infections (STIs)-Gonorrhea HP,486698.6,Mycobacterium riyadhense strain NTM,NTM,Mycobacterium riyadhense,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN12495011,486698,,,,,,,,2021-02-11T00:00:00Z,,PRJNA558523,GCA_016864455.1,CP045092,,King Faisal Specialist Hospital and Research Centre,IonTorrent,64.0x,SPAdes v. 3.13.0,1,0,1,6772223,65.10811,6779,,lungs,,2018-10,Saudi Arabia,Saudi Arabia,,,,Tuberculosis,,,,,,,,,,,,,NTM,collected_by:KFSHRC,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.28,1.19,Respiratory Diseases,Tuberculosis,Respiratory Tract,Respiratory Diseases-Tuberculosis HP,486994.11,Salmonella enterica subsp. enterica serovar Hvittingfoss strain AUSMDU00005056,AUSMDU00005056,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05589873,486994,Hvittingfoss,,,MLST.Salmonella_enterica.434,mlst:ST434,,,2019-11-12T00:00:00Z,33180013,PRJNA556438,GCA_009650055.1,CP045831,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,105x,de novo,1,,1,4744949,52.248,4746,4438,human,,2016,Australia,Australia,,,,Salmonellosis (except human typhoid & paratyphoid),,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",collected_by:not collected,,,,,,,Salmonellosis (except human typhoid & paratyphoid),,,,,,,,,,,,,,99.85,0.04,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases NHP,487.1231,Neisseria meningitidis strain 38277,38277,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04321475,487,,,,MLST.Neisseria_spp.845,,,,2017-01-30T00:00:00Z,,PRJNA305279,GCA_001974965.1,CP015886,NZ_CP015886.1,Public Health Agency of Canada,PacBio,202,HGAP v. 3,1,,1,2264278,51.4,2604,2123,throat,,2014,Canada,Canada,,,,,,,,,,,,Mesophilic,37 C,Aerobic,HostAssociated,,Closed genome of a commensal isolate,collected_by:British Columbia Centre for Disease Control;sample_type:Cell Culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Respiratory Tract,- HP,487.1300,Neisseria meningitidis strain FDAARGOS_214,FDAARGOS_214,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875551,487,,,,MLST.Neisseria_spp.344,,FDA:FDAARGOS_214,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073235.2,CP020401,,US Food and Drug Administration,PacBio,22.34x,CA v. 8.2,1,,1,2397439,51.05,2960,2683,spinal fluid,,,USA,USA:MD,,,,Meningococcal infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:USAMRIID < ATCC < S.E. Branham < F. Mickle,,,,,,,Meningococcal infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.8,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,487.1301,Neisseria meningitidis strain FDAARGOS_215,FDAARGOS_215,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875552,487,,,,MLST.Neisseria_spp.2875,,FDA:FDAARGOS_215,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073275.2,CP020402,,US Food and Drug Administration,PacBio,16.5293667860386x,HGAP v. 3,1,,1,2305808,51.43,2822,2574,spinal fluid,,,USA,USA:MA,,,,Meningococcal infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:USAMRIID,,,,,,,Meningococcal infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,487.1302,Neisseria meningitidis strain FDAARGOS_211,FDAARGOS_211,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875548,487,Group B,,,MLST.Neisseria_spp.2875,,FDA:FDAARGOS_211,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073555.2,CP020422,,US Food and Drug Administration,PacBio,16.6618785920759x,HGAP v. 3,1,,1,2305790,51.43,2823,2575,spinal fluid,,,USA,USA:MA,,,,Meningococcal infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.","collected_by:ATCC < Enzo Biochem, Inc. < ATCC 13090",,,,,,,Meningococcal infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,487.1303,Neisseria meningitidis strain FDAARGOS_209,FDAARGOS_209,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875546,487,Serogroup B,,,MLST.Neisseria_spp.4,,FDA:FDAARGOS_209,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073575.2,CP020420,,US Food and Drug Administration,PacBio,16.4151912652294x,HGAP v. 3,1,,1,2181227,51.89,2680,2439,human,,,United Kingdom,United Kingdom,,,,Meningococcal meningitis,,host_description:Invasive infection,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:ATCC < H Tettelin < R Moxon,,,,,,,Meningococcal meningitis,Missing,Missing,Invasive infection,Missing,,,,,,,,,,100,2.4,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.1306,Neisseria meningitidis strain COL-201504-11,COL-201504-11,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN05560575,487,,,,MLST.Neisseria_spp.11,genotype:ST-11,,,2017-03-31T00:00:00Z,,PRJNA319252,GCA_002075815.1,CP017257,,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,234.3642347,HGAP v. 3,1,,1,2195573,51.65,2599,2203,urethral swab,,2015,USA,"USA: Columbus, Ohio",,,,urethritis,,,,,,,,,,,,,"Epidemics of invasive meningococcal disease (IMD) caused by meningococcal serogroup A have been eliminated from the sub-Saharan African “meningitis belt” by the meningococcal A conjugate vaccine (MACV), yet other serogroups continue to cause epidemics. Neisseria meningitidis serogroup W (NmW) remains a major cause of disease in the region, with most isolates belonging to Clonal Complex 11 (CC11). The genomes of 92 NmW IMD isolates collected between 1994 and 2012 were sequenced, 85 being from selected meningitis belt countries. CC11 isolates were further analyzed to identify the phylogenetic placement of epidemic-associated strains and describe the genetic variation within and between epidemic-associated strains.",collected_by:Columbus STD clinic,,,,,,,urethritis,,,,,,,,,,,,,,99.4,1.2,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,487.1548,Neisseria meningitidis strain M26417,M26417,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07615714,487,,,,MLST.Neisseria_spp.11,,,,2017-10-16T00:00:00Z,28505234,PRJNA400487,GCA_002556585.1,CP023814,,Centers for Disease Control,PacBio,25x,HGAP v. 3,1,,1,2247997,51.59,2788,2589,sterile site,,2013,USA,United States,,,,bacterial meningitis,,,,,,,,,,,,,All meningococcal disease cases among men aged 18-64 years reported to the National Notifiable Disease Surveillance System between January 2012 and June 2015 were reviewed. Characteristics of meningococcal disease cases among MSM and men not known to be MSM (non-MSM) were described. Annualized incidence rates among MSM and non-MSM were compared through calculation of the relative risk and 95% confidence intervals. Isolates from meningococcal disease cases among MSM were characterized using standard microbiological methods and whole genome sequencing.,collected_by:US State Health Department,,,,,,,bacterial meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.1549,Neisseria meningitidis strain M26263,M26263,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07615715,487,,,,MLST.Neisseria_spp.11,,,,2017-10-16T00:00:00Z,28505234,PRJNA400487,GCA_002556605.1,CP023813,,Centers for Disease Control,PacBio,25x,HGAP v. 3,1,,1,2264467,51.56,2807,2609,sterile site,,2013,USA,United States,,,,bacterial meningitis,,,,,,,,,,,,,All meningococcal disease cases among men aged 18-64 years reported to the National Notifiable Disease Surveillance System between January 2012 and June 2015 were reviewed. Characteristics of meningococcal disease cases among MSM and men not known to be MSM (non-MSM) were described. Annualized incidence rates among MSM and non-MSM were compared through calculation of the relative risk and 95% confidence intervals. Isolates from meningococcal disease cases among MSM were characterized using standard microbiological methods and whole genome sequencing.,collected_by:US State Health Department,,,,,,,bacterial meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.2044,Neisseria meningitidis strain M21273,M21273,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN06144986,487,,,,MLST.Neisseria_spp.2724,,,,2018-02-01T00:00:00Z,,PRJNA324131,GCA_002951575.1,CP018907,,Centers for Disease Control and Prevention,PacBio,116.45,HGAP v. 3,1,,1,2203850,51.61318,2806,2648,not collected,,2009,USA,United States,,,,,,,,,,,,,,,,,"Backgound: Neisseria meningitidis (Nm), a Gram-negative diplococci that normally colonizes the nasopharynx, can rarely infect the urogenital tract. Oral sex is the presumptive mode of transmission. On urethral Gram stain, Nm can be confused with the more common sexually-transmitted pathogen Neisseria gonorrhoeae.Methods: In response to an outbreak of Nm urethritis among men at an STD clinic in Columbus, OH, there was an investigation into the epidemiologic, molecular and phylogenetic characteristics of cases identified between January 1 and November 18, 2015. Because the outbreak was identified through the CDC’s Gonococcal Isolate Surveillance Project, only men are included.Results: Seventy-two Nm urethritis cases were confirmed by biochemical and PCR testing. Men with Nm urethritis had a median age of 30.5 years (interquartile range (IQR): 24-38) and a median of 2 sex partners in the last 3 months (IQR: 1-3). Nm cases were overwhelmingly heterosexual (99%) and Black (82%). Nearly all cases had urethral discharge (90%), reported oral sex with a female in last 12 months (96%), and were treated with a regimen appropriate for Ng (94%). Only a minority had urethral chlamydia co-infection (15%). All urethral Nm isolates were non-groupable, part of the ST-11/CC-11 clonal complex, and phylogenetically clustered together.Conclusions: Between January-November 2015, there were 72 urethritis cases due to a clonal strain of Nm among men in Columbus, OH. Since Nm frequently colonizes the nasopharynx, oral sex may be a risk factor for transmission. Further study of this clonal Nm isolate, including short and long-term health consequences, is warranted.",,,,,,,,not collected,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,487.2792,Neisseria meningitidis strain NCTC10025,NCTC10025,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMEA104307683,487,not available: to be reported later,,,MLST.Neisseria_spp.4,,NCTC:10025,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638555.1,LR134525,,SC,,,,1,,1,2186098,51.88258,2504,2071,spinal fluid,,1900-1957,USA,USA: Illinois,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.41,0.21,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,487.3168,Neisseria meningitidis strain 12-221,12-221,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137413,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008329765.1,CP021517,,Orebro University Hospital,PacBio,144x,Celera Assembler v. HGAP v3,1,,1,2167947,51.693146,2645,2397,missing,,2012,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.56,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3169,Neisseria meningitidis strain 11-14,11-14,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137411,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330785.1,CP021519,,Orebro University Hospital,PacBio,132x,Celera Assembler v. HGAP v3,1,,1,2156539,51.75246,2617,2416,missing,,2011,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3170,Neisseria meningitidis strain 14-563,14-563,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137416,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330745.1,CP021516,,Orebro University Hospital,PacBio,197x,Celera Assembler v. HGAP v3,1,,1,2166707,51.709576,2624,2429,missing,,2014,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3171,Neisseria meningitidis strain 12-176,12-176,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137412,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330765.1,CP021518,,Orebro University Hospital,PacBio,186x,Celera Assembler v. HGAP v3,1,,1,2168615,51.674686,2614,2425,missing,,2012,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3172,Neisseria meningitidis strain 11-7,11-7,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137410,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330805.1,CP021520,,Orebro University Hospital,PacBio,151x,Celera Assembler v. HGAP v3,1,,1,2157444,51.76626,2629,2421,missing,,2011,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3173,Neisseria meningitidis strain 09-292,09-292,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137409,487,,,,MLST.Neisseria_spp.4183,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330825.1,CP021521,,Orebro University Hospital,PacBio,135x,Celera Assembler v. HGAP v3,1,,1,2198497,51.55986,2675,2470,missing,,2009,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.38,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3174,Neisseria meningitidis strain 06-178,06-178,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137408,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330845.1,CP021522,,Orebro University Hospital,PacBio,153x,Celera Assembler v. HGAP v3,1,,1,2167920,51.69319,2630,2434,missing,,2006,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3175,Neisseria meningitidis strain 98-182,98-182,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137407,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330865.1,CP021523,,Orebro University Hospital,PacBio,108x,Celera Assembler v. HGAP v3,1,,1,2167995,51.704594,2651,2443,missing,,1998,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3176,Neisseria meningitidis strain 95-134,95-134,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137406,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330885.1,CP021725,,Orebro University Hospital,PacBio,116x,Celera Assembler v. HGAP v3,1,,1,2165984,51.71123,2646,2434,missing,,1995,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.56,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3177,Neisseria meningitidis strain 12-330,12-330,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137414,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330905.1,CP021724,,Orebro University Hospital,PacBio,198x,Celera Assembler v. HGAP v3,1,,1,2169717,51.685772,2620,2431,missing,,2012,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3178,Neisseria meningitidis strain 13-600,13-600,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN07137415,487,,,,,,,,2019-09-09T00:00:00Z,,PRJNA386981,GCA_008330925.1,CP021723,,Orebro University Hospital,PacBio,159x,Celera Assembler v. HGAP v3,1,,1,2170095,51.679443,2621,2432,missing,,2013,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Whole genome sequencing of emergent Neisseria meningitidis serogroup Y,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.65,0.19,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3231,Neisseria meningitidis strain AUSMDU00005726,AUSMDU00005726,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13191641,487,Y,,,,mlst:ST1655,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664675.1,CP045960,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,768x,de novo,1,0,1,2166248,51.755432,2499,2193,blood,,2016,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.75,0.19,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,487.3232,Neisseria meningitidis strain AUSMDU00010537,AUSMDU00010537,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13191640,487,W,,,MLST.Neisseria_spp.11,mlst:ST11,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664695.1,CP045961,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,678x,de novo,1,0,1,2185677,51.656033,2557,2237,blood,,2014,Australia,Australia,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.83,0.21,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,487.3726,Neisseria meningitidis strain 16-579,16-579,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429014,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679665.1,CP030814,,Orebro University Hospital,PacBio,421.4x,Celera Assembler v. HGAP v3,1,0,1,2179401,51.704758,2637,2509,missing,,2016,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3727,Neisseria meningitidis strain 16-306,16-306,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429013,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679705.1,CP030815,,Orebro University Hospital,PacBio,462.3x,Celera Assembler v. HGAP v3,1,0,1,2169328,51.721733,2702,2501,missing,,2016,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.69,0,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3728,Neisseria meningitidis strain 16-92,16-92,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429012,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679735.1,CP030816,,Orebro University Hospital,PacBio,374.8x,Celera Assembler v. HGAP v3,1,0,1,2176177,51.722034,2627,2501,missing,,2016,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3729,Neisseria meningitidis strain 15-236,15-236,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429010,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679795.1,CP030818,,Orebro University Hospital,PacBio,805.3x,Celera Assembler v. HGAP v3,1,0,1,2179010,51.707058,2686,2513,missing,,2015,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.72,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3730,Neisseria meningitidis strain 16-7,16-7,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429011,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679775.1,CP030817,,Orebro University Hospital,PacBio,350.2x,Celera Assembler v. HGAP v3,1,0,1,2197385,51.62923,2784,2539,missing,,2016,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.13,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3731,Neisseria meningitidis strain 15-215,15-215,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429009,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679815.1,CP030819,,Orebro University Hospital,PacBio,258.7x,Celera Assembler v. HGAP v3,1,0,1,2179038,51.70644,2663,2514,missing,,2015,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3732,Neisseria meningitidis strain 15-198,15-198,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429008,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679845.1,CP030820,,Orebro University Hospital,PacBio,793.4x,Celera Assembler v. HGAP v3,1,0,1,2179025,51.705788,2661,2518,missing,,2015,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.51,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3733,Neisseria meningitidis strain 14-627,14-627,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429005,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679865.1,CP030823,,Orebro University Hospital,PacBio,1035.8x,Celera Assembler v. HGAP v3,1,0,1,2196100,51.64009,2677,2535,missing,,2014,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3734,Neisseria meningitidis strain 12-208,12-208,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429003,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679905.1,CP030825,,Orebro University Hospital,PacBio,380x,Celera Assembler v. HGAP v3,1,0,1,2171562,51.722126,2629,2495,missing,,2012,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3735,Neisseria meningitidis strain 14-159,14-159,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429004,487,,,,MLST.Neisseria_spp.11,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679885.1,CP030824,,Orebro University Hospital,PacBio,275.9x,Celera Assembler v. HGAP v3,1,0,1,2170460,51.738155,2697,2491,missing,,2014,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.51,0.1,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3736,Neisseria meningitidis strain 11-251,11-251,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429002,487,,,,MLST.Neisseria_spp.1287,,,,2020-11-24T00:00:00Z,,PRJNA476247,GCA_015679925.1,CP030826,,Orebro University Hospital,PacBio,342x,Celera Assembler v. HGAP v3,1,0,1,2182561,51.69143,2670,2512,missing,,2011,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.77,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3750,Neisseria meningitidis strain 15-193,15-193,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429007,487,,,,MLST.Neisseria_spp.11,,,,2020-12-03T00:00:00Z,,PRJNA476247,GCA_015732665.1,CP030821,,Orebro University Hospital,PacBio,350.9x,Celera Assembler v. HGAP v3,1,0,1,2172196,51.739716,2585,2124,missing,,2015,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,97.94,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3751,Neisseria meningitidis strain 15-123,15-123,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN09429006,487,,,,MLST.Neisseria_spp.11,,,,2020-12-03T00:00:00Z,,PRJNA476247,GCA_015732685.1,CP030822,,Orebro University Hospital,PacBio,408.1x,Celera Assembler v. HGAP v3,1,0,1,2171633,51.73922,2537,2108,missing,,2015,Sweden,Sweden,,,,invasive meningococcal disease,,,,,,,,,,,,,Neisseria meningitidis serogroup W sequencing,,,,,,,,invasive meningococcal disease,,,,,,,,,,,,,,99.37,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.3961,Neisseria meningitidis strain S4,S4,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN19789151,487,,,,MLST.Neisseria_spp.11,,,,2021-06-28T00:00:00Z,,PRJNA739446,GCA_019048825.1,CP077603,,University of Liverpool,PacBio Sequel; Illumina,100.0x,Filtlong v. 0.2.0; Flye v. 2.3.4; Racon,1,0,1,2206600,51.595985,2461,,nasal cavity,,2010,United Kingdom,United Kingdom,,,,meningitis,,,,,,,,,,,,,"Neisseria meningitidis has several strategies to evade complement-mediated killing, and these contribute to its ability to cause septicaemic disease and meningitis. However, the meningococcus is primarily an obligate commensal of the human nasopharynx, and it is unclear why the bacterium has evolved exquisite mechanisms to avoid host immunity. This study describes the sequencing and assembly of genome of S4, an invasive strain of Neisseria meningitidis.","collected_by:Sir William Dunn School of Pathology, University of Oxford",,,,,,,meningitis,,,,,,,,,,,,,,99.83,0.21,Neurological Diseases,Meningitis,Other,Neurological Diseases-Meningitis HP,487.4037,Neisseria meningitidis strain C311,C311,Neisseria meningitidis,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN20308719,487,,,,,,,,2021-07-27T00:00:00Z,,PRJNA748166,GCA_019356015.1,CP079941,,Griffith University,PacBio Sequel,243.0x,HGAP v. v3,1,0,1,2311508,51.264847,2590,2199,csf,,1987,United Kingdom,United Kingdom: Liverpool,,,,meningitis,,,,,,,,,,,,,"N. meningitidis strain C311 has been widely used to study meningococcal pathogenesis in the past 30 years but its genome is not available. The closed, complete and annotated genome sequence of C311 was determined by using Single-Molecule, Read-Time (SMRT) long read genome sequencing.",collected_by:Alder Hey Children's Hospital,,,,,,,meningitis,,,,,,,,,,,,,,99.75,0.19,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,488447.211,Burkholderia contaminans strain SCAID TST1-2021 (11/270) strain SCAID TST1-2021 (11/270) strain SCAID TST1-2021 (11/270),SCAID TST1-2021 (11/270),Burkholderia contaminans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN20982457,488447,,,,MLST.Burkholderia_cepacia_complex.102,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915365.1,"CP082807,CP082808,CP082809,CP082810,CP082811,CP082812",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,91x,Canu v. 2.0,3,3,6,8363142,66.25037,8297,7480,swab from tracheostomic tube,,2021-03-12,Kazakhstan,Kazakhstan: Almaty,,,,"Surgical Procedures, Operative",,,Resistant;Susceptible,AMR Panel,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,"Surgical Procedures, Operative",,,,,,,,,,,,,,98.21,0.48,Surgical Site Infections,,Other,Surgical Site Infections- HP,490.259,Neisseria sicca strain NS20201025,NS20201025,Neisseria sicca,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN18451419,490,,,,,,,,2021-04-05T00:00:00Z,,PRJNA714501,GCA_017753665.1,CP072524,,"First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,200X,SPAdes v. 3.9.1,1,0,1,2566407,51.059555,2731,2343,blood,,2020-10-25,China,China:Hangzhou,,,,,,,,,,,,,,,,,Genome sequence-based identification and analysis of virulence genes in Neisseria. Sicca causing native-valve endocarditis with multiple embolic brain infarcts in a patient with underlying heart disease Genome sequencing and assembly,,Hospital,blood,blood,Homo sapiens blood,,,,,,,,,,,,,Hospital,,,,99.39,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,490.6,Neisseria sicca strain FDAARGOS_260,FDAARGOS_260,Neisseria sicca,Neisseria,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN04875586,490,,,,,,FDA:FDAARGOS_260,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073715.2,CP020452,,US Food and Drug Administration,PacBio,16.04441661x,HGAP v. 3,1,,1,2783913,50.95,3074,2678,blood,,2014-09-15,USA,USA:DC,,male,42Y,Infection with Neisseria sicca,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,,,,,,,Infection with Neisseria sicca,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,492670.1315,Bacillus velezensis LOH112,LOH112,Bacillus velezensis,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN22026941,492670,,,,MLST.Bacillus_subtilis.110,,,,2022-02-17T00:00:00Z,,PRJNA768308,GCA_022313395.1,"CP092110,CP092111",,,Oxford Nanopore,427.0x,Canu v. 1.5,1,1,2,4357259,45.801823,4635,,feces from healthy human,,2020-01-10,China,China: Guangdong,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.63,0.61,,,Gastrointestinal,- HP,49283.17,Paenibacillus thiaminolyticus strain Mbale,Mbale,Paenibacillus thiaminolyticus,Paenibacillus,Paenibacillaceae,Bacillales,Bacilli,Bacillota,SAMN11874974,49283,,,,,,,,2019-07-17T00:00:00Z,,PRJNA552221,GCA_007066225.1,CP041404,,Penn State College of Medicine,Illumina MiSeq; Oxford Nanopore MiniION;,218.0x,Canu v. 05/2018; Bionano Hybrid Scaffold,1,,1,6744588,53.41736,6946,6010,ventricular cerebrospinal fluid,isolate from ventricular cerebrospinal fluid,2016-06-17,Uganda,Uganda,,,,Postinfectious Hydrocephalus,,,,,,,,,,,,,The assembly of a clinical isolate from ventricular cerebrospinal fluid.,collected_by:Steven Schiff,,,,,,,Postinfectious Hydrocephalus,,,,,,,,,,,,,,99.41,1.06,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,498388.3,Escherichia coli C strain C,C,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06645125,498388,,,,"MLST.Escherichia_coli_1.1721,MLST.Escherichia_coli_2.687",,,,2017-04-05T00:00:00Z,,PRJNA380607,GCA_002079225.1,CP020543,,Drexel University College of Medicine,PacBio,184.0x,HGAP Assembly v. 2,1,,1,4617024,50.96,4665,4581,,,2016-04-01,USA,United States,,,,,,,,,,,,,,,,,The last laboratory strain of E. coli to be sequnced. E. coli C is a long time laboratory strain used for phage studies. Recent data shows that it forms much better biofilm than other strains and can be used as a model organism in bacterial biofilm studies.,sample_type:bacterial culture,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,498743.37,Borreliella garinii PBr,PBr,Borreliella garinii,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328476,498743,,,,,,,,2022-12-05T00:00:00Z,,PRJNA327303,,CP075439,,,Illumina MiSeq,10x,SPAdes v. 3.13.0,1,0,1,866149,28.634708,874,,missing,,1985,Germany,Germany,,,,Lyme disease,,,,,,,,,,,,,,collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,95.8,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,504.107,Kingella kingae strain F41215CHC,F41215CHC,Kingella kingae,Kingella,Neisseriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN13028224,504,,,,MLST.Kingella_kingae.25,,,,2020-03-02T00:00:00Z,,PRJNA577516,GCA_011045755.1,CP045141,,Canterbury Health Laboratories,Illumina MiSeq; Oxford Nanopore GridION,290.0x,Flye v. 2.4.2,1,0,1,2014880,46.554287,2287,2084,,,2018-08-13,New Zealand,New Zealand: Christchurch,,,,,,,,,,,,,,,,,Kingella kingae is a cause of invasive infections especially in children less than 4 years old. This isolate was cultured from L3/L4 disc aspirate sample which the patient had failed initial therapy with flucloxacillin. The isolate has been sequenced as a New Zealand reference strain that has a raised MIC to flucloxacillin.,sample_type:Aspirate,,,,,,,,,,,,,,,,,,,,,98.98,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,50719.19,Vibrio diabolicus strain FDAARGOS_96,FDAARGOS_96,Vibrio diabolicus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN03996337,50719,,,,MLST.Vibrio_spp.63,,FDA:FDAARGOS_96,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002953335.1,"CP014094,CP014095,CP014093",,US Food and Drug Administration,PacBio; Illumina,14.506x,HGAP3 v. Feb 2015,2,1,3,5173621,44.85286,5139,4883,blister,,,USA,USA:Fl,,,,Vibrio infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:FDA CFSAN,,,,,,,Vibrio infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,50719.21,Vibrio diabolicus strain FDAARGOS_105,FDAARGOS_105,Vibrio diabolicus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN03996322,50719,,,,,,FDA:FDAARGOS_105,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002953395.1,"CP014036,CP014037",,US Food and Drug Administration,PacBio; Illumina,21.47x,HGAP3 v. Sep 2014,2,,2,5426154,44.815002,5174,5016,human,,,Jordan,Jordan:Amman,,,,Vibrio infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:FDA CFSAN,,,,,,,Vibrio infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,512402.24,Mycobacterium heraklionense SVM_VP21,SVM_VP21,Mycolicibacter heraklionensis,Mycolicibacter,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN29453539,512402,,,,,,,,2022-08-29T00:00:00Z,,PRJNA826325,GCA_024758765.1,CP101406,,,Illumina NovaSeq,450.0x,SPAdes v. v3.11,1,0,1,4882418,67.250534,4580,4502,oral cavity,,2019-04,India,India: NEW DELHI,,,,,,,,,,,,,,,,,,,Human Commensals,Oral Cavity,Oral Cavity,DOI 10.1099/ijs.0.038737-0,,,,,,,,,,,,,Human Commensals,,,,97.1,3.7,,,Oral,- NHP,518636.99,[Clostridium] asparagiforme DSM 15981,DSM 15981,Enterocloster asparagiformis,Enterocloster,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222674,518636,,,,,,DSM:15981,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025149125.1,CP102272,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,6353279,55.511585,6039,5637,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.22,0.63,,,Other,- HP,519.98,Bordetella parapertussis strain CIDM-BPP2,CIDM-BPP2,Bordetella parapertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18200433,519,,,,MLST.Bordetella_spp.19,,,,2021-03-16T00:00:00Z,,PRJNA695314,GCA_017357185.1,CP071602,,Centre for Infectious Diseases and Microbiology - Public Health,Oxford Nanopore; Illumina,72x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,0,1,4775256,68.101814,4614,4418,respiratory,,1993,Australia,Australia,,,,,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,,,,,,,unknown,,,,,,,Unknown,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1000,Bordetella pertussis strain J077,J077,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352197,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007155.1,CP025344,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,363x,HGAP v. 3,1,,1,4108444,67.70444,4112,3926,missing,,2013,USA,USA: MN,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1001,Bordetella pertussis strain C871,C871,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136966,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007215.1,CP025345,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,413x,HGAP v. 3,1,,1,4100074,67.712555,4085,3911,missing,,2000,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1002,Bordetella pertussis strain H742,H742,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136983,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007275.1,CP025346,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,416x,HGAP v. 3,1,,1,4104296,67.70869,4082,3915,missing,,2011,USA,USA: FL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1003,Bordetella pertussis strain H672,H672,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136979,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007335.1,CP025349,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,443x,HGAP v. 3,1,,1,4107426,67.70581,4088,3922,nasopharyngeal swab,,2010,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1004,Bordetella pertussis strain I958,I958,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352193,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007415.1,CP025350,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,371x,HGAP v. 3,1,,1,4108479,67.70499,4098,3924,missing,,2013,USA,USA: NM,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1005,Bordetella pertussis strain F580,F580,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136974,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007475.1,CP025342,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,505x,HGAP v. 3,1,,1,4104318,67.70847,4084,3920,missing,,2007,USA,USA: NC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1006,Bordetella pertussis strain C569,C569,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136964,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007535.1,CP025347,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,382x,HGAP v. 3,1,,1,4105353,67.707695,4091,3915,missing,,2000,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1007,Bordetella pertussis strain J234,J234,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136992,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007625.1,CP025348,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,424x,HGAP v. 3,1,,1,4107445,67.70569,4092,3916,missing,,2013,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1008,Bordetella pertussis strain J384,J384,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08016809,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008415.1,CP025073,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,152x,Unicycler v. 0.4.0,1,,1,4110543,67.70266,4103,3930,missing,,2015,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1009,Bordetella pertussis strain J024,J024,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352194,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008475.1,CP025353,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,406x,HGAP v. 3,1,,1,4106548,67.70575,4105,3922,missing,,2013,USA,USA: NY,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1010,Bordetella pertussis strain E140,E140,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136971,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008555.1,CP025354,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,420x,HGAP v. 3,1,,1,4103234,67.70942,4106,3917,missing,,2002,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1011,Bordetella pertussis strain D919,D919,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136969,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008595.1,CP025355,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,219x,HGAP v. 3,1,,1,4106395,67.70688,4088,3919,missing,,2002,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1012,Bordetella pertussis strain F578,F578,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136973,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008655.1,CP025357,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,400x,HGAP v. 3,1,,1,4097016,67.705444,4076,3909,missing,,2007,USA,USA: MS,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1013,Bordetella pertussis strain H034,H034,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136976,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008715.1,CP025356,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,322x,HGAP v. 3,1,,1,4105484,67.70734,4087,3920,missing,,2009,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1014,Bordetella pertussis strain H642,H642,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136978,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008795.1,CP025360,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,427x,HGAP v. 3,1,,1,4085512,67.69749,4067,3897,missing,,2010,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1015,Bordetella pertussis strain H697,H697,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136981,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008855.1,CP025365,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,375x,HGAP v. 3,1,,1,4104135,67.70874,4079,3914,missing,,2011,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1016,Bordetella pertussis strain F954,F954,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136975,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008915.1,CP025366,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,338x,HGAP v. 3,1,,1,4112103,67.70485,4105,3924,missing,,2007,USA,USA: IL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1017,Bordetella pertussis strain I223,I223,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136989,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008935.1,CP025369,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,336x,HGAP v. 3,1,,1,4102613,67.705605,4083,3920,missing,,2012,USA,USA: FL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1018,Bordetella pertussis strain I120,I120,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136988,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008955.1,CP025370,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,377x,HGAP v. 3,1,,1,4102199,67.710464,4090,3912,nasopharyngeal swab,,2012,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1019,Bordetella pertussis strain H640,H640,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136977,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008975.1,CP025371,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,406x,HGAP v. 3,1,,1,4088701,67.72166,4064,3898,missing,,2010,USA,USA: MI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1020,Bordetella pertussis strain I372,I372,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136990,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004008995.1,CP025372,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,358x,HGAP v. 3,1,,1,4106744,67.703415,4089,3927,nasopharyngeal swab,,2012,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1021,Bordetella pertussis strain H814,H814,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164940,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009015.1,CP025374,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,412x,HGAP v. 3,1,,1,4105351,67.707466,4087,3922,missing,,2007,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1022,Bordetella pertussis strain I439,I439,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164944,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009035.1,CP025375,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,441x,HGAP v. 3,1,,1,4106374,67.70664,4090,3921,missing,,2012,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1023,Bordetella pertussis strain I692,I692,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164948,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009055.1,CP025378,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,394x,HGAP v. 3,1,,1,4105345,67.707634,4087,3914,missing,,2011,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1024,Bordetella pertussis strain I188,I188,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164942,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009075.1,CP025379,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,393x,HGAP v. 3,1,,1,4100921,67.70413,4083,3911,missing,,2012,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1025,Bordetella pertussis strain I598,I598,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164946,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009095.1,CP025380,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,414x,HGAP v. 3,1,,1,4107721,67.70693,4092,3924,missing,,2013,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1026,Bordetella pertussis strain I896,I896,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164949,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009115.1,CP025381,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,410x,HGAP v. 3,1,,1,4101872,67.71018,4091,3915,missing,,2007,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1027,Bordetella pertussis strain H877,H877,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164941,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009135.1,CP025382,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,388x,HGAP v. 3,1,,1,4105345,67.70927,4087,3918,nasopharyngeal swab,,2012,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1028,Bordetella pertussis strain E198,E198,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164936,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009155.1,CP025385,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,203x,HGAP v. 3,1,,1,4101116,67.71123,4089,3914,missing,,2003,USA,USA: KY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,99.77,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1029,Bordetella pertussis strain I623,I623,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164947,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009175.1,CP025386,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,457x,HGAP v. 3,1,,1,4105302,67.70744,4098,3915,missing,,2012,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1030,Bordetella pertussis strain E365,E365,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164937,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009195.1,CP025387,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,309x,HGAP v. 3,1,,1,4103253,67.709404,4084,3915,missing,,2004,USA,USA: MO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1031,Bordetella pertussis strain H920,H920,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352190,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009215.1,CP025352,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,433x,HGAP v. 3,1,,1,4106670,67.70797,4094,3920,missing,,2011,USA,USA: WA,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1032,Bordetella pertussis strain H813,H813,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136986,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009235.1,CP025351,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,371x,HGAP v. 3,1,,1,4106497,67.70549,4082,3920,nasopharyngeal swab,,2011,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1033,Bordetella pertussis strain D322,D322,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136967,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009255.1,CP025358,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,337x,HGAP v. 3,1,,1,4104278,67.708595,4102,3918,missing,,2001,USA,USA: MO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1034,Bordetella pertussis strain E153,E153,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136972,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009275.1,CP025359,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,382x,HGAP v. 3,1,,1,4108487,67.70475,4097,3921,missing,,2003,USA,USA: SC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1035,Bordetella pertussis strain H811,H811,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136985,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009295.1,CP025361,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,453x,HGAP v. 3,1,,1,4110592,67.70283,4089,3924,missing,,2011,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1036,Bordetella pertussis strain H778,H778,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136984,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009315.1,CP025362,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,325x,HGAP v. 3,1,,1,4106328,67.706085,4090,3922,nasopharyngeal swab,,2011,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1037,Bordetella pertussis strain H902,H902,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136987,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009335.1,CP025363,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,434x,HGAP v. 3,1,,1,4105338,67.70785,4083,3918,missing,,2011,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1038,Bordetella pertussis strain H709,H709,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136982,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009355.1,CP025364,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,370x,HGAP v. 3,1,,1,4103241,67.70936,4088,3914,missing,,2010,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1039,Bordetella pertussis strain H677,H677,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136980,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009375.1,CP025367,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,417x,HGAP v. 3,1,,1,4106930,67.7068,4088,3920,missing,,2010,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1040,Bordetella pertussis strain C756,C756,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136965,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009395.1,CP025368,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,337x,HGAP v. 3,1,,1,4104277,67.710464,4091,3916,missing,,2000,USA,USA: TX,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1041,Bordetella pertussis strain H541,H541,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164939,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009415.1,CP025373,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,266x,HGAP v. 3,1,,1,4104306,67.70874,4086,3919,missing,,2010,USA,USA: SC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1042,Bordetella pertussis strain I462,I462,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164945,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009435.1,CP025376,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,432x,HGAP v. 3,1,,1,4107545,67.70463,4085,3917,missing,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1043,Bordetella pertussis strain I323,I323,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164943,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009455.1,CP025377,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,365x,HGAP v. 3,1,,1,4106368,67.70672,4091,3927,nasopharyngeal swab,,2012,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1044,Bordetella pertussis strain J184,J184,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164951,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009475.1,CP025383,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,377x,HGAP v. 3,1,,1,4104293,67.708664,4084,3916,nasopharyngeal swab,,2012,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1045,Bordetella pertussis strain I945,I945,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164950,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009495.1,CP025384,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,206x,HGAP v. 3,1,,1,4107408,67.705475,4093,3925,missing,,2013,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1046,Bordetella pertussis strain G102,G102,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08164938,520,,,,MLST.Bordetella_spp.83,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009515.1,CP025388,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,248x,HGAP v. 3,1,,1,4110608,67.702805,4090,3925,missing,,2008,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1047,Bordetella pertussis strain I892,I892,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08178168,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009535.1,CP025479,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,239x,HGAP v. 3,1,,1,4101882,67.71026,4088,3913,missing,,2007,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1048,Bordetella pertussis strain E087,E087,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136970,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009555.1,CP025480,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,295x,HGAP v. 3,1,,1,4101146,67.713394,4083,3910,missing,,2002,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1049,Bordetella pertussis strain I859,I859,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08178167,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009575.1,CP025477,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,197x,HGAP v. 3,1,,1,4107433,67.70601,4087,3925,missing,,2012,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1050,Bordetella pertussis strain E191,E191,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08178166,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009595.1,CP025478,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,252x,HGAP v. 3,1,,1,4104745,67.703964,4081,3923,missing,,2003,USA,USA: SC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1051,Bordetella pertussis strain D869,D869,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136968,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009635.1,CP025528,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,233x,HGAP v. 3,1,,1,4104044,67.70797,4166,3920,missing,,2002,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1052,Bordetella pertussis strain H624,H624,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08200082,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009655.1,CP025529,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,391x,HGAP v. 3,1,,1,4121896,67.70945,4103,3930,missing,,2010,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1053,Bordetella pertussis strain F569,F569,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08214406,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009675.1,CP025523,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,370x,HGAP v. 3,1,,1,4103262,67.70915,4083,3918,missing,,2006,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1054,Bordetella pertussis strain I705,I705,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08214408,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009695.1,CP025524,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,113x,HGAP v. 3,1,,1,4105347,67.70767,4085,3915,missing,,2011,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1055,Bordetella pertussis strain J139,J139,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08200079,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009715.1,CP025527,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,289x,HGAP v. 3,1,,1,4247121,67.760376,4224,4058,nasopharyngeal swab,,2013,USA,USA:TX,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,99.53,2.31,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1056,Bordetella pertussis strain I955,I955,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352192,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009735.1,CP025531,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,394x,HGAP v. 3,1,,1,4107611,67.70566,4088,3927,missing,,2013,USA,USA: CA,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1057,Bordetella pertussis strain I420,I420,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08214407,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009775.1,CP025525,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,484x,HGAP v. 3,1,,1,4111618,67.70169,4112,3927,missing,,2012,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1058,Bordetella pertussis strain D665,D665,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08200081,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009795.1,CP025526,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,258x,HGAP v. 3,1,,1,4145812,67.7269,4127,3963,nasopharyngeal swab,,2002,USA,USA: NV,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1059,Bordetella pertussis strain D236,D236,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08200080,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004009815.1,CP025530,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,284x,HGAP v. 3,1,,1,4285328,67.7063,4249,4069,missing,,2001,USA,USA: UT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,3.74,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1060,Bordetella pertussis strain FR5810,FR5810,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4700352,520,,,,,,,,2018-11-27T00:00:00Z,,PRJEB27048,GCA_900492145.1,LR130529,,INSTITUT PASTEUR DE PARIS,,,,1,,1,4108173,67.706566,4506,4294,nasopharynx,"recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data",2014,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,"We describe the complete genome sequences of two Bordetella pertussis isolates\; FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species\; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data.;Bacterial culture",,,,,,,,,diseased,,,,,,,,,,,,,97.79,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1092,Bordetella pertussis strain J366,J366,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395641,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634585.1,CP026429,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,284x,HGAP v. 3,1,,1,4110583,67.702614,4092,3924,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1093,Bordetella pertussis strain J364,J364,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395640,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634605.1,CP026430,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,276x,HGAP v. 3,1,,1,4095487,67.696396,4076,3914,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1094,Bordetella pertussis strain J363,J363,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395639,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634625.1,CP026431,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,317x,HGAP v. 3,1,,1,4113166,67.70376,4113,3927,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1095,Bordetella pertussis strain J360,J360,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395638,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634645.1,CP026432,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,253x,HGAP v. 3,1,,1,4110459,67.70176,4144,3927,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1096,Bordetella pertussis strain J359,J359,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395637,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634665.1,CP026433,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,279x,HGAP v. 3,1,,1,4107267,67.70444,4109,3927,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1097,Bordetella pertussis strain J354,J354,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395635,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634685.1,CP026435,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,258x,HGAP v. 3,1,,1,4106370,67.70671,4088,3925,nasopharyngeal swab,,2015,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1098,Bordetella pertussis strain J336,J336,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395634,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634705.1,CP026436,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,267x,HGAP v. 3,1,,1,4107434,67.705505,4095,3920,missing,,2014,Guatemala,Guatemala,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1099,Bordetella pertussis strain J334,J334,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395633,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634725.1,CP026437,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,221x,HGAP v. 3,1,,1,4110578,67.702835,4089,3924,missing,,2014,Guatemala,Guatemala,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1100,Bordetella pertussis strain J330,J330,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395631,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634745.1,CP026439,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,288x,HGAP v. 3,1,,1,4107415,67.70548,4086,3922,missing,,2014,Guatemala,Guatemala,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1101,Bordetella pertussis strain J322,J322,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395629,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634765.1,CP026441,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,282x,HGAP v. 3,1,,1,4106368,67.70655,4091,3922,nasopharyngeal swab,,2015,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1102,Bordetella pertussis strain J275,J275,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395628,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634785.1,CP026442,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,315x,HGAP v. 3,1,,1,4108430,67.704254,4109,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1103,Bordetella pertussis strain J272,J272,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395626,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634805.1,CP026444,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,299x,HGAP v. 3,1,,1,4110578,67.70269,4093,3927,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1104,Bordetella pertussis strain J270,J270,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395625,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634825.1,CP026445,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,292x,HGAP v. 3,1,,1,4110582,67.70272,4089,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1105,Bordetella pertussis strain J393,J393,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395647,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634845.1,CP026428,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,260x,HGAP v. 3,1,,1,4106382,67.7069,4098,3927,nasopharyngeal swab,,2015,USA,USA: WI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1106,Bordetella pertussis strain J357,J357,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395636,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634865.1,CP026434,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,382x,HGAP v. 3,1,,1,4107421,67.70584,4083,3926,missing,,2014,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1107,Bordetella pertussis strain J332,J332,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395632,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634885.1,CP026438,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,207x,HGAP v. 3,1,,1,4109535,67.70364,4087,3923,missing,,2014,Guatemala,Guatemala,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1108,Bordetella pertussis strain J323,J323,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395630,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634905.1,CP026440,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,260x,HGAP v. 3,1,,1,4106376,67.70661,4087,3923,nasopharyngeal swab,,2015,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1109,Bordetella pertussis strain J274,J274,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395627,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004634925.1,CP026443,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,365x,HGAP v. 3,1,,1,4110548,67.70243,4109,3927,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1110,Bordetella pertussis strain J269,J269,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395624,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635085.1,CP026446,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,286x,HGAP v. 3,1,,1,4108484,67.70466,4092,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1111,Bordetella pertussis strain J267,J267,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395622,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635105.1,CP026448,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,254x,HGAP v. 3,1,,1,4110579,67.7027,4095,3926,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1112,Bordetella pertussis strain J266,J266,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395621,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635125.1,CP026449,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,330x,HGAP v. 3,1,,1,4110579,67.7027,4095,3927,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1113,Bordetella pertussis strain J264,J264,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395620,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635145.1,CP026450,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,369x,HGAP v. 3,1,,1,4110583,67.702614,4091,3923,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1114,Bordetella pertussis strain J263,J263,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395619,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635165.1,CP026451,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,303x,HGAP v. 3,1,,1,4110580,67.702736,4093,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1115,Bordetella pertussis strain J260,J260,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395617,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635185.1,CP026453,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,230x,HGAP v. 3,1,,1,4110577,67.70271,4093,3926,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1116,Bordetella pertussis strain J259,J259,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395616,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635205.1,CP026454,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,182x,HGAP v. 3,1,,1,4110580,67.702736,4089,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1117,Bordetella pertussis strain J258,J258,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395615,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635225.1,CP026455,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,165x,HGAP v. 3,1,,1,4110584,67.70277,4090,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1118,Bordetella pertussis strain J257,J257,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395614,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635245.1,CP026456,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,214x,HGAP v. 3,1,,1,4110581,67.70274,4095,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1119,Bordetella pertussis strain J256,J256,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395613,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635265.1,CP026457,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,197x,HGAP v. 3,1,,1,4110580,67.702736,4089,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1120,Bordetella pertussis strain J254,J254,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395611,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635285.1,CP026459,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,196x,HGAP v. 3,1,,1,4110577,67.702736,4094,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1121,Bordetella pertussis strain J253,J253,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395610,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635305.1,CP026460,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,201x,HGAP v. 3,1,,1,4108481,67.70466,4091,3923,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1122,Bordetella pertussis strain J252,J252,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395609,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635325.1,CP026461,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,198x,HGAP v. 3,1,,1,4110577,67.70268,4096,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1123,Bordetella pertussis strain J251,J251,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395608,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635345.1,CP026462,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,228x,HGAP v. 3,1,,1,4110582,67.7027,4093,3922,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1124,Bordetella pertussis strain J249,J249,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395606,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635365.1,CP026464,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,262x,HGAP v. 3,1,,1,4110576,67.7027,4095,3925,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1126,Bordetella pertussis strain J268,J268,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395623,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635405.1,CP026447,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,391x,HGAP v. 3,1,,1,4108457,67.7062,4097,3922,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1127,Bordetella pertussis strain J255,J255,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395612,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635425.1,CP026458,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,206x,HGAP v. 3,1,,1,4110576,67.702675,4092,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1128,Bordetella pertussis strain J250,J250,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395607,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635445.1,CP026463,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,213x,HGAP v. 3,1,,1,4110579,67.7027,4094,3924,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1129,Bordetella pertussis strain J402,J402,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395649,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635465.1,CP026466,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,323x,HGAP v. 3,1,,1,4107550,67.70459,4083,3917,nasopharyngeal swab,,2015,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1130,Bordetella pertussis strain J401,J401,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395648,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635485.1,CP026467,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,355x,HGAP v. 3,1,,1,4113744,67.699524,4093,3927,nasopharyngeal swab,,2015,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1131,Bordetella pertussis strain J392,J392,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395646,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635505.1,CP026468,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,230x,HGAP v. 3,1,,1,4107431,67.7057,4089,3926,nasopharyngeal swab,,2015,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1132,Bordetella pertussis strain J391,J391,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395645,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635525.1,CP026469,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,339x,HGAP v. 3,1,,1,4107431,67.705894,4096,3927,nasopharyngeal swab,,2015,USA,USA: WI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1133,Bordetella pertussis strain J376,J376,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395644,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635545.1,CP026470,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,233x,HGAP v. 3,1,,1,4107552,67.704704,4084,3917,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1134,Bordetella pertussis strain J370,J370,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395643,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635565.1,CP026471,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,336x,HGAP v. 3,1,,1,4107544,67.704544,4084,3924,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1135,Bordetella pertussis strain J367,J367,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395642,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635585.1,CP026472,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,282x,HGAP v. 3,1,,1,4108483,67.704796,4087,3925,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1136,Bordetella pertussis strain J703,J703,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524485,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635605.1,CP026882,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,366x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105128,67.707436,4099,3919,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1137,Bordetella pertussis strain J700,J700,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524483,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635625.1,CP026884,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,236x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4107386,67.705444,4108,3923,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1138,Bordetella pertussis strain J699,J699,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524482,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635645.1,CP026885,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,277x,HGAP v. 3,1,,1,4107132,67.70552,4124,3925,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1139,Bordetella pertussis strain J698,J698,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524481,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635665.1,CP026886,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,245x,HGAP v. 3,1,,1,4107367,67.70539,4123,3924,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1140,Bordetella pertussis strain J697,J697,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524480,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635685.1,CP026887,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,268x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4108309,67.70382,4199,3926,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1141,Bordetella pertussis strain J695,J695,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524479,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635705.1,CP026888,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,285x,HGAP v. 3,1,,1,4105341,67.70763,4087,3921,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1142,Bordetella pertussis strain J693,J693,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524478,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635725.1,CP026889,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,196x,HGAP v. 3,1,,1,4105318,67.70752,4103,3922,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1143,Bordetella pertussis strain J692,J692,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524477,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635745.1,CP026890,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,251x,HGAP v. 3,1,,1,4105332,67.70758,4096,3920,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1144,Bordetella pertussis strain J690,J690,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524475,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635765.1,CP026892,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,250x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105314,67.70744,4098,3921,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1145,Bordetella pertussis strain J628,J628,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524466,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635785.1,CP026901,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,287x,HGAP v. 3,1,,1,4107705,67.706764,4095,3921,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1146,Bordetella pertussis strain J617,J617,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524465,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635805.1,CP026902,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,221x,HGAP v. 3,1,,1,4104279,67.708336,4095,3924,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1147,Bordetella pertussis strain J614,J614,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524463,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635825.1,CP026904,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,187x,HGAP v. 3,1,,1,4104254,67.70819,4105,3924,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1148,Bordetella pertussis strain J606,J606,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524462,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635845.1,CP026905,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,201x,HGAP v. 3,1,,1,4112660,67.700294,4110,3932,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1149,Bordetella pertussis strain J605,J605,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524461,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635865.1,CP026906,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,217x,HGAP v. 3,1,,1,4112682,67.70037,4111,3933,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1150,Bordetella pertussis strain J604,J604,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524460,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635885.1,CP026907,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,269x,HGAP v. 3,1,,1,4111650,67.70151,4101,3928,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1151,Bordetella pertussis strain J603,J603,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524459,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635905.1,CP026908,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,316x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4112699,67.70048,4102,3930,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1152,Bordetella pertussis strain J656,J656,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524467,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635925.1,CP026900,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,332x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4108772,67.70597,4090,3921,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1153,Bordetella pertussis strain J616,J616,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524464,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635945.1,CP026903,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,233x,HGAP v. 3,1,,1,4104267,67.70837,4094,3921,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1154,Bordetella pertussis strain J673,J673,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469407,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635965.1,CP026618,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,338x,HGAP v. 3,1,,1,4107704,67.70678,4095,3922,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1155,Bordetella pertussis strain J650,J650,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469406,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004635985.1,CP026619,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,334x,HGAP v. 3,1,,1,4107707,67.70678,4097,3922,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1156,Bordetella pertussis strain J632,J632,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469405,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636005.1,CP026620,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,333x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4107723,67.7069,4089,3921,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1157,Bordetella pertussis strain J529,J529,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469404,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636025.1,CP026621,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,245x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105348,67.70759,4083,3916,nasopharyngeal swab,,2016,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1158,Bordetella pertussis strain J528,J528,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469403,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636045.1,CP026622,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,251x,HGAP v. 3,1,,1,4104297,67.70865,4084,3915,nasopharyngeal swab,,2016,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1159,Bordetella pertussis strain J527,J527,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469402,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636065.1,CP026623,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,267x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105308,67.70761,4089,3925,nasopharyngeal swab,,2016,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1160,Bordetella pertussis strain J524,J524,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469400,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636085.1,CP026625,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,301x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4107246,67.70576,4116,3929,nasopharyngeal swab,,2015,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1161,Bordetella pertussis strain J523,J523,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469399,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636105.1,CP026626,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,378x,HGAP v. 3,1,,1,4108503,67.70486,4092,3927,nasopharyngeal swab,,2015,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1162,Bordetella pertussis strain J522,J522,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469398,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636125.1,CP026627,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,289x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106373,67.70676,4087,3924,nasopharyngeal swab,,2015,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1163,Bordetella pertussis strain J378,J378,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469395,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636145.1,CP026630,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,263x,HGAP v. 3,1,,1,4106635,67.707794,4081,3919,nasopharyngeal swab,,2015,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1164,Bordetella pertussis strain J374,J374,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469394,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636165.1,CP026631,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,209x,HGAP v. 3,1,,1,4111643,67.701866,4089,3928,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1165,Bordetella pertussis strain J368,J368,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469393,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636185.1,CP026632,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,340x,HGAP v. 3,1,,1,4110592,67.702805,4087,3925,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1166,Bordetella pertussis strain J362,J362,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469392,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636205.1,CP026633,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,371x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4099525,67.70777,4083,3914,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1167,Bordetella pertussis strain J525,J525,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469401,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636225.1,CP026624,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,329x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4107260,67.705864,4092,3928,nasopharyngeal swab,,2015,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1168,Bordetella pertussis strain J424,J424,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469397,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636245.1,CP026628,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,255x,HGAP v. 3,1,,1,4109501,67.70345,4103,3923,nasopharyngeal swab,,2015,USA,USA: WI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1169,Bordetella pertussis strain J386,J386,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469396,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636265.1,CP026629,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,352x,HGAP v. 3,1,,1,4106400,67.70665,4090,3920,nasopharyngeal swab,,2015,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1170,Bordetella pertussis strain A339,A339,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08469391,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636285.1,CP026634,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,308x,HGAP v. 3,1,,1,4131102,67.71537,4117,3937,missing,,1995,USA,USA: HI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1171,Bordetella pertussis strain J526,J526,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471228,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636305.1,CP026663,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,317x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105346,67.707664,4088,3918,nasopharyngeal swab,,2015,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1172,Bordetella pertussis strain J390,J390,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471227,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636325.1,CP026664,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,274x,HGAP v. 3,1,,1,4106379,67.706856,4095,3926,nasopharyngeal swab,,2015,USA,USA: WI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1173,Bordetella pertussis strain J379,J379,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471226,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636345.1,CP026665,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,293x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106636,67.7078,4084,3919,nasopharyngeal swab,,2015,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1174,Bordetella pertussis strain J375,J375,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471225,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636365.1,CP026666,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,287x,HGAP v. 3,1,,1,4106495,67.70535,4087,3919,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1175,Bordetella pertussis strain J373,J373,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471224,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636385.1,CP026667,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,264x,HGAP v. 3,1,,1,4110597,67.7027,4093,3926,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1176,Bordetella pertussis strain J372,J372,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471223,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636405.1,CP026668,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,282x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105473,67.70621,4082,3915,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1177,Bordetella pertussis strain J369,J369,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08471222,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636425.1,CP026669,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,328x,HGAP v. 3,1,,1,4103232,67.709625,4086,3917,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1178,Bordetella pertussis strain J702,J702,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524484,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636445.1,CP026883,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,251x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105107,67.707245,4109,3919,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1179,Bordetella pertussis strain J691,J691,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524476,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636465.1,CP026891,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,337x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4105328,67.707504,4098,3921,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1180,Bordetella pertussis strain J687,J687,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524474,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636485.1,CP026893,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,322x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106343,67.706276,4116,3922,nasopharyngeal swab,,2016,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1181,Bordetella pertussis strain J683,J683,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524473,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636505.1,CP026894,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,307x,HGAP v. 3,1,,1,4110594,67.70231,4101,3922,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1182,Bordetella pertussis strain J682,J682,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524472,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636525.1,CP026895,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,274x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4110562,67.70208,4113,3925,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1183,Bordetella pertussis strain J680,J680,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524471,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636545.1,CP026896,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,312x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4110583,67.702225,4101,3923,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1184,Bordetella pertussis strain J679,J679,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524470,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636565.1,CP026897,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,230x,HGAP v. 3,1,,1,4110580,67.702194,4102,3926,nasopharyngeal swab,,2016,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1185,Bordetella pertussis strain J667,J667,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524469,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636785.1,CP026898,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,229x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4108749,67.70579,4099,3923,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1186,Bordetella pertussis strain J662,J662,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524468,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636805.1,CP026899,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,323x,HGAP v. 3,1,,1,4104253,67.70882,4084,3920,missing,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1187,Bordetella pertussis strain J589,J589,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524458,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636825.1,CP026909,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,295x,HGAP v. 3,1,,1,4105313,67.70775,4108,3919,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1188,Bordetella pertussis strain J588,J588,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524457,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636845.1,CP026910,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,324x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106460,67.705055,4105,3922,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1189,Bordetella pertussis strain J582,J582,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524455,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636865.1,CP026912,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,295x,HGAP v. 3,1,,1,4106349,67.70625,4121,3923,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1190,Bordetella pertussis strain J571,J571,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524454,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636885.1,CP026913,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,351x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106638,67.70755,4103,3922,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1191,Bordetella pertussis strain J567,J567,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524453,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636905.1,CP026914,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,343x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106621,67.707466,4113,3921,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1192,Bordetella pertussis strain J549,J549,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524452,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636925.1,CP026915,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,251x,HGAP v. 3,1,,1,4106572,67.7072,4119,3922,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1193,Bordetella pertussis strain J546,J546,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524451,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636945.1,CP026916,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,238x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106441,67.70486,4096,3918,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1194,Bordetella pertussis strain J132,J132,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524449,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636965.1,CP026918,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,390x,HGAP v. 3,1,,1,4087073,67.6984,4086,3902,nasopharyngeal swab,,2014,Haiti,Haiti,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1195,Bordetella pertussis strain J130,J130,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524448,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004636985.1,CP026919,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,331x,HGAP v. 3,1,,1,4103048,67.70935,4119,3915,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1196,Bordetella pertussis strain J092,J092,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524445,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637005.1,CP026922,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,253x,HGAP v. 3,1,,1,4113725,67.699394,4107,3929,missing,,2014,USA,USA: DE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1197,Bordetella pertussis strain J586,J586,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524456,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637025.1,CP026911,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,311x,HGAP v. 3; Circlator v. 1.5.1,1,,1,4106373,67.70637,4102,3924,nasopharyngeal swab,,2016,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1198,Bordetella pertussis strain J233,J233,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524450,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637045.1,CP026917,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,293x,HGAP v. 3,1,,1,4104389,67.70725,4098,3914,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1199,Bordetella pertussis strain J129,J129,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524447,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637065.1,CP026920,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,409x,HGAP v. 3,1,,1,4107579,67.70533,4098,3930,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1200,Bordetella pertussis strain J118,J118,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08524446,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637085.1,CP026921,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,307x,HGAP v. 3,1,,1,4103077,67.70957,4092,3915,nasopharyngeal swab,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1201,Bordetella pertussis strain J303,J303,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352227,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637105.1,CP026987,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,345x,HGAP v. 3,1,,1,4108452,67.70474,4109,3928,missing,,2014,USA,USA: CO,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1202,Bordetella pertussis strain J247,J247,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352219,520,,,,,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637125.1,CP026988,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,380x,HGAP v. 3,1,,1,4109425,67.702614,4161,3925,missing,,2014,USA,USA: VT,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1203,Bordetella pertussis strain J246,J246,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352218,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637145.1,CP026989,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,299x,HGAP v. 3,1,,1,4103095,67.70855,4159,3923,missing,,2014,USA,USA: VT,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1204,Bordetella pertussis strain J205,J205,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352214,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637165.1,CP026990,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,252x,HGAP v. 3,1,,1,4106403,67.70473,4146,3921,missing,,2014,USA,USA: GA,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1205,Bordetella pertussis strain J204,J204,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352213,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637185.1,CP026991,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,290x,HGAP v. 3,1,,1,4113707,67.69957,4103,3928,missing,,2014,USA,USA: GA,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1206,Bordetella pertussis strain I182,I182,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08214409,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637225.1,CP026996,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,176x,HGAP v. 3,1,,1,4112703,67.70093,4092,3926,missing,,2012,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1207,Bordetella pertussis strain J171,J171,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352209,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637205.1,CP026992,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,294x,HGAP v. 3,1,,1,4104386,67.707375,4089,3916,missing,,2014,USA,USA: CO,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1208,Bordetella pertussis strain J085,J085,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352199,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637245.1,CP026997,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,313x,HGAP v. 3,1,,1,4296902,67.69913,4261,4091,missing,,2013,USA,USA: CO,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,4.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1209,Bordetella pertussis strain J066,J066,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07352196,520,,,,MLST.Bordetella_spp.2,,,,2019-04-05T00:00:00Z,,PRJNA279196,GCA_004637265.1,CP026998,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,329x,HGAP v. 3,1,,1,4107429,67.705734,4089,3923,missing,,2013,USA,USA: CT,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.1210,Bordetella pertussis strain J262,J262,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08395618,520,,,,,,,,2019-04-11T00:00:00Z,,PRJNA279196,GCA_004771055.1,CP026452,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,277x,HGAP v. 3,1,,1,4110580,67.702705,4096,3935,nasopharyngeal swab,,2014,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1226,Bordetella pertussis strain P2013109,P2013109,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN11295233,520,,,,MLST.Bordetella_spp.2,,,,2019-09-09T00:00:00Z,,PRJNA530108,GCA_008330005.1,CP038790,,"WeHealthGene Co., Ltd.",PacBio,290.0x,Celera Assembler v. Version 8.0,1,,1,4126010,67.72027,4059,,nasophyrangeal,,2014-09-25,China,China:Beijing,,,,whooping cough,,,,,,,,,,,,,Comparation analysis between 16 Bordetella pertussis strains.,collected_by:Lin Yuan,,,,,,,whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1232,Bordetella pertussis strain BP82,BP82,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693568,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465165.1,LS483252,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4104282,67.70868,4015,3748,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2014,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1233,Bordetella pertussis strain BP46,BP46,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693567,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465145.1,LS483251,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4104308,67.708664,4009,3742,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2014,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1234,Bordetella pertussis strain BP155,BP155,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693569,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465175.1,LS483253,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4109117,67.70313,4019,3746,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2008,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,99.91,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1235,Bordetella pertussis strain BP6384,BP6384,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693574,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465715.1,LS483257,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4105215,67.70883,4016,3744,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2012,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,99.91,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1236,Bordetella pertussis strain BP6260,BP6260,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693573,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465735.1,LS483256,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4110570,67.70263,4016,3748,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2012,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1237,Bordetella pertussis strain BPK10,BPK10,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693575,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465745.1,LS483255,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4104707,67.70837,4038,3751,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2012,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1238,Bordetella pertussis strain BP6242,BP6242,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693572,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465785.1,LS483259,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4105356,67.70724,4017,3744,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2012,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1239,Bordetella pertussis strain BP318,BP318,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693571,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465925.1,LS483260,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4113685,67.69973,4023,3752,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2015,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,96.99,0.58,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1240,Bordetella pertussis strain BP312,BP312,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA4693570,520,,,,MLST.Bordetella_spp.2,,,,2020-11-19T00:00:00Z,,PRJEB26966,GCA_900465795.1,LS483258,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,0,1,4105753,67.706436,4027,3745,respiratory tract,"isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine)",2008,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of clinical B.pertussis strains, which were isolated in 2008-2015 in the Czech Republic from patients having different pertussis vaccination status (non-vaccinated, vaccinated with whole-cell vaccine and/or acellular vaccine).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.1248,Bordetella pertussis strain CIDM-BP3,CIDM-BP3,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18200431,520,,,,MLST.Bordetella_spp.2,,,,2021-03-16T00:00:00Z,,PRJNA695314,GCA_017357125.1,CP071600,,Centre for Infectious Diseases and Microbiology - Public Health,Oxford Nanopore; Illumina,100x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,0,1,4093865,67.70695,4110,3852,respiratory,,2015,Australia,Australia,,,,pertussis,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,,,,,,,pertussis,,,,,,,NPA,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1249,Bordetella pertussis strain CIDM-BP5,CIDM-BP5,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18200432,520,,,,MLST.Bordetella_spp.2,,,,2021-03-16T00:00:00Z,,PRJNA695314,GCA_017357165.1,CP071601,,Centre for Infectious Diseases and Microbiology - Public Health,Oxford Nanopore; Illumina,119x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,0,1,4104145,67.708595,4079,3861,respiratory,,2008,Australia,Australia,,,,pertussis,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,,,,,,,pertussis,,,,,,,NPA,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1250,Bordetella pertussis strain CIDM-BP2,CIDM-BP2,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18200430,520,,,,,,,,2021-03-16T00:00:00Z,,PRJNA695314,GCA_017357205.1,CP071599,,Centre for Infectious Diseases and Microbiology - Public Health,Oxford Nanopore; Illumina,78x,Flye v. 2.7b; Racon v. 1.3.1; Medaka v.,1,0,1,4109518,67.70458,4121,3896,respiratory,,2011,Australia,Australia,,,,pertussis,,,,,,,,,,,,,Genomic evaluation of Bordetella spp. originating from Australia,collected_by:Centre for Infectious Diseases and Microbiology - Public Health,,,,,,,pertussis,,,,,,,NPA,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.1291,Bordetella pertussis NZ60,NZ60,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585526,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022404855.1,CP054071,,,Oxford Nanopore; Illumina,489x,Unicycler v. 0.4.8,1,0,1,4108959,67.70274,4047,3868,nasopharynx,,2017,New Zealand,New Zealand: Nelson Marlborough,,female,10Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1292,Bordetella pertussis NZ61,NZ61,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585527,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022404835.1,CP054070,,,Oxford Nanopore; Illumina,636x,Unicycler v. 0.4.8,1,0,1,4109504,67.70328,4047,3895,nasopharynx,,2017,New Zealand,New Zealand: Auckland Combined,,female,10Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1293,Bordetella pertussis NZ62,NZ62,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585528,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022404815.1,CP054069,,,Oxford Nanopore; Illumina,221x,Flye v. 2.3.1,1,0,1,4112438,67.6969,4135,3873,nasopharynx,,2017,New Zealand,New Zealand: Nelson Marlborough,,female,3Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1294,Bordetella pertussis NZ58,NZ58,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585524,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022406935.1,CP054073,,,Oxford Nanopore; Illumina,672x,Unicycler v. 0.4.8,1,0,1,4107413,67.7058,4042,3890,pharynx,,2017,New Zealand,New Zealand: Southern,,female,23Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1295,Bordetella pertussis NZ59,NZ59,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585525,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022406915.1,CP054072,,,Oxford Nanopore; Illumina,561x,Flye v. 2.3.1,1,0,1,4109030,67.70238,4048,3872,nasopharynx,,2017,New Zealand,New Zealand: Nelson Marlborough,,male,7Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.67,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1296,Bordetella pertussis NZ56,NZ56,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585523,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022406975.1,CP054075,,,Oxford Nanopore; Illumina,542x,Unicycler v. 0.4.8,1,0,1,4109160,67.70328,4046,3892,nasopharynx,,2012,New Zealand,New Zealand: Auckland Combined,,female,33Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1297,Bordetella pertussis NZ57,NZ57,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385805,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022406955.1,CP054074,,,Oxford Nanopore; Illumina,288x,Flye v. 2.3.1,1,0,1,4105651,67.70505,4129,3864,nasopharynx,,2017,New Zealand,New Zealand: Southern,,female,12Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1298,Bordetella pertussis NZ53,NZ53,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585520,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407035.1,CP054078,,,Oxford Nanopore; Illumina,185x,Flye v. 2.3.1,1,0,1,4108355,67.70009,4154,3870,pernasal,,2012,New Zealand,New Zealand: Canterbury,,male,12Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1299,Bordetella pertussis NZ54,NZ54,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585521,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407015.1,CP054077,,,Oxford Nanopore; Illumina,387x,Unicycler v. 0.4.8,1,0,1,4110567,67.70197,4055,3896,nasopharynx,,2012,New Zealand,New Zealand: Auckland Combined,,female,10Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1300,Bordetella pertussis NZ55,NZ55,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585522,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022406995.1,CP054076,,,Oxford Nanopore; Illumina,375x,Unicycler v. 0.4.8,1,0,1,4107422,67.70497,4048,3893,nasopharynx,,2012,New Zealand,New Zealand: Auckland Combined,,female,15Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1301,Bordetella pertussis NZ51,NZ51,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585518,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407055.1,CP054080,,,Oxford Nanopore; Illumina,105x,Flye v. 2.3.1,1,0,1,4108230,67.69955,4178,3873,nasopharynx,,2012,New Zealand,New Zealand: Bay of Plenty,,male,3M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.13,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1302,Bordetella pertussis NZ49,NZ49,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585516,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407115.1,CP054082,,,Oxford Nanopore; Illumina,404x,Flye v. 2.3.1,1,0,1,4107903,67.7025,4124,3862,pernasal,,2012,New Zealand,New Zealand: Northland,,male,69Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1303,Bordetella pertussis NZ52,NZ52,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585519,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407075.1,CP054079,,,Oxford Nanopore; Illumina,317x,Unicycler v. 0.4.8,1,0,1,4110469,67.70188,4053,3894,nasopharynx,,2012,New Zealand,New Zealand: Auckland Combined,,female,37Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1304,Bordetella pertussis NZ47,NZ47,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385804,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407135.1,CP054084,,,Oxford Nanopore; Illumina,562x,Unicycler v. 0.4.8,1,0,1,4110579,67.702065,4049,3896,nasopharynx,,2012,New Zealand,New Zealand: Southern,,male,1M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1305,Bordetella pertussis NZ50,NZ50,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585517,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407095.1,CP054081,,,Oxford Nanopore; Illumina,178x,Flye v. 2.3.1,1,0,1,4107288,67.701996,4157,3873,sputum,,2012,New Zealand,New Zealand: Auckland Combined,,male,49Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1306,Bordetella pertussis NZ46,NZ46,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585514,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407175.1,CP054085,,,Oxford Nanopore; Illumina,350x,Unicycler v. 0.4.8,1,0,1,4106252,67.70737,4049,3861,nasopharynx,,2011,New Zealand,New Zealand: Southern,,female,8Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1307,Bordetella pertussis NZ45,NZ45,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585513,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407215.1,CP054086,,,Oxford Nanopore; Illumina,159x,Flye v. 2.3.1,1,0,1,4103978,67.70343,4258,3866,pernasal,,2011,New Zealand,New Zealand: Waikato,,female,4Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,97.22,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1308,Bordetella pertussis NZ48,NZ48,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585515,520,,,,,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407155.1,CP054083,,,Oxford Nanopore; Illumina,141x,Flye v. 2.3.1,1,0,1,4105005,67.70311,4217,3863,nasopharynx,,2012,New Zealand,New Zealand: Auckland Combined,,male,54Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.54,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1309,Bordetella pertussis NZ42,NZ42,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385801,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407195.1,CP054089,,,Oxford Nanopore; Illumina,145x,Flye v. 2.3.1,1,0,1,4105636,67.70318,4175,3864,nasopharynx,,2009,New Zealand,New Zealand: Auckland Combined,,male,4Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1310,Bordetella pertussis NZ43,NZ43,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385802,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407255.1,CP054088,,,Oxford Nanopore; Illumina,320x,Flye v. 2.3.1,1,0,1,4105635,67.70477,4110,3863,pernasal,,2010,New Zealand,New Zealand: Waikato,,female,12Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.83,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1311,Bordetella pertussis NZ44,NZ44,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385803,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407235.1,CP054087,,,Oxford Nanopore; Illumina,367x,Flye v. 2.3.1,1,0,1,4106674,67.70299,4113,3865,nasopharynx,,2010,New Zealand,New Zealand: Auckland Combined,,female,2Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1312,Bordetella pertussis NZ38,NZ38,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385797,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407335.1,CP054093,,,Oxford Nanopore; Illumina,348x,Flye v. 2.3.1,1,0,1,4105814,67.70521,4094,3866,nasopharynx,,2008,New Zealand,New Zealand: Southern,,female,32Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.5,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1313,Bordetella pertussis NZ39,NZ39,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385798,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407315.1,CP054092,,,Oxford Nanopore; Illumina,201x,Flye v. 2.3.1,1,0,1,4109715,67.69861,4125,3866,nasopharynx,,2008,New Zealand,New Zealand: Nelson Marlborough,,female,7Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.95,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1314,Bordetella pertussis NZ41,NZ41,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385800,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407275.1,CP054090,,,Oxford Nanopore; Illumina,162x,Flye v. 2.3.1,1,0,1,4104237,67.707855,4118,3860,nasopharynx,,2009,New Zealand,New Zealand: Auckland Combined,,male,3M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1315,Bordetella pertussis NZ40,NZ40,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385799,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407295.1,CP054091,,,Oxford Nanopore; Illumina,420x,Unicycler v. 0.4.8,1,0,1,4103224,67.709145,4044,3861,nasopharynx,,2009,New Zealand,New Zealand: Auckland Combined,,female,5Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1316,Bordetella pertussis NZ34,NZ34,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385793,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407415.1,CP054097,,,Oxford Nanopore; Illumina,173x,Flye v. 2.3.1,1,0,1,4105547,67.70389,4112,3861,nasal,,2005,New Zealand,New Zealand: Waikato,,male,11Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.5,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1317,Bordetella pertussis NZ37,NZ37,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385796,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407355.1,CP054094,,,Oxford Nanopore; Illumina,334x,Flye v. 2.3.1,1,0,1,4129327,67.712006,4119,3886,pernasal,,2006,New Zealand,New Zealand: Capital and Coast,,female,8Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1318,Bordetella pertussis NZ36,NZ36,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385795,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407375.1,CP054095,,,Oxford Nanopore; Illumina,502x,Flye v. 2.3.1,1,0,1,4129691,67.71262,4136,3882,nasal,,2006,New Zealand,New Zealand: Midcentral,,male,1M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1319,Bordetella pertussis NZ35,NZ35,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385794,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407395.1,CP054096,,,Oxford Nanopore; Illumina,486x,Flye v. 2.3.1,1,0,1,4129756,67.71291,4144,3882,nasopharynx,,2005,New Zealand,New Zealand: Midcentral,,female,56Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1320,Bordetella pertussis NZ33,NZ33,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385792,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407435.1,CP054098,,,Oxford Nanopore; Illumina,251x,Flye v. 2.3.1,1,0,1,4101147,67.70706,4141,3866,pernasal,,2005,New Zealand,New Zealand: Southern,,female,11Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1321,Bordetella pertussis NZ30,NZ30,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385789,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407495.1,CP054101,,,Oxford Nanopore; Illumina,278x,Flye v. 2.3.1,1,0,1,4104448,67.70406,4163,3863,nasopharynx,,2004,New Zealand,New Zealand: Auckland Combined,,female,21Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.16,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1322,Bordetella pertussis NZ32,NZ32,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385791,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407455.1,CP054099,,,Oxford Nanopore; Illumina,196x,Flye v. 2.3.1,1,0,1,4124576,67.71416,4203,3881,nasopharynx,,2005,New Zealand,New Zealand: Waikato,,female,2Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.51,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1323,Bordetella pertussis NZ31,NZ31,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385790,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407475.1,CP054100,,,Oxford Nanopore; Illumina,201x,Flye v. 2.3.1,1,0,1,4103226,67.70507,4137,3863,nasopharynx,,2004,New Zealand,New Zealand: Northland,,male,7Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1324,Bordetella pertussis NZ28,NZ28,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385787,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407515.1,CP054102,,,Oxford Nanopore; Illumina,548x,Unicycler v. 0.4.8,1,0,1,4107436,67.705475,4053,3892,nasopharynx,,2016,New Zealand,New Zealand: Southern,,female,1M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1325,Bordetella pertussis NZ27,NZ27,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385786,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407535.1,CP054103,,,Oxford Nanopore; Illumina,197x,Flye v. 2.3.1,1,0,1,4108488,67.70026,4185,3867,nasopharynx,,2015,New Zealand,New Zealand: Southern,,male,9Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.07,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1326,Bordetella pertussis NZ26,NZ26,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385785,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407655.1,CP054104,,,Oxford Nanopore; Illumina,509x,Unicycler v. 0.4.8,1,0,1,4113734,67.70036,4045,3869,nasopharynx,,2015,New Zealand,New Zealand: Auckland Combined,,female,68Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1327,Bordetella pertussis NZ23,NZ23,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385782,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022408035.1,CP054107,,,Oxford Nanopore; Illumina,613x,Unicycler v. 0.4.8,1,0,1,4108473,67.70391,4048,3893,nasopharynx,,2013,New Zealand,New Zealand: Northland,,male,43Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1328,Bordetella pertussis NZ24,NZ24,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385783,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407895.1,CP054106,,,Oxford Nanopore; Illumina,567x,Unicycler v. 0.4.8,1,0,1,4110545,67.7019,4053,3896,nasopharynx,,2014,New Zealand,New Zealand: Southern,,female,70Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1329,Bordetella pertussis NZ25,NZ25,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385784,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022407775.1,CP054105,,,Oxford Nanopore; Illumina,552x,Unicycler v. 0.4.8,1,0,1,4111604,67.70093,4052,3872,nasopharynx,,2014,New Zealand,New Zealand: Waikato,,male,2Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1330,Bordetella pertussis NZ66,NZ66,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585532,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409135.1,CP054065,,,Oxford Nanopore; Illumina,715x,Unicycler v. 0.4.8,1,0,1,4111589,67.70115,4069,3868,nasopharynx,,2018,New Zealand,New Zealand: Nelson Marlborough,,male,2Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1331,Bordetella pertussis NZ65,NZ65,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585531,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409155.1,CP054066,,,Oxford Nanopore; Illumina,325x,Flye v. 2.3.1,1,0,1,4105764,67.70406,4129,3864,nasopharynx,,2018,New Zealand,New Zealand: South Canterbury,,male,1M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1332,Bordetella pertussis NZ64,NZ64,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585530,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409175.1,CP054067,,,Oxford Nanopore; Illumina,825x,Unicycler v. 0.4.8,1,0,1,4105330,67.70803,4046,3890,pernasal,,2018,New Zealand,New Zealand: South Canterbury,,male,16Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1333,Bordetella pertussis NZ22,NZ22,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385781,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409215.1,CP054108,,,Oxford Nanopore; Illumina,388x,Flye v. 2.3.1,1,0,1,4114225,67.69656,4155,3872,nasal,,2013,New Zealand,New Zealand: South Canterbury,,male,5Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1334,Bordetella pertussis NZ63,NZ63,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12585529,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409195.1,CP054068,,,Oxford Nanopore; Illumina,494x,Flye v. 2.3.1,1,0,1,4112099,67.700874,4072,3875,nasopharynx,,2017,New Zealand,New Zealand: Nelson Marlborough,,female,57Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.97,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1335,Bordetella pertussis NZ21,NZ21,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385780,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409235.1,CP054109,,,Oxford Nanopore; Illumina,370x,Unicycler v. 0.4.8,1,0,1,4105329,67.70741,4043,3891,nasal,,2007,New Zealand,New Zealand: Nelson Marlborough,,male,11M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1336,Bordetella pertussis NZ17,NZ17,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385776,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409315.1,CP054113,,,Oxford Nanopore; Illumina,499x,Unicycler v. 0.4.8,1,0,1,4107409,67.70538,4049,3867,pernasal,,2002,New Zealand,New Zealand: Capital and Coast,,female,3Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1337,Bordetella pertussis NZ18,NZ18,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385777,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409295.1,CP054112,,,Oxford Nanopore; Illumina,406x,Unicycler v. 0.4.8,1,0,1,4106161,67.70577,4052,3862,nasopharynx,,2002,New Zealand,New Zealand: Nelson Marlborough,,male,36Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1338,Bordetella pertussis NZ15,NZ15,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385774,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409355.1,CP054115,,,Oxford Nanopore; Illumina,248x,Flye v. 2.3.1,1,0,1,4105505,67.70383,4132,3862,nasopharynx,,2000,New Zealand,New Zealand: Taranaki,,male,9M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.07,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1339,Bordetella pertussis NZ16,NZ16,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385775,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409335.1,CP054114,,,Oxford Nanopore; Illumina,147x,Flye v. 2.3.1,1,0,1,4101679,67.7064,4175,3862,pernasal,,2001,New Zealand,New Zealand: Canterbury,,female,3Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.84,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1340,Bordetella pertussis NZ19,NZ19,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385778,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409255.1,CP054111,,,Oxford Nanopore; Illumina,368x,Flye v. 2.3.1,1,0,1,4102505,67.707634,4153,3862,pernasal,,2003,New Zealand,New Zealand: Midcentral,,male,4Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1341,Bordetella pertussis NZ20,NZ20,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385779,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409275.1,CP054110,,,Oxford Nanopore; Illumina,339x,Flye v. 2.3.1,1,0,1,4106591,67.70287,4153,3867,pernasal,,2007,New Zealand,New Zealand: Waikato,,female,3M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.3,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1342,Bordetella pertussis NZ9,NZ9,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385768,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409415.1,CP054120,,,Oxford Nanopore; Illumina,489x,Unicycler v. 0.4.8,1,0,1,4106091,67.706024,4044,3863,pernasal,,1990,New Zealand,New Zealand: Auckland Combined,,female,11M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1343,Bordetella pertussis NZ13,NZ13,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385772,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409395.1,CP054117,,,Oxford Nanopore; Illumina,404x,Unicycler v. 0.4.8,1,0,1,4129017,67.714714,4083,3882,pernasal,,1997,New Zealand,New Zealand: Capital and Coast,,male,9M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1344,Bordetella pertussis NZ14,NZ14,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385773,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409375.1,CP054116,,,Oxford Nanopore; Illumina,361x,Unicycler v. 0.4.8,1,0,1,4104272,67.70906,4038,3864,nasopharynx,,1999,New Zealand,New Zealand: Southern,,female,4Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1345,Bordetella pertussis NZ12,NZ12,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385771,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409455.1,CP054127,,,Oxford Nanopore; Illumina,260x,Flye v. 2.3.1,1,0,1,4107067,67.70332,4128,3864,nasopharynx,,1994,New Zealand,New Zealand: Capital and Coast,,female,9M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1346,Bordetella pertussis NZ11,NZ11,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385770,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409475.1,CP054118,,,Oxford Nanopore; Illumina,204x,Flye v. 2.3.1,1,0,1,4107545,67.700294,4227,3864,nasopharynx,,1993,New Zealand,New Zealand: Capital and Coast,,male,9Y,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,98.83,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1347,Bordetella pertussis NZ10,NZ10,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385769,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409435.1,CP054119,,,Oxford Nanopore; Illumina,218x,Flye v. 2.3.1,1,0,1,4129934,67.70714,4160,3881,nasopharynx,,1991,New Zealand,New Zealand: Capital and Coast,,female,1M,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.88,0.47,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.1348,Bordetella pertussis NZ7,NZ7,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385766,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409515.1,CP054122,,,Oxford Nanopore; Illumina,370x,Unicycler v. 0.4.8,1,0,1,4134221,67.71271,4070,3886,,,1988,New Zealand,New Zealand,,,,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1349,Bordetella pertussis NZ8,NZ8,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385767,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409495.1,CP054121,,,Oxford Nanopore; Illumina,134x,Flye v. 2.3.1,1,0,1,4105369,67.70232,4248,3862,,,1989,New Zealand,New Zealand: Auckland Combined,,female,9W,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.3,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1350,Bordetella pertussis NZ6,NZ6,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385765,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409535.1,CP054123,,,Oxford Nanopore; Illumina,428x,Unicycler v. 0.4.8,1,0,1,4107406,67.70575,4043,3865,,,1987,New Zealand,New Zealand,,,,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1351,Bordetella pertussis NZ4,NZ4,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385763,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409555.1,CP054124,,,Oxford Nanopore; Illumina,329x,Flye v. 2.3.1,1,0,1,4128172,67.71222,4137,3875,,,1985,New Zealand,New Zealand,,,,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.3,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1352,Bordetella pertussis NZ3,NZ3,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385762,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409575.1,CP054125,,,Oxford Nanopore; Illumina,451x,Unicycler v. 0.4.8,1,0,1,4130100,67.715065,4066,3908,,,1984,New Zealand,New Zealand,,,,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1353,Bordetella pertussis NZ2,NZ2,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12385761,520,,,,MLST.Bordetella_spp.2,,,,2022-02-28T00:00:00Z,35084300,PRJNA556977,GCA_022409595.1,CP054126,,,Oxford Nanopore; Illumina,387x,Flye v. 2.3.1,1,0,1,4131552,67.71119,4110,3888,,,1983,New Zealand,New Zealand,,,,Whooping cough,,,,,,,,,,,,,,collected_by:NZ_ESR,,,,,,,Whooping cough,,,,,,,,,,,,,,99.07,0.47,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,520.1373,Bordetella pertussis J294,J294,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007542,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018039,,,PacBio RSII; Illumina HiSeq,108x,HGAP v. 3,1,0,1,4109951,67.70222,4092,3864,,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1374,Bordetella pertussis I384,I384,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05948795,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017882,,,PacBio RSII; Illumina HiSeq,105x,HGAP v. 3,1,0,1,4108491,67.70486,4038,3861,,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1375,Bordetella pertussis I385,I385,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05948796,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017883,,,PacBio RSII; Illumina HiSeq,107x,HGAP v. 3,1,0,1,4105355,67.70759,4036,3859,,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1376,Bordetella pertussis J074,J074,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05948797,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017884,,,PacBio RSII; Illumina MiSeq,104x,HGAP v. 3,1,0,1,4105450,67.70649,4036,3862,,,2013,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1377,Bordetella pertussis J081,J081,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05948798,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017885,,,PacBio RSII; Illumina MiSeq,163x,HGAP v. 3,1,0,1,4107548,67.70448,4037,3863,,,2013,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1378,Bordetella pertussis J148,J148,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716050,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017923,,,PacBio RSII; Illumina HiSeq,240x,HGAP v. 3,1,0,1,4102575,67.70243,4041,3861,,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,99.7,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1379,Bordetella pertussis J173,J173,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05950788,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017924,,,PacBio RSII; Illumina HiSeq,200x,HGAP v. 3,1,0,1,4106356,67.70667,4048,3859,,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1380,Bordetella pertussis J203,J203,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05950790,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017925,,,PacBio RSII; Illumina HiSeq,222x,HGAP v. 3,1,0,1,4104273,67.708336,4036,3858,,,2014,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1381,Bordetella pertussis J230,J230,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716056,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017926,,,PacBio RSII; Illumina HiSeq,266x,HGAP v. 3,1,0,1,4106384,67.70655,4039,3859,,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1382,Bordetella pertussis J295,J295,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05950791,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP017927,,,PacBio RSII; Illumina HiSeq,245x,HGAP v. 3,1,0,1,4105292,67.70773,4039,3858,,,2014,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1383,Bordetella pertussis J094,J094,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007540,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018037,,,PacBio RSII; Illumina HiSeq,266x,HGAP v. 3,1,0,1,4103789,67.703674,4041,3860,,,2014,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1384,Bordetella pertussis J207,J207,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007541,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018038,,,PacBio RSII; Illumina HiSeq,135x,HGAP v. 3,1,0,1,4108318,67.70352,4098,3870,,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1385,Bordetella pertussis J306,J306,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007544,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018041,,,PacBio RSII; Illumina HiSeq,244x,HGAP v. 3,1,0,1,4103205,67.70924,4045,3855,,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1386,Bordetella pertussis J313,J313,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007545,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018042,,,PacBio RSII; Illumina MiSeq,194x,HGAP v. 3,1,0,1,4109385,67.703,4077,3862,,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.1387,Bordetella pertussis J304,J304,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007543,520,,,,MLST.Bordetella_spp.2,,,,2019-12-17T00:00:00Z,31744907,PRJNA279196,,CP018040,,,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,0,1,4105872,67.70484,4090,3857,,,2014,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,,,,,,,,,pertussis,,,,,,,,,,,,,,99.9,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.505,Bordetella pertussis strain C571,C571,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455331,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001984925.1,CP011167,NZ_CP011167.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,141x,HGAP v. 3,1,,1,4105364,67.71,4049,3626,missing,,2000,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.506,Bordetella pertussis strain C958,C958,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455332,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001984945.1,CP011168,NZ_CP011168.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,223x,HGAP v. 3,1,,1,4100254,67.71,4048,3620,missing,,2001,USA,USA: NJ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.507,Bordetella pertussis strain D521,D521,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455333,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001984965.1,CP011169,NZ_CP011169.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,120x,HGAP v. 3,1,,1,4101097,67.71,4051,3625,missing,,2000,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.508,Bordetella pertussis strain E150,E150,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455335,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985005.1,CP011171,NZ_CP011171.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,163x,HGAP v. 3,1,,1,4104313,67.71,4074,3911,missing,,2003,USA,USA: OH,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.509,Bordetella pertussis strain D879,D879,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455334,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001984985.1,CP011170,NZ_CP011170.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,154x,HGAP v. 3,1,,1,4106400,67.71,4054,3633,missing,,2002,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.510,Bordetella pertussis strain E555,E555,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455336,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985025.1,CP011172,NZ_CP011172.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,159x,HGAP v. 3,1,,1,4102209,67.71,4052,3626,missing,,2004,USA,USA: MT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.511,Bordetella pertussis strain E587,E587,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455337,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985045.1,CP011173,NZ_CP011173.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,179x,HGAP v. 3,1,,1,4101625,67.71,4052,3627,missing,,2005,USA,USA: DE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.512,Bordetella pertussis strain E809,E809,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455338,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985065.1,CP011174,NZ_CP011174.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,230x,HGAP v. 3,1,,1,4103251,67.71,4054,3629,missing,,2005,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.513,Bordetella pertussis strain E976,E976,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455339,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985085.1,CP011175,NZ_CP011175.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,158x,HGAP v. 3,1,,1,4116415,67.7,4072,3619,missing,,2005,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.514,Bordetella pertussis strain F011,F011,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455340,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985105.1,CP011176,NZ_CP011176.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,130x,HGAP v. 3,1,,1,4102201,67.71,4050,3627,missing,,2005,USA,USA: NE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.515,Bordetella pertussis strain F034,F034,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455341,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985125.1,CP011177,NZ_CP011177.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,140x,HGAP v. 3,1,,1,4105889,67.71,4054,3627,missing,,2005,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.516,Bordetella pertussis strain F658,F658,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455342,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985145.1,CP011178,NZ_CP011178.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,133x,HGAP v. 3,1,,1,4107481,67.71,4051,3631,missing,,2008,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.517,Bordetella pertussis strain F670,F670,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455343,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985165.1,CP011179,NZ_CP011179.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,130x,HGAP v. 3,1,,1,4103215,67.71,4050,3629,missing,,2003,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.518,Bordetella pertussis strain F684,F684,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455344,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985185.1,CP011180,,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,143x,HGAP v. 3,1,,1,4106424,67.71,4052,3629,missing,,2008,USA,USA: NC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.519,Bordetella pertussis strain F687,F687,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455345,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985205.1,CP011181,NZ_CP011181.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,145x,HGAP v. 3,1,,1,4108495,67.7,4053,3633,missing,,2008,USA,USA: VA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.520,Bordetella pertussis strain F948,F948,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455346,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985225.1,CP011182,NZ_CP011182.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,158x,HGAP v. 3,1,,1,4106406,67.71,4059,3630,missing,,2007,USA,USA: IL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.521,Bordetella pertussis strain H520,H520,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455347,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985245.1,CP011183,NZ_CP011183.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,104x,HGAP v. 3,1,,1,4102661,67.71,4052,3625,missing,,2009,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.522,Bordetella pertussis strain H579,H579,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455348,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985265.1,CP011184,NZ_CP011184.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,171x,HGAP v. 3,1,,1,4109506,67.7,4054,3630,missing,,2010,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.523,Bordetella pertussis strain H637,H637,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455349,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985285.1,CP011185,NZ_CP011185.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,171x,HGAP v. 3,1,,1,4103696,67.7,4049,3625,missing,,2010,USA,USA: TN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.524,Bordetella pertussis strain H665,H665,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455350,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985305.1,CP011186,NZ_CP011186.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,163x,HGAP v. 3,1,,1,4109528,67.7,4056,3629,missing,,2010,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.525,Bordetella pertussis strain H703,H703,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455351,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985325.1,CP011187,NZ_CP011187.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,128x,HGAP v. 3,1,,1,4107439,67.71,4051,3630,missing,,2010,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.526,Bordetella pertussis strain H707,H707,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455352,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985345.1,CP011188,NZ_CP011188.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,141x,HGAP v. 3,1,,1,4107280,67.71,4054,3632,missing,,2010,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.527,Bordetella pertussis strain H729,H729,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455353,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985365.1,CP011189,NZ_CP011189.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,143x,HGAP v. 3,1,,1,4108484,67.7,4050,3630,missing,,2011,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.528,Bordetella pertussis strain H740,H740,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455354,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985385.1,CP011190,NZ_CP011190.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,134x,HGAP v. 3,1,,1,4111081,67.71,4080,3618,missing,,2011,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.529,Bordetella pertussis strain H754,H754,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455355,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985405.1,CP011191,NZ_CP011191.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,130x,HGAP v. 3,1,,1,4101757,67.71,4050,3626,missing,,2011,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.530,Bordetella pertussis strain H765,H765,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455356,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985425.1,CP011192,NZ_CP011192.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,146x,HGAP v. 3,1,,1,4103252,67.71,4053,3623,missing,,2011,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.531,Bordetella pertussis strain H784,H784,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455357,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985445.1,CP011193,NZ_CP011193.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,110x,HGAP v. 3,1,,1,4106396,67.71,4053,3633,missing,,2011,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.532,Bordetella pertussis strain H800,H800,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455358,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985465.1,CP011194,NZ_CP011194.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,134x,HGAP v. 3,1,,1,4102311,67.71,4049,3630,missing,,2011,USA,USA: MO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.533,Bordetella pertussis strain H806,H806,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455359,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985485.1,CP011195,NZ_CP011195.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,164x,HGAP v. 3,1,,1,4103534,67.71,4053,3627,missing,,2011,USA,USA: FL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.534,Bordetella pertussis strain H810,H810,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455360,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985505.1,CP011196,NZ_CP011196.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,134x,HGAP v. 3,1,,1,4106384,67.71,4049,3627,missing,,2011,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.535,Bordetella pertussis strain H812,H812,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455361,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985525.1,CP011197,NZ_CP011197.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,162x,HGAP v. 3,1,,1,4106501,67.71,4053,3632,missing,,2011,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.536,Bordetella pertussis strain I228,I228,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455362,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985545.1,CP011198,NZ_CP011198.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,168x,HGAP v. 3,1,,1,4111652,67.7,4061,3630,missing,,2012,USA,USA: FL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.537,Bordetella pertussis strain I238,I238,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455363,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985565.1,CP011199,NZ_CP011199.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,128x,HGAP v. 3,1,,1,4104580,67.71,4050,3625,missing,,2012,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.538,Bordetella pertussis strain I373,I373,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455364,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985585.1,CP011200,NZ_CP011200.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,166x,HGAP v. 3,1,,1,4105954,67.71,4052,3629,missing,,2012,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.539,Bordetella pertussis strain I387,I387,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455365,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985605.1,CP011201,NZ_CP011201.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,149x,HGAP v. 3,1,,1,4108494,67.7,4053,3629,missing,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.540,Bordetella pertussis strain I602,I602,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455366,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985625.1,CP011202,NZ_CP011202.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,148x,HGAP v. 3,1,,1,4108484,67.7,4054,3630,missing,,2013,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.541,Bordetella pertussis strain I730,I730,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455367,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985645.1,CP011203,NZ_CP011203.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,253x,HGAP v. 3,1,,1,4106407,67.71,4052,3628,missing,,2013,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.542,Bordetella pertussis strain I752,I752,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455368,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985665.1,CP011204,NZ_CP011204.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,112x,HGAP v. 3,1,,1,4110589,67.7,4051,3633,missing,,2013,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.543,Bordetella pertussis strain I763,I763,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455369,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985685.1,CP011205,NZ_CP011205.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,126x,HGAP v. 3,1,,1,4106397,67.71,4080,3921,missing,,2013,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.544,Bordetella pertussis strain I915,I915,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455370,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985705.1,CP011206,NZ_CP011206.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,191x,HGAP v. 3,1,,1,4106386,67.71,4052,3623,missing,,2010,USA,USA: VT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.545,Bordetella pertussis strain I944,I944,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455371,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985725.1,CP011207,NZ_CP011207.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,114x,HGAP v. 3,1,,1,4112738,67.7,4057,3635,missing,,2013,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.546,Bordetella pertussis strain J018,J018,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03455372,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001985745.1,CP011208,NZ_CP011208.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,145x,HGAP v. 3,1,,1,4103225,67.71,4052,3627,missing,,2013,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.547,Bordetella pertussis strain I106,I106,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854492,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985805.1,CP012080,NZ_CP012080.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,123x,HGAP v. 3,1,,1,4102205,67.71,4047,3624,missing,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.548,Bordetella pertussis strain H852,H852,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854491,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985785.1,CP012079,NZ_CP012079.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,134x,HGAP v. 3,1,,1,4105340,67.71,4052,3625,missing,,2011,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.549,Bordetella pertussis strain H681,H681,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854490,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985765.1,CP012078,NZ_CP012078.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,195x,HGAP v. 3,1,,1,4105309,67.71,4054,3626,missing,,2009,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.550,Bordetella pertussis strain I351,I351,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854493,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985825.1,CP012081,NZ_CP012081.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,123x,HGAP v. 3,1,,1,4108752,67.71,4060,3628,missing,,2012,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.551,Bordetella pertussis strain I743,I743,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854494,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985845.1,CP012082,NZ_CP012082.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,157x,HGAP v. 3,1,,1,4107480,67.71,4062,3627,missing,,2013,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.552,Bordetella pertussis strain I751,I751,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854495,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985865.1,CP012083,NZ_CP012083.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,121x,HGAP v. 3,1,,1,4109556,67.7,4057,3625,missing,,2012,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.553,Bordetella pertussis strain I976,I976,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854496,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985885.1,CP012084,NZ_CP012084.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,121x,HGAP v. 3,1,,1,4104251,67.71,4051,3624,missing,,2013,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.554,Bordetella pertussis strain J010,J010,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854497,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985905.1,CP012085,NZ_CP012085.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,130x,HGAP v. 3,1,,1,4107382,67.71,4054,3626,missing,,2013,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.555,Bordetella pertussis strain J013,J013,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854498,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985925.1,CP012086,NZ_CP012086.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,109x,HGAP v. 3,1,,1,4105333,67.71,4050,3626,missing,,2013,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.556,Bordetella pertussis strain J038,J038,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854499,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985945.1,CP012087,NZ_CP012087.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,100x,HGAP v. 3,1,,1,4107443,67.71,4048,3630,missing,,2013,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.557,Bordetella pertussis strain J107,J107,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854500,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001985965.1,CP012088,NZ_CP012088.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,148x,HGAP v. 3,1,,1,4106377,67.71,4053,3627,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.558,Bordetella pertussis strain J169,J169,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03854501,520,,,,MLST.Bordetella_spp.1,,ATCC: BAA-589,,2017-02-06T00:00:00Z,,PRJNA279196,GCA_001985985.1,CP012089,NZ_CP012089.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,126x,HGAP v. 3,1,,1,4102567,67.71,4042,3621,missing,,,,,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.559,Bordetella pertussis strain G057,G057,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877217,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986005.1,CP012129,NZ_CP012129.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,175x,HGAP v. 3,1,,1,4108471,67.71,4050,3630,missing,,2004,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.560,Bordetella pertussis strain H639,H639,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877218,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986025.1,CP012130,NZ_CP012130.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,182x,HGAP v. 3,1,,1,4088698,67.72,4034,3620,missing,,2010,USA,USA: MI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.561,Bordetella pertussis strain I150,I150,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877219,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986045.1,CP012131,NZ_CP012131.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,121x,HGAP v. 3,1,,1,4107430,67.71,4054,3630,missing,,2012,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.562,Bordetella pertussis strain I187,I187,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877220,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986065.1,CP012132,NZ_CP012132.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,,1,4106507,67.71,4052,3632,missing,,2012,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.563,Bordetella pertussis strain I259,I259,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877221,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986085.1,CP012133,NZ_CP012133.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,156x,HGAP v. 3,1,,1,4105353,67.71,4053,3627,missing,,2012,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.564,Bordetella pertussis strain I464,I464,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877222,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986105.1,CP012134,NZ_CP012134.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,,1,4107433,67.71,4058,3630,missing,,2012,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.565,Bordetella pertussis strain H320,H320,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464271,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986155.1,CP011234,NZ_CP011234.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,258x,HGAP v. 3,1,,1,4109545,67.7,4056,3635,missing,,2009,USA,USA: FL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.566,Bordetella pertussis strain H834,H834,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464273,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986175.1,CP011235,NZ_CP011235.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,102x,HGAP v. 3,1,,1,4103704,67.71,4051,3627,missing,,2009,USA,USA: NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.567,Bordetella pertussis strain H710,H710,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464272,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986195.1,CP011236,NZ_CP011236.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,161x,HGAP v. 3,1,,1,4105333,67.71,4054,3628,missing,,,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.568,Bordetella pertussis strain H851,H851,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464274,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986215.1,CP011237,NZ_CP011237.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,129x,HGAP v. 3,1,,1,4106500,67.71,4052,3631,missing,,2011,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.569,Bordetella pertussis strain H915,H915,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464276,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986255.1,CP011239,NZ_CP011239.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,188x,HGAP v. 3,1,,1,4104277,67.71,4055,3630,missing,,2011,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.570,Bordetella pertussis strain H911,H911,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464275,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986235.1,CP011238,NZ_CP011238.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,114x,HGAP v. 3,1,,1,4102182,67.71,4053,3624,missing,,2012,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.571,Bordetella pertussis strain I075,I075,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464277,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986275.1,CP011240,NZ_CP011240.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,137x,HGAP v. 3,1,,1,4106355,67.71,4052,3629,missing,,2012,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.572,Bordetella pertussis strain I112,I112,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464278,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986295.1,CP011241,NZ_CP011241.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,131x,HGAP v. 3,1,,1,4106385,67.71,4053,3628,missing,,2012,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.573,Bordetella pertussis strain I975,I975,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464279,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986315.1,CP011242,NZ_CP011242.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,102x,HGAP v. 3,1,,1,4106497,67.71,4053,3630,missing,,2013,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.574,Bordetella pertussis strain I998,I998,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464280,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986335.1,CP011243,NZ_CP011243.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,148x,HGAP v. 3,1,,1,4109711,67.7,4055,3631,missing,,2013,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.575,Bordetella pertussis strain J022,J022,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464281,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986355.1,CP011244,NZ_CP011244.1,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,152x,HGAP v. 3,1,,1,4106504,67.71,4051,3630,missing,,2013,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.576,Bordetella pertussis strain C505,C505,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702609,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986375.1,CP011687,NZ_CP011687.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,132x,HGAP v. 3,1,,1,4103277,67.71,4053,3627,missing,,2000,USA,USA:MI,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.577,Bordetella pertussis strain C742,C742,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702610,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986415.1,CP011688,NZ_CP011688.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,139x,HGAP v. 3,1,,1,4103249,67.71,4047,3627,missing,,2000,USA,USA:OH,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.578,Bordetella pertussis strain D175,D175,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702611,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986435.1,CP011689,NZ_CP011689.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,108x,HGAP v. 3,1,,1,4108515,67.7,4056,3632,missing,,2000,USA,USA:CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.579,Bordetella pertussis strain D321,D321,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702612,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986455.1,CP011690,NZ_CP011690.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,108x,HGAP v. 3,1,,1,4104176,67.71,4052,3627,missing,,2001,USA,USA:MO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.580,Bordetella pertussis strain D502,D502,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702613,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986475.1,CP011691,NZ_CP011691.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,104x,HGAP v. 3,1,,1,4101167,67.71,4044,3625,missing,,2001,USA,USA:IL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.581,Bordetella pertussis strain E024,E024,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702614,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986495.1,CP011692,NZ_CP011692.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,111x,HGAP v. 3,1,,1,4101131,67.71,4050,3627,missing,,2003,USA,USA:MD,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.582,Bordetella pertussis strain E530,E530,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702615,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,,PRJNA279196,GCF_001986515.1,CP011693,NZ_CP011693.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,75x,HGAP v. 3,1,,1,4106392,67.71,4052,3628,missing,,2000,USA,USA:MT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.583,Bordetella pertussis strain H346,H346,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702616,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986535.1,CP011694,NZ_CP011694.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,143x,HGAP v. 3,1,,1,4110608,67.7,4053,3631,missing,,2010,USA,USA:GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.584,Bordetella pertussis strain H437,H437,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702617,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986555.1,CP011695,NZ_CP011695.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,157x,HGAP v. 3,1,,1,4105342,67.71,4053,3628,missing,,2006,USA,USA:TN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.585,Bordetella pertussis strain H762,H762,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702618,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986575.1,CP011696,NZ_CP011696.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,124x,HGAP v. 3,1,,1,4105337,67.71,4052,3625,missing,,2011,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.586,Bordetella pertussis strain H763,H763,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702619,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986595.1,CP011697,NZ_CP011697.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,189x,HGAP v. 3,1,,1,4110595,67.71,4054,3629,missing,,2011,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.587,Bordetella pertussis strain H764,H764,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702620,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986615.1,CP011698,NZ_CP011698.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,139x,HGAP v. 3,1,,1,4105334,67.71,4052,3626,missing,,2011,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.588,Bordetella pertussis strain H766,H766,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702621,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986635.1,CP011699,NZ_CP011699.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,133x,HGAP v. 3,1,,1,4104260,67.71,4054,3625,missing,,2011,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.589,Bordetella pertussis strain H768,H768,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702622,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986655.1,CP011700,NZ_CP011700.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,101x,HGAP v. 3,1,,1,4106385,67.71,4050,3626,missing,,2011,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.590,Bordetella pertussis strain H773,H773,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702623,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986675.1,CP011701,NZ_CP011701.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,119x,HGAP v. 3,1,,1,4111638,67.7,4055,3628,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.591,Bordetella pertussis strain H775,H775,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702624,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986695.1,CP011702,NZ_CP011702.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,157x,HGAP v. 3,1,,1,4106491,67.71,4054,3626,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.592,Bordetella pertussis strain H779,H779,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702625,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986715.1,CP011703,NZ_CP011703.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,129x,HGAP v. 3,1,,1,4106294,67.71,4064,3599,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.593,Bordetella pertussis strain H787,H787,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702626,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986735.1,CP011704,NZ_CP011704.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,142x,HGAP v. 3,1,,1,4108479,67.7,4052,3632,missing,,2011,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.594,Bordetella pertussis strain H842,H842,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702627,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986755.1,CP011705,NZ_CP011705.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,109x,HGAP v. 3,1,,1,4111642,67.7,4056,3634,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.595,Bordetella pertussis strain H847,H847,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702628,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986775.1,CP011706,NZ_CP011706.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,130x,HGAP v. 3,1,,1,4103252,67.71,4045,3617,missing,,2011,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.596,Bordetella pertussis strain H849,H849,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702629,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986795.1,CP011707,NZ_CP011707.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,103x,HGAP v. 3,1,,1,4103204,67.71,4050,3626,missing,,2011,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.597,Bordetella pertussis strain H853,H853,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702630,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986815.1,CP011708,NZ_CP011708.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,99x,HGAP v. 3,1,,1,4109537,67.71,4054,3629,missing,,2011,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.598,Bordetella pertussis strain H864,H864,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702631,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986835.1,CP011709,NZ_CP011709.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,90x,HGAP v. 3,1,,1,4106500,67.71,4046,3631,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.599,Bordetella pertussis strain H866,H866,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702632,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986855.1,CP011710,NZ_CP011710.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,147x,HGAP v. 3,1,,1,4111644,67.7,4053,3636,missing,,2011,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.600,Bordetella pertussis strain H878,H878,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702633,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986875.1,CP011711,NZ_CP011711.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,134x,HGAP v. 3,1,,1,4106327,67.71,4051,3626,missing,,2012,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.601,Bordetella pertussis strain H883,H883,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702634,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986895.1,CP011712,NZ_CP011712.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,94x,HGAP v. 3,1,,1,4109547,67.7,4048,3630,missing,,2011,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.602,Bordetella pertussis strain H884,H884,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702635,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986915.1,CP011713,NZ_CP011713.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,126x,HGAP v. 3,1,,1,4109547,67.7,4052,3616,missing,,2011,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.603,Bordetella pertussis strain H910,H910,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702636,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986935.1,CP011714,NZ_CP011714.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,141x,HGAP v. 3,1,,1,4110589,67.7,4053,3634,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.604,Bordetella pertussis strain I069,I069,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702637,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001986955.1,CP011715,NZ_CP011715.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,113x,HGAP v. 3,1,,1,4109549,67.7,4055,3632,missing,,2012,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.605,Bordetella pertussis strain I088,I088,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702638,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986975.1,CP011716,NZ_CP011716.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,163x,HGAP v. 3,1,,1,4112692,67.7,4059,3634,missing,,2012,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.606,Bordetella pertussis strain I089,I089,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702639,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001986995.1,CP011717,NZ_CP011717.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,92x,HGAP v. 3,1,,1,4110588,67.7,4051,3629,missing,,2012,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.607,Bordetella pertussis strain I110,I110,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702640,520,,,,MLST.Bordetella_spp.83,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001987015.1,CP011718,NZ_CP011718.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,120x,HGAP v. 3,1,,1,4111608,67.7,4054,3633,missing,,2012,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.608,Bordetella pertussis strain I111,I111,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702641,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001987035.1,CP011719,NZ_CP011719.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,156x,HGAP v. 3,1,,1,4106381,67.71,4049,3628,missing,,2012,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.609,Bordetella pertussis strain I113,I113,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702642,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987055.1,CP011720,NZ_CP011720.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,155x,HGAP v. 3,1,,1,4103237,67.71,4046,3626,missing,,2012,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.610,Bordetella pertussis strain I127,I127,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702643,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987075.1,CP011721,NZ_CP011721.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,163x,HGAP v. 3,1,,1,4103220,67.71,4055,3627,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.611,Bordetella pertussis strain I257,I257,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702646,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987135.1,CP011724,NZ_CP011724.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,87x,HGAP v. 3,1,,1,4104251,67.71,4053,3627,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.612,Bordetella pertussis strain I135,I135,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702644,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987095.1,CP011722,NZ_CP011722.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,91x,HGAP v. 3,1,,1,4109544,67.7,4049,3631,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.613,Bordetella pertussis strain I136,I136,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702645,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987115.1,CP011723,NZ_CP011723.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,110x,HGAP v. 3,1,,1,4107454,67.71,4060,3629,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.614,Bordetella pertussis strain I263,I263,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702647,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987155.1,CP011725,NZ_CP011725.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,116x,HGAP v. 3,1,,1,4104253,67.71,4052,3627,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.615,Bordetella pertussis strain I270,I270,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702648,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987175.1,CP011726,NZ_CP011726.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,156x,HGAP v. 3,1,,1,4103217,67.71,4051,3626,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.616,Bordetella pertussis strain I271,I271,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702649,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987195.1,CP011727,NZ_CP011727.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,158x,HGAP v. 3,1,,1,4109543,67.7,4056,3634,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.617,Bordetella pertussis strain I273,I273,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702650,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987215.1,CP011728,NZ_CP011728.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,90x,HGAP v. 3,1,,1,4110433,67.7,4054,3635,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.618,Bordetella pertussis strain I289,I289,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702651,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987235.1,CP011729,NZ_CP011729.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,97x,HGAP v. 3,1,,1,4106397,67.71,4049,3629,missing,,2012,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.619,Bordetella pertussis strain I315,I315,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702652,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987255.1,CP011730,NZ_CP011730.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,171x,HGAP v. 3,1,,1,4108498,67.7,4054,3629,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.620,Bordetella pertussis strain I318,I318,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702653,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987275.1,CP011731,NZ_CP011731.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,184x,HGAP v. 3,1,,1,4107427,67.71,4052,3631,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.621,Bordetella pertussis strain I331,I331,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702654,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001987295.1,CP011732,NZ_CP011732.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,185x,HGAP v. 3,1,,1,4104202,67.71,4058,3632,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.622,Bordetella pertussis strain I350,I350,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702655,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987315.1,CP011733,NZ_CP011733.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,150x,HGAP v. 3,1,,1,4107435,67.71,4048,3629,missing,,2012,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.623,Bordetella pertussis strain I375,I375,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702656,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987335.1,CP011734,NZ_CP011734.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,113x,HGAP v. 3,1,,1,4113693,67.7,4063,3636,missing,,2012,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.624,Bordetella pertussis strain I379,I379,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702657,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987355.1,CP011735,NZ_CP011735.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,106x,HGAP v. 3,1,,1,4104294,67.71,4053,3626,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.625,Bordetella pertussis strain I380,I380,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702658,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987375.1,CP011736,NZ_CP011736.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,130x,HGAP v. 3,1,,1,4091930,67.69,4036,3615,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.626,Bordetella pertussis strain I382,I382,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702659,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987395.1,CP011737,NZ_CP011737.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,149x,HGAP v. 3,1,,1,4110505,67.7,4054,3629,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.627,Bordetella pertussis strain I386,I386,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702660,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987415.1,CP011738,NZ_CP011738.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,89x,HGAP v. 3,1,,1,4104275,67.71,4052,3627,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.628,Bordetella pertussis strain I452,I452,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702661,520,,,,MLST.Bordetella_spp.2,,,,2017-02-14T00:00:00Z,28167525,PRJNA279196,GCF_001987435.1,CP011739,NZ_CP011739.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,85x,HGAP v. 3,1,,1,4109548,67.7,4054,3631,missing,,2012,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.629,Bordetella pertussis strain I461,I461,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702662,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987455.1,CP011740,NZ_CP011740.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,153x,HGAP v. 3,1,,1,4106406,67.71,4052,3628,missing,,2012,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.630,Bordetella pertussis strain I728,I728,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702663,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987475.1,CP011741,NZ_CP011741.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,107x,HGAP v. 3,1,,1,4107398,67.71,4059,3628,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.631,Bordetella pertussis strain I735,I735,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702664,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987495.1,CP011742,NZ_CP011742.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,104x,HGAP v. 3,1,,1,4105343,67.71,4052,3626,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.632,Bordetella pertussis strain I754,I754,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702665,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987515.1,CP011743,NZ_CP011743.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,108x,HGAP v. 3,1,,1,4109174,67.7,4054,3632,missing,,2013,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.633,Bordetella pertussis strain I755,I755,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702666,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987535.1,CP011744,NZ_CP011744.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,112x,HGAP v. 3,1,,1,4111653,67.7,4060,3629,missing,,2013,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.634,Bordetella pertussis strain I762,I762,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702667,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987555.1,CP011745,NZ_CP011745.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,133x,HGAP v. 3,1,,1,4110592,67.7,4058,3633,missing,,2013,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.635,Bordetella pertussis strain I959,I959,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702668,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987575.1,CP011746,NZ_CP011746.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,127x,HGAP v. 3,1,,1,4104353,67.71,4050,3630,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.636,Bordetella pertussis strain I965,I965,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702669,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987595.1,CP011747,NZ_CP011747.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,137x,HGAP v. 3,1,,1,4108598,67.7,4057,3633,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.637,Bordetella pertussis strain I968,I968,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702670,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987615.1,CP011748,NZ_CP011748.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,164x,HGAP v. 3,1,,1,4107604,67.71,4056,3632,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.638,Bordetella pertussis strain I977,I977,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702671,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987635.1,CP011749,NZ_CP011749.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,128x,HGAP v. 3,1,,1,4111640,67.7,4055,3636,missing,,2013,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.639,Bordetella pertussis strain I978,I978,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702672,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987655.1,CP011750,NZ_CP011750.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,121x,HGAP v. 3,1,,1,4110591,67.7,4055,3633,missing,,2013,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.640,Bordetella pertussis strain J012,J012,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702673,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987675.1,CP011751,NZ_CP011751.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,94x,HGAP v. 3,1,,1,4110595,67.7,4052,3631,missing,,2013,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.641,Bordetella pertussis strain J016,J016,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702674,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987695.1,CP011752,NZ_CP011752.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,107x,HGAP v. 3,1,,1,4103226,67.71,4049,3625,missing,,2013,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.642,Bordetella pertussis strain J019,J019,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702675,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987715.1,CP011753,NZ_CP011753.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,84x,HGAP v. 3,1,,1,4107558,67.7,4049,3634,missing,,2013,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.643,Bordetella pertussis strain J021,J021,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702676,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987735.1,CP011754,NZ_CP011754.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,129x,HGAP v. 3,1,,1,4106673,67.71,4052,3628,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.644,Bordetella pertussis strain J023,J023,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702677,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987755.1,CP011755,NZ_CP011755.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,108x,HGAP v. 3,1,,1,4106503,67.71,4055,3631,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.645,Bordetella pertussis strain J027,J027,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702678,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987775.1,CP011756,NZ_CP011756.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,131x,HGAP v. 3,1,,1,4109543,67.7,4052,3630,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.646,Bordetella pertussis strain J030,J030,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702679,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987795.1,CP011757,NZ_CP011757.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,117x,HGAP v. 3,1,,1,4105288,67.71,4047,3626,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.647,Bordetella pertussis strain J039,J039,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702680,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987815.1,CP011758,NZ_CP011758.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,137x,HGAP v. 3,1,,1,4107448,67.71,4047,3629,missing,,,USA,USA:missing,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.648,Bordetella pertussis strain J068,J068,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702681,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987835.1,CP011759,NZ_CP011759.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,113x,HGAP v. 3,1,,1,4107434,67.71,4051,3628,missing,,2013,USA,USA:CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.649,Bordetella pertussis strain J072,J072,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702682,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987855.1,CP011760,NZ_CP011760.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,124x,HGAP v. 3,1,,1,4113747,67.7,4058,3635,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.650,Bordetella pertussis strain J073,J073,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702683,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987875.1,CP011761,NZ_CP011761.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,181x,HGAP v. 3,1,,1,4112724,67.7,4057,3636,missing,,2013,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.651,Bordetella pertussis strain J076,J076,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702684,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987895.1,CP011762,NZ_CP011762.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,109x,HGAP v. 3,1,,1,4105464,67.71,4054,3630,missing,,2013,USA,USA:NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.652,Bordetella pertussis strain J090,J090,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702685,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987915.1,CP011763,NZ_CP011763.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,95x,HGAP v. 3,1,,1,4106346,67.71,4053,3627,missing,,2013,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.653,Bordetella pertussis strain J091,J091,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702686,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987935.1,CP011764,NZ_CP011764.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,115x,HGAP v. 3,1,,1,4106381,67.71,4052,3625,missing,,2014,USA,USA:CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.654,Bordetella pertussis strain J098,J098,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702687,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987955.1,CP011765,NZ_CP011765.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,110x,HGAP v. 3,1,,1,4107474,67.71,4053,3631,missing,,2014,USA,USA:NM,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.655,Bordetella pertussis strain J100,J100,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702688,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987975.1,CP011766,NZ_CP011766.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,80x,HGAP v. 3,1,,1,4109710,67.7,4053,3631,missing,,2014,USA,USA:OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.656,Bordetella pertussis strain J110,J110,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702689,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001987995.1,CP011767,NZ_CP011767.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,122x,HGAP v. 3,1,,1,4106384,67.71,4051,3628,missing,,2014,USA,USA:MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.657,Bordetella pertussis strain J115,J115,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03702690,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988015.1,CP011768,NZ_CP011768.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,123x,HGAP v. 3,1,,1,4106397,67.71,4055,3628,missing,,2014,USA,USA:NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.658,Bordetella pertussis strain B201,B201,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221179,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988035.1,CP013075,NZ_CP013075.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,86x,HGAP v. 3,1,,1,4122649,67.72,4089,3712,missing,,1955,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.659,Bordetella pertussis strain B227,B227,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221180,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988055.1,CP013076,NZ_CP013076.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,121x,HGAP v. 3,1,,1,4134432,67.71,4079,3735,missing,,1967,United Kingdom,United Kingdom,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.660,Bordetella pertussis strain C549,C549,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221181,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988075.1,CP013077,NZ_CP013077.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,160x,HGAP v. 3,1,,1,4106401,67.71,4061,3709,missing,,2000,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.661,Bordetella pertussis strain C734,C734,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221182,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988095.1,CP013078,NZ_CP013078.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,147x,HGAP v. 3,1,,1,4102201,67.71,4054,3702,missing,,2000,USA,USA: ID,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.662,Bordetella pertussis strain C757,C757,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221183,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988115.1,CP013079,NZ_CP013079.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,124x,HGAP v. 3,1,,1,4106366,67.71,4060,3708,missing,,2000,USA,USA: TX,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.663,Bordetella pertussis strain E194,E194,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221184,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988135.1,CP013080,NZ_CP013080.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,195x,HGAP v. 3,1,,1,4103209,67.71,4052,3709,missing,,2003,USA,USA: WA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.664,Bordetella pertussis strain E602,E602,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221185,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988155.1,CP013081,NZ_CP013081.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,184x,HGAP v. 3,1,,1,4108490,67.7,4060,3711,missing,,2005,USA,USA: DE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.665,Bordetella pertussis strain H682,H682,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221187,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988195.1,CP013083,NZ_CP013083.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,220x,HGAP v. 3,1,,1,4104309,67.71,4059,3704,missing,,2009,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.666,Bordetella pertussis strain H382,H382,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221186,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988175.1,CP013082,NZ_CP013082.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,193x,HGAP v. 3,1,,1,4106392,67.71,4060,3708,missing,,2010,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.667,Bordetella pertussis strain H698,H698,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221188,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988215.1,CP013084,NZ_CP013084.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,195x,HGAP v. 3,1,,1,4104135,67.71,4047,3706,missing,,2010,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.668,Bordetella pertussis strain H706,H706,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221189,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988235.1,CP013085,NZ_CP013085.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,213x,HGAP v. 3,1,,1,4105094,67.71,4059,3707,missing,,2010,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.669,Bordetella pertussis strain H730,H730,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221190,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988255.1,CP013086,NZ_CP013086.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,165x,HGAP v. 3,1,,1,4102201,67.71,4050,3710,missing,,2011,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.670,Bordetella pertussis strain H771,H771,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221191,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988275.1,CP013087,NZ_CP013087.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,197x,HGAP v. 3,1,,1,4105345,67.71,4058,3711,missing,,2011,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.671,Bordetella pertussis strain J178,J178,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221192,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988295.1,CP013088,NZ_CP013088.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,116x,HGAP v. 3,1,,1,4107422,67.71,4063,3707,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.672,Bordetella pertussis strain J179,J179,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221193,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988315.1,CP013089,NZ_CP013089.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,108x,HGAP v. 3,1,,1,4113730,67.7,4059,3713,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.673,Bordetella pertussis strain J191,J191,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221194,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988335.1,CP013090,NZ_CP013090.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,95x,HGAP v. 3,1,,1,4111645,67.7,4071,3713,missing,,2014,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.674,Bordetella pertussis strain J192,J192,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221195,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988355.1,CP013091,NZ_CP013091.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,118x,HGAP v. 3,1,,1,4112694,67.7,4066,3715,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.675,Bordetella pertussis strain J193,J193,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221196,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988375.1,CP013092,NZ_CP013092.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,101x,HGAP v. 3,1,,1,4105331,67.71,4052,3708,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.676,Bordetella pertussis strain J197,J197,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221198,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988415.1,CP013094,NZ_CP013094.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,122x,HGAP v. 3,1,,1,4107421,67.71,4058,3709,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.677,Bordetella pertussis strain J201,J201,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221199,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988435.1,CP013095,NZ_CP013095.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,110x,HGAP v. 3,1,,1,4103283,67.71,4052,3708,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.678,Bordetella pertussis strain J194,J194,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221197,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988395.1,CP013093,NZ_CP013093.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,,1,4106379,67.71,4054,3707,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.679,Bordetella pertussis strain J225,J225,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04221200,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988455.1,CP013096,NZ_CP013096.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,158x,HGAP v. 3,1,,1,4106294,67.71,4054,3713,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.680,Bordetella pertussis strain J296,J296,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383599,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988475.1,CP013863,NZ_CP013863.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,86x,HGAP v. 3,1,,1,4107428,67.71,4058,3709,missing,,2014,USA,USA: CT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.681,Bordetella pertussis strain J300,J300,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383600,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988495.1,CP013864,NZ_CP013864.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,87x,HGAP v. 3,1,,1,4105330,67.71,4055,3708,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.682,Bordetella pertussis strain J305,J305,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383601,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988515.1,CP013865,NZ_CP013865.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,104x,HGAP v. 3,1,,1,4111657,67.7,4062,3719,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.683,Bordetella pertussis strain J311,J311,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383602,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988535.1,CP013866,NZ_CP013866.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,,1,4103242,67.71,4052,3708,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.684,Bordetella pertussis strain C975,C975,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383559,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988555.1,CP013868,NZ_CP013868.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,151x,HGAP v. 3,1,,1,4104403,67.71,4058,3708,missing,,2000,USA,USA: IL,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.685,Bordetella pertussis strain E368,E368,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383560,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988575.1,CP013869,NZ_CP013869.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,162x,HGAP v. 3,1,,1,4104277,67.71,4056,3706,missing,,2004,USA,USA: MO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.686,Bordetella pertussis strain F501,F501,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383561,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988595.1,CP013870,NZ_CP013870.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,124x,HGAP v. 3,1,,1,4101167,67.71,4057,3709,missing,,2004,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.687,Bordetella pertussis strain F657,F657,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383562,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988615.1,CP013871,NZ_CP013871.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,223x,HGAP v. 3,1,,1,4104234,67.71,4059,3707,missing,,2007,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.688,Bordetella pertussis strain F778,F778,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383563,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988635.1,CP013872,NZ_CP013872.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,155x,HGAP v. 3,1,,1,4090785,67.72,4037,3701,missing,,2004,USA,USA: OH,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.689,Bordetella pertussis strain F934,F934,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383564,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988655.1,CP013873,NZ_CP013873.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,187x,HGAP v. 3,1,,1,4105353,67.71,4054,3709,missing,,2009,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.690,Bordetella pertussis strain G085,G085,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383565,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988675.1,CP013874,NZ_CP013874.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,158x,HGAP v. 3,1,,1,4106376,67.71,4058,3710,missing,,2008,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.691,Bordetella pertussis strain G807,G807,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383566,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988695.1,CP013875,NZ_CP013875.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,204x,HGAP v. 3,1,,1,4102202,67.71,4052,3706,missing,,2005,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.692,Bordetella pertussis strain G965,G965,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383567,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988715.1,CP013876,NZ_CP013876.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,130x,HGAP v. 3,1,,1,4105340,67.71,4059,3711,missing,,2002,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.693,Bordetella pertussis strain H348,H348,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383568,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988735.1,CP013877,NZ_CP013877.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,169x,HGAP v. 3,1,,1,4106382,67.71,4058,3704,missing,,2010,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.694,Bordetella pertussis strain H361,H361,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383569,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988755.1,CP013878,NZ_CP013878.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,98x,HGAP v. 3,1,,1,4107431,67.71,4058,3712,missing,,2010,USA,USA: MA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.695,Bordetella pertussis strain H533,H533,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383570,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988775.1,CP013879,NZ_CP013879.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,149x,HGAP v. 3,1,,1,4108283,67.7,4053,3711,missing,,2009,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.696,Bordetella pertussis strain H540,H540,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383571,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988795.1,CP013880,NZ_CP013880.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,131x,HGAP v. 3,1,,1,4105291,67.71,4053,3709,missing,,2010,USA,USA: SC,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.697,Bordetella pertussis strain H636,H636,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383572,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988815.1,CP013881,NZ_CP013881.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,107x,HGAP v. 3,1,,1,4105336,67.71,4055,3709,missing,,2010,USA,USA: TN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.698,Bordetella pertussis strain H876,H876,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383573,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988835.1,CP013882,NZ_CP013882.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,120x,HGAP v. 3,1,,1,4105347,67.71,4056,3711,missing,,2012,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.699,Bordetella pertussis strain I093,I093,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383574,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988855.1,CP013883,NZ_CP013883.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,129x,HGAP v. 3,1,,1,4101532,67.71,4075,3680,missing,,2012,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.700,Bordetella pertussis strain J093,J093,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383575,520,,,,MLST.Bordetella_spp.83,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988875.1,CP013884,NZ_CP013884.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,65x,HGAP v. 3,1,,1,4113750,67.7,4064,3712,missing,,2014,USA,USA: DE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.701,Bordetella pertussis strain J097,J097,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383576,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988895.1,CP013885,NZ_CP013885.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,191x,HGAP v. 3,1,,1,4107418,67.71,4063,3700,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.702,Bordetella pertussis strain J099,J099,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383577,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988915.1,CP013886,NZ_CP013886.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,113x,HGAP v. 3,1,,1,4112678,67.7,4066,3704,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.703,Bordetella pertussis strain J103,J103,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383578,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001988995.1,CP013887,NZ_CP013887.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,187x,HGAP v. 3,1,,1,4107419,67.71,4061,3701,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.704,Bordetella pertussis strain J104,J104,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383579,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989015.1,CP013888,NZ_CP013888.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,146x,HGAP v. 3,1,,1,4108480,67.7,4058,3707,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.705,Bordetella pertussis strain J120,J120,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383581,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989035.1,CP013890,NZ_CP013890.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,171x,HGAP v. 3,1,,1,4109522,67.7,4054,3711,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.706,Bordetella pertussis strain J121,J121,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383582,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989055.1,CP013891,NZ_CP013891.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,142x,HGAP v. 3,1,,1,4103084,67.71,4053,3700,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.707,Bordetella pertussis strain J124,J124,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383584,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989095.1,CP013893,NZ_CP013893.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,156x,HGAP v. 3,1,,1,4107607,67.71,4066,3703,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.708,Bordetella pertussis strain J122,J122,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383583,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989075.1,CP013892,NZ_CP013892.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,124x,HGAP v. 3,1,,1,4107596,67.71,4063,3705,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.709,Bordetella pertussis strain J149,J149,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383585,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989115.1,CP013894,NZ_CP013894.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,139x,HGAP v. 3,1,,1,4105638,67.71,4054,3706,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.710,Bordetella pertussis strain J155,J155,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383587,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989135.1,CP013896,NZ_CP013896.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,154x,HGAP v. 3,1,,1,4106378,67.71,4058,3706,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.711,Bordetella pertussis strain J159,J159,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383588,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989155.1,CP013897,NZ_CP013897.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,115x,HGAP v. 3,1,,1,4107438,67.71,4053,3707,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.712,Bordetella pertussis strain J161,J161,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383589,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989175.1,CP013898,NZ_CP013898.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,131x,HGAP v. 3,1,,1,4106377,67.71,4058,3706,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.713,Bordetella pertussis strain J162,J162,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383590,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989195.1,CP013899,NZ_CP013899.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,152x,HGAP v. 3,1,,1,4102183,67.71,4063,3691,missing,,2014,USA,USA: GA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.714,Bordetella pertussis strain J174,J174,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383591,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989215.1,CP013900,NZ_CP013900.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,114x,HGAP v. 3,1,,1,4108659,67.7,4061,3707,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.715,Bordetella pertussis strain J198,J198,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383593,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989235.1,CP013902,NZ_CP013902.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,148x,HGAP v. 3,1,,1,4113756,67.7,4060,3716,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.716,Bordetella pertussis strain J206,J206,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383594,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989255.1,CP013903,NZ_CP013903.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,123x,HGAP v. 3,1,,1,4110604,67.7,4062,3718,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.717,Bordetella pertussis strain J208,J208,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383595,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989275.1,CP013904,NZ_CP013904.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,131x,HGAP v. 3,1,,1,4108471,67.7,4062,3712,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.718,Bordetella pertussis strain J210,J210,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383596,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989295.1,CP013905,NZ_CP013905.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,154x,HGAP v. 3,1,,1,4110596,67.7,4057,3717,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.719,Bordetella pertussis strain J277,J277,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383598,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989315.1,CP013907,NZ_CP013907.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,123x,HGAP v. 3,1,,1,4108658,67.7,4060,3712,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.720,Bordetella pertussis strain J096,J096,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04388406,520,,,,MLST.Bordetella_spp.2,,,,2017-02-06T00:00:00Z,27303739,PRJNA279196,GCF_001989335.1,CP013951,NZ_CP013951.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,234x,HGAP v. 3,1,,1,4105309,67.71,4063,3857,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.721,Bordetella pertussis strain J105,J105,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383580,520,,,,MLST.Bordetella_spp.2,,,,2017-02-15T00:00:00Z,28167525,PRJNA279196,GCF_002018515.1,CP013889,NZ_CP013889.1,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,136x,HGAP v. 3,1,,1,4106364,67.71,4056,3702,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.729,Bordetella pertussis strain J152,J152,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383586,520,,,,MLST.Bordetella_spp.2,,,,2017-02-15T00:00:00Z,28167525,PRJNA279196,GCA_002068675.1,CP013895,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,131x,HGAP v. 3,1,,1,4110587,67.7,4063,3704,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.730,Bordetella pertussis strain J175,J175,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383592,520,,,,MLST.Bordetella_spp.2,,,,2017-02-15T00:00:00Z,28167525,PRJNA279196,GCA_002068975.1,CP013901,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,135x,HGAP v. 3,1,,1,4106390,67.71,4055,3711,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.731,Bordetella pertussis strain J276,J276,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383597,520,,,,MLST.Bordetella_spp.2,,,,2017-02-15T00:00:00Z,28167525,PRJNA279196,GCA_002069155.1,CP013906,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,137x,HGAP v. 3,1,,1,4108478,67.7,4058,3711,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.737,Bordetella pertussis strain J078,J078,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07137592,520,,,,MLST.Bordetella_spp.2,,,,2017-08-03T00:00:00Z,,PRJNA279196,GCA_002240435.1,CP021401,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,122x,HGAP v. 3,1,,1,4100915,67.71,4070,3905,missing,,2013,USA,USA: MN,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.738,Bordetella pertussis strain H696,H696,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07137591,520,,,,MLST.Bordetella_spp.2,,,,2017-08-03T00:00:00Z,,PRJNA279196,GCA_002240475.1,CP021402,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,104x,HGAP v. 3,1,,1,4103125,67.71,4075,3904,missing,,2011,USA,USA: CA,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.739,Bordetella pertussis strain J473,J473,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07137593,520,,,,MLST.Bordetella_spp.83,,,,2017-08-03T00:00:00Z,,PRJNA279196,GCA_002240495.1,CP021403,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,156x,HGAP v. 3,1,,1,4114583,67.7,4167,3906,missing,,2016,USA,USA: NY,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.740,Bordetella pertussis strain J625,J625,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN07327524,520,,,,MLST.Bordetella_spp.2,,,,2017-08-03T00:00:00Z,,PRJNA279196,GCA_002240515.1,CP022362,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,182x,HGAP v. 3,1,,1,4110338,67.7,4090,3925,missing,,2016,USA,USA: VT,,,,,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,520.742,Bordetella pertussis strain E945,E945,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583817,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002285955.1,CP016956,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,194x,HGAP v. 3,1,,1,4127835,67.72,4073,3873,missing,,2005,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.743,Bordetella pertussis strain B226,B226,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583809,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002285975.1,CP016957,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,226x,HGAP v. 3,1,,1,4126037,67.72,4077,3875,missing,,1967,United Kingdom,United Kingdom,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",passage_history:CDC <-- FDA,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.744,Bordetella pertussis strain E537,E537,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583815,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002285995.1,CP016958,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,192x,HGAP v. 3,1,,1,4110590,67.7,4054,3863,missing,,2001,USA,USA: MT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.745,Bordetella pertussis strain D422,D422,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583811,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286015.1,CP016959,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,204x,HGAP v. 3,1,,1,4107441,67.71,4060,3860,missing,,2002,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.746,Bordetella pertussis strain D735,D735,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583813,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286035.1,CP016960,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,192x,HGAP v. 3,1,,1,4106298,67.7,4066,3863,missing,,2000,USA,USA: OH,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.747,Bordetella pertussis strain C934,C934,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583810,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286055.1,CP016961,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,221x,HGAP v. 3,1,,1,4104297,67.71,4055,3858,missing,,2000,USA,USA: NJ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.748,Bordetella pertussis strain E898,E898,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583816,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286075.1,CP016962,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,170x,HGAP v. 3,1,,1,4103239,67.71,4060,3855,missing,,2005,USA,USA: AZ,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.749,Bordetella pertussis strain D799,D799,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583814,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286095.1,CP016963,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,195x,HGAP v. 3,1,,1,4103196,67.71,4055,3856,missing,,2002,USA,USA: ID,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.750,Bordetella pertussis strain D717,D717,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583812,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286115.1,CP016964,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,188x,HGAP v. 3,1,,1,4102255,67.71,4055,3860,missing,,2002,USA,USA: NV,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.751,Bordetella pertussis strain E541,E541,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583850,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286135.1,CP016966,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,190x,HGAP v. 3,1,,1,4105336,67.71,4057,3859,missing,,2003,USA,USA: MT,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.752,Bordetella pertussis strain E025,E025,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583849,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286155.1,CP016967,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,186x,HGAP v. 3,1,,1,4101132,67.71,4055,3855,missing,,2003,USA,USA: MD,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.753,Bordetella pertussis strain D925,D925,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583848,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286175.1,CP016968,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,192x,HGAP v. 3,1,,1,4106392,67.71,4052,3859,missing,,2002,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.754,Bordetella pertussis strain J160,J160,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716053,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286295.1,CP017119,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,160x,HGAP v. 3,1,,1,4112627,67.7,4089,3863,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.755,Bordetella pertussis strain J209,J209,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716055,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286315.1,CP017120,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,72x,HGAP v. 3,1,,1,4107500,67.7,4073,3864,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.756,Bordetella pertussis strain J172,J172,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716054,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286335.1,CP017121,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,171x,HGAP v. 3,1,,1,4107375,67.7,4069,3862,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.757,Bordetella pertussis strain J154,J154,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716052,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286355.1,CP017122,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,172x,HGAP v. 3,1,,1,4106367,67.71,4069,3860,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.758,Bordetella pertussis strain J153,J153,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05716051,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002286375.1,CP017123,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,167x,HGAP v. 3,1,,1,4106365,67.71,4063,3860,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.761,Bordetella pertussis strain F013,F013,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05583818,520,,,,MLST.Bordetella_spp.2,,,,2017-09-05T00:00:00Z,,PRJNA279196,GCA_002310915.1,CP016965,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,195x,HGAP v. 3,1,,1,4101245,67.71,4053,3854,missing,,2005,USA,USA: NE,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.769,Bordetella pertussis strain J226,J226,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751698,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442635.1,CP017159,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,134.6x,HGAP v. 3,1,,1,4107365,67.71,4083,3859,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.770,Bordetella pertussis strain J165,J165,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751699,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442615.1,CP017158,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,187.9x,HGAP v. 3,1,,1,4111636,67.7,4078,3867,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.771,Bordetella pertussis strain J223,J223,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751696,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442655.1,CP017160,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,130.8x,HGAP v. 3,1,,1,4107128,67.7,4160,3862,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,1.8,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.772,Bordetella pertussis strain J151,J151,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751694,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442675.1,CP017161,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,254.2x,HGAP v. 3,1,,1,4106441,67.71,4081,3863,missing,,2014,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.773,Bordetella pertussis strain J108,J108,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751692,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442715.1,CP017163,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,290x,HGAP v. 3,1,,1,4106326,67.71,4092,3858,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.774,Bordetella pertussis strain J109,J109,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751693,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442695.1,CP017162,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,259.5x,HGAP v. 3,1,,1,4106343,67.71,4075,3859,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.775,Bordetella pertussis strain J224,J224,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751697,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442735.1,CP017164,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,152.5x,HGAP v. 3,1,,1,4106189,67.7,4112,3858,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,1.2,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.776,Bordetella pertussis strain J170,J170,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751700,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442775.1,CP017166,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,190.5x,HGAP v. 3,1,,1,4105315,67.71,4062,3858,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.777,Bordetella pertussis strain J222,J222,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751695,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442755.1,CP017165,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,126.4x,HGAP v. 3,1,,1,4106009,67.7,4183,3866,missing,,2014,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,1.8,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.778,Bordetella pertussis strain J308,J308,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751701,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442795.1,CP017167,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,148.9x,HGAP v. 3,1,,1,4103236,67.71,4062,3855,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.779,Bordetella pertussis strain J310,J310,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05751702,520,,,,MLST.Bordetella_spp.2,,,,2017-10-04T00:00:00Z,,PRJNA279196,GCA_002442815.1,CP017168,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,212.5x,HGAP v. 3,1,,1,4102178,67.71,4067,3855,missing,,2014,USA,USA: NY,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.819,Bordetella pertussis strain J199,J199,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03464282,520,,,,MLST.Bordetella_spp.2,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892665.1,CP011245,,Centers for Disease Control and Prevention,Illumina MiSeq; PacBio,65x,HGAP v. 3,1,,1,4109686,67.70367,4063,3625,missing,,2014,USA,USA: CO,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.820,Bordetella pertussis strain J014,J014,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03877223,520,,,,MLST.Bordetella_spp.2,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892685.1,CP012135,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,106x,HGAP v. 3,1,,1,4107409,67.70565,4054,3629,missing,,2013,USA,USA: MN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.821,Bordetella pertussis strain J365,J365,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04383603,520,,,,MLST.Bordetella_spp.2,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892705.1,CP013867,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,114x,HGAP v. 3,1,,1,4082563,67.70487,4021,3686,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.822,Bordetella pertussis strain J043,J043,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05333714,520,,,,MLST.Bordetella_spp.1,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892725.1,CP016887,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,141x,HGAP v. 3,1,,1,4102813,67.704155,4104,3853,missing,,1947,USA,United States,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.823,Bordetella pertussis strain J042,J042,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05333713,520,,,,MLST.Bordetella_spp.1,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892745.1,CP019869,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,207x,HGAP v. 3,1,,1,4162596,67.7071,4120,3955,missing,,1947,USA,United States,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",passage_history:CDC <-- UMich <-- NIH,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.824,Bordetella pertussis strain B199,B199,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04388407,520,,,,MLST.Bordetella_spp.1,,,,2018-01-19T00:00:00Z,,PRJNA279196,GCA_002892765.1,CP022361,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,162x,HGAP v. 3,1,,1,4314502,67.729836,4273,4102,missing,,1935,USA,USA: PA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,99.4,3.1,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.908,Bordetella pertussis strain UK36,UK36,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09721533,520,,,,MLST.Bordetella_spp.83,,,,2018-08-03T00:00:00Z,,PRJNA478201,GCA_003355025.1,CP031289,,University of Bath,Oxford Nanopore Technologies; Illumina,397.0x,Canu v. 1.7; Unicycler v. 0.4.5,1,,1,4107923,67.70322,4088,3907,nasopharynx,,2012-03-06,United Kingdom,United Kingdom: Slough,,,,Whooping cough,,,,,,,,,,,,,"Long read sequencing offers the potential to construct single contig assemblies for complex genomes, such as the highly repetitive genome of the pathogen which causes whooping cough, Bordetella pertussis. Several hundred Insertion Sequence element copies in the B. pertussis genome have meant that full genome resolution has not been possible using reads shorter than 1000bp. We have conducted nanopore long read sequencing of several B. pertussis strains from the United Kingdom's 2012 outbreak, enabling the construction of closed, single contig assemblies for each. These closed genomes allowed visualisation and confirmation of extensive inter-strain genomic rearrangements, which had previously been predicted by Pulsed Field Gel Electrophoresis typing. Going forwards, long read sequencing may allow us to understand phenotypic differences between closely-related strains in this resurging pathogen.",,,,,,,,Whooping cough,,,,,,,This sample group is the combination of the 2 individual BioSamples: SAMEA1570035and SAMN09500967,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.909,Bordetella pertussis strain UK38,UK38,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09721534,520,,,,MLST.Bordetella_spp.83,,,,2018-08-03T00:00:00Z,,PRJNA478201,GCA_003355045.1,CP031112,,University of Bath,Oxford Nanopore Technologies; Illumina,380.0x,Canu v. 0.7; Unicycler v. 0.4.5,1,,1,4108026,67.70429,4105,3908,nasopharynx,,2012-03-05,United Kingdom,United Kingdom: Slough,,,,Whooping cough,,,,,,,,,,,,,"Long read sequencing offers the potential to construct single contig assemblies for complex genomes, such as the highly repetitive genome of the pathogen which causes whooping cough, Bordetella pertussis. Several hundred Insertion Sequence element copies in the B. pertussis genome have meant that full genome resolution has not been possible using reads shorter than 1000bp. We have conducted nanopore long read sequencing of several B. pertussis strains from the United Kingdom's 2012 outbreak, enabling the construction of closed, single contig assemblies for each. These closed genomes allowed visualisation and confirmation of extensive inter-strain genomic rearrangements, which had previously been predicted by Pulsed Field Gel Electrophoresis typing. Going forwards, long read sequencing may allow us to understand phenotypic differences between closely-related strains in this resurging pathogen.",,,,,,,,Whooping cough,,,,,,,This sample group is the combination of the 2 individual BioSamples: SAMEA1570050 and SAMN09500966,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.910,Bordetella pertussis strain UK39,UK39,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09721535,520,,,,MLST.Bordetella_spp.83,,,,2018-08-03T00:00:00Z,,PRJNA478201,GCA_003355065.1,CP031113,,University of Bath,Oxford Nanopore Technologies; Illumina,271.0x,Canu v. 1.7; Unicycler v. 0.4.5,1,,1,4108152,67.70414,4084,3901,nasopharynx,,2012-03-14,United Kingdom,United Kingdom: Southampton,,,,Whooping cough,,,,,,,,,,,,,"Long read sequencing offers the potential to construct single contig assemblies for complex genomes, such as the highly repetitive genome of the pathogen which causes whooping cough, Bordetella pertussis. Several hundred Insertion Sequence element copies in the B. pertussis genome have meant that full genome resolution has not been possible using reads shorter than 1000bp. We have conducted nanopore long read sequencing of several B. pertussis strains from the United Kingdom's 2012 outbreak, enabling the construction of closed, single contig assemblies for each. These closed genomes allowed visualisation and confirmation of extensive inter-strain genomic rearrangements, which had previously been predicted by Pulsed Field Gel Electrophoresis typing. Going forwards, long read sequencing may allow us to understand phenotypic differences between closely-related strains in this resurging pathogen.",,,,,,,,Whooping cough,,,,,,,This sample group is the combination of the 2 individual BioSamples: SAMEA1570041 and SAMN09500968,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.911,Bordetella pertussis strain UK76,UK76,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09721537,520,,,,MLST.Bordetella_spp.2,,,,2018-08-03T00:00:00Z,,PRJNA478201,GCA_003355085.1,CP031114,,University of Bath,Oxford Nanopore Technologies; Illumina,482.0x,Canu v. 0.7; Unicycler v. 0.4.5,1,,1,4112629,67.70132,4096,3929,nasopharynx,,2012-06-06,United Kingdom,United Kingdom: Bristol,,,,Whooping cough,,,,,,,,,,,,,"Long read sequencing offers the potential to construct single contig assemblies for complex genomes, such as the highly repetitive genome of the pathogen which causes whooping cough, Bordetella pertussis. Several hundred Insertion Sequence element copies in the B. pertussis genome have meant that full genome resolution has not been possible using reads shorter than 1000bp. We have conducted nanopore long read sequencing of several B. pertussis strains from the United Kingdom's 2012 outbreak, enabling the construction of closed, single contig assemblies for each. These closed genomes allowed visualisation and confirmation of extensive inter-strain genomic rearrangements, which had previously been predicted by Pulsed Field Gel Electrophoresis typing. Going forwards, long read sequencing may allow us to understand phenotypic differences between closely-related strains in this resurging pathogen.",,,,,,,,Whooping cough,,,,,,,This sample group is the combination of the 2 individual BioSamples: SAMEA2060461 and SAMN09500970,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,520.913,Bordetella pertussis strain Tohama,Tohama,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09862822,520,,,,MLST.Bordetella_spp.1,,,,2018-08-29T00:00:00Z,,PRJNA486745,GCA_003431345.1,CP031787,,Institut Pasteur,Oxford Nanopore MiniION,1X,Unicycler/0.4.4 v. Unicycler/0.4.4,1,,1,4102412,67.70458,4024,,respiratory sample,"recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data",1954,Japan,Japan,,,,Pertussis,,,,,,,,,,,,,"We describe the complete genome sequences of two Bordetella pertussis isolates\; FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species\; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data.",collected_by:Sato,,,,,,,Pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.914,Bordetella pertussis strain FR5810,FR5810,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN09862835,520,,,,,,,,2018-08-29T00:00:00Z,,PRJNA486745,GCA_003431425.1,CP031788,,Institut Pasteur,Oxford Nanopore MiniION,1X,Unicycler/0.4.4 v. Unicycler/0.4.4,1,,1,4108173,67.706566,4506,,respiratory sample,"recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data",2014,France,France,,,,Pertussis,,,,,,,,,,,,,"We describe the complete genome sequences of two Bordetella pertussis isolates\; FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species\; obtained using a hybrid sequencing approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq-500 sequence data.;many frameshifted proteins",collected_by:Institut Pasteur,,,,,,,Pertussis,,,,,,,,,,,,,,99.4,4.2,Respiratory Diseases,Pertussis,Respiratory Tract,Respiratory Diseases-Pertussis HP,520.927,Bordetella pertussis strain VS366,VS366,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA1062146,520,,,,MLST.Bordetella_spp.2,,,,2018-10-03T00:00:00Z,,PRJEB25820,GCA_900327835.1,LS398589,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,,1,4144451,67.70918,4073,3778,respiratory tract,isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine,1954-65,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of B. pertussis strains, which were isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.928,Bordetella pertussis strain VS393,VS393,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA1062147,520,,,,MLST.Bordetella_spp.2,,,,2018-10-03T00:00:00Z,,PRJEB25820,GCA_900327845.1,LS398590,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,,1,4160081,67.696785,4079,3790,respiratory tract,isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine,1954-65,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of B. pertussis strains, which were isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.929,Bordetella pertussis strain VS377,VS377,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA1062148,520,,,,MLST.Bordetella_spp.2,,,,2018-10-03T00:00:00Z,,PRJEB25820,GCA_900327855.1,LS398604,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,,1,4160618,67.699104,4086,3791,respiratory tract,isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine,1954-65,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of B. pertussis strains, which were isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.930,Bordetella pertussis strain VS401,VS401,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA1062149,520,,,,MLST.Bordetella_spp.2,,,,2018-10-03T00:00:00Z,,PRJEB25820,GCA_900327865.1,LS398605,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,,1,4162738,67.695854,4090,3794,respiratory tract,isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine,1954-65,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of B. pertussis strains, which were isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine.",,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.931,Bordetella pertussis strain VS67,VS67,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA1062145,520,,,,MLST.Bordetella_spp.2,,,,2018-10-03T00:00:00Z,,PRJEB25820,GCA_900327875.1,LS398588,,"Institute of Microbiology of the Czech Academy of Sciences, v.v.i.",,,,1,,1,4137378,67.70909,4064,3769,respiratory tract,isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine,1954-65,Czech Republic,Czech Republic,,,,,,host_health_state:diseased,,,,,,,,,,,"This study aims at characterization of genotypic and phenotypic traits of B. pertussis strains, which were isolated in 1954-1965 in the Czech Republic and used as components of the whole-cell vaccine.",,,,,,,,,diseased,,,,,,,,,,,,,100,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,520.991,Bordetella pertussis strain BPD2,BPD2,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10457990,520,,,,MLST.Bordetella_spp.2,,,,2018-12-02T00:00:00Z,,PRJNA506315,GCA_003855595.1,CP034101,,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,195.0x,Unicycler v. v0.4.6,1,,1,4104911,67.70286,4098,3921,np swab,,2017,India,India: New Delhi,,,,Pertussis,,,,,,,,,,,,,Complete genome sequence of Bordetella pertussis,collected_by:Maharishi Valmiki Infectious Diseases Hospital Delhi,,,,,,,Pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.992,Bordetella pertussis strain BPD1,BPD1,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10457989,520,,,,MLST.Bordetella_spp.2,,,,2018-12-04T00:00:00Z,,PRJNA506314,GCA_003860305.1,CP034182,,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,203.0x,Unicycler v. v0.4.6,1,,1,4126211,67.702866,4159,3941,np swab,,2017,India,India: New Delhi,,,,Pertussis,,,,,,,,,,,,,complete genome sequence of Bordetella pertussis clinical isolate,collected_by:Maharishi Valmiki Infectious Diseases Hospital Delhi,,,,,,,Pertussis,,,,,,,,,,,,,,100,2.34,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.994,Bordetella pertussis strain J358,J358,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04388409,520,,,,MLST.Bordetella_spp.2,,,,2019-01-03T00:00:00Z,,PRJNA279196,GCA_003991035.1,CP014212,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,248x,HGAP v. 3,1,,1,4110595,67.70283,4057,3864,missing,,2014,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.995,Bordetella pertussis strain J377,J377,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN04388408,520,,,,MLST.Bordetella_spp.2,,,,2019-01-03T00:00:00Z,,PRJNA279196,GCA_003991055.1,CP014211,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,176x,HGAP v. 3,1,,1,4106512,67.70544,4058,3861,missing,,2015,USA,USA: CA,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.996,Bordetella pertussis strain C927,C927,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05333715,520,,,,MLST.Bordetella_spp.24,,ATCC:9340,,2019-01-03T00:00:00Z,,PRJNA279196,GCA_003991095.1,CP016339,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,200x,HGAP v. 3,1,,1,4095467,67.71057,4053,3843,missing,,,,,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",passage_history:CDC <-- UCLA <-- ATCC,,,,,,,pertussis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.997,Bordetella pertussis strain I094,I094,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007762,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004006155.1,CP018036,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,82x,HGAP v. 3,1,,1,4111426,67.70011,4169,3863,missing,,2012,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.998,Bordetella pertussis strain H782,H782,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06007763,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004006615.1,CP018035,,Centers for Disease Control and Prevention,PacBio RSII; Illumina MiSeq,169x,HGAP v. 3,1,,1,4108455,67.70445,4068,3861,missing,,2011,USA,USA: OR,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,520.999,Bordetella pertussis strain J185,J185,Bordetella pertussis,Bordetella,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN08136991,520,,,,MLST.Bordetella_spp.2,,,,2019-01-09T00:00:00Z,,PRJNA279196,GCA_004007095.1,CP025343,,Centers for Disease Control and Prevention,PacBio RSII; Illumina HiSeq,344x,HGAP v. 3,1,,1,4106374,67.70654,4098,3925,missing,,2013,USA,USA: IN,,,,pertussis,,,,,,,,,,,,,"This project is an effort by the Pertussis and Diphtheria Laboratory at the Centers for Disease Control and Prevention to study the genomic diversity of B. pertussis isolates collected in the United States. Isolates have been selected for sequencing with the intent to broadly sample representative phenotypes, genotypes, geographic locations, and disease severity. Comparative analyses of these data should shed new light on genome evolution while informing the development of novel molecular typing strategies for this important bacterial pathogen.",,,,,,,,pertussis,,,,,,,,,,,,,,100,0.47,Respiratory Diseases,Pertussis,Other,Respiratory Diseases-Pertussis HP,523796.82,Staphylococcus aureus subsp. aureus ST398 strain 2012-3,2012-3,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06856373,523796,,,,MLST.Staphylococcus_aureus.398,,,,2021-11-16T00:00:00Z,,PRJNA385005,GCA_020881895.1,CP021178,,Renji Hospital,Illumina,357.8,HGAP v. 3.0,1,0,1,2715600,32.95684,2682,2689,missing,,2012-03,China,China: Shanghai,,,,fatal sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The first CA-MRSA ST398 genome isolated from human without livestock contact and harboring prophage 3,collected_by:Min Li,,,,,,,fatal sepsis,,,,,,,,,,,,,,99.51,0.08,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis NHP,525283.9,Fusobacterium nucleatum subsp. nucleatum ATCC 23726,ATCC 23726,Fusobacterium nucleatum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN08501025,525283,,,,,,ATCC:23726,,2018-03-26T00:00:00Z,,PRJNA433545,GCA_003019785.1,CP028109,,Virginia Tech,"Illumina, MinION",35x,Unicycler v. 0.4.3,1,,1,2299539,27.180925,2175,2112,urogentical tract,,,,,env_biome:terrestrial biome [ENVO:00000446],,,,,,,,,,,,,,,,"Complete Fusobacterium genomes generated by MinION and Illumina sequencing, followed by assembly with Unicycler.",,,,,https://www.atcc.org/products/all/23726.aspx,,Homo Sapiens,,Healthy,,,,,,,,commensal,terrestrial biome [ENVO:00000446],,,,100,0,,,Other,- NHP,53345.73,Enterococcus durans strain 4928STDY7071430,4928STDY7071430,Enterococcus durans,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104567538,53345,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164665.1,LR607335,,SC,,,,1,,1,3128540,38.038956,2997,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.13,0.75,,,Other,- NHP,53345.74,Enterococcus durans strain 4928STDY7387704,4928STDY7387704,Enterococcus durans,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA104694341,53345,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166615.1,LR607372,,SC,,,,1,,1,3195719,37.98997,3092,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97,0.75,,,Other,- HP,53436.3,Treponema pallidum subsp. endemicum strain Iraq B,Iraq B,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN08290048,53436,,,,,,,,2019-02-14T00:00:00Z,,PRJNA428415,GCA_004194495.1,CP032303,,"Masaryk University, Faculty of Medicine",Illumina MiSeq,1000.0x,IDBA_UD v. 1.1.1,1,,1,1137653,52.778217,1034,1062,lesion,,1951,Iraq,Iraq,,female,7 years,endemic syphilis,,,,,,,,,,,,,"Complete genome sequencing of Treponema pallidum subsp. endemicum strain Iraq B, the causative agent of endemic syphilis.",,,,,,,,endemic syphilis,,,,,,,,,,,,,,99.97,0,Sexually Transmitted Infections (STIs),Syphilis,Other,Sexually Transmitted Infections (STIs)-Syphilis HP,53436.6,Treponema pallidum subsp. endemicum C279,C279,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN19981495,53436,,,,,,,,2022-04-26T00:00:00Z,,PRJNA742865,GCA_023116935.1,CP078090,,,,,,1,0,1,1137501,52.777847,1035,1054,genital ulcer,,2017,Cuba,Cuba,,male,,bejel,,,,,,,,,,,,,,"collected_by:A A Noda\; Tropical Medicine Institute Pedro Kouri, Havana, Cuba",,,,,,,bejel,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,53436.7,Treponema pallidum subsp. endemicum C77,C77,Treponema pallidum,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN20000520,53436,,,,,,,,2022-04-26T00:00:00Z,,PRJNA743168,GCA_023117035.1,CP081507,,,Illumina,5.0x,SPAdes v. 3.11.1,1,0,1,1137664,52.73971,1435,239,genital ulcer,,2014,Cuba,Cuba,,male,,bejel,,,,,,,,,,,,,,"collected_by:Angel A. Noda, Institute of Tropical Medicine Pedro Kouri",,,,,,,bejel,,,,,,,,,,,,,,95.8,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,537006.36,Parabacteroides johnsonii DSM 18315,DSM 18315,Parabacteroides johnsonii,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222700,537006,,,,,,DSM:18315,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025151045.1,CP102285,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4749455,45.21401,4088,3759,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.62,0,,,Other,- NHP,537007.56,Blautia hansenii DSM 20583,DSM 20583,Blautia hansenii,Blautia,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222664,537007,,,,,,DSM:20583,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147655.1,CP102264,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3065591,39.04027,3080,2980,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.36,0,,,Other,- NHP,537011.447,Prevotella copri DSM 18205,DSM 18205,Segatella copri,Segatella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222705,537011,,,,,,DSM:18205,,2022-09-12T00:00:00Z,,PRJNA746600,,CP102288,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3325514,45.154495,2909,2707,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,98.31,0.68,,,Other,- HP,539813.21,Enterobacter mori strain 08-091,08-091,Enterobacter mori,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18011300,539813,,,,,,,,2021-06-02T00:00:00Z,,PRJNA703085,GCA_018638795.1,"CP071063,CP071064",,"Huashan Hospital, Fudan University","Illumina, Oxford Nanopore ONT",248x,HGAP v. 2020-09-01T00:00:00,1,1,2,4986313,55.39983,4685,4565,ascites,,2008-01,China,China:Shanghai,,male,65,not collected,,,,,,,,,,,,,Enterobacter mori clinical isolate 08-091 producing qnrE3,collected_by:Huashan Hospital,,,,,,,not collected,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,54005.7,Peptoniphilus harei strain NCTC13077,NCTC13077,Peptoniphilus harei,Peptoniphilus,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMEA104224812,54005,not available: to be reported later,,,,,NCTC:13077,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638565.1,LR134524,,SC,,,,1,,1,1739102,34.41851,1626,1577,pus,,1986,United Kingdom,United Kingdom,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,99.3,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,54006.4,Peptoniphilus ivorii strain NCTC13079,NCTC13079,Peptoniphilus ivorii,Peptoniphilus,Peptoniphilaceae,Tissierellales,Tissierellia,Bacillota,SAMEA104224813,54006,not available: to be reported later,,,,,NCTC:13079,,2018-12-19T00:00:00Z,,PRJEB6403,GCA_900638585.1,LR134523,,SC,,,,1,,1,1587771,53.220142,1559,1505,abdominal skin swab,,1987,United Kingdom,United Kingdom,,,,,,host_health_state:disease,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,disease,,,98.95,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,54291.111,Raoultella ornithinolytica strain YDC775_2,YDC775_2,Raoultella ornithinolytica,Raoultella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10388008,54291,,,,,,,,2018-11-20T00:00:00Z,,PRJNA499091,GCA_003798165.1,"CP033683,CP033682",,University of Pittsburgh,PacBio,268.0x,HGAP v. 3,1,1,2,5459882,55.795307,5478,5076,abdominal abscess,,2016-04,USA,USA:Pittsburgh,,,,Abdominal abscess,,,,,,,,,,,,,Carbapenem resistance in Raoultella ornithinolytica due to presence of OXA-232 enzyme,collected_by:University of Pittsburgh,,,,,,,Abdominal abscess,,,,,,,,,,,,,,99.65,1.35,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,54291.34,Raoultella ornithinolytica strain Ro24724,Ro24724,Raoultella ornithinolytica,Raoultella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06909736,54291,,,,,,,,2017-07-05T00:00:00Z,,PRJNA385928,GCA_002214825.1,"CP021329,CP021328",,Zhejiang University,PacBio,400.0x,HGAP v. 3.0,1,1,2,5944351,55.23,5926,5618,necrotic tissue,,2014-08-21,China,China: Hangzhou,,male,13,wound infection post surgery,,host_disease_outcome:cure,,,,,,,,,,,Emergence of Raoultella ornithinolytica coproducing IMP-4 and KPC-2 carbapenemases in China,collected_by:Beiwen Zheng,,,,,,,wound infection post surgery,,cure,,,,,,,,,,,,100,1.3,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,54388.356,Salmonella enterica subsp. enterica serovar Paratyphi A strain 45157,45157,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19708132,54388,Paratyphi A,,,MLST.Salmonella_enterica.129,,,,2021-06-22T00:00:00Z,22190395,PRJNA737743,GCA_018986895.1,CP076727,,Sheba medical center,Illumina MiSeq,100.0x,Newbler v. april-2012,1,0,1,4495821,52.182056,4674,4293,blood,,2009-10-27,Nepal,Nepal,,,,Enteric fever (paratyphoid fever),,,,,,,,,,,,,Genetic and molecular characterization of an S. Paratyphi A strain accounted for a recent paratyphoid outbreak in Nepal that affected at least 37 travelers,collected_by:Ohad Gal-Mor,,,,,,,Enteric fever (paratyphoid fever),,,,,,,,,,,,,,100,0.04,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever NHP,544645.229,Butyricimonas virosa strain DSM 23226,DSM 23226,Butyricimonas virosa,Butyricimonas,Odoribacteraceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222670,544645,,,,,,DSM:23226,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025148635.1,CP102269,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4813254,42.44002,4142,3901,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.46,0,,,Other,- HP,545.123,Citrobacter koseri strain SCAID URN1-2019,SCAID URN1-2019,Citrobacter koseri,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14653268,545,,,,,,,,2020-05-03T00:00:00Z,,PRJNA627194,GCA_012955585.1,CP052059,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,30x,Bowtie v. 1.2.3,1,0,1,4650688,53.889866,4483,4231,urine,,2019-05-04,Kazakhstan,Kazakhstan: Almaty,,female,29,chronic cystitis,,host_disease_outcome:Chronic disease;host_disease_stage:Chronic cystitis,Intermediate;Resistant;Susceptible,AMR Panel,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,chronic cystitis,,Chronic disease,,Chronic cystitis,,,,,,,,,,99.88,0.32,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,545.196,Citrobacter koseri strain NJ,NJ,Citrobacter koseri,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14371231,545,,,,,,,,2021-08-03T00:00:00Z,,PRJNA612390,GCA_019443705.1,CP050078,,"Huashan Hospital, Fudan University",Illumina HiSeq; Oxford Nanopore MiniION,200.0x,Unicycler v. v0.4.8,1,0,1,4767913,53.711655,4614,4390,urine,isolated from patient with UTI and Bacteremia,2019-10-10,China,China: Jiangsu,,,,UTI,,,,,,,,,,,,,A Citrobacter koseri strain isolated from patient with UTI and Bacteremia.,collected_by:Yanliang Zhang,,,,,,,UTI,,,,,,,,,,,,,,99.88,0.54,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI NHP,545.36,Citrobacter koseri strain 0123A_53_520,0123A_53_520,Citrobacter koseri,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05509313,545,,,,,,,,2017-01-04T00:00:00Z,,PRJNA327106,GCA_001931885.1,CP017665,,None,Illumina HiSeq,520.0,IDBA_UD v. 1.1.1,1,,1,4752495,53.91,4539,,infant 1 dol 23 gut,,2013-2014,USA,"USA: Pittsburgh, Magee-Womens Hospital of UPMC",,,,,,,,,,,,,,,,,"Simultaneous longitudinal metagenomic sequencing of the mouth, skin, and gut microbiomes of two premature infants during the first month of life;derived from metagenome",sample_type:metagenomic assembly,,,,,,,,,,,,,,This biosample is a metagenomic assembly obtained from the human gut metagenome sample: SAMN05301478,,,,,,,99.7,0,,,Other,- HP,545.38,Citrobacter koseri strain FDAARGOS_287,FDAARGOS_287,Citrobacter koseri,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173300,545,,,,,,FDA:FDAARGOS_287,,2017-06-27T00:00:00Z,,PRJNA231221,GCA_002208985.3,"CP022073,CP022074,CP022075",,US Food and Drug Administration,PacBio,16.071077666678x,"SMRT v. 2.3.0, HGAP v. 3.0",1,2,3,4936094,53.76,5060,4747,clean catch urine,,2014-11-04,USA,USA:DC,,female,17Y,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,2.2,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,546.1125,Citrobacter freundii strain CF48846,CF48846,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933277,546,,,,MLST.Citrobacter_freundii.65,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939595.1,"CP070544,CP070543,CP070542,CP070541,CP070540,CP070539,CP070538",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,6,7,5551777,51.470062,5562,5262,endotracheal tube swab,,2019-02-02,Czech Republic,Czech Republic: Ostrov,,,,Acute respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Ostrov,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,100,0.42,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,546.1126,Citrobacter freundii strain CF49969,CF49969,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933282,546,,,,MLST.Citrobacter_freundii.8,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939615.1,"CP070549,CP070548,CP070547,CP070546,CP070545",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,4,5,5485671,51.60798,5548,5251,urine (permanent catheter),,2019-04-10,Czech Republic,Czech Republic: Turnov,,,,Fever,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Panochova nemocnice Turnov,,,,,,,Fever,,,,,,,,,,,,,,100,0.74,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,546.1127,Citrobacter freundii strain CF50935,CF50935,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933285,546,,,,MLST.Citrobacter_freundii.65,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939655.1,"CP070559,CP070558,CP070557,CP070556,CP070555,CP070554",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,5,6,5608362,51.40756,5604,5320,abscess,,2019-05-23,Czech Republic,Czech Republic: Koln,,,,Diverticular disease of intestine,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Koln,,,,,,,Diverticular disease of intestine,,,,,,,,,,,,,,99.93,0.58,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,546.1129,Citrobacter freundii strain CF49141,CF49141,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933278,546,,,,,,,,2021-03-01T00:00:00Z,,PRJNA700516,GCA_017114565.1,JAFIQF000000000,,Charles University in Prague,PacBio Sequel,250x,Microbial Assembly v. 1.1,2,6,8,5788351,51.666096,5869,5554,urine,,2019-02-18,Czech Republic,Czech Republic: Praha,,,,Dissection of aorta,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Krlovsk Vinohrady,,,,,,,Dissection of aorta,,,,,,,,,,,,,,100,1.69,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,546.1295,Citrobacter freundii strain DY2010,DY2010,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21601121,546,,,,MLST.Citrobacter_freundii.22,,,,2021-11-09T00:00:00Z,,PRJNA766039,GCA_020809005.1,"CP086287,CP086288,CP086289,CP086290",,The First Affiliated Hospital of Wenzhou Medical University,Illumina NovaSeq,200X,SPAdes v. 3.9.1,1,3,4,5260876,51.63239,5171,4984,urine,,2020-01-24,China,China: Dongyang,,,,bacterial sepsis,,,,,,,,,,,,,Here we first report the isolation and comparative genomics of two blaNDM-5 producing Citrobacter freundii (C. freundii) isolates from one single patient with bloodstream and urinary tract infection.,collected_by:Affiliated Dongyang Hospital of Wenzhou Medical University,,,,,,,bacterial sepsis,,,,,,,,,,,,,,99.7,0.46,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,546.1298,Citrobacter freundii strain 56415CZ,56415CZ,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22377426,546,,,,,,,,2021-11-01T00:00:00Z,,PRJNA772913,GCA_020695525.1,"CP085726,CP085727,CP085728",,Charles University in Prague,PacBio Sequel,518x,Microbial assembly v. v.1,1,2,3,5349058,51.467697,5357,5084,rectal swab,,2020-02,Czech Republic,Czech Republic: Prague,,,,Biliary acute pancreatitis,,,,,,,,,,,,,Molecular characterization of VIM-producing Enterobacterales from Czech hospitals,collected_by:Vseobecna fakultni nemocnice v Praze,,,,,,,Biliary acute pancreatitis,,,,,,,,,,,,,,99.7,0.72,Gastrointestinal Diseases,Pancreatic Disorders,Gastrointestinal,Gastrointestinal Diseases-Pancreatic Disorders HP,546.1602,Citrobacter freundii CRCB-101,CRCB-101,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07944242,546,,,,,,,,2017-11-20T00:00:00Z,,PRJNA416193,,"CP024819,CP024820",,,PacBio,486x,RS HGAP v. 3,1,1,2,5357480,52.05701,5208,5111,open pus,,2015,South Korea,South Korea: Incheon,,,,not collected,,,,,,,,,,,,,,collected_by:KCDC,,,,,,,not collected,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,546.1609,Citrobacter freundii CF1807,CF1807,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31693425,546,,,,,,,,2022-11-20T00:00:00Z,,PRJNA900524,,"CP110894,CP110891,CP110892,CP110896,CP110890,CP110893,CP110895,CP110898,CP110897",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,8,9,5783339,51.60849,5953,5655,urine,,2018-07-17,China,China,,,,Urinary tract infection,,,,,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.6,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,546.1610,Citrobacter freundii CFA1707,CFA1707,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31693747,546,,,,,,,,2022-11-20T00:00:00Z,,PRJNA900549,,"CP110914,CP110911,CP110908,CP110913,CP110915,CP110907,CP110909,CP110912,CP110910",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,8,9,5697627,51.64645,5856,5571,blood,,2017-07-28,China,China,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0.6,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,546.1611,Citrobacter freundii CF2206,CF2206,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31693662,546,,,,,,,,2022-11-20T00:00:00Z,,PRJNA900539,,"CP110900,CP110904,CP110899,CP110903,CP110906,CP110905,CP110901,CP110902",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,7,8,5561304,51.61207,5678,5413,urine,,2022-06-23,China,China,,,,Urinary tract infection,,,,,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,546.1782,Citrobacter freundii CF5125,CF5125,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34580837,546,,,,MLST.Citrobacter_freundii.18,,,,2023-05-18T00:00:00Z,,PRJNA967229,,"CP125310,CP125311,CP125312,CP125313,CP125314",,,Illumina NovaSeq; PacBio,85.54x,Hifiasm v. 0.13-r308; Canu v. 1.7,1,4,5,5596899,51.74576,5730,5504,urine,,2022,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,546.402,Citrobacter freundii strain B9-C2,B9-C2,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08631944,546,,,,MLST.Citrobacter_freundii.11,,,,2018-03-27T00:00:00Z,,PRJNA436768,GCA_003019835.1,CP027849,,University of Malaya,Illumina MiSeq,30.0x,IDBA-UD v. 1.0.9,1,,1,5028563,52.32941,4578,4277,stool,,2014-07-10,Malaysia,Malaysia: Kuala Lumpur,,,,,,,,,,,,,,,,,Multidrug resistant C. freundii and K. pneumoniae isolated from clinical stool samples,sample_type:single cell;biomaterial_provider:Mmb Bacte;collected_by:Polly Yap,,,,,,,,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,546.462,Citrobacter freundii strain UMH19,UMH19,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729551,546,,,,MLST.Citrobacter_freundii.11,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665535.1,"CP024673,CP024674",,University of Michigan,PacBio,217x,HGAP v. 2,1,1,2,5053452,51.919994,5041,4960,,,2013-10,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.98,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.463,Citrobacter freundii strain UMH15,UMH15,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729547,546,,,,MLST.Citrobacter_freundii.307,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665595.1,CP024679,,University of Michigan,PacBio,270x,HGAP v. 2,1,,1,5343952,51.80013,5388,5256,,,2014-06,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,99.9,0.47,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.464,Citrobacter freundii strain UMH14,UMH14,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729546,546,,,,MLST.Citrobacter_freundii.212,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665615.1,"CP024680,CP024681,CP024682",,University of Michigan,PacBio,229x,HGAP v. 2,1,2,3,5064975,51.75066,5016,4889,,,2014-07,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,99.9,0.35,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.465,Citrobacter freundii strain UMH13,UMH13,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729545,546,,,,MLST.Citrobacter_freundii.98,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665635.1,CP024683,,University of Michigan,PacBio,239x,HGAP v. 2,1,,1,4917351,51.88511,4822,4723,,,2014-04,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.86,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.466,Citrobacter freundii strain HM38,HM38,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729552,546,,,,,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665655.1,CP024672,,University of Michigan,PacBio,234x,HGAP v. 2,1,,1,4899014,51.701057,4867,4737,,,2012-02,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.13,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.467,Citrobacter freundii strain UMH16,UMH16,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729548,546,,,,MLST.Citrobacter_freundii.114,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665675.1,"CP024677,CP024678",,University of Michigan,PacBio,207x,HGAP v. 2,1,1,2,5246590,51.65723,5254,5130,,,2014-06,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,99.9,1.35,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,546.682,Citrobacter freundii strain C50,C50,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289284,546,,,,MLST.Citrobacter_freundii.8,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931485.1,"CP042478,CP042479,CP042480",,University of Oxford,Oxford Nanopore MiniION,2240x,Unicycler v. SEP-2017,1,2,3,5514965,51.805244,5535,5331,clinical sample,,2014-05-29,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,0.89,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,546.759,Citrobacter freundii strain SCAID PHRX1-2019,SCAID PHRX1-2019,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14653284,546,,,,,,,,2020-05-03T00:00:00Z,,PRJNA627194,GCA_012955545.1,CP052058,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,14x,Bowtie v. 1.2.3,1,0,1,4664379,51.94257,4520,4312,oropharyngeal swab of pharynx,,2019-08-01,Kazakhstan,Kazakhstan: Almaty,,female,55,Tonsilitis,,host_disease_outcome:Recovery;host_disease_stage:Acute tonsilitis,Resistant;Susceptible;Intermediate,AMR Panel,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Tonsilitis,,Recovery,,Acute tonsilitis,,,,,,,,,,99.85,0.04,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,546.801,Citrobacter freundii strain M92,M92,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15394190,546,,,,,,,,2020-07-06T00:00:00Z,,PRJNA642348,GCA_013389635.1,"CP058318,CP058319,CP058320",,Chinese Academy of Agricultural Sciences,Oxford Nanopore MiniION; Illumina HiSeq,100.0x,Unicycler v. 0.4.3,1,2,3,5667960,51.816067,5815,5511,,,2019-07-12,China,China: Heilongjiang,,,,,,,,,,,,,,,,,Characterization of a novel hybrid plasmid coharboring blaKPC-2 and qnrVC4 in a clinical Citrobacter freundii strain,sample_type:single cell,,,,,,,,,,,,,,,,,,,,,100,1.69,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,546.867,Citrobacter freundii strain CIFR51929,CIFR51929,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15589939,546,,,,,,,,2020-07-29T00:00:00Z,,PRJNA647548,GCA_013874155.1,"CP059427,CP059428,CP059429",,Charles University in Prague,PacBio Sequel,390.0x,Microbial Assembly v. SMRT Link v.9,1,2,3,5567320,51.444485,5572,5285,stool,,2019,Czech Republic,Czech Republic: Prague,,,,gastric ulcers,,,,,,,,,,,,,VIM/MCR producers in the Czech republic,collected_by:Vseobecna fakultni nemocnice v Praze,,,,,,,gastric ulcers,,,,,,,,,,,,,,100,0.82,Gastrointestinal Diseases,Gastritis and Ulcers,Gastrointestinal,Gastrointestinal Diseases-Gastritis and Ulcers HP,546.894,Citrobacter freundii strain IDR1900015725-01-02,IDR1900015725-01-02,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15086848,546,,,,,,,,2020-08-12T00:00:00Z,,PRJNA636827,GCA_014169975.1,"CP054278,CP054280,CP054281,CP054279",,"Wadsworth Center, New York State Department of Health",Illumina MiSeq; Oxford Nanopore MiniION,159x,Flye v. 2.6,1,3,4,5257552,51.914597,5189,4954,rectal swab,,2019-01,USA,USA:Maine,,,,,,,,,,,,,,,,,"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.",collected_by:Maine Center for Disease Control and Prevention,,,,,,,Unknown,,,,,,,,,,,,,,99.87,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,546.919,Citrobacter freundii strain IDR1800045912-01-00,IDR1800045912-01-00,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15086845,546,,,,MLST.Citrobacter_freundii.22,,,,2020-08-12T00:00:00Z,,PRJNA636827,GCA_014170055.1,"CP054294,CP054295,CP054300,CP054299,CP054297,CP054296,CP054298",,"Wadsworth Center, New York State Department of Health",Illumina MiSeq; Oxford Nanopore MiniION,183x,Unicycler v. 0.4.8,1,6,7,5276672,51.77684,5201,4985,urine,,2018-10,USA,USA:Maine,,,,,,,,,,,,,,,,,"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.",collected_by:Maine Center for Disease Control and Prevention,,,,,,,Unknown,,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,546.920,Citrobacter freundii strain N18-04128,N18-04128,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506077,546,,,,MLST.Citrobacter_freundii.22,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189285.1,"CP047279,CP047280",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,68.0x,Unicycler v. 0.4.7,1,1,2,5458361,51.812458,5522,5237,rectum,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,100,0.34,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,546.921,Citrobacter freundii strain N18-04078,N18-04078,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506022,546,,,,MLST.Citrobacter_freundii.22,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189355.1,"CP047273,CP047274",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,60.0x,Unicycler v. 0.4.7,1,1,2,5493723,51.789597,5483,5246,missing,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,100,0.34,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,546.922,Citrobacter freundii strain N18-04085,N18-04085,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506036,546,,,,MLST.Citrobacter_freundii.22,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189375.1,"CP047275,CP047276",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,86.0x,Unicycler v. 0.4.7,1,1,2,5449384,51.80103,5455,5213,rectum,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,100,0.34,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,546.936,Citrobacter freundii strain N16-03880,N16-03880,Citrobacter freundii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11505996,546,,,,MLST.Citrobacter_freundii.22,,,,2020-09-24T00:00:00Z,32766684,PRJNA534306,GCA_014725915.1,"CP047269,CP047270",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,110.0x,Unicycler v. 0.4.7,1,1,2,5546039,51.821434,5565,5321,trachea,,2016,Canada,Canada,,,,not collected,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,548.1098,Klebsiella aerogenes 722,722,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173987,548,,,,,genotype:ST93,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917575.1,"CP103639,CP103640,CP103641",,,Oxford Nanopore GridION,38x,Flye v. 2.8.3-b1695,1,2,3,5483132,54.9974,5344,5135,blood,,2018-07-20,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,548.1099,Klebsiella aerogenes 4417,4417,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174061,548,,,,,genotype:ST208,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918355.1,"CP103664,CP103665,CP103666,CP103667,CP103668,CP103669,CP103670,CP103671",,,Oxford Nanopore GridION,470x,Flye v. 2.8.3-b1695,1,7,8,5868480,54.239292,5883,5605,blood,,2018-05-11,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,548.1154,Klebsiella aerogenes S2_CRE2,S2_CRE2,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387622,548,,,,,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074446,CP074447",,,Illumina NextSeq; PacBio Sequel,400x,Unicycler v. v0.4.7,1,1,2,5191437,55.134098,4959,4744,bal,,2017-01-21,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,548.1155,Klebsiella aerogenes S8_CRE8,S8_CRE8,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387628,548,,,,,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074517,CP074518",,,Illumina NextSeq; PacBio Sequel,260x,Unicycler v. v0.4.7,1,1,2,5251454,55.113403,5053,4872,"urine, clean catch",,2017-02-21,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,548.1156,Klebsiella aerogenes S33_CRE34,S33_CRE34,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387652,548,,,,,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074545,CP074546,CP074547",,,Illumina NextSeq; PacBio Sequel,301x,Unicycler v. v0.4.7,1,2,3,5487446,54.83633,5415,5190,lt groin wound,,2017-12-18,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,548.614,Klebsiella aerogenes strain 4928STDY7071344,4928STDY7071344,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567454,548,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164615.1,LR607333,,SC,,,,1,,1,5726555,55.23375,5013,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.81,0.1,,,Other,- HP,548.625,Klebsiella aerogenes strain C9,C9,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289361,548,,,,,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931665.1,"CP042530,CP042531,CP042532,CP042533",,University of Oxford,Oxford Nanopore MiniION,1407x,Unicycler v. SEP-2017,1,3,4,5390662,54.844376,5332,5154,clinical sample,,2008-06-28,Australia,Australia: Sydney,,,,,,,,,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,548.687,Klebsiella aerogenes strain 18-2341,18-2341,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14249374,548,,,,,,,,2020-03-08T00:00:00Z,,PRJNA554399,GCA_011067245.1,"CP049600,CP049601,CP049602",,Seoul Metropolitan Government Research Institute of Public Health and Environment,PacBio RSII; Illumina HiSeq,159.0x,HGAP v. 3.0,1,2,3,5406045,54.982616,5280,5046,missing,,2018-11-26,South Korea,South Korea: Seoul,,,,Klebsiella Infections,,,,,,,,,,,,,The purpose of this project is to characterize carbapenem-resistant Enterobacteriaceae in South Korea.,collected_by:Seoul Metropolitan Government Research Institute of Public Health and Environment,,,,,,,Klebsiella Infections,,,,,,,,,,,,,,100,0.44,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,548.809,Klebsiella aerogenes strain EA46506,EA46506,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933261,548,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939495.1,"CP070520,CP070519",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,1,2,5197914,54.986576,5072,4854,rectal swab,,2018-09-11,Czech Republic,Czech Republic: Hradec Krlov,,,,Dyspnea,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Hradec Krlov,,,,,,,Dyspnea,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,548.928,Klebsiella aerogenes strain SL269 strain Klebsiella aerogenes SL269,Klebsiella aerogenes SL269,Klebsiella aerogenes,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00389787,548,,,,,,,,2021-10-01T00:00:00Z,,PRJDB11945,GCA_020886955.1,"AP024918,AP024919,AP024920",,"Department of Microbiology, Juntendo University",Oxford nanopore MinION; Illumina Miseq,90x,Unicycler v. 0.4.7,1,2,3,5071587,55.381382,4925,4798,,,2018-07-23,Japan,Japan:Tokyo,,,,,,,,,,,,,,,,,The aim of this project is to analyze a transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-beta-lactamase in three clinical isolates of Enterobacteriaceae from one patient.,"biomaterial_provider:St. Luke's International Hospital, Tokyo",not applicable,not applicable,Blood,not applicable,A transferrable IncL/M plasmid harboring IMP-1,,,Bacteremia,,,,,,,,,not applicable,,,,99.47,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.1143,Enterobacter cloacae strain A1137,A1137,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07162522,550,,,,MLST.Enterobacter_cloacae.738,,,,2017-06-16T00:00:00Z,,PRJNA387717,GCA_002197345.1,CP021851,,Beijing Institute of Microbiology and Epidemiology,Illumina MiSeq,188.0x,Newbler v. 3.0,1,,1,5090134,55.26,4887,,isolated from a clinical multi-drug resistant enterobacter cloacae,,,,,,,,,,,,,,,,,,,,,Complete genome sequence of Enterobacter cloacae A1137,biomaterial_provider:Zhe Zhan,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.1232,Enterobacter cloacae strain M12X01451,M12X01451,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05831100,550,,,,MLST.Enterobacter_cloacae.922,,,,2017-08-01T00:00:00Z,,PRJNA341281,GCA_002303275.1,"CP017475,CP017473",,USDA,Illumina; PacBio,95,RS_HGAP v. Assembly.3,1,1,2,5087499,54.86,4853,4726,stool,,,,,,,,,,,,,,,,,,,,,Comparative genomics of shiga toxin producing Enterobacter Cloacae with Shiga toxin producing Escherichia coli,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.7,0.6,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,550.1235,Enterobacter cloacae strain MS7884A,MS7884A,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06765483,550,,,,,,,,2017-07-31T00:00:00Z,,PRJNA383436,GCA_002237465.1,"CP022532,CP022533,CP022534",,University of Queensland,PacBio,179.0x,HGAP v. 2.0,1,2,3,5267121,54.91,5161,4968,endotracheal tube,,2015-06-15,Australia,Australia,,,,,,,,,,,,,,,,,Hospital outbreak of IMP4 carbapenemase-producing Enterobacter cloacae,,,,,,,,N/A,,,,,,,Originally submitted as Enterobacter cloacae but changed in March 2019 because of ANI results to Enterobacter hormaechei,,,,,,,98.2,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,550.1527,Enterobacter cloacae strain PIMB10EC27,PIMB10EC27,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06448868,550,,,,MLST.Enterobacter_cloacae.513,,,,2018-04-05T00:00:00Z,,PRJNA376861,GCA_002982195.1,"CP020089,CP020090,CP020091",,Pasteur Institute in Ho Chi Minh City,PacBio,30.0x,HGAP v. SEP-2016,1,2,3,5419249,54.336754,5407,5238,urine,,2010,Viet Nam,Viet Nam,,male,,urinary tract infection,,host_health_state:Ho Chi Minh,,,,,,,,,,,Genome sequencing of a multidrug-resistance enterobacter cloacae clinical isolate.,collected_by:Binh Dan Hospital,,,,,,,urinary tract infection,Ho Chi Minh,,,,,,,,,,,,,96.9,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,550.1583,Enterobacter cloacae strain 20710,20710,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09425565,550,,,,MLST.Enterobacter_cloacae.200,,,,2018-06-25T00:00:00Z,,PRJNA476055,GCA_003264955.1,"CP030076,CP030077,CP030078,CP030079,CP030080,CP030081",,Zhejiang University,PacBio,100.0x,HGAP v. 3,1,5,6,5545020,54.57672,5636,5497,sptum,,2011-08,China,China:Shandong,,,,pneumonia,,,,,,,,,,,,,Complete Sequence of two Enterobacter cloacae Coproducing IMP-34 and VIM-1 Carbapenemases in China,collected_by:Zhou Kai,,,,,,,pneumonia,,,,,,,Originally submitted as Enterobacter cloacae but changed in March 2019 because of ANI results to Enterobacter hormaechei,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,550.2251,Enterobacter cloacae strain EN3600,EN3600,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10844942,550,,,,MLST.Enterobacter_cloacae.25,,,,2019-02-09T00:00:00Z,,PRJNA517781,GCA_004151605.1,"CP035633,CP035634,CP035635,CP035636,CP035637,CP035638",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,100X,HGAP v. 2,1,5,6,5484425,55.00039,5653,5488,blood,,2015-05,China,China:Anhui,,,,bloodstream infection,,,,,,,,,,,,,"Complete genome sequence of an IMP-8, CTX-M-14, and QnrS1 co-producing Enterobacter cloacae strain isolated from a patient with wound infection",collected_by:Yuanyuan Dai,,,,,,,bloodstream infection,,,,,,,,,,,,,,99.97,1.92,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,550.2442,Enterobacter cloacae strain 4928STDY7071342,4928STDY7071342,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567452,550,,,,MLST.Enterobacter_cloacae.145,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164655.1,LR607337,,SC,,,,1,,1,5063609,54.992584,4760,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.97,0.48,,,Other,- NHP,550.2443,Enterobacter cloacae strain 4928STDY7071341,4928STDY7071341,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567451,550,,,,MLST.Enterobacter_cloacae.145,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164705.1,LR607332,,SC,,,,1,,1,5077894,54.984196,4781,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.37,0.48,,,Other,- NHP,550.2450,Enterobacter cloacae strain 4928STDY7071648,4928STDY7071648,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567754,550,,,,MLST.Enterobacter_cloacae.286,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166375.1,LR607344,,SC,,,,1,,1,5132545,55.394577,4572,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.72,0.61,,,Other,- NHP,550.2451,Enterobacter cloacae strain 4928STDY7071160,4928STDY7071160,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567259,550,,,,MLST.Enterobacter_cloacae.168,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166405.1,LR607347,,SC,,,,1,,1,5598694,55.121094,5012,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.97,0.59,,,Other,- NHP,550.2452,Enterobacter cloacae strain 4928STDY7071173,4928STDY7071173,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567284,550,,,,MLST.Enterobacter_cloacae.145,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166455.1,LR607339,,SC,,,,1,,1,5002290,55.40687,4489,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.37,0.82,,,Other,- NHP,550.2453,Enterobacter cloacae strain 4928STDY7071152,4928STDY7071152,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567276,550,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166485.1,LR607340,,SC,,,,1,,1,4975856,55.452244,4762,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.47,0.62,,,Other,- NHP,550.2454,Enterobacter cloacae strain 4928STDY7071163,4928STDY7071163,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567262,550,,,,MLST.Enterobacter_cloacae.268,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166535.1,LR607345,,SC,,,,1,,1,4738893,55.82544,4117,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.69,0.04,,,Other,- NHP,550.2455,Enterobacter cloacae strain 4928STDY7387798,4928STDY7387798,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694437,550,,,,MLST.Enterobacter_cloacae.141,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166595.1,LR607364,,SC,,,,1,,1,5016704,55.503212,4537,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.11,0.33,,,Other,- NHP,550.2456,Enterobacter cloacae strain 4928STDY7387746,4928STDY7387746,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694383,550,,,,MLST.Enterobacter_cloacae.104,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166715.1,LR607370,,SC,,,,1,,1,5332468,55.39854,4534,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.24,0.33,,,Other,- NHP,550.2457,Enterobacter cloacae strain 4928STDY7387752,4928STDY7387752,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694389,550,,,,MLST.Enterobacter_cloacae.104,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166805.1,LR607379,,SC,,,,1,,1,5114720,55.368916,4474,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.92,0.33,,,Other,- HP,550.3005,Enterobacter cloacae strain 14240244101,14240244101,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999973,550,,,,,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864115.1,CP045487,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,101.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,5006044,55.04846,4687,,,,2014,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.97,0.43,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.3006,Enterobacter cloacae strain 99101,99101,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999971,550,,,,,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864095.1,CP045486,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,128.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,4594958,55.885017,4268,,,,2017,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.95,0.48,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.3007,Enterobacter cloacae strain 88701,88701,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12999970,550,,,,,,,,2021-02-11T00:00:00Z,,PRJNA576640,GCA_016864075.1,CP045485,,University Medical Center Groningen,Illumina MiSeq; Oxford Nanopore MiniION,135.0x,CLC Genomics Workbench v. 11; Unicycler,1,0,1,4483402,55.75159,4212,,,,2017,Netherlands,Netherlands: Groningen,,,,,,,,,,,,,,,,,Comparative multi-omics analysis of clinical Enterobacter spp. isolates uncovers differences in the expression of determinants for antibiotic resistance and virulence,sample_type:bone infection,,,,,,,,,,,,,,,,,,,,,99.92,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.3207,Enterobacter cloacae strain SL264 strain Enterobacter cloacae SL264,Enterobacter cloacae SL264,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00389785,550,,,,MLST.Enterobacter_cloacae.175,,,,2021-10-01T00:00:00Z,,PRJDB11945,GCA_020886835.1,"AP024913,AP024914,AP024915",,"Department of Microbiology, Juntendo University",Oxford nanopore MinION; Illumina Miseq,104x,Unicycler v. 0.4.7,1,2,3,5069484,55.384354,4915,4789,,,2018-04-25,Japan,Japan:Tokyo,,,,,,,,,,,,,,,,,The aim of this project is to analyze a transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-beta-lactamase in three clinical isolates of Enterobacteriaceae from one patient.,"biomaterial_provider:St. Luke's International Hospital, Tokyo",not applicable,not applicable,Pancreatic fluid,not applicable,A transferrable IncL/M plasmid harboring IMP-1,,,Pancreatitis,,,,,,,,,not applicable,,,,99.47,0.25,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,550.3829,Enterobacter cloacae EFN743,EFN743,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26208495,550,,,,MLST.Enterobacter_cloacae.456,,,,2022-06-27T00:00:00Z,,PRJNA473419,GCA_023920605.1,"CP092635,CP092637,CP092638,CP092636",,,Illumina MiniSeq; Oxford Nanopore,159.0x,Unicycler hybrid assembly v. 0.4.8,1,3,4,5407505,54.57737,5285,5117,urine,,2019,Ghana,Ghana,,,,UTI,,,,,,,,,,,,,,collected_by:ENRH_Hospital staff,,,,,,,UTI,,,,,,,,,,,,,,100,0.3,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,550.3830,Enterobacter cloacae P7536,P7536,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18256316,550,,,,,,,,2022-07-05T00:00:00Z,,PRJNA713617,GCA_024138875.1,"CP071792,CP071791,CP071788,CP071789,CP071790",,,Illumina MiSeq; Oxford Nanopore MinION,20.0x,SPAdes v. May 2020,1,4,5,5569846,54.569534,5673,5365,rectal swab,,2018,France,France: Marseille,,,,disease carrier,,,,,,,,,,,,,,collected_by:IHU Mediterranee Infection,,,,,,,disease carrier,,,,,,,,,,,,,,99.1,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,550.3911,Enterobacter cloacae 3143,3143,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174020,550,,,,,genotype:ST995,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917615.1,"CP103611,CP103612,CP103613",,,Oxford Nanopore GridION,109x,Flye v. 2.8.3-b1695,1,2,3,5108863,54.789608,4910,4784,blood,,2018-10-31,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,550.3973,Enterobacter cloacae 2340913,2340913,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31029877,550,,,,MLST.Enterobacter_cloacae.25,,,,2022-10-30T00:00:00Z,,PRJNA884522,GCA_025908355.1,"CP109673,CP109674",,,Oxford Nanopore PromethION,100X,Flye v. v.2.8.3; Minimap2 v. v.2.17;,1,1,2,4961506,55.610104,4829,4680,ascites,,2019-06-21,Taiwan,Taiwan,,female,,peritonitis,,host_disease_outcome:death;host_disease_stage:multiple organ failure;host_health_state:liver cirrhosis,,,,,,,,,,,,collected_by:Yuan's General Hospital,,,,,,,peritonitis,liver cirrhosis,death,,multiple organ failure,,,,,,,,,,100,0.1,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,550.3974,Enterobacter cloacae 49483,49483,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31029875,550,,,,MLST.Enterobacter_cloacae.25,,,,2022-10-30T00:00:00Z,,PRJNA884522,GCA_025908375.1,"CP109679,CP109680",,,Oxford Nanopore PromethION,100X,Flye v. v2.8.3; Minimap2 v. v.2.17; Racon,1,1,2,4917639,55.638184,4746,4612,blood,,2019-02-05,Taiwan,Taiwan,,male,,bacterial sepsis,,host_disease_outcome:death;host_disease_stage:severe septic shock,,,,,,,,,,,,collected_by:Yuan's General hospital,,,,,,,bacterial sepsis,,death,,severe septic shock,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,550.3992,Enterobacter cloacae 2312040,2312040,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31029876,550,,,,MLST.Enterobacter_cloacae.78,,,,2022-10-30T00:00:00Z,,PRJNA884522,,"CP109676,CP109675,CP109677,CP109678",,,Oxford Nanopore PromethION,100X,Flye v. v.2.8.3; Minimap2 v. v.2.17;,1,3,4,5044190,54.997612,4889,4734,blood,,2019-05-07,Taiwan,Taiwan,,male,,bacterial sepsis,,host_disease_outcome:death;host_disease_stage:severe septic shock,,,,,,,,,,,,collected_by:Yuan's General Hospital,,,,,,,bacterial sepsis,,death,,severe septic shock,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,550.4023,Enterobacter cloacae S36_CRE37,S36_CRE37,Enterobacter cloacae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387654,550,,,,,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074548,CP074549,CP074550,CP074551,CP074552",,,Illumina NextSeq; PacBio Sequel,361x,Unicycler v. v0.4.7,1,4,5,5038189,55.26704,4950,4766,urine cc,,2017-10-03,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,556499.3,Propionibacterium acidifaciens strain FDAARGOS_576 strain Not applicable,Not applicable,Propionibacterium acidifaciens,Propionibacterium,Propionibacteriaceae,Propionibacteriales,Actinomycetes,Actinomycetota,SAMN10228556,556499,,,,,,FDA:FDAARGOS_576,,2018-11-20T00:00:00Z,,PRJNA231221,GCA_003798325.1,CP033719,,US Food and Drug Administration,Pacbio; Illumina,11.56x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,3072768,70.58913,2915,2566,subgingival plaque,,1983,,,,male,53y,moderate periodontitis,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI < J Izard,,,,,,,moderate periodontitis,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,98.46,0.33,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,562.102131,Escherichia coli Ec-050-T5-ESBL,Ec-050-T5-ESBL,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108723,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759745.1,"CP086490,CP086491,CP086492,CP086493,CP086494,CP086495,CP086496,CP086497,CP086498,CP086499",,,Illumina NovaSeq; Oxford Nanopore MiniION,225x,Unicycler v. 0.4.8,1,9,10,5330360,50.62782,5500,5120,stool,,2018,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102132,Escherichia coli Ec-050-T5-MAC,Ec-050-T5-MAC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108722,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759725.1,"CP086500,CP086501,CP086502,CP086503,CP086504,CP086505,CP086506,CP086507,CP086508,CP086509",,,Illumina NovaSeq; Oxford Nanopore MiniION,275x,Unicycler v. 0.4.8,1,9,10,5333616,50.627865,5507,5126,stool,,2018,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102133,Escherichia coli Ec-050-T20-MAC,Ec-050-T20-MAC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108724,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759765.1,"CP086480,CP086481,CP086482,CP086483,CP086484,CP086485,CP086486,CP086487,CP086488,CP086489",,,Illumina NovaSeq; Oxford Nanopore MiniION,308x,Unicycler v. 0.4.8,1,9,10,5333341,50.627552,5509,5124,stool,,2018,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102134,Escherichia coli Ec-050-T20-ESBL,Ec-050-T20-ESBL,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108725,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759785.1,"CP086470,CP086471,CP086472,CP086473,CP086474,CP086475,CP086476,CP086477,CP086478,CP086479",,,Illumina NovaSeq; Oxford Nanopore MiniION,390x,Unicycler v. 0.4.8,1,9,10,5331662,50.625957,5506,5122,stool,,2018,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102135,Escherichia coli Ec-042-T5-MAC,Ec-042-T5-MAC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108717,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759825.1,"CP086538,CP086539,CP086540,CP086541,CP086542,CP086543",,,Illumina NovaSeq; Oxford Nanopore MiniION,430x,Unicycler v. 0.4.8,1,5,6,4808531,50.467075,4855,4578,stool,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102136,Escherichia coli Ec-050-T0,Ec-050-T0,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108721,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759805.1,"CP086510,CP086511,CP086512,CP086513,CP086514,CP086515,CP086516,CP086517,CP086518,CP086519",,,Illumina NovaSeq; Oxford Nanopore MiniION,271x,Unicycler v. 0.4.8,1,9,10,5332076,50.626774,5502,5121,stool,,2018,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102137,Escherichia coli Ec-042-T5-ESBL,Ec-042-T5-ESBL,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108718,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759845.1,"CP086532,CP086533,CP086534,CP086535,CP086536,CP086537",,,Illumina NovaSeq; Oxford Nanopore MiniION,325x,Unicycler v. 0.4.8,1,5,6,4808193,50.467503,4851,4573,stool,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102138,Escherichia coli Ec-042-T20-ESBL,Ec-042-T20-ESBL,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108720,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759885.1,"CP086520,CP086521,CP086522,CP086523,CP086524,CP086525",,,Illumina NovaSeq; Oxford Nanopore MiniION,273x,Unicycler v. 0.4.8,1,5,6,4808210,50.46737,4856,4572,stool,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102139,Escherichia coli Ec-042-T20-MAC,Ec-042-T20-MAC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108719,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759865.1,"CP086526,CP086527,CP086528,CP086529,CP086530,CP086531",,,Illumina NovaSeq; Oxford Nanopore MiniION,290x,Unicycler v. 0.4.8,1,5,6,4809001,50.467968,4848,4577,stool,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102140,Escherichia coli Ec-042-T0,Ec-042-T0,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108716,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759905.1,"CP086544,CP086545,CP086546,CP086547,CP086548,CP086549",,,Illumina NovaSeq; Oxford Nanopore MiniION,294x,Unicycler v. 0.4.8,1,5,6,4808195,50.4674,4854,4574,stool,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.102351,Escherichia coli EC6868,EC6868,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27258442,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2022-04-12T00:00:00Z,,PRJNA822684,GCA_022918835.1,"CP095083,CP095084,CP095085",,,Illumina HiSeq; PacBio,147.74x,HGAP v. 4; FALCON v. 0.3,1,2,3,5405505,50.73367,5572,5190,vaginal secretion,,2021-12,China,China:Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,562.102352,Escherichia coli w264,w264,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27258894,562,,,,MLST.Escherichia_coli_2.398,,,,2022-04-12T00:00:00Z,,PRJNA822691,GCA_022919055.1,"CP095088,CP095089",,,Illumina HiSeq; PacBio,368.41x,HGAP v. 4; FALCON v. 0.3,1,1,2,4736388,50.852104,4765,4510,vaginal secretion,,2021-12,China,China:Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Ling Wang,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,562.102792,Escherichia coli EC9682,EC9682,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27395225,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2022-04-14T00:00:00Z,,PRJNA824219,GCA_022982975.1,"CP095271,CP095272,CP095273",,,Illumina HiSeq; PacBio,156.45x,HGAP v. 4; FALCON v. 0.3,1,2,3,5412376,50.631203,5539,5215,vaginal secretion,,2021-10,China,China:Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,562.102816,Escherichia coli 779,779,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22826253,562,,,,"MLST.Escherichia_coli_2.88,MLST.Escherichia_coli_1.2480",,,,2022-04-18T00:00:00Z,35411158,PRJNA776738,GCA_023024425.1,"CP086220,CP086221,CP086222,CP086223,CP086224,CP086225,CP086226,CP086227,CP086228",,,Oxford Nanopore GridION; Illumina HiSeq,100.0x,Unicycler v. 0.4.8,1,8,9,5667876,50.372326,5864,5515,urine,,2016-11-03,China,China: Zhejiang,,,,urinary tract infection,,,,,,,,,,,,,,collected_by:Danni Bao,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.103951,Escherichia coli EC6563,EC6563,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27615948,562,,,,"MLST.Escherichia_coli_1.3941,MLST.Escherichia_coli_2.83",,,,2022-04-25T00:00:00Z,,PRJNA827647,GCA_023100765.1,"CP095856,CP095859,CP095857,CP095858",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,3,4,5251855,50.545647,5343,5013,urine,,2020-11-25,China,China,,,,Urinary tract infection,,,,,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.104048,Escherichia coli EC6622,EC6622,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27776107,562,,,,"MLST.Escherichia_coli_1.58,MLST.Escherichia_coli_2.87",,,,2022-05-04T00:00:00Z,,PRJNA832063,GCA_023238365.1,"CP096587,CP096588,CP096589",,,Illumina HiSeq; PacBio,164.89x,HGAP v. 4; FALCON v. 0.3,1,2,3,5160509,50.65543,5217,4947,urine,,2021,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.104233,Escherichia coli UPEC-245U/190328,UPEC-245U/190328,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14277527,562,,,"Escherichia coli, UPEC","MLST.Escherichia_coli_2.469,MLST.Escherichia_coli_1.295",,,,2021-08-03T00:00:00Z,,PRJNA610084,GCA_023376095.1,"CP049845,CP049851,CP049850,CP049849,CP049848,CP049847,CP049846",,,Illumina HiSeq; Oxford Nanopore MiniION,208.905x,Unicycler v. v0.4.1,1,6,7,5301911,50.689423,5356,5080,bladder epithelial biopsy from 30-year-old female patient with recurrent urinary tract infection,,2019-03-28,Mexico,Mexico: Mexico City,,female,30 years,Recurrent urinary tract infection,,host_description:30-year-old female patient with recurrent urinary tract infection;host_disease_outcome:chronic disease;host_disease_stage:chronic disease;host_health_state:chronic disease;host_subject_id:Not applicable,,,,,,,,,,,,collected_by:Hospital Militar de Especialidades de la mujer y neonatologia;specimen_voucher:Not collected,,,,,,,Recurrent urinary tract infection,chronic disease,chronic disease,30-year-old female patient with recurrent urinary tract infection,chronic disease,"Escherichia coli, UPEC",,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.107118,Escherichia coli EC20017429,EC20017429,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18140782,562,,,,MLST.Escherichia_coli_1.17,,,,2022-06-27T00:00:00Z,,PRJNA698617,GCA_023921205.1,"CP071711,CP071712,CP071713,CP071714,CP071715,CP071716",,,Nanopore Technology,150.0x,Unicycler v. Galaxy version 0.4.8.0,1,5,6,5959220,50.499947,6304,5827,missing,,2017-04-29,Canada,Canada: Quebec,,,,gastroenteritis,,,,,,,,,,,,,,collected_by:LSPQ,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108529,Escherichia coli C31,C31,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30011701,562,,,,MLST.Escherichia_coli_1.131,,,,2022-08-06T00:00:00Z,,PRJNA863061,GCA_024579775.1,"CP102061,CP102063,CP102064,CP102062",,,Illumina NovaSeq; Oxford Nanopore,180.0x,SPAdes v. v3.15.5,1,3,4,5333774,50.81239,5424,5157,urine,,,Singapore,Singapore,,,,Urine infection,,,,,,,,,,,,,,collected_by:National University of Singapore Hospital,,,,,,,Urine infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.108537,Escherichia coli WY517-2,WY517-2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917423,562,,,,MLST.Escherichia_coli_2.21,genotype:LT-IIc4 EplBA,,,2022-08-08T00:00:00Z,,PRJNA320137,GCA_024584845.1,"CP076259,CP076261,CP076260",,,Illumina MiSeq 2 x 250 bp,131x,Geneious v. 6.1.7,1,2,3,5012694,50.694675,4999,4720,child,,1984-01-01,Nigeria,Nigeria,,,,diarrhea,,,,,,,,,,,,,,collected_by:Peter Echeverria,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108540,Escherichia coli 0-4,0-4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917421,562,,,,,genotype:LT-IIc2 EplBA,,,2022-08-08T00:00:00Z,,PRJNA320137,GCA_024584885.1,"CP076262,CP076263",,,Illumina MiSeq 2 x 250 bp,87x,Geneious v. 6.1.7,1,1,2,5062962,50.69009,5084,4829,adult,,1979-01-01,Brazil,Brazil,,,,diarrhea,,,,,,,,,,,,,,collected_by:Luis Trabulsi,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108541,Escherichia coli E21845/O/A,E21845/O/A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917414,562,,,,MLST.Escherichia_coli_1.1308,genotype:LT-IIc2 EplBA,,,2022-08-08T00:00:00Z,,PRJNA320137,GCA_024585005.1,"CP076272,CP076273",,,Illumina MiSeq 2 x 250 bp,100x,Geneious v. 6.1.7,1,1,2,5082499,50.731796,5040,,adult,,1984-01-01,Thailand,Thailand,,,,diarrhea,,,,,,,,,,,,,,collected_by:Silvia Scotland,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108542,Escherichia coli D217-5,D217-5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917419,562,,,,,genotype:LT-IIc3 EplBA,,,2022-08-08T00:00:00Z,,PRJNA320137,GCA_024584925.1,"CP076268,CP076269",,,Illumina MiSeq 2 x 250 bp,125x,Geneious v. 6.1.7,1,1,2,4863595,50.78733,4810,4582,child,,1985-01-01,Thailand,Thailand,,,,diarrhea,,,,,,,,,,,,,,collected_by:Peter Echeverria,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108543,Escherichia coli 442/2,442/2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917418,562,,,,MLST.Escherichia_coli_2.314,genotype:LT-IIc2 EplBA,,,2022-08-08T00:00:00Z,,PRJNA320137,GCA_024584945.1,"CP076282,CP076283,CP076284",,,Illumina MiSeq 2 x 250 bp,128x,Geneious v. 6.1.7,1,2,3,4968009,50.689983,4982,4723,adult,,1979-01-01,Brazil,Brazil,,,,diarrhea,,,,,,,,,,,,,,collected_by:Luis Trabulsi,,,,,,,diarrhea,,,,,,,,,,,,,,100,0.1,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.108812,Escherichia coli SCAID WND1-2022 (119) strain SCAID WND1-2022 (119),SCAID WND1-2022 (119),Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30333619,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734835.1,"CP102947,CP102948,CP102949",,,PacBio Sequel,164x,Velvet v. 1.2.10,1,2,3,5237864,50.72497,5360,5046,bile duct discharge,,2022-02,Kazakhstan,Kazakhstan: Almaty,,,,cholangitis,,,Resistant;Susceptible;Intermediate,AMR Panel,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,cholangitis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,562.108813,Escherichia coli XH989,XH989,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30247557,562,,,,MLST.Escherichia_coli_2.88,,,,2022-08-24T00:00:00Z,,PRJNA868478,GCA_024735245.1,"CP102679,CP102676,CP102678,CP102677",,,Illumina; Oxford Nanopore MinION,100.0x,Raven v. 1.8.1; polypolish v. 0.5.0,1,3,4,5280985,50.65216,5426,5104,urine,,2015-05-18,China,China:Hangzhou,,,,UTI,,,,,,,,,,,,,,collected_by:Sir Run Run Shaw Hospital,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.108814,Escherichia coli XH987,XH987,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30247543,562,,,,MLST.Escherichia_coli_2.88,,,,2022-08-24T00:00:00Z,,PRJNA868478,GCA_024735225.1,"CP102675,CP102673,CP102672,CP102674",,,Oxford Nanopore MinION; Illumina,100.0x,Raven v. 1.8.1; polypolish v. 0.5.0,1,3,4,5258359,50.643555,5398,5077,urine,,2015-04-16,China,China:Hangzhou,,,,UTI,,,,,,,,,,,,,,collected_by:Sir Run Run Shaw Hospital,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.109883,Escherichia coli strain 2021CK-01784,2021CK-01784,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24145077,562,,,,MLST.Escherichia_coli_1.501,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025259645.1,"CP104371,CP104372",,Utah Public Health Laboratory Infectious Disease submission group,Illumina MiSeq; Oxford Nanopore GridION,286.0x,Unicycler v. 0,1,1,2,5049286,50.651577,4966,4746,rectal swab,,2021-12-08,,USA,,,,,,,,,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,99.97,0.49,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.110580,Escherichia coli ECO3183,ECO3183,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30869335,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",,,,2022-09-25T00:00:00Z,,PRJNA880665,GCA_025398915.1,"CP104721,CP104722,CP104723",,,PacBio; Illumina,200.0x,SMRT Link v. v5.1.0,1,2,3,5083529,50.791527,5124,4823,urine,,2019-04,China,China: Tianjin,,,,urinary tract infection,,,,,,,,,,,,,,collected_by:Shuangqing Liu,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.110755,Escherichia coli 3045,3045,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174015,562,,,,"MLST.Escherichia_coli_1.44,MLST.Escherichia_coli_2.2",genotype:ST44,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917235.1,"CP103570,CP103571,CP103572,CP103573,CP103574,CP103575,CP103576",,,Oxford Nanopore GridION,289x,Flye v. 2.8.3-b1695,1,6,7,5034395,50.948822,5085,4789,blood,,2019-04-25,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110756,Escherichia coli 4314,4314,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174056,562,,,,"MLST.Escherichia_coli_1.224,MLST.Escherichia_coli_2.479",genotype:ST224,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917275.1,"CP103609,CP103610",,,Oxford Nanopore GridION,326x,Flye v. 2.8.3-b1695,1,1,2,4990445,50.86805,4922,4702,blood,,2018-11-29,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110757,Escherichia coli 3059,3059,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174016,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",genotype:ST38,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917375.1,CP103559,,,Oxford Nanopore GridION,208x,Flye v. 2.8.3-b1695,1,0,1,5337629,50.602825,5347,5057,blood,,2019-05-22,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110758,Escherichia coli 4848,4848,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174075,562,,,,"MLST.Escherichia_coli_1.44,MLST.Escherichia_coli_2.2",genotype:ST44,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917355.1,"CP103596,CP103597,CP103598,CP103599,CP103600,CP103601,CP103602,CP103603,CP103604",,,Oxford Nanopore GridION,58x,Flye v. 2.8.3-b1695,1,8,9,5014932,50.75915,5109,4782,blood,,2019-01-10,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110759,Escherichia coli 2900,2900,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174010,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",genotype:ST405,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917475.1,"CP103633,CP103634",,,Oxford Nanopore GridION,85x,Flye v. 2.8.3-b1695,1,1,2,5347110,50.63494,5348,5063,blood,,2018-07-20,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110760,Escherichia coli 4750,4750,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174072,562,,,,"MLST.Escherichia_coli_1.1193,MLST.Escherichia_coli_2.53",genotype:ST1193,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917535.1,"CP103589,CP103590,CP103591",,,Oxford Nanopore GridION,96x,Flye v. 2.8.3-b1695,1,2,3,5376110,50.615555,5458,5129,blood,,2019-01-23,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110761,Escherichia coli 5283,5283,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174091,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",genotype:ST405,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917655.1,"CP103762,CP103763,CP103764,CP103765,CP103766,CP103767",,,Oxford Nanopore GridION,242x,Flye v. 2.8.3-b1695,1,5,6,5402248,50.633163,5468,5173,blood,,2020-02-08,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110762,Escherichia coli 4621,4621,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174065,562,,,,"MLST.Escherichia_coli_2.14,MLST.Escherichia_coli_1.68",genotype:ST68,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917715.1,"CP103479,CP103480,CP103481,CP103482,CP103483,CP103484,CP103485,CP103486",,,Oxford Nanopore GridION,345x,Flye v. 2.8.3-b1695,1,7,8,5494983,50.545307,5489,5189,blood,,2019-12-22,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110763,Escherichia coli 4238,4238,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174054,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917735.1,"CP103533,CP103534,CP103535,CP103536,CP103537,CP103538,CP103539",,,Oxford Nanopore GridION,186x,Flye v. 2.8.3-b1695,1,6,7,5125971,50.676956,5214,4898,blood,,2019-09-28,USA,USA: Houston,,,,,,,,,,,,,,,,,,,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110764,Escherichia coli 5270,5270,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174089,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",genotype:ST167,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917795.1,"CP103529,CP103530,CP103531,CP103532",,,Oxford Nanopore GridION,532x,Flye v. 2.8.3-b1695,1,3,4,5192842,50.749878,5251,4930,blood,,2019-10-22,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110765,Escherichia coli 5264,5264,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174088,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",genotype:ST167,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917815.1,"CP103540,CP103541,CP103542,CP103543",,,Oxford Nanopore GridION,343x,Flye v. 2.8.3-b1695,1,3,4,4891501,50.809006,4915,4630,blood,,2019-09-25,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110766,Escherichia coli 5444,5444,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174095,562,,,,"MLST.Escherichia_coli_1.44,MLST.Escherichia_coli_2.2",genotype:ST44,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917955.1,"CP103515,CP103516,CP103517,CP103518,CP103519,CP103520",,,Oxford Nanopore GridION,209x,Flye v. 2.8.3-b1695,1,5,6,5020180,50.898273,5142,4829,blood,,2019-11-07,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110767,Escherichia coli 3090,3090,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174017,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",genotype:ST167,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917995.1,"CP103745,CP103746,CP103747,CP103748,CP103749,CP103750",,,Oxford Nanopore GridION,85x,Flye v. 2.8.3-b1695,1,5,6,5166096,50.83268,5265,4933,blood,,2016-10-27,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110768,Escherichia coli 2779 - blood draw same patient as MB9267,2779 - blood draw same patient as MB9267,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174006,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",genotype:ST405,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918015.1,"CP103521,CP103522,CP103523,CP103524,CP103525,CP103526,CP103527,CP103528",,,Oxford Nanopore GridION,91x,Flye v. 2.8.3-b1695,1,7,8,5353028,50.628468,5390,5111,blood draw same patient as mb9267,,2019-10-28,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110769,Escherichia coli 3036,3036,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174012,562,,,,"MLST.Escherichia_coli_2.21,MLST.Escherichia_coli_1.155",genotype:ST155,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918035.1,"CP103544,CP103545,CP103546,CP103547",,,Oxford Nanopore GridION,254x,Flye v. 2.8.3-b1695,1,3,4,5010740,50.616695,5024,4744,blood,,2019-09-20,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110770,Escherichia coli 4973,4973,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174076,562,,,,MLST.Escherichia_coli_1.648,genotype:ST648,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918135.1,"CP103468,CP103469,CP103478,CP103470,CP103471,CP103472,CP103473,CP103474,CP103475,CP103476,CP103477",,,Oxford Nanopore GridION,250x,Flye v. 2.8.3-b1695,1,10,11,5413924,50.32564,5489,5188,blood,,2020-01-09,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110771,Escherichia coli 4069,4069,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174050,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",genotype:ST38,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918155.1,CP103673,,,Oxford Nanopore GridION,275x,Flye v. 2.8.3-b1695,1,0,1,5087395,50.648438,4993,4721,blood,,2018-01-13,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110772,Escherichia coli 3985,3985,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174042,562,,,,"MLST.Escherichia_coli_2.19,MLST.Escherichia_coli_1.156",genotype:ST156,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918195.1,"CP103623,CP103624,CP103625",,,Oxford Nanopore GridION,221x,Flye v. 2.8.3-b1695,1,2,3,4929699,50.814808,4866,4635,blood,,2018-09-07,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110773,Escherichia coli 4012,4012,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174046,562,,,,"MLST.Escherichia_coli_1.90,MLST.Escherichia_coli_2.66",genotype:ST90,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918275.1,"CP103626,CP103627,CP103628,CP103629,CP103630,CP103631,CP103632",,,Oxford Nanopore GridION,273x,Flye v. 2.8.3-b1695,1,6,7,5106755,50.7115,5138,4857,blood,,2018-08-21,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110774,Escherichia coli 961,961,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173990,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.617",,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918295.1,"CP103645,CP103646,CP103647,CP103648,CP103649,CP103650,CP103651,CP103652,CP103653",,,Oxford Nanopore GridION,61x,Flye v. 2.8.3-b1695,1,8,9,5226855,50.83858,5322,4992,blood,,2018-06-18,USA,USA: Houston,,,,,,,,,,,,,,,,,,,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110775,Escherichia coli ST361,ST361,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174001,562,,,,"MLST.Escherichia_coli_1.361,MLST.Escherichia_coli_2.650",,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918335.1,"CP103704,CP103705,CP103706,CP103708,CP103709,CP103707",,,Oxford Nanopore GridION,48x,Flye v. 2.8.3-b1695,1,5,6,5084854,50.772766,5153,4855,blood,,2017-02-23,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110776,Escherichia coli 3150,3150,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174021,562,,,,MLST.Escherichia_coli_1.648,genotype:ST648,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918375.1,"CP103657,CP103658,CP103659,CP103660,CP103661,CP103662,CP103663",,,Oxford Nanopore GridION,449x,Flye v. 2.8.3-b1695,1,6,7,5615964,50.465763,5719,5419,blood,,2018-05-21,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110777,Escherichia coli ST12468,ST12468,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174027,562,,,,,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918755.1,"CP103694,CP103695,CP103696",,,Oxford Nanopore GridION,417x,Flye v. 2.8.3-b1695,1,2,3,4895987,50.78022,4929,4700,blood,,2017-06-13,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110778,Escherichia coli 3359,3359,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174032,562,,,,"MLST.Escherichia_coli_1.450,MLST.Escherichia_coli_2.132",genotype:ST450,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918775.1,"CP103739,CP103740,CP103741",,,Oxford Nanopore GridION,140x,Flye v. 2.8.3-b1695,1,2,3,5156253,50.86403,5294,5002,blood,,2016-11-20,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.6,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110779,Escherichia coli 1579,1579,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173996,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",genotype:ST405,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918815.1,"CP103718,CP103719,CP103720,CP103721",,,Oxford Nanopore GridION,104x,Flye v. 2.8.3-b1695,1,3,4,5468527,50.65452,5521,5229,blood,,2017-01-13,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110780,Escherichia coli p10B,p10B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13948682,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.10",genotype:ST10,,,2022-09-04T00:00:00Z,33164081,PRJNA603908,GCA_024918895.1,"CP103758,CP103759,CP103760,CP103761",,,Oxford Nanopore GridION,265x,Flye v. 2.8.3-b1695,1,3,4,4886452,50.782654,4938,4670,blood,,2015-01/2016-07,USA,USA:Houston,,,,bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.110781,Escherichia coli p11B,p11B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13948685,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",genotype:ST131,,,2022-09-04T00:00:00Z,33164081,PRJNA603908,GCA_024918915.1,"CP103755,CP103756,CP103757",,,Oxford Nanopore GridION,73x,Flye v. 2.8.3-b1695,1,2,3,5546857,50.72689,5763,5437,blood,,2015-01/2016-07,USA,USA:Houston,,,,bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia NHP,562.110982,Escherichia coli B-JRPT-4119,B-JRPT-4119,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30996451,562,,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",,,,2022-10-11T00:00:00Z,,PRJNA883762,GCA_025642235.1,CP106756,,,Oxford Nanopore GridION,864.0x,Flye v. 2.9,1,0,1,4724630,50.81598,4733,4470,human stool,,2021-12-14,Sweden,Sweden,,,,healthy,,,,,,,,,,,,,,,Human gut microbiome,fecal samples,human stool,Petrone et al. 2022 (In press),,,healthy,,,,,,,,,,Human gut microbiome,,,,100,0.1,,,Gastrointestinal,- NHP,562.112383,Escherichia coli KR001_HIC_0034,KR001_HIC_0034,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31100334,562,,,,"MLST.Escherichia_coli_2.666,MLST.Escherichia_coli_1.297",,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757665.1,CP107197,,,PacBio Sequel II,115x,HiCanu v. 2.1.1,1,0,1,4778506,50.751156,4688,4481,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- HP,562.112391,Escherichia coli HUM3355,HUM3355,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26232716,562,,,,MLST.Escherichia_coli_1.361,,,,2022-10-21T00:00:00Z,,PRJNA810075,GCA_025782825.1,"CP093317,CP093318,CP093319,CP093320",,,Oxford Nanopore MinION; Illumina MiSeq,100X,Trycycler v. 0.4.1; Flye v. 2.8.1; Raven,1,3,4,5134820,50.952087,5164,4895,faecal sample,,2012,Botswana,Botswana: Kasane,,,,diarrhea,,,Resistant;Intermediate,AMR Panel,,,,,,,,,,"collected_by:Center for African Resources: Animals, Communities and Land Use (CARACAL)",,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.112421,Escherichia coli EC488,EC488,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30088785,562,,,,MLST.Escherichia_coli_1.648,,,,2022-11-01T00:00:00Z,,PRJNA865002,GCA_025946585.1,"CP109874,CP109875,CP109884,CP109877,CP109878,CP109879,CP109880,CP109881,CP109882,CP109883,CP109876",,,Oxford Nanopore,100.0x,SPAdes v. v0.4.8,1,10,11,5573675,50.632175,5687,5367,urine,,2021-08-04,China,China,,,,Tuberculosis,,,,,,,,,,,,,,collected_by:Xianhong He,,,,,,,Tuberculosis,,,,,,,,,,,,,,99.7,0,Respiratory Diseases,Tuberculosis,Urinary Tract,Respiratory Diseases-Tuberculosis HP,562.114671,Escherichia coli BH100,BH100,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08117235,562,,,UPEC,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.33",,,,2018-01-04T00:00:00Z,,PRJNA389912,,"CP025251,CP025252,CP025253",,,Illumina HiSeq,984.0x,SPAdes v. 3.6,1,2,3,5270937,50.485672,5301,5255,urine,,1974,Brazil,Brazil: Belo Horizonte,,female,,Urinary tract infection,,,,,,,,,,,,,,collected_by:Edmar Chartone Souza,,,,,,,Urinary tract infection,,,,,UPEC,,,,,,,,,100,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.115253,Escherichia coli GN02050,GN02050,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361453,562,,,,"MLST.Escherichia_coli_2.55,MLST.Escherichia_coli_1.144",genotype:144,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095505,CP095504,CP095503,CP095502,CP095507,CP095506,CP095509,CP095508",,,PacBio Sequel,508x,HGAP v. 6.0.0.47841,1,7,8,5289801,50.655064,5399,5113,blood,,2002,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115254,Escherichia coli GN02270,GN02270,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361456,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",genotype:69,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095510,CP095511,CP095512,CP095513",,,PacBio Sequel,335x,HGAP v. 6.0.0.47841,1,3,4,5363149,50.744926,5422,5116,blood,,2004,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115255,Escherichia coli GN02323,GN02323,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361457,562,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",genotype:73,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095514,CP095515,CP095517,CP095516",,,PacBio Sequel,488x,HGAP v. 6.0.0.47841,1,3,4,5248807,50.438698,5264,4961,blood,,2004,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115256,Escherichia coli GN02350,GN02350,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361458,562,,,,"MLST.Escherichia_coli_2.36,MLST.Escherichia_coli_1.12",genotype:12,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095518,CP095519",,,PacBio Sequel,756x,HGAP v. 6.0.0.47841,1,1,2,5333286,50.44498,5328,5013,blood,,2005,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115257,Escherichia coli GN05505,GN05505,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361466,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",genotype:69,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095526,CP095525,CP095528,CP095527",,,PacBio Sequel,217x,HGAP v. 6.0.0.47841,1,3,4,5391862,50.723053,5504,5200,blood,,2013,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115258,Escherichia coli GN04171,GN04171,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361461,562,,,,MLST.Escherichia_coli_1.131,genotype:131,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095520,CP095521,CP095524,CP095522,CP095523",,,PacBio Sequel,259x,HGAP v. 6.0.0.47841,1,4,5,5100549,50.80257,5205,4959,blood,,2011,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.9,0.1,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115259,Escherichia coli GN02461,GN02461,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361468,562,,,,MLST.Escherichia_coli_1.68,genotype:68,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095533,CP095535,CP095534,CP095537,CP095536",,,PacBio Sequel,304x,HGAP v. 6.0.0.47841,1,4,5,5321280,50.57877,5211,4945,blood,,2006,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115260,Escherichia coli GN06156,GN06156,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361467,562,,,,MLST.Escherichia_coli_1.69,genotype:69,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095529,CP095532,CP095530,CP095531",,,PacBio Sequel,571x,Flye v. 2.4.2,1,3,4,5040973,50.70075,4921,4711,blood,,2014,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115261,Escherichia coli GN04592,GN04592,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361463,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",genotype:69,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095538,CP095539",,,PacBio Sequel,396x,HGAP v. 6.0.0.47841,1,1,2,5368107,50.694798,5441,5147,blood,,2012,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115262,Escherichia coli GN03204,GN03204,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361470,562,,,,MLST.Escherichia_coli_1.131,genotype:131,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095540,CP095541",,,PacBio Sequel,560x,HGAP v. 6.0.0.47841,1,1,2,5003919,50.79123,5021,4760,blood,,2009,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115271,Escherichia coli 16843,16843,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31927828,562,,,,MLST.Escherichia_coli_1.127,,,,2022-12-07T00:00:00Z,,PRJNA906551,,CP113503,,,IonTorrent,64.0x,SPAdes v. 3.12,1,0,1,5167586,50.396645,5202,4841,urine,,2017-06-16,Russia,Russia: Saratov,,,,Chronic cystitis,,,,,,,,,,,,,,collected_by:RARI,,,,,,,Chronic cystitis,,,,,,,,,,,,,,99.9,1.2,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.115279,Escherichia coli GN03344,GN03344,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27361471,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:131,,,2022-12-05T00:00:00Z,,PRJNA823807,,"CP095544,CP095542,CP095543,CP095545,CP095546,CP095547,CP095548,CP095549",,,PacBio Sequel,562x,Flye v. 2.4.2,1,7,8,5208456,50.7738,5308,5028,blood,,2010,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.115444,Escherichia coli KE26,KE26,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32080938,562,,,UPEC,MLST.Escherichia_coli_1.4713,,,,1900-01-01T00:00:00Z,,PRJNA909323,,JAPVBU000000000,,,Illumina NextSeq; Oxford Nanopore MinION,414x,Unicycler v. 0.4.8,1,3,4,5044943,50.633656,5061,4814,urine,,2022-08-15,USA,"USA: Dallas, Texas",,female,65,Urinary Tract Infection,,,,,,,,,,,,,,collected_by:UTD/UTSW,,,,,,,Urinary Tract Infection,,,,,UPEC,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.115445,Escherichia coli KE21,KE21,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32080935,562,,,UPEC,MLST.Escherichia_coli_1.131,,,,1900-01-01T00:00:00Z,,PRJNA909323,,JAPVBX000000000,,,Illumina NextSeq; Oxford Nanopore MinION,288x,Unicycler v. 0.4.8,1,2,3,5144037,50.714508,5182,4933,urine,,2022-08-15,USA,"USA: Dallas, Texas",,female,78,Urinary Tract Infection,,,,,,,,,,,,,,collected_by:UTD/UTSW,,,,,,,Urinary Tract Infection,,,,,UPEC,,,,,,,,,100,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.121921,Escherichia coli EH031,EH031,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562882,562,O26:H11,,STEC,MLST.Escherichia_coli_2.481,,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027162,AP027163,AP027164",,,MinION,340x,Flye v. 2.9,1,2,3,5922257,50.602734,6164,5811,missing,,1989,Belgium,Belgium,,,,,,,,,,,,,,,,,,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.121922,Escherichia coli H19,H19,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562883,562,O26:H11,,STEC,"MLST.Escherichia_coli_2.481,MLST.Escherichia_coli_1.21",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027165,AP027166,AP027167,AP027168,AP027169",,,MinION,177x,Flye v. 2.9,1,4,5,5809914,50.668186,6007,5668,missing,,1967,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.121923,Escherichia coli 2313,2313,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562881,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027159,AP027160,AP027161",,,MinION,268x,Flye v. 2.9,1,2,3,5905973,50.694424,6171,5794,missing,,2004,Japan,Japan:Toyama,,,,,,,,,,,,,,,,,,collected_by:Toyama Institute of Health,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.121925,Escherichia coli EH2252,EH2252,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562885,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027176,AP027177,AP027178,AP027179,AP027180",,,MinION,70x,Flye v. 2.9,1,4,5,6113694,50.58153,6438,6050,missing,,2013,Belgium,Belgium,,,,diarrhea/bloody diarrhea,,,,,,,,,,,,,,,,,,,,,diarrhea/bloody diarrhea,,,,,STEC,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.121926,Escherichia coli 98E11,98E11,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562886,562,O26:H11,,STEC,"MLST.Escherichia_coli_2.481,MLST.Escherichia_coli_1.21",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027181,AP027182,AP027183,AP027184",,,MinION,95x,Flye v. 2.9,1,3,4,5965160,50.595543,6275,5893,missing,,1998,Japan,Japan:Fukuoka,,,,diarrhea/bloody diarrhea,,,,,,,,,,,,,,collected_by:Fukuoka Institute of Health and Environmental Sciences,,,,,,,diarrhea/bloody diarrhea,,,,,STEC,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.121927,Escherichia coli 02E060,02E060,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562890,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027197,AP027198,AP027199,AP027200,AP027201",,,MinION,235x,Flye v. 2.9,1,4,5,5882574,50.60113,6164,5795,missing,,2002,Japan,Japan:Fukuoka,,,,diarrhea,,,,,,,,,,,,,,collected_by:Fukuoka Institute of Health and Environmental Sciences,,,,,,,diarrhea,,,,,STEC,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.121928,Escherichia coli 10153,10153,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562889,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027191,AP027192,AP027193,AP027194,AP027195,AP027196",,,MinION,58x,Flye v. 2.9,1,5,6,6107920,50.6144,6456,6072,missing,,1999,Japan,Japan:Miyazaki,,,,diarrhea/bloody diarrhea,,,,,,,,,,,,,,collected_by:Miyazaki Prefectural Institute for Public Health and Environment,,,,,,,diarrhea/bloody diarrhea,,,,,STEC,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.121929,Escherichia coli PV0838,PV0838,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562888,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027188,AP027189,AP027190",,,MinION,244x,Flye v. 2.9,1,2,3,5847772,50.69736,6144,5786,missing,,2008,Japan,Japan:Osaka,,,,diarrhea,,,,,,,,,,,,,,collected_by:Osaka Institute of Public Health,,,,,,,diarrhea,,,,,STEC,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.121930,Escherichia coli NIID080884,NIID080884,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00562887,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2023-01-13T00:00:00Z,,PRJDB14896,,"AP027185,AP027186,AP027187",,,MinION,196x,Flye v. 2.9,1,2,3,5819666,50.65074,6077,5711,missing,,2008,Japan,Japan,,,,,,,,,,,,,,,,,,collected_by:National Institute of Infectious Diseases,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.121960,Escherichia coli STEC1575,STEC1575,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32736966,562,,,,MLST.Escherichia_coli_1.906,,,,2023-01-24T00:00:00Z,,PRJNA923774,,"CP116044,CP116045",,,PacBio,300.0x,SPAdes v. v3.9.0,1,1,2,5044589,50.636555,5049,4811,patient,,2021,China,China: Beijing,,,,diarrhear,,,,,,,,,,,,,,collected_by:China CDC,,,,,,,diarrhear,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases NHP,562.121962,Escherichia coli FAH,FAH,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32691645,562,,,,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2023-01-24T00:00:00Z,,PRJNA923252,,"CP116035,CP116036,CP116037",,,Oxford Nanopore PromethION,300.0x,unicycler v. 0.5.0,1,2,3,5227536,50.58184,5373,5064,feces from healthy subject,,,China,China: Guangzhou,,,,,,,,,,,,,,,,,,sample_type:Batceria culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,562.122068,Escherichia coli EC9952,EC9952,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30844958,562,,,,MLST.Escherichia_coli_2.202,,,,2023-02-02T00:00:00Z,,PRJNA880509,,"CP104595,CP104596,CP104597",,,Illumina HiSeq; PacBio,58.67x,Hifiasm v. 0.13-r308; Canu v. 2.2,1,2,3,5088602,50.671246,5099,4818,blood,,2022-06,China,China:Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.122162,Escherichia coli XH2172,XH2172,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32746371,562,,,,MLST.Escherichia_coli_1.410,,,,2023-02-06T00:00:00Z,,PRJNA924115,,"CP116900,CP116901",,,Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,1,2,4887613,50.611168,4908,4635,blood,,2020-05-17,China,China,,,,Bloodstream infection,,,,,,,,,,,,,,collected_by:zhangxiaofan,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.122163,Escherichia coli YL03,YL03,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26675664,562,,,,MLST.Escherichia_coli_1.405,,,,2023-02-06T00:00:00Z,,PRJNA816326,,"CP093548,CP093549,CP093550,CP093551,CP093552",,,PacBio,80.0x,FALCON v. 0.3.0,1,4,5,5349338,50.74099,5366,5065,missing,,2020-12-17,China,China: guangzhou,,,,bacterial sepsis,,,,,,,,,,,,,,collected_by:qian xu,,,,,,,bacterial sepsis,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,562.124141,Escherichia coli GN4554,GN4554,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30273450,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2023-03-14T00:00:00Z,,PRJNA861980,,"CP102694,CP102695,CP102696,CP102697,CP102698,CP102699,CP102700",,,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Unicycler v. v0.4.8,1,6,7,4956679,50.653492,5014,4738,urine,,2021-06,Jamaica,Jamaica,,,,urine tract infections,,,,,,,,,,,,,,collected_by:Camille-Ann Thoms-Rodriguez,,,,,,,urine tract infections,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.124994,Escherichia coli ST3,ST3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33902174,562,,,,MLST.Escherichia_coli_2.3,,,,2023-04-08T00:00:00Z,,PRJNA948410,,"CP121087,CP121089,CP121088",,,Illumina iSeq; Oxford Nanopore MinION,160.0x,Unicycler v. 0.5.0,1,2,3,5141453,50.732662,5114,4860,blood,,2022-12-06,Italy,Italy: Verona,,,,Meningitis,,,,,,,,,,,,,,collected_by:Azienda Ospedaliera Universitaria Integrata,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Blood and Circulatory System,Neurological Diseases-Meningitis HP,562.126118,Escherichia coli 5132,5132,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32977680,562,,,,"MLST.Escherichia_coli_1.1193,MLST.Escherichia_coli_2.53",genotype:ST1193,,,2023-04-24T00:00:00Z,,PRJNA924946,,"CP123231,CP123232,CP123233,CP123234,CP123235,CP123236",,,Oxford Nanopore GridION,106.0x,Flye v. 2.9.1-b1780,1,5,6,5180851,50.59024,5275,4959,blood,,2020-10-02,USA,USA: Houston,,,,bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.126119,Escherichia coli EC0430,EC0430,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34178803,562,,,,"MLST.Escherichia_coli_1.2179,MLST.Escherichia_coli_2.595",,,,2023-04-23T00:00:00Z,,PRJNA955656,,"CP123046,CP123047,CP123048,CP123049",,,Illumina NovaSeq; PacBio Sequel,41.32x,Hifiasm v. 0.13-r308; Canu v. 1.7; Pilon,1,3,4,5203912,50.789215,5241,4931,sputum,,2022-09,China,China: Zhuhai,,,,pneumonia,,,,,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,562.126120,Escherichia coli 4588,4588,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32977832,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.744",genotype:ST744,,,2023-04-24T00:00:00Z,,PRJNA924946,,"CP123237,CP123238,CP123239",,,Oxford Nanopore GridION,105.0x,Flye v. 2.9.1-b1780,1,2,3,4950007,50.641502,5057,4786,blood,,2018-12-21,USA,USA: Houston,,,,bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,bacteremia,,,,,,,,,,,,,,99.7,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.129227,Escherichia coli JNE141411,JNE141411,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566465,562,,,,MLST.Escherichia_coli_1.156,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027256,AP027257",,,Illumina MiSeq; PacBio RS II,162.6x,Unicycler v. 0.5.0,1,1,2,5235036,50.725132,5225,4917,feces,,2014,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129229,Escherichia coli JNE131328,JNE131328,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566111,562,,,,MLST.Escherichia_coli_1.2484,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027212,AP027213,AP027214,AP027215,AP027216",,,Illumina MiSeq; PacBio Sequel IIe,162.5x,Unicycler v. 0.5.0; Trycycler v. 0.5.3,1,4,5,5202722,50.722794,5202,4893,feces,,2013,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129471,Escherichia coli JNE170426,JNE170426,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566110,562,,,,,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027217,AP027218,AP027219,AP027220",,,Illumina MiSeq; PacBio Sequel IIe,63.3x,Unicycler v. 0.5.0; Trycycler v. 0.5.3,1,3,4,5281796,50.80518,5281,4936,feces,,2017,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129472,Escherichia coli JNE120393,JNE120393,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566463,562,,,,MLST.Escherichia_coli_1.223,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027246,AP027247,AP027248,AP027249,AP027250,AP027251,AP027252,AP027253",,,Illumina MiSeq; PacBio RS II,157.4x,Unicycler v. 0.5.0,1,7,8,5259148,50.788795,5314,4988,feces,,2012,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129473,Escherichia coli JNE151685,JNE151685,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566466,562,,,,,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027258,AP027259,AP027260,AP027261",,,Illumina MiSeq; PacBio RS II,108.6x,Unicycler v. 0.5.0,1,3,4,5209051,50.852142,5225,4905,feces,,2015,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129474,Escherichia coli JNE082640,JNE082640,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566112,562,,,,MLST.Escherichia_coli_1.679,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027206,AP027207,AP027208,AP027209,AP027210,AP027211",,,Illumina MiSeq; PacBio Sequel IIe,53.4x,Unicycler v. 0.5.0; Trycycler v. 0.5.3,1,5,6,5109215,50.747227,5078,4761,feces,,2008,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129475,Escherichia coli JNE120442,JNE120442,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00566464,562,,,,MLST.Escherichia_coli_1.657,,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027254,AP027255",,,Illumina MiSeq; PacBio RS II,158.4x,Unicycler v. 0.5.0,1,1,2,5127983,50.97006,5111,4850,feces,,2012,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.129476,Escherichia coli JNE181771,JNE181771,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00565531,562,,,,"MLST.Escherichia_coli_1.205,MLST.Escherichia_coli_2.537",,,,2023-05-30T00:00:00Z,,PRJDB14917,,"AP027156,AP027157,AP027158",,,Illumina MiSeq; PacBio Sequel IIe,120x,Unicycler v. 0.5.0; Trycycler v 0.5.3,1,2,3,5125506,50.762794,5065,4763,feces,,2018,Japan,Japan,,,,,,,,,,,,,,,,,,biomaterial_provider:National Institute of Infectious Diseases,missing,missing,missing,missing,Complete genome of LEE-negative Shiga toxin-producing Escherichia coli,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.131861,Escherichia coli strain_139,strain_139,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773961,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128448,,,Illumina,48x,SPAdes v. v3.15.5,1,0,1,5152092,50.78285,5334,5097,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.131862,Escherichia coli strain_67,strain_67,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773954,562,,,,MLST.Escherichia_coli_1.5687,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128443,,,Illumina,57x,SPAdes v. v3.15.5,1,0,1,4882485,50.833557,5072,4801,sputum,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,98.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,562.131863,Escherichia coli strain_88,strain_88,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773957,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128446,,,Illumina,54x,SPAdes v. v3.15.5,1,0,1,5341472,50.425472,5518,5233,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,98.8,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.131864,Escherichia coli strain_137,strain_137,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773960,562,,,,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128447,,,Illumina,46x,SPAdes v. v3.15.5,1,0,1,5055851,50.650116,5178,4930,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.131871,Escherichia coli strain_32,strain_32,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773951,562,,,,"MLST.Escherichia_coli_1.43,MLST.Escherichia_coli_2.165",,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128440,,,Illumina,33x,SPAdes v. v3.15.5,1,0,1,4776229,50.474796,4982,4748,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,99.7,0.7,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.131872,Escherichia coli strain_15,strain_15,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773950,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128439,,,Illumina,35x,SPAdes v. v3.15.5,1,0,1,5196605,50.47696,5393,5124,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,,,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.131922,Escherichia coli STEC1589,STEC1589,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269400,562,,,,"MLST.Escherichia_coli_2.202,MLST.Escherichia_coli_1.75",,,,2023-07-10T00:00:00Z,,PRJNA990487,,"CP129269,CP129270",,,PacBio Sequel,44.0x,SOAPdenovo v. v3.9.0,1,1,2,5222294,50.5709,5278,4958,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131926,Escherichia coli STEC1586,STEC1586,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269289,562,,,,"MLST.Escherichia_coli_1.75,MLST.Escherichia_coli_2.202",,,,2023-07-10T00:00:00Z,,PRJNA990487,,"CP129257,CP129258",,,PacBio Sequel,42.0x,SOAPdenovo v. v3.9.0,1,1,2,4782612,50.705807,4838,4551,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,90.8,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131927,Escherichia coli STEC1588,STEC1588,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269387,562,,,,"MLST.Escherichia_coli_1.2308,MLST.Escherichia_coli_2.294",,,,2023-07-10T00:00:00Z,,PRJNA990487,,"CP129263,CP129264,CP129265,CP129266,CP129267,CP129268",,,PacBio Sequel,43.0x,SOAPdenovo v. v3.9.0,1,5,6,5134479,50.68331,5184,4901,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131928,Escherichia coli STEC1585,STEC1585,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269257,562,,,,MLST.Escherichia_coli_2.357,,,,2023-07-10T00:00:00Z,,PRJNA990487,,"CP129252,CP129253,CP129254,CP129255,CP129256",,,PacBio Sequel,40.0x,SOAPdenovo v. v3.9.0,1,4,5,5477080,50.65714,5672,5287,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131929,Escherichia coli STEC1587,STEC1587,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269290,562,,,,"MLST.Escherichia_coli_1.971,MLST.Escherichia_coli_2.87",,,,2023-07-10T00:00:00Z,,PRJNA990487,,"CP129259,CP129260,CP129261,CP129262",,,PacBio Sequel,40.0x,SOAPdenovo v. v3.9.0,1,3,4,5143769,50.814568,5232,4954,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131930,Escherichia coli 1344_LBHALD,1344_LBHALD,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35984967,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.692",,,,2023-07-10T00:00:00Z,,PRJNA987639,,"CP129240,CP129241,CP129242,CP129243,CP129244",,,Illumina,70.0x,SPAdes v. 3.15.4,1,4,5,5044676,50.61887,5217,4984,urine,,2018-01-20,Senegal,Senegal: Dakar,,,,community-acquired urinary tract infection,,,,,,,,,,,,,,collected_by:Bacteriology laboratory of Aristide Le Dantec National University teaching hospital in Dakar Senegal,,,,,,,community-acquired urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.131940,Escherichia coli STEC434,STEC434,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269677,562,,,,"MLST.Escherichia_coli_2.363,MLST.Escherichia_coli_1.937",,,,2023-07-12T00:00:00Z,,PRJNA990487,,CP129383,,,PacBio Sequel,43.0x,SOAPdenovo v. v3.9.0,1,0,1,5011978,50.753494,4978,4727,,,2014,China,China: Guangdong,,,,,,,,,,,,,,,,,,sample_type:stool,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131945,Escherichia coli STEC435,STEC435,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269922,562,,,,MLST.Escherichia_coli_1.33,,,,2023-07-11T00:00:00Z,,PRJNA990487,,"CP129348,CP129349,CP129350,CP129351",,,PacBio Sequel,40.0x,SOAPdenovo v. v3.9.0,1,3,4,5083774,50.814514,5121,4838,,,2013,China,China: Qinghai,,,,,,,,,,,,,,,,,,sample_type:stool,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.131949,Escherichia coli STEC1590,STEC1590,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36269620,562,,,,"MLST.Escherichia_coli_2.202,MLST.Escherichia_coli_1.75",,,,2023-07-11T00:00:00Z,,PRJNA990487,,"CP129345,CP129346,CP129347",,,PacBio Sequel,42.0x,SOAPdenovo v. v3.9.0,1,2,3,5278067,50.589638,5361,5026,,,2021,China,China: Guangxi,,,,,,,,,,,,,,,,,,sample_type:anal swab,,,,,,,,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.132096,Escherichia coli MS20674,MS20674,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934299,562,,,,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",genotype:ST1193,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082062,CP082063,CP082064,CP082065,CP082066",,,Oxford Nanopore MiniION,171x,flye v. 2.5,1,4,5,5151870,50.62467,5174,4859,csf,,2019,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Adam Irwin,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132097,Escherichia coli MS20675,MS20675,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934300,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",genotype:ST69,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082056,CP082057,CP082058,CP082059,CP082060,CP082061",,,Oxford Nanopore MiniION,73x,flye v. 2.5,1,5,6,5430852,50.76942,5559,5224,csf,,2019,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Adam Irwin,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132102,Escherichia coli MS15236,MS15236,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934289,562,,,,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.22",genotype:ST127,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082094,CP082095,CP082096",,,Oxford Nanopore MiniION,58x,flye v. 2.5,1,2,3,5226528,50.549618,5242,4911,csf,,,Sweden,Sweden,,,,Meningitis,,,,,,,,,,,,,,collected_by:Annelie Brauner,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132103,Escherichia coli MS21324,MS21324,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934303,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",genotype:ST95,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082045,CP082046",,,Oxford Nanopore MiniION,121x,flye v. 2.5,1,1,2,5056674,50.621555,5064,4775,blood,,2020,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Adam Irwin,,,,,,,Meningitis,,,,,,,,,,,,,,100,0.1,Neurological Diseases,Meningitis,Blood and Circulatory System,Neurological Diseases-Meningitis HP,562.132104,Escherichia coli MS21199,MS21199,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934302,562,,,,MLST.Escherichia_coli_2.53,genotype:ST11637,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082047,CP082048,CP082049,CP082050,CP082051,CP082052",,,Oxford Nanopore MiniION,37x,flye v. 2.5,1,5,6,5073611,50.563118,5123,4808,csf,,2019,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Adam Irwin,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132105,Escherichia coli MS15052,MS15052,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934288,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",genotype:ST95,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082097,CP082098,CP082099",,,Oxford Nanopore MiniION,17x,flye v. 2.5,1,2,3,5328955,50.658806,5486,5166,csf,,,Sweden,Sweden,,,,Meningitis,,,,,,,,,,,,,,collected_by:Annelie Brauner,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132106,Escherichia coli MS20677,MS20677,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934301,562,,,,"MLST.Escherichia_coli_1.1193,MLST.Escherichia_coli_2.53",genotype:ST1193,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082053,CP082054,CP082055",,,Oxford Nanopore MiniION,29x,flye v. 2.5,1,2,3,5063065,50.66577,5094,4804,csf,,2019,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Adam Irwin,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132109,Escherichia coli MS20657,MS20657,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934295,562,,,,"MLST.Escherichia_coli_1.567,MLST.Escherichia_coli_2.82",genotype:ST567,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082077,CP082078,CP082079",,,Oxford Nanopore MiniION,180x,flye v. 2.5,1,2,3,4996041,50.59666,5028,4722,blood,,,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,99.9,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132110,Escherichia coli MS15046,MS15046,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934286,562,,,,"MLST.Escherichia_coli_2.4,MLST.Escherichia_coli_1.73",genotype:ST73,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082103,CP082104,CP082105,CP082106",,,Oxford Nanopore MiniION,126x,flye v. 2.5,1,3,4,5448521,50.439156,5519,5151,csf,,,Sweden,Sweden,,,,Meningitis,,,,,,,,,,,,,,collected_by:Annelie Brauner,,,,,,,Meningitis,,,,,,,,,,,,,,100,0.1,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132111,Escherichia coli MS15047,MS15047,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934287,562,,,,"MLST.Escherichia_coli_2.132,MLST.Escherichia_coli_1.48",genotype:ST48,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082100,CP082101,CP082102",,,Oxford Nanopore MiniION,118x,flye v. 2.5,1,2,3,4922876,50.936077,4937,4643,csf,,,Sweden,Sweden,,,,Meningitis,,,,,,,,,,,,,,collected_by:Annelie Brauner,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132112,Escherichia coli MS20645,MS20645,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934290,562,,,,"MLST.Escherichia_coli_2.6,MLST.Escherichia_coli_1.14",genotype:ST537,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082091,CP082092,CP082093",,,Oxford Nanopore MiniION,30x,flye v. 2.5,1,2,3,5280661,50.583534,5392,5024,blood,,1975,Finland,Finland,,,,Meningitis,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,Meningitis,,,,,,,,,,,,,,100,0.2,Neurological Diseases,Meningitis,Blood and Circulatory System,Neurological Diseases-Meningitis HP,562.132114,Escherichia coli MS20673,MS20673,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934298,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",genotype:ST95,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082067,CP082068,CP082069,CP082070,CP082071,CP082072",,,Oxford Nanopore MiniION,77x,flye v. 2.5,1,5,6,5173642,50.726105,5223,4914,csf,,2019,Australia,Australia,,,,Meningitis,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,Meningitis,,,,,,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.132115,Escherichia coli MS20658,MS20658,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934296,562,,,,"MLST.Escherichia_coli_2.36,MLST.Escherichia_coli_1.12",genotype:ST12,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082075,CP082076",,,Oxford Nanopore MiniION,55x,flye v. 2.5,1,1,2,5077633,50.53069,5037,4766,blood,,,Finland,Finland,,,,Meningitis,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,Meningitis,,,,,,,,,,,,,,98.8,0.1,Neurological Diseases,Meningitis,Blood and Circulatory System,Neurological Diseases-Meningitis HP,562.132116,Escherichia coli MS20654,MS20654,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934293,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",genotype:ST95,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082083,CP082084",,,Oxford Nanopore MiniION,359x,flye v. 2.5,1,1,2,5203382,50.631207,5257,4958,blood,,,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132117,Escherichia coli MS20649,MS20649,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934291,562,,,,"MLST.Escherichia_coli_1.23,MLST.Escherichia_coli_2.7",genotype:ST23,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082087,CP082088,CP082089,CP082090",,,Oxford Nanopore MiniION,80x,flye v. 2.5,1,3,4,5042319,50.710358,5043,4751,blood,,1976,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132118,Escherichia coli MS20655,MS20655,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934294,562,,,,"MLST.Escherichia_coli_1.390,MLST.Escherichia_coli_2.1",genotype:ST390,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082080,CP082081,CP082082",,,Oxford Nanopore MiniION,40x,flye v. 2.5,1,2,3,5108804,50.713787,5134,4847,blood,,,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,99.8,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132119,Escherichia coli MS20659,MS20659,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934297,562,,,,"MLST.Escherichia_coli_1.141,MLST.Escherichia_coli_2.129",genotype:ST141,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082073,CP082074",,,Oxford Nanopore MiniION,67x,flye v. 2.5,1,1,2,5218850,50.530422,5206,4927,blood,,,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,99.9,0.6,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132123,Escherichia coli MS20653,MS20653,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20934292,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",genotype:ST95,,,2023-07-21T00:00:00Z,,PRJNA757133,,"CP082085,CP082086",,,Oxford Nanopore MiniION,27x,flye v. 2.5,1,1,2,5323322,50.548756,5415,5094,blood,,,Finland,Finland,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,collected_by:Benita Westerlund-Wilkstrom,,,,,,,sepsis/meningeal involvement,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.132138,Escherichia coli 11899A_LBHALD,11899A_LBHALD,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35842356,562,,,,MLST.Escherichia_coli_1.167,,,,2023-07-24T00:00:00Z,,PRJNA986545,,"CP130447,CP130448,CP130449",,,Illumina,70.0x,SPAdes v. 3.15.4,1,2,3,5088163,50.718834,5306,5036,leg pus,,2018-01-20,Senegal,Senegal: Dakar,,,,Hospital-acquired infection after surgery,,,,,,,,,,,,,,collected_by:Bacteriology laboratory of Aristide Le Dantec National University teaching hospital in Dakar Senegal,,,,,,,Hospital-acquired infection after surgery,,,,,,,,,,,,,,100,0,Nosocomial Infections,Other Nosocomial Infections,Skin and Soft Tissue,Nosocomial Infections-Other Nosocomial Infections HP,562.132162,Escherichia coli SM107,SM107,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36664847,562,,,,"MLST.Escherichia_coli_2.31,MLST.Escherichia_coli_1.1011",,,,2023-07-30T00:00:00Z,,PRJNA997113,,"CP130667,CP130670,CP130671,CP130672,CP130673,CP130669,CP130668",,,Oxford Nanopore GridION; Illumina HiSeq,100.0x,Unicycler v. 0.5.0,1,6,7,5511563,50.48183,5600,5301,urine,,2022-10-26,China,China: Sanmen,,,,Infection,,,,,,,,,,,,,,collected_by:Danni Bao,,,,,,,Infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.13544,Escherichia coli strain MRSN352231,MRSN352231,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06029893,562,,,,MLST.Escherichia_coli_1.617,,,,2016-11-28T00:00:00Z,,PRJNA353939,GCF_001886535.1,"CP018103,CP018108,CP018107,CP018105,CP018106,CP018104","NZ_CP018103.1,NZ_CP018108.1,NZ_CP018107.1,NZ_CP018105.1,NZ_CP018106.1,NZ_CP018104.1",Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,300.0x,HGAP v. 2.0,1,5,6,5200916,50.75,5310,5057,clinical,,2016-07,Germany,Germany,,,,,,,,,,,,,,,,,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,collected_by:MRSN,,,,,,,Unknown,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13545,Escherichia coli strain MRSN346638,MRSN346638,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06029895,562,,,,MLST.Escherichia_coli_1.617,,,,2016-11-28T00:00:00Z,,PRJNA353939,GCF_001886555.1,"CP018115,CP018116,CP018120,CP018119,CP018118,CP018117","NZ_CP018115.1,NZ_CP018116.1,NZ_CP018120.1,NZ_CP018119.1,NZ_CP018118.1,NZ_CP018117.1",Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,300.0x,HGAP v. 2.0,1,5,6,5116498,50.76,5213,4964,clinical,,2016-07,USA,United States,,,,,,,,,,,,,,,,,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,collected_by:MRSN,,,,,,,Unknown,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13546,Escherichia coli strain MRSN346355,MRSN346355,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06029896,562,,,,MLST.Escherichia_coli_1.617,,,,2016-11-28T00:00:00Z,,PRJNA353939,GCF_001886575.1,"CP018121,CP018122,CP018126,CP018125,CP018124,CP018123","NZ_CP018121.1,NZ_CP018122.1,NZ_CP018126.1,NZ_CP018125.1,NZ_CP018124.1,NZ_CP018123.1",Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,300.0x,HGAP v. 2.0,1,5,6,5114354,50.76,5208,4957,clinical,,2016-07,USA,United States,,,,,,,,,,,,,,,,,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,collected_by:MRSN,,,,,,,Unknown,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13547,Escherichia coli strain MRSN346595,MRSN346595,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06029894,562,,,,MLST.Escherichia_coli_1.617,,,,2016-11-28T00:00:00Z,,PRJNA353939,GCF_001886755.1,"CP018109,CP018110,CP018114,CP018113,CP018112,CP018111","NZ_CP018109.1,NZ_CP018110.1,NZ_CP018114.1,NZ_CP018113.1,NZ_CP018112.1,NZ_CP018111.1",Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,300.0x,HGAP v. 2.0,1,5,6,5116627,50.76,5213,4963,clinical,,2016-07,USA,United States,,,,,,,,,,,,,,,,,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,collected_by:MRSN,,,,,,,Unknown,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13550,Escherichia coli strain FMU073332,FMU073332,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05945146,562,O6:H16,,ETEC,"MLST.Escherichia_coli_1.4,MLST.Escherichia_coli_2.215","genotype:st+, lt+, lngA+, cstH+, ecpA+, etpA+, etpB+, tibA-, leoA-, tia-, eatA-, cfAI, cfAIII-, cs1-.",,,2016-12-02T00:00:00Z,,PRJNA350704,GCF_001888075.1,"CP017844,CP017848,CP017845,CP017846,CP017847","NZ_CP017844.1,NZ_CP017848.1,NZ_CP017845.1,NZ_CP017846.1,NZ_CP017847.1",Centro de Ciencias Genomicas,Illumina HiSeq and PacBio RSII,290X,"HGAP_3 in SMRT analysis v. 2.3, Spades v.",1,4,5,5022828,50.52,5217,4936,faeces; feces,,1987,Mexico,"Mexico: Tlaltizpan, Morelos",,,730 days,ETEC infection,,host_description:child,,,,,,,,,,,description og genes involved in pathogenicity,"collected_by:Carlos Eslava Campos, Armando Navarro Ocana, Alejandro Cravioto",,,,,,,ETEC infection,,,child,,ETEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.13551,Escherichia coli strain 155,155,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05544764,562,O157:H7,,EHEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2016-12-07T00:00:00Z,,PRJNA336330,GCF_001890205.1,"CP018237,CP018238","NZ_CP018237.1,NZ_CP018238.1",United State Department of Agriculture,PacBio,103X,Celera 8.1 v. Mar-2014,1,1,2,5604428,50.5,6087,5955,human,,2012,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",collected_by:Publich Health England,,,,,,,missing,,,,,EHEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13552,Escherichia coli strain 272,272,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05544766,562,O157:H7,,EHEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2016-12-07T00:00:00Z,,PRJNA336330,GCF_001890225.1,"CP018239,CP018240","NZ_CP018239.1,NZ_CP018240.1",United State Department of Agriculture,PacBio,165X,Celera 8.1 v. Apr-2014,1,1,2,5568363,50.44,6024,5909,human,,2013,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",collected_by:Publich Health England,,,,,,,missing,,,,,EHEC,,,,,,,,,99.3,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13553,Escherichia coli strain 472,472,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05544767,562,O157:H7,,EHEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2016-12-07T00:00:00Z,,PRJNA336330,GCF_001890245.1,"CP018245,CP018246","NZ_CP018245.1,NZ_CP018246.1",United State Department of Agriculture,PacBio,207X,Celera 8.1 v. Jan-2015,1,1,2,5608872,50.46,6101,5975,human,,2012,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",collected_by:Publich Health England,,,,,,,missing,,,,,EHEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13554,Escherichia coli strain 350,350,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05544765,562,O157:H7,,EHEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2016-12-07T00:00:00Z,,PRJNA336330,GCF_001890265.1,"CP018243,CP018244","NZ_CP018243.1,NZ_CP018244.1",United State Department of Agriculture,PacBio,283X,Celera 8.1 v. Jan-2015,1,1,2,5504345,50.49,5897,5829,human,,2011,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",collected_by:Publich Health England,,,,,,,missing,,,,,EHEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13557,Escherichia coli strain 319,319,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05544768,562,O157:H7,,EHEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2016-12-07T00:00:00Z,,PRJNA336330,GCF_001890325.1,"CP018241,CP018242","NZ_CP018241.1,NZ_CP018242.1",United State Department of Agriculture,PacBio,132X,Celera 8.1 v. Mar-2014,1,1,2,5567385,50.49,5977,5890,human,,2012,United Kingdom,United Kingdom,,,,,,,,,,,,,,,,,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",collected_by:Publich Health England,,,,,,,missing,,,,,EHEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.13559,Escherichia coli strain MRSN346647,MRSN346647,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06067968,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.535",,,,2016-12-07T00:00:00Z,,PRJNA353939,GCF_001890365.1,"CP018206,CP018207,CP018208","NZ_CP018206.1,NZ_CP018207.1,NZ_CP018208.1",Walter Reed Army Institute of Research,PacBio; Illumina MiSeq,200.0x,HGAP v. 2.0,1,2,3,5158613,50.62,5312,5212,clinical,,2016-07,USA,United States,,,,,,,,,,,,,,,,,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,collected_by:MRSN,,,,,,,Unknown,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.14013,Escherichia coli strain 2016C-3936C1,2016C-3936C1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06159501,562,O157:H48,,,MLST.Escherichia_coli_1.2732,,,,2017-01-06T00:00:00Z,,PRJNA218110,GCF_001938625.1,"CP018770,CP018773,CP018771,CP018772,CP018774,CP018775",,CDC,PacBio,100.0x,PacBio Hierarchical Genome Assembly,1,5,6,5439080,50.46,5704,5664,,,,USA,USA: Conneticut,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,na,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.14016,Escherichia coli strain SLK172,SLK172,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05853574,562,,,,"MLST.Escherichia_coli_1.189,MLST.Escherichia_coli_2.809",,,,2017-01-05T00:00:00Z,,PRJNA344951,GCF_001936315.1,"CP017631,CP017632,CP017633","NZ_CP017631.1,NZ_CP017632.1,NZ_CP017633.1",China National Center For Food Safety and Risk Assessment,,,,1,2,3,5773662,50.43,6129,5746,faeces; feces,,2015-11,China,China: Beijing,,,,Diarrhea,,,,,,,,,,,,,An isolate came from a diarrheal patient,"collected_by:Lili Wang, Qian Chen",,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.4,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.15193,Escherichia coli strain Ecol_276,Ecol_276,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511184,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002011965.1,"CP018953,CP018952,CP018951,CP018950,CP018949","NZ_CP018953.1,NZ_CP018952.1,NZ_CP018951.1,NZ_CP018950.1,NZ_CP018949.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5126305,50.74,5416,5388,,,2010,USA,USA: Pittsburgh,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15194,Escherichia coli strain Ecol_224,Ecol_224,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511177,562,,,,"MLST.Escherichia_coli_1.101,MLST.Escherichia_coli_2.88",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002011945.1,"CP018948,CP018947,CP018946,CP018944,CP018943,CP018942,CP018941,CP018940,CP018945","NZ_CP018948.1,NZ_CP018947.1,NZ_CP018946.1,NZ_CP018944.1,NZ_CP018943.1,NZ_CP018942.1,NZ_CP018941.1,NZ_CP018940.1,NZ_CP018945.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,8,9,5223096,50.7,5561,5521,,,2010,Viet Nam,Viet Nam: Hanoi,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15195,Escherichia coli strain Ecol_316,Ecol_316,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511183,562,,,,"MLST.Escherichia_coli_1.393,MLST.Escherichia_coli_2.494",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002011985.1,"CP018957,CP018955,CP018954,CP018956","NZ_CP018957.1,NZ_CP018955.1,NZ_CP018954.1,NZ_CP018956.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,3,4,5471138,50.82,5699,5661,,,2011,USA,USA: Caguas,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15196,Escherichia coli strain Ecol_517,Ecol_517,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511179,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012005.1,"CP018965,CP018964,CP018963","NZ_CP018965.1,NZ_CP018964.1,NZ_CP018963.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,2,3,4968096,50.67,5230,5172,,,2011,Brazil,Brazil: Rio de Janeiro,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15197,Escherichia coli strain Ecol_542,Ecol_542,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511186,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012025.1,"CP018970,CP018969,CP018967,CP018966,CP018968","NZ_CP018970.1,NZ_CP018969.1,NZ_CP018967.1,NZ_CP018966.1,NZ_CP018968.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5395325,50.81,5770,5733,,,2011,Viet Nam,Viet Nam: Ho Chi Minh City,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15198,Escherichia coli strain Ecol_545,Ecol_545,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511169,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.535",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012045.1,"CP018976,CP018975,CP018973,CP018972,CP018971,CP018974","NZ_CP018976.1,NZ_CP018975.1,NZ_CP018973.1,NZ_CP018972.1,NZ_CP018971.1,NZ_CP018974.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,5,6,5276034,50.63,5495,5440,,,2011,Viet Nam,Viet Nam: Ho Chi Minh City,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15199,Escherichia coli strain Ecol_656,Ecol_656,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511161,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012065.1,"CP018979,CP018978,CP018977","NZ_CP018979.1,NZ_CP018978.1,NZ_CP018977.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,2,3,5405139,50.8,5758,5690,,,2012,USA,USA: Caguas,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15200,Escherichia coli strain Ecol_AZ146,Ecol_AZ146,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511152,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012085.1,"CP018991,CP018990,CP018988,CP018987,CP018986,CP018985,CP018984,CP018989","NZ_CP018991.1,NZ_CP018990.1,NZ_CP018988.1,NZ_CP018987.1,NZ_CP018986.1,NZ_CP018985.1,NZ_CP018984.1,NZ_CP018989.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,7,8,5727407,50.71,6232,6150,,,2012,Italy,Italy: Pisa,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15201,Escherichia coli strain Ecol_AZ147,Ecol_AZ147,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511182,562,,,,"MLST.Escherichia_coli_1.540,MLST.Escherichia_coli_2.716",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012105.1,"CP018995,CP018994,CP018993,CP018992","NZ_CP018995.1,NZ_CP018994.1,NZ_CP018993.1,NZ_CP018992.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,3,4,5090480,50.89,5370,5348,,,2012,Israel,Israel: Kfar Sava,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15202,Escherichia coli strain Ecol_AZ155,Ecol_AZ155,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511168,562,,,,"MLST.Escherichia_coli_1.44,MLST.Escherichia_coli_2.2",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012125.1,"CP019005,CP019002,CP019003,CP019004,CP019001","NZ_CP019005.1,NZ_CP019002.1,NZ_CP019003.1,NZ_CP019004.1,NZ_CP019001.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5090221,50.89,5389,5366,,,2013,China,China: Beijing,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15203,Escherichia coli strain Ecol_AZ159,Ecol_AZ159,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511159,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012145.1,"CP019008,CP019007,CP019006","NZ_CP019008.1,NZ_CP019007.1,NZ_CP019006.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,2,3,5101928,50.64,5280,5258,,,2013,Colombia,Colombia: Bogota,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15204,Escherichia coli strain Ecol_AZ162,Ecol_AZ162,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511185,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012165.1,"CP019015,CP019013,CP019014","NZ_CP019015.1,NZ_CP019013.1,NZ_CP019014.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,2,3,5351874,50.72,5640,5607,,,2013,USA,USA: Boston,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15205,Escherichia coli strain Ecol_422,Ecol_422,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511153,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012185.1,"CP018962,CP018961,CP018960,CP018958,CP018959","NZ_CP018962.1,NZ_CP018961.1,NZ_CP018960.1,NZ_CP018958.1,NZ_CP018959.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5215799,50.59,5509,5488,,,2011,Ecuador,Ecuador: Quito,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15206,Escherichia coli strain Ecol_867,Ecol_867,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511148,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012205.1,"CP018983,CP018982,CP018980,CP018981","NZ_CP018983.1,NZ_CP018982.1,NZ_CP018980.1,NZ_CP018981.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,3,4,5065803,50.83,5282,5263,,,2013,Canada,Canada: Toronto,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15208,Escherichia coli strain Ecol_AZ153,Ecol_AZ153,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511160,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012245.1,"CP019000,CP018998,CP018997,CP018996,CP018999","NZ_CP019000.1,NZ_CP018998.1,NZ_CP018997.1,NZ_CP018996.1,NZ_CP018999.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5252746,50.9,5579,5544,,,2013,China,China: Beijing,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15209,Escherichia coli strain Ecol_AZ161,Ecol_AZ161,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511166,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012265.1,"CP019012,CP019011,CP019009,CP019010","NZ_CP019012.1,NZ_CP019011.1,NZ_CP019009.1,NZ_CP019010.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,3,4,5173038,50.88,5424,5403,,,2013,USA,USA: Lafayette,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.15210,Escherichia coli strain Ecol_244,Ecol_244,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05511157,562,,,,MLST.Escherichia_coli_1.131,,,,2017-03-03T00:00:00Z,,PRJNA316786,GCF_002012305.1,"CP019020,CP019019,CP019018,CP019016,CP019017","NZ_CP019020.1,NZ_CP019019.1,NZ_CP019018.1,NZ_CP019016.1,NZ_CP019017.1",University of Oxford,PacBio,XX,HGAP v. unspecified,1,4,5,5383061,50.43,5701,5592,,,2010,Argentina,Argentina: Buenos Aires,,,,,,,,,,,,,,,,,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.16465,Escherichia coli strain Z1002,Z1002,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06924979,562,,,,MLST.Escherichia_coli_1.405,,,,2017-05-16T00:00:00Z,27506685,PRJNA386069,GCA_002142675.1,"CP021202,CP021203,CP021204,CP021205,CP021206",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,204.0x,SmrtPipe v. 2.3.0,1,4,5,5628524,50.54,5934,5805,blood,isolated from a patient with bloodstream infection,2014-09-06,China,China:Jining,,,,bloodstream infection,,,,,,,,,,,,,"This is a genome of Escherichia coli strain Z1002, isolated from a patient with bloodstream infection. This strain is capable of coproducing MCR-1 and NDM-1.","collected_by:Affiliated Hospital of Jining Medical University, China",,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.7,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.16466,Escherichia coli strain 5CRE51,5CRE51,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06828737,562,,,,"MLST.Escherichia_coli_1.617,MLST.Escherichia_coli_2.741",,,,2017-05-16T00:00:00Z,,PRJNA384104,GCA_002142695.1,"CP021175,CP021176,CP021177",,"Centers for Disease Control, Tawian",PacBio,100x,Celera Assembler v. HGAP3,1,2,3,5256426,50.62,5520,5370,urine,,2016-01,Taiwan,Taiwan: Tainan,,,,Urinary tract infection,,,Susceptible;Resistant;Not defined,AMR Panel,,,,,,,,,Investigation of colistin resistance gene mcr-1 in clinical isolate,"collected_by:Centers for Disease Control, Taiwan",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.16467,Escherichia coli strain strain Z247,strain Z247,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06925129,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.9",,,,2017-05-16T00:00:00Z,27506685,PRJNA386074,GCA_002142715.1,"CP021207,CP021208,CP021209,CP021210",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",PacBio,165.0x,SmrtPipe v. 2.3.0,1,3,4,5400073,50.4,5662,5511,blood,isolated from a patient with bloodstream infection,2015-09-11,China,China:Hefei,,,,bloodstream infection,,,,,,,,,,,,,"This is a genome of Escherichia coli strain Z2474, isolated from a patient with bloodstream infection. This strain is capable of coproducing MCR-1 and NDM-1.","collected_by:Anhui Provincial Hospital, China",,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.4,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.16499,Escherichia coli strain WI1 isolate,WI1 isolate,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA19195168,562,,,,"MLST.Escherichia_coli_1.1288,MLST.Escherichia_coli_2.2",,,,2017-04-20T00:00:00Z,,PRJEB18462,GCA_900174625.1,"LT838196,LT838197,LT838198,LT838199",,CHU Clermont-ferrand,,,,1,3,4,5008891,50.79,5019,4862,clinical isolate,,2016,,,,,,,,host_health_state:diseased,,,,,,,,,,,The spread of mcr-1-encoding plasmids into carbapenem-resistant Enterobacteriaceae raises concern about the emergence of untreatable bacteria. We report the acquisition of mcr-1 in a carbapenem resistant E. coli after a 3-week course of colistin in a patient repatriated to France from Portugal.,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.17359,Escherichia coli strain 81009,81009,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06808253,562,O25b:H4,,ExPEC,MLST.Escherichia_coli_1.131,,,,2017-05-24T00:00:00Z,,PRJNA383781,GCA_002157245.1,"CP021179,CP021180",,Arsanis Biosciences GmbH,PacBio,275.0x,Celera Assembler v. HGAP4,1,1,2,5147804,50.8,5116,4822,urine,,2009-10-25,United Arab Emirates,"United Arab Emirates: Tawam Hospital, Al Ain",,male,76,Bacteriuria,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Finished quality genome assembly of Escherichia coli 81009, an ST131-O25b:H4 prototype with multi-drug resistance phenotype",collected_by:Sylvia El Kurdi,,,,,,,Bacteriuria,,,,,ExPEC,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,562.17710,Escherichia coli strain EC974,EC974,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07192703,562,,,,"MLST.Escherichia_coli_1.219,MLST.Escherichia_coli_2.867",,,,2017-06-15T00:00:00Z,,PRJNA389338,GCA_002196475.1,"CP021840,CP021841,CP021842,CP021843",,National Yang Ming University,PacBio,143.0x,HGAP version 3.0 v. 3.0,1,3,4,5457692,50.53,5577,5480,urine; urinary tract infection,,2007-08-24,Taiwan,Taiwan,,,,Urinary Tract Infection,,,,,,,,,,,,,EC974 and EC1515 were isolated from a patient with recurrent urinary tract infection,collected_by:National Cheng Kung University Hospital,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.17711,Escherichia coli strain EC1515,EC1515,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07192704,562,,,,"MLST.Escherichia_coli_1.219,MLST.Escherichia_coli_2.867",,,,2017-06-15T00:00:00Z,,PRJNA389338,GCA_002196495.1,"CP021844,CP021845,CP021846,CP021847",,National Yang Ming University,PacBio,193.0x,HGAP v. 3.0,1,3,4,5468903,50.55,5590,5492,urine; urinary tract infection,,2007-12-10,Taiwan,Taiwan,,,,Urinary Tract Infection,,,,,,,,,,,,,EC974 and EC1515 were isolated from a patient with recurrent urinary tract infection,collected_by:National Cheng Kung University Hospital,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.17735,Escherichia coli strain FORC_043,FORC_043,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05520965,562,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2017-07-05T00:00:00Z,,PRJNA338095,GCA_002214745.2,CP016828,,Seoul National University,PacBio,124.49x,PacBio SMRT Analysis v. 2.3.0,1,,1,5244443,50.75,5334,5328,human stool,isolated from stool of foodborne poisoning patient in South Korea,2008-06-03,South Korea,South Korea: Gyeonggi-do,,,,Not reported,,,,,,,,,,,,,Enterohaemorrhagic Escherichia coli is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,collected_by:Korea Center for Disease Control and Prevention,,,,,,,Not reported,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.19158,Escherichia coli strain PA45B,PA45B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06920354,562,O2:K1:H7,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2017-09-05T00:00:00Z,,PRJNA385892,GCA_002285755.1,"CP021288,CP021289",,University of Queensland,PacBio,120.0x,HGAP v. 2.0,1,1,2,5221926,50.52,5243,4883,,,2010,Australia,Australia: Brisbane,,,,,,,,,,,,,,,,,"Uropathogenic Escherichia coli (UPEC) are responsible for the majority of urinary tract infections (UTIs). UPEC strains possess an array of virulence-associated factors that aid in their colonization, survival and persistence in the urinary tract. One such factor is the polysaccharide K capsule, which provides protection against host innate immune factors. Among the different K capsule types, the K1 serotype is strongly associated with UPEC strains that cause UTI, bloodstream infections and meningitis. In this study, we employed a combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon directed insertion-site sequencing (TraDIS) to identify genes associated with K1 capsule production in the clinical urosepsis isolate PA45B.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.19192,Escherichia coli strain ETEC-2265,ETEC-2265,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07503734,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2017-09-14T00:00:00Z,,PRJNA398221,GCA_002302315.1,"CP023346,CP023347,CP023348",,Karolinska Institutet,PacBio,596x,HGAP3 v. 3,1,2,3,5319464,50.64,5631,5512,diarrheal stool,,2006-03-22,Bangladesh,Bangladesh: Dhaka,,,,Secretory diarrhea,,,,,,,,,,,,,"Genomic comparison of Enterotoxigenic E. coli collected from diarrheal stool in Dhaka, Bangladesh 2006.",collected_by:Asa Sjoling,,,,,,,Secretory diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.19193,Escherichia coli strain ETEC-2264,ETEC-2264,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07503733,562,,,,MLST.Escherichia_coli_1.5305,,,,2017-09-14T00:00:00Z,,PRJNA398221,GCA_002302335.1,"CP023349,CP023350,CP023351,CP023352",,Karolinska Institutet,PacBio,894x,HGAP3 v. 3,1,3,4,5207995,50.69,5464,5356,diarrheal stool,,2006-03-21,Bangladesh,Bangladesh: Dhaka,,,,Secretory diarrhea,,,,,,,,,,,,,"Genomic comparison of Enterotoxigenic E. coli collected from diarrheal stool in Dhaka, Bangladesh 2006.",collected_by:Asa Sjoling,,,,,,,Secretory diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.20517,Escherichia coli strain FDAARGOS_401,FDAARGOS_401,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07312445,562,O104:H4,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,FDA:FDAARGOS_401,,2017-09-28T00:00:00Z,,PRJNA231221,GCA_002393465.1,"CP023531,CP023530",,US Food and Drug Administration,PacBio; Illumina,15.54x,"SMRT v. 2.3.0, HGAP v. 3",1,1,2,5387375,50.67,5705,5574,stool,,2009,Georgia,Georgia,,,,Bloody diarrhea,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < CDC,,,,,,,Bloody diarrhea,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.22326,Escherichia coli strain UFU_EC98,UFU_EC98,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07746131,562,,,,"MLST.Escherichia_coli_1.156,MLST.Escherichia_coli_2.19",,,,2017-10-30T00:00:00Z,,PRJNA413419,GCA_002736085.1,"CP024092,CP024093,CP024094,CP024095",,Londrina State University,Illumina HiSeq,134.0x,CLC Genomics Workbench v. v10,1,3,4,5017436,50.59,5123,5048,urine,isolated from human urine in 2014,2014-07-29,Brazil,Brazil: Minas Gerais,,,,Urinary tract infection,,,,,,,,,,,,,Escherichia coli EC98 was isolated from human urine in 2014. The antibiotic resistance is a main characteristic of this strain.,collected_by:Federal University of Uberlandia,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.22331,Escherichia coli strain ATCC 43886,ATCC 43886,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916957,562,,,,"MLST.Escherichia_coli_1.1312,MLST.Escherichia_coli_2.155",,ATCC: 43886,,2017-11-02T00:00:00Z,,PRJNA218110,GCA_002741295.1,"CP024256,CP024254,CP024255",,CDC,PacBio,148.0x,HGAP v. 3,1,2,3,5117901,50.73,5213,,"feces, human",,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.22333,Escherichia coli strain ATCC 43896,ATCC 43896,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01917241,562,,,,MLST.Escherichia_coli_1.7256,,ATCC: 43896,,2017-11-02T00:00:00Z,,PRJNA218110,GCA_002741355.1,"CP024278,CP024279,CP024280,CP024281",,CDC,PacBio,107.0x,HGAP v. 3,1,3,4,5254447,50.7,5246,,infant diarrheic stool,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.22350,Escherichia coli strain BH100,BH100,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07210972,562,,,,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.33",,,,2017-11-13T00:00:00Z,,PRJNA389912,GCA_002763515.1,"CP024650,CP024651,CP024652",,UFMG,IonTorrent,145.98x,Newbler v. 2.9,1,2,3,5389362,50.45,5600,5466,urine,"isolated from a patient with urinary tract infection in Belo Horizonte, Brazil",1974,Brazil,Brazil: Belo Horizonte,,female,,Urinary tract infection,,,,,,,,,,,,,"Escherichia coli BH100 was isolated from a patient with urinary tract infection in Belo Horizonte, Brazil.",collected_by:Edmar Chartone Souza,,,,,,,Urinary tract infection,,,,,,,,,,,,,,97.4,4.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.28183,Escherichia coli strain BH100L,BH100L,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08118424,562,,,UPEC,MLST.Escherichia_coli_1.127,,,,2018-01-17T00:00:00Z,,PRJNA389912,GCA_002887715.1,CP025716,,UFMG,Illumina HiSeq,888.0x,SPAdes v. 2.9,1,,1,5033214,50.53016,5014,4824,urine,"isolated from a patient with urinary tract infection in Belo Horizonte, Brazil",1974,Brazil,Brazil: Belo Horizonte,,female,,Urinary tract infection,,,,,,,,,,,,,"Escherichia coli BH100 was isolated from a patient with urinary tract infection in Belo Horizonte, Brazil.",collected_by:Edmar Chartone Souza,,,,,,,Urinary tract infection,,,,,UPEC,,,,,,,,,96.7,1.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.28203,Escherichia coli strain BH100N,BH100N,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08272629,562,,,UPEC,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.33",,,,2018-01-26T00:00:00Z,,PRJNA389912,GCA_002900305.1,CP025703,,UFMG,Illumina HiSeq,368.0x,SPAdes v. 2.9,1,,1,5116034,50.436626,5129,4980,urine,"isolated from a patient with urinary tract infection in Belo Horizonte, Brazil",1974,Brazil,Brazil: Belo Horizonte,,female,,Urinary tract infection,,,,,,,,,,,,,"Escherichia coli BH100 was isolated from a patient with urinary tract infection in Belo Horizonte, Brazil.",collected_by:Edmar Chartone Souza,,,,,,,Urinary tract infection,,,,,UPEC,,,,,,,,,97.8,2.6,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.28386,Escherichia coli strain FDAARGOS_144,FDAARGOS_144,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03996288,562,,,,"MLST.Escherichia_coli_1.538,MLST.Escherichia_coli_2.221",,FDA:FDAARGOS_144,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002944935.1,"CP014111,CP014110,CP014112,CP014109",,US Food and Drug Administration,PacBio; Illumina,19.454x,HGAP3 v. Oct 2014,1,3,4,5022152,50.671803,5164,5098,urine,,2014-03-21,USA,USA:DC,,female,21Y,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.28391,Escherichia coli strain FHI_NMBU_03,FHI_NMBU_03,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06250205,562,O81:H6,,ExPEC/IPEC,"MLST.Escherichia_coli_1.28,MLST.Escherichia_coli_2.300",,,,2018-02-06T00:00:00Z,,PRJNA362852,GCA_002951855.1,"CP019455,CP019456",,Norwegian University of Life Sciences,Oxford Nanopore MinION; Illumina MiSeq,21.6x,CANU v. DEC-2016,1,1,2,4844877,50.628242,4957,4918,fecal sample,,2012-09,Norway,Norway: south east,,,,Diarrhea,,host_disease_outcome:recovery,,,,,,,,,,,Sequence characterization of hybrid IPEC/ExPEC isolates of Escherichia coli,collected_by:Norwegian Institute of Public Health,,,,,,,Diarrhea,,recovery,,,ExPEC/IPEC,,,,,,,,,99.3,0.4,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.28405,Escherichia coli strain HS13-1,HS13-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08409128,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2018-02-04T00:00:00Z,,PRJNA431867,GCA_002953435.1,"CP026491,CP026493,CP026494,CP026492",,The Hong Kong Polytechnic University,MinION; Illumina NextSeq 500,60.0x,Canu v. 1.3,1,3,4,5554216,50.42204,5897,5706,faecal sample,,2017,China,China:Shenzhen,,,,diarrhea,,,,,,,,,,,,,Rapid resolution of complete sequences of chromosome and plasmids for MDR bacteria using the MinION sequencing platform,collected_by:Miaomiao Xie,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,562.28692,Escherichia coli strain 2015C-3163,2015C-3163,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579553,562,O103:H2,,STEC,MLST.Escherichia_coli_1.17,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017375.1,"CP027219,CP027220",,CDC,PacBio,73.109x,HGAP v. 3,1,1,2,5594293,50.68857,5784,,stool,,2014-06,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28693,Escherichia coli strain 2015C-3101,2015C-3101,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579554,562,O111:H8,,STEC,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017455.1,"CP027221,CP027222,CP027223",,CDC,PacBio,70.272x,HGAP v. 3,1,2,3,5434211,50.56147,5643,,stool,,2014-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28695,Escherichia coli strain 2014C-4135,2014C-4135,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579556,562,O113:H21,,STEC,MLST.Escherichia_coli_2.366,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017615.1,"CP027310,CP027311",,CDC,PacBio,110.963x,HGAP v. 3,1,1,2,5082486,50.76199,5057,,stool,,2014-05,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28697,Escherichia coli strain 2013C-3033,2013C-3033,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579559,562,O146:H21,,STEC,MLST.Escherichia_coli_1.442,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017765.1,"CP027323,CP027324",,CDC,PacBio,230.753x,HGAP v. 3,1,1,2,5553868,50.78079,5650,,stool,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28698,Escherichia coli strain 2013C-4830,2013C-4830,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579560,562,O165:H25,,STEC,"MLST.Escherichia_coli_1.119,MLST.Escherichia_coli_2.341",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017805.1,"CP027325,CP027326,CP027327",,CDC,PacBio,122.932x,HGAP v. 3,1,2,3,5303516,50.608105,5639,,missing,,2013-10,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.28699,Escherichia coli strain 2014C-3741,2014C-3741,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579561,562,O174:H8,,STEC,"MLST.Escherichia_coli_1.13,MLST.Escherichia_coli_2.420",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017885.1,"CP027328,CP027329,CP027330",,CDC,PacBio,197.393x,Canu v. 1.6,1,2,3,5626021,50.67876,5754,,missing,,2013-10,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.28700,Escherichia coli strain 2014C-3051,2014C-3051,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579564,562,O71:H11,,STEC,MLST.Escherichia_coli_1.21,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017915.1,"CP027338,CP027339",,CDC,PacBio,92.732x,HGAP v. 3,1,1,2,5690119,50.64274,5975,,stool,,2013-03,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28706,Escherichia coli strain 2013C-3252,2013C-3252,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN02991246,562,O69:H11,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018055.1,"CP027442,CP027443,CP027444",,CDC,PacBio,81.78x,HGAP v. 3,1,2,3,5823288,50.628166,6109,,stool,,2012-07,USA,United States,,,20-29,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,Missing,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28708,Escherichia coli strain 2013C-3492,2013C-3492,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579580,562,O172:H25,,STEC,"MLST.Escherichia_coli_1.660,MLST.Escherichia_coli_2.341",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018075.1,"CP027445,CP027446",,CDC,PacBio,93.11x,HGAP v. 3,1,1,2,5270374,50.618874,5603,,stool,,2013-03,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.6,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28716,Escherichia coli strain 2012C-4502,2012C-4502,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579579,562,O185:H28,,STEC,MLST.Escherichia_coli_1.658,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018255.1,"CP027440,CP027441",,CDC,PacBio,127.87x,HGAP v. 3,1,1,2,5066380,50.918762,5022,,stool,,2012-09,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28721,Escherichia coli strain 00-3076,00-3076,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579602,562,O113:H21,,STEC,MLST.Escherichia_coli_1.2484,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018355.1,"CP027584,CP027585",,CDC,PacBio,186.121x,HGAP v. 3,1,1,2,5158555,50.772495,5135,,urine,,2000,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.28723,Escherichia coli strain 2013C-3304,2013C-3304,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579606,562,O71:H8,,STEC,"MLST.Escherichia_coli_1.2836,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018415.1,"CP027593,CP027594,CP027595,CP027596",,CDC,PacBio,112.231x,HGAP v. 3,1,3,4,5448869,50.678253,5636,,stool,,2013-01,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28729,Escherichia coli strain 2013C-4225,2013C-4225,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579596,562,O103:H11,,STEC,MLST.Escherichia_coli_1.723,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018555.1,"CP027577,CP027578",,CDC,PacBio,76.725x,HGAP v. 3,1,1,2,5734160,50.678078,5979,,stool,,2013-04,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28731,Escherichia coli strain 2012EL-2448,2012EL-2448,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579603,562,O91:H14,,STEC,,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018615.1,CP027586,,CDC,PacBio,169.219x,HGAP v. 3,1,,1,5272286,50.84161,5394,,stool,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28736,Escherichia coli strain 2015C-3107,2015C-3107,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579558,562,O121:H19,,STEC,MLST.Escherichia_coli_1.655,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018695.1,"CP027317,CP027318",,CDC,PacBio,120.949x,HGAP v. 3,1,1,2,5470214,50.628567,5651,,stool,,2014-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.28745,Escherichia coli strain 2014C-3057,2014C-3057,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579576,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018895.1,"CP027387,CP027386",,CDC,PacBio,81.261x,HGAP v. 3,1,1,2,5700435,50.611294,5965,,stool,,2013-05,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29036,Escherichia coli strain APEC 01,APEC 01,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196152,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028815.1,CP028310,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4609982,50.83303,4500,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.29037,Escherichia coli strain CFT073,CFT073,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196153,562,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028795.1,CP028309,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4721099,50.760834,4615,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.29038,Escherichia coli strain E24377A,E24377A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196154,562,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028775.1,CP028308,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4721864,50.736443,4636,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.29088,Escherichia coli strain MS7163,MS7163,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08469740,562,O45:K1:H7,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2018-03-27T00:00:00Z,,PRJNA427051,GCA_003020885.1,"CP026853,CP026854,CP026855",,University of Queensland,PacBio,100.0x,HGAP v. 2.0,1,2,3,5292507,50.67965,5360,5031,urine,,,Slovakia,Slovakia,,,,,,,,,,,,,,,,,"Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection. Curli are extracellular amyloid fibres that enhance UPEC virulence by their capacity to mediate adhesion and biofilm formation. In this study, we examined the function and regulation of curli in the UPEC pyelonephritis strain MS7163 that expressed these fibres at human physiological temperature. We also performed a large genetic screen and identified multiple genes involved in curli production, including several genes that were novel or poorly characterized with respect to curli synthesis.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.29089,Escherichia coli strain 2015C-3125,2015C-3125,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579601,562,O145:H28,,STEC,MLST.Escherichia_coli_1.32,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019235.1,"CP027763,CP027764,CP027765",,CDC,PacBio,83.737x,HGAP v. 3,1,2,3,5604464,50.675606,5907,,stool,,2014-09,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29090,Escherichia coli strain 2013C-3342,2013C-3342,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579610,562,O117:H8,,STEC,"MLST.Escherichia_coli_1.2836,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019215.1,"CP027766,CP027767",,CDC,PacBio,119.094x,HGAP v. 3,1,1,2,5555996,50.638515,5765,,stool,,2013-02,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29092,Escherichia coli strain 2013C-4187,2013C-4187,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579590,562,O71:H11,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019175.1,"CP027546,CP027547",,CDC,PacBio,69.884x,HGAP v. 3,1,1,2,5605298,50.652134,5802,,stool,,2013-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29093,Escherichia coli strain 2013C-3264,2013C-3264,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN02991245,562,E. coli O103:H25,,,"MLST.Escherichia_coli_1.343,MLST.Escherichia_coli_2.591",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019155.1,"CP027544,CP027545",,CDC,PacBio,79.656x,HGAP v. 3,1,1,2,5587496,50.58561,5936,,stool,,2012-08,USA,United States,,,60-69,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,Missing,,,,,,,,,,,,,,100,2.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29094,Escherichia coli strain 2013C-4248,2013C-4248,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579589,562,O186:H2,,STEC,"MLST.Escherichia_coli_1.1967,MLST.Escherichia_coli_2.135",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019135.1,"CP027464,CP027465,CP027466,CP027467,CP027468,CP027469,CP027470,CP027471",,CDC,PacBio,157.835x,HGAP v. 3,1,7,8,5914235,50.548683,6278,,stool,,2013-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29098,Escherichia coli strain 2014C-4423,2014C-4423,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579584,562,O121:H19,,STEC,MLST.Escherichia_coli_1.655,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019055.1,"CP027454,CP027455,CP027456",,CDC,PacBio,69.53x,HGAP v. 3,1,2,3,5491859,50.596565,5707,,stool,,2014-08,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29099,Escherichia coli strain 2014C-3075,2014C-3075,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579581,562,O36:H42,,STEC,MLST.Escherichia_coli_1.967,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003019035.1,"CP027447,CP027448",,CDC,PacBio,157.52x,HGAP v. 3,1,1,2,5339468,50.58221,5253,,stool,,2013-06,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29104,Escherichia coli strain 2011C-4251,2011C-4251,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579577,562,O45:H2,,STEC,MLST.Escherichia_coli_2.135,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018915.1,"CP027388,CP027389",,CDC,PacBio,100.369x,HGAP v. 3,1,1,2,5508088,50.682816,5634,,missing,,2011-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.29105,Escherichia coli strain 05-3629,05-3629,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579574,562,O8:H16,,STEC,MLST.Escherichia_coli_1.2602,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018855.1,"CP027373,CP027374,CP027375",,CDC,PacBio,169.936x,HGAP v. 3,1,2,3,5114662,50.71428,5062,,stool,,2005-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29107,Escherichia coli strain 2013C-4991,2013C-4991,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579568,562,O80:H2,,STEC,"MLST.Escherichia_coli_1.301,MLST.Escherichia_coli_2.917",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018815.1,"CP027355,CP027356,CP027357,CP027358",,CDC,PacBio,96.531x,HGAP v. 3,1,3,4,5680429,50.515232,5926,,stool,,2013-11,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,99.6,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29110,Escherichia coli strain 2014C-4587,2014C-4587,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579566,562,OUND:H19,,STEC,"MLST.Escherichia_coli_1.205,MLST.Escherichia_coli_2.537",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018755.1,"CP027342,CP027343",,CDC,PacBio,89.272x,HGAP v. 3,1,1,2,5171573,50.77024,5139,,stool,,2014-10,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29111,Escherichia coli strain 2014C-3716,2014C-3716,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579562,562,O26:H11,,STEC,"MLST.Escherichia_coli_1.29,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018735.1,"CP027335,CP027336,CP027337",,CDC,PacBio,134.69x,HGAP v. 3,1,2,3,5775245,50.67994,6097,,stool,,2014-04,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29112,Escherichia coli strain 2013C-3277,2013C-3277,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN02991240,562,E. coli O26:H11,,,"MLST.Escherichia_coli_1.29,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018715.1,"CP027331,CP027332,CP027333,CP027334",,CDC,PacBio,44.034x,HGAP v. 3,1,3,4,5687465,50.638203,6018,,stool,,2012-10,USA,United States,,,0-4,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,Missing,,,,,,,,,,,,,,100,2.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29113,Escherichia coli strain 2014C-3550,2014C-3550,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579557,562,O118:H16,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018675.1,"CP027313,CP027314,CP027315,CP027316",,CDC,PacBio,104.403x,HGAP v. 3,1,3,4,5877677,50.672604,6183,,stool,,2014-04,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29114,Escherichia coli strain 2013C-3181,2013C-3181,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN02991250,562,E. coli O113:H21,,,MLST.Escherichia_coli_1.3695,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018655.1,CP027312,,CDC,PacBio,110.444x,HGAP v. 3,1,,1,5167951,50.78357,5138,,stool,,2013-01,USA,United States,,,80-89,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,Missing,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29117,Escherichia coli strain 2013C-4538,2013C-4538,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579598,562,O118:H16,,STEC,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018575.1,"CP027582,CP027583",,CDC,PacBio,94.362x,HGAP v. 3,1,1,2,5768767,50.619137,6011,,stool,,2013-08,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29120,Escherichia coli strain 2015C-4498,2015C-4498,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579594,562,O117:H8,,STEC,MLST.Escherichia_coli_1.2836,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018495.1,"CP027552,CP027553",,CDC,PacBio,118.255x,HGAP v. 3,1,1,2,5501497,50.611423,5748,,rectal swab,,2015-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29121,Escherichia coli strain 2015C-4136CT1,2015C-4136CT1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579593,562,O145:H34,,STEC,"MLST.Escherichia_coli_1.722,MLST.Escherichia_coli_2.788",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018475.1,"CP027550,CP027551",,CDC,PacBio,78.081x,HGAP v. 3,1,1,2,4999728,50.590492,5098,,stool,,2015-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29122,Escherichia coli strain 97-3250,97-3250,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08638904,562,O26:H11,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018455.1,"CP027599,CP027600,CP027601",,CDC,PacBio,113.492x,HGAP v. 3,1,2,3,6156163,50.584072,6577,,stool,,1997-08,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29124,Escherichia coli strain 2014C-3011,2014C-3011,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579605,562,O177:H25,,STEC,MLST.Escherichia_coli_1.659,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018395.1,"CP027591,CP027589,CP027590,CP027592",,CDC,PacBio,142.9x,HGAP v. 3,1,3,4,5353744,50.52862,5805,,stool,,2013-12,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,99.6,2.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29125,Escherichia coli strain 2013C-4974,2013C-4974,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579604,562,O5:H9,,STEC,MLST.Escherichia_coli_1.342,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018375.1,"CP027587,CP027588",,CDC,PacBio,96.558x,HGAP v. 3,1,1,2,5293669,50.64168,5571,,stool,,2013-11,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,2.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29126,Escherichia coli strain 2013C-4282,2013C-4282,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579597,562,O77:H45,,STEC,"MLST.Escherichia_coli_1.7083,MLST.Escherichia_coli_2.675",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018335.1,"CP027579,CP027580,CP027581",,CDC,PacBio,98.187x,HGAP v. 3,1,2,3,5203410,50.44469,5056,,stool,,2013-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29127,Escherichia coli strain 2013C-3513,2013C-3513,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579595,562,O186:H11,,STEC,MLST.Escherichia_coli_1.21,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018315.1,"CP027555,CP027554,CP027556",,CDC,PacBio,121.607x,HGAP v. 3,1,2,3,5746114,50.552044,6066,,missing,,2013-03,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.29129,Escherichia coli strain 2014C-3097,2014C-3097,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579582,562,O181:H49,,STEC,MLST.Escherichia_coli_1.173,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018275.1,"CP027449,CP027450,CP027451",,CDC,PacBio,60.29x,HGAP v. 3,1,2,3,5285744,50.80159,5278,,stool,,2013-08,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29130,Escherichia coli strain 2012C-4221,2012C-4221,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579578,562,O101:H6,,STEC,MLST.Escherichia_coli_1.5350,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018235.1,"CP027437,CP027438,CP027439",,CDC,PacBio,94.01x,HGAP v. 3,1,2,3,5194649,50.51219,5125,,stool,,2012-09,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29131,Escherichia coli strain 2015C-3905,2015C-3905,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579573,562,O181:H49,,STEC,MLST.Escherichia_coli_1.173,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018215.1,"CP027371,CP027372",,CDC,PacBio,185.611x,HGAP v. 3,1,1,2,5077047,50.861553,4995,,stool,,2015-06,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29132,Escherichia coli strain 2014C-3061,2014C-3061,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579591,562,O156:H25,,STEC,"MLST.Escherichia_coli_1.300,MLST.Escherichia_coli_2.591",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018155.1,"CP027548,CP027549",,CDC,PacBio,67.785x,HGAP v. 3,1,1,2,5398051,50.569714,5649,,stool,,2013-05,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29133,Escherichia coli strain 2014C-3338,2014C-3338,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579583,562,O183:H18,,STEC,"MLST.Escherichia_coli_1.657,MLST.Escherichia_coli_2.385",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003018095.1,"CP027452,CP027453",,CDC,PacBio,44.21x,HGAP v. 3,1,1,2,4958625,50.878902,4960,,stool,,2013-11,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,1.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29134,Escherichia coli strain 2014C-3307,2014C-3307,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579572,562,O178:H19,,STEC,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.537",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017995.1,"CP027368,CP027369,CP027370",,CDC,PacBio,126.946x,HGAP v. 3,1,2,3,5251777,50.75482,5318,,stool,,2014-02,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,2.3,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29137,Escherichia coli strain 2015C-3121,2015C-3121,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579565,562,O91:H14,,STEC,MLST.Escherichia_coli_1.33,,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017935.1,"CP027340,CP027341",,CDC,PacBio,64.661x,HGAP v. 3,1,1,2,5470775,50.788963,5753,,stool,,2014-08,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,99.6,0.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.29138,Escherichia coli strain 2015C-3108,2015C-3108,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08579555,562,O111:H8,,STEC,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,,,2018-03-26T00:00:00Z,,PRJNA218110,GCA_003017555.1,"CP027307,CP027308,CP027309",,CDC,PacBio,75.219x,HGAP v. 3,1,2,3,5521830,50.6096,5751,,stool,,2014-07,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,STEC,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.30340,Escherichia coli strain DA33133,DA33133,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245645,562,ST2,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003180975.1,"CP029574,CP029575",,Uppsala University,PacBio; Illumina HiSeq 2000,30.0x,CLC Genomics workbench v. 11.0.1,1,1,2,4928362,50.867184,5088,4993,feces,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.30341,Escherichia coli strain DA33137,DA33137,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245647,562,ST44,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.44",,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003180995.1,"CP029579,CP029580,CP029581",,Uppsala University,PacBio; Illumina MiSeq,30.0x,CLC Genomics workbench v. 11.0.1,1,2,3,5441874,50.631126,5661,5568,,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.30342,Escherichia coli strain DA33135,DA33135,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245744,562,ST506,,,MLST.Escherichia_coli_1.131,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181035.1,"CP029576,CP029577,CP029578",,Uppsala University,PacBio; Illumina HiSeq 2000,50.0x,CLC Genomics workbench v. 11.0.1,1,2,3,5253091,50.798588,5520,5406,,,,Sweden,Sweden,,,,,,,,,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.30348,Escherichia coli strain H17,H17,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06833089,562,,,,"MLST.Escherichia_coli_1.354,MLST.Escherichia_coli_2.39",,,,2018-06-06T00:00:00Z,,PRJNA384272,GCA_003194125.1,"CP021193,CP021194,CP021195,CP021196,CP021197,CP021198",,"SRRSH hospital, Zhejiang university",PacBio,66.69x,SMRT Analysis v. 2.3.0,1,5,6,5896485,50.34347,6478,6140,hospital,,2012-10,China,China: Hefei,,,,UTI,,,,,,,,,,,,,Antibiotic resistance of bacteria;many frameshifted proteins,collected_by:SRRSH hospital,,,,,,,UTI,,,,,,,,,,,,,,100,2.2,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,562.30349,Escherichia coli strain CCUG 70745,CCUG 70745,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07602583,562,,,,"MLST.Escherichia_coli_1.648,MLST.Escherichia_coli_2.599",,,,2018-06-06T00:00:00Z,,PRJNA401330,GCA_003194265.1,"CP023258,CP023259,CP023260,CP023261,CP023262,CP023263,CP023264",,Chalmers University of Technology,Illumina MiSeq; PacBio,77.0x,SPAdes v. v3.7.0,1,6,7,5235096,50.492283,5495,5364,feces,,2013-01-09,Sweden,Sweden: Gothenburg,,,,,,,Intermediate;Resistant;Susceptible;Not defined,AMR Panel,,,,,,,,,"In this study, we aimed to characterize the resistome of highly multi-resistant pathogens, all phenotypically resistant to at least one carbapenem antibiotic.","collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,N/A,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.30361,Escherichia coli strain SD134209,SD134209,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09278797,562,,,,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,,,2018-06-09T00:00:00Z,,PRJNA473579,GCA_003203755.1,"CP029692,CP029690,CP029691",,"United States Department of Agriculture, Agricultural Research Service",PacBio; Illumina MiSeq,200.0x,HGAP v. 2.3; Geneious Reference Assembly,1,2,3,5626456,50.44049,6172,5920,feces,,2001,USA,USA: South Dakota,,,,bloody diarrhea,,,,,,,,,,,,,"Non-O157 Shiga toxin-producing Escherichia coli (STEC) are a common source of foodborne illness. STEC O111 are among the most prevalent non-O157 STEC serogroups and the third most commonly reported in the United States. Here, we report the complete genomic sequences of three O111:H8 strains that display a distinct aggregation phenotype.",collected_by:South Dakota Department of Health,,,,,,,bloody diarrhea,,,,,,,,,,,,,,100,0.4,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.31000,Escherichia coli strain WI2 isolate,WI2 isolate,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA19195918,562,,,,"MLST.Escherichia_coli_1.1288,MLST.Escherichia_coli_2.2",,,,2017-04-20T00:00:00Z,,PRJEB18462,GCA_900174635.1,"LT838200,LT838202,LT838203,LT838204,LT838201",,CHU Clermont-ferrand,,,,1,4,5,5053216,50.722054,5077,4906,clinical isolate,,2016,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,The spread of mcr-1-encoding plasmids into carbapenem-resistant Enterobacteriaceae raises concern about the emergence of untreatable bacteria. We report the acquisition of mcr-1 in a carbapenem resistant E. coli after a 3-week course of colistin in a patient repatriated to France from Portugal.,,,,,,,,,diseased,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.33453,Escherichia coli strain MCJCHV-1,MCJCHV-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09462202,562,O75:H5:K1,,Escherichia coli- NMEC,"MLST.Escherichia_coli_1.1193,MLST.Escherichia_coli_2.53",,,,2018-07-27T00:00:00Z,,PRJNA476955,GCA_003344465.1,"CP030111,CP030112,CP030113,CP030114,CP030115,CP030116",,University of Georgia,PacBio,320.0x,Canu v. 1.5,1,5,6,5042521,50.59128,5213,5113,csf,,2015,USA,"USA: Nashville, TN",,female,30 days,Neonatal bacterial meningitis,,host_disease_outcome:death,,,,,,,,,,,"Neonatal meningitis Escherichia coli (NMEC) is the second-leading cause of neonatal bacterial meningitis (NBM) worldwide. We report the genome sequence of a multi-drug resistant, NMEC serotype O75:H5:K1 strain mcjchv-1 (NMEC-O75), which resulted in the death of an infant. The O75 serogroup is rare among NMEC isolates.",collected_by:Monroe Carell Jr. Children's Hospital at Vanderbilt University,,,,,,,Neonatal bacterial meningitis,,death,,,Escherichia coli- NMEC,,,,,,,,,100,0,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.33455,Escherichia coli strain Es_ST80_L1_NDM_10_2017,Es_ST80_L1_NDM_10_2017,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09710898,562,O2:H7,,,MLST.Escherichia_coli_1.80,genotype:ST80,,,2018-07-31T00:00:00Z,,PRJNA482002,GCA_003346835.1,"CP031215,CP031216",,Public Health England,Oxford Nanopore MiniION; Illumina HiSeq,500.0x,miniasm v. 0.2-r168-dirty; racon,1,1,2,5313245,50.328903,5634,5386,rectal swab,,2017-10-26,United Kingdom,United Kingdom,,male,64,screen,,,,,,,,,,,,,"Inc L/M NDM plasmids are currently relatively rare, yet we have observed a number (in multiple bacterial genera) of late. This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.",collected_by:Hospital in London,,,,,,,screen,,,,,,,,,,,,,,100,3.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.33462,Escherichia coli strain Es_ST410_NW1_NDM_09_2017,Es_ST410_NW1_NDM_09_2017,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09693981,562,O8:H21,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",genotype:ST410;genotype:ST410;genotype:ST410;genotype:ST410;genotype:ST410,,,2018-08-01T00:00:00Z,,PRJNA482002,GCA_003351385.1,"CP031231,CP031232,CP031233,CP031234,CP031235",,Public Health England,Oxford Nanopore MiniION; Illumina HiSeq,500.0x,miniasm v. 0.2-r168-dirty; racon,1,4,5,5086148,50.709023,5461,5240,rectal swab,,2017-09-28,United Kingdom,United Kingdom,,,,screen,,,,,,,,,,,,,"Inc L/M NDM plasmids are currently relatively rare, yet we have observed a number (in multiple bacterial genera) of late. This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.;many frameshifted proteins",collected_by:Hospital in North West England,,,,,,,screen,,,,,,,,,,,,,,100,3.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.33466,Escherichia coli strain Es_ST2350_SE1_NDM_03_2018,Es_ST2350_SE1_NDM_03_2018,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09729056,562,O8:H49,,,MLST.Escherichia_coli_1.2350,genotype:ST2350,,,2018-08-05T00:00:00Z,,PRJNA482002,GCA_003355175.1,"CP031321,CP031323,CP031322",,Public Health England,Oxford Nanopore MiniION; Illumina HiSeq,500.0x,miniasm v. 0.2-r168-dirty; racon,1,2,3,4891336,50.79753,5097,4928,rectal swab,,2018-03-22,United Kingdom,United Kingdom,,female,82,screen,,,,,,,,,,,,,"Inc L/M NDM plasmids are currently relatively rare, yet we have observed a number (in multiple bacterial genera) of late. This project involved sequencing a number of isolates with Inc L/M NDM plasmids using both minION and Illumina platforms to accurately determine the plasmid sequences and assess any potential transmission between organisms. The project included both epidemiologically related and unrelated isolates.",collected_by:Hospital in South East England,,,,,,,screen,,,,,,,,,,,,,,100,2.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.33716,Escherichia coli strain ST410,ST410,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09273490,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2018-08-08T00:00:00Z,,PRJNA473419,GCA_003367575.1,"CP029630,CP029631",,Tokyo Medical and Dental University,PacBio,142.7x,HGAP v. 3,1,1,2,4938383,50.539185,5173,5020,urine,,2015-06,Ghana,Ghana: Tamale,,,,Urinary tract infection,,,,,,,,,,,,,AMR-GhanaOur aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana， and further to explore major resistance mechanisms involved.,collected_by:Tamale Teaching Hospital,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,2.2,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.34017,Escherichia coli strain FORC_069,FORC_069,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07436715,562,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,,,2018-09-07T00:00:00Z,,PRJNA396801,GCA_003491165.1,"CP023061,CP023062",,Seoul National University,PacBio,198.52x,SMRT Analysis v. 2.3.0,1,1,2,5267223,50.66332,5399,5413,human stool,"isolated from the stool of a food-poisoned patient in Seoul, Korea",2016-01-01,South Korea,South Korea: Seoul,,,,diffusal diarrhea,,,,,,,,,,,,,"As a food-borne pathogen, Escherichia coli exhibits profound food-poisoning activities with high fatality, every year. This strain was isolated from the stool of a food-poisoned patient in Seoul, Korea.",collected_by:National Culture Collection for Pathogens,,,,,,,diffusal diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.36160,Escherichia coli strain 118UI,118UI,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10112494,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2018-10-09T00:00:00Z,,PRJNA492884,GCA_003627855.1,"CP032515,CP032517,CP032516",,"Center for Genomic Sciences, National Autonomous University of Mexico (UNAM)",Illumina MiSeq and PacBio Sequel,221.79x,Unicycler v. 0.4.1,1,2,3,5300729,50.72538,5427,5236,urine,,2009-01-28,Mexico,Mexico: Mexico City,,female,17 years,Cystitis,,host_description:Patient admitted to the Orthopedics service,,,,,,,,,,,Uropathogenic Escherichia coli complete genome,collected_by:Hospital Infantil de Mexico Federico Gomez,,,,,,,Cystitis,,,Patient admitted to the Orthopedics service,,,,,,,,,,,99.97,0.09,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.36203,Escherichia coli strain CHL5009T,CHL5009T,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10225034,562,,,,"MLST.Escherichia_coli_1.101,MLST.Escherichia_coli_2.88",,,,2018-10-18T00:00:00Z,,PRJNA495393,GCA_003666405.1,"CP032936,CP032937,CP032943,CP032942,CP032941,CP032940,CP032939,CP032938",,Canterbury Health Laboratories,Oxford Nanopore; Illumina MiSeq,19.0x,Unicycler v. 0.4.4; Canu v. 1.7.1,1,7,8,5222791,50.46724,5461,5215,urine,,2017-10,New Zealand,New Zealand: Christchurch,,,,Urinary tract infection,,,,,,,,,,,,,The characterisation of the first human case of E . coli harbouring mcr gene in New Zealand. This isolate is the first documented case of the mcr gene found in New Zealand. Two types of mcr genes (mcr-1 and mcr-3) were found on different plasmids with the mcr-3 gene inserted in a region near blaCTX-M-55 gene.,collected_by:Canterbury Health Laboratories,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.56,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.38629,Escherichia coli strain 4/2-1,4/2-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760933,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.664",,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856575.1,"CP023834,CP023835,CP023836,CP023837,CP023838",,Uppsala University,Pacific bio + Miseq,13x,CLC Genomics workbench v. 10,1,4,5,4928465,50.764507,5098,4977,feces,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.67,0.39,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.38630,Escherichia coli strain 4/0,4/0,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760930,562,,,,MLST.Escherichia_coli_1.131,,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856615.1,"CP023849,CP023850,CP023851,CP023852",,Uppsala University,Pacific bio + Miseq,17x,CLC Genomics workbench v. 10,1,3,4,5503245,50.66827,5784,5673,uti,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.85,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.38631,Escherichia coli strain 4/4,4/4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760938,562,,,,MLST.Escherichia_coli_1.131,,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856655.1,"CP023826,CP023827,CP023828,CP023829,CP023830,CP023831,CP023832,CP023833",,Uppsala University,Pacific bio + Miseq,24x,CLC Genomics workbench v. 10,1,7,8,5377516,50.724686,5713,5603,feces,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.38632,Escherichia coli strain 2/0,2/0,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760925,562,,,,MLST.Escherichia_coli_1.131,,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856635.1,"CP023853,CP023854,CP023855,CP023856,CP023857,CP023858",,Uppsala University,Pacific bio + Miseq,17x,CLC Genomics workbench v. 10,1,5,6,5319417,50.71227,5553,5439,uti,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.38633,Escherichia coli strain 7/2,7/2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760941,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856675.1,"CP023820,CP023821,CP023822,CP023823,CP023824,CP023825",,Uppsala University,Pacific bio + Miseq,20x,CLC Genomics workbench v. 10,1,5,6,5295885,50.65886,5513,5420,feces,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.38634,Escherichia coli strain 4/1-1,4/1-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760931,562,,,,MLST.Escherichia_coli_1.131,,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856695.1,"CP023844,CP023845,CP023846,CP023847,CP023848",,Uppsala University,Pacific bio + Miseq,10x,CLC Genomics workbench v. 10,1,4,5,5371977,50.661983,5661,5533,feces,,2009,Sweden,Sweden,,,,,,,,,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.38635,Escherichia coli strain SA186,SA186,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07411973,562,O25b,,UPEC,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.527",genotype:ST131,,,2018-12-03T00:00:00Z,,PRJNA395653,GCA_003856995.1,"CP022730,CP022731,CP022732,CP022733,CP022734,CP022735",,King Abdullah International Medical Research Center (KAIMRC),PacBio,185.73x,HGAP3 SMART v. 2.3.0; Canu v. 1.0,1,5,6,5585941,50.380573,5849,5707,urine,,2012-01-13,Saudi Arabia,Saudi Arabia:Riyadh,,female,2,Urinary tract infection,,host_description:Out Patient;host_subject_id:UPEC,,,,,,,,,,,"Complete Genome Sequence of Escherichia coli Strain SA186, a Uropathogenic E.coli strain of ST131 Encoding Colistin Resistance Determinant MCR-1",collected_by:Majed Alghoribi,,,,,,,Urinary tract infection,,,Out Patient,,UPEC,,Uropathogenic Escherichia coli,,,,,,,99.97,0.38,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.39125,Escherichia coli strain 504838,504838,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161196,562,,,,MLST.Escherichia_coli_1.173,,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956165.1,"CP025856,CP025857,CP025858",,"University of Maryland, School of Medicine",PacBio,24.71x,Canu v. v.1.2,1,2,3,5302308,50.68104,5388,,stool,,2010-09-13,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.62,0.71,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39126,Escherichia coli strain 504237,504237,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161313,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956185.1,"CP025862,CP025863,CP025864",,"University of Maryland, School of Medicine",PacBio,16.96x,HGAP v. v.3,1,2,3,5200734,50.619606,5210,,stool,,2010-03-22,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.41,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39127,Escherichia coli strain 204446,204446,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161280,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956205.1,"CP025910,CP025911,CP025912",,"University of Maryland, School of Medicine",PacBio,25.43x,Celera Assembler v. v.8.2,1,2,3,5335684,50.72006,5404,,stool,,2010-11-03,Mali,Mali,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.47,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39128,Escherichia coli strain 203740,203740,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161275,562,,,,"MLST.Escherichia_coli_1.1312,MLST.Escherichia_coli_2.155",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956225.1,"CP025913,CP025915,CP025914",,"University of Maryland, School of Medicine",PacBio,18.79x,HGAP v. v.3,1,2,3,5038713,50.71676,5047,,stool,,2010-03-30,Mali,Mali,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.82,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39129,Escherichia coli strain 214-4,214-4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161344,562,,,,"MLST.Escherichia_coli_1.398,MLST.Escherichia_coli_2.858",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956245.1,"CP025840,CP025841",,"University of Maryland, School of Medicine",PacBio,15.34x,HGAP v. v.3,1,1,2,5271236,50.60297,5380,,stool,,1974,Mexico,Mexico,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Centers for Disease Control (CDC),,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.66,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39130,Escherichia coli strain 510016,510016,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161314,562,,,,MLST.Escherichia_coli_1.1201,,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956265.1,"CP025851,CP025852,CP025853,CP025854,CP025855",,"University of Maryland, School of Medicine",PacBio,26.12x,Celera Assembler v. v.8.2,1,4,5,5116904,50.71588,5214,,stool,,2012-01-04,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.71,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39131,Escherichia coli strain 503829,503829,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161311,562,,,,"MLST.Escherichia_coli_1.94,MLST.Escherichia_coli_2.58",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956285.1,"CP025869,CP025870,CP025871,CP025872",,"University of Maryland, School of Medicine",PacBio,20.07x,Canu v. v.1.2,1,3,4,5150622,50.51751,5204,,stool,,2009-10-02,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.52,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39132,Escherichia coli strain 300709,300709,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161146,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956305.1,"CP025903,CP025905,CP025904",,"University of Maryland, School of Medicine",PacBio,20.17x,HGAP v. v.3,1,2,3,5034709,50.553963,5087,,stool,,2008-08-03,Mozambique,Mozambique,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.19,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39133,Escherichia coli strain 103605,103605,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161256,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956325.1,"CP025920,CP025921,CP025922",,"University of Maryland, School of Medicine",PacBio,26.08x,Canu v. v.1.2,1,2,3,5347793,50.710583,5410,,stool,,2010-08-26,Gambia,Gambia,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.47,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39134,Escherichia coli strain 720632,720632,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161340,562,,,,"MLST.Escherichia_coli_1.1564,MLST.Escherichia_coli_2.843",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956345.1,"CP025842,CP025843,CP025845,CP025846,CP025844",,"University of Maryland, School of Medicine",PacBio,18.52x,HGAP v. v.3,1,4,5,5078039,50.94581,5249,,stool,,2012-05-07,Pakistan,Pakistan,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39135,Escherichia coli strain 602354,602354,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161318,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956365.1,"CP025847,CP025848",,"University of Maryland, School of Medicine",PacBio,42.18x,Canu v. v.1.2,1,1,2,5207077,50.692165,5208,,stool,,2009-04-08,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.41,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39136,Escherichia coli strain 600468,600468,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161317,562,,,,"MLST.Escherichia_coli_1.517,MLST.Escherichia_coli_2.546",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956385.1,"CP025849,CP025850",,"University of Maryland, School of Medicine",PacBio,45.37x,Canu v. v.1.2,1,1,2,4977019,50.72384,4885,,stool,,2008-04-22,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,1.03,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39137,Escherichia coli strain 504239,504239,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161195,562,,,,MLST.Escherichia_coli_2.661,,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956405.1,"CP025859,CP025860,CP025861",,"University of Maryland, School of Medicine",PacBio,30.31x,Canu v. v.1.2,1,2,3,5237282,50.71495,5302,,stool,,2010-03-22,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.44,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39138,Escherichia coli strain 504211,504211,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161312,562,,,,"MLST.Escherichia_coli_1.94,MLST.Escherichia_coli_2.58",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956425.1,"CP025865,CP025868,CP025867,CP025866",,"University of Maryland, School of Medicine",PacBio,24.11x,Canu v. v.1.2,1,3,4,5179575,50.538643,5222,,stool,,2010-02-22,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.52,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39139,Escherichia coli strain 503440,503440,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161308,562,,,,MLST.Escherichia_coli_2.58,,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956445.1,"CP025881,CP025883,CP025882,CP025885,CP025884",,"University of Maryland, School of Medicine",PacBio,25.81x,Canu v. v.1.2,1,4,5,5284416,50.53862,5380,,stool,,2009-06-07,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.54,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39140,Escherichia coli strain 503025,503025,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161306,562,,,,"MLST.Escherichia_coli_1.94,MLST.Escherichia_coli_2.58",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956465.1,"CP025892,CP025894,CP025893,CP025895",,"University of Maryland, School of Medicine",PacBio,26.07x,Celera Assembler v. v.8.2,1,3,4,5169235,50.54717,5213,,stool,,2009-03-15,India,India,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.85,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39141,Escherichia coli strain 120899,120899,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08161259,562,,,,"MLST.Escherichia_coli_1.443,MLST.Escherichia_coli_2.5",,,,2018-12-19T00:00:00Z,,PRJNA421191,GCA_003956485.1,"CP025916,CP025917,CP025919,CP025918",,"University of Maryland, School of Medicine",PacBio,18.33x,Canu v. v.1.2,1,3,4,5388677,50.696804,5475,,stool,,2012-07-09,Gambia,Gambia,,,,diarrhea,,,,,,,,,,,,,Genome sequencing of ETEC,collected_by:Global Enteric Multicenter Study (GEMS),,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.62,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.39409,Escherichia coli strain EC17GD31,EC17GD31,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09717320,562,,,,MLST.Escherichia_coli_1.457,,,,2019-01-03T00:00:00Z,,PRJNA482900,GCA_003991155.1,"CP031293,CP031295,CP031294,CP031296,CP031297",,Pasteur Institute in Ho Chi Minh City,Illumina MiSeq; Oxford Nanopore MiniION,130.0x,Canu v. 1.6; SPAdes v. 3.11.1,1,4,5,5580091,50.352493,5820,5685,blood,"isolated in Vietnam in 2017 which showed resistance to both carbapenem and colistin, was sequenced by the MinION nanopore and the Illumina MiSeq system",2017-03-20,Viet Nam,Viet Nam: Ho Chi Minh city,,female,85,"Pneumonia, acute kidney injury, cerebral infarction",,,,,,,,,,,,,"whole genome of a clinical Escherichia coli isolated in Vietnam in 2017 which showed resistance to both carbapenem and colistin, was sequenced by the MinION nanopore and the Illumina MiSeq system.",collected_by:Nhan Dan Gia Dinh hospital,,,,,,,"Pneumonia, acute kidney injury, cerebral infarction",,,,,,,,,,,,,,99.97,1.06,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,562.39410,Escherichia coli strain C4435,C4435,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08706591,562,O25:H4,,Escherichia coli - AIEC,MLST.Escherichia_coli_1.131,,,,2019-01-08T00:00:00Z,,PRJNA438133,GCA_003999775.1,CP027851,,Benemerita Universidad Autonoma de Puebla,Illumina NextSeq,1.13x,SPAdes v. 3.9.0,1,,1,5199428,50.639473,5597,5475,peritoneal fluid,,2010-09-22,Mexico,Mexico: Puebla,,female,1 month,,,host_subject_id:#22,,,,,,,,,,,"Four samples isolated from healthy donors and one isolated from peritoneal fluid from a 1 month old girl, none of them refer symptoms of Inflammatory Bowel Disease",collected_by:Hospital para el Nino Poblano,,,,,,,None,,,,,Escherichia coli - AIEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,562.39449,Escherichia coli strain E-1246,E-1246,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08222594,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2019-01-10T00:00:00Z,,PRJNA427077,GCA_004011015.1,"CP025573,CP025574,CP025575",,Uppsala University,Illumina MiSeq; PacBio,50.0x,CLC Genomics Workbench v. 11,1,2,3,5560834,50.51399,5800,5666,"outbreak at the neonatal ward at karolinska hospital, sweden","isolate from an outbreak at the neonatal ward at Karolinska hospital, Sweden",2008,Sweden,Sweden: Stockholm,,,,,,,,,,,,,,,,,"One Escherichia coli and one Klebsiella pneumoniae isolate from an outbreak at the neonatal ward at Karolinska hospital, Sweden.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.39506,Escherichia coli strain ecoli019,ecoli019,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4916090,562,,,,MLST.Escherichia_coli_1.8346,,,,2018-11-27T00:00:00Z,,PRJEB28660,GCA_900618295.1,LR130532,,"BIOZENTRUM, UNIVERSITY OF BASEL",,,,1,,1,5009390,50.872383,4981,4713,hospital,,2016,Switzerland,Switzerland,,,,,,host_health_state:diseased,,,,,,,,,,,"Carbapenemase-producing bacteria are resistant against almost all beta-lactam and cephalosporin class antibiotics and represent a growing health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished Carbapenemase and ESBL producing genomes sequenced using Oxford Nanopore and Illumina technologies. We observed the rapid movement of Carbapenemases between distinct genomic neighborhoods, sequence types, and species boundaries using this diverse collection of high quality closed genomes and their associated plasmids.;Clinically isolated MDRO",collected_by:University Basel Hospital,,,,,,,,diseased,,,,,,,,,,,,,99.93,1.93,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.45330,Escherichia coli strain EC25,EC25,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10743440,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2019-01-21T00:00:00Z,,PRJNA515159,GCA_004088295.1,"CP035123,CP035124,CP035126,CP035127,CP035128,CP035125",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. 0.4.7,1,5,6,5069694,50.658047,5233,4956,urine,,2017-08-17,China,China: Hangzhou,,,,Pulmonary infection,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis of carbapenem-resistant Escherichia coli,collected_by:Fang He,,,,,,,Pulmonary infection,,,,,,,,,,,,,,99.01,0.33,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases NHP,562.45389,Escherichia coli strain RS571,RS571,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10535911,562,,,,MLST.Escherichia_coli_1.648,,,,2019-01-25T00:00:00Z,,PRJNA509034,GCA_004114395.1,"CP034389,CP034390,CP034391,CP034392",,Cardiff University,Oxford Nanopore MiniION,627.0x,Unicycler v. 0.4.6,1,3,4,5348132,50.346157,5468,5164,rectal swab,,2018-05-16,Bangladesh,Bangladesh: Dhaka,,,,,,,,,,,,,,,,,First report of mcr-1 carried by IncH12 plasmid in Escherichia coli from human normal flora in Bangladesh,sample_type:Pure culture one microbial species,,,,,,,,,,,,,,,,,,,,,99.93,0.2,,,Gastrointestinal,- HP,562.45394,Escherichia coli strain BR03-DEC,BR03-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748446,562,ST2179,,,"MLST.Escherichia_coli_2.595,MLST.Escherichia_coli_1.2179",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116595.1,CP035321,,Sao Paulo State University,Illumina NextSeq,213.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,,1,5038603,50.764866,5150,4914,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.42,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45395,Escherichia coli strain BR07-DEC,BR07-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748581,562,ST2179,,,"MLST.Escherichia_coli_2.595,MLST.Escherichia_coli_1.2179",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116695.1,"CP035322,CP035323,CP035324",,Sao Paulo State University,Illumina NextSeq,254.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,2,3,5087428,50.744022,5243,5012,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Resistant;Susceptible;Intermediate,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.42,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45396,Escherichia coli strain BR10-DEC,BR10-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748585,562,ST2509,,,MLST.Escherichia_coli_1.2509,,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116795.1,"CP035360,CP035361,CP035362,CP035363,CP035364,CP035365",,Sao Paulo State University,Illumina NextSeq,259.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,5,6,5094768,50.76092,5178,4962,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.76,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45397,Escherichia coli strain BR12-DEC,BR12-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748588,562,ST410,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116815.1,"CP035325,CP035326,CP035327,CP035328,CP035329",,Sao Paulo State University,Illumina NextSeq,253.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,4,5,4848972,50.6427,4986,4748,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Intermediate;Resistant,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.26,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45398,Escherichia coli strain BR14-DEC,BR14-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748593,562,ST1193,,,MLST.Escherichia_coli_1.1193,,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116855.1,CP035330,,Sao Paulo State University,Illumina NextSeq,300.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,,1,5110451,50.631485,5318,5072,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.39,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45399,Escherichia coli strain BR25-DEC,BR25-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748596,562,ST641,,,"MLST.Escherichia_coli_2.86,MLST.Escherichia_coli_1.641",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116875.1,"CP035331,CP035332,CP035333,CP035334",,Sao Paulo State University,Illumina NextSeq,325.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,3,4,4960880,50.518612,5091,4846,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.18,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45400,Escherichia coli strain BR29-DEC,BR29-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748603,562,ST224,,,"MLST.Escherichia_coli_2.479,MLST.Escherichia_coli_1.224",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116895.1,"CP035339,CP035335,CP035345,CP035346,CP035347,CP035348,CP035336,CP035337,CP035338,CP035340,CP035341,CP035342",,Sao Paulo State University,Illumina NextSeq,264.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,13,14,5010100,50.818615,5120,4902,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Resistant;Intermediate,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45401,Escherichia coli strain BR32-DEC,BR32-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748605,562,ST617,,,MLST.Escherichia_coli_1.617,,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116915.1,"CP035350,CP035349,CP035351",,Sao Paulo State University,Illumina NextSeq,111.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,2,3,4848573,50.79566,4954,4715,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Resistant;Intermediate;Susceptible,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.67,0.04,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45403,Escherichia coli strain BR64-DEC,BR64-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748607,562,ST224,,,"MLST.Escherichia_coli_2.479,MLST.Escherichia_coli_1.224",,,,2019-01-29T00:00:00Z,,PRJNA511007,GCA_004116935.1,"CP035354,CP035352,CP035353,CP035355,CP035356,CP035357,CP035358,CP035359",,Sao Paulo State University,Illumina NextSeq,227.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,7,8,5030024,50.83097,5141,4915,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Susceptible;Resistant;Intermediate,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.16,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45404,Escherichia coli strain BR43-DEC,BR43-DEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10748606,562,ST131,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2019-01-30T00:00:00Z,,PRJNA511007,GCA_004118895.1,"CP035377,CP035378,CP035379",,Sao Paulo State University,Illumina NextSeq,151.0x,A5-miseq v. AUGUST-2016; MeDuSa v. 1.6;,1,2,3,5161342,50.58899,5377,5155,urine,,2015,Brazil,"Brazil: Botucatu, Sao Paulo State",,,,Urinary tract infection,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"11 uropathogenic Escherichia coli genomes isolated in Hospital da Clinicas de Botucatu, Sao Paulo - Brazil",collected_by:Hospital das Clinincas Botucatu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.33,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.45430,Escherichia coli strain U13A,U13A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10817700,562,,,,MLST.Escherichia_coli_1.131,,,,2019-02-03T00:00:00Z,,PRJNA516747,GCA_004135165.1,"CP035477,CP035478,CP035479,CP035480,CP035481,CP035482,CP035483",,The University of Queensland,PacBio RSII; Illumina NextSeq,120.0x,HGAP v. 2.3.0,1,6,7,5300616,50.77806,5357,5015,urine,isolated over a 5-year period (2012-2016) from the urine and feces of a single individual,2013,USA,USA:Utah,,,,,,,,,,,,,,,,,"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.",,,,,,,,not applicable,,,,,,,,,,,,,,99.97,0.75,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45434,Escherichia coli strain U14A,U14A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10836813,562,,,,MLST.Escherichia_coli_1.131,,,,2019-02-04T00:00:00Z,,PRJNA516748,GCA_004135915.1,"CP035516,CP035517,CP035518,CP035519,CP035520,CP035521,CP035522",,The University of Queensland,PacBio RSII; Illumina NextSeq,109.0x,HGAP v. 2.3.0,1,6,7,5300575,50.77702,5357,5020,urine,isolated over a 5-year period (2012-2016) from the urine and feces of a single individual,2015,USA,USA:Utah,,,,,,,,,,,,,,,,,"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.",,,,,,,,not applicable,,,,,,,,,,,,,,99.97,0.75,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45438,Escherichia coli strain U12A,U12A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10817475,562,,,,MLST.Escherichia_coli_1.131,,,,2019-02-04T00:00:00Z,,PRJNA516746,GCA_004141955.1,"CP035476,CP035468,CP035469,CP035470,CP035471,CP035472,CP035473,CP035474,CP035475",,The University of Queensland,PacBio RSII; Illumina NextSeq,80.0x,HGAP v. 2.3.0,1,8,9,5384821,50.761242,5466,5126,urine,isolated over a 5-year period (2012-2016) from the urine and feces of a single individual,2012,USA,USA:Utah,,,,,,,,,,,,,,,,,"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.",,,,,,,,not applicable,,,,,,,,,,,,,,99.97,0.75,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45584,Escherichia coli strain U15A,U15A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10837069,562,,,,MLST.Escherichia_coli_1.131,,,,2019-02-13T00:00:00Z,,PRJNA516749,GCA_004193755.1,"CP035720,CP035721,CP035722,CP035723,CP035724,CP035725,CP035726",,The University of Queensland,PacBio RSII; Illumina NextSeq,108.0x,HGAP v. 2.3.0,1,6,7,5128015,50.851276,5141,4830,urine,isolated over a 5-year period (2012-2016) from the urine and feces of a single individual,2015,USA,USA:Utah,,,,,,,,,,,,,,,,,"Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.",,,,,,,,not applicable,,,,,,,,,,,,,,99.97,0.4,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45679,Escherichia coli strain S65EC,S65EC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10879429,562,,,,MLST.Escherichia_coli_1.131,genotype:ST131,,,2019-02-26T00:00:00Z,,PRJNA517996,GCA_004299805.1,"CP036245,CP036244",,University of Queensland,PacBio RSII; Illumina,60.0x,HGAP v. OCT-2017,1,1,2,5334561,50.704002,5349,5029,urine,,2009-11,Australia,Australia,,,,,,,,,,,,,,,,,"Uropathogenic E. coli (UPEC) is the major causative pathogen for urinary tract infections. Nearly half of UPEC express hemolysin A, and hemolysin expression is associated with pyelonephritis and urosepsis strains, which indicated its link to increased virulence in UPEC. In this study, we analysed hemolysin production in ST131, and investigated the genes involved in hemolysin production and activity.",sample_type:monoisolate,,,,,,,,,,,,,,,,,,,,,99.97,0.67,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45704,Escherichia coli strain CFSAN027346,CFSAN027346,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10604455,562,,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2019-03-20T00:00:00Z,,PRJNA230969,GCA_004358365.1,"CP037945,CP037946,CP037947",,FDA/CFSAN,PacBio RSII,450x,HGAP v. 3,1,2,3,5761749,50.635685,6228,5874,stool,,1999,USA,USA,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,"collected_by:E. coli Reference Center -Pennsylvania State University, University Park, PA",,,,,,,missing,,,,,,,,,,,,,,99.97,0.38,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.45706,Escherichia coli strain CFSAN027343,CFSAN027343,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10604454,562,,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",,,,2019-03-20T00:00:00Z,,PRJNA230969,GCA_004358405.1,"CP037943,CP037944",,FDA/CFSAN,PacBio RSII,400x,HGAP v. 3,1,1,2,5778004,50.67982,6226,5893,stool,,1999,Argentina,Argentina,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,"collected_by:E. coli Reference Center -Pennsylvania State University, University Park, PA",,,,,,,missing,,,,,,,,,,,,,,99.97,0.38,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.45845,Escherichia coli strain 103,103,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04096281,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",,,,2019-04-02T00:00:00Z,,PRJNA278886,GCA_004564175.1,"CP020495,CP020496,CP020497",,Brigham & Women's Hospital,PacBio,299.66x,HGAP v. 3,1,2,3,5330963,50.6359,5555,5457,urine,,2015,USA,USA:Boston,,male,81,,,host_subject_id:Ecoli-15,Susceptible;Resistant,AMR Panel,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,missing,,,,,,,,,,,,,,99.97,0.69,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.45973,Escherichia coli strain 28Eco12,28Eco12,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08963308,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2019-04-09T00:00:00Z,,PRJNA451184,GCA_004759025.1,"CP038505,CP038506",,Universidad El Bosque,PacBio,266.0x,HGAP v. 2.3.0,1,1,2,5435394,50.512897,5559,5270,urine,,2013-09-05,Colombia,Colombia,,,,Urinary tract infection,,,,,,,,,,,,,Carbapenem resistant clinical isolate,collected_by:Bacterial Molecular Genetics Laboratory,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.09,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.46197,Escherichia coli strain 382634_2f strain not applicable,not applicable,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11266257,562,,,,"MLST.Escherichia_coli_2.586,MLST.Escherichia_coli_1.122",,,,2019-04-23T00:00:00Z,,PRJNA315192,GCA_004804205.1,CP039403,,Health Protection Agency,Oxford Nanopore MiniION,372.24x,Unicycler v. 0.4.2,1,,1,4702395,50.731106,4717,4535,feces,,2017,,,,,,Gastroenteritis,,,,,,,,,,,,,Routine surveillance of E. coli &\; Shigella by Public Health England,"collected_by:Gastrointestinal Bacteria Reference Unit, Public Health England",,,,,,,Gastroenteritis,,,,,,,,,,,,,,99.97,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.48248,Escherichia coli strain B36,B36,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128441,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,102.100.100.25765,,2019-01-10T00:00:00Z,,PRJEB29930,GCA_900622635.1,"LR130545,LR130546,LR130547",,Bioplatforms Australia,,,,1,2,3,5261718,50.85972,5253,,blood,,,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.",,,,,,,,,diseased,,,,,,,,,,,,,99.74,0.37,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.48249,Escherichia coli strain MS14385,MS14385,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128442,562,,,,MLST.Escherichia_coli_1.648,,102.100.100.25767,,2019-01-10T00:00:00Z,,PRJEB29930,GCA_900622655.1,"LR130555,LR130556,LR130557,LR130558,LR130559,LR130560,LR130561",,Bioplatforms Australia,,,,1,6,7,5461091,50.301414,5493,,blood,,,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.",,,,,,,,,diseased,,,,,,,,,,,,,99.62,0.64,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.48250,Escherichia coli strain MS14386,MS14386,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128443,562,,,,"MLST.Escherichia_coli_1.224,MLST.Escherichia_coli_2.479",,102.100.100.25768,,2019-01-10T00:00:00Z,,PRJEB29930,GCA_900622665.1,"LR130552,LR130553,LR130554",,Bioplatforms Australia,,,,1,2,3,5058016,50.880287,4954,,blood,,,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.",,,,,,,,,diseased,,,,,,,,,,,,,99.97,0.57,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.48251,Escherichia coli strain MS14387,MS14387,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128445,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,102.100.100.25769,,2019-01-10T00:00:00Z,,PRJEB29930,GCA_900622685.1,"LR130564,LR130565,LR130566",,Bioplatforms Australia,,,,1,2,3,5232331,50.759193,5157,,blood,,2009-09-03,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.",,,,,,,,,diseased,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.48252,Escherichia coli strain MS14384,MS14384,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128444,562,,,,MLST.Escherichia_coli_1.963,,102.100.100.25766,,2019-01-10T00:00:00Z,,PRJEB29930,GCA_900622695.1,"LR130562,LR130563",,Bioplatforms Australia,,,,1,1,2,5186043,50.71782,5042,,blood,,,,,,,,,,host_health_state:diseased,,,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Escherichia coli.",,,,,,,,,diseased,,,,,,,,,,,,,99.97,0.36,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.50212,Escherichia coli strain Combat2C1,Combat2C1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06219546,562,,,,"MLST.Escherichia_coli_2.32,MLST.Escherichia_coli_1.127",,,,2018-02-05T00:00:00Z,,PRJNA361032,GCA_002951675.1,"CP019243,CP019244",,The University of Hong Kong,PacBio,215.0x,HGAP v. NOV-2016,1,1,2,5273479,50.478878,5500,5356,urine,,2004-07,Hong Kong,Hong Kong,,,,Urinary infection,,,,,,,,,,,,,oqxAB positive Escherichia coli Genome sequencing and assembly,collected_by:Ho Pak-Leung,,,,,,,Urinary infection,,,,,,,,,,,,,,99.97,0.07,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.50213,Escherichia coli strain Combat13F7,Combat13F7,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06219547,562,,,,MLST.Escherichia_coli_1.3902,,,,2018-02-05T00:00:00Z,,PRJNA361032,GCA_002951695.1,"CP019245,CP019246,CP019247,CP019248,CP019249",,The University of Hong Kong,PacBio,234.0x,HGAP v. NOV-2016,1,4,5,5085448,50.685287,5319,5215,urine,,2004-10,Hong Kong,Hong Kong,,,,Urinary infection,,,,,,,,,,,,,oqxAB positive Escherichia coli Genome sequencing and assembly,collected_by:Ho Pak-Leung,,,,,,,Urinary infection,,,,,,,,,,,,,,99.97,0.83,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.50214,Escherichia coli strain 13KWH46,13KWH46,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06219548,562,,,,MLST.Escherichia_coli_1.602,,,,2018-02-05T00:00:00Z,,PRJNA361032,GCA_002951715.1,"CP019250,CP019251,CP019252,CP019253,CP019254,CP019255",,The University of Hong Kong,PacBio,236.0x,HGAP v. NOV-2016,1,5,6,5386699,50.65124,5782,5618,urine,,2013-05,Hong Kong,Hong Kong,,,,Urinary infection,,,,,,,,,,,,,oqxAB positive Escherichia coli Genome sequencing and assembly,collected_by:Ho Pak-Leung,,,,,,,Urinary infection,,,,,,,,,,,,,,99.2,0.87,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.50217,Escherichia coli strain 13TMH22,13TMH22,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06219549,562,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-02-05T00:00:00Z,,PRJNA361032,GCA_002951755.1,"CP019256,CP019257,CP019258",,The University of Hong Kong,PacBio,175.0x,HGAP v. NOV-2016,1,2,3,4901615,50.783016,5150,5100,urine,,2013-05,Hong Kong,Hong Kong,,,,Urinary infection,,,,,,,,,,,,,oqxAB positive Escherichia coli Genome sequencing and assembly,collected_by:Ho Pak-Leung,,,,,,,Urinary infection,,,,,,,,,,,,,,99.67,0.86,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.50219,Escherichia coli strain Combat11I9,Combat11I9,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07187744,562,,,,MLST.Escherichia_coli_1.2847,,,,2018-02-02T00:00:00Z,,PRJNA361032,GCA_002952095.1,"CP021726,CP021727,CP021728,CP021729,CP021730",,The University of Hong Kong,PacBio,203.0x,HGAP v. Feb-2015,1,4,5,5592499,50.405926,5828,5658,urine,,2004-10,Hong Kong,Hong Kong,,,,Urinary infection,,,,,,,,,,,,,oqxAB positive Escherichia coli Genome sequencing and assembly,collected_by:Dr. HO Pak-Leung,,,,,,,Urinary infection,,,,,,,,,,,,,,99.97,0.08,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.50407,Escherichia coli strain FC853_EC,FC853_EC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11974795,562,,,,,,,,2019-06-17T00:00:00Z,,PRJNA547676,GCA_006351885.1,"CP040919,CP040920,CP040921,CP040922,CP040923",,Christian Medical College,IonTorrent; MinION,21.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,4,5,5545145,50.418682,5818,5439,feces,,2017,India,India: Vellore,,,,Gastroenteritis,,,,,,,,,,,,,Azithromycin resistant E. coli isolated from human stool specimen,collected_by:Christian Medical College,,,,,,,Gastroenteritis,,,,,,,,,,,,,,99.27,0.6,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.50492,Escherichia coli strain MSHS 472,MSHS 472,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12158201,562,O82:NM,,UPEC,MLST.Escherichia_coli_2.88,,,,2019-07-09T00:00:00Z,,PRJNA551565,GCA_006777065.1,"CP041302,CP041301",,McGill University,PacBio,138.0x,HGAP v. May-2015; Celera Assembler v.,1,1,2,4932910,50.60437,5015,4727,urine from healthy adult with cystitis,,2006-03-16,Canada,Canada: Montreal,,,,cystitis,,host_health_state:Healthy with symptomatic cystitis,,,,,,,,,,,This strain was sequenced as part of a study that investigated the activity of the outer membrane protease OmpT among uropathogenic Escherichia coli clinical isolates.,collected_by:Student health services McGill University,,,,,,,cystitis,Healthy with symptomatic cystitis,,,,UPEC,,,,,,,,,99.93,1.05,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.50493,Escherichia coli strain MSHS 133,MSHS 133,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12158203,562,O24:NM,,,MLST.Escherichia_coli_2.48,,,,2019-07-09T00:00:00Z,,PRJNA551566,GCA_006777085.1,"CP041304,CP041303",,McGill University,PacBio,138.0x,Celera Assembler v. May-2015; HGAP v.,1,1,2,5103743,50.712605,5223,4970,urine from healthy adult with cystitis,,2005-10-11,Canada,Canada: Montreal,,,,cystitis,,host_health_state:Healthy with symptomatic cystitis,,,,,,,,,,,This strain was sequenced as part of a study that investigated the activity of the outer membrane protease OmpT among uropathogenic Escherichia coli clinical isolates.,collected_by:Student health services McGill University,,,,,,,cystitis,Healthy with symptomatic cystitis,,,,,,,,,,,,,99.97,0.33,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.50508,Escherichia coli strain 69,69,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163104,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007107705.1,"CP041522,CP041523,CP041524,CP041525",,Duke University,PacBio Sequel,74x,HGAP v. 4,1,3,4,5417941,50.725555,5589,5311,blood,,2014,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.11,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50509,Escherichia coli strain 95,95,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163102,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007107905.1,"CP041526,CP041527,CP041528",,Duke University,PacBio Sequel,126x,HGAP v. 4,1,2,3,5066291,50.76236,5205,4939,blood,,2013,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.87,0.39,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50510,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163101,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007108085.1,"CP041529,CP041530,CP041531",,Duke University,PacBio Sequel,50x,HGAP v. 4,1,2,3,5214119,50.821697,5399,5125,blood,,2012,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.36,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50511,Escherichia coli strain 963,963,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163100,562,,,,MLST.Escherichia_coli_1.963,,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007108305.1,"CP041532,CP041533,CP041534",,Duke University,PacBio Sequel,100x,HGAP v. 4,1,2,3,5253812,50.697525,5296,5013,blood,,2012,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.36,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50512,Escherichia coli strain 95,95,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163098,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007108505.1,"CP041535,CP041536,CP041537",,Duke University,PacBio Sequel,151x,HGAP v. 4,1,2,3,5279974,50.63761,5478,5213,blood,,2010,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.89,0.11,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50513,Escherichia coli strain 73,73,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163097,562,,,,,,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007108685.1,"CP041538,CP041539,CP041540",,Duke University,PacBio Sequel,62x,HGAP v. 4,1,2,3,5408216,50.42573,5679,5316,blood,,2008,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.87,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50514,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163096,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007108845.1,"CP041541,CP041542,CP041543",,Duke University,PacBio Sequel,162x,HGAP v. 4,1,2,3,5253264,50.70367,5424,5179,blood,,2008,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.87,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50515,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163095,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109005.1,"CP041544,CP041545",,Duke University,PacBio Sequel,117x,HGAP v. 4,1,1,2,5313308,50.763382,5489,5243,blood,,2007,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.33,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50516,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163094,562,,,,MLST.Escherichia_coli_1.131,,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109165.1,"CP041546,CP041547,CP041548,CP041549",,Duke University,PacBio Sequel,125x,HGAP v. 4,1,3,4,5440285,50.76175,5625,5383,blood,,2006,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.51,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50517,Escherichia coli strain 144,144,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163093,562,,,,"MLST.Escherichia_coli_2.55,MLST.Escherichia_coli_1.144",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109305.1,"CP041550,CP041551,CP041552,CP041553,CP041554,CP041555",,Duke University,PacBio Sequel,100x,HGAP v. 4,1,5,6,5368883,50.54842,5636,5356,blood,,2003,USA,USA,,,,Bloodstream infection,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Vance G. Fowler Jr.,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.97,0.17,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.50518,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163092,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109325.1,"CP041556,CP041557,CP041558",,Duke University,PacBio Sequel,50x,HGAP v. 4,1,2,3,5316481,50.85747,5512,5274,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50519,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163091,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109345.1,"CP041559,CP041560,CP041561,CP041562",,Duke University,PacBio Sequel,50x,HGAP v. 4,1,3,4,5399064,50.85198,5631,5385,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.36,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50520,Escherichia coli strain 405,405,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163090,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109365.1,"CP041563,CP041564,CP041565,CP041566,CP041567,CP041568,CP041569,CP041570,CP041571",,Duke University,PacBio Sequel,100x,HGAP v. 4,1,8,9,5720802,50.516632,5982,5664,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50521,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163089,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109385.1,"CP041572,CP041573,CP041574,CP041575,CP041576,CP041577",,Duke University,PacBio Sequel,50x,HGAP v. 4,1,5,6,5353799,50.71572,5593,5298,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.36,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50522,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163088,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109425.1,"CP041578,CP041579,CP041580",,Duke University,PacBio Sequel,50x,HGAP v. 4,1,2,3,5398583,50.763596,5667,5380,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50523,Escherichia coli strain 3057,3057,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163087,562,,,,"MLST.Escherichia_coli_2.435,MLST.Escherichia_coli_1.3057",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109445.1,"CP041520,CP041521",,Duke University,PacBio Sequel,97x,HGAP v. 4,1,1,2,5016621,50.425762,4954,4718,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50524,Escherichia coli strain 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12163086,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2019-07-18T00:00:00Z,,PRJNA551684,GCA_007109465.1,"CP041581,CP041582,CP041583",,Duke University,PacBio Sequel,78x,HGAP v. 4,1,2,3,5364246,50.754456,5613,5324,unknown,,,USA,USA,,,,,,,,,,,,,,,,,"Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer (i.e. conjugation) are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide large scale, quantitative analysis of HGT in widespread and multidrug resistant E. coli pathogens of pressing clinical concern. We find a substantial proportion of clinical E. coli pathogens (≥25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied mechanism of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates (F(6, 53) = 111.6, p < 0.0001, ANOVA) with transfer efficiency that varies over 5 orders of magnitude. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.",collected_by:Deverick Anderson,,,,,,,Unknown,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.50569,Escherichia coli strain UPEC132,UPEC132,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11664985,562,,,,MLST.Escherichia_coli_2.36,,,,2019-08-05T00:00:00Z,,PRJNA543375,GCA_007833875.1,"CP040456,CP040454,CP040455",,Tianjin Centers for Disease Control and Prevention,PacBio Sequel,50.0x,FALCON v. JAN-2019,1,2,3,5452963,50.514114,5436,,urinary,,1992-02-08,China,China: Tianjin,,,,,,,,,,,,,,,,,To study the antimicrobial resistance and virulence mechanism of uropathogenic Escherichia coli,sample_type:culture,,,,,,,,,,,,,,,,,,,,,99.97,0.08,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.50776,Escherichia coli strain AR Bank #0349,AR Bank #0349,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12272266,562,,,,"MLST.Escherichia_coli_2.594,MLST.Escherichia_coli_1.457",,,,2019-08-30T00:00:00Z,,PRJNA554502,GCA_008152105.1,"CP041996,CP041997",,USDA-ARS,PacBio RSII; Illumina MiSeq,277.0x,Unicycler v. 0.4.4; Canu v. 1.8; Pilon v.,1,1,2,5273509,50.39819,5288,5047,missing,,,,,,,,"Gastroenteritis, diarrhea, UTI, pneumonia, food poisoning",,,,,,,,,,,,,complete genome sequence of Escherichia coli AR Bank # 0349,,,,,,,,"Gastroenteritis, diarrhea, UTI, pneumonia, food poisoning",,,,,,,,,,,,,,99.97,0.16,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,562.50817,Escherichia coli strain ESBL 15,ESBL 15,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12275742,562,,,,"MLST.Escherichia_coli_1.40,MLST.Escherichia_coli_2.126",genotype:ST40,,,2019-09-12T00:00:00Z,31485077,PRJNA554638,GCA_008370755.1,"CP041678,CP041679,CP041680,CP041681",,ETH Zurich,Illumina MiSeq; Oxford Nanopore MiniION,105.0x,Unicycler v. 0.4.7,1,3,4,5099245,50.63834,5260,4959,rectum,"isolated at the University Hospital Basel and Felix Platter Hospital, as part of a hospital transmission study",2013-08-08,Switzerland,Switzerland: Basel,,,,colonisation,,,,,,,,,,,,,"ESBL-producing E. coli isolated at the University Hospital Basel and Felix Platter Hospital, as part of a hospital transmission study.",collected_by:University Hospital Basel,,,,,,,colonisation,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.50847,Escherichia coli strain ETEC6,ETEC6,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12263012,562,,,,MLST.Escherichia_coli_1.48,,,,2019-09-13T00:00:00Z,,PRJNA554338,GCA_008375335.1,CP041627,,Harvard Medical School,Illumina MiSeq; Oxford Nanopore MiniION,70.4x,SPAdes v. 3.13.0,1,,1,4790657,50.89895,4921,4641,missing,,2016-09-24,Bangladesh,Bangladesh,,,,,,,,,,,,,,,,,Importance of transplacental or milk antibodies in protection of neonates from enteric pathogens,collected_by:Wenjing Zhao,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,562.51001,Escherichia coli strain 4928STDY7071353,4928STDY7071353,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567463,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164685.1,LR607328,,SC,,,,1,,1,5132864,50.608727,4933,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.67,0.08,,,Other,- NHP,562.51002,Escherichia coli strain 4928STDY7071340,4928STDY7071340,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567450,562,,,,"MLST.Escherichia_coli_1.104,MLST.Escherichia_coli_2.519",,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164715.1,LR607331,,SC,,,,1,,1,5120867,50.696087,4769,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.37,0.23,,,Other,- HP,562.51580,Escherichia coli strain NZRM4169,NZRM4169,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10177969,562,O157:H7,,Escherichia coli -STEC,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2019-10-09T00:00:00Z,,PRJNA494713,GCA_008925965.1,"CP032789,CP032790",,United State Department of Agriculture,PacBio RSII,173x,HGAP v. 2.3.0,1,1,2,5596785,50.480072,5995,5711,missing,,2003,New Zealand,New Zealand,,,,,,,,,,,,,,,,,The aim of this project is to provided complete closed Shiga toxin-containing Escherichia coli O157:H7 genomes from New Zealand to use for genomic comparison with STEC O157:H7 strains from other countries.,collected_by:Not collected,,,,,,,not collected,,,,,Escherichia coli -STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.51581,Escherichia coli strain NZRM4165,NZRM4165,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10177968,562,O157:HNM,,Escherichia coli -STEC,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2019-10-09T00:00:00Z,,PRJNA494713,GCA_008926085.1,"CP032791,CP032792",,United State Department of Agriculture,PacBio RSII,186x,HGAP v. 2.3.0,1,1,2,5504500,50.474377,5843,5552,missing,,2003,New Zealand,New Zealand,,,,,,,,,,,,,,,,,The aim of this project is to provided complete closed Shiga toxin-containing Escherichia coli O157:H7 genomes from New Zealand to use for genomic comparison with STEC O157:H7 strains from other countries.,collected_by:Not collected,,,,,,,not collected,,,,,Escherichia coli -STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.51602,Escherichia coli strain XDL,XDL,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10691120,562,,,,"MLST.Escherichia_coli_1.354,MLST.Escherichia_coli_2.39",,,,2019-10-09T00:00:00Z,31154009,PRJNA512967,GCA_008949495.1,SAIZ00000000,,Sir Run Run Shaw Hospital,PacBio RSII,100x,Unicycler v. 0.4.7,1,5,6,5540143,50.222313,5664,5347,blood,isolated from blood of a patient,2017-09-20,China,China: Hangzhou,,,,Bloodstream infections,,,,,,,,,,,,,This study is to identified a new variant of mcr-1 gene in Escherichia coli XDL isolated from blood of a patient.,collected_by:Feng Zhao,,,,,,,Bloodstream infections,,,,,,,,,,,,,,99.93,0.71,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.52507,Escherichia coli strain 04-00955,04-00955,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10740161,562,,,,MLST.Escherichia_coli_1.141,,,,2019-10-28T00:00:00Z,,PRJNA514979,GCA_004564035.1,CP035498,,"Muenster university hospital, University of Muenster,",PacBio Sequel,1x,HGAP v. 4,1,,1,5349824,50.58075,5441,5178,stool,,2004,Germany,Germany,,,,Diarrhea,,,,,,,,,,,,,Heteropathogenic Shiga toxin (Stx)-producing Escherichia coli (STEC) of multilocus sequence type (MLST ST) 141 cause both urinary tract infection and diarrhea in humans. We could show previously that they possess virulence genes typical for STEC and uropathogenic E. coli (UPEC) and are phylogenetically positioned between these pathogroups. However the origin and evolution of these strains with respect to other pathogroups is unknown. Our aim is to investigate the origin and the evolution of ST141 using phylogenomics.,"collected_by:Institute of Hygiene, University Hospital Muenster, Muenster, Germany",,,,,,,Diarrhea,,,,,,,,,,,,,,99.97,0.12,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.52722,Escherichia coli strain AUSMDU00014361,AUSMDU00014361,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11008224,562,O26:H11,,,"MLST.Escherichia_coli_1.29,MLST.Escherichia_coli_2.481",mlst:ST29,,,2019-11-12T00:00:00Z,33180013,PRJNA556438,GCA_009650035.1,"CP045827,CP045828,CP045829,CP045830",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,89.0x,de novo,1,3,4,5774445,50.653336,6165,5675,missing,,2015,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.53932,Escherichia coli strain AUSMDU00002545,AUSMDU00002545,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191633,562,O157:H7,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",mlst:ST11,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664455.1,"CP045975,CP045976",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,68x,de novo,1,1,2,5647778,50.47716,5895,5464,missing,,2013,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.53977,Escherichia coli strain EC2,EC2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12307470,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",genotype:ST167,,,2019-11-29T00:00:00Z,,PRJNA555326,GCA_009720465.1,"CP041955,CP041956,CP041957,CP041958,CP041959,CP041960",,The University of Texas Health Science Center at Houston,Oxford Nanopore GridION,715x,Celera Assembler v. 1.8,1,5,6,5201916,50.653183,5294,5020,urine,,2017-09-29,USA,USA:Houston,,,,sepsis,,,,,,,,,,,,,"Submission of consensus genome assemblies from a critically ill patient with polymicrobial infections due to multi-drug resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa who had traveled to India and was also colonized by Candida auris. A precision medicine approach using whole genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181. This case illustrates the rapidly evolving landscape of resistance and its challenges to clinicians.",collected_by:William R. Miller,,,,,,,sepsis,,,,,,,,,,,,,,99.67,0.24,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,562.53978,Escherichia coli strain ECO2947,ECO2947,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13335779,562,,,,,,,,2019-11-30T00:00:00Z,,PRJNA590596,GCA_009720605.1,"CP046259,CP046261,CP046260",,Center for Disease Control and Prevention of PLA,Illumina HiSeq; Oxford Nanopore MiniION,130.0x,unicycler v. v0.4.8-beta,1,2,3,5059444,50.741127,5087,4810,pus,,2018-07-14,China,China:guangzhou,,,,,,,,,,,,,,,,,Multidrug-resistant Enterobacter cloacae harboring blaNDM-5 recovered from China,collected_by:Lanfen Lu,,,,,,,none,,,,,,,,,,,,,,99.93,0.16,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,562.54033,Escherichia coli strain P225M,P225M,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12789774,562,,,,"MLST.Escherichia_coli_2.478,MLST.Escherichia_coli_1.10",,,,2019-12-18T00:00:00Z,,PRJNA566431,GCA_009762495.1,"CP044346,CP044348,CP044347",,Tufts University,Oxford Nanopore MinION; Illumina NextSeq,20.0x,Unicycler v. 2018-07-01T00:00:00,1,2,3,5008304,50.93493,5322,4845,healthy human (stool),"recovered from food and healthy, gut-colonized humans in Cambodia are described",2015,Cambodia,Cambodia,,,,,,,,,,,,,,,,,"The complete nucletotide sequences of 5 ESBL-producing E. coli recovered from food and healthy, gut-colonized humans in Cambodia are described. Hybrid assemblies (Illumina + Minion) revealed ESBL genes were primarily plasmid encoded.",collected_by:Institut Pasteur du Cambodge,,,,,,,,,,,,,,,,,,,,,97.98,0.04,,,Gastrointestinal,- NHP,562.54034,Escherichia coli strain P276M,P276M,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12789775,562,,,,MLST.Escherichia_coli_1.48,,,,2019-12-18T00:00:00Z,,PRJNA566431,GCA_009762385.1,"CP044293,CP044294",,Tufts University,Oxford Nanopore MinION; Illumina NextSeq,20.0x,Unicycler v. 2018-07-01T00:00:00,1,1,2,4642465,50.702118,4769,4434,healthy human (stool),"recovered from food and healthy, gut-colonized humans in Cambodia are described",2015,Cambodia,Cambodia,,,,,,,,,,,,,,,,,"The complete nucletotide sequences of 5 ESBL-producing E. coli recovered from food and healthy, gut-colonized humans in Cambodia are described. Hybrid assemblies (Illumina + Minion) revealed ESBL genes were primarily plasmid encoded.",collected_by:Institut Pasteur du Cambodge,,,,,,,,,,,,,,,,,,,,,98.83,0.1,,,Gastrointestinal,- HP,562.55131,Escherichia coli strain NCCP 15739,NCCP 15739,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12302771,562,,,,,,,,2020-01-14T00:00:00Z,,PRJNA555173,GCA_009873355.1,"CP041747,CP041748",,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,181.0x,SPAdes v. 3.1,1,1,2,5567406,50.486385,6125,5562,stool,,2010-07-19,South Korea,South Korea: Busan,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Escherichia,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,99.67,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.55132,Escherichia coli strain NCCP 15955,NCCP 15955,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12302778,562,,,,"MLST.Escherichia_coli_2.367,MLST.Escherichia_coli_1.10",,,,2020-01-14T00:00:00Z,,PRJNA555176,GCA_009873375.1,CP041749,,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,261.0x,SPAdes v. 3.1,1,0,1,4820620,50.586666,5084,4701,stool,,2014-01-01,South Korea,South Korea: Jeonnam,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Escherichia,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,90.78,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.55133,Escherichia coli strain NCCP 14539,NCCP 14539,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12302750,562,,,,"MLST.Escherichia_coli_2.480,MLST.Escherichia_coli_1.16",,NCCP:14539,,2020-01-14T00:00:00Z,,PRJNA555167,GCA_009873415.1,CP042981,,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,225.0x,SPAdes v. 3.1,1,0,1,5315402,50.610245,5962,5274,stool,,2003-01-01,South Korea,South Korea: Gwangju,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Escherichia,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,99.26,0.08,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.55134,Escherichia coli strain NCCP 14540,NCCP 14540,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12302764,562,,,,MLST.Escherichia_coli_2.481,,NCCP:14540,,2020-01-14T00:00:00Z,,PRJNA555170,GCA_009873435.1,CP042982,,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,220.0x,SPAdes v. 3.1,1,0,1,5538597,50.573547,6249,5626,stool,,2003-01-01,South Korea,South Korea: Gyeonggi,,,,diarrhea,,,,,,,,,,,,,A clinical isolate of the genus Escherichia,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,95.57,0.35,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases NHP,562.55235,Escherichia coli strain 2EC1,2EC1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13756204,562,,,,MLST.Escherichia_coli_1.4977,,,,2020-01-19T00:00:00Z,,PRJNA599529,GCA_009905115.1,"CP047571,CP047572,CP047573,CP047574,CP047575",,Temasek Life Sciences Laboratory Limited,Oxford Nanopore MiniION; Illumina NovaSeq,421.0x,Unicycler v. v0.4.8,1,4,5,4868589,50.89801,4929,4616,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-01,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.93,0.45,,,Gastrointestinal,- NHP,562.55236,Escherichia coli strain 94EC,94EC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13756518,562,,,,MLST.Escherichia_coli_1.156,,,,2020-01-19T00:00:00Z,,PRJNA599529,GCA_009905135.1,"CP047576,CP047577,CP047578,CP047579,CP047580,CP047581,CP047582",,Temasek Life Sciences Laboratory Limited,Oxford Nanopore MiniION; Illumina NovaSeq,433.0x,Unicycler v. v0.4.8,1,6,7,5240704,50.546913,5269,4971,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.93,0.35,,,Gastrointestinal,- HP,562.58133,Escherichia coli strain 201609,201609,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13880799,562,,,,MLST.Escherichia_coli_1.648,genotype:ST648,,,2020-02-03T00:00:00Z,,PRJNA602061,GCA_010092965.1,CP048107,,Institute of Microbiology,Oxford Nanopore GridION,140.0x,canu v. v1.3,1,0,1,5195374,50.414425,5209,4830,urine,,2016-09,China,"China: Jiangsu,Xuzhou",,,,recurrent urinary tract infection,,,,,,,,,,,,,"A clinical ESBL, Carbapenemase and MCR-1-producing Escherichia coli ST648 isolate Carrying Three Resistance Plasmids",collected_by:the Affiliated Hospital of Xuzhou Medical University;lab_host:not applicable,,,,,,,recurrent urinary tract infection,,,,,,,,,,,,,,99.57,0.16,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.58217,Escherichia coli strain E138,E138,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00108729,562,,,,,,,,2020-02-01T00:00:00Z,,PRJDB6565,GCA_010724935.1,AP022351,,"Thailand-Japan Research Collaboration Center on Emerging and Re-emerging infections, Research Institute for Microbial Diseases, Osaka University",GridION; Illumina MiSeq,202x,flye v. 2.6,1,0,1,4812157,50.81345,4748,4501,human stool,,2015-12,Japan,Japan:Osaka,,,,,,,,,,,,,,,,,"The purpose of this project is to investigate whether and to what extent infections caused by carbapenem-resistant Enterobacteriaceae are expanding in Osaka, Japan\; to identify plasmids and its carrying carbapenemase genes responsible for the resistance\; to unveil the mechanism whereby resistant bacteria spread in this region.",,not applicable,not applicable,feces,missing,Molecular epidemiology of carbapenem-resistant Enterobacteriaceae,,,,,,,,,,,,not applicable,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.58218,Escherichia coli strain E302,E302,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00186874,562,,,,MLST.Escherichia_coli_1.131,,,,2020-02-01T00:00:00Z,,PRJDB6565,GCA_010725305.1,AP022362,,"Thailand-Japan Research Collaboration Center on Emerging and Re-emerging infections, Research Institute for Microbial Diseases, Osaka University","GridION, Illumina MiSeq",1x,flye v. 2.6,1,0,1,5237933,50.84433,5268,4976,human stool,,2015-12-01,Japan,Japan:Osaka,,,,,,,,,,,,,,,,,"The purpose of this project is to investigate whether and to what extent infections caused by carbapenem-resistant Enterobacteriaceae are expanding in Osaka, Japan\; to identify plasmids and its carrying carbapenemase genes responsible for the resistance\; to unveil the mechanism whereby resistant bacteria spread in this region.",,not applicable,not applicable,not applicable,missing,Molecular epidemiology of carbapenem-resistant Enterobacteriaceae,,,,,,,,,,,,not applicable,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.58277,Escherichia coli strain 190693,190693,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14137859,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.315",,,,2020-02-26T00:00:00Z,,PRJNA607545,GCA_011022275.1,CP048934,,Liverpool School of Tropical Medicine,Oxford Nanopore MiniION; Illumina MiSeq,76.0x,Unicycler v. 0.4.7,1,0,1,5151952,50.643017,5127,4827,blood culture,,2016-11-15,United Kingdom,United Kingdom: Liverpool,,,,Bacteremia,,,,,,,,,,,,,"Clonal pair of clinical isolates of E. coli, one isolate is TZP susceptible and one isolate is TZP resistant",collected_by:The Royal Liverpool University Hospital,,,,,,,Bacteremia,,,,,,,,,,,,,,99.93,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.58366,Escherichia coli strain EC28,EC28,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14149865,562,,,,"MLST.Escherichia_coli_1.429,MLST.Escherichia_coli_2.634",,,,2020-03-01T00:00:00Z,,PRJNA607867,GCA_011044355.1,"CP049101,CP049102,CP049104,CP049105,CP049106,CP049103",,Zhejiang Provincial People's Hospital,Oxford Nanopore GridION; Illumina NextSeq,250.0x,Unicycler v. v. 0.4.7,1,5,6,5260133,50.275307,5300,5015,urine,,2018-06-03,China,China:Hangzhou,,,,urinary tract infection,,,,,,,,,,,,,Escherichia coli EC28,collected_by:Fang He,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.97,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.59215,Escherichia coli strain 8-3-DC15,8-3-DC15,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14482837,562,,,,MLST.Escherichia_coli_1.270,,,,2020-04-09T00:00:00Z,29266651,PRJNA616136,GCA_012221365.1,"CP050862,CP050863,CP050864",,Monash University,Illumina NextSeq; Oxford Nanopore MiniION,34x,Unicycler v. 0.4.8,1,2,3,5142316,50.824005,5456,5140,colonoscopy,,2010,Australia,Australia: Canberra,,,,Crohn's disease,,,,,,,,,,,,,Completion of two ST270 EIEC genomes for use as references,collected_by:David Gordon,,,,,,,Crohn's disease,,,,,,,,,,,,,,99.57,0.2,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,562.59216,Escherichia coli strain 8-3-Ti3,8-3-Ti3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14482836,562,,,,MLST.Escherichia_coli_1.270,,,,2020-04-09T00:00:00Z,29266651,PRJNA616136,GCA_012221565.1,"CP050865,CP050866,CP050867",,Monash University,Illumina NextSeq; Oxford Nanopore MiniION,35x,Unicycler v. 0.4.8,1,2,3,5141082,50.823658,5459,5137,colonoscopy,,2010,Australia,Australia: Canberra,,,,Crohn's disease,,,,,,,,,,,,,Completion of two ST270 EIEC genomes for use as references,collected_by:David Gordon,,,,,,,Crohn's disease,,,,,,,,,,,,,,99.57,0.2,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases NHP,562.60261,Escherichia coli strain SCU-102,SCU-102,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609768,562,,,,"MLST.Escherichia_coli_1.973,MLST.Escherichia_coli_2.597",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934435.1,CP051753,,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",67x,Unicycler v. 0.4.8,1,0,1,4863332,50.590275,4687,4460,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.07,,,Gastrointestinal,- NHP,562.60262,Escherichia coli strain SCU-105,SCU-105,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609770,562,,,,"MLST.Escherichia_coli_2.77,MLST.Escherichia_coli_1.394",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934455.1,"CP051738,CP051739,CP051740,CP051741,CP051742,CP051743",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",57x,Unicycler v. 0.4.8,1,5,6,5367348,50.43474,5387,5055,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.38,,,Gastrointestinal,- NHP,562.60263,Escherichia coli strain SCU-108,SCU-108,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609773,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934475.1,"CP051735,CP051736,CP051737",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",37x,Unicycler v. 0.4.8,1,2,3,5239110,50.594395,5315,4999,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.42,,,Gastrointestinal,- NHP,562.60264,Escherichia coli strain SCU-109,SCU-109,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609774,562,,,,MLST.Escherichia_coli_1.963,,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934495.1,"CP051733,CP051734",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",32x,Unicycler v. 0.4.8,1,1,2,5144298,50.72255,5050,4764,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.36,,,Gastrointestinal,- NHP,562.60265,Escherichia coli strain SCU-111,SCU-111,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609775,562,,,,"MLST.Escherichia_coli_1.491,MLST.Escherichia_coli_2.375",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934515.1,"CP051727,CP051732,CP051728,CP051729,CP051730,CP051731",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",120x,Unicycler v. 0.4.8,1,5,6,5079785,50.70494,5014,4738,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.82,1.13,,,Gastrointestinal,- NHP,562.60266,Escherichia coli strain SCU-112,SCU-112,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609776,562,,,,MLST.Escherichia_coli_1.73,,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934535.1,"CP051725,CP051726",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",25x,Unicycler v. 0.4.8,1,1,2,5198425,50.531303,5154,4846,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.08,,,Gastrointestinal,- NHP,562.60267,Escherichia coli strain SCU-116,SCU-116,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609778,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934555.1,"CP051719,CP051720,CP051721,CP051722,CP051723,CP051724",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",21x,Unicycler v. 0.4.8,1,5,6,5167467,50.760864,5165,4877,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.33,,,Gastrointestinal,- NHP,562.60268,Escherichia coli strain SCU-118,SCU-118,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609779,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.10",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934575.1,"CP051716,CP051717,CP051718",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",30x,Unicycler v. 0.4.8,1,2,3,4702137,50.65988,4672,4397,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.1,,,Gastrointestinal,- NHP,562.60269,Escherichia coli strain SCU-124,SCU-124,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609784,562,,,,"MLST.Escherichia_coli_1.357,MLST.Escherichia_coli_2.404",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934635.1,"CP051706,CP051707,CP051708,CP051709,CP051710",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",36x,Unicycler v. 0.4.8,1,4,5,4954354,50.56611,5006,4702,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.85,0.36,,,Gastrointestinal,- NHP,562.60270,Escherichia coli strain SCU-123,SCU-123,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609783,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934615.1,"CP051711,CP051712,CP051713",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",44x,Unicycler v. 0.4.8,1,2,3,5260004,50.631367,5325,5009,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.39,,,Gastrointestinal,- NHP,562.60271,Escherichia coli strain SCU-122,SCU-122,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609782,562,,,,"MLST.Escherichia_coli_2.694,MLST.Escherichia_coli_1.95",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934595.1,"CP051714,CP051715",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",20x,Unicycler v. 0.4.8,1,1,2,5025250,50.622257,4992,4705,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.39,,,Gastrointestinal,- NHP,562.60272,Escherichia coli strain SCU-152,SCU-152,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609787,562,,,,MLST.Escherichia_coli_1.54,,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934675.1,"CP051698,CP051699",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",24x,Unicycler v. 0.4.8,1,1,2,4874580,50.869,4841,4524,rectal swab from healthy college student,,2013,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.93,0.1,,,Gastrointestinal,- NHP,562.60273,Escherichia coli strain SCU-125,SCU-125,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609785,562,,,,"MLST.Escherichia_coli_2.55,MLST.Escherichia_coli_1.144",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934655.1,"CP051700,CP051701,CP051702,CP051703,CP051704,CP051705",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",14x,Unicycler v. 0.4.8,1,5,6,5280374,50.763767,5351,5076,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.17,,,Gastrointestinal,- NHP,562.60274,Escherichia coli strain SCU-301,SCU-301,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609790,562,,,,MLST.Escherichia_coli_1.967,,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934695.1,"CP051751,CP051752",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",20x,Unicycler v. 0.4.8,1,1,2,5060858,50.613018,4981,4702,rectal swab from healthy college student,,,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.17,,,Gastrointestinal,- NHP,562.60275,Escherichia coli strain SCU-313,SCU-313,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609793,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934715.1,"CP051694,CP051695,CP051696,CP051697",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",28x,Unicycler v. 0.4.8,1,3,4,5264512,50.817265,5325,4973,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.47,,,Gastrointestinal,- NHP,562.60277,Escherichia coli strain SCU-387,SCU-387,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609795,562,,,,"MLST.Escherichia_coli_2.6,MLST.Escherichia_coli_1.14",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934765.1,"CP051688,CP051689,CP051690,CP051691",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",18x,Unicycler v. 0.4.8,1,3,4,5514160,50.49032,5666,5241,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.89,0.04,,,Gastrointestinal,- NHP,562.60278,Escherichia coli strain SCU-486,SCU-486,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609802,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934815.1,"CP051749,CP051750",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",30x,Unicycler v. 0.4.8,1,1,2,5282735,50.512413,5497,4989,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.55,0.47,,,Gastrointestinal,- NHP,562.60279,Escherichia coli strain SCU-484,SCU-484,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609800,562,,,,"MLST.Escherichia_coli_1.998,MLST.Escherichia_coli_2.129",,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934785.1,"CP051744,CP051745,CP051746,CP051747,CP051748",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",38x,Unicycler v. 0.4.8,1,4,5,5236765,50.56681,5263,4913,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.11,,,Gastrointestinal,- HP,562.60286,Escherichia coli strain SCAID URN1-2019,SCAID URN1-2019,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14653305,562,,,,"MLST.Escherichia_coli_1.998,MLST.Escherichia_coli_2.129",,,,2020-05-03T00:00:00Z,,PRJNA627194,GCA_012955465.1,CP052057,,Scientific Center for Anti-infectious Drugs (SCAID),IonTorrent,16x,Bowtie v. 1.2.3,1,0,1,4937450,50.705578,5028,4577,urine,,2019-03-08,Kazakhstan,Kazakhstan: Almaty,,female,71,Chronic cystitis,,host_disease_outcome:Chronic disease;host_disease_stage:Chronic cystitis,Resistant;Susceptible,AMR Panel,,,,,,,,,"Creating experimental models on the basis of clinical isolates that are characterized by multiple drug resistance, in order to clarify the universality of the reversion phenomenon","collected_by:Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,Chronic cystitis,,Chronic disease,,Chronic cystitis,,,,,,,,,,98.59,3.62,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI NHP,562.60288,Escherichia coli strain SCU-101,SCU-101,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14125718,562,,,,"MLST.Escherichia_coli_1.1262,MLST.Escherichia_coli_2.29",,,,2020-05-05T00:00:00Z,,PRJNA607272,GCA_012974565.1,CP048920,,Santa Clara University,Illumina MiSeq; Oxford Nanopore MiniION,163.0x,Unicycler v. 0.4.8,1,0,1,5357129,50.45962,5374,5041,rectal swab from college student,,2015,USA,"USA: Santa Clara, CA",,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:Rectal swab streaked on Chromagar Orientation agar,,,,,,,,,,,,,,,,,,,,,99.97,0.08,,,Gastrointestinal,- NHP,562.60433,Escherichia coli strain SCU-482,SCU-482,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609798,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",,,,2020-05-13T00:00:00Z,,PRJNA624897,GCA_013085025.1,"CP053247,CP053248,CP053249,CP053250",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",34x,Unicycler v. 0.4.8,1,3,4,5304260,50.78735,5456,5040,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.09,,,Gastrointestinal,- NHP,562.60434,Escherichia coli strain SCU-306,SCU-306,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609791,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2020-05-13T00:00:00Z,,PRJNA624897,GCA_013084945.1,"CP053231,CP053232,CP053233",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",29x,Unicycler v. 0.4.8,1,2,3,5270261,50.53501,5409,5004,rectal swab from healthy college student,,,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.89,,,Gastrointestinal,- NHP,562.60435,Escherichia coli strain SCU-485,SCU-485,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609801,562,,,,"MLST.Escherichia_coli_1.420,MLST.Escherichia_coli_2.61",,,,2020-05-13T00:00:00Z,,PRJNA624897,GCA_013085205.1,"CP053245,CP053246",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",27x,Unicycler v. 0.4.8,1,1,2,4787332,50.639355,4775,4495,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- NHP,562.60436,Escherichia coli strain SCU-106,SCU-106,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609771,562,,,,,,,,2020-05-13T00:00:00Z,,PRJNA624897,GCA_013085185.1,"CP053234,CP053235,CP053244,CP053236,CP053237,CP053238,CP053239,CP053240,CP053241,CP053242,CP053243",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",14x,Unicycler v. 0.4.8,1,10,11,5507015,50.75924,5658,5269,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.78,0.1,,,Gastrointestinal,- NHP,562.60437,Escherichia coli strain SCU-308,SCU-308,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609792,562,,,,"MLST.Escherichia_coli_2.24,MLST.Escherichia_coli_1.58",,,,2020-05-14T00:00:00Z,,PRJNA624897,GCA_013085865.1,"CP053281,CP053282,CP053283",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",33x,Unicycler v. 0.4.8,1,2,3,5202081,50.76534,5340,4905,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.87,0.41,,,Gastrointestinal,- NHP,562.60438,Escherichia coli strain SCU-204,SCU-204,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609789,562,,,,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2020-05-14T00:00:00Z,,PRJNA624897,GCA_013085905.1,"CP053251,CP053253,CP053252,CP053254,CP053255",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",102x,Flye v. 2.6,1,4,5,5348913,50.481785,5557,5110,rectal swab from healthy college student,,2013,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.85,0.39,,,Gastrointestinal,- NHP,562.61462,Escherichia coli strain SCU-318,SCU-318,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609794,562,,,,MLST.Escherichia_coli_1.106,,,,2020-04-30T00:00:00Z,,PRJNA624897,GCA_012934735.1,"CP051692,CP051693",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",22x,Flye v. 2.6,1,1,2,5019349,50.627583,5327,4684,rectal swab from healthy college student,,,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99,0.19,,,Gastrointestinal,- NHP,562.61487,Escherichia coli strain SCU-171,SCU-171,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943544,562,,,,MLST.Escherichia_coli_1.657,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315715.1,"CP054363,CP054364,CP054365,CP054366,CP054367",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",74x,Unicycler v. 0.4.8,1,4,5,5370190,50.76628,5522,5168,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.09,,,Gastrointestinal,- NHP,562.61488,Escherichia coli strain SCU-172,SCU-172,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943545,562,,,,MLST.Escherichia_coli_1.379,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315695.1,"CP054353,CP054354,CP054355,CP054356,CP054357,CP054358,CP054359,CP054360,CP054361,CP054362",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",78x,Unicycler v. 0.4.8,1,9,10,5428728,50.78858,5610,5273,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.86,0.06,,,Gastrointestinal,- NHP,562.61489,Escherichia coli strain SCU-115,SCU-115,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943543,562,,,,MLST.Escherichia_coli_1.1155,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315735.1,"CP054368,CP054369,CP054370",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",70x,Unicycler v. 0.4.8,1,2,3,5084986,50.59412,5100,4788,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.33,,,Gastrointestinal,- NHP,562.61490,Escherichia coli strain SCU-176,SCU-176,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943547,562,,,,"MLST.Escherichia_coli_1.550,MLST.Escherichia_coli_2.6",,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315675.1,"CP054345,CP054346,CP054347,CP054348,CP054349,CP054350,CP054351,CP054352",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",100x,Unicycler v. 0.4.8,1,7,8,5088045,50.5315,5107,4797,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.22,,,Gastrointestinal,- NHP,562.61491,Escherichia coli strain SCU-104,SCU-104,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609769,562,,,,MLST.Escherichia_coli_2.2,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315995.1,"CP053284,CP053285",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",47x,Unicycler v. 0.4.8,1,1,2,5245988,50.71895,5308,4960,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.09,,,Gastrointestinal,- NHP,562.61492,Escherichia coli strain SCU-316,SCU-316,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943536,562,,,,"MLST.Escherichia_coli_1.57,MLST.Escherichia_coli_2.305",,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315755.1,CP054371,,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",95x,Unicycler v. 0.4.8,1,0,1,4957282,50.726063,4880,4570,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.67,0.04,,,Gastrointestinal,- NHP,562.61493,Escherichia coli strain SCU-390,SCU-390,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609796,562,,,,MLST.Escherichia_coli_2.53,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315875.1,"CP054319,CP054321,CP054320,CP054322,CP054323,CP054324",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",13x,Flye v. 2.6,1,5,6,5147113,50.553894,6067,4901,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,98.15,0.69,,,Gastrointestinal,- NHP,562.61494,Escherichia coli strain SCU-479,SCU-479,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609797,562,,,,MLST.Escherichia_coli_1.2279,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315855.1,"CP054317,CP054318",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",31x,Flye v. 2.6,1,1,2,5303425,50.634636,6140,5034,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.21,0.62,,,Gastrointestinal,- NHP,562.61495,Escherichia coli strain SCU-483,SCU-483,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609799,562,,,,,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315835.1,"CP054314,CP054316,CP054315",,Santa Clara University,Illumina MiSeq; Oxford Nanopore MinION,43x,Flye v. 2.6,1,2,3,5084433,50.776184,5879,4867,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.14,0.04,,,Gastrointestinal,- NHP,562.61496,Escherichia coli strain SCU-121,SCU-121,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609781,562,,,,MLST.Escherichia_coli_1.91,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315915.1,"CP054328,CP054329,CP054330,CP054331,CP054332,CP054333,CP054334",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",12x,Flye v. 2.6,1,6,7,5044654,50.619816,6010,4791,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,97.31,0.14,,,Gastrointestinal,- NHP,562.61497,Escherichia coli strain SCU-120,SCU-120,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609780,562,,,,MLST.Escherichia_coli_1.648,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315935.1,"CP054335,CP054336,CP054337,CP054338,CP054339,CP054340,CP054341,CP054342",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",35x,Flye v. 2.6,1,7,8,5457435,50.55694,6180,5202,rectal swab from healthy college student,,2016,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.31,0.58,,,Gastrointestinal,- NHP,562.61498,Escherichia coli strain SCU-147,SCU-147,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609786,562,,,,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315895.1,"CP054325,CP054326,CP054327",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",34x,Flye v. 2.6,1,2,3,5179875,50.54766,6121,4908,rectal swab from healthy college student,,2013,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,97.77,1.12,,,Gastrointestinal,- NHP,562.61499,Escherichia coli strain SCU-113,SCU-113,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609777,562,,,,,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013315975.1,CP051765,,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",86x,Unicycler v. 0.4.8,1,0,1,4765874,50.866577,4630,4422,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.93,0.35,,,Gastrointestinal,- HP,562.61501,Escherichia coli strain MS6193,MS6193,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13155539,562,,,,"MLST.Escherichia_coli_2.88,MLST.Escherichia_coli_1.2480",,,,2020-06-10T00:00:00Z,,PRJNA580336,GCA_013317085.1,"CP047405,CP047406,CP047407,CP047408",,The University of Melbourne,PacBio RSII; Illumina HiSeq,86.7x,HGAP v. 2.3.0,1,3,4,5146790,50.737217,5092,4849,clinical sample: urine,,2003-2009,India,India: South,,,,urinary tract infection,,,,,,,,,,,,,"Extraintestinal pathogenic Escherichia coli (ExPEC) are the leading cause of urinary and systemic infections, where antibiotic resistance complicates successful treatment. Carbapenems are considered a last-resort antibiotic, however the spread of plasmid-encoded carbapenemases such as the New-Delhi Metallo-beta-Lactamase (blaNDM-1) challenges their effectiveness. E. coli ST101 is an emerging, atypical multidrug resistant ExPEC lineage, highly associated with the carriage of blaNDM-1. In this study we analysed the phylogeny and antimicrobial resistance of ST101 isolates from the UK and India.",collected_by:Timothy R Walsh,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.93,0.16,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases NHP,562.61516,Escherichia coli strain SCU-103,SCU-103,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943534,562,,,,,,,,2020-06-14T00:00:00Z,,PRJNA624897,GCA_013341375.1,"CP054457,CP054458,CP054459,CP054460,CP054461,CP054462,CP054463,CP054464",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",57x,"Flye, Unicycler v. 2.6, 0.4.8",1,7,8,5443100,50.912937,6991,5353,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,96.72,0.19,,,Gastrointestinal,- NHP,562.61517,Escherichia coli strain SCU-488,SCU-488,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943542,562,,,,MLST.Escherichia_coli_2.1,,,,2020-06-14T00:00:00Z,,PRJNA624897,GCA_013341335.1,"CP054449,CP054450,CP054451,CP054452,CP054453",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",44x,Flye v. 2.6,1,4,5,5239746,50.626118,6160,4995,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.04,0.39,,,Gastrointestinal,- NHP,562.61518,Escherichia coli strain SCU-487,SCU-487,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943541,562,,,,MLST.Escherichia_coli_1.95,,,,2020-06-14T00:00:00Z,,PRJNA624897,GCA_013341355.1,"CP054454,CP054455,CP054456",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",47x,"Flye, Unicycler v. 2.6, 0.4.8",1,2,3,5109488,50.56405,5899,4836,rectal swab from healthy college student,,2018,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,98.94,0.07,,,Gastrointestinal,- NHP,562.61573,Escherichia coli strain SCU-182,SCU-182,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943535,562,,,,MLST.Escherichia_coli_1.131,,,,2020-06-10T00:00:00Z,,PRJNA624897,GCA_013344585.1,"CP054372,CP054373,CP054374,CP054375,CP054376,CP054377,CP054378",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",91x,"Flye, Unicycler v. 2.6, 0.4.8",1,6,7,5192998,50.814114,5245,4940,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.36,,,Gastrointestinal,- NHP,562.61584,Escherichia coli strain SCU-164,SCU-164,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609788,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2020-06-16T00:00:00Z,,PRJNA624897,GCA_013347985.1,"CP054343,CP054344",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",47x,Unicycler v. 0.4.8,1,1,2,5535386,50.605064,5615,5250,rectal swab from healthy college student,,,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.95,0.13,,,Gastrointestinal,- HP,562.61593,Escherichia coli strain MS6192,MS6192,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13155204,562,,,ExPEC,"MLST.Escherichia_coli_2.88,MLST.Escherichia_coli_1.2480",,,,2020-06-17T00:00:00Z,,PRJNA580334,GCA_013357345.1,"CP054940,CP054941,CP054942,CP054943,CP054944",,The University of Melbourne,PacBio RS; Illumina HiSeq,112.93x,HGAP v. 2.3.0,1,4,5,5188554,50.71916,5169,4896,clinical sample: urine,,2003-2009,India,India:South,,,,urinary tract infection,,,,,,,,,,,,,"Extraintestinal pathogenic Escherichia coli (ExPEC) are the leading cause of urinary and systemic infections, where antibiotic resistance complicates successful treatment. Carbapenems are considered a last-resort antibiotic, however the spread of plasmid-encoded carbapenemases such as the New-Delhi Metallo-beta-Lactamase (blaNDM-1) challenges their effectiveness. E. coli ST101 is an emerging, atypical multidrug resistant ExPEC lineage, highly associated with the carriage of blaNDM-1. In this study we analysed the phylogeny and antimicrobial resistance of ST101 isolates from the UK and India.",collected_by:Timothy R Walsh,,,,,,,urinary tract infection,,,,,ExPEC,,,,,,,,,99.93,0.16,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases NHP,562.61595,Escherichia coli strain SCU-397,SCU-397,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943538,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2020-06-18T00:00:00Z,,PRJNA624897,GCA_013358385.1,"CP054828,CP054829,CP054830",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",28x,Flye v. 2.6,1,2,3,5618031,50.58957,6471,5398,rectal swab from healthy college student,,,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,98.93,0.3,,,Gastrointestinal,- NHP,562.61628,Escherichia coli strain SCU-321,SCU-321,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14943537,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",,,,2020-06-23T00:00:00Z,,PRJNA624897,GCA_013368055.1,CP055158,,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",66x,Flye v. 2.6,1,0,1,4684295,50.867825,5592,4445,rectal swab from healthy college student,,2017,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,98.06,0.19,,,Gastrointestinal,- HP,562.61705,Escherichia coli strain EcPF40,EcPF40,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075998,562,,,UPEC,"MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372305.1,"CP054214,CP054215,CP054216,CP054217,CP054218",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","64x, 315x",Unicycler v. v.0.4.14,1,4,5,5210779,50.643677,5281,4966,urine,,2019-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.39,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61706,Escherichia coli strain EcPF18,EcPF18,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075997,562,,,UPEC,MLST.Escherichia_coli_1.131,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372325.1,"CP054219,CP054220,CP054221,CP054222,CP054223",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","310x, 161x",Unicycler v. v.0.4.13,1,4,5,5232916,50.70009,5287,4987,urine,,2018-07,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.33,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61707,Escherichia coli strain EcPF15,EcPF15,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075995,562,,,UPEC,MLST.Escherichia_coli_1.394,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372365.1,"CP054227,CP054228,CP054229",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","70x, 250x",Unicycler v. v.0.4.11,1,2,3,4938634,50.478897,4770,4536,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.04,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61708,Escherichia coli strain EcPF16,EcPF16,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075996,562,,,UPEC,MLST.Escherichia_coli_1.216,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372345.1,"CP054224,CP054225,CP054226",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","231x, 197x",Unicycler v. v.0.4.12,1,2,3,4851525,50.94013,4877,4595,urine,,2018-07,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.77,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61709,Escherichia coli strain EcPF14,EcPF14,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075994,562,,,UPEC,MLST.Escherichia_coli_1.73,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372385.1,"CP054230,CP054231",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","83x, 338x",Unicycler v. v.0.4.10,1,1,2,5137006,50.505352,5103,4800,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.04,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61710,Escherichia coli strain EcPF5,EcPF5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075992,562,,,UPEC,MLST.Escherichia_coli_1.73,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372425.1,"CP054236,CP054237,CP054238",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","75x, 273x",Unicycler v. v.0.4.8,1,2,3,5280618,50.46485,5272,4943,urine,,2018-04,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.08,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.61711,Escherichia coli strain EcPF7,EcPF7,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15075993,562,,,UPEC,MLST.Escherichia_coli_1.2279,,,,2020-06-24T00:00:00Z,,PRJNA636382,GCA_013372405.1,"CP054232,CP054233,CP054234,CP054235",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","74x, 122x",Unicycler v. v.0.4.9,1,3,4,5131782,50.71786,5189,4890,urine,,2018-05,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.69,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.62716,Escherichia coli strain 357900 strain not applicable,not applicable,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04917416,562,,,,MLST.Escherichia_coli_1.2484,genotype:LT-IIc1 EplBA,,,2020-06-30T00:00:00Z,,PRJNA320137,GCA_013376895.1,CP038859,,University of Colroado Anschutz Medical Campus,Illumina MiSeq,71.0x,Geneious v. 6.1.7,1,0,1,4875596,50.679077,4832,4633,unknown,,1985-06-10,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,representative isolates producing type II heat-labile enterotoxin variants,collected_by:Peter Echeverria,,,,,,,diarrhea,,,,,,ETECtypeII_357900,,,,,,,,99.93,0.1,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases NHP,562.62729,Escherichia coli strain M1/5,M1/5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14840032,562,,,,MLST.Escherichia_coli_1.550,,,,2020-07-06T00:00:00Z,,PRJNA630566,GCA_013390265.1,"CP053296,CP053298,CP053297",,University of Muenster,PacBio RS; Illumina MiSeq,230.0x,HGAP v. 3,1,2,3,5288136,50.627876,5354,5023,feces,isolate from a healthy human donor,1994,Germany,Germany,,,,,,,,,,,,,,,,,"Comparative genome sequence analysis should help to better understand genomic differences between extraintestinal pathogenic and commensal Escherichia coli strains. For this purpose, we sequenced the complete genome of a fecal E. coli isolate from a healthy human donor.",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.39,,,Gastrointestinal,- HP,562.62763,Escherichia coli strain K56-43-un,K56-43-un,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14823672,562,,,,"MLST.Escherichia_coli_2.51,MLST.Escherichia_coli_1.537",,,,2020-07-08T00:00:00Z,,PRJNA630076,GCA_013394575.1,CP053079,,UiT-The Arctic University of Norway,Illumina NextSeq; PacBio,292.0x,Unicycler v. v0.4.7,1,0,1,5140708,50.35964,5153,4851,urine,,2007,Greece,Greece,,,,urinary tract infection,,,,,,,,,,,,,"Evolution, selection, and spread of antibiotic resistance.","collected_by:Gunnar Kahlmeter, Hanna Oden Poulsen",,,,,,,urinary tract infection,,,,,,,,,,,,,,99.91,0.14,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.62803,Escherichia coli strain EC2,EC2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15402835,562,,,,MLST.Escherichia_coli_1.10,,,,2020-07-12T00:00:00Z,,PRJNA643009,GCA_013402855.1,"CP058571,CP058572,CP058573",,Curtin University,Illumina NextSeq; Oxford Nanopore MiniION,195.0x,Flye v. 2.6; Racon v. 1.2.15; Pilon v.,1,2,3,5344123,50.795444,5480,5110,urinary tract,,2019,Australia,Australia,,,,urinary tract infection,,,,,,,,,,,,,Identification and Characterisation of Fosfomycin Resistance in Escherichia coliUrinary Tract Infection Isolates from Australia,collected_by:Hospital staff,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.82,0.09,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.62804,Escherichia coli strain EC1,EC1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15410927,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2020-07-12T00:00:00Z,,PRJNA643009,GCA_013402895.1,"CP058574,CP058575,CP058576,CP058577",,Curtin University,Oxford Nanopore MiniION; Illumina NextSeq,626.0x,Flye v. 2.6; Racon v. 1.4.15; Pilon v.,1,3,4,5292065,50.845066,5361,5043,urinary tract,,2019,Australia,Australia,,,,urinary tract infection,,,,,,,,,,,,,Identification and Characterisation of Fosfomycin Resistance in Escherichia coliUrinary Tract Infection Isolates from Australia,collected_by:Hospital staff,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.97,0.68,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.63039,Escherichia coli strain 2D,2D,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15502380,562,,,,MLST.Escherichia_coli_1.354,,,,2020-07-20T00:00:00Z,,PRJNA608094,GCA_013425955.1,"CP059003,CP059005,CP059007,CP059008,CP059004,CP059006",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Illumina HiSeq; Oxford Nanopore,100.0x,Unicycler v. 0.4.8,1,5,6,5363300,50.600395,5391,5079,blood,,2019-01-26,China,China: Yueqing,,female,,Bloodstream infection,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis of tigecycline and colistin resistant Escherichia coli,collected_by:Wei Zheng,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.93,0.28,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,562.63790,Escherichia coli strain E2348/69,E2348/69,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13901561,562,,,,"MLST.Escherichia_coli_2.491,MLST.Escherichia_coli_1.15",,,,2020-08-09T00:00:00Z,,PRJNA602597,GCA_014117345.1,"CP059840,CP059842,CP059841",,"University of Maryland, Baltimore",Illumina HiSeq 4000; Pacbio Sequel II,2000x,Unicycler v. 0.4.8,1,2,3,5045776,50.51752,5092,,stool,,1969,United Kingdom,United Kingdom: Taunton,,,,diarrhea,,,,,,,,,,,,,"To assess the quality of long read sequencing for de novo genome assembly, raw sequence read data for Escherichia coli and for Drosophila ananassae were generated across multiple sequencing platforms and library preps: PacBio RS II, PacBio Sequel II, PacBio HiFi, Oxford Nanopore Technologies MinION rapid ligation, Oxford Nanopore Technologies MinION extended ligation, and Illumina paired end.",biomaterial_provider:David Rasko,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.63852,Escherichia coli strain IDR1900005638-01-02,IDR1900005638-01-02,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15086849,562,,,,"MLST.Escherichia_coli_2.399,MLST.Escherichia_coli_1.2178",,,,2020-08-12T00:00:00Z,,PRJNA636827,GCA_014169995.1,"CP054282,CP054284,CP054283",,"Wadsworth Center, New York State Department of Health",Illumina MiSeq; Oxford Nanopore MiniION,234x,Unicycler v. 0.4.8,1,2,3,4779842,50.8176,4659,4432,rectal swab,,2019-01,USA,USA:Maine,,,,,,,,,,,,,,,,,"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.",collected_by:Maine Center for Disease Control and Prevention,,,,,,,Unknown,,,,,,,,,,,,,,99.93,0.12,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,562.63869,Escherichia coli strain RH-001-CS,RH-001-CS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342432,562,,,,MLST.Escherichia_coli_1.410,,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216355.1,CP050193,,"icddr,b",Illumina NextSeq,240x,ABySS v. 4.1,1,0,1,5689720,50.538788,5633,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,95.17,0.39,,,Gastrointestinal,- NHP,562.63872,Escherichia coli strain RH-004-CS,RH-004-CS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342435,562,,,,MLST.Escherichia_coli_1.226,,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216415.1,CP050196,,"icddr,b",Illumina NextSeq,258x,ABySS v. 4.1,1,0,1,5552603,50.680832,4985,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.94,0.39,,,Gastrointestinal,- NHP,562.63874,Escherichia coli strain RH-024-CS,RH-024-CS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342438,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216475.1,CP050199,,"icddr,b",Illumina NextSeq,122x,ABySS v. 4.1,1,0,1,5816894,50.43059,5426,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.05,0.25,,,Gastrointestinal,- NHP,562.63875,Escherichia coli strain RH-004-MS,RH-004-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342436,562,,,,MLST.Escherichia_coli_1.226,,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216455.1,CP050197,,"icddr,b",Illumina NextSeq,226x,ABySS v. 4.1,1,0,1,5818100,50.64085,5124,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.94,0.36,,,Gastrointestinal,- NHP,562.63876,Escherichia coli strain RH-024-MS,RH-024-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342439,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216555.1,CP050200,,"icddr,b",Illumina NextSeq,151x,ABySS v. 4.1,1,0,1,5907241,50.41078,5481,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.97,0.25,,,Gastrointestinal,- NHP,562.63879,Escherichia coli strain RH-045-MS,RH-045-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342442,562,,,,MLST.Escherichia_coli_1.226,,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216715.1,CP050203,,"icddr,b",Illumina NextSeq,196x,ABySS v. 4.1,1,0,1,6042336,50.736427,5636,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.67,0.36,,,Gastrointestinal,- NHP,562.63882,Escherichia coli strain RH-048-MS,RH-048-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342445,562,,,,"MLST.Escherichia_coli_1.224,MLST.Escherichia_coli_2.479",,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216775.1,CP050206,,"icddr,b",Illumina NextSeq,163x,ABySS v. 4.1,1,0,1,5879432,50.572906,5615,,human feces,,2017,Bangladesh,Bangladesh: Hajiganj,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,94,0.39,,,Gastrointestinal,- NHP,562.63888,Escherichia coli strain RM-065-MS,RM-065-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342451,562,,,,MLST.Escherichia_coli_1.2705,,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014216915.1,CP050212,,"icddr,b",Illumina NextSeq,254x,ABySS v. 4.1,1,0,1,6051927,50.70107,5180,,human feces,,2017,Bangladesh,Bangladesh: Matlab,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- NHP,562.63896,Escherichia coli strain RM-103-CS,RM-103-CS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342459,562,,,,"MLST.Escherichia_coli_1.1290,MLST.Escherichia_coli_2.367",,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014217075.1,CP050220,,"icddr,b",Illumina NextSeq,160x,ABySS v. 4.1,1,0,1,5747079,50.366703,5720,,human feces,,2017,Bangladesh,Bangladesh: Matlab,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,92.23,0.07,,,Gastrointestinal,- NHP,562.63897,Escherichia coli strain RM-103-MS,RM-103-MS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14342460,562,,,,"MLST.Escherichia_coli_2.367,MLST.Escherichia_coli_1.1290",,,,2020-08-17T00:00:00Z,,PRJNA607650,GCA_014217095.1,CP050221,,"icddr,b",Illumina NextSeq,256x,ABySS v. 4.1,1,0,1,5707033,50.58984,5539,,human feces,,2017,Bangladesh,Bangladesh: Matlab,,,,Healthy Individual,,,,,,,,,,,,,E. coli whole genome sequence comparison,collected_by:Laboratory of Food Safety and One Health,,,,,,,Healthy Individual,,,,,,,,,,,,,,96.42,0.1,,,Gastrointestinal,- HP,562.64260,Escherichia coli strain N18-04097,N18-04097,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506046,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189395.1,"CP047277,CP047278",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,76.0x,Unicycler v. 0.4.7,1,1,2,5030994,50.9744,5056,4758,rectum,,2018,Canada,Canada,,,,,,,,,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,99.97,0.23,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,562.66551,Escherichia coli strain G8,G8,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693150,562,,,,MLST.Escherichia_coli_1.10,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295215.1,"CP060057,CP060060,CP060059,CP060058",,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,859x,Unicycler v. 0.4.8,1,3,4,5404155,50.84475,5622,5199,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- NHP,562.66552,Escherichia coli strain G4/9,G4/9,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693147,562,,,,MLST.Escherichia_coli_1.10,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295255.1,"CP060073,CP060074",,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,485x,Unicycler v. 0.4.8,1,1,2,4673472,50.730934,4582,4313,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.37,0.07,,,Gastrointestinal,- NHP,562.66553,Escherichia coli strain G3/10,G3/10,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693146,562,,,,MLST.Escherichia_coli_1.472,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295275.1,"CP060075,CP060077,CP060078,CP060079,CP060081,CP060076,CP060080,CP060082",,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,181x,Unicycler v. 0.4.8,1,7,8,5115106,50.834938,5191,4853,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.93,1.56,,,Gastrointestinal,- NHP,562.66554,Escherichia coli strain G5,G5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693148,562,,,,MLST.Escherichia_coli_1.10,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295295.1,"CP060065,CP060070,CP060072,CP060069,CP060071,CP060068,CP060066,CP060067",,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,696x,Unicycler v. 0.4.8,1,7,8,5052732,50.94036,5153,4786,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.97,0.12,,,Gastrointestinal,- NHP,562.66555,Escherichia coli strain G1/2,G1/2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693145,562,,,,MLST.Escherichia_coli_1.10,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295315.1,CP060083,,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,482x,Unicycler v. 0.4.8,1,0,1,5288297,50.904404,5460,5057,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- HP,562.66742,Escherichia coli strain EC931,EC931,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14164122,562,,,,"MLST.Escherichia_coli_2.83,MLST.Escherichia_coli_1.773",,,,2020-09-10T00:00:00Z,,PRJNA608094,GCA_014522225.1,"CP049118,CP049119,CP049130,CP049131,CP049120,CP049123,CP049124,CP049125,CP049126,CP049127,CP049128,CP049129",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Illumina HiSeq; Oxford Nanopore MiniION,100.0x,SPAdes v. 3.12; Unicycler v. 0.4.8,1,13,14,5139627,50.724167,5243,4938,urine,,2017-02-10,China,China: Yiwu,,,,Urinary tract infection,,,,,,,,,,,,,Whole genome sequencing and comparative genomic analysis of tigecycline and colistin resistant Escherichia coli,collected_by:Jianyong Wu,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.97,0.04,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.66743,Escherichia coli strain UPEC_U013,UPEC_U013,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15421091,562,,,,MLST.Escherichia_coli_1.73,,,,2020-09-10T00:00:00Z,,PRJNA643643,GCA_014522245.1,CP058596,,Chung Shan Medical University,Illumina MiSeq; Oxford Nanopore MiniION,10.0x,Unicycler v. May-2020,1,0,1,5203972,50.43434,5188,4890,urine,,2014-11-03,Taiwan,Taiwan: Chia-Yi,,,,UTI,,,,,,,,,,,,,A clinical isolate of uropathogenic Escherichia coli carrying a colibactin-producing gene cluster in its genome,collected_by:Yeong Chin Jou,,,,,,,UTI,,,,,,,,,,,,,,99.97,0.08,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.66849,Escherichia coli strain DA61218,DA61218,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16073343,562,,,,MLST.Escherichia_coli_1.73,,,,2020-09-15T00:00:00Z,,PRJNA662022,GCA_014541045.1,"CP061206,CP061207",,Uppsala University,Illumina MiSeq,221.0x,CLC NGS Cell v. 20.3,1,1,2,5234024,50.51257,5193,4873,,,2017-02,Sweden,Sweden,,,,,,,,,,,,,,,,,"Escherichia coli strain DA61218 chromosome, complete genome.",sample_type:Clinical Isolate,,,,,,,,,,,,,,,,,,,,,99.87,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.66854,Escherichia coli strain M11957,M11957,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16077359,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.525",,,,2020-09-19T00:00:00Z,,PRJNA662169,GCA_014656605.1,"CP061337,CP061338",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,50x,flye v. AUG-2020; Unicycler v. AUG-2020,1,1,2,5037044,50.663445,4979,4728,feces,,2019,Australia,Australia,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,WGS of STEC ST69,collected_by:Queensland Health,,,,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,,99.97,0.12,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.66855,Escherichia coli strain M00057,M00057,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16077358,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.525",,,,2020-09-19T00:00:00Z,,PRJNA662169,GCA_014656625.1,"CP061339,CP061340",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,50x,flye v. AUG-2020; Unicycler v. AUG-2020,1,1,2,5040622,50.660652,4981,4721,feces,,2020,Australia,Australia,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,WGS of STEC ST69,collected_by:Queensland Health,,,,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,,99.97,0.12,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.66856,Escherichia coli strain HUE1,HUE1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00241721,562,,,,"MLST.Escherichia_coli_2.37,MLST.Escherichia_coli_1.48",,,,2020-09-09T00:00:00Z,,PRJDB10417,GCA_014679325.1,"AP023427,AP023428,AP023429,AP023430,AP023431,AP023432",,"Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Department of Veterinary Medicine, Rakuno Gakuen University",Illumina MiSeq; Nanopore MinION,220x,Unicycler v. 0.4.8-beta,1,5,6,4742352,50.81833,4671,4462,urinary catheter,,2008,,,,,,,,,,,,,,,,,,,"Antimicrobial-resistant bacteria have spread rapidly all over the world and are an important global health issue. Inappropriate use of antibiotics is one of the reasons of their occurrence. In this context, phage therapy, by using bacteriophages which specifically infect to bacteria, has been received significant attention as an alternative approach to classical antibiotic therapy. On the other hand, further understandings of interaction between bacteria and phages are required to develop phage therapy because bacteria can acquire phage-resistance in the therapy. To investigate mechanisms underlying phage infection to the host and identify the receptors, whole genome information is necessary. This study will facilitate the understandings of life cycle of phage and phage-resistance.",,not applicable,not applicable,not applicable,not applicable,Analysis of HUE1 sequence,,,,,,,,,,,,not applicable,,,,99.97,0.11,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.66875,Escherichia coli strain JS316,JS316,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15455438,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2020-09-30T00:00:00Z,,PRJNA644256,GCA_014826015.1,"CP058618,CP058621,CP058619,CP058620,CP058622,CP058623",,University Hospital Frankfurt,Illumina; Oxford Nanopore,100.0x,Unicycler v. 0.4.8,1,5,6,4939208,50.651257,4959,4665,rectal swab,,2019-12,Germany,Germany,,,,Infection control,,,,,,,,,,,,,Sequencing of carbapenem resistant Enterobacterales for comparative genomics,"collected_by:Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt",,,,,,,Infection control,,,,,,,,,,,,,,99.93,0.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.66917,Escherichia coli strain UTI89,UTI89,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16237063,562,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,,,2020-10-07T00:00:00Z,,PRJNA664911,GCA_014858525.1,CP062228,,SASTRA University,Illumina MiSeq,10.0x,ABySS v. 2.3,1,0,1,5065741,50.604263,5033,4748,urine pellicle,,2018-09-20,India,India: Thanjavur,,,,,,,,,,,,,,,,,Uropathogenic e.coli will cause urinary tract infection which one major nosocomial infection. In our observation UTI89 strain shown heterogen colonies regarding the biofilm formation. If we can understand the interaction between these variants will give some insight to the treatment.,sample_type:Bacterial culture;biomaterial_provider:Dr. CS Srinandan;collected_by:Sandeep miryala,,,,,,,,,,,,,,,,,,,,,99.97,0.12,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.67171,Escherichia coli strain 188B,188B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16330218,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",,,,2020-10-20T00:00:00Z,,PRJNA666802,GCA_014898615.1,"CP062970,CP062971,CP062972",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5133811,51.35106,4858,4282,"blood culture, ankara",,2018-02-12,Turkey,Turkey: Ankara,,,,E coli sepsis,,,,,,,,,,,,,This project was carried out to identified molecular mechanisms that might be responsible for heteroresistance between E. coli and Klebsiella pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,E coli sepsis,,,,,,,,,,,,,,98.77,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.67172,Escherichia coli strain 188,188,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16327877,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2020-10-20T00:00:00Z,,PRJNA666802,GCA_014898635.1,"CP062967,CP062968,CP062969",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5133298,51.29379,4821,4196,blood sample,,2018-06-12,Turkey,Turkey: Ankara,,,,Sepsis,,,,,,,,,,,,,This project was carried out to identified molecular mechanisms that might be responsible for heteroresistance between E. coli and Klebsiella pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,Sepsis,,,,,,,,,,,,,,98.79,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.67248,Escherichia coli strain M7424,M7424,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16435111,562,,,,"MLST.Escherichia_coli_2.525,MLST.Escherichia_coli_1.69",,,,2020-10-27T00:00:00Z,,PRJNA662169,GCA_014962565.1,"CP063153,CP063154,CP063155,CP063156",,Queensland Health Forensic and Scientific Services,Oxford Nanopore GridION; Illumina NextSeq,40.0x,Flye v. OCT-2020; Unicycler v. OCT-2020,1,3,4,5154279,50.511215,5125,4846,feces,,2014,Australia,Australia,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,WGS of STEC ST69,collected_by:Queensland Health,,,,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,562.68395,Escherichia coli strain G6/7,G6/7,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15693149,562,,,,MLST.Escherichia_coli_1.10,,,,2020-08-25T00:00:00Z,,PRJNA650131,GCA_014295235.1,"CP060061,CP060064,CP060063,CP060062",,University of Arkansas for Medical Sciences,Oxford Nanopore MiniION,791x,Unicycler v. 0.4.8,1,3,4,5434724,50.85548,5642,5230,feces from healthy individual,,1954,Germany,Germany,,,,,,,,,,,,,,,,,"Some Escherichia coli strains have been shown to provide beneficial effects on human and animal health. Six of those strains are contained in the probiotic drug Symbioflor2, provided by SymbioPharm (Herborn-Hoerbach, Germany). While this product is used in humans for decades without severe side effects and in this way considered as safe, it is an essential step to ensure complete safety by evaluating their whole genomic content.",sample_type:isolate;passage_history:multiple passages,,,,,,,,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- HP,562.68765,Escherichia coli strain 1EC213,1EC213,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15945290,562,OUT:H4,,,MLST.Escherichia_coli_1.940,genotype:ST940,,,2020-12-29T00:00:00Z,,PRJNA473419,GCA_016432785.1,"CP061101,CP061102,CP061103,CP061104,CP061105,CP061106,CP061107",,Tokyo Medical and Dental University,Illumina MiSeq; Oxford Nanopore MinION,412x,Unicycler v. V0.4.8,1,6,7,4991513,50.591393,5058,4730,,,2018-07-31,Ghana,Ghana: Western region,,,,,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.","sample_type:cell culture;biomaterial_provider:Public Health Laboratory , Sekondi, Ghana",,,,,,,,,,,,,,,,,,,,,99.97,0.56,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.68766,Escherichia coli strain 1EC187,1EC187,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15945289,562,O8:H9,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",genotype:ST410,,,2020-12-29T00:00:00Z,,PRJNA473419,GCA_016432805.1,"CP061108,CP061109,CP061110,CP061111,CP061112",,Tokyo Medical and Dental University,Illumina MiSeq; Oxford Nanopore MinION,485x,Unicycler v. v0.4.8,1,4,5,5054351,50.536774,5065,4752,,,2018-02-16,Ghana,Ghana: Western region,,,,,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.","sample_type:cell culture;biomaterial_provider:Public Health Laboratory , Sekondi, Ghana",,,,,,,,,,,,,,,,,,,,,99.93,1.05,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.69512,Escherichia coli strain QEC11-421,QEC11-421,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14049568,562,,,,"MLST.Escherichia_coli_1.48,MLST.Escherichia_coli_2.132",,,,2020-12-30T00:00:00Z,32966910,PRJNA604918,GCA_016446335.1,"CP048821,CP048822,CP048823,CP048824,CP048825,CP048826",,"Sir Run Run Shaw Hospital, Zhejiang University School of Medicine",Illumina HiSeq; Oxford Nanopore MiniION,150.0x,Unicycler v. 0.4.8,1,5,6,5084514,50.711296,5078,4849,sputum,,2011,China,China: Quzhou,,,,,,,,,,,,,,,,,Clinical prevalence of mcr-1-harboring Escherichia coli in China: a multi-centre genomic survey,collected_by:Jun Lu,,,,,,,unknown,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,562.70502,Escherichia coli strain RIVM_C030256,RIVM_C030256,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373201,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775805.1,CP068825,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5086785,50.753532,5041,4754,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70503,Escherichia coli strain RIVM_C029952,RIVM_C029952,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373197,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775825.1,CP068821,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5280943,50.645218,5318,4987,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.67,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70504,Escherichia coli strain RIVM_C018567,RIVM_C018567,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373181,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775845.1,CP068805,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5215672,50.662407,5211,4914,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70505,Escherichia coli strain RIVM_C030300,RIVM_C030300,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373202,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775865.1,CP068826,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5256124,50.527424,5237,4922,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70506,Escherichia coli strain RIVM_C030453,RIVM_C030453,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373205,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775885.1,CP068829,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5209229,50.564854,5176,4876,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70507,Escherichia coli strain RIVM_C029951,RIVM_C029951,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373196,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775965.1,CP068820,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5197546,50.481785,5174,4870,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70508,Escherichia coli strain RIVM_C030371,RIVM_C030371,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373203,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775985.1,CP068827,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5348975,50.631607,5337,5002,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70509,Escherichia coli strain RIVM_C029324,RIVM_C029324,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373198,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775925.1,CP068822,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5191412,50.431885,5149,4833,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70510,Escherichia coli strain RIVM_C029020,RIVM_C029020,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373188,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775945.1,CP068812,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5251089,50.613846,5197,4872,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70511,Escherichia coli strain RIVM_C030443,RIVM_C030443,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373204,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016775905.1,CP068828,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5104263,50.636692,5047,4776,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70512,Escherichia coli strain RIVM_C028568,RIVM_C028568,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373187,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776145.1,CP068811,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5210247,50.67468,5212,4882,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.83,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70513,Escherichia coli strain RIVM_C029033,RIVM_C029033,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373189,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776165.1,CP068813,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5230678,50.596558,5230,4898,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70514,Escherichia coli strain RIVM_C029494,RIVM_C029494,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373199,562,,,,MLST.Escherichia_coli_1.1722,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776005.1,CP068823,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,4935988,50.497166,4765,4550,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70515,Escherichia coli strain RIVM_C028613,RIVM_C028613,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373190,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776085.1,CP068814,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5385668,50.565964,5404,5052,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70516,Escherichia coli strain RIVM_C017997,RIVM_C017997,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373173,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776065.1,CP068800,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5174511,50.45663,5112,4820,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70517,Escherichia coli strain RIVM_C018563,RIVM_C018563,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373180,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776045.1,CP068804,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5180503,50.52519,5129,4845,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70518,Escherichia coli strain RIVM_C028497,RIVM_C028497,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373185,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776125.1,CP068809,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5086007,50.548435,5041,4736,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70519,Escherichia coli strain RIVM_C018576,RIVM_C018576,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373182,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776265.1,CP068806,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5089794,50.756042,5043,4758,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70520,Escherichia coli strain RIVM_C029042,RIVM_C029042,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373195,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776105.1,CP068819,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5188564,50.619324,5173,4877,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70521,Escherichia coli strain RIVM_C028536,RIVM_C028536,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373186,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776245.1,CP068810,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5279417,50.458073,5273,4962,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70522,Escherichia coli strain RIVM_C028724,RIVM_C028724,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373192,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776225.1,CP068816,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5165070,50.447643,5131,4810,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70523,Escherichia coli strain RIVM_C017887,RIVM_C017887,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373172,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776305.1,CP068799,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5227631,50.440823,5203,4881,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70524,Escherichia coli strain RIVM_C028620,RIVM_C028620,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373191,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776285.1,CP068815,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5192168,50.432304,5152,4833,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70525,Escherichia coli strain RIVM_C018220,RIVM_C018220,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373176,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776385.1,CP068801,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5343645,50.60256,5400,5062,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70526,Escherichia coli strain RIVM_C030197,RIVM_C030197,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373200,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776025.1,CP068824,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5256191,50.527405,5210,4920,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70527,Escherichia coli strain RIVM_C028803,RIVM_C028803,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373194,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776205.1,CP068818,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5262652,50.628525,5302,5002,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.74,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70528,Escherichia coli strain RIVM_C018249,RIVM_C018249,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373177,562,,,,"MLST.Escherichia_coli_2.678,MLST.Escherichia_coli_1.349",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776365.1,CP068802,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,4983069,50.715153,4883,4634,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70529,Escherichia coli strain RIVM_C028786,RIVM_C028786,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373193,562,,,,MLST.Escherichia_coli_1.127,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776185.1,CP068817,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5220173,50.458233,5208,4876,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70530,Escherichia coli strain RIVM_C018583,RIVM_C018583,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373183,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776325.1,CP068807,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5419042,50.551296,5455,5103,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70531,Escherichia coli strain RIVM_C018404,RIVM_C018404,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373178,562,,,,MLST.Escherichia_coli_1.940,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016776345.1,CP068803,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,4832919,50.683117,4843,4540,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70532,Escherichia coli strain RIVM_C018699,RIVM_C018699,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373184,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016779865.1,CP068808,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5294629,50.622887,5320,4999,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70533,Escherichia coli strain RIVM_C011532,RIVM_C011532,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373164,562,,,,"MLST.Escherichia_coli_1.361,MLST.Escherichia_coli_2.650",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016780285.1,CP068795,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,4884056,50.70681,4881,4589,,,2016,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.93,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70534,Escherichia coli strain RIVM_C012087,RIVM_C012087,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373165,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016780415.1,CP068796,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5185152,50.52847,5141,4858,,,2016,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70536,Escherichia coli strain RIVM_C018707,RIVM_C018707,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17497583,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016780575.1,CP068830,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5280569,50.623558,5278,4961,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70596,Escherichia coli strain RIVM_C036689,RIVM_C036689,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373174,562,,,,,,,,2021-02-02T00:00:00Z,,PRJNA691727,GCA_016801475.1,CP068995,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,4805003,50.621937,4732,4467,,,2019,Netherlands,Netherlands,,,,,,,,,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.62,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.70601,Escherichia coli strain RUT3575,RUT3575,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13031455,562,,,,"MLST.Escherichia_coli_2.692,MLST.Escherichia_coli_1.410",,,,2021-02-03T00:00:00Z,,PRJNA577622,GCA_016803855.1,"CP048010,CP048013,CP048011,CP048012,CP048009",,Hospital Universitari Vall d'Hebron,Illumina Miseq andOxford Nanopore MiniION,64x,Unicycler v. Unicycler v0.4.7,1,4,5,4986271,50.540073,5000,4697,rectal swab of patient hospitalized for an unrelated disease,,2018-11,Spain,Spain: Barcelona,,male,63,Human carrier,,,,,,,,,,,,,Escherichia coli clinical isolates ST410 co-producers of NDM-5 and OXA-181 collected from a traveler returning from Pakistan. Dissemination within the same hospital room was evidenced. Stability studies were conducted which showed a rapid NDM-5 loss in the absence of antimicrobial pressure.,collected_by:Vall d'Hebron University Hospital,,,,,,,Human carrier,,,,,,,,,,,,,,99.93,0.23,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.70602,Escherichia coli strain FHI_NMBU_11,FHI_NMBU_11,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13164804,562,O128ab:H2,,STEC,"MLST.Escherichia_coli_1.25,MLST.Escherichia_coli_2.130",genotype:ST25,,,2021-02-03T00:00:00Z,,PRJNA362852,GCA_016803875.1,"CP045712,CP045713,CP045714,CP045715,CP045716,CP045717",,Norwegian University of Life Sciences,Oxford Nanopore MiniION; Illumina MiSeq,42.57x,Unicycler v. 0.4.7.0,1,5,6,5565139,50.610416,5732,5344,feces,,2012-12,Norway,Norway:South-east,,,,Diarrhea,,,,,,,,,,,,,Sequence characterization of hybrid IPEC/ExPEC isolates of Escherichia coli,collected_by:Norwegian Institute of Public Health,,,,,,,Diarrhea,,,,,STEC,,,,,,,,,99.93,0.73,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.70603,Escherichia coli strain FHI_NMBU_10,FHI_NMBU_10,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13476489,562,O146:H21,,STEC,"MLST.Escherichia_coli_2.350,MLST.Escherichia_coli_1.829",genotype:ST829,,,2021-02-03T00:00:00Z,,PRJNA593384,GCA_016803915.1,"CP046539,CP046540,CP046541,CP046542,CP046543,CP046544,CP046545",,Norwegian University of Life Sciences,Oxford Nanopore MiniION; Illumina MiSeq,62.21x,Unicycler v. 0.4.8.0,1,6,7,5402470,50.796913,5515,5189,feces,,2012-12,Norway,Norway:South-east,,,,Diarrhea,,,,,,,,,,,,,Sequencing of enteropathogenic Escherichia coli clinical isolates,collected_by:Norwegian Institute of Public Health,,,,,,,Diarrhea,,,,,STEC,,,,,,,,,99.93,0.45,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.71815,Escherichia coli strain ESC53083,ESC53083,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933302,562,,,,MLST.Escherichia_coli_1.131,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939795.1,"CP070593,CP070592,CP070591,CP070590,CP070589,CP070588,CP070587",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,6,7,5181914,50.87462,5263,4958,stool,,2019-09-19,Czech Republic,Czech Republic: Hradec Krlov,,,,Acute respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Hradec Krlov,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,99.92,0.33,Respiratory Diseases,Other Respiratory Diseases,Gastrointestinal,Respiratory Diseases-Other Respiratory Diseases NHP,562.71836,Escherichia coli strain 99COLEC,99COLEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17807537,562,,,,,,,,2021-03-01T00:00:00Z,,PRJNA599529,GCA_017088405.1,"CP070902,CP070903,CP070904,CP070905",,Temasek Life Sciences Laboratory Limited,Illumina NovaSeq Oxford Nanopore MiniION,548x,Unicycler v. 0.4.8,1,3,4,4947804,50.407856,4924,4612,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.04,,,Gastrointestinal,- NHP,562.71837,Escherichia coli strain 40EC,40EC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17807534,562,,,,MLST.Escherichia_coli_1.4088,,,,2021-03-01T00:00:00Z,,PRJNA599529,GCA_017088445.1,"CP070920,CP070921,CP070922,CP070923,CP070924,CP070925,CP070926,CP070927,CP070928,CP070929",,Temasek Life Sciences Laboratory Limited,Illumina NovaSeq Oxford Nanopore MiniION,378x,Unicycler v. 0.4.8,1,9,10,5254905,50.500496,5323,4998,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.93,0.31,,,Gastrointestinal,- NHP,562.71838,Escherichia coli strain 88COLEC,88COLEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17807536,562,,,,"MLST.Escherichia_coli_1.1011,MLST.Escherichia_coli_2.31",,,,2021-03-01T00:00:00Z,,PRJNA599529,GCA_017088425.1,"CP070906,CP070907,CP070908,CP070909,CP070910,CP070911,CP070912,CP070913",,Temasek Life Sciences Laboratory Limited,Illumina NovaSeq Oxford Nanopore MiniION,367x,Unicycler v. 0.4.8,1,7,8,5157225,50.515247,5062,4789,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.52,,,Gastrointestinal,- NHP,562.71839,Escherichia coli strain 65COLEC,65COLEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17807535,562,,,,MLST.Escherichia_coli_1.2705,,,,2021-03-01T00:00:00Z,,PRJNA599529,GCA_017088465.1,"CP070914,CP070915,CP070916,CP070917,CP070918,CP070919",,Temasek Life Sciences Laboratory Limited,Illumina NovaSeq Oxford Nanopore MiniION,363x,Unicycler v. 0.4.8,1,5,6,5055327,50.527573,5041,4737,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.08,,,Gastrointestinal,- NHP,562.71840,Escherichia coli strain 30COLEC,30COLEC,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17807533,562,,,,"MLST.Escherichia_coli_2.647,MLST.Escherichia_coli_1.2325",,,,2021-03-01T00:00:00Z,,PRJNA599529,GCA_017088485.1,"CP070930,CP070931,CP070932,CP070933,CP070934",,Temasek Life Sciences Laboratory Limited,Illumina NovaSeq Oxford Nanopore MiniION,454x,Unicycler v. 0.4.8,1,4,5,4761190,50.70411,4727,4443,feces,isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore,2019-02,Singapore,Singapore,,,,,,,,,,,,,,,,,"In this project, we isolated antibiotic resistant bacteria from the gut microbiota of healthy individuals in Singapore. Their genomes were sequenced and analysed to identify resistance mechanisms, plasmids and mode of antibiotic resistance gene acquisition.",sample_type:Bacterial pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.19,,,Gastrointestinal,- HP,562.72254,Escherichia coli strain IR53017,IR53017,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561275,562,,,,MLST.Escherichia_coli_1.648,,,,2021-03-09T00:00:00Z,,PRJNA672237,GCA_017310445.1,"CP064103,CP064104,CP064105,CP064106,CP064107",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,5628624,50.46569,5789,5416,,,2015-07-01,China,China: Beijing,,,,,,,,,,,,,,,,,"aimed to investigate the molecular epidemiology, transmission and evolution of XA-48-producing Enterobacterales and pOXA-48",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.18,1.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.72316,Escherichia coli strain EcPNK004,EcPNK004,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18131652,562,,,UPEC,"MLST.Escherichia_coli_2.494,MLST.Escherichia_coli_1.393",,,,2021-03-14T00:00:00Z,,PRJNA636382,GCA_017352035.1,"CP071439,CP071440",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","113x, 787x",Unicycler v. v.0.4.8,1,1,2,5111999,50.696587,5002,4732,urine,,2017-08,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.97,0.04,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.72317,Escherichia coli strain EcPNK006,EcPNK006,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18131653,562,,,UPEC,MLST.Escherichia_coli_1.46,,,,2021-03-14T00:00:00Z,,PRJNA636382,GCA_017352055.1,"CP071436,CP071437,CP071438",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","116x, 836x",Unicycler v. v.0.4.8,1,2,3,4622527,50.70711,4642,4360,urine,,2017-08,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.67,0.04,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.72318,Escherichia coli strain EcPF20,EcPF20,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18131651,562,,,UPEC,"MLST.Escherichia_coli_2.24,MLST.Escherichia_coli_1.58",,,,2021-03-14T00:00:00Z,,PRJNA636382,GCA_017352075.1,"CP071441,CP071442,CP071443",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","182x, 163x",Unicycler v. v.0.4.8,1,2,3,5076468,50.865562,5054,4760,urine,,2018-08,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here we report the complete genome sequences of ten UPEC isolates obtained from the urine of postmenopausal women suffering from rUTI.,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,UPEC,,,,,,,,,99.93,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,562.72349,Escherichia coli strain UPEC129,UPEC129,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16443699,562,,,UPEC,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2021-03-16T00:00:00Z,,PRJNA669570,GCA_017356665.1,"CP071522,CP071523,CP071524",,INSERM IRSD U1220,PacBio RSII; Illumina HiSeq,50.0x,Unicycler v. MAY-2019,1,2,3,5133980,50.641277,5178,4889,urine,,2011,Japan,Japan,,,,Urinary tract infection,,,,,,,,,,,,,We analyzed the genome sequences E. coli strains originating from human and bovine hosts in order to provide insights into the acquisition of the pks island in the E. coli population.,"collected_by:Microbiology, Graduate School of Medical Sciences, Kyushu University",,,,,,,Urinary tract infection,,,,,UPEC,,,,,,,,,99.97,0.39,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.73338,Escherichia coli strain AR Bank #0346,AR Bank #0346,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12263369,562,,,,"MLST.Escherichia_coli_1.744,MLST.Escherichia_coli_2.2",,,,2021-03-24T00:00:00Z,,PRJNA554345,GCA_017579865.1,"CP066366,CP066367,CP066368",,USDA-ARS,PacBio RSII; PacBio Sequel; Illumina,256.0x,CANU v. 2.1,1,2,3,4885435,50.675323,4925,4623,missing,,,,,,,,"Gastroenteritis, diarrhea, UTI, pneumonia, food poisoning",,,,,,,,,,,,,complete genome sequence of Escherichia coli AR Bank # 0346,,,,,,,,"Gastroenteritis, diarrhea, UTI, pneumonia, food poisoning",,,,,,,,,,,,,,99.3,0.04,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,562.74604,Escherichia coli strain EC-JS426,EC-JS426,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18475704,562,,,,"MLST.Escherichia_coli_2.58,MLST.Escherichia_coli_1.448",,,,2021-04-04T00:00:00Z,,PRJNA644256,GCA_017743075.1,"CP072322,CP072324,CP072323",,University Hospital Frankfurt,Illumina; Oxford Nanopore,100.0x,Unicycler v. v0.4.8,1,2,3,5036724,50.86296,5004,4725,rectal swab,,2013,Germany,Germany,,,,Infection control,,,,,,,,,,,,,Sequencing of carbapenem resistant Enterobacterales for comparative genomics,"collected_by:Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt",,,,,,,Infection control,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,562.74672,Escherichia coli strain SCU-101,SCU-101,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14609767,562,,,,"MLST.Escherichia_coli_2.29,MLST.Escherichia_coli_1.1262",,,,2021-04-07T00:00:00Z,32759337,PRJNA624897,GCA_017815815.1,"CP051849,CP051850,CP051851,CP051852",,Santa Clara University,"Illumina MiSeq, Oxford Nanopore MiniION",91x,Unicycler v. 0.4.8,1,3,4,5370586,50.453526,5398,5070,rectal swab from healthy college student,,2015,USA,USA: California,,,,,,,,,,,,,,,,,"This study explores genomic diversity in commensal E. coli isolates from healthy college students. Commensal E. coli are near-ubiquitous components of the human gut microbiome, as well as a major cause of urinary tract infections. This study's goals are to document variation in genome structure in commensal E. coli, including plasmids, as well as variation in genetically-determined traits such as antibiotic resistance, adhesion, motility, and metabolism.",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.97,0.08,,,Gastrointestinal,- HP,562.74679,Escherichia coli strain ECONC427,ECONC427,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18053058,562,,,,MLST.Escherichia_coli_2.3,,,,2021-04-08T00:00:00Z,33789206,PRJNA704692,GCA_017869465.1,"CP071133,CP071135,CP071134,CP071136",,Case Western Reserve University,Oxford Nanopore MinION,50.0x,Flye v. 2.8.3,1,3,4,5417778,50.503277,5803,5114,urine,,2019-03,USA,USA: NC,,female,76,Urinary tract infection,,,,,,,,,,,,,Detection of mcr-1 gene in a clinical Escherichia coli strain in North Carolina: first report,collected_by:Department of PAthology Wake Forest School of MEdicine,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.64,0.09,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.74744,Escherichia coli strain C5,C5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18605473,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,ATCC:700973,,2021-04-17T00:00:00Z,,PRJNA719409,GCA_018064225.1,"CP072911,CP072912",,University of Michigan,Oxford Nanopore GridION,100.0x,Flye v2.8.3 v. March-2021,1,1,2,5162996,50.628338,5607,4881,cerebrospinal fluid from newborn infant,,1975,,,,,,meningitis,,,,,,,,,,,,,Sequence and annotation of ATCC 700973,,,,,,,,meningitis,,,,,,,,,,,,,,99.12,0.08,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,562.74746,Escherichia coli strain 2547,2547,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18652183,562,,,,MLST.Escherichia_coli_1.131,,,,2021-04-19T00:00:00Z,,PRJNA720498,GCA_018075305.1,"CP072980,CP072982,CP072981",,Zhejiang Provincial People's Hospital,PacBio,200X,CLC NGS Cell v. 10.0,1,2,3,5359540,50.67144,5501,5166,sputum,,2018-02-08,China,China: zhejiang,,,,infenction,,,,,,,,,,,,,Complete Genome Sequence of Two Novel KPC-2-Producing IncU Multidrug-Resistant Plasmids from International High-Risk Clones Escherichia coli in China,collected_by:Xi Li,,,,,,,infenction,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,562.74747,Escherichia coli strain EC2341,EC2341,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18652119,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2021-04-19T00:00:00Z,,PRJNA720492,GCA_018075285.1,"CP072976,CP072977,CP072978,CP072979",,Zhejiang Provincial People's Hospital,PacBio,200X,CLC NGS Cell v. 10.0,1,3,4,5098723,50.64115,5185,4829,pus,,2017-10-21,China,China: Zhejiang,,,,infenction,,,,,,,,,,,,,"this is the first report of E. coli strains carrying blaKPC-2 gene on IncU plasmids. Emergence of IncU type blaKPC-2-positve plasmid highlights further dissemination of blaKPC-2 in Enterobacteriaceae. Therefore, it is imperative that effective measures are taken immediately to control the spread of these blaKPC-2-positive plasmids.",collected_by:Xi Li,,,,,,,infenction,,,,,,,,,,,,,,99.59,0.26,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,562.74755,Escherichia coli strain 3347558,3347558,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17736024,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2021-04-22T00:00:00Z,,PRJNA698767,GCA_018128405.1,"CP071073,CP071074,CP071075,CP071076,CP071077,CP071078,CP071079",,,Illumina NovaSeq; Oxford Nanopore MiniION,144x,Unicycler v. 0.4.8,1,6,7,5631387,50.76673,5750,5409,rectal swab,,2020,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,99.97,0.3,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.75631,Escherichia coli strain PK5074,PK5074,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18615003,562,,,,MLST.Escherichia_coli_1.48,,,,2021-04-12T00:00:00Z,,PRJNA719724,GCA_017903455.1,"CP072802,CP072805,CP072804,CP072806,CP072803,CP072807",,Yangzhou University,Illumina HiSeq; Oxford Nanopore MinION,100.0x,Unicycler v. 0.4.4,1,5,6,5321746,50.53351,5422,5086,urine sample,,2019-12-17,Pakistan,Pakistan: Faisalabad,,,,Urinary Tract Infection,,,,,,,,,,,,,Co-existence of tet(X4) and mcr-1 in an Escherichia coli clinical isolate recovered from a patient in Pakistan,collected_by:Dr. Mashkoor,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,99.97,0.73,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.75650,Escherichia coli strain 179,179,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16339631,562,,,,MLST.Escherichia_coli_1.46,,,,2021-04-29T00:00:00Z,,PRJNA666983,GCA_018208275.1,"CP062924,CP062925,CP062926",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5127133,51.148613,4753,4183,"blood culture, ankara",,2018-05-12,Turkey,Turkey: Ankara,,,,E coli sepsis,,,,,,,,,,,,,This study was carried out to identify the molecular mechanisms that might be responsible for hereroresistance between E. coli and K. pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,E coli sepsis,,,,,,,,,,,,,,99.25,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.75651,Escherichia coli strain 91A,91A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16354875,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",,,,2021-04-29T00:00:00Z,,PRJNA666983,GCA_018208335.1,"CP062930,CP062931,CP062932",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5133181,51.297684,4797,4220,"blood culture, ankara",,2018-08-01,Turkey,Turkey: Ankara,,,,E coli sepsis,,,,,,,,,,,,,This study was carried out to identify the molecular mechanisms that might be responsible for hereroresistance between E. coli and K. pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,E coli sepsis,,,,,,,,,,,,,,98.71,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.75652,Escherichia coli strain 179A,179A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16339682,562,,,,MLST.Escherichia_coli_1.46,,,,2021-04-29T00:00:00Z,,PRJNA666802,GCA_018208295.1,"CP062927,CP062928,CP062929",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5127129,51.149925,4755,4181,"blood culture, ankara",,2018-05-12,Turkey,Turkey: Ankara,,,,E coli sepsis,,,,,,,,,,,,,This project was carried out to identified molecular mechanisms that might be responsible for heteroresistance between E. coli and Klebsiella pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,E coli sepsis,,,,,,,,,,,,,,99.25,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.75653,Escherichia coli strain 71,71,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16354869,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",,,,2021-04-29T00:00:00Z,,PRJNA666983,GCA_018208315.1,"CP062933,CP062934,CP062935",,Ankara Yildirim Beyazit University,IonTorrent,20.0x,Bowtie 2 v. 2.3.5,1,2,3,5133210,51.29814,4790,4218,"blood culture, ankara",,2018-08-01,Turkey,Turkey: Ankara,,,,E coli sepsis,,,,,,,,,,,,,This study was carried out to identify the molecular mechanisms that might be responsible for hereroresistance between E. coli and K. pneumoniae clinical isolates,collected_by:Banu Sancak,,,,,,,E coli sepsis,,,,,,,,,,,,,,98.77,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.76357,Escherichia coli strain Survcare253,Survcare253,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19349419,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.2851",,,,2021-06-08T00:00:00Z,,PRJNA732846,GCA_018771465.1,"CP076305,CP076309,CP076308,CP076306,CP076307,CP076310,CP076311",,Justus-Liebig-University Giessen,Illumina NextSeq; Oxford Nanopore MinION,560x,Unicycler v. v.0.4.7,1,6,7,5037534,50.49945,5156,4845,"urine, catheter urine",,2019,Germany,Germany: Hesse,,,,Infection,,,,,,,,,,,,,Our study goals to molecular investigation on resistance mechanisms of CMY-42 encoding artreonam and avibactam resistant Eschichia coli.,collected_by:IMM Giessen,,,,,,,Infection,,,,,,,,,,,,,,99.93,0.59,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.76358,Escherichia coli strain Survcare045,Survcare045,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19349416,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",,,,2021-06-08T00:00:00Z,,PRJNA732846,GCA_018771545.1,"CP076318,CP076315,CP076319,CP076320,CP076321,CP076312,CP076313,CP076314,CP076316,CP076317",,Justus-Liebig-University Giessen,Illumina NextSeq; Oxford Nanopore MinION,109x,Unicycler v. v.0.4.7,1,9,10,5181753,50.793797,5263,4899,skin swab,,2018,Germany,Germany: Hesse,,,,Infection,,,,,,,,,,,,,Our study goals to molecular investigation on resistance mechanisms of CMY-42 encoding artreonam and avibactam resistant Eschichia coli.,collected_by:IMM Giessen,,,,,,,Infection,,,,,,,,,,,,,,99.67,0.15,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,562.76359,Escherichia coli strain Survcare321,Survcare321,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19349425,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",,,,2021-06-08T00:00:00Z,,PRJNA732846,GCA_018771585.1,"CP076301,CP076302,CP076303,CP076304",,Justus-Liebig-University Giessen,Illumina NextSeq; Oxford Nanopore MinION,531x,Unicycler v. v.0.4.7,1,3,4,5371977,50.612,5356,5051,"urine, catheter urine",,2019,Germany,Germany: Hesse,,,,Infection,,,,,,,,,,,,,Our study goals to molecular investigation on resistance mechanisms of CMY-42 encoding artreonam and avibactam resistant Eschichia coli.,collected_by:IMM Giessen,,,,,,,Infection,,,,,,,,,,,,,,99.67,0.14,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.76453,Escherichia coli strain E2,E2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13031456,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.692",,,,2021-06-15T00:00:00Z,27048740,PRJNA577622,GCA_018884065.1,"CP048915,CP048917,CP048919,CP048916,CP048918",,Hospital Universitari Vall d'Hebron,Oxford Nanopore MiniION; Illumina MiSeq,70.0x,Unicycler v. v0.4.7,1,4,5,4998048,50.56514,5008,4716,ascitic fluid,,2015,Egypt,Egypt:Giza,,female,52,post-hepatitis cirrhosis,,,,,,,,,,,,,Escherichia coli clinical isolates ST410 co-producers of NDM-5 and OXA-181 collected from a traveler returning from Pakistan. Dissemination within the same hospital room was evidenced. Stability studies were conducted which showed a rapid NDM-5 loss in the absence of antimicrobial pressure.,collected_by:Theodor Bilharz Research Institut,,,,,,,post-hepatitis cirrhosis,,,,,,,,,,,,,,99.93,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.76454,Escherichia coli strain B7A,B7A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904681,562,,,,"MLST.Escherichia_coli_1.94,MLST.Escherichia_coli_2.58",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884265.1,"CP035812,CP035816,CP035815,CP035814,CP035813",,"University of Maryland, School of Medicine",PacBio RSII,14.99x,HGAP v. 3,1,4,5,5240296,50.77841,5280,,stool,,,,,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76455,Escherichia coli strain WS3294A,WS3294A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904679,562,,,,"MLST.Escherichia_coli_2.366,MLST.Escherichia_coli_1.2484",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884305.1,"CP035819,CP035820,CP035821",,"University of Maryland, School of Medicine",PacBio RSII,17.56x,Canu v. v.1.2,1,2,3,5227380,50.794834,5235,,stool,,,Egypt,Egypt,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.19,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76456,Escherichia coli strain WS4437A-1,WS4437A-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904678,562,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884325.1,"CP035822,CP035825,CP035824,CP035823",,"University of Maryland, School of Medicine",PacBio RSII,16.64x,Canu v. v.1.4,1,3,4,5032644,50.546253,5060,,stool,,,Saudi Arabia,Saudi Arabia,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.25,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76457,Escherichia coli strain E7476,E7476,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904680,562,,,,"MLST.Escherichia_coli_1.58,MLST.Escherichia_coli_2.87",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884285.1,"CP035817,CP035818",,"University of Maryland, School of Medicine",PacBio RSII,23.86x,Canu v. v.1.4,1,1,2,5170332,50.587234,5173,,stool,,,South Africa,South Africa,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76458,Escherichia coli strain 025542-1,025542-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904676,562,,,,MLST.Escherichia_coli_1.173,,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884345.1,"CP035832,CP035835,CP035834,CP035833",,"University of Maryland, School of Medicine",PacBio RSII,16.81x,Canu v. v.1.2,1,3,4,5367095,50.560574,5366,,stool,,,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76459,Escherichia coli strain E275 a,E275 a,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07947704,562,,,,MLST.Escherichia_coli_1.4121,,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884485.1,"CP035865,CP035867,CP035866,CP035869,CP035868",,"University of Maryland, School of Medicine",PacBio RSII,16.87x,Canu v. v.1.4,1,4,5,5371942,50.726402,5410,,stool,,,Chile,Chile: Santiago,,,,ETEC gastroenteritis,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,collected_by:Roberto Vidal,,,,,,,ETEC gastroenteritis,,,,,,,,,,,,,,99.97,0.42,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76460,Escherichia coli strain TW10722,TW10722,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904674,562,,,,"MLST.Escherichia_coli_2.5,MLST.Escherichia_coli_1.443",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884385.1,"CP035841,CP035843,CP035842,CP035845,CP035844",,"University of Maryland, School of Medicine",PacBio RSII,24.21x,Canu v. v.1.4,1,4,5,5652056,50.66342,5761,,stool,,,Guinea-Bissau,Guinea-Bissau,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.62,1.61,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76461,Escherichia coli strain E2528-C1,E2528-C1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904671,562,,,,"MLST.Escherichia_coli_2.155,MLST.Escherichia_coli_1.1312",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884505.1,"CP035870,CP035873,CP035872,CP035871",,"University of Maryland, School of Medicine",PacBio RSII,12.17x,HGAP v. 3,1,3,4,5158259,50.695652,5193,,stool,,,,,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.82,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76462,Escherichia coli strain WS1933D,WS1933D,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904675,562,,,,MLST.Escherichia_coli_2.661,,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884365.1,"CP035836,CP035837,CP035840,CP035839,CP035838",,"University of Maryland, School of Medicine",PacBio RSII,14.67x,Canu v. v.1.4,1,4,5,5362911,50.81742,5433,,stool,,,Egypt,Egypt,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.59,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76463,Escherichia coli strain TW10598,TW10598,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904673,562,,,,"MLST.Escherichia_coli_1.4,MLST.Escherichia_coli_2.215",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884405.1,"CP035846,CP035847,CP035849,CP035848",,"University of Maryland, School of Medicine",PacBio RSII,23.31x,Canu v. v.1.4,1,3,4,5138413,50.662315,5191,,stool,,,Guinea-Bissau,Guinea-Bissau,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.84,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76464,Escherichia coli strain TD225-C4,TD225-C4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904672,562,,,,"MLST.Escherichia_coli_2.65,MLST.Escherichia_coli_1.410",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884465.1,"CP035860,CP035862,CP035861,CP035864,CP035863",,"University of Maryland, School of Medicine",PacBio RSII,19.9x,Canu v. v.1.2,1,4,5,5238275,50.512585,5330,,stool,,,Mexico,Mexico,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.62,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76465,Escherichia coli strain WS0115A,WS0115A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904668,562,,,,MLST.Escherichia_coli_1.2368,,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884565.1,"CP035882,CP035883",,"University of Maryland, School of Medicine",PacBio RSII,27.53x,Canu v. v.1.2,1,1,2,5015532,50.83706,4961,,stool,,,Egypt,Egypt,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.19,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76466,Escherichia coli strain DS26-1,DS26-1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904669,562,,,,"MLST.Escherichia_coli_1.423,MLST.Escherichia_coli_2.69",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884545.1,"CP035879,CP035880,CP035881",,"University of Maryland, School of Medicine",PacBio RSII,29.67x,Canu v. v.1.2,1,2,3,5294813,50.785458,5342,,stool,,,Saudi Arabia,Saudi Arabia,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.96,0.62,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76467,Escherichia coli strain B2C,B2C,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904670,562,,,,"MLST.Escherichia_coli_1.4,MLST.Escherichia_coli_2.215",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884525.1,"CP035874,CP035875,CP035878,CP035877,CP035876",,"University of Maryland, School of Medicine",PacBio RSII,25.43x,Canu v. v.1.4,1,4,5,5223561,50.607296,5250,,stool,,,Viet Nam,Viet Nam,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.97,0.92,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.76468,Escherichia coli strain LSN03-016011/A,LSN03-016011/A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10904667,562,,,,"MLST.Escherichia_coli_2.717,MLST.Escherichia_coli_1.88",,,,2021-06-15T00:00:00Z,,PRJNA521509,GCA_018884585.1,"CP035884,CP035885",,"University of Maryland, School of Medicine",PacBio RSII,13.96x,HGAP v. 3,1,1,2,5194852,50.735672,5086,,stool,,,Turkey,Turkey,,,,diarrhea,,,,,,,,,,,,,Complete genome assemblies of clinical enterotoxigenic Escherichia coli reference isolates,,,,,,,,diarrhea,,,,,,,,,,,,,,99.93,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,562.77177,Escherichia coli strain ST865,ST865,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19769895,562,,,,,,,,2021-07-02T00:00:00Z,,PRJNA739030,GCA_019091005.1,"CP077649,CP077650,CP077651",,China CDC,PacBio; Illumina HiSeq,300x,Unicycler v. v0.4.8,1,2,3,4944083,50.611084,4933,4662,diarrhea from outbreaks of food poisoning,,2019-05-29,China,China: Guangxi,,,,,,,,,,,,,,,,,descript the genome characteristics of E.coli,collected_by:Xiong Yanwen,,,,,,,,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.78000,Escherichia coli strain EC45,EC45,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15486686,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.410",,,,2021-07-27T00:00:00Z,,PRJNA473419,GCA_019355475.1,"CP059125,CP059126,CP059127,CP059128,CP059129",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; Illumina MiSeq,1600x,Unicycler v. v0.4.8,1,4,5,5141554,50.573914,5195,4861,,,2016,Ghana,Ghana,,,,,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:urine,,,,,,,,,,,,,,,,,,,,,99.93,0.77,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.78001,Escherichia coli strain Ec42,Ec42,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15486687,562,,,,MLST.Escherichia_coli_1.617,,,,2021-07-27T00:00:00Z,,PRJNA473419,GCA_019355455.1,"CP059119,CP059120,CP059121,CP059122,CP059123,CP059124",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; Illumina MiSeq,1300x,Unicycler v. v0.4.8,1,5,6,5267266,50.673004,5333,4986,,,2016,Ghana,Ghana,,,,,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:urine,,,,,,,,,,,,,,,,,,,,,99.67,0.89,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.78002,Escherichia coli strain Ec55,Ec55,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15486685,562,,,,MLST.Escherichia_coli_1.131,,,,2021-07-27T00:00:00Z,,PRJNA473419,GCA_019355495.1,"CP059130,CP059131,CP059132,CP059133,CP059134",,Tokyo Medical and Dental University,Oxford Nanopore MiniION; Illumina MiSeq,1000x,Unicycler v. v0.4.8,1,4,5,5392098,50.786465,5471,5152,,,2016,Ghana,Ghana,,,,,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",sample_type:Urine,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.78020,Escherichia coli strain M70,M70,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20339878,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,,,2021-07-31T00:00:00Z,,PRJNA748602,GCA_019428565.1,CP080118,,University of Veterinary Sciences Brno,Illumina MiSeq; PacBio Sequel,557x,SMRT Link v. 6.0,1,0,1,5168848,50.763634,5172,4894,"human, urinary tract infection",,2010,Czech Republic,Czech Republic: Brno,,,,urinary tract infection,,,,,,,,,,,,,"The whole-genome sequences of Escherichia coli ST131 H30Rx subclone of human, animal and environmental origin",,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.97,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78024,Escherichia coli strain M45,M45,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20339877,562,,,,MLST.Escherichia_coli_1.131,,,,2021-07-31T00:00:00Z,,PRJNA748602,GCA_019428585.1,CP080119,,University of Veterinary Sciences Brno,Illumina MiSeq; PacBio Sequel,300x,SMRT Link v. 6.0,1,0,1,5185411,50.774742,5231,4946,"human, urinary tract infection",,2010,Czech Republic,Czech Republic: Brno,,,,urinary tract infection,,,,,,,,,,,,,"The whole-genome sequences of Escherichia coli ST131 H30Rx subclone of human, animal and environmental origin",,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.97,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78026,Escherichia coli strain M24,M24,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20339876,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2021-07-31T00:00:00Z,,PRJNA748602,GCA_019428605.1,CP080120,,University of Veterinary Sciences Brno,Illumina MiSeq; PacBio Sequel,340x,SMRT Link v. 6.0,1,0,1,5271974,50.65518,5291,4996,"human, urinary tract infection",,2009,Czech Republic,Czech Republic: Brno,,,,urinary tract infection,,,,,,,,,,,,,"The whole-genome sequences of Escherichia coli ST131 H30Rx subclone of human, animal and environmental origin",,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.97,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78042,Escherichia coli strain L3452210II,L3452210II,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19604719,562,,,,"MLST.Escherichia_coli_1.410,MLST.Escherichia_coli_2.471",,,,2021-08-02T00:00:00Z,,PRJNA735932,GCA_019434375.1,"CP076527,CP076528,CP076529,CP076530,CP076531",,University of Bern,Oxford Nanopore MinION; Illumina NovaSeq,82.0x,Unicycler v. v.0.4.8,1,4,5,4965434,50.63189,5012,4709,rectal swab,,2021-04,Switzerland,Switzerland,,,,Covid-19,,,,,,,,,,,,,Genome sequencing of a cephalosporin- and ertapenem-resistant Escherichia coli isolated from a human rectal swab sample,collected_by:Institute for Infectious Diseases Bern,,,,,,,Covid-19,,,,,,,,,,,,,,99.93,0.16,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.78057,Escherichia coli strain PK5086,PK5086,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20445367,562,,,,"MLST.Escherichia_coli_2.692,MLST.Escherichia_coli_1.410",,,,2021-08-03T00:00:00Z,,PRJNA750217,GCA_019443365.1,"CP080370,CP080374,CP080373,CP080372,CP080371",,Yangzhou University,Illumina HiSeq; Oxford Nanopore MinION,100.0x,Unicycler v. 0.4.4,1,4,5,5042256,50.60947,5060,4766,missing,,2019-12-23,Pakistan,Pakistan: Faisalabad,,,,,,,,,,,,,,,,,Emergence of plasmid-mediated tigecycline resistance gene tet(X4) in Escherichia coli clinical isolates from Pakistan,collected_by:Mashkoor Mohsin,,,,,,,missing,,,,,,,,,,,,,,99.93,0.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.78059,Escherichia coli strain UPEC-455U/190220,UPEC-455U/190220,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14277528,562,,,"Escherichia coli, UPEC","MLST.Escherichia_coli_1.1193,MLST.Escherichia_coli_2.53",,,,2021-08-03T00:00:00Z,,PRJNA610084,GCA_019443605.1,"CP049839,CP049843,CP049842,CP049841,CP049844,CP049840",,Universidad Nacional Autonoma de Mexico,Illumina HiSeq; Oxford Nanopore MiniION,286.563x,Unicycler v. v0.4.1,1,5,6,5192928,50.628056,5246,4930,biopsy of human bladder epithelium; bladder epithelial biopsy from 60-year-old female patient with recurrent urinary tract infection,,2019-02-20,Mexico,Mexico: Mexico City,,female,60 years,Recurrent urinary tract infection,,host_description:60-year-old female patient with recurrent urinary tract infection;host_disease_outcome:chronic disease;host_disease_stage:chronic disease;host_health_state:chronic disease;host_subject_id:Not applicable,,,,,,,,,,,Genome sequences of E.coli producing recurrent infections,collected_by:Hospital Militar de Especialidades de la mujer y neonatologia;passage_history:Not applicable;specimen_voucher:Not collected,,,,,,,Recurrent urinary tract infection,chronic disease,chronic disease,60-year-old female patient with recurrent urinary tract infection,chronic disease,"Escherichia coli, UPEC",,,,,,,,,99.97,0.39,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78060,Escherichia coli strain UPEC-774U/190308,UPEC-774U/190308,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14277526,562,,,"Escherichia coli, UPEC","MLST.Escherichia_coli_2.53,MLST.Escherichia_coli_1.1193",,,,2021-08-03T00:00:00Z,,PRJNA610084,GCA_019443685.1,"CP049852,CP049856,CP049855,CP049854,CP049853",,Universidad Nacional Autonoma de Mexico,Illumina HiSeq; Oxford Nanopore MiniION,189.523x,Unicycler v. v0.4.1,1,4,5,5107728,50.655125,5141,4835,biopsy of human bladder epithelium; bladder epithelial biopsy from 50-year-old female patient with recurrent urinary tract infection,,2019-03-08,Mexico,Mexico: Mexico City,,female,50 years,Recurrent urinary tract infection,,host_description:50-year-old female patient with recurrent urinary tract infection;host_disease_outcome:chronic disease;host_disease_stage:chronic disease;host_health_state:chronic disease;host_subject_id:Not applicable,,,,,,,,,,,Genome sequences of E.coli producing recurrent infections,collected_by:Hospital Militar de Especialidades de la mujer y neonatologia;passage_history:Not applicable;specimen_voucher:Not collected,,,,,,,Recurrent urinary tract infection,chronic disease,chronic disease,50-year-old female patient with recurrent urinary tract infection,chronic disease,"Escherichia coli, UPEC",,,,,,,,,99.97,0.39,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78282,Escherichia coli strain 31HGR-CBG,31HGR-CBG,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20391559,562,O101:H4,,UPEC,"MLST.Escherichia_coli_1.44,MLST.Escherichia_coli_2.2",,,,2021-08-16T00:00:00Z,,PRJNA749581,GCA_019614135.1,"CP080645,CP080646",,INSTITUTO POLITECNICO NACIONAL,Illumina MiniSeq,98x,MEGAHIT v. 1.1.2,1,1,2,4820169,50.868523,4963,4703,urine,,2018,Mexico,Mexico,,,,Urinary infection,,,,,,,,,,,,,"Antimicrobial resistance is a global concern around the world. Escherichia coli due to its genomic flexibility acquire antimicrobial resistance genes by horizontal gene transfer. This project aims to evaluate the mobile genetic elements involved in the spread of antimicrobial resistance from clinical, food, and environmental sources in Northeast Mexico.",collected_by:Laboratorio Interaccion Ambiente-Microorganismo,,,,,,,Urinary infection,,,,,UPEC,,,,,,,,,99.55,0.19,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.78283,Escherichia coli strain ST866,ST866,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19769896,562,,,,,,,,2021-08-16T00:00:00Z,,PRJNA739030,GCA_019614825.1,"CP077646,CP077647,CP077648",,China CDC,PacBio; Illumina HiSeq,300x,Unicycler v. v0.4.8,1,2,3,4944441,50.61114,4935,4662,outbreaks of food poisoning,,2019-05-28,China,China: Guangxi,,,,,,,,,,,,,,,,,descript the genome characteristics of E.coli,collected_by:Xiong Yanwen,,,,,,,,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.78338,Escherichia coli strain Ec1079,Ec1079,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20802105,562,,,,"MLST.Escherichia_coli_2.692,MLST.Escherichia_coli_1.410",,,,2021-08-23T00:00:00Z,,PRJNA473419,GCA_019720795.1,"CP081306,CP081307,CP081308,CP081309,CP081310",,Tokyo Medical and Dental University,Oxford Nanopore; MGI DNBSEQ-G400FAST,100.0x,Unicycler v. 0.4.8,1,4,5,5049881,50.485744,5123,4826,urine,,2015,Ghana,Ghana,,,,Urinary tract infection,,,,,,,,,,,,,"Our aim of the project is to investigate the current status of antimicrobial resistance among clinical isolates from Ghana, and further to explore major resistance mechanisms involved.",collected_by:Tamale teaching hospital,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.93,0.56,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.79122,Escherichia coli strain SCAID URN1-2021 (19/278) strain SCAID URN1-2021 (19/278) strain SCAID URN1-2021 (19/278),SCAID URN1-2021 (19/278),Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982449,562,,,,MLST.Escherichia_coli_2.53,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915505.1,"CP082824,CP082825,CP082826",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,362x,Canu v. 2.0,1,2,3,5362922,50.60564,5499,5148,urine,,2021-03-26,Kazakhstan,Kazakhstan: Almaty,,,,pyelonephritis,,,Resistant;Susceptible,AMR Panel,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,pyelonephritis,,,,,,,,,,,,,,99.97,0.39,Urinary Tract Diseases,Upper UTI/Kidney Diseases,Urinary Tract,Urinary Tract Diseases-Upper UTI/Kidney Diseases HP,562.79123,Escherichia coli strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128) strain SCAID WND1-2021 (1/128),SCAID WND1-2021 (1/128),Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982447,562,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915525.1,"CP082831,CP082832",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,334x,Canu v. 2.0,1,1,2,5636010,50.61146,5889,5465,swab from wound,,2021-02-16,Kazakhstan,Kazakhstan: Almaty,,,,wound discharge,,,Resistant;Susceptible;Intermediate,AMR Panel,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,wound discharge,,,,,,,,,,,,,,99.97,1.07,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,562.79124,Escherichia coli strain SCAID WND2-2021 (3/145) strain SCAID WND2-2021 (3/145) strain SCAID WND2-2021 (3/145),SCAID WND2-2021 (3/145),Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982448,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915545.1,"CP082827,CP082828,CP082829,CP082830",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,397x,Canu v. 2.0,1,3,4,5411762,50.706924,5475,5135,swab from wound,,2021-02-16,Kazakhstan,Kazakhstan: Almaty,,,,wound discharge,,,Resistant;Susceptible;Intermediate,AMR Panel,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,wound discharge,,,,,,,,,,,,,,99.97,0.09,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,562.79210,Escherichia coli strain FUJ80154,FUJ80154,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00317522,562,,,,MLST.Escherichia_coli_1.648,,,,2021-09-01T00:00:00Z,,PRJDB11569,GCA_019973795.1,"AP024687,AP024688,AP024689,AP024690,AP024691,AP024692,AP024693",,"Microbiology, Fujita Health University School of Medicine",MiSeq; MinION,108x,Unicycler v. 0.4.9b,1,6,7,5352063,50.54522,5263,4958,,,2019-08-21,Japan,Japan:Aichi,,,,,,,,,,,,,,,,,Illumina and Oxford NANOPORE hybrid assembly of Eschericha coli clinical isolates producing NDM-5 and OXA-48.,,not applicable,not applicable,not applicable,not applicable,Whole genome sequense of carbapenemase producing Escherichia coli,,,,,,,,,,,,not applicable,,,,99.97,0.85,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.79211,Escherichia coli strain FUJ80155,FUJ80155,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00317523,562,,,,MLST.Escherichia_coli_1.648,,,,2021-09-01T00:00:00Z,,PRJDB11569,GCA_019973815.1,"AP024694,AP024695,AP024696,AP024697,AP024698,AP024699,AP024700,AP024701",,"Microbiology, Fujita Health University School of Medicine",MiSeq; MinION,106x,Unicycler v. 0.4.9b,1,7,8,5527700,50.54896,5536,5191,,,2019-09-25,Japan,Japan:Aichi,,,,,,,,,,,,,,,,,Illumina and Oxford NANOPORE hybrid assembly of Eschericha coli clinical isolates producing NDM-5 and OXA-48.,,not applicable,not applicable,not applicable,not applicable,Whole genome sequense of carbapenemase producing Escherichia coli,,,,,,,,,,,,not applicable,,,,99.93,0.79,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86574,Escherichia coli strain SCPM-O-B-9427,SCPM-O-B-9427,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22830670,562,,,,"MLST.Escherichia_coli_2.290,MLST.Escherichia_coli_1.678",,,,2021-11-09T00:00:00Z,,PRJNA269675,GCA_020808965.1,"CP086259,CP086260,CP086261,CP086262,CP086263,CP086264",,SRCAMB,Oxford Nanopore MinION; Illumina MiSeq,53.0x,Unicycler v. 0.4.7,1,5,6,5492674,50.624996,5655,5283,feces,,2018-07-30,Russia,Russia: Saint-Petersburg,,,,,,,,,,,,,,,,,"Genome sequencing of bacteria from State collection of pathogenic microorganisms Obolensk. Collection includes bacteria, fungi, and cell-lines.",sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,99.93,0.49,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.86576,Escherichia coli strain EH41 strain not applicable,not applicable,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13045723,562,O113:H21,,EHEC,MLST.Escherichia_coli_2.366,,,,2021-11-09T00:00:00Z,,PRJNA548004,GCA_020809385.1,"CP045213,CP045215,CP045214",,University of Texas at San Antonio,"Oxford Nanopore MinION, Illumina MiSeq",24x,SPAdes v. v3.5,1,2,3,5216538,50.729374,5329,5054,feces,,2002,,Australia,,,,Hemolytic uremic syndrome,,,,,,,,,,,,,Pathogenome and phylogenomic classification of global EHEC O113:21 isolates,,,,,,,,Hemolytic uremic syndrome,,,,,EHEC,,,,,,,,,99.93,0.23,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.86743,Escherichia coli strain RIVM_C039629,RIVM_C039629,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569039,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883235.1,"CP086616,CP086617",,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,1,2,5305264,50.626812,5353,5028,,,2021,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.69,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86744,Escherichia coli strain RIVM_C039227,RIVM_C039227,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569037,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883255.1,"CP086618,CP086619",,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,1,2,5336151,50.619743,5398,5079,,,2021,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.69,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86745,Escherichia coli strain RIVM_C039205,RIVM_C039205,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569035,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883275.1,"CP086620,CP086621",,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,1,2,5366928,50.647762,5458,5126,,,2021,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86746,Escherichia coli strain RIVM_C037884,RIVM_C037884,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569034,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883295.1,CP086622,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5262226,50.558434,5327,4992,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86747,Escherichia coli strain RIVM_C037794,RIVM_C037794,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569033,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883315.1,CP086623,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5248035,50.579292,5281,4974,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86748,Escherichia coli strain RIVM_C037791,RIVM_C037791,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569032,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883335.1,CP086624,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5242232,50.59755,5279,4972,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86749,Escherichia coli strain RIVM_C037166,RIVM_C037166,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569031,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883355.1,CP086625,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5254248,50.57816,5288,4988,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.43,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86750,Escherichia coli strain RIVM_C037134,RIVM_C037134,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569030,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883375.1,CP086626,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5230471,50.59837,5252,4953,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86751,Escherichia coli strain RIVM_C036569,RIVM_C036569,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569028,562,,,,"MLST.Escherichia_coli_2.8,MLST.Escherichia_coli_1.38",,,,2021-11-18T00:00:00Z,,PRJNA774636,GCA_020883395.1,CP086627,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5199059,50.620758,5204,4905,,,2020,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86845,Escherichia coli strain 127,127,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8065684,562,,,,MLST.Escherichia_coli_1.127,,,,2021-10-21T00:00:00Z,,PRJEB42440,GCA_905332355.1,HG994850,,CNAG-CRG,,,,1,0,1,5184627,50.44895,5056,4781,hospital universitari germans trias i pujol (badalona),"isolated from 41 Spanish hospitals and sequenced both with long and short reads to perform hybrid assemblies which allowed us to define their genetic characteristics, the genomic mechanisms which bear the carbapenemase-enzymes, the mechanisms associated with other antimicrobials, the molecular epidemiology of 16S rRNA methyltransferases, and to define the gene clusters implicated in the successful spread of K. pneumoniae ST-15 in Spain",2018,,Spain,,,,,,host_health_state:diseased,,,,,,,,,,,"To get a wide view of the distribution, the characteristics and the mechanisms of resistance to carbapenem in Enterobacteria in Spain, 461 strains were isolated from 41 Spanish hospitals and sequenced both with long and short reads to perform hybrid assemblies which allowed us to define their genetic characteristics, the genomic mechanisms which bear the carbapenemase-enzymes, the mechanisms associated with other antimicrobials, the molecular epidemiology of 16S rRNA methyltransferases, and to define the gene clusters implicated in the successful spread of K. pneumoniae ST-15 in Spain.",,,,,,,,,diseased,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.86846,Escherichia coli strain 127,127,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8065773,562,,,,MLST.Escherichia_coli_1.127,,,,2021-10-21T00:00:00Z,,PRJEB42440,GCA_905332365.1,HG994851,,CNAG-CRG,,,,1,0,1,5131774,50.47017,5004,4736,hospital universitario son de espases (palma de mallorca),"isolated from 41 Spanish hospitals and sequenced both with long and short reads to perform hybrid assemblies which allowed us to define their genetic characteristics, the genomic mechanisms which bear the carbapenemase-enzymes, the mechanisms associated with other antimicrobials, the molecular epidemiology of 16S rRNA methyltransferases, and to define the gene clusters implicated in the successful spread of K. pneumoniae ST-15 in Spain",2018,,Spain,,,,,,host_health_state:diseased,,,,,,,,,,,"To get a wide view of the distribution, the characteristics and the mechanisms of resistance to carbapenem in Enterobacteria in Spain, 461 strains were isolated from 41 Spanish hospitals and sequenced both with long and short reads to perform hybrid assemblies which allowed us to define their genetic characteristics, the genomic mechanisms which bear the carbapenemase-enzymes, the mechanisms associated with other antimicrobials, the molecular epidemiology of 16S rRNA methyltransferases, and to define the gene clusters implicated in the successful spread of K. pneumoniae ST-15 in Spain.",,,,,,,,,diseased,,,,,,,,,,,,,99.97,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.88798,Escherichia coli strain RIVM_C019217,RIVM_C019217,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22569026,562,,,,"MLST.Escherichia_coli_1.38,MLST.Escherichia_coli_2.8",,,,2021-11-24T00:00:00Z,,PRJNA774636,GCA_020971745.1,"CP087377,CP087378",,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,1,2,5378081,50.656116,5464,5135,,,2019,,Netherlands,,,,,,,,,,,,,,,,,"The Dutch national surveillance of carbapenemase-producing Enterobacterales from 2016 to 2021 revealed a genetic cluster of 17 Escherichia coli ST38 isolates from phylotype D and producing the OXA-244 carbapenemase. Isolates carry multiple putative urovirulence factors, harbor a MDR plasmid, and were retrieved from urine in 53% of the cases.",sample_type:Chromosome,,,,,,,,,,,,,,,,,,,,,99.97,0.69,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.89934,Escherichia coli STO_Bone2,STO_Bone2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15006795,562,,,,"MLST.Escherichia_coli_2.44,MLST.Escherichia_coli_1.405",,,,2022-01-18T00:00:00Z,,PRJNA634765,GCA_021498145.1,"CP054161,CP054165,CP054162,CP054164,CP054163",,,PacBio RSII,1043x,HGAP v. 3,1,4,5,5323759,50.599323,5264,4970,bone infection of foot,,2005-01-01,Sweden,Sweden: Stockholm,,,,Focal infection,,,,,,,,,,,,,,collected_by:Karolinska University Hospital,,,,,,,Focal infection,,,,,,,,,,,,,,99.97,0.19,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,562.89935,Escherichia coli STO_Bone1B,STO_Bone1B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15006794,562,,,,MLST.Escherichia_coli_1.940,,,,2022-01-18T00:00:00Z,,PRJNA634765,GCA_021498165.1,"CP054169,CP054166,CP054167,CP054168",,,PacBio RSII,1210x,HGAP v. 3,1,3,4,5011905,50.79438,5027,4681,bone infection of foot,,2005-01-01,Sweden,Sweden: Stockholm,,,,Focal infection,,,,,,,,,,,,,,collected_by:Karolinska University Hospital,,,,,,,Focal infection,,,,,,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,562.91930,Escherichia coli EC12,EC12,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17849355,562,O63:H6,,,"MLST.Escherichia_coli_2.586,MLST.Escherichia_coli_1.583",,,,2022-01-06T00:00:00Z,34679522,PRJNA701164,GCA_021378315.1,"CP070229,CP070230,CP070231",,,Oxford Nanopore MinION; Illumina NovaSeq,100.0x,Unicycler v. 0.4.8,1,2,3,5173402,50.556328,5412,5069,stool,,2020-06-20,South Korea,South Korea:Seoul,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,,collected_by:Samsung Medical Center,,,,,,,Hemolytic-Uremic Syndrome,,,,,,,,,,,,,,99.79,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,562.91935,Escherichia coli UCS1,UCS1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21558688,562,O25:H4,,UPEC,MLST.Escherichia_coli_1.131,,,,2022-01-07T00:00:00Z,34696479,PRJNA765452,GCA_021383885.1,CP084679,,,Illumina MiSeq,248x,Geneious v. 2021-07-19 12:20,1,0,1,5109337,50.75248,5171,4893,urine (recurrent uti),,2019-03-17,USA,USA: San Diego,,,56,Urinary Tract Infection,,,,,,,,,,,,,,collected_by:University of San Diego Health,,,,,,,Urinary Tract Infection,,,,,UPEC,,,,,,,,,99.97,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.91936,Escherichia coli UCS1.1,UCS1.1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21558689,562,O25:H4,,,MLST.Escherichia_coli_1.131,,,,2022-01-07T00:00:00Z,34696479,PRJNA765452,GCA_021383905.1,CP084678,,,Illumina MiSeq,215x,Geneious v. 2021-07-19 12:20,1,0,1,5109228,50.751865,5171,4908,urine (asymptomatic uti),,2020-05-19,USA,USA: San Diego,,,56,Urinary Tract Infection,,,,,,,,,,,,,,collected_by:University of San Diego Health,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,99.97,0.37,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,562.92062,Escherichia coli B379,B379,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24645352,562,,,,"MLST.Escherichia_coli_2.446,MLST.Escherichia_coli_1.746",,,,2022-01-12T00:00:00Z,,PRJNA515159,GCA_021441985.1,"CP090456,CP090457,CP090458,CP090460,CP090461,CP090459",,,Illumina NovaSeq; Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.8,1,5,6,5152502,50.8734,5201,4886,pus,,2021-08-02,China,China: Hangzhou,,female,,Appendicitis,,,,,,,,,,,,,,collected_by:Meina Yue,,,,,,,Appendicitis,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,562.93985,Escherichia coli elppa1,elppa1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169124,562,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_021655655.1,"CP083534,CP083535,CP083536,CP083537,CP083538",,,Oxford Nanopore,113x,flye v. 2.8,1,4,5,5375429,50.680496,5570,5279,blood,,2019-10,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.97,0.99,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94069,Escherichia coli NDM4,NDM4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398205,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",genotype:ST167,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149605.1,"CP083877,CP083878,CP083879",,,Oxford Nanopore MiniION + Illumina MiSeq,330x,Canu v. JAN-2021,1,2,3,4902558,50.819183,4968,4642,pelvic abcsess,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.67,0.09,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,562.94070,Escherichia coli NDM5,NDM5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398207,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",genotype:ST167,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149625.1,"CP083872,CP083873,CP083874,CP083875,CP083876",,,Oxford Nanopore MiniION + Illumina MiSeq,285x,Canu v. JAN-2021,1,4,5,5017598,50.94585,5098,4786,urine,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.67,0.33,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.94071,Escherichia coli NDM1,NDM1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398202,562,,,,MLST.Escherichia_coli_1.90,genotype:ST90,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149645.1,"CP083888,CP083889,CP083890,CP083891,CP083892,CP083893,CP083894,CP083895,CP083896",,,Oxford Nanopore MiniION + Illumina MiSeq,67x,Canu v. JAN-2021,1,8,9,5249684,50.664345,5329,4995,blood,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.94073,Escherichia coli NDM2,NDM2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398203,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.10",genotype:ST10,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149665.1,"CP083886,CP083884,CP083885,CP083887",,,Oxford Nanopore MiniION + Illumina MiSeq,63x,Canu v. JAN-2021,1,3,4,4958906,50.799953,5012,4690,blood,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.67,0.45,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,562.94075,Escherichia coli NDM3,NDM3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398204,562,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",genotype:ST167,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149685.1,"CP083880,CP083881,CP083882,CP083883",,,Oxford Nanopore MiniION + Illumina MiSeq,277x,Canu v. JAN-2021,1,3,4,4954894,50.744717,5033,4716,urine,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.67,0.09,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.94076,Escherichia coli NDM6,NDM6,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21398206,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",genotype:ST167,,,2021-09-27T00:00:00Z,,PRJNA762553,GCA_020149705.1,"CP083869,CP083867,CP083868,CP083870,CP083871",,,Oxford Nanopore MiniION + Illumina MiSeq,234x,Canu v. JAN-2021,1,4,5,5003849,51.069706,5136,4762,urine,,2020,USA,USA: Baltimore,,,,Intraabdominal Infections,,,,,,,,,,,,,,collected_by:Johns Hopkins University,,,,,,,Intraabdominal Infections,,,,,,,,,,,,,,99.31,0.98,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,562.94146,Escherichia coli NEC1,NEC1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975553,562,,,,"MLST.Escherichia_coli_2.500,MLST.Escherichia_coli_1.1284",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029835.1,CP091155,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4781904,50.81518,4650,4374,blood,,2020-08-31,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.37,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94147,Escherichia coli NEC3,NEC3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975952,562,,,,MLST.Escherichia_coli_1.167,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029855.1,CP091157,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4677158,50.856133,4560,4271,blood,,2020-07-12,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,98.48,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94148,Escherichia coli NEC4,NEC4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24976033,562,,,,"MLST.Escherichia_coli_2.650,MLST.Escherichia_coli_1.361",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029875.1,CP091158,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4783211,50.73406,4664,4395,blood,,2019-10-20,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.93,0.14,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94151,Escherichia coli NEC5,NEC5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24976404,562,,,,MLST.Escherichia_coli_1.405,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029895.1,CP091159,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5154825,50.52126,5053,4770,blood,,2020-11-22,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94155,Escherichia coli NEC6,NEC6,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24976414,562,,,,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.22",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029915.1,CP091160,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4967275,50.574856,4908,4626,blood,,2020-09-01,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.81,0.07,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94156,Escherichia coli NEC8,NEC8,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24976522,562,,,,MLST.Escherichia_coli_1.424,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029935.1,CP091161,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4778181,50.736813,4674,4399,blood,,2019-09-20,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.93,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94157,Escherichia coli NEC10,NEC10,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24977493,562,,,,MLST.Escherichia_coli_1.167,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029955.1,CP091162,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4720910,50.89503,4617,4335,blood,,2020-09-02,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.31,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94158,Escherichia coli NEC11,NEC11,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24979483,562,,,,"MLST.Escherichia_coli_2.471,MLST.Escherichia_coli_1.2851",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029975.1,CP091163,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4814956,50.691383,4790,4480,blood,,2019-10-02,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.52,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94159,Escherichia coli NEC12,NEC12,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24979498,562,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029995.1,CP091164,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4689227,50.796623,4569,4300,blood,,2019-10-28,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,96.4,0.06,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94160,Escherichia coli NEC13,NEC13,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24985826,562,,,,MLST.Escherichia_coli_1.450,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022030015.1,CP091165,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4887515,50.79556,4772,4446,blood,,2020-11-18,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.91,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94161,Escherichia coli NEC2,NEC2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975554,562,,,,"MLST.Escherichia_coli_1.2851,MLST.Escherichia_coli_2.471",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022030035.1,CP091156,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4837004,50.713146,4811,4499,blood,,2020-08-29,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.52,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94162,Escherichia coli NEC9,NEC9,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24977285,562,,,,"MLST.Escherichia_coli_2.650,MLST.Escherichia_coli_1.361",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022030055.1,CP091298,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4747633,50.766693,4648,4378,blood,,2019-11-26,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.93,0.14,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94163,Escherichia coli NEC14,NEC14,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24992592,562,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.506",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022030995.1,CP091166,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4817002,50.692463,4755,4488,blood,,2019-12-23,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.33,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94164,Escherichia coli NEC16,NEC16,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25000402,562,,,,"MLST.Escherichia_coli_2.3,MLST.Escherichia_coli_1.69",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022031015.1,CP091167,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4963880,50.662926,4851,4610,blood,,2020-09-02,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94165,Escherichia coli NEC17,NEC17,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25000409,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022031035.1,CP091168,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4959888,50.620876,4826,4587,blood,,2020-03-15,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.39,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94166,Escherichia coli NEC18,NEC18,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25000427,562,,,,MLST.Escherichia_coli_1.131,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022031055.1,CP091169,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4849845,50.742393,4766,4527,blood,,2020-10-17,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.81,0.48,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94167,Escherichia coli NEC19,NEC19,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25001171,562,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022031075.1,CP091170,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,4996618,50.543797,4911,4660,blood,,2020-08-24,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.08,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94168,Escherichia coli NEC20,NEC20,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25001173,562,,,,"MLST.Escherichia_coli_1.69,MLST.Escherichia_coli_2.3",,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022031095.1,CP091171,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5055567,50.765354,4951,4667,blood,,2020-11-12,India,India,,,,Sepsis,,,,,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,562.94172,Escherichia coli elppa10,elppa10,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169133,562,,,,"MLST.Escherichia_coli_2.24,MLST.Escherichia_coli_1.58",,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827555.1,"CP083478,CP083479,CP083480",,,Oxford Nanopore,103x,flye v. 2.8,1,2,3,5063468,50.821926,5082,4805,blood,,2019-12,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.93,0.65,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94173,Escherichia coli elppa9,elppa9,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169132,562,,,,"MLST.Escherichia_coli_2.477,MLST.Escherichia_coli_1.405",,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827575.1,"CP083481,CP083482,CP083483,CP083484,CP083485,CP083486,CP083487,CP083488,CP083489,CP083490",,,Oxford Nanopore,177x,flye v. 2.8,1,9,10,5509639,50.730873,5563,5258,blood,,2019-04,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.97,0.45,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94174,Escherichia coli elppa8,elppa8,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169131,562,,,,MLST.Escherichia_coli_1.167,,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827595.1,"CP083492,CP083491,CP083493,CP083494,CP083495,CP083496",,,Oxford Nanopore,77x,flye v. 2.8,1,5,6,5290898,50.678658,5572,5080,blood,,2019-04,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.52,0.65,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94175,Escherichia coli elppa6,elppa6,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169129,562,,,,"MLST.Escherichia_coli_2.87,MLST.Escherichia_coli_1.58",,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827615.1,"CP083497,CP083498,CP083499,CP083500,CP083501,CP083502",,,Oxford Nanopore,108x,flye v. 2.8,1,5,6,5138601,50.78242,5178,4874,blood,,2019-01,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.93,0.91,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94176,Escherichia coli elppa5,elppa5,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169128,562,,,,"MLST.Escherichia_coli_1.405,MLST.Escherichia_coli_2.477",,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827635.1,"CP083503,CP083504,CP083505,CP083506,CP083507,CP083508,CP083509,CP083510,CP083511",,,Oxford Nanopore,59x,flye v. 2.8,1,8,9,5379061,50.74817,5426,5138,blood,,2019-11,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.97,0.04,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94177,Escherichia coli elppa4,elppa4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169127,562,,,,MLST.Escherichia_coli_1.349,,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827655.1,"CP083512,CP083513,CP083514,CP083515,CP083516",,,Oxford Nanopore,114x,flye v. 2.8,1,4,5,5424313,50.661163,5483,5175,blood,,2019-08,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.97,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94178,Escherichia coli elppa2,elppa2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21169125,562,,,,MLST.Escherichia_coli_1.1485,,,,2021-11-10T00:00:00Z,,PRJNA610462,GCA_020827895.1,"CP083530,CP083531,CP083532,CP083533",,,Oxford Nanopore,60x,flye v. 2.8,1,3,4,5384690,50.233032,5505,5032,blood,,2019-10,Taiwan,Taiwan,,,,bacteremia,,,,,,,,,,,,,,collected_by:National Chung Cheng University,,,,,,,bacteremia,,,,,,,,,,,,,,99.42,0.14,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,562.94312,Escherichia coli STO_Bone4,STO_Bone4,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15006796,562,,,,,,,,2022-01-24T00:00:00Z,,PRJNA634765,GCA_021559635.1,"CP054251,CP054250,CP054249,CP054252,CP054253,CP054248",,,PacBio RSII,91.77x,HGAP v. 3,1,5,6,5406858,50.818405,6385,5257,bone infection of foot,,2013-06-09,Sweden,Sweden: Stockholm,,,,Focal infection,,,,,,,,,,,,,,collected_by:Karolinska University Hospital,,,,,,,Focal infection,,,,,,,,,,,,,,98.19,1.3,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,562.94317,Escherichia coli STO_Bone7,STO_Bone7,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15006798,562,,,,,,,,2022-01-24T00:00:00Z,,PRJNA634765,GCA_021562195.1,"CP054239,CP054243,CP054240,CP054241,CP054242",,,PacBio RSII,178.91x,HGAP v. 3,1,4,5,5329642,50.781742,6344,5177,bone infection of foot,,2015-10-24,Sweden,Sweden: Stockholm,,,,Focal infection,,,,,,,,,,,,,,collected_by:Karolinska University Hospital,,,,,,,Focal infection,,,,,,,,,,,,,,98.35,0.6,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,562.96053,Escherichia coli 131,131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22456104,562,,,,MLST.Escherichia_coli_1.131,,,,2022-03-15T00:00:00Z,,PRJNA773238,GCA_022569795.1,CP093011,,,Illumina MiSeq,30.0x,SPAdes v. 3.11.1,1,0,1,5219097,50.62391,5337,5042,hospital,,2017,South Africa,South Africa,,,,Sepsis,,,,,,,,,,,,,,collected_by:Stellenbosch University,,,,,,,Sepsis,,,,,,,,,,,,,,99.97,0.67,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,562.96077,Escherichia coli EC-14-2-9,EC-14-2-9,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26549971,562,,,,"MLST.Escherichia_coli_1.167,MLST.Escherichia_coli_2.2",,,,2022-03-17T00:00:00Z,,PRJNA814402,GCA_022605345.1,"CP093283,CP093284,CP093285,CP093287,CP093288,CP093286",,,Illumina MiSeq,1.0x,CLC NGS Cell v. 21.0,1,5,6,5303628,50.425896,5404,5049,sputum,,2014-12-19,China,China: Zhengzhou,,,,Aortitis infection,,,,,,,,,,,,,,collected_by:Zhengzhou University,,,,,,,Aortitis infection,,,,,,,,,,,,,,99.67,0.24,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- NHP,562.96286,Escherichia coli H3,H3,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04100030,562,,,,"MLST.Escherichia_coli_2.478,MLST.Escherichia_coli_1.10",,,,2022-03-07T00:00:00Z,33319232,PRJNA293615,GCA_022492975.1,CP028732,,,PacBio,60x,HGAP v. 3.2.3,1,0,1,4906030,50.634483,5057,4981,feces,,2000,Mexico,Mexico,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,commensal,,,,,99.97,0.04,,,Gastrointestinal,- NHP,562.96289,Escherichia coli H2,H2,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04100029,562,,,,"MLST.Escherichia_coli_2.86,MLST.Escherichia_coli_1.641",,,,2022-03-07T00:00:00Z,,PRJNA293615,GCA_022493015.1,CP028733,,,PacBio,60x,HGAP v. 3.2.3,1,0,1,4816573,50.55142,4955,4850,feces,,1999,Mexico,Mexico,,,,,,,,,,,,,,,,,,sample_type:whole organism,,,,,,,,,,,,,,,,commensal,,,,,99.89,0.04,,,Gastrointestinal,- HP,564.44,Escherichia fergusonii strain ATCC 35473,ATCC 35473,Escherichia fergusonii,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916852,564,,,,,,ATCC: 35473,,2019-08-22T00:00:00Z,,PRJNA218110,GCA_008064875.1,CP042942,,CDC,PacBio,113.35X,HGAP v. 3,1,,1,4657720,49.823174,4555,,feces,,,USA,USA: New Mexico|USA: NewMexico,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.75,0.52,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,564.45,Escherichia fergusonii strain ATCC 35471,ATCC 35471,Escherichia fergusonii,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916802,564,,,,MLST.Escherichia_coli_1.4419,,ATCC: 35471,,2019-08-22T00:00:00Z,,PRJNA218110,GCA_008064895.1,"CP042945,CP042943,CP042944",,CDC,PacBio,123.44X,HGAP v. 3,1,2,3,4755297,49.945988,4688,,feces,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.67,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,565.13,Atlantibacter hermannii strain ATCC 33651,ATCC 33651,Atlantibacter hermannii,Atlantibacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01915842,565,,,,,,ATCC: 33651,,2019-08-22T00:00:00Z,,PRJNA218110,GCA_008064855.1,CP042941,,CDC,PacBio,197.10X,HGAP v. 3,1,,1,4315318,54.331985,4061,,"arm wound, 24-year-old male",,,USA,USA: New Mexico|USA: NewMexico,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.2,0.87,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,566.7,Pseudescherichia vulneris strain 4928STDY7071515,4928STDY7071515,Pseudescherichia vulneris,Pseudescherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567622,566,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164725.1,LR607338,,SC,,,,1,,1,4398823,57.353264,3848,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,95.92,0.51,,,Other,- HP,569579.3,Escherichia coli NU14 strain NU14,NU14,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06314223,569579,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,,,2017-03-10T00:00:00Z,,PRJNA373796,GCF_002024865.1,CP019777,NZ_CP019777.1,National University of Singapore and Genome Institute of Singapore,PacBio,300.0x,HGAP3 v. 3,1,,1,5076615,50.59,5206,5102,urine,,1986,USA,United States,,female,,Urinary tract infection,,,,,,,,,,,,,Sequencing of uropathogenic E. coli strain NU14,"collected_by:Scott J. Hultgren, William R. Schwan, Anthony J. Schaeffer, James L. Duncan",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,571.1454,Klebsiella oxytoca Kox71,Kox71,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286080,571,,,,,,,,2021-12-19T00:00:00Z,,PRJNA781656,GCA_021228655.1,"CP089392,CP089393,CP089394",,,Oxford Nanopore MinION; Illumina HiSeq,48x,Flye v. v2.8,1,2,3,6435969,54.579163,6372,5971,urine,,2018-05-07,Australia,Australia: Melbourne,,,,urinary tract infection,,,,,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,99.7,0.23,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,571.1456,Klebsiella oxytoca Kox100,Kox100,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286083,571,,,,,,,,2021-12-19T00:00:00Z,,PRJNA781656,GCA_021228775.1,"CP089411,CP089412,CP089413",,,Oxford Nanopore MinION; Illumina HiSeq,35x,Flye v. v2.8,1,2,3,6160838,54.822445,6028,5670,blood,,2018-06-15,Australia,Australia: Melbourne,,,,blood infection,,,,,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,blood infection,,,,,,,,,,,,,,100,0.08,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,571.1525,Klebsiella oxytoca ST34,ST34,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173998,571,,,,MLST.Klebsiella_oxytoca.34,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918735.1,"CP103690,CP103691,CP103692,CP103693",,,Oxford Nanopore GridION,155x,Flye v. 2.8.3-b1695,1,3,4,6420321,54.860497,6361,6000,blood,,2017-06-28,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,571.1737,Klebsiella oxytoca RSM6895,RSM6895,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36411529,571,,,,,,,,2023-07-19T00:00:00Z,,PRJNA992249,,CP130257,,,Illumina NovaSeq,600.0x,Unicycler v. 0.4.8,1,0,1,5910306,55.023575,5878,5578,rectal swab,,2022-03-02,Uganda,Uganda: Kampala,,,,Gastrointestinal infections,,,,,,,,,,,,,,collected_by:Simon Sekyanzi,,,,,,,Gastrointestinal infections,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,571.1739,Klebsiella oxytoca RSM6774,RSM6774,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36411192,571,,,,MLST.Klebsiella_oxytoca.2,,,,2023-07-19T00:00:00Z,,PRJNA992249,,CP130256,,,Illumina NovaSeq,600.0x,Unicycler v. 0.4.8; Medusa v. 1.3,1,0,1,5734157,55.143982,5554,5272,blood,,2022-03-02,Uganda,Uganda: Kampala,,,,Blood infection,,,,,,,,,,,,,,collected_by:Robert Ebwong,,,,,,,Blood infection,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,571.1740,Klebsiella oxytoca RSM5034,RSM5034,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36347001,571,,,,,,,,2023-07-26T00:00:00Z,,PRJNA992249,,CP130582,,,Illumina NovaSeq,652.0x,SPAdes v. 3.15; Medusa v. 1.3,1,0,1,5726898,55.25794,5524,5244,feces,,2022-03-02,Uganda,Uganda: Kampala,,,,Gastroenteritis,,,,,,,,,,,,,,collected_by:Robert Ebwong,,,,,,,Gastroenteritis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,571.213,Klebsiella oxytoca strain CAV1752,CAV1752,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03733848,571,,,,MLST.Klebsiella_oxytoca.144,,,,2016-12-13T00:00:00Z,,PRJNA246471,GCF_001970835.1,"CP018362,CP018360,CP018361,CP018357,CP018358,CP018359","NZ_CP018362.1,NZ_CP018360.1,NZ_CP018361.1,NZ_CP018357.1,NZ_CP018358.1,NZ_CP018359.1",University of Oxford,PacBio,110x,HGAP v. unspecified,1,5,6,6394387,55.9,6415,6144,perirectal,,2012-12,USA,USA:Virginia,,,,,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,571.319,Klebsiella oxytoca strain FDAARGOS_335,FDAARGOS_335,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173348,571,,,,MLST.Klebsiella_oxytoca.147,,FDA:FDAARGOS_335,,2018-03-09T00:00:00Z,,PRJNA231221,GCA_002984395.1,"CP027426,CP027425",,US Food and Drug Administration,PacBio; Illumina,15.9487981715526x,"SMRT v. 2.3.0, HGAP v. 3.0",1,1,2,6049823,55.082916,5935,5710,urine catheter,,2015-02-11,USA,USA:DC,,female,4Y,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases NHP,571.705,Klebsiella oxytoca strain 4928STDY7071292,4928STDY7071292,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567402,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164635.1,LR607327,,SC,,,,1,,1,6017355,55.879894,5769,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.7,0.37,,,Other,- NHP,571.706,Klebsiella oxytoca strain 4928STDY7071328,4928STDY7071328,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567438,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164675.1,LR607336,,SC,,,,1,,1,6099119,56.40208,5338,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.7,0.11,,,Other,- NHP,571.728,Klebsiella oxytoca strain 4928STDY7071186,4928STDY7071186,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567297,571,,,,MLST.Klebsiella_oxytoca.29,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166415.1,LR607342,,SC,,,,1,,1,6014703,55.683193,5865,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,100,1.32,,,Other,- NHP,571.729,Klebsiella oxytoca strain 4928STDY7071171,4928STDY7071171,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567282,571,,,,MLST.Klebsiella_oxytoca.88,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166425.1,LR607351,,SC,,,,1,,1,6484331,55.928566,6060,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.95,0.46,,,Other,- NHP,571.730,Klebsiella oxytoca strain 4928STDY7071151,4928STDY7071151,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567275,571,,,,MLST.Klebsiella_oxytoca.36,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166465.1,LR607350,,SC,,,,1,,1,6835957,55.043636,6297,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.39,0.97,,,Other,- NHP,571.731,Klebsiella oxytoca strain 4928STDY7071187,4928STDY7071187,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567298,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166545.1,LR607341,,SC,,,,1,,1,7064570,55.79775,6234,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,100,0.13,,,Other,- NHP,571.732,Klebsiella oxytoca strain 4928STDY7387706,4928STDY7387706,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694343,571,,,,MLST.Klebsiella_oxytoca.44,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166555.1,LR607367,,SC,,,,1,,1,6744573,56.337402,5706,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,95.97,0.18,,,Other,- NHP,571.733,Klebsiella oxytoca strain 4928STDY7387759,4928STDY7387759,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694396,571,,,,MLST.Klebsiella_oxytoca.84,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166585.1,LR607369,,SC,,,,1,,1,5932716,56.62123,5251,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.48,0.22,,,Other,- NHP,571.734,Klebsiella oxytoca strain 4928STDY7387738,4928STDY7387738,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694375,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166625.1,LR607366,,SC,,,,1,,1,5906467,56.650475,5372,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97.9,0.22,,,Other,- NHP,571.735,Klebsiella oxytoca strain 4928STDY7387762,4928STDY7387762,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694399,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166675.1,LR607363,,SC,,,,1,,1,6666581,56.172295,5640,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97.47,0.11,,,Other,- NHP,571.736,Klebsiella oxytoca strain 4928STDY7387763,4928STDY7387763,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694400,571,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166735.1,LR607357,,SC,,,,1,,1,6634074,56.122574,5694,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.07,0.07,,,Other,- NHP,571.737,Klebsiella oxytoca strain 4928STDY7387739,4928STDY7387739,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694376,571,,,,MLST.Klebsiella_oxytoca.40,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166795.1,LR607380,,SC,,,,1,,1,6281729,56.233994,5691,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,98.73,0.22,,,Other,- HP,571.978,Klebsiella oxytoca strain IR5392,IR5392,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561276,571,,,,MLST.Klebsiella_oxytoca.34,,,,2021-03-09T00:00:00Z,,PRJNA672237,GCA_017310465.1,"CP064108,CP064109,CP064110,CP064111,CP064112",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,6366360,54.55062,6337,5922,,,2015-08-20,China,China: Beijing,,,,,,,,,,,,,,,,,"aimed to investigate the molecular epidemiology, transmission and evolution of XA-48-producing Enterobacterales and pOXA-48",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,571.990,Klebsiella oxytoca strain KoPF10,KoPF10,Klebsiella oxytoca,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18675296,571,,,,MLST.Klebsiella_oxytoca.48,,,,2021-04-15T00:00:00Z,,PRJNA683049,GCA_017968865.1,CP072914,,University of Texas at Dallas,Illumina NextSeq; Oxford Nanopore MinION,323.5x,Unicycler v. 0.4.8,1,0,1,5822988,55.015312,5656,5346,urine,,2018-05,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six Klebsiella spp. isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.41,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.12457,Klebsiella pneumoniae strain BK13043,BK13043,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06701573,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2017-05-23T00:00:00Z,,PRJNA376414,GCA_002156725.1,"CP020837,CP020838,CP020839,CP020840",,Houston Methodist Hospital,PacBio,121x,HGAP v. v2,1,3,4,5896654,56.99,6053,5881,unknown,,2004,USA,"USA: New York, New York City",,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",,,,,,,,Unknown,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.12458,Klebsiella pneumoniae strain KPN1482,KPN1482,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06438459,573,,,,MLST.Klebsiella_pneumoniae.37,genotype:ST37\; Capsule locus KL105,,,2017-05-23T00:00:00Z,,PRJNA376414,GCA_002156745.1,"CP020841,CP020842,CP020843,CP020844,CP020846,CP020845",,Houston Methodist Hospital,PacBio,201x,HGAP v. v2,1,5,6,5965284,56.71,6244,6014,respiratory,,2014-06-11,USA,USA: Houston,,,,Klebsiella Infections,,host_description:HMH:KPN:1482,Resistant;Susceptible,Computational Prediction,,,,,,,,,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",collected_by:Houston Methodist Hospital,,,,,,,Klebsiella Infections,,,HMH:KPN:1482,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.12459,Klebsiella pneumoniae strain KPN1481,KPN1481,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06438458,573,,,,MLST.Klebsiella_pneumoniae.906,genotype:ST906\; Capsule locus KL10,,,2017-05-23T00:00:00Z,,PRJNA376414,GCA_002156765.1,"CP020847,CP020848,CP020851,CP020852,CP020850,CP020849",,Houston Methodist Hospital,PacBio,95x,HGAP v. v2,1,5,6,6106127,56.73,6291,6026,urine,,2014-06-10,USA,USA: Houston,,,,Klebsiella Infections,,host_description:HMH:KPN:1481,Susceptible;Resistant,Computational Prediction,,,,,,,,,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",collected_by:Houston Methodist Hospital,,,,,,,Klebsiella Infections,,,HMH:KPN:1481,,,,Originally submitted as Klebsiella pneumoniae but changed in October 2018 because of ANI results to Klebsiella variicola,,,,,,,98.3,2.4,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.12460,Klebsiella pneumoniae strain KPN528,KPN528,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06437491,573,,,,MLST.Klebsiella_pneumoniae.14,genotype:ST14\; Capsule locus KL2,,,2017-05-23T00:00:00Z,,PRJNA376414,GCA_002156785.1,"CP020853,CP020854,CP020855,CP020856",,Houston Methodist Hospital,PacBio,232x,HGAP v. v2,1,3,4,5973075,56.7,6186,5898,respiratory,,2012-12-02,USA,USA: Houston,,,,Klebsiella Infections,,host_description:HMH:KPN:528,Resistant;Susceptible,Computational Prediction,,,,,,,,,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",collected_by:Houston Methodist Hospital,,,,,,,Klebsiella Infections,,,HMH:KPN:528,,,,,,,,,,,100,2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.12792,Klebsiella pneumoniae strain 19051,19051,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07187263,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2017-06-27T00:00:00Z,,PRJNA388820,GCA_002209405.1,CP022023,,Beijing Institute of Microbiology and Epidemiology,PacBio,86.0x,SOAPdenovo v. 1.0,1,,1,5332976,57.41,5128,,urine,,,,,,,62,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae 19051 chromosome,biomaterial_provider:Beijing Institute of Microbiology and Epidemiology;sample_type:clinical,,,,,,,,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.15329,Klebsiella pneumoniae strain KSB1_5D,KSB1_5D,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06112197,573,,,,MLST.Klebsiella_pneumoniae.340,mlst:ST340,,,2017-11-02T00:00:00Z,29340588,PRJNA351909,GCA_002741685.1,"CP024191,CP024192,CP024193,CP024194,CP024195,CP024196,CP024197",,University of Melbourne,Illumina HiSeq,83x,Unicycler v. 0.4.0,1,6,7,5768890,57.06,5938,5800,rectal swab,,2013-08-27,Australia,Australia: Melbourne,,,,carriage,Rectal swab,,Resistant;Susceptible,AMR Panel,,,,,,,,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,collected_by:University of Melbourne,,,,,,,carriage,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.15379,Klebsiella pneumoniae strain P1428,P1428,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05231874,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2017-11-07T00:00:00Z,,PRJNA325419,GCA_002761315.1,CP017994,,Peking University People's Hospital,PacBio,100.0x,HGAP v. 2.0,1,,1,5633290,57.13,5582,5356,sputum,,2007-09-08,China,China: Beijing,,male,62,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of the chromosome of a clinical Klebsiella pneumoniae isolate 1428,collected_by:Fujian Provincial Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,1.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.16440,Klebsiella pneumoniae strain 459,459,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05231873,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2017-12-07T00:00:00Z,,PRJNA325418,GCA_002814015.1,CP018306,,Peking University People's Hospital,not specified,not specified,not specified v. not specified,1,,1,5320942,57.4,5401,5416,sputum,,2008-10-08,China,China,,female,49,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of the chromosome of a clinical Klebsiella pneumoniae isolate 459,collected_by:Fujian Provincial Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.16472,Klebsiella pneumoniae strain KP8,KP8,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08117208,573,,,,MLST.Klebsiella_pneumoniae.485,,,,2017-12-20T00:00:00Z,,PRJNA420654,GCA_002845865.1,CP025089,,Department of Laboratory Medicine,Illumina MiSeq,99.0x,A5-miseq v. v20150522,1,,1,5478203,57.31,5329,,,,2009-04-18,China,China: Shanghai,,,,,,,Susceptible,Computational Prediction,,,,,,,,,High a virulence strains;missing tRNA genes,sample_type:The liver abscess puncture fluid,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.16473,Klebsiella pneumoniae strain KP11,KP11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4773868,573,,,,MLST.Klebsiella_pneumoniae.700,mlst:11,,,2017-12-20T00:00:00Z,33092694,PRJNA420766,GCA_002845885.1,CP025092,,Department of Laboratory Medicine,Illumina MiSeq,99.0x,A5-miseq v. v20150522,1,,1,4766628,57.55,4585,,blood,,2009-04-18,Brazil,China: Shanghai,,,,,Blood,,Susceptible,Computational Prediction,,,,,,,,,have a high virulence strains.;genome length too small;missing tRNA genes,sample_type:The liver abscess puncture fluid,,,,,,,,diseased,,,,,,,,,,,,,90.1,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.16474,Klebsiella pneumoniae strain KP9,KP9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08117209,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2017-12-20T00:00:00Z,,PRJNA420765,GCA_002845905.1,CP025090,,Department of Laboratory Medicine,Illumina MiSeq,99.0x,A5-miseq v. v20150522,1,,1,5339613,57.42,5160,,,,2009-04-18,China,China: Shanghai,,,,,,,Susceptible,Computational Prediction,,,,,,,,,have High virulence strains,sample_type:The liver abscess puncture fluid,,,,,,,,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.16475,Klebsiella pneumoniae strain KP10,KP10,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4773867,573,,,,MLST.Klebsiella_pneumoniae.29,mlst:11,,,2017-12-20T00:00:00Z,33092694,PRJNA420767,GCA_002845925.1,CP025091,,Department of Laboratory Medicine,Illumina MiSeq,99.0x,A5-miseq v. v20150522,1,,1,5061821,57.87,4845,,blood,,2009-04-18,Brazil,China: Shanghai,,,,,Blood,,Susceptible,Computational Prediction,,,,,,,,,their have a high virulence strains,sample_type:The liver abscess puncture fluid,,,,,,,,diseased,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.16477,Klebsiella pneumoniae strain KP7,KP7,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08117788,573,,,,MLST.Klebsiella_pneumoniae.1941,,,,2017-12-20T00:00:00Z,,PRJNA420616,GCA_002845965.1,CP025088,,Department of Laboratory Medicine,Illumina MiSeq,99.0x,A5-miseq v. v20150522,1,,1,5405065,57.38,5195,,,,2009-04-18,China,China: shanghai,,,,,,,Susceptible,Computational Prediction,,,,,,,,,High virulence strains,sample_type:The liver abscess puncture fluid,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.17803,Klebsiella pneumoniae strain Kp81,Kp81,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08298849,573,,,,MLST.Klebsiella_pneumoniae.340,,,,2018-01-17T00:00:00Z,,PRJNA428749,GCA_002887435.1,"CP025816,CP025817,CP025818",,Londrina State University,Illumina,240.0x,CLC v. CLC Genomic Workbench 8,1,2,3,5314129,57.432728,5466,5339,urine,isolated from human urine in 2014,2014-07-29,Brazil,Brazil:Minas Gerais,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Klebsiella pneumoniae Kp81 is a strain isolated from human urine in 2014. The antibiotic resistance is a main characteristic of this strain.;missing tRNA genes,collected_by:Federal University of Uberlandia,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.17909,Klebsiella pneumoniae strain FDAARGOS_156,FDAARGOS_156,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03996301,573,,,,MLST.Klebsiella_pneumoniae.13,,FDA:FDAARGOS_156,,2018-02-20T00:00:00Z,,PRJNA231221,GCA_002951635.1,"CP014123,CP014121,CP014124,CP014125,CP014122",,US Food and Drug Administration,PacBio; Illumina,19.325x,HGAP3 v. Oct 2014,1,4,5,5550639,57.100292,5602,5426,urine,,2014-05-11,USA,USA:DC,,male,9M,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,99.7,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.17910,Klebsiella pneumoniae strain HZW25,HZW25,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08135572,573,,,,MLST.Klebsiella_pneumoniae.34,,,,2018-03-02T00:00:00Z,,PRJNA421241,GCA_002966875.1,"CP025211,CP025212,CP025213,CP025214,CP025215",,The First Affiliated Hospital College of Medicine Zhejiang University,PacBio,221.0x,Canu v. V1.5,1,4,5,5604335,56.98831,5951,5650,blie,,2016-03-05,China,China: Hangzhou,,,36,Acute cholangitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae strain HZW25 isolated from blie of a patient with acute cholangitis;many frameshifted proteins,collected_by:Chen Qiong,,,,,,,Acute cholangitis,,,,,,,,,,,,,,100,2.8,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,573.17919,Klebsiella pneumoniae strain KPHS1249,KPHS1249,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08582315,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2018-03-06T00:00:00Z,,PRJNA435632,GCA_002970895.1,CP027189,,"Jinshan Hospital, Shanghai Medical College, Fudan University",PacBio; Illumina HiSeq,124.0x,smrtlink v. version 4.1,1,,1,5458646,57.44346,5416,5275,wound,,2008-06-11,China,China,,,,wood infection,,,Susceptible,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae subsp. pneumoniae strain KPHS1249, complete genome","collected_by:Gang Li, Tang Yu,Jiang Xiaofei",,,,,,,wood infection,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.17920,Klebsiella pneumoniae strain DA48896,DA48896,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05908511,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2018-03-16T00:00:00Z,29220374,PRJNA348457,GCA_003006175.1,"CP024429,CP024430,CP024431,CP024432,CP024433,CP024434,CP024435,CP024436",,Uppsala University,Illumina MiSeq; PacBio,50.0x,CLC Genomics Workbench v. 10,1,7,8,5752275,56.840538,5883,5707,trachaeal secretion,,2015-06,Pakistan,Pakistan,,,,Trachaeal secretion,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of a clinical Klebsiella pneumoniae encoding OXA181 beta lactamase.,collected_by:Fouzia Nahid,,,,,,,Trachaeal secretion,,,,,,,,,,,,,,98,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.17931,Klebsiella pneumoniae strain NH25,NH25,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08022168,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2018-04-03T00:00:00Z,,PRJNA418211,GCA_003031325.1,"CP024874,CP024875,CP024876,CP024877,CP024878,CP024879",,Chiang Mai University,PacBio,131.0x,CANU v. SEP-2017,1,5,6,5947820,56.754913,6155,5965,sputum,,2016-08,Thailand,Thailand,,,,Klebsiella pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Extensive drug resistant Klebsiella pneumoniae NH25, clinical isolate",collected_by:Nan Hospital,,,,,,,Klebsiella pneumoniae,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.17935,Klebsiella pneumoniae strain Kp589,Kp589,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08904739,573,,,,MLST.Klebsiella_pneumoniae.405,,,,2018-04-18T00:00:00Z,,PRJNA449447,GCA_003056445.1,"CP028816,CP028817,CP028819,CP028820,CP028821,CP028822,CP028823,CP028824,CP028825,CP028818",,Hospital Universitari Vall d'Hebron,Illumina MiSeq; MinION,1.0x,Unicycler assembly pipeline v. 0.4.4,1,9,10,5778569,56.990215,5851,5681,amniotic fluid,,2012-01-16,Spain,Spain: Barcelona,,,,Chorioamnionitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,K. pneumoniae KP589 whole Genome Sequencing,collected_by:Hospital Vall d'Hebron,,,,,,,Chorioamnionitis,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18085,Klebsiella pneumoniae strain 616,616,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08391417,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2018-05-01T00:00:00Z,,PRJNA431464,GCA_003076555.1,"CP026495,CP026496,CP026497",,University of Melbourne,Oxford Nanopore minION; Illumina MiniSeq,119.0x,Unicycler v. v0.4.4,1,2,3,5359558,57.406395,5333,5232,urine,,2009,Iran,Iran,,,,urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Whole genome sequencing for Klebsiella pneumoniae 616, a novel reference genome for Klebsiella pneumoniae sequence type 307.",collected_by:Mohammad Ali Boroumand,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.18238,Klebsiella pneumoniae strain NH54,NH54,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08026708,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2018-04-03T00:00:00Z,,PRJNA418370,GCA_003031345.1,"CP024916,CP024917,CP024918,CP024919",,Chiang Mai University,CANU,129.0x,CANU v. JUL-2017,1,3,4,5640638,57.102512,5800,5641,rectal swab,,2016-09,Thailand,Thailand,,,,Klebsiella pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing MDR Klebsiella pneumoniae NH54 clinical isolate,collected_by:rectal swab,,,,,,,Klebsiella pneumoniae,,,,,,,,,,,,,,100,1,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.18239,Klebsiella pneumoniae strain CFSAN054111,CFSAN054111,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08663449,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2018-04-02T00:00:00Z,,PRJNA243331,GCA_003030145.1,"CP028176,CP028177,CP028178,CP028179",,FDA/CFSAN,PacBio,430.0x,HGAP v. 3.0,1,3,4,5535332,57.209866,5608,5465,human,,2012-05-10,Germany,Germany,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,collected_by:DTU National Food Institute,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18240,Klebsiella pneumoniae strain CFSAN054110,CFSAN054110,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08663443,573,,,,MLST.Klebsiella_pneumoniae.512,,,,2018-04-02T00:00:00Z,,PRJNA243331,GCA_003030045.1,"CP028180,CP028181,CP028182",,FDA/CFSAN,PacBio,395.0x,HGAP v. 3.0,1,2,3,5709497,57.110565,5885,5751,human,,2013-04-16,Denmark,Denmark,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,collected_by:DTU National Food Institute,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18464,Klebsiella pneumoniae strain DA33140,DA33140,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245749,573,ST147,,,MLST.Klebsiella_pneumoniae.147,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181055.1,"CP029582,CP029583,CP029584,CP029585,CP029586",,Uppsala University,PacBio; Illumina MiSeq,20.0x,CLC Genomics workbench v. 11.0.1,1,4,5,5657209,57.031162,5714,5556,,,,Sweden,Sweden,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18465,Klebsiella pneumoniae strain DA33141,DA33141,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245752,573,ST16,,,MLST.Klebsiella_pneumoniae.16,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181095.1,"CP029587,CP029588,CP029589",,Uppsala University,PacBio; Illumina HiSeq 2000,90.0x,CLC Genomics workbench v. 11.0.1,1,2,3,5477813,57.3628,5599,5461,,,,Sweden,Sweden,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18466,Klebsiella pneumoniae strain DA33144,DA33144,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09245753,573,ST16,,,MLST.Klebsiella_pneumoniae.16,,,,2018-05-31T00:00:00Z,,PRJNA472712,GCA_003181135.1,"CP029590,CP029591,CP029592",,Uppsala University,PacBio; Illumina MiSeq,30.0x,CLC Genomics workbench v. 11.0.1,1,2,3,5482460,57.364998,5596,5467,,,,Sweden,Sweden,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Prevalence and mechanisms of antibiotic heteroresistance in clinical isolates,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.18472,Klebsiella pneumoniae strain 203,203,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05774083,573,,,,MLST.Klebsiella_pneumoniae.983,,,,2018-06-05T00:00:00Z,,PRJNA278886,GCA_003186535.1,"CP021165,CP021166",,Brigham & Women's Hospital,PacBio,320.0x,HGAP v. v.3.0,1,1,2,5380271,57.36423,5384,5273,urine,,2016,USA,USA:Boston,,female,40,,,host_subject_id:Kpneumoniae-23,Susceptible;Resistant,AMR Panel,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,missing,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.18476,Klebsiella pneumoniae strain CCUG 70742,CCUG 70742,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07602587,573,,,,MLST.Klebsiella_pneumoniae.147,,CCUG:70742,,2018-06-06T00:00:00Z,,PRJNA401330,GCA_003194285.1,"CP023249,CP023250,CP023251,CP023252,CP023253",,Chalmers University of Technology,Illumina MiSeq; PacBio,71.0x,SPAdes v. v3.7.0,1,4,5,5391141,57.40553,5405,5286,urine,,2012-01-20,Sweden,Sweden: Gothenburg,,,,acute cystitis,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,,,,,,,,,"In this study, we aimed to characterize the resistome of highly multi-resistant pathogens, all phenotypically resistant to at least one carbapenem antibiotic.","collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,acute cystitis,,,,,,,,,,,,,,100,0.3,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.18477,Klebsiella pneumoniae strain CCUG 70747,CCUG 70747,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07602916,573,,,,MLST.Klebsiella_pneumoniae.17,,CCUG:70747,,2018-06-06T00:00:00Z,,PRJNA401330,GCA_003194325.1,"CP023441,CP023442,CP023443,CP023444",,Chalmers University of Technology,Illumina MiSeq; PacBio,66.0x,SPAdes v. v3.7.0,1,3,4,5561916,57.269325,5657,5525,wound,,2013-08-14,Sweden,Sweden: Gothenburg,,,,,,,Resistant;Susceptible;Not defined,AMR Panel,,,,,,,,,"In this study, we aimed to characterize the resistome of highly multi-resistant pathogens, all phenotypically resistant to at least one carbapenem antibiotic.","collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,N/A,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.18541,Klebsiella pneumoniae strain TVGHCRE225,TVGHCRE225,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07672549,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2018-06-08T00:00:00Z,29800340,PRJNA408002,GCA_003203435.1,"CP023722,CP023723,CP023724,CP023725",,Taipei Veterans General Hospital and National Yang-Ming University,PacBio,132.92x,SMRT portal v. 2.3.0,1,3,4,6107937,56.48986,6162,,intraabdominal abscess,,2014-08-13,Taiwan,Taiwan: Taipei,,,,sepsis,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"A hyper-virulent multi-drug resistant KP isolate of strain ST11 discovered at VGHTPE, Taiwan",collected_by:Taipei Veterans General Hospital,,,,,,,sepsis,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Sepsis,Skin and Soft Tissue,Bloodstream Infections-Sepsis HP,573.18713,Klebsiella pneumoniae strain CNR48,CNR48,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104569902,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2018-06-30T00:00:00Z,,PRJEB24842,GCA_900323945.1,LS399318,,UCA,,,,1,,1,5138672,57.701153,4985,4850,urine,isolated in France and Overseas between 2012 and 2013,2012,France,France,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,DHA-1-producing Klebsiella spp strains have been isolated in France and Overseas between 2012 and 2013. They have been sequenced by Illumina technology.,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.19949,Klebsiella pneumoniae strain F1,F1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08378650,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2018-08-08T00:00:00Z,,PRJNA430804,GCA_003367555.1,"CP026130,CP026131",,Peking University People's Hospital,PacBio,144.06x,SOAPdenovo v. 2.3.0,1,1,2,5682889,57.391724,5853,5734,urine,,2014-05-20,China,China: Fujian Province,,male,61,pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F1.,collected_by:Fujian Provincial Hospital,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.19950,Klebsiella pneumoniae strain KP30835,KP30835,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04457966,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2018-08-09T00:00:00Z,,PRJNA311034,GCA_003368025.1,"CP027697,CP027696,CP027695,CP027698,CP027699,CP027700",,USAMRIID,PacBio,363.0x,HGAP v. 2.3,1,5,6,5941188,56.877495,6639,6039,,,2015-12-01,,,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Whole genome long-read sequencing of isolates of Klebsiella and Acinetobacter;many frameshifted proteins,collected_by:USAMRIID,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,4.8,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.20005,Klebsiella pneumoniae strain 160111,160111,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09279554,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2018-08-28T00:00:00Z,,PRJNA473597,GCA_003429545.1,"CP029689,CP030130,CP030131,CP030132,CP030133,CP030134,CP030135",,Chung Shan Medical University,Illumina MiSeq; PacBio,100.0x,CLC NGS Cell v. 10.1.1,1,6,7,5805104,57.124542,6067,5907,urine,isolated carbapenem-resistant K. pneumoniae strains from a hospital-wide surveillance,2014-12-02,Taiwan,Taiwan,,,,Urinary tract infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"We isolated carbapenem-resistant K. pneumoniae strains from a hospital-wide surveillance. This strain KPC160111 was found to co-produce OXA-48- and KPC-2-type carbapenemase. Considering the potential threat of this multi-drug resistant strains to our public heath, we performed WGS analysis of this strain. The genome sequence data will provide in-depth understanding of how multi-drug resistant K. pneumoniae has evolved.",collected_by:Chung Shan Medical University Hospital,,,,,,,Urinary tract infections,,,,,,,,,,,,,,100,1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.20030,Klebsiella pneumoniae strain 1050,1050,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07638733,573,,,,MLST.Klebsiella_pneumoniae.54,,,,2018-09-04T00:00:00Z,30144503,PRJNA407116,GCA_003443755.1,"CP023416,CP023417,CP023418,CP023419,CP023420,CP023421",,Hospital Universitario La Paz,Illumina HiSeq; Oxford Nanopore,100.0x,Unicycler v. SEP-2017,1,5,6,5977633,56.845913,6210,5985,hospital,,2016-06,Spain,Spain: Madrid,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole-genome sequence of a clinical isolate of Klebsiella pneumoniae resistant to all antibiotics currently in use,sample_type:Bilis,,,,,,,,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.22547,Klebsiella pneumoniae strain ST307PT04,ST307PT04,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07421006,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2018-09-26T00:00:00Z,,PRJNA396106,GCA_003597695.1,"CP022916,CP022917,CP022918",,Yonsei University College of Medicine,PacBio,339.55x,SMRT Analysis (RS_HGAP_Assembly.2) v.,1,2,3,5584541,57.240334,5617,5473,rectal swab,,20-02,South Korea,South Korea: Seoul,,male,80,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC-pruducing Klebsiella pneumoniae,collected_by:Yonsei University College of Medicine,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,0.33,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.22548,Klebsiella pneumoniae strain ST307PT02,ST307PT02,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07421004,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2018-09-26T00:00:00Z,,PRJNA396106,GCA_003597715.1,"CP022922,CP022923",,Yonsei University College of Medicine,PacBio,368.02x,SMRT Analysis (RS_HGAP_Assembly.2) v.,1,1,2,5570673,57.242706,5590,5455,sputum,,2014-11-27,South Korea,South Korea: Seoul,,male,72,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC-pruducing Klebsiella pneumoniae,collected_by:Yonsei University College of Medicine,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,0.33,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.22549,Klebsiella pneumoniae strain ST307PT03,ST307PT03,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07421005,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2018-09-26T00:00:00Z,,PRJNA396106,GCA_003597735.1,"CP022919,CP022920,CP022921",,Yonsei University College of Medicine,PacBio,267.17x,SMRT Analysis (RS_HGAP_Assembly.2) v.,1,2,3,5584763,57.24026,5611,5473,sputum,,2015-01-31,South Korea,South Korea: Seoul,,male,80,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC-pruducing Klebsiella pneumoniae,collected_by:Yonsei University College of Medicine,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,0.33,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.22550,Klebsiella pneumoniae strain ST307PT01,ST307PT01,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07421000,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2018-09-26T00:00:00Z,,PRJNA396106,GCA_003597755.1,"CP022924,CP022926,CP022925",,Yonsei University College of Medicine,PacBio,441.47x,SMRT Analysis (RS_HGAP_Assembly.2) v.,1,2,3,5613520,57.204445,5696,5510,sputum,,2014-10-25,South Korea,South Korea: Seoul,,male,74,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC-pruducing Klebsiella pneumoniae,collected_by:Yonsei University College of Medicine,,,,,,,Pneumonia,,,,,,,,,,,,,,99.7,0.33,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.23138,Klebsiella pneumoniae strain KP_NORM_BLD_2014_104014,KP_NORM_BLD_2014_104014,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5063299,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2018-12-02T00:00:00Z,,PRJNA505543,GCA_003855315.1,"CP034045,CP034046,CP034047,CP034048,CP034049,CP034050,CP034051,CP034052",,University of Melbourne,Illumina,250x,SPAdes v. 3.6.2,1,7,8,5920038,56.578167,5991,5796,blood,,2014,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,Two Norwegian Kp strains with virulence and AMR encoded on single plasmid vectors;KP_NORM_BLD_2014_104014,,,,,,,,,diseased,,,,,,,,,,,,,100,1.09,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.23139,Klebsiella pneumoniae strain KP_NORM_BLD_2015_112126,KP_NORM_BLD_2015_112126,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5063300,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2018-12-02T00:00:00Z,,PRJNA505543,GCA_003855335.1,"CP034053,CP034054,CP034055,CP034056,CP034057",,University of Melbourne,Illumina,51x,SPAdes v. 3.6.2,1,4,5,5841099,56.670277,5885,5686,blood,,2015,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,Two Norwegian Kp strains with virulence and AMR encoded on single plasmid vectors;KP_NORM_BLD_2015_112126,,,,,,,,,diseased,,,,,,,,,,,,,100,1.09,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.23140,Klebsiella pneumoniae strain KP17-15,KP17-15,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10439690,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2018-12-02T00:00:00Z,,PRJNA505940,GCA_003855535.1,CP034076,,Zhengzhou University,Illumina; MinION,12.0x,CLC Genomics Workbench v. 10.0,1,,1,5379069,57.320457,5296,5172,blood,"isolated from a local hospital in the Pingdingshan city, central region of Henan province, China in November 2017",2017-11-03,China,China: Henan,,,,pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae KP17-15 was isolated from a local hospital in the Pingdingshan city, central region of Henan province, China in November 2017. Strain KP17-15 was recovered from the blood culture of patient A, a 62-year-old man who was admitted to the respiratory intensive care unit (RICU) with a diagnosis of chronic obstructive pulmonary disease with pulmonary infection on November 3.",collected_by:a local hospital in the Pingdingshan city,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.5,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases HP,573.23143,Klebsiella pneumoniae strain BJCFK909,BJCFK909,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10473953,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2018-12-03T00:00:00Z,,PRJNA506788,GCA_003856475.1,"CP034123,CP034124,CP034125,CP034126,CP034127",,Zhejiang Hospital,Oxford Nanopore GridION; Illumina HiSeq,300.0x,minimap v. 2.0; miniasm v. 2.0,1,4,5,5871807,56.999233,6130,5934,respiratory tract,,2018-09,China,China: zhejiang,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To investigate the mechanism of resistance of clinical isolates of Klebsiella pneumoniae to carbapenems,collected_by:shilei dong,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.12,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.23144,Klebsiella pneumoniae strain 4/1-2,4/1-2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07760932,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2018-12-03T00:00:00Z,,PRJNA413669,GCA_003856595.1,"CP023839,CP023840,CP023841,CP023842,CP023843",,Uppsala University,Pacific bio + Miseq,13x,CLC Genomics workbench v. 10,1,4,5,5657200,57.031147,5704,5534,feces,,2009,Sweden,Sweden,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We have followed three patients over the course of one year after an initial urinary tract infection caused by ESBL-producing Enterobacteriaceae. The complete genomes including plasmids were sequenced for isolates 0, 1, 3, 6 and 12 months post UTI.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,100,1.14,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.23194,Klebsiella pneumoniae strain cr-hvkp3,cr-hvkp3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07811429,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2018-12-10T00:00:00Z,,PRJNA351750,GCA_003932915.1,"CP024707,CP024708,CP024709",,Peking University Third Hospital,PacBio,170.0x,SMRT Analysis v. v2.1 software package,1,2,3,5655284,56.84512,5684,5495,blood,isolated from carbepenem resistant hypervirulent Klebsiella pneumoniae,2014-08-01,China,China:beijing,,,,blood stream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The complete DNA sequence of the two plasmids (pPUTH1 and pPUTH2) isolated from carbepenem resistant hypervirulent Klebsiella pneumoniae.,collected_by:Peking University Third Hospital,,,,,,,blood stream infection,,,,,,,,,,,,,,100,2.04,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.23231,Klebsiella pneumoniae strain TOP52_1721_U1,TOP52_1721_U1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09928108,573,,,,MLST.Klebsiella_pneumoniae.152,,,,2018-12-20T00:00:00Z,,PRJNA488268,GCA_003957455.1,"CP031938,CP031939,CP031940",,Washington University School of Medicine,PacBio RS; Illumina HiSeq,100.0x,HGAP v. V5.0.1.9585,1,2,3,5467441,57.294937,5500,5384,urine,,,,,,,,urinary tract infection,,,Susceptible,Computational Prediction,,,,,,,,,Klebsiella pneumoniae sequence,collected_by:David Rosen,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0.25,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.23266,Klebsiella pneumoniae strain NB5306,NB5306,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10662038,573,,,,MLST.Klebsiella_pneumoniae.437,,,,2019-01-09T00:00:00Z,,PRJNA512142,GCA_004006035.1,"CP034760,CP034761,CP034762,CP034763,CP034764,CP034765",,Ningbo First Hospital,Oxford Nanopore MiniION,20.0x,ABySS v. Jun-2018,1,5,6,5360721,57.494205,5414,5291,blood,,2014-09-24,China,China: Ningbo,,,,bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae strain NB5306, nanopore",collected_by:Xing-bei Weng,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.02,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.23267,Klebsiella pneumoniae strain 08EU827,08EU827,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08222595,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2019-01-10T00:00:00Z,,PRJNA427077,GCA_004010995.1,"CP025576,CP025577,CP025578,CP025579,CP025580",,Uppsala University,Illumina MiSeq; PacBio,57.0x,CLC Genomics Workbench v. 11,1,4,5,5582414,57.146084,5622,5459,"outbreak at the neonatal ward at karolinska hospital, sweden","isolate from an outbreak at the neonatal ward at Karolinska hospital, Sweden",2008,Sweden,Sweden: Stockholm,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"One Escherichia coli and one Klebsiella pneumoniae isolate from an outbreak at the neonatal ward at Karolinska hospital, Sweden.",sample_type:Bacterial isolate,,,,,,,,,,,,,,,,,,,,,99.95,0.48,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.25593,Klebsiella pneumoniae strain F5,F5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08378686,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-01-30T00:00:00Z,,PRJNA430814,GCA_004119955.1,"CP026132,CP026133,CP026134,CP026135",,Peking University People's Hospital,PacBio,94.9x,SOAPdenovo v. 2.3.0,1,3,4,5916981,57.15298,6130,5982,sputum,,2014-05-22,China,China: Fujian Province,,female,80,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F5.,collected_by:Fujian Provincial Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.95,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.25594,Klebsiella pneumoniae strain F77,F77,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08378909,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-01-30T00:00:00Z,,PRJNA430818,GCA_004119975.1,"CP026136,CP026137,CP026138,CP026139",,Peking University People's Hospital,PacBio,136.57x,SOAPdenovo v. 2.3.0,1,3,4,5840818,57.207653,6042,5885,bile,,2014-09-18,China,China: Fujian Province,,male,77,abdominal infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F77.,collected_by:Fujian Provincial Hospital,,,,,,,abdominal infection,,,,,,,,,,,,,,100,0.95,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.25595,Klebsiella pneumoniae strain F127,F127,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08379292,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-01-30T00:00:00Z,,PRJNA430866,GCA_004119995.1,"CP026140,CP026141,CP026142",,Peking University People's Hospital,PacBio,208.21x,SOAPdenovo v. 2.3.0,1,2,3,5735314,57.339405,5934,5808,ascites,,2014-11-30,China,China: Fujian Province,,female,61,gaslrointestinal perforation,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F127.,collected_by:Fujian Provincial Hospital,,,,,,,gaslrointestinal perforation,,,,,,,,,,,,,,99.7,0.84,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,573.25596,Klebsiella pneumoniae strain F10(AN) strain F10(AN) strain F10(AN),F10(AN),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380931,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2019-01-30T00:00:00Z,,PRJNA430912,GCA_004120015.1,"CP026153,CP026154",,Peking University People's Hospital,PacBio,209.501907x,SOAPdenovo v. 2.3.0,1,1,2,5578129,57.277145,5709,5558,sputum,,2011-06-17,China,China: Fujian Province,,male,40,pulmonary infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F10(AN).,collected_by:Fujian Provincial Hospital,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.33,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.25597,Klebsiella pneumoniae strain F93-1,F93-1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380941,573,,,,MLST.Klebsiella_pneumoniae.343,,,,2019-01-30T00:00:00Z,,PRJNA430926,GCA_004120035.1,"CP026160,CP026161",,Peking University People's Hospital,PacBio,417.9066061x,SOAPdenovo v. 2.3.0,1,1,2,5356474,57.315224,5378,5252,sputum,,2014-10-14,China,China: Fujian Province,,male,40,pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F93-1.,collected_by:Fujian Provincial Hospital,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.06,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.25598,Klebsiella pneumoniae strain F13,F13,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380933,573,,,,MLST.Klebsiella_pneumoniae.661,,,,2019-01-30T00:00:00Z,,PRJNA430916,GCA_004120055.1,"CP026162,CP026163",,Peking University People's Hospital,PacBio,200.0x,SOAPdenovo v. 2.3.0,1,1,2,5492069,57.14901,5542,5392,urine,,2014-06-13,China,China: Fujian Province,,female,47,urinary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F13.,collected_by:Fujian Provincial Hospital,,,,,,,urinary infection,,,,,,,,,,,,,,100,1.31,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.25599,Klebsiella pneumoniae strain F132,F132,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380929,573,,,,,,,,2019-01-30T00:00:00Z,,PRJNA430910,GCA_004120075.1,"CP026145,CP026146,CP026147,CP026148",,Peking University People's Hospital,PacBio,151.77x,SOAPdenovo v. 2.3.0,1,3,4,5782958,57.243008,6072,5814,end of the catheter,,2014-12-07,China,China: Fujian Province,,male,84,sepsis shock,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F132.,collected_by:Fujian Provincial Hospital,,,,,,,sepsis shock,,,,,,,,,,,,,,99.17,0.95,Bloodstream Infections,Sepsis,Medical Device,Bloodstream Infections-Sepsis HP,573.25600,Klebsiella pneumoniae strain F138,F138,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380930,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-01-30T00:00:00Z,,PRJNA430911,GCA_004120095.1,"CP026149,CP026150,CP026151,CP026152",,Peking University People's Hospital,PacBio,123.86x,SOAPdenovo v. 2.3.0,1,3,4,5881983,57.15914,6110,5926,blood,,2014-12-02,China,China: Fujian Province,,male,64,pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F138.,collected_by:Fujian Provincial Hospital,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.95,Respiratory Diseases,Other Respiratory Diseases,Blood and Circulatory System,Respiratory Diseases-Other Respiratory Diseases HP,573.25601,Klebsiella pneumoniae strain B12(AN) strain B12(AN) strain B12(AN),B12(AN),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380949,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-01-30T00:00:00Z,,PRJNA430932,GCA_004120115.1,"CP026155,CP026156",,Peking University People's Hospital,PacBio,213.72875x,SOAPdenovo v. 2.3.0,1,1,2,5642913,57.198383,5770,5640,sputum,,2011-05-12,China,China: Inner Mongolia Autonomous Prefecture,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate B12(AN).,collected_by:The First Affiliated Hospital of Baotou Medical College,,,,,,,Not available,,,,,,,,,,,,,,100,0.32,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.25602,Klebsiella pneumoniae strain F89-1,F89-1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380938,573,,,,,,,,2019-01-30T00:00:00Z,,PRJNA430923,GCA_004120135.1,CP026159,,Peking University People's Hospital,PacBio,304.428323x,SOAPdenovo v. 2.3.0,1,,1,5272353,57.52297,5284,5169,sputum,,2014-10-11,China,China: Fujian Province,,female,,respiratory distress syndrome of newborn,,,Susceptible,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F89-1.,collected_by:Fujian Provincial Hospital,,,,,,,respiratory distress syndrome of newborn,,,,,,,,,,,,,,99.7,0.04,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.25603,Klebsiella pneumoniae strain F81,F81,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380935,573,,,,MLST.Klebsiella_pneumoniae.1764,,,,2019-01-30T00:00:00Z,,PRJNA430920,GCA_004120155.1,"CP026164,CP026165,CP026166",,Peking University People's Hospital,PacBio,200.0x,SOAPdenovo v. 2.3.0,1,2,3,5487061,57.19723,5537,5395,incision secretion,,2014-09-23,China,China: Fujian Province,,female,55,skin and soft tissue infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F81.,collected_by:Fujian Provincial Hospital,,,,,,,skin and soft tissue infection,,,,,,,,,,,,,,100,0.9,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,573.25604,Klebsiella pneumoniae strain F93-2,F93-2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08380932,573,,,,MLST.Klebsiella_pneumoniae.17,,,,2019-01-30T00:00:00Z,,PRJNA430915,GCA_004120175.1,"CP026157,CP026158",,Peking University People's Hospital,PacBio,238.8754981x,SOAPdenovo v. 2.3.0,1,1,2,5202611,57.560406,5195,5092,sputum,,2014-10-14,China,China: Fujian Province,,male,40,pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete nucleotide sequence of a clinical Klebsiella pneumoniae isolate F93-2.,collected_by:Fujian Provincial Hospital,,,,,,,pulmonary infection,,,,,,,,,,,,,,100,0.14,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.25630,Klebsiella pneumoniae strain NH34,NH34,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10531975,573,,,,MLST.Klebsiella_pneumoniae.14,,,,2019-02-04T00:00:00Z,,PRJNA508868,GCA_004135795.1,"CP034408,CP034406,CP034407",,Chiang Mai University,PacBio,112.0x,CANU v. SEP-2018,1,2,3,5831084,56.734375,6067,5718,sputum,,2014-09,Thailand,Thailand: Chiang Mai,,,,Gastroenteritis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,whole genome sequencing XDR Klebsiella pneumoniae NH34,collected_by:Nan hospital,,,,,,,Gastroenteritis,,,,,,,,,,,,,,99.5,0.61,Gastrointestinal Diseases,Diarrheal Diseases,Respiratory Tract,Gastrointestinal Diseases-Diarrheal Diseases HP,573.25657,Klebsiella pneumoniae strain BA4656,BA4656,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10908921,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2019-02-19T00:00:00Z,,PRJNA521675,GCA_004209795.1,"CP035905,CP035912,CP035911,CP035908,CP035907,CP035910,CP035906,CP035909",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,58.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,7,8,6138784,56.693947,6629,6129,blood,,2018,India,India,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Characterisation of hypervirulent multidrug resistant Klebsiella pneumoniae,"collected_by:Christian Medical College, Vellore, India",,,,,,,Bacteremia,,,,,,,,,,,,,,99.85,1.59,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25675,Klebsiella pneumoniae strain BA1559,BA1559,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10956433,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2019-02-25T00:00:00Z,,PRJNA522835,GCA_004295385.1,"CP036187,CP036189,CP036188",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,58.1x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,2,3,5663110,57.017754,5740,5550,blood,,2018,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,VBA1559 Klebsiella pneumoniae,"collected_by:Christian Medical College, Vellore, India",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.33,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25676,Klebsiella pneumoniae strain BA34918,BA34918,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10956502,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2019-02-25T00:00:00Z,,PRJNA522836,GCA_004295405.1,"CP036190,CP036198,CP036197,CP036196,CP036192,CP036194,CP036193,CP036195,CP036191",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,37.6x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,8,9,6181364,56.620625,6495,6170,blood,,2017,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,VBA34918 Klebsiella pneumoniae,"collected_by:Christian Medical College, Vellore, India",,,,,,,Bacteremia,,,,,,,,,,,,,,99.93,1.88,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25677,Klebsiella pneumoniae strain B31,B31,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10910564,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2019-02-25T00:00:00Z,,PRJNA521748,GCA_004295605.1,CP035929,,UFMG,Illumina HiSeq Paired-end,400x,SPAdes v. 3.9.1,1,,1,5273146,57.46855,5040,5041,bronchoalveolar lavage,,,,,,female,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The isolate was obtained from the bronchoalveolar lavage of afemale patient admitted to an intensive care unit in the northeast of Brazil.,,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.25786,Klebsiella pneumoniae strain BP327,BP327,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10963497,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2019-02-28T00:00:00Z,,PRJNA523082,GCA_004319525.1,"CP036335,CP036338,CP036337,CP036336",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,62.3x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,3,4,5881158,56.561344,6021,5790,blood,,2018,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae BP329 hybrid assembly,"collected_by:Christian Medical College, Vellore, India",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.48,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25801,Klebsiella pneumoniae strain 18CPO060,18CPO060,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10678732,573,,,,MLST.Klebsiella_pneumoniae.86,,,,2019-03-07T00:00:00Z,,PRJNA512469,GCA_004332075.1,"CP034778,CP034777,CP034776",,Public Health Agency of Canada,Illumina NextSeq,77.0x,Unicycler v. 0.4.7,1,2,3,5616401,57.10639,5681,5482,rectal swab,,2018-10-09,Canada,Canada: Montreal,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Investigating hypervirulent Klebsiella pneumoniae isolates in carbapenemase producing isolates in Canada,collected_by:PHAC,,,,,,,none,,,,,,,,,,,,,,100,0.73,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.25927,Klebsiella pneumoniae strain ST23,ST23,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11054834,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2019-04-30T00:00:00Z,,PRJNA288601,GCA_004924315.1,"CP037742,CP037744,CP037743",,Centers for Disease Control and Prevention. Division of Healthcare Quality Promotion,Illumina MiSeq; Oxford Nanopore MiniION,91.04x,Unicycler v. v0.4.4,1,2,3,5741563,57.144264,5762,5564,urine,,2016-06,USA,USA: MN,,,,urinary tract infection,,,Susceptible;Resistant;Intermediate;Not defined,Computational Prediction,,,,,,,,,"The Multi-Site Gram-Negative Bacilli Surveillance Initiative or MuGSI is a part of the CDC’s Emerging Infections Program (EIP) Healthcare-Associated Infections Community Interface (HAIC) activity. Through MuGSI, CDC is conducting active population- and laboratory-based surveillance in a defined surveillance catchment for six carbapenem-resistant organisms which include Escherichia coli, Enterobacter cloacae, Enterobacter aerogenes, Klebsiella pneumoniae, Klebsiella oxytoca, and Acinetobacter baumannii.",collected_by:MN Dept. of Health,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.55,0.42,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.25949,Klebsiella pneumoniae strain R1701,R1701,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11089893,573,,,,,,,,2019-05-08T00:00:00Z,,PRJNA485133,GCA_005239265.1,"CP039968,CP039969,CP039970,CP039971,CP039972,CP039973",,University of Pittsburgh,Oxford Nanopore PromethION,75x,Unicycler v. v0.4.6,1,5,6,5897286,56.932426,6052,5812,blood,,2016-10,USA,USA:Pittsburgh,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reduced Ceftazidime and Ertapenem Susceptibility Due to Production of OXA-2 in Klebsiella pneumoniae ST258,collected_by:University of Pittsburgh,,,,,,,Bacteremia,,,,,,,,,,,,,,99.26,0.04,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25950,Klebsiella pneumoniae strain R1761,R1761,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11089894,573,,,,,,,,2019-05-08T00:00:00Z,,PRJNA485133,GCA_005239285.1,"CP039974,CP039975,CP039976,CP039977,CP039978,CP039979,CP039980,CP039981,CP039982,CP039983,CP039984,CP039985",,University of Pittsburgh,Oxford Nanopore PromethION,123x,Unicycler v. v0.4.6,1,13,14,5899919,56.919308,6106,5893,bronchoalveolar lavage,,2016-12,USA,USA:Pittsburgh,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Reduced Ceftazidime and Ertapenem Susceptibility Due to Production of OXA-2 in Klebsiella pneumoniae ST258,collected_by:University of Pittsburgh,,,,,,,Pneumonia,,,,,,,,,,,,,,99.26,0.22,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.25951,Klebsiella pneumoniae strain CRKP I,CRKP I,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11047257,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-05-14T00:00:00Z,31005731,PRJNA525329,GCA_005347525.1,CP037927,,RAJIV GANDHI CENTRE FOR BIOTECHNOLOGY,Illumina MiSeq,140.0x,SPAdes v. 3.0.0.,1,,1,5318075,57.489414,5431,5219,blood,,2018-06-20,India,India,,female,,bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"colistin resistant Klebsiella pneumoniae isolated from the blood culture of a female patient with chronic kidney disease from Kerala, India",collected_by:Sabu Thomas,,,,,,,bacteremia,,,,,,,,,,,,,,99.33,0.02,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.25981,Klebsiella pneumoniae strain CR-HvKP1,CR-HvKP1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09487516,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-05-27T00:00:00Z,,PRJNA477921,GCA_005853785.1,"CP040533,CP040535,CP040534,CP040536,CP040537,CP040538",,The Hong Kong Polytechnic University,Illumina NextSeq 500,50x,v0.4.4 v. v0.4.4,1,5,6,5862723,56.921177,6091,5872,blood,,2016,China,China,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Complete genomes of 3 isolates of ST11 carbapenemase-producing hypervirulent K. pneumoniae were generated by the Oxford nanopore MinION platform, to obtain a better understanding of the genetic characteristic of this emerging ‘superbug’.",,,,,LB,,,,,,,,,,,,,blood,,,,99.4,0.02,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.25982,Klebsiella pneumoniae strain CR-HvKP5,CR-HvKP5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09487518,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-05-27T00:00:00Z,,PRJNA477921,GCA_005854025.1,"CP040545,CP040547,CP040546,CP040548,CP040549,CP040550",,The Hong Kong Polytechnic University,Illumina NextSeq 500,50x,v0.4.4 v. v0.4.4,1,5,6,5880866,56.93437,6103,5891,blood,,2016,China,China,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Complete genomes of 3 isolates of ST11 carbapenemase-producing hypervirulent K. pneumoniae were generated by the Oxford nanopore MinION platform, to obtain a better understanding of the genetic characteristic of this emerging ‘superbug’.",,,,,LB,,,,,,,,,,,,,blood,,,,99.11,0.12,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.25983,Klebsiella pneumoniae strain CR-HvKP4,CR-HvKP4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09487517,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-05-27T00:00:00Z,,PRJNA477921,GCA_005854245.1,"CP040539,CP040540,CP040542,CP040543,CP040544,CP040541",,The Hong Kong Polytechnic University,Illumina NextSeq 500,50x,v0.4.4 v. v0.4.4,1,5,6,5861748,56.92858,6101,5873,blood,,2016,China,China,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Complete genomes of 3 isolates of ST11 carbapenemase-producing hypervirulent K. pneumoniae were generated by the Oxford nanopore MinION platform, to obtain a better understanding of the genetic characteristic of this emerging ‘superbug’.",,,,,LB,,,,,,,,,,,,,blood,,,,99.7,0.12,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.25985,Klebsiella pneumoniae strain KpvST147B_SE1_1_NDM,KpvST147B_SE1_1_NDM,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11835544,573,,,,MLST.Klebsiella_pneumoniae.147,genotype:ST147,,,2019-06-04T00:00:00Z,,PRJNA483246,GCA_005944305.1,"CP040724,CP040725,CP040727,CP040729,CP040728,CP040726,CP040730,CP040731",,Public Health England,Oxford Nanopore MiniION; Illumina HiSeq,243.0x,miniasm v. 0.2-r168-dirty; racon,1,7,8,6109775,56.339176,6436,6013,rectal swab,,2019-01-14,United Kingdom,United Kingdom,,,88,screen,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae is known for its antibiotic resistance and for its virulence (referred to as hypervirulence), but until recently these two traits were not combined in the same organism. This project looks at 'high-risk clones' for antibiotic resistance that also carry a virulence plasmid, even having antibiotic resistance genes in that virulence plasmid. This is of serious public health concern.",collected_by:Hospital in South East England,,,,,,,screen,,,,,,,,,,,,,,99.95,2.28,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.26069,Klebsiella pneumoniae strain AJ218,AJ218,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128437,573,,,,,,102.100.100.25726,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622605.1,"LR130541,LR130542",,Bioplatforms Australia,,,,1,1,2,5668371,57.144497,5510,,urine,,2002-06-26,Australia,Australia,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,1.08,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.26070,Klebsiella pneumoniae strain KPC2,KPC2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5128438,573,,,,MLST.Klebsiella_pneumoniae.258,,102.100.100.25728,,2019-01-10T00:00:00Z,,PRJEB29928,GCA_900622645.1,"LR130548,LR130549,LR130550,LR130551",,Bioplatforms Australia,,,,1,3,4,5664402,57.145504,5605,,,,,,,,,,,,host_health_state:diseased,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies.The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. The following project contains the complete genomes and sequence data for Klebsiella pneumoniae & Klebsiella variicola",,,,,,,,,diseased,,,,,,,,,,,,,100,0.02,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.27188,Klebsiella pneumoniae strain BWHC1,BWHC1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03657213,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2018-04-03T00:00:00Z,,PRJNA278886,GCA_003031505.1,"CP020498,CP020499,CP020500",,Brigham & Women's Hospital,PacBio,498.14x,HGAP v. 3,1,2,3,5535407,57.32778,5613,5491,urine,,2012-05-12,USA,USA: Boston,,,,AML (BMT),,,Resistant;Susceptible,Computational Prediction,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:BWH,,,,,,,missing,,,,,,,,,,,,,,100,0.02,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.27316,Klebsiella pneumoniae strain DA12090,DA12090,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09271081,573,,,,MLST.Klebsiella_pneumoniae.14,,,,2019-08-05T00:00:00Z,,PRJNA473316,GCA_007833575.1,"CP030072,CP030071",,Uppsala University,PacBio; Illumina MiSeq,40.0x,CLC Genomics workbench v. 11,1,1,2,5497463,57.262867,5519,5399,urine,,,USA,USA: Walter Reed Army Medical Center,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae CAS55 whole genome sequence from PacBio + MiSeq data.,,,,,,,,UTI,,,,,,,,,,,,,,100,0.04,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.27317,Klebsiella pneumoniae strain PIMB15ND2KP27,PIMB15ND2KP27,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09104544,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2019-08-07T00:00:00Z,,PRJNA470778,GCA_007873865.1,"CP041639,CP041641,CP041640,CP041642",,Pasteur Institute in Ho Chi Minh City,Illumina MiSeq; Oxford Nanopore MiniION,110.0x,Canu v. 1.6; SPAdes v. 3.11.1,1,3,4,5736143,57.149864,5898,5715,,"isolated in Vietnam in 2015 which showed strong resistance to most antibiotics, including both carbapenem and colistin, was sequenced by Minion Nanopore and Illumina Miseq system",2015-03-18,Viet Nam,Viet Nam: Ho Chi Minh,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"In this study, whole genome of a clinical Klebsiella pneumoniae isolated in Vietnam in 2015 which showed strong resistance to most antibiotics, including both carbapenem and colistin, was sequenced by Minion Nanopore and Illumina Miseq system. The genome sequence was further analyzed by bioinformatic software for genetic characteristics that are responsible for antibiotic resistance of this strain.",sample_type:sputum,,,,,,,,,,,,,,,,,,,,,100,0.56,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.27361,Klebsiella pneumoniae strain 18-2374,18-2374,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12264830,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2019-08-22T00:00:00Z,,PRJNA554399,GCA_008065415.1,"CP041927,CP041928,CP041929,CP041930,CP041931",,Seoul Metropolitan Government Research Institute of Public Health and Environment,PacBio RSII,147x,HGAP v. 3.0,1,4,5,5704733,57.059566,5834,5630,missing,,2018-12-12,South Korea,South Korea: Seoul,,,,Klebsiella infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The purpose of this project is to characterize carbapenem-resistant Enterobacteriaceae in South Korea.,collected_by:Seoul Metropolitan Government Research Institute of Public Health and Environment,,,,,,,Klebsiella infections,,,,,,,,,,,,,,100,0.61,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.27403,Klebsiella pneumoniae strain KLP268,KLP268,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12588286,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2019-08-28T00:00:00Z,,PRJNA529592,GCA_008121515.1,"CP043047,CP043050,CP043048,CP043049",,University of Pittsburgh,PacBio RS,190.0x,HGAP v. 2.3,1,3,4,5908298,56.93132,6048,5822,not collected,,2016,USA,"USA: Pittsburgh, Pennsylvania",,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,WGS surveillance of K. pneumoniae ST258 was performed for hospital infection prevention.,collected_by:University of Pittsburgh Medical Center,,,,,,,not collected,,,,,,,,,,,,,,100,0.02,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.27404,Klebsiella pneumoniae strain KP1677,KP1677,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11998170,573,,,,,,,,2019-08-28T00:00:00Z,,PRJNA548051,GCA_008122285.1,CP041022,,National Yang-Ming University,PacBio RSII,170.0x,HGAP v. AUG-2017,1,,1,5371084,57.510105,5377,5121,sputum,,2015-11-11,Taiwan,Taiwan,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Genomes of hypervirulent Klebsiella pneumoniae strains in Taiwan,sample_type:bacterial culture,,,,,,,,,,,,,,,,,,,,,99.61,0.66,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.27405,Klebsiella pneumoniae strain KP1692,KP1692,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11998171,573,,,,MLST.Klebsiella_pneumoniae.268,,,,2019-08-28T00:00:00Z,,PRJNA548051,GCA_008122305.1,"CP041023,CP041024",,National Yang-Ming University,PacBio RSII,170.0x,HGAP v. AUG-2017,1,1,2,5573436,57.23288,5706,5345,sputum,,2015-11-23,Taiwan,Taiwan,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Genomes of hypervirulent Klebsiella pneumoniae strains in Taiwan,sample_type:bacterial culture,,,,,,,,,,,,,,,,,,,,,99.52,1.29,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.27416,Klebsiella pneumoniae strain P094-1,P094-1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10986063,573,,,,,,,,2019-09-11T00:00:00Z,,PRJNA563201,GCA_008369685.1,CP043562,,P094-1,PacBio,107.68x,SOAPdenovo v. 2016.8,1,,1,5058062,57.65999,5001,,sputum,,2013,China,China: Chongqing,,,,disease o respiratory system,,,Susceptible,Computational Prediction,,,,,,,,,"procaryotic breed klebsiella pneumoniae P094-1, clinical isolated from a human'sputum",collected_by:sputum,,,,,,,disease o respiratory system,,,,,,,,,,,,,,99.08,0.85,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases NHP,573.27692,Klebsiella pneumoniae strain 4928STDY7071295,4928STDY7071295,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567405,573,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902164625.1,LR607330,,SC,,,,1,,1,5287159,58.104218,5031,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.99,0.29,,,Other,- NHP,573.27714,Klebsiella pneumoniae strain 4928STDY7071681,4928STDY7071681,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4608428,573,,,,MLST.Klebsiella_pneumoniae.1001,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166475.1,LR607343,,SC,,,,1,,1,5379736,57.898716,4865,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.69,0.22,,,Other,- NHP,573.27715,Klebsiella pneumoniae strain 4928STDY7071680,4928STDY7071680,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4608427,573,,,,MLST.Klebsiella_pneumoniae.1001,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166495.1,LR607348,,SC,,,,1,,1,5311295,57.87035,4875,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.4,0.19,,,Other,- NHP,573.27716,Klebsiella pneumoniae strain 4928STDY7071137,4928STDY7071137,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104567248,573,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166515.1,LR607352,,SC,,,,1,,1,4894925,58.373833,4486,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,97.85,0.04,,,Other,- NHP,573.27717,Klebsiella pneumoniae strain 4928STDY7387736,4928STDY7387736,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694373,573,,,,MLST.Klebsiella_pneumoniae.639,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166565.1,LR607362,,SC,,,,1,,1,5861889,57.360737,5553,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.7,0.43,,,Other,- NHP,573.27718,Klebsiella pneumoniae strain 4928STDY7387799,4928STDY7387799,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694438,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166635.1,LR607360,,SC,,,,1,,1,5782096,57.347355,5516,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.94,0.41,,,Other,- NHP,573.27719,Klebsiella pneumoniae strain 4928STDY7387808,4928STDY7387808,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694444,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166705.1,LR607368,,SC,,,,1,,1,5830367,57.346233,5508,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,100,0.41,,,Other,- NHP,573.27720,Klebsiella pneumoniae strain 4928STDY7387758,4928STDY7387758,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694395,573,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166725.1,LR607358,,SC,,,,1,,1,5989149,57.792355,5362,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,99.4,0.07,,,Other,- NHP,573.27721,Klebsiella pneumoniae strain 4928STDY7387729,4928STDY7387729,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104694366,573,,,,MLST.Klebsiella_pneumoniae.105,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166745.1,LR607373,,SC,,,,1,,1,5568802,57.456837,5218,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,Susceptible,Computational Prediction,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",,,,,,,,,,,,,,,,,,,carriage,,,100,0.27,,,Other,- HP,573.27957,Klebsiella pneumoniae strain KP65,KP65,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12813532,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-09-30T00:00:00Z,,PRJNA573505,GCA_008728415.1,"CP044258,CP044260,CP044259",,Zhejiang Provincial People's Hospital,Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. v. 0.4.7,1,2,3,5592496,57.30368,5714,5547,urine,,2018-05-18,China,China:Hangzhou,,,,urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae KP65,collected_by:Fang He,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.4,0.27,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.27958,Klebsiella pneumoniae strain KP58,KP58,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12228410,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2019-09-30T00:00:00Z,,PRJNA553055,GCA_008728695.1,"CP041373,CP041374,CP041375,CP041376,CP041377,CP041378",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. 0.4.7,1,5,6,5920915,56.94623,6153,5913,urine,,2018-05-04,China,China: Hangzhou,,,,Pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing and comparative genomic analysis of Klebsiella pneumoniae isolates,collected_by:Fang He,,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,0.12,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.28016,Klebsiella pneumoniae strain C51,C51,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289282,573,,,,MLST.Klebsiella_pneumoniae.12,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931345.1,"CP042481,CP042482,CP042483,CP042484,CP042485,CP042486,CP042487",,University of Oxford,Oxford Nanopore MiniION,2228x,Unicycler v. SEP-2017,1,6,7,5686533,57.192562,5751,5532,clinical sample,,2014-05-30,Australia,Australia: Sydney,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,0.37,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.28017,Klebsiella pneumoniae strain C2,C2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12289275,573,,,,MLST.Klebsiella_pneumoniae.1109,,,,2019-10-09T00:00:00Z,,PRJNA550014,GCA_008931565.1,"CP042520,CP042521,CP042522,CP042523",,University of Oxford,Oxford Nanopore MiniION,4072x,Unicycler v. SEP-2017,1,3,4,5503501,57.28588,5539,5359,clinical sample,,2007-01-17,Australia,Australia: Sydney,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Genome sequencing (Illumina, MinION) was used to investigate a 10-year (2006-2015) outbreak of blaIMP-4-containing organisms in a burns unit (BU) in a hospital in Sydney, Australia. 154 carbapenem non-susceptible, ESBL-producing or multi-drug resistant (MDR) isolates (58 clinical, 96 environmental) were analysed, of which 113 contained blaIMP-4. This study illustrates the persistence, diversity and evolution of genetic backgrounds disseminating blaIMP-4 amongst both human and environmental reservoirs during a prolonged outbreak.",sample_type:Whole organism;collected_by:Concord Repatriation Hospital Sydney Australia,,,,,,,,,,,,,,,,,,,,,100,0.37,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.28586,Klebsiella pneumoniae strain SMU18037509,SMU18037509,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13135504,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2019-11-05T00:00:00Z,,PRJNA579868,GCA_009556655.1,"CP045661,CP045662,CP045663",,Saitama medical university,Illumina MiSeq; Oxford Nanopore,65.0x,SPAdes v. 2019-10-20,1,2,3,5514092,57.250477,5466,5284,blood from patient with community-acquired emphysematous osteomyelitis,,2018-03,Japan,Japan,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of Klebsiella pneumoniae isolated from patient with community-acquired emphysematous osteomyelitis,sample_type:Culture,,,,,,,,,,,,,,,,,,,,,99.7,0.65,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.28604,Klebsiella pneumoniae strain TK421,TK421,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13161584,573,,,,,,,,2019-11-06T00:00:00Z,,PRJNA449090,GCA_009601745.1,"CP045694,CP045691,CP045692,CP045693",,Northwestern University Feinberg School of Medicine,PacBio RSII; Illumina MiSeq,535.0x,Unicycler v. 0.4.8,1,3,4,5565050,57.086853,5538,5224,blood,,2013,USA,USA:Chicago,,,,bacteremia,,,Susceptible,Computational Prediction,,,,,,,,,Sequencing and assembly of clinical isolates of Klebsiella pneumoniae,,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.77,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.29092,Klebsiella pneumoniae strain KP2,KP2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12307651,573,,,,MLST.Klebsiella_pneumoniae.16,genotype:ST16,,,2019-11-29T00:00:00Z,,PRJNA555326,GCA_009720445.1,"CP041946,CP041947,CP041948,CP041949,CP041950,CP041951,CP041952,CP041953,CP041954",,The University of Texas Health Science Center at Houston,Oxford Nanopore GridION,448x,Celera Assembler v. 1.8,1,8,9,5738478,56.935028,5911,5704,urine,,2017-09-29,USA,USA:Houston,,,,sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Submission of consensus genome assemblies from a critically ill patient with polymicrobial infections due to multi-drug resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa who had traveled to India and was also colonized by Candida auris. A precision medicine approach using whole genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181. This case illustrates the rapidly evolving landscape of resistance and its challenges to clinicians.",collected_by:William R. Miller,,,,,,,sepsis,,,,,,,,,,,,,,100,0.14,Bloodstream Infections,Sepsis,Urinary Tract,Bloodstream Infections-Sepsis HP,573.29093,Klebsiella pneumoniae strain JUNP 254 strain JUNP254,JUNP254,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00186795,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2019-11-19T00:00:00Z,,PRJDB8799,GCA_009731405.1,AP021880,,"Department of Microbiology, Juntendo University School of Medicine",Illuminia MiSeq; Oxford nanopore MinION,50x,Unicycler v. 0.4.8,1,0,1,5422388,57.28362,5312,5106,human sputum,,2018,Nepal,Nepal:Kathmandu,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae clinical isolates co-harboring blaNDM-5 and blaOXA-181/-232 were detected in medical settings in Nepal.,,missing,missing,missing,missing,Carbapenem-resistant Klebsiella pneumoniae in Nepal,,,,,,,,,,,,missing,,,,100,0.74,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.29484,Klebsiella pneumoniae strain XJ-K2,XJ-K2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09988182,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-08T00:00:00Z,,PRJNA489756,GCA_009834285.1,"CP032240,CP032241,CP032242,CP032243",,Chengdu Medical College,Illumina; PacBio,192.0x,FALCON v. v0.3.0.,1,3,4,5903938,56.937523,6168,5992,blood,,2018-05-12,China,China:Shanghai,,,,blood stream infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To find the relevant resistance genes and study the resistant mechanism among Klebsiella pneumoniae,collected_by:The Northern Division of Huashan Hospital Affiliated to Hudan University,,,,,,,blood stream infections,,,,,,,,,,,,,,100,0.12,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.29491,Klebsiella pneumoniae strain Kp36,Kp36,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13671318,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-11T00:00:00Z,,PRJNA597257,GCA_009856585.1,"CP047192,CP047193,CP047194,CP047195,CP047196",,Fudan University,PacBio,12x,CLC NGS Cell v. 2.3,1,4,5,5978162,56.91808,6112,5792,,,2019-01-10,China,China: Shanghai,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Phage-host interactions,collected_by:Demeng Tan,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.7,0.12,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.29506,Klebsiella pneumoniae strain WSD411,WSD411,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12877715,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2020-01-15T00:00:00Z,,PRJNA575105,GCA_009884415.1,"CP045674,CP045682,CP045683,CP045684,CP045685,CP045686,CP045675,CP045676,CP045677,CP045678,CP045679,CP045680",,"Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University",Oxford Nanopore MinION,12.0x,CLC Genomic Workbench v. 9.0,1,12,13,5930400,56.729362,5825,,rectum,,2018-08-26,China,China,,,84,"fracture, pulmonary embolism (PE), atrial fibrillation (Af), Chronic renal failure (CRF) and acute respiratory failure (ARF)",,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"To characterize the clinical Klebsiella pneumoniae isolate harboring blaOXA-48-like on the different type plasmids in China. The Plasmid DNA was sequenced using Nanopore MinION and Illumina platform. The strain was resistant to ertapenem. The blaOXA-232 was located on the pOXA-232_WSD, which found in the different clonality of Klebsiella pneumoniae isolates of the same patient. This is the first report of the K. pneumoniae isolate positive for blaOXA-48 in China, and our results suggested that the horizontal transfer of blaOXA-232 in vivo via plasmids, which played an essential role in the transmission and prevalence of the blaOXA-48 gene.","collected_by:Sir Run Run Shaw Hospital, Zhejiang University School of Medicine (Hangzhou, China)",,,,,,,"fracture, pulmonary embolism (PE), atrial fibrillation (Af), Chronic renal failure (CRF) and acute respiratory failure (ARF)",,,,,,,,,,,,,,100,2.07,Respiratory Diseases,Other Respiratory Diseases,Gastrointestinal,Respiratory Diseases-Other Respiratory Diseases HP,573.29567,Klebsiella pneumoniae strain LSH-KPN148,LSH-KPN148,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11602135,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-22T00:00:00Z,,PRJNA541650,GCA_009914235.1,"CP040122,CP040123,CP040124,CP040125",,"Lishui Hospital, Zhejiang University School of Medicine",Illumina HiSeq; PacBio,40.0x,SPAdes v. v3.11.1; HGAP v. 2016,1,3,4,5754454,57.148464,5706,,sputum,,2015-09-01,China,China,,,,Severe pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,It is the genome sequence of a clinical Klebsiella pneumoniae strain.,collected_by:Hui Ding,,,,,,,Severe pneumonia,,,,,,,,,,,,,,99.95,0.12,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.29580,Klebsiella pneumoniae strain 721005,721005,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499703,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009930975.1,"CP030292,CP030293,CP030294,CP030295",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,151x,HGAP v. version 3,1,3,4,5967847,56.736694,6218,6065,physical,,2013,China,China: Ningbo,,male,60,Urinary system infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dongsheng Zhou,,,,,,,Urinary system infection,,,,,,,,,,,,,,99.7,0.22,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.29581,Klebsiella pneumoniae strain 309074,309074,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499702,573,,,,MLST.Klebsiella_pneumoniae.1,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009930995.1,"CP030296,CP030297,CP030298,CP030299",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,160x,HGAP v. version 3,1,3,4,5622482,57.176743,5715,5584,physical,,2013,China,China: Handan,,female,47,Respiratory System Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dongsheng Zhou,,,,,,,Respiratory System Infection,,,,,,,,,,,,,,100,0.32,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,573.29582,Klebsiella pneumoniae strain 283747,283747,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499701,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931015.1,"CP030300,CP030301",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,95x,HGAP v. version 3,1,1,2,5648422,57.29423,5814,5706,physical,,2015,China,China: Guangzhou,,male,77,Respiratory System Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dongsheng Zhou,,,,,,,Respiratory System Infection,,,,,,,,,,,,,,100,0.12,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,573.29583,Klebsiella pneumoniae strain 205880,205880,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499700,573,,,,MLST.Klebsiella_pneumoniae.290,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931035.1,"CP030302,CP030303,CP030304,CP030305,CP030306,CP030307,CP030308,CP030309,CP030310",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,60x,HGAP v. version 3,1,8,9,6097855,56.691772,6345,6158,physical,,2012,China,China: Chongqing,,,,Respiratory System Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dongsheng Zhou,,,,,,,Respiratory System Infection,,,,,,,,,,,,,,100,0.88,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,573.29584,Klebsiella pneumoniae strain 11311,11311,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499694,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931055.1,"CP030313,CP030314",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,124x,HGAP v. version 3,1,1,2,5473107,57.27725,5455,5327,physical,,2013,China,China: Beijing,,male,48,Mediastinal Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dingxia Shen,,,,,,,Mediastinal Abscess,,,,,,,,,,,,,,100,1.15,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.29585,Klebsiella pneumoniae strain 11454,11454,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499696,573,,,,MLST.Klebsiella_pneumoniae.86,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931075.1,"CP030311,CP030312",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,95x,HGAP v. version 3,1,1,2,5410532,57.329536,5405,5268,physical,,2014,China,China: Beijing,,female,66,Liver Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dingxia Shen,,,,,,,Liver Abscess,,,,,,,,,,,,,,100,0.65,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.29586,Klebsiella pneumoniae strain 11305,11305,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499693,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931095.1,"CP030315,CP030316",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,103x,HGAP v. version 3,1,1,2,5383617,57.40895,5418,5288,physical,,2013,China,China: Beijing,,female,31,Septic Shock,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dingxia Shen,,,,,,,Septic Shock,,,,,,,,,,,,,,100,0.52,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,573.29587,Klebsiella pneumoniae strain 11021,11021,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499692,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931155.1,"CP030317,CP030318,CP030319",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,55x,HGAP v. version 3,1,2,3,5856161,57.105072,6070,5945,physical,,2014,China,China: Chongqing,,,,Urinary System Infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dongsheng Zhou,,,,,,,Urinary System Infection,,,,,,,,,,,,,,100,0.24,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.29588,Klebsiella pneumoniae strain 23,23,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09499691,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2020-01-27T00:00:00Z,,PRJNA477755,GCA_009931175.1,"CP030320,CP030321,CP030322",,"Beijing Institute of Genomics,Chinese Academy of Sciences",PacBio,82x,HGAP v. version 3,1,2,3,5598689,57.103313,5626,5491,physical,,2011,China,China: Beijing,,female,81,Perisplenic Abscess,,,Susceptible,Computational Prediction,,,,,,,,,We selected 14 K.p strains to study the mechanisms of DNA methylation using pacbio SMRT sequencing technology.,collected_by:Dingxia Shen,,,,,,,Perisplenic Abscess,,,,,,,,,,,,,,100,1.4,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.30814,Klebsiella pneumoniae strain C2660,C2660,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11479264,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-02-05T00:00:00Z,31911273,PRJNA534178,GCA_010183645.1,"CP039808,CP039809,CP039810,CP039811,CP039812",,Peking University People's Hospital,PacBio RSII + Illumina NextSeq,240x (PacBio) + 200x (Illumina)x,Unicycler v. 0.4.6,1,4,5,5919068,57.014668,6141,5976,pus,,2017-08-01,China,China:Beijing,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,WGS (NGS and TGS) on eight Klebsiella pneumoniae strains which carry both blaKPC-2 and blaNDM-1,sample_type:culture,,,,,,,,,,,,,,,,,,,,,99.67,0.64,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.30828,Klebsiella pneumoniae strain KP18-3-8,KP18-3-8,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13978114,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-02-12T00:00:00Z,,PRJNA604666,GCA_010450855.1,CP048430,,zhengzhou university,Illumina; PacBio,12.0x,CLC Genomics workbench v. 10.0,1,0,1,5547989,57.287605,5544,5495,urine,,2018-07-14,China,China,,male,,Respiratory Diseases,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,the goal of project is to identify Klebsiella pneumoniae strain KP18-3-8,collected_by:Zhengzhou University,,,,,,,Respiratory Diseases,,,,,,,,,,,,,,100,0.12,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.30990,Klebsiella pneumoniae strain QD23,QD23,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12559024,573,,,,MLST.Klebsiella_pneumoniae.1,,,,2020-03-02T00:00:00Z,,PRJNA559783,GCA_011045595.1,CP042858,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,5803733,57.00319,5938,5742,urine,,2015,China,China: Shandong,,,,Fever,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete sequence of chromosome of strain QD23,,,,,,,,Fever,,,,,,,,,,,,,,100,0.37,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.31228,Klebsiella pneumoniae strain 16HN-263,16HN-263,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10353651,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-06T00:00:00Z,,PRJNA503173,GCA_011066505.1,"CP045263,CP045265,CP045266,CP045264",,The Hong Kong Polytechnic University,Illumina NextSeq; Oxford Nanopore MiniION,100.0x,Unicycler v. v0.4.7,1,3,4,5743792,57.124302,5906,5704,blood,,2016,China,China,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Carbapenem-resistant hypervirulent Klebsiella pneumonia,sample_type:genomic DNA,,,,,,,,,,,,,,,,,,,,,100,0.17,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.31239,Klebsiella pneumoniae strain KPC160121 strain Not collected,Not collected,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11246289,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-10T00:00:00Z,,PRJNA528846,GCA_011106605.1,"CP040028,CP040032,CP040029,CP040031,CP040030",,Chung Shan Medical University,Oxford Nanopore MiniION; Illumina MiSeq,10.0x,Unicycler v. May-2018,1,4,5,5778064,56.892933,5947,5746,pus,isolated from a single hospital and subjected for comparative genomic analysis,2015-01-30,Taiwan,Taiwan:Taichung,,,,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Outbreak strains of OXA-48 K. pneumoniae were isolated from a single hospital and subjected for comparative genomic analysis.,collected_by:CSMUH,,,,,,,pneumonia,,,,,,,,,,,,,,99.4,0.52,Respiratory Diseases,Pneumonia,Skin and Soft Tissue,Respiratory Diseases-Pneumonia HP,573.31240,Klebsiella pneumoniae strain KPC160117 strain Not collected,Not collected,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11246288,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-10T00:00:00Z,,PRJNA528846,GCA_011106775.1,"CP040033,CP040037,CP040034,CP040036,CP040035",,Chung Shan Medical University,Oxford Nanopore MiniION; Illumina MiSeq,10.0x,Unicycler v. May-2018,1,4,5,5777370,56.89355,5952,5747,urine,isolated from a single hospital and subjected for comparative genomic analysis,2014-12-19,Taiwan,Taiwan:Taichung,,,,urinary tract infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Outbreak strains of OXA-48 K. pneumoniae were isolated from a single hospital and subjected for comparative genomic analysis.,collected_by:CSMUH,,,,,,,urinary tract infections,,,,,,,,,,,,,,99.4,0.52,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.31241,Klebsiella pneumoniae strain KPC160125 strain Not collected,Not collected,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11246290,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-10T00:00:00Z,,PRJNA528846,GCA_011106795.1,"CP040038,CP040039",,Chung Shan Medical University,Oxford Nanopore MiniION; Illumina MiSeq,10.0x,Unicycler v. May-2018,1,1,2,5556926,57.096424,5655,5473,urine,isolated from a single hospital and subjected for comparative genomic analysis,2015-02-10,Taiwan,Taiwan:Taichung,,,,urinary tract infections,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak strains of OXA-48 K. pneumoniae were isolated from a single hospital and subjected for comparative genomic analysis.,collected_by:CSMUH,,,,,,,urinary tract infections,,,,,,,,,,,,,,99.4,0.26,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.31242,Klebsiella pneumoniae strain KPC160132 strain Not collected,Not collected,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11246291,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-10T00:00:00Z,,PRJNA528846,GCA_011129215.1,"CP040023,CP040027,CP040024,CP040026,CP040025",,Chung Shan Medical University,Oxford Nanopore MiniION; Illumina MiSeq,10.0x,unicycler v. May-2018,1,4,5,5826480,56.79084,6008,5800,blood,isolated from a single hospital and subjected for comparative genomic analysis,2015-04-01,Taiwan,Taiwan:Taichung,,,,bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Outbreak strains of OXA-48 K. pneumoniae were isolated from a single hospital and subjected for comparative genomic analysis.,collected_by:CSMUH,,,,,,,bacteremia,,,,,,,,,,,,,,99.26,0.63,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.31286,Klebsiella pneumoniae strain 9949,9949,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13702289,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-03-29T00:00:00Z,,PRJNA598275,GCA_011765405.1,"CP050280,CP050281,CP050282,CP050283,CP050284",,First Affiliated Hospital of Nanchang University,PacBio RSII,150.0x,Celera Assembler v. 2019-11,1,4,5,6048138,56.791958,7303,6106,blood,,2017-12-07,China,China:Nanchang,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae,collected_by:Liu Yang,,,,,,,Sepsis,,,,,,,,,,,,,,97.27,0.27,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.31287,Klebsiella pneumoniae strain 10553,10553,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13683895,573,,,,,,,,2020-03-29T00:00:00Z,,PRJNA597816,GCA_011765385.1,"CP050275,CP050276,CP050277,CP050278,CP050279",,First Affiliated Hospital of Nanchang University,PacBio RSII,150.0x,Celera Assembler v. NOV-2019,1,4,5,6099601,56.6771,8157,6183,blood,,2017-12-26,China,"China:Jiangxi,Nanchang",,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,klebsiella pneumoniae,collected_by:Liu Yang,,,,,,,Sepsis,,,,,,,,,,,,,,96.04,0.31,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.31288,Klebsiella pneumoniae strain 9630,9630,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13707218,573,,,,,,,,2020-03-29T00:00:00Z,,PRJNA598527,GCA_011765425.1,"CP050285,CP050286,CP050287,CP050288",,First Affiliated Hospital of Nanchang University,PacBio RSII,150.0x,Celera Assembler v. 2019-11,1,3,4,5787752,57.01243,8410,5865,blood,,2017-11-27,China,"China:Jiangxi,Nanchang",,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae,collected_by:Liu Yang,,,,,,,Sepsis,,,,,,,,,,,,,,93.92,1.01,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.31293,Klebsiella pneumoniae strain NMI4661_17,NMI4661_17,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12715042,573,,,,MLST.Klebsiella_pneumoniae.45,genotype:ST45,,,2020-03-31T00:00:00Z,,PRJNA564526,GCA_011784905.1,"CP050455,CP050456,CP050457,CP050458",,National Medicines Institute,Illumina MiSeq; Oxford Nanopore MiniION,1.0x,Unicycler v. v0.4.8,1,3,4,5582160,57.16476,5569,5428,bal,,2017-06-08,Poland,Poland: Cracow,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella pneumoniae ST45 producing GES-5 beta-lactamase.,collected_by:National Medicines Institute,,,,,,,pneumonia,,,,,,,,,,,,,,99.7,0.83,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31338,Klebsiella pneumoniae strain SCH6109,SCH6109,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14482422,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2020-04-08T00:00:00Z,,PRJNA616107,GCA_012168575.1,"CP050858,CP050859,CP050860",,"Renji Hospital, School of Medicine, Shanghai Jiaotong University",Oxford Nanopore PromethION,200.0x,CANU v. 1.7,1,2,3,5749977,57.007236,5986,5642,urine,,2016,China,China: Shanghai,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The emergence of NDM-1-producing Klebsiella pneumoniae carrying a novel recombinant virulence plasmid,collected_by:Zhen Shen,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.79,0.79,Bloodstream Infections,Other Bloodstream Infections,Urinary Tract,Bloodstream Infections-Other Bloodstream Infections HP,573.31384,Klebsiella pneumoniae strain MRK9,MRK9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10712994,573,,,,MLST.Klebsiella_pneumoniae.14,,,,2020-01-28T00:00:00Z,,PRJNA513450,GCA_009937845.1,"CP043859,CP043860,CP043861,CP043862,CP043863,CP043864",,"ICMR- National Institute of Pathology and VVMC Safdarjung Hospital Campus, New Delhi -110029",Illumina HiSeq,48.1x,SPAdes v. 3.13.0,1,5,6,5940676,56.929295,6075,5906,urine,,2018-01-23,India,"India: Safdarjung Hospital, New Delhi",,,,Nosocomical Infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Nosocomial and community acquired infections caused by multidrug resistant (MDR) Gram-negative bacteria (GNB), represent a growing problem worldwide. These organisms are responsible for a spectrum of infections\; ranging from urinary tract infections (UTI), meningitis, septicaemia, pneumonia, to wound and device-associated infections. Polymyxins (polymyxin B and colistin) are increasingly used as antibiotic of last resort, however, emergence of polymyxin resistance (PR) is increasingly observed among bacterial pathogens. Polymyxin resistance is mediated by increased expression of efflux pumps, capsule formation and alterations in LPS of bacterial outer membrane. In recent years emergence of plasmid mediated resistance due to mcr-genes poses a threat for the rapid global spread. Analysis of the factors responsible for decreased susceptibility to polymyxin, is believed to enhance understanding of antibiotic resistance and in identifying novel markers of polymyxin resistance for rapid identification of resistance in healthcare settings. In this study, we screened and characterized the colistin resistant bacteria. We also aimed to identify the resistant determinants of colistin in the resistant isolates.",collected_by:Mudsser Azam,,,,,,,Nosocomical Infection,,,,,,,,,,,,,,100,1.28,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.31749,Klebsiella pneumoniae strain SB5881,SB5881,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA6634591,573,ST66-K2,,,MLST.Klebsiella_pneumoniae.66,,,,2020-04-23T00:00:00Z,,PRJEB37472,GCA_902827215.1,"LR792628,LR792630,LR792629,LR792631",,Institut Pasteur,,,,1,3,4,5707999,57.058838,5625,,blood,isolated in 1935 in Indonesia and was selected as the reference strain of capsular serotype K2,2018-02-18,France,France,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"One of the main K. pneumoniae laboratory reference strains is Kp52.145 (=B5055). It was isolated in 1935 in Indonesia and was selected as the reference strain of capsular serotype K2. Kp52.145 belongs to Sequence-type (ST) 66 and is a highly virulent strain from which the virulence plasmid of Klebsiella and the role of aerobactin in virulence were discovered. This strain is also used as a reference strain for its ability to escape molecular pathways relevant in the activation of the immune response. Important virulence factors (plasmid-carried rmpA/rmpA2, iut, iro, and integrative conjugative elements (ICEs)-carried yersiniabactin [ybt] and colibactin [clb]) are harbored by this strain. In contrast to the prominent role of this reference strain in laboratory work, after almost a century, the K. pneumoniae sublineage ST66-K2 was almost never observed again in clinical and epidemiological studies, with only one report in in Australia in 2002 (isolate AJ210). In this study, we describe the clinical and molecular characteristics of a ST66-K2 community-acquired infection in France in 2018. Four Kp isolates were recovered from blood (18/02\; SB5881), urine (18/02\; SB5882), CSF (19/02\; SB5883) and otorrhea (19/02\; SB5884) samples. They were involved in the different infectious site (bacteremia, bacteriuria, meningitis and acute otitis media, respectively). The four isolates were analyzed phenotypically and genotypically.",,,,,,,,,diseased,,,,,,,,,,,,,100,1.45,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.31861,Klebsiella pneumoniae strain MS14393,MS14393,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14859483,573,,,,MLST.Klebsiella_pneumoniae.515,,,,2020-06-09T00:00:00Z,,PRJNA631348,GCA_013305325.1,"CP054303,CP054304,CP054305",,The University of Queensland,PacBio RSII,75.0x,CANU v. 1.3,1,2,3,5834466,56.881332,5769,5474,rectal swab,,2016,Australia,Australia: Brisbane,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,This project contains the complete Klebsiella pneumoniae genome MS14393 relating to the study of an outbreak of carbapenem-resistant Acinetobacter baumannii (CR-Ab) and other associated gram-negative bacilli in a Brisbane ICU and burns ward between 2016-2018.,,,,,,,,N/A,,,,,,,,,,,,,,100,0.62,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.31865,Klebsiella pneumoniae strain KP20194b2,KP20194b2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186440,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013348885.1,"CP054762,CP054763,CP054764,CP054765,CP054766,CP054767",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5883119,57.024563,5999,5755,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-12,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31867,Klebsiella pneumoniae strain KP20194c,KP20194c,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186441,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013348925.1,"CP054756,CP054757,CP054758,CP054759,CP054760,CP054761",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5871874,57.03709,5981,5739,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-13,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31868,Klebsiella pneumoniae strain KP20194e,KP20194e,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186446,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013348965.1,"CP054726,CP054727,CP054728,CP054729,CP054730,CP054731",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5882289,57.024178,5996,5754,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-25,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31869,Klebsiella pneumoniae strain KP20194d,KP20194d,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186445,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013348945.1,"CP054732,CP054733,CP054734,CP054735,CP054736,CP054737",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5871563,57.03684,5979,5739,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-24,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31871,Klebsiella pneumoniae strain KP20194c3,KP20194c3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186442,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013349025.1,"CP054750,CP054751,CP054752,CP054753,CP054754,CP054755",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5883673,57.023735,5995,5754,bed sheets,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-15,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.31873,Klebsiella pneumoniae strain KP20194b,KP20194b,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186439,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013349045.1,"CP054768,CP054769,CP054770,CP054771,CP054772,CP054773",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5881004,57.024567,5985,5751,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-03,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.31875,Klebsiella pneumoniae strain KP20194a,KP20194a,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15186437,573,ST11-K64,,,MLST.Klebsiella_pneumoniae.11,,,,2020-06-17T00:00:00Z,,PRJNA638288,GCA_013349085.1,"CP054780,CP054781,CP054782,CP054783,CP054784,CP054785",,"The Second Affiliated Hospital, University of South China",Oxford Nanopore,200x,SPAdes v. 3.14,1,5,6,5882292,57.024014,5995,5755,sputum,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-04-03,China,China: Hunan,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:Xiaotuan Zhang,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.32416,Klebsiella pneumoniae strain IDR1800050501-01-02,IDR1800050501-01-02,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15086847,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2020-08-12T00:00:00Z,,PRJNA636827,GCA_014170015.1,"CP054285,CP054287,CP054286,CP054288",,"Wadsworth Center, New York State Department of Health",Illumina MiSeq; Oxford Nanopore MiniION,187x,Flye v. 2.6,1,3,4,5643101,57.12581,5659,5398,rectal swab,,2018-11,USA,USA:Maine,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.",collected_by:Maine Center for Disease Control and Prevention,,,,,,,Unknown,,,,,,,,,,,,,,99.9,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.32417,Klebsiella pneumoniae strain IDR1900025266-01-00,IDR1900025266-01-00,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15086846,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2020-08-12T00:00:00Z,,PRJNA636827,GCA_014170035.1,"CP054289,CP054291,CP054290,CP054293,CP054292",,"Wadsworth Center, New York State Department of Health",Illumina MiSeq; Oxford Nanopore MiniION,156x,Flye v. 2.6,1,4,5,5651598,57.11944,5694,5409,wound,,2018-10,USA,USA:Maine,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the U.S. and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.",collected_by:Maine Center for Disease Control and Prevention,,,,,,,Unknown,,,,,,,,,,,,,,99.96,0.33,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.32518,Klebsiella pneumoniae strain N16-03892,N16-03892,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11506009,573,,,,MLST.Klebsiella_pneumoniae.1454,,,,2020-08-14T00:00:00Z,32766684,PRJNA534306,GCA_014189335.1,"CP047271,CP047272",,Public Health Agency of Canada,Illumina NextSeq; Oxford Nanopore MiniION,116.0x,Unicycler v. 0.4.7,1,1,2,5577703,57.259647,5606,5331,rectum,,2016,Canada,Canada,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The purpose of investigating these isolates was to determine the mechanism of carbapenem resistance and the relatedness of strains in the outbreak,collected_by:LSPQ,,,,,,,not collected,,,,,,,,,,,,,,100,0.53,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.33817,Klebsiella pneumoniae strain ent1077,ent1077,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15816123,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2020-08-26T00:00:00Z,,PRJNA657141,GCA_014304835.1,"CP060281,CP060284,CP060282,CP060283",,National University of Singapore,Oxford Nanopore,150.0x,Unicycler v. July-2020,1,3,4,5835779,56.72883,5824,5575,rectal swab,,2014,Singapore,Singapore,,,,Klebsiella infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Whole genome sequencing of multidrug-resistant hypervirulent Klebsiella pneumoniae strains from Singapore,collected_by:NCID Singapore,,,,,,,Klebsiella infection,,,,,,,,,,,,,,100,2.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.33823,Klebsiella pneumoniae strain KP120,KP120,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15903654,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2020-09-01T00:00:00Z,,PRJNA659360,GCA_014361115.1,"CP060744,CP060747,CP060745,CP060746",,"Huashan Hospital, Fudan University","Illumina, PacBio",690x,SPAdes v. v3.5.5,1,3,4,5524151,57.213734,5560,5328,bile,,2011,China,China:Shanghai,,female,65,biliary tract infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,CTX-M-215-producing Escherichia coli strain EC96 and CTX-M-125-producing Klebsiella pneumoniae strain KP120,"collected_by:Institute of Antibiotics Huashan Hospital, Fudan University",,,,,,,biliary tract infection,,,,,,,,,,,,,,99.7,0.14,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,573.33849,Klebsiella pneumoniae strain P35,P35,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14770898,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2020-09-11T00:00:00Z,,PRJNA629309,GCA_014524525.1,"CP053035,CP053036,CP053037,CP053038,CP053039,CP053040,CP053041",,Universidade Federal de Sao Paulo,Illumina MiSeq; Oxford Nanopore MiniION,120.0x,Unicycler v. v0.4.0,1,6,7,5676295,57.105244,5662,5515,blood,"recovered from bloodstream infections in a teaching hospital in Sao Paulo, Brazil",2015-05,Brazil,Brazil: Sao Paulo,,male,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Evaluation of KPC-2-producing K. pneumoniae ST15 recovered from bloodstream infections in a teaching hospital in Sao Paulo, Brazil.",collected_by:Laboratorio Alerta,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.85,0.04,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.34011,Klebsiella pneumoniae strain 33Kpn12,33Kpn12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16246721,573,,,,MLST.Klebsiella_pneumoniae.504,,,,2020-10-13T00:00:00Z,,PRJNA665232,GCA_014883955.1,"CP062792,CP062793,CP062794",,Universidad El Bosque,PacBio RSII,203.0x,HGAP v. 2.3,1,2,3,5418559,57.219254,5377,5107,percutaneous abscess drainage,,2015-03-30,Colombia,Colombia: Bogota,,female,,Site-operative infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC carbapenemase-producing K. pneumoniae isolates in a Colombian high complexity hospital,collected_by:Bacterial Molecular Genetics Laboratory,,,,,,,Site-operative infection,,,,,,,,,,,,,,100,0.33,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.34030,Klebsiella pneumoniae strain MAR14-456,MAR14-456,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16386297,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-10-29T00:00:00Z,,PRJNA667838,GCA_015074925.1,"CP063277,CP063279,CP063278,CP063280",,Central Research Institute of Epidemiology,Oxford Nanopore MinION; Illumina MiSeq,100.0x,Unicycler v. v0.4.8-beta,1,3,4,5869421,56.872784,5920,5656,postoperative wound,"isolated in February 2014 from postoperative wound in a patient who later developed multiple abscesses, fatal sepsis and septic shock despite multiple surgical interventions and combination therapy with high-dose meropenem, amikacin and tigecycline",2014-02,Russia,Russia:Moscow,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Between February 2013 and November 2015 a nosocomial outbreak due to multidrug resistant hvKP occurred in the neurosurgical ICU in Moscow, Russia. K. pneumoniae isolate MAR14-456 representing this outbreak was isolated in February 2014 from postoperative wound in a patient who later developed multiple abscesses, fatal sepsis and septic shock despite multiple surgical interventions and combination therapy with high-dose meropenem, amikacin and tigecycline.","collected_by:4N .N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, Russia",,,,,,,Sepsis,,,,,,,,,,,,,,99.6,1.18,Bloodstream Infections,Sepsis,Skin and Soft Tissue,Bloodstream Infections-Sepsis HP,573.34070,Klebsiella pneumoniae strain KP19-3023,KP19-3023,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16418109,573,,,,,,,,2020-11-05T00:00:00Z,,PRJNA668652,GCA_015238555.1,"CP063747,CP063749,CP063748,CP063746",,Zhengzhou University,Illumina; MinION,12.0x,CLC Genomics workbench v. 10.0,1,3,4,5840602,56.806576,5832,5626,sputum,,2019-10-27,China,China,,male,,cirrhosis and hepatitis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"the Klebsiella pneumoniae strain KP19-3023 , complete sequence.",collected_by:Zhengzhou University,,,,,,,cirrhosis and hepatitis,,,,,,,,,,,,,,100,0.19,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.34071,Klebsiella pneumoniae strain ZRKP01,ZRKP01,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14411773,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-05T00:00:00Z,,PRJNA613645,GCA_015239295.1,"CP050354,CP050355,CP050356,CP050357,CP050358,CP050359",,GensKey Gene Technology Co. Ltd.,Oxford Nanopore,62x,Unicycler v. version 0.4.8,1,5,6,5892312,56.983406,6001,5898,sputum,,2019-10-14,China,China,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Genome sequence, compariation and selecion analysis of Ceftazidime- Avibactam-Resistant, Meropenem-Susceptible Klebsiella pneumoniae Isolates","collected_by:Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, P. R. China",,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.34072,Klebsiella pneumoniae strain ZRKP03,ZRKP03,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14411775,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-05T00:00:00Z,,PRJNA613645,GCA_015238895.1,"CP050342,CP050343,CP050344,CP050345,CP050346,CP050347",,GensKey Gene Technology Co. Ltd.,Oxford Nanopore,117x,Unicycler v. version 0.4.8,1,5,6,5857642,56.99206,5965,5861,bronchoalveolar lavage,,2019-11-18,China,China,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Genome sequence, compariation and selecion analysis of Ceftazidime- Avibactam-Resistant, Meropenem-Susceptible Klebsiella pneumoniae Isolates","collected_by:Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, P. R. China",,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.34073,Klebsiella pneumoniae strain ZRKP02,ZRKP02,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14411774,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-05T00:00:00Z,,PRJNA613645,GCA_015239135.1,"CP050348,CP050349,CP050350,CP050351,CP050352,CP050353",,GensKey Gene Technology Co. Ltd.,Oxford Nanopore,92x,Unicycler v. version 0.4.8,1,5,6,5877289,56.984863,5994,5884,sputum,,2019-10-29,China,China,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Genome sequence, compariation and selecion analysis of Ceftazidime- Avibactam-Resistant, Meropenem-Susceptible Klebsiella pneumoniae Isolates","collected_by:Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, P. R. China",,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.34074,Klebsiella pneumoniae strain ZRKP04,ZRKP04,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14411776,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-05T00:00:00Z,,PRJNA613645,GCA_015238655.1,"CP050336,CP050337,CP050338,CP050339,CP050340,CP050341",,GensKey Gene Technology Co. Ltd.,Oxford Nanopore,111x,Unicycler v. version 0.4.8,1,5,6,5887750,56.987595,5996,5892,bronchoalveolar lavage,,2019-11-23,China,China,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Genome sequence, compariation and selecion analysis of Ceftazidime- Avibactam-Resistant, Meropenem-Susceptible Klebsiella pneumoniae Isolates","collected_by:Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, P. R. China",,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.34075,Klebsiella pneumoniae strain FRPDR,FRPDR,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16451036,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-05T00:00:00Z,,PRJNA669320,GCA_015243235.1,"CP063759,CP063760,CP063762,CP063763,CP063764,CP063765,CP063761",,University of Science and Technology of China,Complete Genomics,15.66x,Unicycler v. 0.4.9b,1,6,7,6029648,56.864246,6100,,missing,,2020-05-06,China,China: Anhui,,,,Cerebral hemorrhage,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Clinical strain, isolated from sputum of patients with cerebral hemorrhage",collected_by:Zhao Liping,,,,,,,Cerebral hemorrhage,,,,,,,,,,,,,,100,0.12,Neurological Diseases,Other Brain Infections,Other,Neurological Diseases-Other Brain Infections HP,573.34124,Klebsiella pneumoniae strain 3214,3214,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08915824,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-11-09T00:00:00Z,,PRJNA449686,GCA_015290985.1,"CP028850,CP028853,CP028855,CP028856,CP028857,CP028854,CP028851,CP028852",,Qingdao Agricultural Universtiy,PacBio,406.0x,SOAPdenovo v. v2.04,1,7,8,6171644,56.39256,6427,6183,sputum,,2017-03,China,China:Qingdao,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Characterization of Klebsiella pneumoniae strain,collected_by:Weiqi Su,,,,,,,pneumonia,,,,,,,,,,,,,,100,1.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.34145,Klebsiella pneumoniae strain JX-CR-hvKP-4,JX-CR-hvKP-4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561284,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015355995.1,"CP064235,CP064236,CP064237,CP064238,CP064239,CP064240",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,259x,HGAP v. 3,1,5,6,5965960,56.875843,6018,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34146,Klebsiella pneumoniae strain JX-CR-hvKP-6,JX-CR-hvKP-6,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561429,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015355955.1,"CP064229,CP064230,CP064231",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,241x,HGAP v. 3,1,2,3,5739454,57.13214,5560,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.18,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34147,Klebsiella pneumoniae strain JX-CR-hvKP-5,JX-CR-hvKP-5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561285,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015355975.1,"CP064232,CP064233,CP064234",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,235x,HGAP v. 3,1,2,3,5739446,57.132153,5569,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,1.18,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34148,Klebsiella pneumoniae strain JX-CR-hvKP-3,JX-CR-hvKP-3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561283,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015356015.1,"CP064241,CP064242,CP064243,CP064244,CP064245",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,258x,HGAP v. 3,1,4,5,5853213,56.936935,5878,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.4,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34149,Klebsiella pneumoniae strain JX-CR-hvKP-1,JX-CR-hvKP-1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561274,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015356055.1,"CP064252,CP064253,CP064254,CP064255,CP064256,CP064257",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,255x,HGAP v. 3,1,5,6,5827883,57.153206,5828,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.7,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34150,Klebsiella pneumoniae strain JX-CR-hvKP-2,JX-CR-hvKP-2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16561282,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-11-12T00:00:00Z,,PRJNA672246,GCA_015356035.1,"CP064246,CP064247,CP064248,CP064249,CP064250,CP064251",,"First Affiliated Hospital of Nanchang University, Nanchang University",PacBio RSII,174x,HGAP v. 3,1,5,6,5995772,56.993595,6030,,,,2018-2019,China,China:Nanchang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Prevalence of the NTEKPC-I on IncFrepB plasmids among Hypervirulent Klebsiella pneumoniae isolates in Jiangxi Province, South China",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.7,0.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.34159,Klebsiella pneumoniae strain 33Kpn9,33Kpn9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16246830,573,,,,MLST.Klebsiella_pneumoniae.846,,,,2020-11-15T00:00:00Z,,PRJNA665234,GCA_015475915.1,"CP064296,CP064298,CP064297",,Universidad El Bosque,PacBio RSII,133.7x,HGAP v. 2.3,1,2,3,5721946,57.14951,5788,5489,ascites fluid,,2015-03-19,Colombia,Colombia: Bogota,,female,,Peritonitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,KPC carbapenemase-producing K. pneumoniae (KPC-Kp) isolates in a Colombian high complexity hospital,collected_by:Bacterial Molecular Genetics Laboratory,,,,,,,Peritonitis,,,,,,,,,,,,,,99.11,0.68,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,573.34234,Klebsiella pneumoniae strain INF357-sc-2280189,INF357,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357260,573,,,,MLST.Klebsiella_pneumoniae.30,mlst:ST30,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904863125.1,"LR890217,LR890218,LR890219,LR890220,LR890221,LR890222,LR890223,LR890224",,Monash University,Illumina HiSeq,,,1,7,8,5434792,57.250416,5282,,urine,,2014-03-28,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.05,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34239,Klebsiella pneumoniae strain INF133-sc-2279960,INF133,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357033,573,,,,MLST.Klebsiella_pneumoniae.323,mlst:ST323,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904863195.1,"LR890189,LR890190,LR890191,LR890192,LR890193,LR890194,LR890195,LR890196,LR890197",,Monash University,Illumina HiSeq,,,1,8,9,5830162,56.752316,5726,,wound swab,,2013-07-29,Australia,,,,,,Wound swab,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.88,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.34246,Klebsiella pneumoniae strain INF354-sc-2280183,INF354,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357254,573,,,,MLST.Klebsiella_pneumoniae.29,mlst:ST29,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904863325.1,"LR890369,LR890370,LR890371,LR890372,LR890373",,Monash University,Illumina HiSeq,,,1,4,5,5671180,57.105366,5549,,urine,,2014-03-31,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,1.5,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34248,Klebsiella pneumoniae strain INF148-sc-2279987,INF148,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357060,573,,,,MLST.Klebsiella_pneumoniae.323,mlst:ST323,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904863355.1,"LR890381,LR890382,LR890383",,Monash University,Illumina HiSeq,,,1,2,3,5467726,57.35582,5250,,urine,,2013-08-14,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.84,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34250,Klebsiella pneumoniae strain INF250-sc-2280154,INF250,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357225,573,,,,MLST.Klebsiella_pneumoniae.29,mlst:ST29,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904863395.1,"LR890374,LR890375,LR890376,LR890377,LR890378,LR890379,LR890380",,Monash University,Illumina HiSeq,,,1,6,7,5683515,57.097923,5540,,urine,,2013-12-02,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,1.5,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34261,Klebsiella pneumoniae strain INF313-sc-2280106,INF313,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357177,573,,,,MLST.Klebsiella_pneumoniae.29,mlst:ST29,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904864535.1,"LR890415,LR890416,LR890417,LR890418,LR890419,LR890420,LR890421",,Monash University,Illumina HiSeq,,,1,6,7,5688260,57.090763,5576,,urine,,2014-02-17,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,1.5,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34278,Klebsiella pneumoniae strain INF142-sc-2279977,INF142,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357050,573,,,,MLST.Klebsiella_pneumoniae.340,mlst:ST340,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904865785.1,"LR890547,LR890548,LR890549,LR890550,LR890551,LR890552,LR890553",,Monash University,Illumina HiSeq,,,1,6,7,5740875,57.062157,5701,,urine,,2013-08-07,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.39,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34284,Klebsiella pneumoniae strain INF327-sc-2280132,INF327,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357203,573,,,,MLST.Klebsiella_pneumoniae.323,mlst:ST323,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904866195.1,"LR890571,LR890572,LR890573,LR890574,LR890575",,Monash University,Illumina HiSeq,,,1,4,5,5676080,56.85873,5522,,urine,,2014-03-03,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.88,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34294,Klebsiella pneumoniae strain INF279-sc-2280202,INF279,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357273,573,,,,MLST.Klebsiella_pneumoniae.29,mlst:ST29,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904866405.1,"LR890679,LR890680,LR890681,LR890682,LR890683,LR890684,LR890685",,Monash University,Illumina HiSeq,,,1,6,7,5685961,57.09267,5568,,urine,,2014-01-06,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,1.5,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.34297,Klebsiella pneumoniae strain INF065-sc-2279980,INF065,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3357053,573,,,,,mlst:ST2998,,,2020-10-30T00:00:00Z,29340588,PRJEB6891,GCA_904866425.1,"LR890665,LR890666,LR890667,LR890668",,Monash University,Illumina HiSeq,,,1,3,4,5565136,57.127842,5390,,urine,,2013-05-27,Australia,,,,,,Urine,,Resistant;Susceptible,AMR Panel,,,,,,,,,Whole genome sequencing of antimicrobial resistant organisms from an Australian ICU,,,,,,,,,,,,,,,,,,,diseased,,,100,0.76,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.35025,Klebsiella pneumoniae strain KPN110,KPN110,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16685805,573,,,,MLST.Klebsiella_pneumoniae.323,,,,2020-11-29T00:00:00Z,,PRJNA674961,GCA_015694065.1,"CP065172,CP065173,CP065174,CP065175,CP065176",,Monash University,Oxford Nanopore MinION,122x,Unicycler v. 0.4.7,1,4,5,5955584,56.670162,5960,5717,urine,,2017-05-19,Australia,Australia: Melbourne,,,,urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Whole-genome sequencing of Klebsiella pneumoniae species complex isolates collected from hospital patients in Melbourne, Australia.","collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,100,1.92,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.35026,Klebsiella pneumoniae strain KPN114,KPN114,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16685806,573,,,,MLST.Klebsiella_pneumoniae.29,,,,2020-11-29T00:00:00Z,,PRJNA674961,GCA_015694085.1,"CP065167,CP065168,CP065169,CP065170,CP065171",,Monash University,Oxford Nanopore MinION,141x,Unicycler v. 0.4.7,1,4,5,5602288,57.15979,5542,5332,urine,,2017-05-18,Australia,Australia: Melbourne,,,,urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Whole-genome sequencing of Klebsiella pneumoniae species complex isolates collected from hospital patients in Melbourne, Australia.","collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urinary tract infection,,,,,,,,,,,,,,100,1.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.35063,Klebsiella pneumoniae strain FK 6768,FK 6768,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17005574,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2020-12-13T00:00:00Z,,PRJNA682695,GCA_015999625.1,"CP065554,CP065555,CP065556,CP065557,CP065558,CP065559",,First affiliated hospital of Wenzhou medical university,PacBio Sequel,50.0x,HGAP v. SEP-2020,1,5,6,5868563,56.990597,6165,5731,feces,,2019-05-23,China,China,,male,45,"multiple injuries, traumatic brain herniation",,,Susceptible;Resistant,Computational Prediction,,,,,,,,,tetA Variant mediating Tigecycline Resistance Evolution in KPC-2-producing Klebsiella pneumoniae during tigecycline treatment,"collected_by:Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University",,,,,,,"multiple injuries, traumatic brain herniation",,,,,,,,,,,,,,99.52,0.12,Neurological Diseases,Other Brain Infections,Gastrointestinal,Neurological Diseases-Other Brain Infections HP,573.35099,Klebsiella pneumoniae strain KpPF25,KpPF25,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016749,573,,,,MLST.Klebsiella_pneumoniae.1440,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016066025.1,"CP065825,CP065826,CP065827,CP065828,CP065829,CP065830",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","311x, 154x",Unicycler v. v.0.4.8,1,5,6,5469485,57.32589,5396,5222,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.57,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.35100,Klebsiella pneumoniae strain KpC5,KpC5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016747,573,,,,MLST.Klebsiella_pneumoniae.507,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016066475.1,"CP065833,CP065834,CP065835,CP065836,CP065837",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","284x, 150x",Unicycler v. v.0.4.8,1,4,5,5421580,57.12095,5383,5183,urine,,2018-05,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,Susceptible,Computational Prediction,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.61,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.35101,Klebsiella pneumoniae strain KpC11,KpC11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17016748,573,,,,MLST.Klebsiella_pneumoniae.225,,,,2020-12-15T00:00:00Z,,PRJNA683049,GCA_016066295.1,"CP065831,CP065832",,University of Texas at Dallas,"Illumina NextSeq, ONT MinION","401x, 148x",Unicycler v. v.0.4.8,1,1,2,5676463,57.06987,5689,5472,urine,,2018-06,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,Susceptible,Computational Prediction,,,,,,,,,"Recurrent Urinary Tract Infection (rUTI) poses a major health issue, especially among postmenopausal women. Klebsiella spp. account for ~15%-17% of rUTIs, with Klebsiella pneumoniae being the most prevalent. We report the complete genome sequences of six K. pneumoniae isolates acquired from the urine of postmenopausal women diagnosed with rUTI.",collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,100,0.33,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.35511,Klebsiella pneumoniae strain 1970_kpn,1970_kpn,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10935845,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-01-10T00:00:00Z,,PRJNA522420,GCA_016598795.1,"CP066855,CP066857,CP066858,CP066856",,Pediatric Research and Clinical Center for Infectious Diseases (PRCCID),Illumina; Oxford Nanopore MinION; Sanger,92.40058475417054x,SPAdes v. 3.10.1,1,3,4,5797747,56.637062,5842,5567,urine,,2018-04-04,Russia,Russia: Saint-Petersburg,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Whole genome sequencing of hypervirulent Klebsiella pneumoniae isolates circulating in Saint Petersburg, Russia",collected_by:State Budgetary Healthcare Institution Saint-Petersburg clinical scientific and practical center for special types of medical care (oncology-oriented),,,,,,,not applicable,,,,,,,,,,,,,,99.7,1.34,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.36092,Klebsiella pneumoniae strain RIVM_C014073,RIVM_C014073,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373167,573,,,,MLST.Klebsiella_pneumoniae.45,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016780025.1,CP068797,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5401998,57.328808,5360,5176,,,2017,Netherlands,Netherlands,,,,,,,Susceptible,Computational Prediction,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,100,0.83,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.36093,Klebsiella pneumoniae strain RIVM_C015043,RIVM_C015043,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373170,573,,,,MLST.Klebsiella_pneumoniae.377,,,,2021-02-01T00:00:00Z,,PRJNA691727,GCA_016780145.1,CP068798,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5442266,57.32794,5390,5196,,,2017,Netherlands,Netherlands,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,100,0.86,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.36094,Klebsiella pneumoniae strain fekpn2511,fekpn2511,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17506720,573,,,,MLST.Klebsiella_pneumoniae.290,,,,2021-02-02T00:00:00Z,,PRJNA638288,GCA_016800965.1,"CP068972,CP068973,CP068974,CP068975,CP068976",,"The Second Affiliated Hospital, University of South China",Illumina MiSeq; Oxford Nanopore,50.0x,unicycler v. 0.4.8; SPAdes v. 3.1.14,1,4,5,5537477,57.14931,5474,5275,urine,"isolated from the ward environment at the same time, which harbor different chromosome indels",2019-12-25,China,"China:Hengyang, Hunan",,male,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.",collected_by:XiaoTuan Zhang,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.22,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.36095,Klebsiella pneumoniae strain 33Kpn22,33Kpn22,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16246926,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2021-02-02T00:00:00Z,,PRJNA665239,GCA_016801375.1,"CP069046,CP069047,CP069048,CP069049,CP069051,CP069050",,Universidad El Bosque,PacBio RSII,131.7x,HGAP v. 2.3,1,5,6,6102548,56.58084,6198,5827,blood,,2015-04-11,Colombia,Colombia: Bogota,,female,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,KPC carbapenemase-producing K. pneumoniae isolates in a Colombian high complexity hospital,collected_by:Bacterial Molecular Genetics Laboratory,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36096,Klebsiella pneumoniae strain RIVM_C018500,RIVM_C018500,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373179,573,,,,MLST.Klebsiella_pneumoniae.45,,,,2021-02-02T00:00:00Z,,PRJNA691727,GCA_016801495.1,CP068997,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5340301,57.378513,5278,5092,,,2019,Netherlands,Netherlands,,,,,,,Susceptible,Computational Prediction,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,100,0.83,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.36097,Klebsiella pneumoniae strain RIVM_C015657,RIVM_C015657,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17373171,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-02-02T00:00:00Z,,PRJNA691727,GCA_016801575.1,CP068994,,National Institute for Public Health and the Environment,Oxford Nanopore MiniION,30x,Unicycler v. 0.4.4,1,0,1,5430483,57.14282,5411,5193,,,2017,Netherlands,Netherlands,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,OXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.,sample_type:chromosome,,,,,,,,,,,,,,,,,,,,,99.11,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.36149,Klebsiella pneumoniae strain K8,K8,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450830,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-02-11T00:00:00Z,,PRJNA615326,GCA_016864275.1,CP050819,,Gumushane University,Illumina NovaSeq,0.9712677102699x,GS De Novo Assembler v. 23.12.2019,1,0,1,5334176,57.93543,4885,,urine,,2017-12-07,Turkey,Turkey,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,To determine resistance and virulence factors genes of K.pneumoniae by WGS,collected_by:FDH,,,,,,,pneumonia,,,,,,,,,,,,,,99.55,0.04,Respiratory Diseases,Pneumonia,Urinary Tract,Respiratory Diseases-Pneumonia HP,573.36591,Klebsiella pneumoniae strain B960,B960,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17911762,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701798,GCA_016925215.1,"CP070410,CP070411,CP070412,CP070413,CP070414",,Christian Medical College,Illumina; Oxford Nanopore,123.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5506598,57.096905,5463,5258,blood,,2021,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,MDR Klebsiella pneumoniae B960,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36592,Klebsiella pneumoniae strain B1347,B1347,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17911845,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701804,GCA_016925235.1,"CP070415,CP070416,CP070417,CP070418,CP070419",,Christian Medical College,Illumina; Oxford Nanopore,72.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5504416,57.09654,5468,5257,blood,,2021,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B1347,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36593,Klebsiella pneumoniae strain B3824,B3824,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17911903,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701806,GCA_016925275.1,"CP070425,CP070426,CP070427,CP070428,CP070429",,Christian Medical College,Illumina; Oxford Nanopore,127.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5505287,57.098057,5464,5257,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B3824,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36594,Klebsiella pneumoniae strain B3923,B3923,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17912169,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701810,GCA_016925295.1,"CP070430,CP070431,CP070432,CP070433,CP070434",,Christian Medical College,Illumina; Oxford Nanopore,115.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5504407,57.09638,5470,5257,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of MDR K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36595,Klebsiella pneumoniae strain B5617,B5617,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17914336,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2021-02-24T00:00:00Z,,PRJNA701817,GCA_016925315.1,"CP070435,CP070436,CP070437,CP070438,CP070439",,Christian Medical College,Illumina; Oxford Nanopore,97.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,4,5,5841424,56.95529,5879,5663,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome sequencing of MDR K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.93,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36596,Klebsiella pneumoniae strain B12097,B12097,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17915080,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701847,GCA_016925355.1,"CP070445,CP070446,CP070447,CP070448",,Christian Medical College,Illumina; Oxford Nanopore,118.0x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,3,4,5493060,57.134895,5444,5240,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of MDR K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36597,Klebsiella pneumoniae strain B18064,B18064,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17915099,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701849,GCA_016925375.1,"CP070449,CP070450,CP070451,CP070452,CP070453",,Christian Medical College,Illumina; Oxford Nanopore,79.0x,Canu v. 1.8,1,4,5,5506617,57.097397,5466,5258,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B18064,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36598,Klebsiella pneumoniae strain B28484,B28484,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17915109,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-02-24T00:00:00Z,,PRJNA701851,GCA_016925415.1,"CP070459,CP070460,CP070461,CP070462,CP070463",,Christian Medical College,Illumina; Oxford Nanopore,94.0x,Canu v. 1.8,1,4,5,5507133,57.08197,5461,5257,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B28484,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36599,Klebsiella pneumoniae strain B28906,B28906,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17915140,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2021-02-24T00:00:00Z,,PRJNA701854,GCA_016925435.1,"CP070464,CP070465,CP070466",,Christian Medical College,Illumina; Oxford Nanopore,98.0x,Canu v. 1.8,1,2,3,5450493,57.335693,5323,5147,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of MDR Klebsiella pneumoniae B28906,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.36601,Klebsiella pneumoniae strain KP47693,KP47693,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933269,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939535.1,"CP070528,CP070527,CP070529,CP070526,CP070525",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,4,5,5516587,57.18505,5487,5253,swab from around the abdominal drainage,,2018-11-26,Czech Republic,Czech Republic: Praha,,,,Idiopathic acute pancreatitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Veobecn fakultn nemocnice v Praze,,,,,,,Idiopathic acute pancreatitis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Pancreatic Disorders,Abdominal,Gastrointestinal Diseases-Pancreatic Disorders HP,573.36602,Klebsiella pneumoniae strain KP52813,KP52813,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933300,573,,,,MLST.Klebsiella_pneumoniae.846,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939775.1,"CP070586,CP070585,CP070584,CP070583,CP070582,CP070581,CP070580",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,6,7,5725869,57.163307,5723,5504,sputum,,2019-09-03,Czech Republic,Czech Republic: Nymburk,,,,Chronic respiratory failure,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Chronic respiratory failure,,,,,,,,,,,,,,100,0.98,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.36603,Klebsiella pneumoniae strain KP51069,KP51069,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933286,573,,,,MLST.Klebsiella_pneumoniae.512,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939675.1,"CP070564,CP070563,CP070562,CP070561,CP070560",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,4,5,5681342,57.07333,5720,5511,urine,,2019-05-27,Czech Republic,Czech Republic: Tinec,,,,Low back pain,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Tinec,,,,,,,Low back pain,,,,,,,,,,,,,,100,0.02,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.36604,Klebsiella pneumoniae strain KP51248,KP51248,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933289,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939695.1,"CP070568,CP070567,CP070566,CP070565",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,5600113,57.11194,5610,5359,rectal swab,,2019-06-14,Czech Republic,Czech Republic: Ostrava,,,,Unspecified infectious diseases,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Zdravotn stav se sdlem v Ostrav,,,,,,,Unspecified infectious diseases,,,,,,,,,,,,,,100,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.36605,Klebsiella pneumoniae strain KP52810,KP52810,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933298,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939755.1,"CP070579,CP070578,CP070577,CP070576",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,5676569,57.20286,5670,5480,pressure ulcer swab,,2019-09-03,Czech Republic,Czech Republic: Nymburk,,,,Acute respiratory failure,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,100,0.18,Respiratory Diseases,Other Respiratory Diseases,Skin and Soft Tissue,Respiratory Diseases-Other Respiratory Diseases HP,573.36606,Klebsiella pneumoniae strain KPA9853,KPA9853,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933305,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939835.1,"CP070602,CP070601,CP070600,CP070599",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,5514856,57.189453,5471,5247,urine,,2019-10-08,Czech Republic,Czech Republic: Mlnk,,,,Acute pancreatitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Mlnk,,,,,,,Acute pancreatitis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Pancreatic Disorders,Urinary Tract,Gastrointestinal Diseases-Pancreatic Disorders HP,573.36607,Klebsiella pneumoniae strain KPA4411,KPA4411,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933304,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939815.1,"CP070598,CP070597,CP070596,CP070595,CP070594",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,4,5,5698780,57.16927,5706,5509,endotracheal cannula,,2019-06-17,Czech Republic,Czech Republic: Mstec Krlov,,,,Chronic respiratory failure,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Mstsk nemocnice Mstec Krlov,,,,,,,Chronic respiratory failure,,,,,,,,,,,,,,100,0.44,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.36608,Klebsiella pneumoniae strain JNQH116,JNQH116,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17976248,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2021-03-01T00:00:00Z,,PRJNA702614,GCA_017084505.1,"CP070898,CP070899,CP070900,CP070901",,The First Affiliated Hospital of Shandong First Medical University,Oxford Nanopore MinION; Illumina NovaSeq,98.0x,SPAdes v. 3.14; Unicycler v. v0.4.9b,1,3,4,5650669,57.10844,5585,5368,cerebrospinal fluid,"isolated from Shandong, China",2020-04-20,China,China,,,,meningitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The studies are aimed at determining the characteristics of epidemiology, antimicrobial resistance and pathogenicity for carbapenem resistant enterobacteriaceae, especially for strains isolated from Shandong, China.",collected_by:Mingju Hao,,,,,,,meningitis,,,,,,,,,,,,,,100,1.38,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,573.36651,Klebsiella pneumoniae strain IR5065,IR5065,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676897,573,,,,MLST.Klebsiella_pneumoniae.383,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310305.1,"CP061948,CP061949,CP061950,CP061951",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,3,4,5773950,56.6131,5917,5605,blood,,2013-04-29,China,China: Beijing,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.79,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.36652,Klebsiella pneumoniae strain IR5654,IR5654,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676890,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310325.1,"CP061952,CP061953,CP061954,CP061955,CP061956",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,5672130,57.123974,5669,5486,urine,,2015-11-01,China,China: Beijing,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.36653,Klebsiella pneumoniae strain IR5726,IR5726,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676889,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310345.1,"CP061957,CP061958,CP061959,CP061960",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,3,4,5801912,57.165104,5862,5628,sputum,,2017-08-09,China,China: Beijing,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.9,0.27,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.36654,Klebsiella pneumoniae strain LZK001,LZK001,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676887,573,,,,MLST.Klebsiella_pneumoniae.1393,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310385.1,"CP061965,CP061966,CP061967,CP061968,CP061969",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,5541471,57.07091,5501,5261,bile,,2015-02-03,China,China: Lanzhou,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.65,1.2,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.36655,Klebsiella pneumoniae strain JNK002,JNK002,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676888,573,,,,MLST.Klebsiella_pneumoniae.395,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310365.1,"CP061961,CP061962,CP061963,CP061964",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,3,4,5859393,56.650253,6009,5724,urine,,2015-11-10,China,China: Jinan,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.7,0.99,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.36656,Klebsiella pneumoniae strain IR5086,IR5086,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676882,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310425.1,"CP061975,CP061976,CP061977,CP061978,CP061979",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,5717198,56.8528,5733,5487,sputum,,2014-02-11,China,China: Beijing,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.36657,Klebsiella pneumoniae strain IR5755,IR5755,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15676885,573,,,,MLST.Klebsiella_pneumoniae.1128,,,,2021-03-09T00:00:00Z,,PRJNA648010,GCA_017310405.1,"CP061970,CP061971,CP061972,CP061973,CP061974",,Chinese PLA General Hospital,Illumina HiSeq,100X,SOAPdenovo v. 2.21,1,4,5,5797218,56.937897,5856,5613,urine,,2018-04-13,China,China: Beijing,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The aim of this study was to investigate the emergence, the nosocomial transmission, evolution, and persistence of OXA-48-producing Klebsiella pneumoniae",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0.69,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.36681,Klebsiella pneumoniae strain JS161205112,JS161205112,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18106513,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2021-03-10T00:00:00Z,,PRJNA705944,GCA_017315205.1,"CP071324,CP071323",,"Jinshan Hospital, Shanghai Medical College, Fudan University",PacBio,124.0x,smrtlink v. version 4.1,1,1,2,5618722,56.909863,5557,5323,sputum,,2016-12-05,China,China: Shanghai,,,,pneumonia,,,Susceptible,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae subsp. pneumoniae strain JS161205112, complete genome",collected_by:Gang Li,,,,,,,pneumonia,,,,,,,,,,,,,,100,1.49,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.36684,Klebsiella pneumoniae strain C2244,C2244,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18160617,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-03-14T00:00:00Z,,PRJNA707017,GCA_017351975.1,CP071464,,Peking University People's Hospital,PacBio; Illumina,100.0x,Unicycler v. 0.4.5,1,0,1,5461348,57.336834,5349,,sputum,,2017-05-07,China,China:Beijing,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Clinical Klebsiella pneumoniae isolate C2244,collected_by:Longyang Jin,,,,,,,pneumonia,,,,,,,,,,,,,,99.45,0.12,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.37198,Klebsiella pneumoniae strain B33769,B33769,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18478625,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2021-04-04T00:00:00Z,,PRJNA717115,GCA_017742895.1,"CP072422,CP072423,CP072424",,Christian Medical College,Illumina; Oxford Nanopore,104.9x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,2,3,5450492,57.33545,5324,5147,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.37199,Klebsiella pneumoniae strain B4650,B4650,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18478563,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-04-04T00:00:00Z,,PRJNA717121,GCA_017742915.1,"CP072408,CP072409,CP072410,CP072411,CP072412",,Christian Medical College,Illumina; Oxford Nanopore,54.93x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,5505129,57.098007,5469,5257,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.37200,Klebsiella pneumoniae strain B32278,B32278,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18478623,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-04-04T00:00:00Z,,PRJNA717116,GCA_017742935.1,"CP072413,CP072414,CP072415,CP072416,CP072417,CP072418,CP072419,CP072420,CP072421",,Christian Medical College,Illumina; Oxford Nanopore,38.7x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,8,9,5507145,57.096027,5465,5258,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.37201,Klebsiella pneumoniae strain B13243,B13243,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18478480,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-04-04T00:00:00Z,,PRJNA717133,GCA_017742955.1,"CP072403,CP072404,CP072405,CP072406,CP072407",,Christian Medical College,Illumina; Oxford Nanopore,59.7x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,4,5,5505287,57.09786,5468,5257,blood,,2015,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of K. pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.56,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.37202,Klebsiella pneumoniae strain KPN236,KPN236,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18450111,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-04-04T00:00:00Z,,PRJNA716566,GCA_017743095.1,"CP072492,CP072493",,Guangdong Medical University,Illumina HiSeq,100.0x,ABySS v. 2.0.2,1,1,2,5628645,57.210396,5482,5278,sputum,,2020-11-15,China,China:Zhanjiang,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"hypervirulent Klebsiella pneumoniae isolated from hospital patients,complete genome",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,1.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.37203,Klebsiella pneumoniae strain KPN246,KPN246,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18450112,573,,,,MLST.Klebsiella_pneumoniae.660,,,,2021-04-04T00:00:00Z,,PRJNA716566,GCA_017743115.1,"CP072494,CP072495",,Guangdong Medical University,Illumina HiSeq,100.0x,ABySS v. 2.0.2,1,1,2,5530510,57.02997,5466,5247,sputum,,2020-11-15,China,China:Zhanjiang,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"hypervirulent Klebsiella pneumoniae isolated from hospital patients,complete genome",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,1.01,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.37204,Klebsiella pneumoniae strain KPN247,KPN247,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18450113,573,,,,,,,,2021-04-04T00:00:00Z,,PRJNA716566,GCA_017743135.1,"CP072496,CP072497,CP072498,CP072499",,Guangdong Medical University,Illumina HiSeq,100.0x,ABySS v. 2.0.2,1,3,4,5514453,57.257446,5427,5270,sputum,,2020-11-15,China,China:Zhanjiang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"hypervirulent Klebsiella pneumoniae isolated from hospital patients,complete genome",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.37205,Klebsiella pneumoniae strain KP1517,KP1517,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15052358,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-04-06T00:00:00Z,,PRJNA635754,GCA_017809835.1,"CP072463,CP072464,CP072465,CP072466",,Nankai University,PacBio; Illumina,80 x,SMRT Link v. 5.1.0,1,3,4,5864329,56.935944,5944,5727,urine,,2018-11-19,China,China: Tianjin,,,,Urinary tract infections,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,We find a pan-resistant isolate of Klebsiella pneumoniae and explore its resistance mechanism.,collected_by:Shuangqing Liu,,,,,,,Urinary tract infections,,,,,,,,,,,,,,99.11,0.49,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.37213,Klebsiella pneumoniae strain KPN234,KPN234,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18450110,573,,,,MLST.Klebsiella_pneumoniae.420,,,,2021-04-07T00:00:00Z,,PRJNA716566,GCA_017815715.1,"CP072653,CP072654",,Guangdong Medical University,Illumina HiSeq,100.0x,ABySS v. 2.0.2,1,1,2,5431899,57.300385,5316,5132,sputum,,2020-11-15,China,China:Zhanjiang,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"hypervirulent Klebsiella pneumoniae isolated from hospital patients,complete genome",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.77,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.37301,Klebsiella pneumoniae strain 3347684I,3347684I,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17736023,573,,,,MLST.Klebsiella_pneumoniae.268,,,,2021-04-22T00:00:00Z,,PRJNA698767,GCA_018128445.1,"CP071080,CP071081,CP071082,CP071083,CP071084,CP071085",,,Illumina NovaSeq; Oxford Nanopore MiniION,255x,Unicycler v. 0.4.8,1,5,6,5689667,57.06274,5627,5417,central nervous catheter,,2020,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0.38,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,573.37302,Klebsiella pneumoniae strain 3347689I,3347689I,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17736022,573,,,,MLST.Klebsiella_pneumoniae.395,,,,2021-04-22T00:00:00Z,,PRJNA698767,GCA_018128465.1,"CP071086,CP071087,CP071088,CP071089",,,Illumina NovaSeq; Oxford Nanopore MiniION,129x,Unicycler v. 0.4.8,1,3,4,5857083,56.941467,5953,5722,outer malleolus,,2020,Switzerland,Switzerland,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,1.34,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.37707,Klebsiella pneumoniae strain Kpn 1693,Kpn 1693,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13741660,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-05-05T00:00:00Z,,PRJNA599216,GCA_018279185.1,"CP047595,CP047597,CP047596",,Chinese Academy of Medical Sciences &Peking Union Medical College,PacBio,100.0x,SMRT Link v. v5.1.0,1,2,3,5593962,57.229885,5470,5189,sputum,,2016-09-15,China,"China:Hebei, Zhangjiakou",,,,Bronchiectasis,,,Susceptible,Computational Prediction,,,,,,,,,"We reported a multidrug-resistant hypervirulent Klebsiella pneumoniae (hvKp) named as Kpn 1693.Bioinformatic analysis revealed that Kpn 1693 harbored one chromosome of 5,331,308 bp (cKpn1693), and two plasmids of 192,347 bp (IncHI1B, pKpn1693-Vir) and 70,307 bp (IncFII, pKpn1693-CTXM) respectively.",collected_by:CAMS Collection Center of Pathogen Microorganisms (CAMS-CCPM-AP),,,,,,,Bronchiectasis,,,,,,,,,,,,,,99.54,1.18,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.37762,Klebsiella pneumoniae strain B30155,B30155,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19104983,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2021-05-18T00:00:00Z,,PRJNA728855,GCA_018394355.1,"CP074580,CP074581,CP074582,CP074583",,Christian Medical College,Illumina; Oxford Nanopore,97.36x,Canu v. 1.8; Unicycler Hybrid v. 0.4.7,1,3,4,5450289,57.33487,5328,5149,blood,,2014,India,India: Vellore,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Klebsiella pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.37793,Klebsiella pneumoniae strain DD521,DD521,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19073635,573,,,,,,,,2021-05-24T00:00:00Z,,PRJNA728250,GCA_018454365.1,"CP075316,CP075317,CP075318,CP075319,CP075320",,Hohai University,Illumina HiSeq; Oxford Nanopore,120x,SMRT Link v. 5.1.0; Unicycle v. 1.0,1,4,5,5748663,56.836903,5680,5454,hospital,,2021-01-12,China,"China: Lushi County, Sanmenxia City, Henan Provience",,male,66 years old,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Acinetobacter baumannii and Klebsiella pneumoniae were isolated, and the two strains are both multidrug resistant, incuding carbopenems. Therefore, their genomes were sequenced to characterize the drug resistance genes.",collected_by:Dao-Feng Zhang,,,,,,,pneumonia,,,,,,,,,,,,,,100,1.55,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.38179,Klebsiella pneumoniae strain 2016_49,2016_49,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16657684,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-06-01T00:00:00Z,,PRJNA674482,GCA_018604345.1,"CP068015,CP068016,CP068017",,ITACYL,Illumina MiSeq; Oxford Nanopore MinION,53.0x,SPAdes v. v3.14.0; Unicycler v. v0.4.8,1,2,3,5913209,56.935787,5916,5644,sputum,,2016-06-05,Spain,Spain: Valladolid,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Illumina and ONT reads,collected_by:Hospital Universitario Rio Hortega,,,,,,,Pneumonia,,,,,,,,,,,,,,99.9,0.79,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.38180,Klebsiella pneumoniae strain GR390,GR390,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18317283,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-06-01T00:00:00Z,,PRJNA714767,GCA_018604385.1,"CP075890,CP075891,CP075892,CP075893,CP075894",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,175.0x,CANU v. v.1.7; UNICYCLER HYBRID v.,1,4,5,5808550,57.004276,5841,5617,blood,,2015,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Klebsiella pneumoniae_GR390,collected_by:Wockhardt Research Centre,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.09,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.38213,Klebsiella pneumoniae strain K186,K186,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19522986,573,,,,MLST.Klebsiella_pneumoniae.437,,,,2021-06-15T00:00:00Z,,PRJNA734734,GCA_018885345.1,"CP076518,CP076519,CP076520,CP076521",,Zhejiang University,Illumina; Oxford Nanopore,1.0x,Unicycle v. v 0.3.0,1,3,4,5674372,57.118214,5703,5497,feces,,2017-09-23,China,China: Hangzhou,,,,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,To surveil the evolution of Hv-CRKP strains,collected_by:Liu Lizhang,,,,,,,pneumonia,,,,,,,,,,,,,,99.85,0.07,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.38830,Klebsiella pneumoniae strain Kp1,Kp1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7708245,573,,,,MLST.Klebsiella_pneumoniae.39,,,,2021-07-06T00:00:00Z,,PRJEB41835,GCA_910589455.1,"OU342706,OU342707,OU342708,OU342709,OU342710",,Institut Pasteur,,,,1,4,5,5846198,57.01131,5790,5474,urine,,2005-10-06,Spain,Spain,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Outbreaks of carbapenemase-producing Klebsiella pneumoniae (CPKp) represent a major threat for hospitals. We molecularly characterized the first out- break of VIM-1-producing K. pneumoniae in Spain, which raised fears about the spread of this strain or of the plasmid carrying blaVIM-1. Through in-depth genomic analysis of 18 isolates recovered between October 2005 and September 2007, we show that 17 ST39 isolates were clonal, whereas the last isolate had acquired the VIM-1 plasmid from the epidemic clone. The index isolate carried 31 antibiotic resist- ance genes (ARGs) and was resistant to almost all antibiotics tested. Later isolates further gained mutations in efflux pump regulators ramR and opxR, deletion of mgrB (colistin resistance), and frameshift mutations in ompK36 (b-lactam resistance) likely selected by antibiotic usage. Comparison with publicly available genome sequences and literature review revealed no sign of dissemination of this CPKp strain. However, the VIM-1 plasmid was found in diverse Enterobacterales species, although restricted to Spain. One isolate became urease negative following IS5075 transposition into ureC. Analysis of 9,755 K. pneumoniae genomes showed the same ureC::IS5075 inser- tion in 14.1% of the isolates and explained why urease activity is a variable identifi- cation trait for K. pneumoniae. Transposition into ureC results from the similarity of its 39 end and the terminal inverted repeats of Tn21-like transposons, the targets of IS5075 and related insertion sequences (ISs). As these transposons frequently carry ARGs, this might explain the frequent chromosomal invasion by these ISs and ureC inactivation in multidrug-resistant isolates.",,,,,,,,,diseased,,,,,,,,,,,,,100,0.83,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.39711,Klebsiella pneumoniae strain KP-CT77,KP-CT77,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20375149,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-02T00:00:00Z,,PRJNA749500,GCA_019434295.1,"CP080303,CP080307,CP080308,CP080305,CP080304,CP080306",,The Second Affiliated Hospital of Zhejiang University School of Medicine,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,5,6,5916103,56.896965,6050,5807,the same patient,isolated from the same patient,2020,China,China:Hangzhou,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To investigate three clonally related carbapenem-resistant hypervirulent Klebsiella pneumoniae strains consecutively isolated from the same patient.,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.39712,Klebsiella pneumoniae strain KP-426,KP-426,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20373013,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-02T00:00:00Z,,PRJNA749500,GCA_019434255.1,"CP080309,CP080313,CP080315,CP080311,CP080310,CP080314,CP080312",,The Second Affiliated Hospital of Zhejiang University School of Medicine,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,6,7,5919746,56.895294,6053,5809,the same patient,isolated from the same patient,2020,China,China:Hangzhou,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To investigate three clonally related carbapenem-resistant hypervirulent Klebsiella pneumoniae strains consecutively isolated from the same patient.,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.39713,Klebsiella pneumoniae strain KP-C76,KP-C76,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20373014,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-02T00:00:00Z,,PRJNA749500,GCA_019434275.1,"CP080297,CP080302,CP080299,CP080298,CP080301,CP080300",,The Second Affiliated Hospital of Zhejiang University School of Medicine,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,5,6,5894462,56.98072,6013,5772,the same patient,isolated from the same patient,2020,China,China:Hangzhou,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,To investigate three clonally related carbapenem-resistant hypervirulent Klebsiella pneumoniae strains consecutively isolated from the same patient.,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.39715,Klebsiella pneumoniae strain K191663,K191663,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20422817,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2021-08-03T00:00:00Z,,PRJNA749815,GCA_019443545.1,"CP080353,CP080359,CP080354,CP080355,CP080361,CP080356,CP080357,CP080360,CP080358",,Southwest medical university,Illumina HiSeq; PacBio RSII,100.0x,SOAPdenovo v. 2.04; unicycler v. 0.4.7,1,8,9,5731197,56.99469,5791,5599,blood,,2019-11-07,China,China:wuxi,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,whole genome sequencing of clinical strains,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.43,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.39716,Klebsiella pneumoniae strain K191773,K191773,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20422820,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2021-08-03T00:00:00Z,,PRJNA749815,GCA_019443585.1,"CP080362,CP080365,CP080366,CP080367,CP080368,CP080364,CP080363",,Southwest medical university,Illumina HiSeq; PacBio RSII,100.0x,SOAPdenovo v. 2.04; unicycler v. 0.4.7,1,6,7,5844036,56.866573,5928,5708,sputum,,2019-12-03,China,China:wuxi,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,whole genome sequencing of clinical strains,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.61,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.39717,Klebsiella pneumoniae strain K191659,K191659,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20422816,573,,,,MLST.Klebsiella_pneumoniae.656,,,,2021-08-03T00:00:00Z,,PRJNA749815,GCA_019443565.1,"CP080346,CP080352,CP080347,CP080348,CP080349,CP080350,CP080351",,Southwest medical university,Illumina HiSeq; PacBio RSII,100.0x,SOAPdenovo v. 2.04; unicycler v. 0.4.7,1,6,7,5825598,56.739807,5844,5562,sputum,,2019-10-24,China,China:wuxi,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,whole genome sequencing of clinical strains,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.15,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.39751,Klebsiella pneumoniae strain ZJ27003,ZJ27003,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17108663,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-08-05T00:00:00Z,34141626,PRJNA686203,GCA_019454345.1,"CP067060,CP067062,CP067061",,"Sir Run Run Shaw Hospital, Collage of Medicine, Zhejiang University",nanopore,100.0x,Unicycler v. 0.4.7,1,2,3,5606745,57.35702,5474,5270,sputum,,2017-02-27,China,"China: Huzhou, Hangzhou, Zhejiang Province",,,,chronic obstructive pulmonary disease,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Aim to characterize clinical carbapenem-resistant ST23 K. pneumoniae isolate ZJ27003 and its harbored blaKPC-2 plasmid p27003_KPC.,collected_by:Ping Zhang,,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,100,0.93,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.39752,Klebsiella pneumoniae strain ER17974.3,ER17974.3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15567838,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2021-08-05T00:00:00Z,34141583,PRJNA646893,GCA_019455345.1,"CP059295,CP059296",,Icahn School of Medicine,PacBio RSII,11.148128220335842x,HGAP v. 3,1,1,2,5605979,56.90478,5579,5297,blood,,2020,USA,USA:New York City,,,,Lemierres syndrome,,,Susceptible,Computational Prediction,,,,,,,,,Hypervirulent Klebsiella pneumoniae,collected_by:Mount Sinai Hospital,,,,,,,Lemierres syndrome,,,,,,,,,,,,,,99.85,1.15,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.39840,Klebsiella pneumoniae,Klebsiella pneumoniae,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8995931,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-08-04T00:00:00Z,,PRJEB37819,GCA_911728565.1,OU453210,,Erasmus University Medical Center,,,,1,0,1,5497511,57.03172,5400,,human,derived from 14 patients,2016,Netherlands,Netherlands,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Background. The global spread of colistin resistance poses a healthcare threat. However, the epidemiology of mcr-1-carrying-plasmids in a local healthcare setting is largely unknown. In this study, we aim to characterize plasmids and their transmission in mcr-1 positive isolates identified from a large hospital in the Netherlands.Methods. We retrospectively included all clinical mcr-1-carrying isolates from patients hospitalized in years 2010-2018. In principle, extracted plasmids from mcr-1 positive isolates were sequenced using a combination of short (iSeq) and long (MinION) reads chemistries. The plasmid hybrid assemblies had their incompatibility type (Inc type) and genetic background characterized. A comparison was performed of the detected plasmids with all public available mcr-1-carrying-plasmids. Results. We confirmed the presence of the mcr-1 in 22 isolates, derived from 14 patients. We identified 21 plasmids, which were described with incompatibility type of IncX4, IncI2, IncHI2 and double Inc types\; IncHI2/IncN and IncHI2/IncQ. Additionally, the mcr-1 was identified in the chromosome of a prevalent strain of K. pneumoniae (ST147). Genomic analysis of available mcr-1-carrying-plasmids indicated plasmidal transmission in the hospital through patients and species. Conclusion. In a small collection of isolates, we observed multiple plasmidal transmission cases such as intrapatient-interspecific and among patients hospitalized in different years. Mcr-1 plasmids have a diverse genetic background which can corelate with the Inc type. Plasmid enrichment, and genetic background in all available plasmids contributed in defining transmissions. Understanding the transmission of mcr-1-carrying plasmids, the spread of the mcr-1 gene can be observed, studied and hopefully limited in a local tertiary care center and eventually globally. ",,,,,,,,,,,,,,,,,,,,,,100,0.58,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.40306,Klebsiella pneumoniae strain KP_NORM_BLD_2012_85054,KP_NORM_BLD_2012_85054,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4724625,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2021-08-30T00:00:00Z,,PRJNA723772,GCA_019797985.1,"CP073627,CP073628,CP073629",,Stavanger University Hospital,Illumina MiSeq; Oxford Nanopore,50.0x,SPAdes v. 3.13.0,1,2,3,5531852,57.293705,5406,5230,blood,,2012,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Norwegian Klebsiella pneumoniae study.,,,,,,,,,diseased,,,,,,,,,,,,,99.7,0.48,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.40307,Klebsiella pneumoniae strain KP_NORM_BLD_2014_96855,KP_NORM_BLD_2014_96855,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8602828,573,,,,MLST.Klebsiella_pneumoniae.420,,,,2021-08-30T00:00:00Z,,PRJNA723772,GCA_019798005.1,"CP073783,CP073784,CP073785,CP073786,CP073787",,Stavanger University Hospital,Illumina HiSeq; Oxford Nanopore,317x,SPAdes v. 3.13.0,1,4,5,5671312,57.03758,5579,5364,blood,,2014,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Norwegian Klebsiella pneumoniae study.,,,,,,,,,diseased,,,,,,,,,,,,,100,0.97,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.40308,Klebsiella pneumoniae strain KP_NORM_BLD_2015_115359,KP_NORM_BLD_2015_115359,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8602827,573,,,,,,,,2021-08-30T00:00:00Z,,PRJNA723772,GCA_019798025.1,"CP073788,CP073789,CP073790",,Stavanger University Hospital,Illumina MiSeq; Oxford Nanopore,64x,SPAdes v. 3.13.0,1,2,3,5544555,57.242104,5453,5258,blood,,2015,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Norwegian Klebsiella pneumoniae study.,,,,,,,,,diseased,,,,,,,,,,,,,100,0.57,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.40309,Klebsiella pneumoniae strain KP_NORM_BLD_2010_71621,KP_NORM_BLD_2010_71621,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8602826,573,,,,,,,,2021-08-30T00:00:00Z,,PRJNA723772,GCA_019798185.1,"CP073791,CP073792,CP073793,CP073794,CP073795,CP073796",,Stavanger University Hospital,Illumina MiSeq; Oxford Nanopore,58x,SPAdes v. 3.13.0,1,5,6,5574001,57.297928,5541,5372,blood,,2010,Norway,Norway,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,The Norwegian Klebsiella pneumoniae study.,,,,,,,,,diseased,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.40317,Klebsiella pneumoniae strain KP18-2138,KP18-2138,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20928637,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-31T00:00:00Z,,PRJNA540114,GCA_019823875.1,"CP082032,CP082033,CP082035,CP082034",,Zhengzhou University,Oxford Nanopore,12x,unicycler v. v.0.4.8,1,3,4,5773264,57.116096,5770,,blood,isolated from China，for bacteria resistance,2018-12-19,China,China,,,,Septic shock,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,Septic shock,,,,,,,,,,,,,,100,0.17,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.40318,Klebsiella pneumoniae strain KP18-238,KP18-238,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20928632,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-31T00:00:00Z,,PRJNA540114,GCA_019823855.1,"CP082014,CP082016,CP082013,CP082017,CP082015",,Zhengzhou University,Illumina,12x,unicycler v. v.0.4.8,1,4,5,5848221,57.05328,5856,,blood,isolated from China，for bacteria resistance,2018-10-04,China,China,,,,Brain congestion,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,Brain congestion,,,,,,,,,,,,,,100,0.17,Neurological Diseases,Other Brain Infections,Blood and Circulatory System,Neurological Diseases-Other Brain Infections HP,573.40319,Klebsiella pneumoniae strain KP18-2050,KP18-2050,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20928633,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-31T00:00:00Z,,PRJNA540114,GCA_019823835.1,"CP082019,CP082021,CP082022,CP082018,CP082020",,Zhengzhou University,Illumina,12x,unicycler v. v.0.4.8,1,4,5,6021475,56.885963,6044,,blood,isolated from China，for bacteria resistance,2018-11-13,China,China,,,,Septicemia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,Septicemia,,,,,,,,,,,,,,100,0.17,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.40322,Klebsiella pneumoniae strain KP18-2113,KP18-2113,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20928636,573,,,,,,,,2021-08-31T00:00:00Z,,PRJNA540114,GCA_019823895.1,"CP082029,CP082031,CP082028,CP082030",,Zhengzhou University,Oxford Nanopore,12x,unicycler v. v.0.4.8,1,3,4,5814793,56.9191,5655,,blood,isolated from China，for bacteria resistance,2018-12-02,China,China,,,,Fever,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,Fever,,,,,,,,,,,,,,100,1.31,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.40323,Klebsiella pneumoniae strain KP19-2196,KP19-2196,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20928639,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-08-31T00:00:00Z,,PRJNA540114,GCA_019823915.1,"CP082041,CP082043,CP082044,CP082040,CP082042",,Zhengzhou University,Oxford Nanopore,12x,unicycler v. v.0.4.8,1,4,5,6005752,56.906845,6006,,hydrothorax,isolated from China，for bacteria resistance,2019-02-23,China,China,,,,Severe pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,Severe pneumonia,,,,,,,,,,,,,,100,0.32,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.40330,Klebsiella pneumoniae strain GIMC1002:Kpn-3Ts64,GIMC1002:Kpn-3Ts64,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12618964,573,,,,MLST.Klebsiella_pneumoniae.395,genotype:ST395,,,2021-09-02T00:00:00Z,,PRJNA561493,GCA_019856575.1,"CP082240,CP082241,CP082242",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina,130.0x,CLC Genomics Workbench v. 20; SPAdes,1,2,3,5777346,56.71978,5882,5620,sputum,,2016-02-02,Russia,Russia:Moscow,,,,pulmonaryartery thrombembolia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Main pathogens causing nosocomial infections in intensive care units.,collected_by:Fedosova NF,,,,,,,pulmonaryartery thrombembolia,,,,,,,,,,,,,,99.7,0.99,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.40354,Klebsiella pneumoniae strain SCAID PHRX1-2021 (13/97) strain SCAID PHRX1-2021 (13/97) strain SCAID PHRX1-2021 (13/97),SCAID PHRX1-2021 (13/97),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982458,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915305.1,"CP082805,CP082806",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,153x,Canu v. 2.0,1,1,2,5716056,57.151314,5698,5403,swab from pharynx,,2021-03-16,Kazakhstan,Kazakhstan: Almaty,,,,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,pneumonia,,,,,,,,,,,,,,99.55,1.54,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.40355,Klebsiella pneumoniae strain SCAID PHRX2-2021 (20/245) strain SCAID PHRX2-2021 (20/245) strain SCAID PHRX2-2021 (20/245),SCAID PHRX2-2021 (20/245),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982460,573,,,,MLST.Klebsiella_pneumoniae.380,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915325.1,"CP082796,CP082797,CP082798",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,209x,Canu v. 2.0,1,2,3,5576938,57.197678,5458,5242,swab from pharynx,,2021-03-26,Kazakhstan,Kazakhstan: Almaty,,,,pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,pneumonia,,,,,,,,,,,,,,100,1.03,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.40356,Klebsiella pneumoniae strain SCAID TST1-2021 (15/226) strain SCAID TST1-2021 (15/226) strain SCAID TST1-2021 (15/226),SCAID TST1-2021 (15/226),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20982459,573,,,,MLST.Klebsiella_pneumoniae.1486,,,,2021-09-15T00:00:00Z,,PRJNA754843,GCA_019915345.1,"CP082799,CP082800,CP082801,CP082802,CP082803,CP082804",,Scientific Center for Anti-infectious Drugs (SCAID),PacBio Sequel,238x,Canu v. 2.0,1,5,6,5642663,57.177773,5608,5407,swab from tracheostomic tube,,2021-03-16,Kazakhstan,Kazakhstan: Almaty,,,,"Surgical Procedures, Operative",,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Experimental models of clinical isolates for clarifying the universality of the reversion phenomenon,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology;passage_history:2",,,,,,,"Surgical Procedures, Operative",,,,,,,,,,,,,,100,2,Surgical Site Infections,,Other,Surgical Site Infections- HP,573.40472,Klebsiella pneumoniae strain KP294,KP294,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21399028,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2021-09-21T00:00:00Z,,PRJNA757181,GCA_020080145.1,"CP083445,CP083446,CP083447",,Yongchuan Hospital of Chongqing Medical University,Oxford Nanopore PromethION,500.0x,canu v. 1.6,1,2,3,5657623,57.05108,5697,5469,secretion,,2020-05-30,China,"China:Yongchuan District, Chongqing",,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, the objectives of our study were the following: (i) to describe the prevalence of clinical CRE isolates, (ii) to identify the mechanisms and clonal relatedness among these CRE strains, (iii) to examine the genetic context of IMP-4.",sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,1.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.41281,Klebsiella pneumoniae strain B17602,B17602,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21848771,573,,,,MLST.Klebsiella_pneumoniae.35,,,,2021-10-04T00:00:00Z,,PRJNA766467,GCA_020221715.1,"CP084168,CP084169,CP084170,CP084171",,Christian Medical College,Illumina; Oxford Nanopore,92.3x,Canu v. 1.8; Unicycler hybrid v. 0.4.7,1,3,4,5450177,57.33445,5339,5167,blood,,2015,,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome sequencing of Klebsiella pneumoniae,collected_by:Christian Medical College,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.15,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.41289,Klebsiella pneumoniae strain HJM-ERG332,HJM-ERG332,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21491216,573,,,,MLST.Klebsiella_pneumoniae.392,,,,2021-10-07T00:00:00Z,,PRJNA764253,GCA_020341575.1,"CP084332,CP084333,CP084334,CP084335",,InDRE,Illumina MiSeq,74.56x,CLC NGS Cell v. 21.0.5,1,3,4,5380559,57.693413,5200,4984,urine,,2016-08-02,Mexico,Mexico: Mexico City,,,,,,,Susceptible,Computational Prediction,,,,,,,,,"Complete Genome of Klebsiella pneumoniae isolated from six patients, after a nosocomial outbreak with bad and fatal consequences in Mexico City",collected_by:Mendieta-Condado Edgar Escobar-Escamilla Noe Ramirez -Gonzalez Jose Ernesto Cortes-Ortiz Iliana Alejandra Bravata-Alcantara Juan Carlos Garces-Ayala Fabiola Araiza Rodriguez Adnan,,,,,,,,,,,,,,,,,,,,,99.63,0.29,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.41303,Klebsiella pneumoniae strain C1672,C1672,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18897823,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2021-10-14T00:00:00Z,,PRJNA725642,GCA_020496635.1,"CP073917,CP073918,CP073919",,Peking University People's hospital,Illumina; PacBio,1.0x,Unicycler v. 0.4.7,1,2,3,5915234,56.372005,5892,5607,sputum,,2016-04-17,China,China: Jiangsu,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Carbapenem resistance conferred by blaIMP-4 in K2-ST65 hypervirulent Klebsiella pneumoniae,collected_by:Peking University People's Hospital,,,,,,,Pneumonia,,,,,,,,,,,,,,100,2.16,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.41304,Klebsiella pneumoniae strain C2051,C2051,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18897888,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2021-10-14T00:00:00Z,,PRJNA725646,GCA_020496675.1,"CP073920,CP073923,CP073922,CP073921",,Peking University People's hospital,Illumina; PacBio,1.0x,Unicycler v. 0.4.7,1,3,4,5702904,56.754383,5713,5478,blood,,2015-12-23,China,China: Gansu,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Carbapenem resistance conferred by blaIMP-4 in K2-ST65 hypervirulent Klebsiella pneumoniae,collected_by:Peking University People's Hospitla,,,,,,,Bacteremia,,,,,,,,,,,,,,100,1.52,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.41311,Klebsiella pneumoniae strain SB1139,SB1139,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024792,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525505.1,CP084859,,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,0,1,5385248,57.31686,5326,5159,feces,,2002,,Netherlands,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.14,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.41312,Klebsiella pneumoniae strain SA12,SA12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024790,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525485.1,"CP084866,CP084867",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5661819,57.179893,5591,5372,liver abscess,,2008,,France,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,1.01,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.41313,Klebsiella pneumoniae strain SB1170,SB1170,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024793,573,,,,MLST.Klebsiella_pneumoniae.45,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525645.1,"CP084856,CP084857,CP084858",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,2,3,5644528,57.077457,5610,5401,feces,,2002,,Netherlands,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,1.25,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.41314,Klebsiella pneumoniae strain SB1067,SB1067,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024791,573,,,,MLST.Klebsiella_pneumoniae.17,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525845.1,"CP084860,CP084861,CP084862,CP084863,CP084864,CP084865",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,5,6,5510448,57.251354,5475,5303,feces,,2002,,Netherlands,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.89,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.41316,Klebsiella pneumoniae strain T69,T69,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024799,573,,,,MLST.Klebsiella_pneumoniae.375,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525865.1,"CP084823,CP084824",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5564218,57.214222,5525,5287,liver abscess,,2010,,France,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,1.37,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.41317,Klebsiella pneumoniae strain SA1,SA1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024789,573,,,,MLST.Klebsiella_pneumoniae.86,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020525885.1,"CP084868,CP084869",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5563569,57.144993,5505,5299,blood/pneumoniae,,2008,,France,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,1.03,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.41320,Klebsiella pneumoniae strain SB2390,SB2390,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024794,573,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020526005.1,"CP084852,CP084853,CP084854,CP084855",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,3,4,5697330,57.085495,5625,5448,urinary tract,,2002,,Curacao,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.54,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.41321,Klebsiella pneumoniae strain 04A025,04A025,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024781,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020526025.1,"CP084871,CP084872",,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,1,2,5504965,57.267994,5397,5241,blood,,1997,,France,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.41323,Klebsiella pneumoniae strain BJ1,BJ1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024782,573,,,,MLST.Klebsiella_pneumoniae.380,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020526065.1,CP084870,,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,0,1,5258072,57.597767,5039,4899,liver abscess,,2011,,France,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.63,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.41324,Klebsiella pneumoniae strain 03-9138-2,03-9138-2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22024780,573,,,,MLST.Klebsiella_pneumoniae.65,,,,2021-10-19T00:00:00Z,,PRJNA768294,GCA_020526045.1,CP084873,,Monash University,Minion (Oxford Nanopore) and NextSeq,50x,Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3;,1,0,1,5157573,57.404095,5042,4887,anal abscess,,2003,,Martinique,,,,,,,Susceptible,Computational Prediction,,,,,,,,,Complete genomes from a range of Klebsiella species across the Klebsiella pneumoniae species complex. Some genomes overlapping with PRJEB15325,"sample_type:Whole organism;biomaterial_provider:Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia",,,,,,,,,,,,,,,,,,,,,100,0.83,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.41326,Klebsiella pneumoniae strain Kp36336,Kp36336,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17075437,573,,,,MLST.Klebsiella_pneumoniae.893,,,,2021-10-25T00:00:00Z,,PRJNA686374,GCA_020544485.1,"CP066511,CP066512,CP066513,CP066514,CP066515",,KU Leuven,Illumina MiniSeq; Oxford Nanopore,110.0x,Unicycler v. 0.4.8,1,4,5,6085754,56.429684,6172,5856,tissue samples,,2019,Belgium,Belgium:Brussels,,,,Fracture fixation infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Pre-adaptated bacteriophage-antibiotic combination therapy in a patient with fracture-related infection due to pandrug-resistant Klebsiella pneumoniae,collected_by:Hopital academique Erasme,,,,,,,Fracture fixation infection,,,,,,,,,,,,,,100,1.24,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.42339,Klebsiella pneumoniae strain Kp1,Kp1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22815109,573,,,,MLST.Klebsiella_pneumoniae.1017,,,,2021-11-09T00:00:00Z,,PRJNA776717,GCA_020808985.1,"CP086285,CP086286",,Shanghai Jiao Tong University,PacBio,235.0x,HGAP v. v4,1,1,2,5338291,57.34116,5162,,feces,,2020-08,China,China:Shanghai,,,,infection,,,Susceptible,Computational Prediction,,,,,,,,,pubngchun-Intestinal isolation,collected_by:Pubingchun,,,,,,,infection,,,,,,,,,,,,,,100,0.91,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.42340,Klebsiella pneumoniae strain Kp1604,Kp1604,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22374975,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2021-10-27T00:00:00Z,,PRJNA772526,GCA_020641015.1,"CP085478,CP085479,CP085480",,Shanghai Jiao Tong University,PacBio,232.0x,HGAP v. v4,1,2,3,5459550,57.19409,5255,,blood,,2015,China,China:Shanghai,,,,infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Klebsiella Pneumoniae,collected_by:Shanghai Jiao Tong University,,,,,,,infection,,,,,,,,,,,,,,100,1.48,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.43313,Klebsiella pneumoniae strain TH12852,TH12852,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23002891,573,,,,,,,,2021-11-22T00:00:00Z,,PRJNA778913,GCA_020911785.1,CP087122,,Tsinghua University,PacBio Sequel,120X,HGAP v. 1.2,1,0,1,5531835,57.098515,5467,5287,blood,,,China,China: Tsinghua University,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,The genome of Klebsiella pneumoniae isolates TH12908 (K1) and TH12852 (K23) were sequenced to study the role of capsule locus on virulence.,"collected_by:Changgeng Hospital(Beijing, China)",,,,,,,Sepsis,,,,,,,,,,,,,,99.9,0.42,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.43314,Klebsiella pneumoniae strain TH12908,TH12908,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23002890,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-11-22T00:00:00Z,,PRJNA778913,GCA_020911805.1,CP087123,,Tsinghua University,PacBio Sequel,120X,HGAP v. 1.2,1,0,1,5692842,57.156033,5612,5382,blood,,,China,China: Tsinghua University,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,The genome of Klebsiella pneumoniae isolates TH12908 (K1) and TH12852 (K23) were sequenced to study the role of capsule locus on virulence.,"collected_by:Changgeng Hospital(Beijing, China)",,,,,,,Sepsis,,,,,,,,,,,,,,100,1.05,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.43318,Klebsiella pneumoniae strain YZH2487,YZH2487,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23249428,573,,,,MLST.Klebsiella_pneumoniae.617,,,,2021-11-28T00:00:00Z,,PRJNA781387,GCA_020991145.1,"CP087706,CP087707,CP087708,CP087709",,Yangzhou University,PacBio RS,100.0x,HGAP v. 4,1,3,4,5720680,57.021595,5730,5523,sputum,,2020-10-24,China,China: Yangzhou,,,,Acute severe pancreatitis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"whole genome sequences of Klebsiella pneumoniae YZH22127, YZH2429 and YZH2487",collected_by:Li Guiling,,,,,,,Acute severe pancreatitis,,,,,,,,,,,,,,100,1.13,Gastrointestinal Diseases,Pancreatic Disorders,Respiratory Tract,Gastrointestinal Diseases-Pancreatic Disorders HP,573.43350,Klebsiella pneumoniae strain KP-PA,KP-PA,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20218086,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-12-06T00:00:00Z,,PRJNA746592,GCA_021057265.1,"CP084984,CP084985",,Sapienza University of Rome,Illumina,50x,SPAdes v. 3.14.1,1,1,2,5761820,56.73657,6018,5538,unknown,,,,Italy,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,HvKp ESBL infections are associated with high mortality and may complicate the course of patients with severe COVID-19.,"collected_by:Microbiology Unit, Azienda Universitaria Ospedaliera Pisana",,,,,,,unknown,,,,,,,,,,,,,,98.56,1.28,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.43421,Klebsiella pneumoniae strain 7011.62,7011.62,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016533,573,,,,MLST.Klebsiella_pneumoniae.152,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137655.1,"CP082985,CP082986,CP082987",,University of Bern,Illumina NovaSeq and Oxford Nanopore,389.6399x,Unicycler v. 0.4.8,1,2,3,5706648,56.739647,5730,5487,not applicable,,2018,,Switzerland,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,not applicable,,,,,,,,,,,,,,100,0.26,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.43422,Klebsiella pneumoniae strain 7008.20,7008.20,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016532,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137675.1,"CP082988,CP082989,CP082990,CP082991,CP082992,CP082993,CP082994",,University of Bern,Illumina NovaSeq and Oxford Nanopore,331.0631x,Unicycler v. 0.4.8,1,6,7,5870019,56.89041,5885,5663,rectal swab,,2018,,Switzerland,,,,None/screening,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,None/screening,,,,,,,,,,,,,,100,1.48,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.43423,Klebsiella pneumoniae strain 6911.28,6911.28,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016531,573,,,,MLST.Klebsiella_pneumoniae.437,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137695.1,"CP082995,CP082996,CP082997,CP082998,CP082999",,University of Bern,Illumina NovaSeq and Oxford Nanopore,187.6888x,Unicycler v. 0.4.8,1,4,5,5441835,57.364822,5414,5264,blood,,2018,,Switzerland,,,,Sepsis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,Sepsis,,,,,,,,,,,,,,100,0.02,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.43424,Klebsiella pneumoniae strain 6712.08,6712.08,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016529,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137715.1,"CP083000,CP083001,CP083002,CP083003,CP083004,CP083005,CP083006",,University of Bern,Illumina NovaSeq and Oxford Nanopore,197.2725x,Unicycler v. 0.4.8,1,6,7,5652918,57.02299,5712,5463,not applicable,,2018,,Switzerland,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,not applicable,,,,,,,,,,,,,,100,0.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.43425,Klebsiella pneumoniae strain 6711.43,6711.43,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016528,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137735.1,"CP083007,CP083008,CP083009,CP083010",,University of Bern,Illumina NovaSeq and Oxford Nanopore,218.7681x,Unicycler v. 0.4.8,1,3,4,5676882,57.11156,5723,5517,rectal swab,,2018,,Switzerland,,,,None/screening,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,None/screening,,,,,,,,,,,,,,100,0.02,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.43426,Klebsiella pneumoniae strain 6710.71,6710.71,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016527,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137755.1,"CP083011,CP083012,CP083013,CP083014,CP083015",,University of Bern,Illumina NovaSeq and Oxford Nanopore,205.4498x,Unicycler v. 0.4.8,1,4,5,5630871,57.0524,5703,5458,not applicable,,2018,,Switzerland,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,not applicable,,,,,,,,,,,,,,99.99,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.43427,Klebsiella pneumoniae strain 6709.15-I,6709.15-I,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016534,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137775.1,"CP083016,CP083017,CP083018,CP083019,CP083020",,University of Bern,Illumina NovaSeq and Oxford Nanopore,328.832x,Unicycler v. 0.4.8,1,4,5,5521180,57.142567,5531,5309,urine,,2018,,Switzerland,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,UTI,,,,,,,,,,,,,,99.7,0.33,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.43428,Klebsiella pneumoniae strain 6611.48,6611.48,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016525,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137795.1,"CP083021,CP083022,CP083023,CP083024,CP083025",,University of Bern,Illumina NovaSeq and Oxford Nanopore,229.2595x,Unicycler v. 0.4.8,1,4,5,5537776,57.151985,5551,5330,urine,,2017,,Switzerland,,,,UTI,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,UTI,,,,,,,,,,,,,,100,0.33,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.43429,Klebsiella pneumoniae strain 6604.68,6604.68,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016524,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137815.1,"CP083026,CP083027,CP083028,CP083029,CP083030,CP083031",,University of Bern,Illumina NovaSeq and Oxford Nanopore,204.287x,Unicycler v. 0.4.8,1,5,6,5565437,57.12283,5588,5363,blood,,2017,,Switzerland,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,Sepsis,,,,,,,,,,,,,,100,0.33,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.43430,Klebsiella pneumoniae strain 5208.51,5208.51,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016539,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137835.1,"CP083032,CP083033,CP083034,CP083035",,University of Bern,Illumina NovaSeq and Oxford Nanopore,372.2797x,Unicycler v. 0.4.8,1,3,4,5647468,57.16229,5610,5433,not applicable,,2013,,Switzerland,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,not applicable,,,,,,,,,,,,,,100,1.14,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.43431,Klebsiella pneumoniae strain 4906.28,4906.28,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21016535,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2021-12-09T00:00:00Z,,PRJNA759850,GCA_021137855.1,"CP083036,CP083037,CP083038,CP083039,CP083040,CP083041,CP083042",,University of Bern,Illumina NovaSeq and Oxford Nanopore,359.2643x,Unicycler v. 0.4.8,1,6,7,5794280,56.871536,5852,5606,tracheobronchial,,2013,,Switzerland,,,,not applicable,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,A subset of carbapenem non-susceptible Klebsiella pneumoniae isolates from human sources between 2013 and 2020 in Switzerland (PRJNA758223) was investigated and characterized by short and long read sequencing (Illumina and Nanopore). Hybrid assemblies were generated with Unicycler (v0.4.8) by combining Illumina short read (NovaSeq 6000 sequencer\; 2 x 150-bp paired-end reads) and Nanopore long read (MinION\; FLO-MIN 106D R9 flow cell\; SQK-RBK004 1D library) sequencing technologies.,"collected_by:Institute for Infectious Diseases (IFIK), University of Bern, Friedbuehlstrasse 51, 3001 Bern, Switzerland",,,,,,,not applicable,,,,,,,,,,,,,,100,0.33,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.43556,Klebsiella pneumoniae strain DJ,DJ,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7556989,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-11-25T00:00:00Z,,PRJEB41234,GCA_920103885.1,"OV049808,OV049809,OV049810,OV049811,OV049812,OV049813,OV049814,OV049815,OV049816",,Genopole Institut Pasteur,,,,1,8,9,5808477,56.93031,5759,,urine,isolate from India exploring the genetics mechanism behind the observed phenotypic profile,2016,,India,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,"In this study, we describe a pandrug resistant ST147 Kp clinical isolate from India exploring the genetics mechanism behind the observed phenotypic profile. Furthermore, we investigated the genomic insights of 218 K. pneumoniae CG147 whole-genome sequences publicly available in order to provide a deeper understanding of the evolution and global molecular epidemiology (phylogeny, antimicrobial resistance and virulence genes, plasmid profiles) of this increasingly successful MDR worldwide lineage.",,,,,,,,,diseased,,,,,,,,,,,,,99.76,1.22,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.43868,Klebsiella pneumoniae KpBO_TO5,KpBO_TO5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24648678,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-01-16T00:00:00Z,,PRJNA794363,GCA_021484985.1,"CP090623,CP090624,CP090625",,,Oxford Nanopore MinION; Illumina iSeq,20x,Unicycler v. 0.4.8,1,2,3,5582290,57.276188,5588,5434,blood,,2021-09-04,Italy,Italy,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Turin,not applicable,not applicable,not applicable,,,,Klebsiella pneumoniae infection,,,,,,,,,,not applicable,,,,100,0.02,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.43869,Klebsiella pneumoniae KpBO_TO3,KpBO_TO3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24648677,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-01-16T00:00:00Z,,PRJNA794363,GCA_021485005.1,"CP090626,CP090627,CP090628",,,Oxford Nanopore MinION; Illumina iSeq,20x,Unicycler v. 0.4.8,1,2,3,5572350,57.26654,5591,5428,blood,,2021-07-01,Italy,Italy,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Turin,not applicable,not applicable,not applicable,,,,Klebsiella pneumoniae infection,,,,,,,,,,not applicable,,,,100,0.02,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.43870,Klebsiella pneumoniae KpBO_TO1,KpBO_TO1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24648676,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-01-16T00:00:00Z,,PRJNA794363,GCA_021485025.1,"CP090629,CP090630,CP090631",,,Oxford Nanopore MinION; Illumina iSeq,20x,Unicycler v. 0.4.8,1,2,3,5570298,57.270435,5592,5426,rectal swab,,2021-04-23,Italy,Italy,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Turin,not applicable,not applicable,not applicable,,,,Klebsiella pneumoniae infection,,,,,,,,,,not applicable,,,,100,0.02,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.43896,Klebsiella pneumoniae ONE259,ONE259,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17023568,573,,,,MLST.Klebsiella_pneumoniae.340,,,,2022-01-18T00:00:00Z,,PRJNA683169,GCA_021496095.1,"CP090931,CP090932,CP090933,CP090934,CP090935,CP090936,CP090937,CP090938,CP090939",,,Illumina NextSeq; Oxford Nanopore MinION,144.0x,Uniciclyer v. v0.4.8,1,8,9,5766661,56.713615,5842,5576,catheter,,2011,Brazil,Brazil: Sao Paulo,,,,Medical device-related infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Doroti Garcia,,,,,,,Medical device-related infection,,,,,,,,,,,,,,99.7,0.84,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,573.43899,Klebsiella pneumoniae KP697,KP697,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17023459,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-18T00:00:00Z,,PRJNA683150,GCA_021497485.1,"CP066151,CP066152,CP066153,CP066154,CP066155",,,Oxford Nanopore MinION,100x,CLC NGS Cell v. 10.0,1,4,5,5916024,56.955315,6022,5783,sputum,,2020-06-23,China,China:Zhejiang,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Xi Li,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.42,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.43944,Klebsiella pneumoniae KP29105,KP29105,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24562924,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2022-01-20T00:00:00Z,,PRJNA788123,GCA_021535085.1,"CP091061,CP091062,CP091063",,,Oxford Nanopore MiniION,58x,SPAdes v. v3.13.1,1,2,3,5812172,56.996284,5750,5506,sputum,,2020-03,China,China: Beijing,,,,COPD,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Laboratory of Clinical Microbiology and Infectious Diseases,,,,,,,COPD,,,,,,,,,,,,,,100,1.37,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,573.43945,Klebsiella pneumoniae KP30086,KP30086,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24562925,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2022-01-20T00:00:00Z,,PRJNA788123,GCA_021535105.1,"CP091058,CP091059,CP091060",,,Oxford Nanopore MiniION,58x,SPAdes v. v3.13.1,1,2,3,5808098,57.00596,5743,5506,sputum,,2020-05,China,China: Beijing,,,,COPD,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:Laboratory of Clinical Microbiology and Infectious Diseases,,,,,,,COPD,,,,,,,,,,,,,,100,1.37,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,573.44624,Klebsiella pneumoniae KPN342,KPN342,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23286194,573,,,,,,,,2021-12-19T00:00:00Z,,PRJNA674961,GCA_021228815.1,"CP089383,CP089384",,,Illumina HiSeq; Oxford Nanopore MinION,73x,Unicycler v. v0.4.8,1,1,2,5415589,57.3848,5284,5153,urine,,2017-10-16,Australia,Australia: Melbourne,,,,urine infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Microbiology Unit & Department of Infectious Diseases, Alfred Hospital",,,,,,,urine infection,,,,,,,,,,,,,,100,0.52,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.44640,Klebsiella pneumoniae KP29499,KP29499,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23898336,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2021-12-21T00:00:00Z,,PRJNA788123,GCA_021249265.1,"CP089598,CP089599,CP089600",,,Oxford Nanopore MiniION,58x,SPAdes v. v3.13.1,1,2,3,5883732,56.881176,5849,5588,sputum,,2020-04,China,China: Beijing,,,,COPD,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Laboratory of Clinical Microbiology and Infectious Diseases,,,,,,,COPD,,,,,,,,,,,,,,100,1.37,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,573.44711,Klebsiella pneumoniae KP46,KP46,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24255899,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2022-01-10T00:00:00Z,,PRJNA553055,GCA_021397585.1,"CP090126,CP090127,CP090128,CP090129,CP090130,CP090131,CP090132",,,Illumina NovaSeq; Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.8,1,6,7,5674521,57.062614,5659,5449,cerebral spinal fluid,,2017-12-14,China,China: Hangzhou,,,,Meningitis,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Qingyang Sun,,,,,,,Meningitis,,,,,,,,,,,,,,99.7,0.79,Neurological Diseases,Meningitis,Central Nervous System,Neurological Diseases-Meningitis HP,573.44713,Klebsiella pneumoniae JNKPN26,JNKPN26,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24425642,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-10T00:00:00Z,,PRJNA792451,GCA_021398155.1,"CP090203,CP090204,CP090205,CP090206",,,Oxford Nanopore,100.0x,SOAPdenovo v. 1.0,1,3,4,5962370,56.872353,6108,5868,sputum,,2019-02-28,China,China:Shandong province,,,,bacterial infectious disease,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Yingying Hao,,,,,,,bacterial infectious disease,,,,,,,,,,,,,,99.7,0.97,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.44714,Klebsiella pneumoniae C2582,C2582,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20065586,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-10T00:00:00Z,34925264,PRJNA744016,GCA_021398425.1,"CP079208,CP079211,CP079210,CP079209",,,PacBio; Illumina HiSeq,1.0x,Unicycler v. 0.4.7,1,3,4,5969891,56.7704,6100,5840,blood,,2017-08-29,China,China: Jinan,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Peking University People's Hospital,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0.53,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.44809,Klebsiella pneumoniae F94,F94,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24579938,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-11T00:00:00Z,,PRJNA793723,GCA_021431985.1,CP090398,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,5453822,57.408623,5411,5250,urine,,2021,China,China: Zhejiang,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.7,0.12,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.44810,Klebsiella pneumoniae F4,F4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24579953,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2022-01-11T00:00:00Z,,PRJNA793726,GCA_021432005.1,CP090397,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,5249104,57.462875,5075,4924,sputum,,2019,China,China: Zhejiang,,,,Pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.44815,Klebsiella pneumoniae kp7450,kp7450,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24662597,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2022-01-12T00:00:00Z,,PRJNA794878,GCA_021442045.1,"CP090468,CP090469,CP090470,CP090471,CP090472,CP090473,CP090474",,,PacBio,236.0x,HGAP v. 2020-01,1,6,7,5811072,56.8249,5774,5538,human,,2020-01,China,China:Shanghai,,,,infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:Lijianhui,,,,,,,infection,,,,,,,,,,,,,,100,1.57,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.44816,Klebsiella pneumoniae kp5152,kp5152,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24662261,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-12T00:00:00Z,,PRJNA794878,GCA_021442065.1,"CP090462,CP090463,CP090464,CP090465,CP090466,CP090467",,,PacBio,188.0x,HGAP v. 2020-01,1,5,6,5887462,56.9897,6003,5770,urine,,2020-01,China,China:Shanghai,,,,infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Qinjinhong,,,,,,,infection,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.45120,Klebsiella pneumoniae NKP1,NKP1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24220679,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028875.1,CP090310,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5599846,57.203293,5387,5090,blood,,2019-09-22,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,97.15,0.21,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45121,Klebsiella pneumoniae NKP2,NKP2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24867401,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028895.1,CP091297,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5258558,57.666122,5177,4988,blood,,2020-06-14,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.14,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45122,Klebsiella pneumoniae NKP3,NKP3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24967500,573,,,,MLST.Klebsiella_pneumoniae.280,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028915.1,CP091822,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5294789,57.746387,5092,4942,blood,,2019-10-26,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,98.81,0.13,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45123,Klebsiella pneumoniae NKP4,NKP4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24967761,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028935.1,CP091823,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5573804,57.347122,5370,5157,blood,,2019-10-02,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.43,0.53,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45124,Klebsiella pneumoniae NKP5,NKP5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24967844,573,,,,MLST.Klebsiella_pneumoniae.273,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028955.1,CP091824,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5306031,57.47059,5223,5045,blood,,2019-09-06,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.29,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45125,Klebsiella pneumoniae NKP9,NKP9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24973042,573,,,,MLST.Klebsiella_pneumoniae.2096,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029015.1,CP091827,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5377832,57.621044,5152,4960,blood,,2019-09-19,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.98,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45126,Klebsiella pneumoniae NKP8,NKP8,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24972771,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022028995.1,CP091826,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5176534,57.86983,4917,4774,blood,,2020-11-17,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45127,Klebsiella pneumoniae NKP10,NKP10,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24973877,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029035.1,CP091828,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5385666,57.598316,5164,4976,blood,,2020-09-13,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45128,Klebsiella pneumoniae NKP11,NKP11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24974170,573,,,,MLST.Klebsiella_pneumoniae.48,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029055.1,CP091829,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5351254,57.585236,5227,5055,blood,,2020-09-10,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.26,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45129,Klebsiella pneumoniae NKP12,NKP12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24974173,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029075.1,CP091830,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5491410,57.369003,5412,5230,blood,,2020-03-02,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.4,0.64,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45130,Klebsiella pneumoniae NKP13,NKP13,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24974277,573,,,,MLST.Klebsiella_pneumoniae.437,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029095.1,CP091831,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5228844,57.641537,5137,4998,blood,,2019-10-04,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.02,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45131,Klebsiella pneumoniae NKP14,NKP14,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24974278,573,,,,MLST.Klebsiella_pneumoniae.48,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029115.1,CP091832,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5217763,57.646324,5076,4925,blood,,2020-09-12,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.04,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45132,Klebsiella pneumoniae NKP16,NKP16,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975185,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029235.1,CP091150,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5390249,57.510754,5141,4957,blood,,2020-09-20,India,India,,,,Sepsis,,,Susceptible,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.43,0.32,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45133,Klebsiella pneumoniae NKP17,NKP17,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975186,573,,,,MLST.Klebsiella_pneumoniae.437,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029355.1,CP091151,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5229609,57.64069,5135,4998,blood,,2019-10-02,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.02,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45134,Klebsiella pneumoniae NKP19,NKP19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975504,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029475.1,CP091153,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5592329,57.21734,5563,5264,blood,,2020-09-02,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,97.75,2.44,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45135,Klebsiella pneumoniae NKP18,NKP18,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975495,573,,,,,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029595.1,CP091152,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5479687,57.370285,5398,5197,blood,,2019-07-09,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,98.6,0.78,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45136,Klebsiella pneumoniae NKP20,NKP20,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24975514,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-07T00:00:00Z,,PRJNA790696,GCA_022029735.1,CP091154,,,Illumina HiSeq,100.0x,Unicycler v. 3.0,1,0,1,5550612,57.349052,5458,5273,blood,,2020-12-05,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:JSSAHER,,,,,,,Sepsis,,,,,,,,,,,,,,99.86,0.79,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.45162,Klebsiella pneumoniae JNQH373,JNQH373,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25378372,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2022-02-13T00:00:00Z,,PRJNA801716,GCA_022213425.1,"CP091978,CP091979,CP091980",,,Oxford Nanopore GridION,245.0x,unicycler v. 0.4.9b,1,2,3,5694272,57.106915,5634,5408,blood,,2019-08,China,China,,,,pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Mingju Hao,,,,,,,pneumoniae,,,,,,,,,,,,,,100,1.76,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.45771,Klebsiella pneumoniae KP-1Pi,KP-1Pi,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15437778,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-23T00:00:00Z,,PRJNA643814,GCA_022369925.1,"CP071027,CP071031,CP071030,CP071028,CP071029",,,Illumina MiSeq; Oxford Nanopore MiniION,90.0x,Unicycler v. 0.4.8,1,4,5,5883186,56.586346,5901,5636,blood,,2018-07-19,Italy,Italy: Pisa,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Diagnostic Microbiology and Virology Unit, Pisa",,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,1.39,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.45772,Klebsiella pneumoniae KP-135LU,KP-135LU,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15437788,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-23T00:00:00Z,,PRJNA643814,GCA_022369815.1,"CP070890,CP070894,CP070891,CP070893,CP070892",,,Illumina MiSeq; Oxford Nanopore MinION,270.0x,Unicycler v. 0.4.8,1,4,5,5874438,56.60169,5892,5629,blood,,2019-07-05,Italy,Italy: Lucca,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Diagnostic Microbiology and Virology Unit, Lucca",,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,1.39,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.45778,Klebsiella pneumoniae KP-26Pi,KP-26Pi,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15437767,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-23T00:00:00Z,,PRJNA643814,GCA_022370195.1,"CP072925,CP072930,CP072928,CP072926,CP072929,CP072927",,,Illumina MiSeq; Oxford Nanopore MinION,90x,Unicycler v. 0.4.8,1,5,6,5893567,56.609768,5927,5649,blood,,2019-05-12,Italy,Italy: Pisa,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Diagnostic Microbiology and Virology Unit, Pisa",,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,1.68,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.45779,Klebsiella pneumoniae KP-12Pi,KP-12Pi,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15437790,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-02-23T00:00:00Z,,PRJNA643814,GCA_022370035.1,"CP072917,CP072923,CP072924,CP072921,CP072918,CP072922,CP072920,CP072919",,,Illumina MiSeq; Oxford Nanopore MinION,95x,Unicycler v. 0.4.8,1,7,8,6010286,56.506737,6062,5767,blood,,2019-01-12,Italy,Italy: Pisa,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Diagnostic Microbiology and Virology Unit, Pisa",,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,1.68,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.45865,Klebsiella pneumoniae bat16,bat16,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26209580,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-03-07T00:00:00Z,,PRJNA809903,GCA_022492875.1,"CP092759,CP092760,CP092761,CP092762,CP092763,CP092764",,,Illumina iSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,5,6,5861552,56.96998,5996,5713,blood,,2020-02-06,Italy,Italy: Bologna,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,Klebsiella pneumoniae infection,,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,,,,,,,,,,,,,,,100,0.08,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.45866,Klebsiella pneumoniae bat17,bat17,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26209581,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-03-07T00:00:00Z,,PRJNA809903,GCA_022492855.1,"CP092753,CP092754,CP092755,CP092756,CP092757,CP092758",,,Illumina iSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,5,6,5846862,56.975674,5983,5699,rectal swab,,2020-03-10,Italy,Italy: Bologna,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,Klebsiella pneumoniae infection,,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,,,,,,,,,,,,,,,100,0.08,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.45868,Klebsiella pneumoniae bat15,bat15,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26209579,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-03-07T00:00:00Z,,PRJNA809903,GCA_022492895.1,"CP092765,CP092766,CP092767,CP092768,CP092769,CP092770",,,Illumina iSeq; Oxford Nanopore MinION,20x,Unicycler v. v0.4.8,1,5,6,5847041,56.974854,5894,5700,rectal swab,,2020-02-13,Italy,Italy: Bologna,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,Klebsiella pneumoniae infection,,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,,,,,,,,,,,,,,,100,0.08,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.45896,Klebsiella pneumoniae XH1508,XH1508,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26270981,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-03-09T00:00:00Z,,PRJNA810585,GCA_022533505.1,"CP092786,CP092787,CP092788,CP092789,CP092790,CP092791,CP092792",,,Illumina; Oxford Nanopore MinION,300x,Unicycler v. 0.48,1,6,7,5932890,56.86119,6075,5838,pus,,2019-05-10,China,China:Hangzhou,,,,multiple injuries,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Xiaoting Hua,,,,,,,multiple injuries,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.45897,Klebsiella pneumoniae F11,F11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26292662,573,,,,MLST.Klebsiella_pneumoniae.1,,,,2022-03-10T00:00:00Z,,PRJNA810945,GCA_022539425.1,"CP092901,CP092902,CP092903,CP092904,CP092905",,,Illumina NovaSeq; PacBio Sequel,154.0x,Canu v. 2.2,1,4,5,5763236,56.82035,5724,5312,sputum specimen,,2019-12-31,China,China:Taizhou,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Dongguo Wang,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.83,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.45898,Klebsiella pneumoniae XH1507,XH1507,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26270980,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-03-09T00:00:00Z,,PRJNA810585,GCA_022533525.1,"CP092793,CP092794,CP092795,CP092796,CP092797,CP092798,CP092799,CP092800",,,Illumina; Oxford Nanopore MinION,300x,Unicycler v. 0.48,1,7,8,5943955,56.858757,6090,5850,pus,,2019-05-10,China,China:Hangzhou,,,,multiple injuries,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Xiaoting Hua,,,,,,,multiple injuries,,,,,,,,,,,,,,100,0.12,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.47121,Klebsiella pneumoniae Bio73,Bio73,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26668026,573,,,,MLST.Klebsiella_pneumoniae.2096,,,,2022-03-27T00:00:00Z,,PRJNA816291,GCA_022699305.1,"CP093852,CP093853",,,Illumina NovaSeq,250.0x,PATRIC Auto strategy(combined assembly,1,1,2,6069456,56.25738,6189,5888,sputum of human,,2016-07-23,Turkey,Turkey: Kayseri,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Pinar Sagiroglu,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.47124,Klebsiella pneumoniae Bio4,Bio4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26668785,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-27T00:00:00Z,,PRJNA816299,GCA_022699405.1,CP093850,,,Illumina NovaSeq,250.0x,PATRIC Auto strategy(combined assembly,1,0,1,5496155,57.240707,5453,5310,blood culture,,2018-03-21,Turkey,Turkey: Kayseri,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Pinar Sagiroglu,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.47125,Klebsiella pneumoniae Bio13,Bio13,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26669095,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-27T00:00:00Z,,PRJNA816318,GCA_022699425.1,CP093851,,,Illumina NovaSeq,250.0x,PATRIC Auto strategy(combined assembly,1,0,1,5496864,57.241257,5460,5302,respiratory system,,2018-03-20,Turkey,Turkey: Kayseri,,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Pinar Sagiroglu,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.47126,Klebsiella pneumoniae SP968,SP968,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16178551,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2022-03-28T00:00:00Z,,PRJNA663420,GCA_022701055.1,"CP069203,CP069212,CP069207,CP069211,CP069204,CP069205,CP069206,CP069208,CP069209,CP069210",,,Illumina HiSeq; Oxford Nanopore MinION,68.2x,SPAdes v. August 2020; unicycler v.,1,9,10,5609903,56.965477,5594,5362,endotracheal aspirate,,2019,India,India,,,,respiratory infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,respiratory infection,,,,,,,,,,,,,,99.9,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.47127,Klebsiella pneumoniae SP4663,SP4663,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16177882,573,,,,,,,,2022-03-28T00:00:00Z,,PRJNA663727,GCA_022701075.1,"CP069365,CP069366,CP069367,CP069368,CP069369",,,Illumina HiSeq,170.3x,SPAdes v. August 2020,1,4,5,5819528,56.30687,5932,5432,endotracheal aspirate,,2019,India,India,,,,respiratory infection,,,Susceptible,Computational Prediction,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,respiratory infection,,,,,,,,,,,,,,99.7,2.5,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.47152,Klebsiella pneumoniae Bio3,Bio3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26655402,573,,,,MLST.Klebsiella_pneumoniae.2096,,,,2022-03-29T00:00:00Z,,PRJNA816050,GCA_022749215.1,"CP094227,CP094228",,,Illumina NovaSeq,250.0x,PATRIC Auto v. 3.6.12,1,1,2,6058685,56.257404,6170,5876,"erciyes university, faculty of medicine",,2019-07-30,Turkey,Turkey,,,,Urinary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Pinar Sagiroglu,,,,,,,Urinary infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.47154,Klebsiella pneumoniae MCL-2017-2-T5-MAC,MCL-2017-2-T5-MAC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108727,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759625.1,"CP086464,CP086465,CP086466",,,Illumina NovaSeq; Oxford Nanopore MiniION,462x,Unicycler v. 0.4.8,1,2,3,5703394,57.07179,5651,5460,missing,,2017,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.47155,Klebsiella pneumoniae MCL-2017-2-T5-ESBL,MCL-2017-2-T5-ESBL,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108728,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759645.1,"CP086461,CP086462,CP086463",,,Illumina NovaSeq; Oxford Nanopore MiniION,247x,Unicycler v. 0.4.8,1,2,3,5703095,57.071537,5651,5460,missing,,2017,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.47156,Klebsiella pneumoniae MCL-2017-2-T20-MAC,MCL-2017-2-T20-MAC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108729,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759665.1,"CP086458,CP086459,CP086460",,,Illumina NovaSeq; Oxford Nanopore MiniION,431x,Unicycler v. 0.4.8,1,2,3,5703389,57.07184,5649,5461,missing,,2017,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.47157,Klebsiella pneumoniae MCL-2017-2-T20-ESBL,MCL-2017-2-T20-ESBL,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108730,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759685.1,"CP086455,CP086456,CP086457",,,Illumina NovaSeq; Oxford Nanopore MiniION,420x,Unicycler v. 0.4.8,1,2,3,5703097,57.071533,5649,5460,missing,,2017,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.47158,Klebsiella pneumoniae MCL-2017-2-T0,MCL-2017-2-T0,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108726,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759705.1,"CP086467,CP086468,CP086469",,,Illumina NovaSeq; Oxford Nanopore MiniION,278x,Unicycler v. 0.4.8,1,2,3,5703400,57.0718,5656,5459,missing,,2017,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.47159,Klebsiella pneumoniae AE-2247421-T5-MAC,AE-2247421-T5-MAC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108732,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759925.1,"CP086439,CP086440,CP086441,CP086442,CP086443,CP086444,CP086445,CP086446",,,Illumina NovaSeq; Oxford Nanopore MiniION,452x,Unicycler v. 0.4.8,1,7,8,5938471,56.727196,6056,5789,stool,,2013,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.47160,Klebsiella pneumoniae AE-2247421-T5-ESBL,AE-2247421-T5-ESBL,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108733,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759945.1,"CP086431,CP086432,CP086433,CP086434,CP086435,CP086436,CP086437,CP086438",,,Illumina NovaSeq; Oxford Nanopore MiniION,269x,Unicycler v. 0.4.8,1,7,8,5927416,56.737423,6036,5776,stool,,2013,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.47161,Klebsiella pneumoniae AE-2247421-T20-MAC,AE-2247421-T20-MAC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108734,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759965.1,"CP086423,CP086424,CP086425,CP086426,CP086427,CP086428,CP086429,CP086430",,,Illumina NovaSeq; Oxford Nanopore MiniION,238x,Unicycler v. 0.4.8,1,7,8,5939313,56.728935,6054,5791,stool,,2013,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.47162,Klebsiella pneumoniae AE-2247421-T0,AE-2247421-T0,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108731,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022760005.1,"CP086447,CP086448,CP086449,CP086450,CP086451,CP086452,CP086453,CP086454",,,Illumina NovaSeq; Oxford Nanopore MiniION,223x,Unicycler v. 0.4.8,1,7,8,5960745,56.696,6081,5810,stool,,2013,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.47163,Klebsiella pneumoniae AE-2247421-T20-ESBL,AE-2247421-T20-ESBL,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22108735,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-03-30T00:00:00Z,,PRJNA769291,GCA_022759985.1,"CP086416,CP086417,CP086418,CP086419,CP086420,CP086421,CP086422",,,Illumina NovaSeq; Oxford Nanopore MiniION,299x,Unicycler v. 0.4.8,1,6,7,5862987,56.795486,5957,5694,stool,,2013,Switzerland,Switzerland,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.47269,Klebsiella pneumoniae KP16,KP16,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23012466,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-04-06T00:00:00Z,,PRJNA779111,GCA_022828555.1,"CP087146,CP087147,CP087148,CP087149,CP087150",,,Oxford Nanopore MinION; Illumina NovaSeq,100x,SPAdes v. 3.15.0,1,4,5,5903660,56.958515,6028,5787,sputum,,2021,China,China: zhejiang,,,,surgical site infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Zhang Rong,,,,,,,surgical site infection,,,,,,,,,,,,,,100,0,Surgical Site Infections,,Respiratory Tract,Surgical Site Infections- HP,573.47270,Klebsiella pneumoniae KP15,KP15,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23012467,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-04-06T00:00:00Z,,PRJNA779111,GCA_022828525.1,"CP087142,CP087143,CP087144,CP087145",,,Illumina NovaSeq; Oxford Nanopore MinION,100x,SPAdes v. 3.15.0,1,3,4,5906614,56.95009,6038,5790,secretion,,2021,China,China: zhejiang,,,,surgical site infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Zhang Rong,,,,,,,surgical site infection,,,,,,,,,,,,,,100,0.1,Surgical Site Infections,,Other,Surgical Site Infections- HP,573.47271,Klebsiella pneumoniae KP14,KP14,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23012465,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-04-06T00:00:00Z,,PRJNA779111,GCA_022828575.1,"CP087151,CP087152,CP087153,CP087154,CP087155",,,Oxford Nanopore MinION; Illumina NovaSeq,100x,SPAdes v. 3.15.0,1,4,5,5903661,56.958538,6032,5787,sputum,,2021,China,China: zhejiang,,,,surgical site infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Zhang Rong,,,,,,,surgical site infection,,,,,,,,,,,,,,100,0,Surgical Site Infections,,Respiratory Tract,Surgical Site Infections- HP,573.47327,Klebsiella pneumoniae AZS099,AZS099,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23040723,573,,,,MLST.Klebsiella_pneumoniae.20,,,,2022-04-18T00:00:00Z,,PRJNA692086,GCA_023025805.1,"CP086761,CP086763,CP086762",,,PacBio Sequel; Illumina NovaSeq,200.0x,Unicycler v. v0.4.8,1,2,3,5498475,57.236633,5427,5262,bloodstream specimen,,2018-08-21,China,China,,,,bloodstream infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,,collected_by:PUMCH,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.48017,Klebsiella pneumoniae KP5362,KP5362,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27606095,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-04-24T00:00:00Z,,PRJNA827194,GCA_023093995.1,"CP095762,CP095763,CP095764",,,Illumina HiSeq; PacBio,138.98x,HGAP v. 4; FALCON v. 0.3,1,2,3,5587292,57.073822,5596,5375,sputum,,2021-12-20,China,China:Zhuhai,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Haile Huang,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.48119,Klebsiella pneumoniae bo714,bo714,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27594434,573,,,,MLST.Klebsiella_pneumoniae.512,genotype:ST512,,,2022-04-24T00:00:00Z,,PRJNA827023,GCA_023184535.1,"CP095776,CP095779,CP095778,CP095777",,,Illumina iSeq; Oxford Nanopore MinION,20.0x,Unicycler v. 0.4.8,1,3,4,5876068,56.958973,5949,5745,bronchial aspirate,,2021-03-23,Italy,Italy: Bologna,,,,Klebsiella pneumoniae infection,,,Resistant,Computational Prediction,,,,,,,,,,collected_by:IRCCS Policlinico S. Orsola - Malpighi,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.48146,Klebsiella pneumoniae Bio19,Bio19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26678607,573,,,,MLST.Klebsiella_pneumoniae.530,,,,2022-05-07T00:00:00Z,,PRJNA816493,GCA_023272735.1,"CP096810,CP096811",,,Illumina NovaSeq 6000,300.0x,PATRIC Auto algorithm(combined assembly,1,1,2,5747989,56.7769,5799,5577,sputum,,2016-02-14,Iraq,"Iraq: Al-Yarmouk Teaching Hospital, Baghdad",,,,pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Mohammed Hasan Nabeel Almashat,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.48279,Klebsiella pneumoniae NTU107224,NTU107224,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28105843,573,,,,MLST.Klebsiella_pneumoniae.8,,,,2022-05-17T00:00:00Z,,PRJNA835626,GCA_023379965.1,"CP097248,CP097249,CP097250",,,Oxford Nanopore MinION,115.0x,Flye v. 2.9,1,2,3,5456678,56.897274,5489,5274,blood,,2018-08-30,Taiwan,Taiwan,,not collected,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:Po-Ren Hsueh,,,,,,,Bacteremia,,,,,,,,,,,,,,96.5,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.48282,Klebsiella pneumoniae BA30371,BA30371,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17214426,573,,,,MLST.Klebsiella_pneumoniae.985,,,,2022-05-23T00:00:00Z,,PRJNA663420,GCA_023518335.1,"CP067372,CP067373,CP067374",,,Illumina HiSeq; Oxford Nanopore MinION,75.9x,Unicycler v. August 2020,1,2,3,5540851,57.2052,5438,5243,blood,,2019,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.48283,Klebsiella pneumoniae B9122,B9122,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17214286,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-05-23T00:00:00Z,,PRJNA663420,GCA_023518315.1,"CP067370,CP067371",,,Oxford Nanopore MinION; Illumina HiSeq,97.9x,Unicycler v. August 2020,1,1,2,5576801,57.21949,5466,5278,blood,,2015,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.49108,Klebsiella pneumoniae TH12846,TH12846,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28907143,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-06-14T00:00:00Z,,PRJNA846980,GCA_023715965.1,CP098769,,,PacBio Sequel,120X,HGAP v. 1.2,1,0,1,5366061,57.482555,5343,5153,blood,,,China,China: Tsinghua University,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,"collected_by:PLA 302 Hospital (Beijing, China)",,,,,,,Sepsis,,,,,,,,,,,,,,100,1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.49163,Klebsiella pneumoniae CNR146C9,CNR146C9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA11998055,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-05-01T00:00:00Z,,PRJEB49056,GCA_924899195.1,"OV408202,OV408203,OV408204,OV408205",,,,,,1,3,4,5784236,57.070614,5635,5334,rectal swab,,2017-08-06,France,France,,,,,,host_health_state:diseased,Susceptible;Resistant,Computational Prediction,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.49402,Klebsiella pneumoniae EFN 299,EFN 299,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26139404,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-06-27T00:00:00Z,,PRJNA473419,GCA_023920325.1,"CP092589,CP092590,CP092592,CP092593,CP092594,CP092595,CP092596,CP092591",,,Illumina MiniSeq; Oxford Nanopore,42.7x,Unicycler hybrid assembly v. 0.4.8,1,7,8,5729441,56.864204,5796,5579,sputum culture,,2018,Ghana,Ghana,,,,Respiratory disease,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:ENRH_Hospital staff,,,,,,,Respiratory disease,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.49406,Klebsiella pneumoniae PM27,PM27,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19589280,573,,,,,,,,2022-06-30T00:00:00Z,,PRJNA735573,GCA_024081805.1,"CP076453,CP076455,CP076454",,,Illumina NextSeq; Nanopore MinION,100.0x,Unicycler v. v0.4.8,1,2,3,5670661,57.07996,5653,5365,blood,,2015,Hong Kong,Hong Kong,,,,sepsis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:CMC,,,,,,,sepsis,,,,,,,,,,,,,,99.9,0.2,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.49553,Klebsiella pneumoniae XHKP6,XHKP6,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17173497,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-07-20T00:00:00Z,,PRJNA688319,GCA_024346655.1,"CP066887,CP066888,CP066889,CP066890",,,PacBio RSII,294.0x,HGAP v. 2.3,1,3,4,5645164,57.306095,5590,,venipuncture tube,,2010-09-13,China,China: Shanghai,,,,"Severe pneumonia, acute respiratory failure",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Xinhua Hospital,,,,,,,"Severe pneumonia, acute respiratory failure",,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.49554,Klebsiella pneumoniae XHKP75,XHKP75,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17173614,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-07-20T00:00:00Z,,PRJNA688329,GCA_024346735.1,"CP066895,CP066896,CP066897,CP066898,CP066899",,,PacBio RSII,383.0x,HGAP v. 2.3,1,4,5,5868873,57.090775,5852,,sputum,,2013-07-29,China,China: Shanghai,,,,"Septic shock, multiple organ failure",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Xinhua Hospital,,,,,,,"Septic shock, multiple organ failure",,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Respiratory Tract,Bloodstream Infections-Sepsis HP,573.49556,Klebsiella pneumoniae XHKP309,XHKP309,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17173631,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-07-20T00:00:00Z,,PRJNA688350,GCA_024346775.1,"CP066900,CP066901,CP066902,CP066903",,,PacBio RSII,285.0x,HGAP v. 2.3,1,3,4,5633251,57.282715,5579,,urine,,2015-12-14,China,China: Shanghai,,,,"Urinary tract infection, Left hydronephrosis after surgery",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Xinhua Hospital,,,,,,,"Urinary tract infection, Left hydronephrosis after surgery",,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.49558,Klebsiella pneumoniae XHKPN083,XHKPN083,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17173860,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-07-20T00:00:00Z,,PRJNA688366,GCA_024346855.1,"CP066910,CP066911,CP066912,CP066913,CP066914",,,PacBio Sequel,440.0x,HGAP v. 6,1,4,5,5804025,56.827614,5779,,tracheal intubation,,2017-10-30,China,China: Shanghai,,,,"Cerebral hemorrhage, pulmonary infection",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Xinhua Hospital,,,,,,,"Cerebral hemorrhage, pulmonary infection",,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.49891,Klebsiella pneumoniae K-28,K-28,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24790942,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-08-01T00:00:00Z,,PRJNA795853,GCA_024498895.1,"CP090834,CP090835",,,Illumina PE150; Nanopore,422.7x,Unicycler v. 0.4.9,1,1,2,5437674,57.41223,5404,5247,blood,,2018,China,China: Beijing,,,,Blood stream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Wentao NI,,,,,,,Blood stream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.49892,Klebsiella pneumoniae KPK3,KPK3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24394412,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-08-01T00:00:00Z,,PRJNA792222,GCA_024498655.1,"CP090343,CP090344,CP090345,CP090346",,,Oxford Nanopore,209.0x,Canu v.1.7 v. MAR-2021,1,3,4,5831253,57.045013,5933,5699,clinical isolate,,2020-12-04,China,China,,,,brain infarction,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine,,,,,,,brain infarction,,,,,,,,,,,,,,100,0,Neurological Diseases,Other Brain Infections,Other,Neurological Diseases-Other Brain Infections HP,573.50061,Klebsiella pneumoniae B3,B3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09519601,573,,,,MLST.Klebsiella_pneumoniae.274,,,,2022-08-08T00:00:00Z,,PRJNA478567,GCA_024585205.1,"CP030725,CP030728,CP030726,CP030727,CP030729,CP030730,CP030731,CP030732",,,Illumina MiSeq; Pacbio,129x,Unicycler v. 0.4.1,1,7,8,5913147,56.60686,6023,5851,feces,,2013-10-17,Sweden,Sweden: Gothenburg,,,,Pneumonia; Cerebral Hemorrhage,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,Pneumonia; Cerebral Hemorrhage,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.50062,Klebsiella pneumoniae B4,B4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09519602,573,,,,MLST.Klebsiella_pneumoniae.274,,,,2022-08-08T00:00:00Z,,PRJNA478567,GCA_024585185.1,"CP030717,CP030718,CP030719,CP030720,CP030721,CP030722,CP030723,CP030724",,,Illumina MiSeq; Pacbio,140x,Unicycler v. 0.4.1,1,7,8,5918070,56.59698,6041,5857,feces,,2014-01-07,Sweden,Sweden: Gothenburg,,,,Pneumonia; Cerebral Hemorrhage,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,Pneumonia; Cerebral Hemorrhage,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.50063,Klebsiella pneumoniae B2,B2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09519600,573,,,,MLST.Klebsiella_pneumoniae.274,,,,2022-08-08T00:00:00Z,,PRJNA478567,GCA_024585225.1,"CP030733,CP030734,CP030735,CP030736,CP030737,CP030738,CP030739,CP030740",,,Illumina MiSeq; Pacbio,141x,Unicycler v. 0.4.1,1,7,8,5918321,56.6032,6045,5860,feces,,2013-04-17,Sweden,Sweden: Gothenburg,,,,Pneumonia; Cerebral Hemorrhage,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,Pneumonia; Cerebral Hemorrhage,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.50064,Klebsiella pneumoniae B1,B1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09519599,573,,,,MLST.Klebsiella_pneumoniae.274,,,,2022-08-08T00:00:00Z,,PRJNA478567,GCA_024585245.1,"CP030741,CP030742,CP030743,CP030744,CP030745,CP030746,CP030747,CP030748",,,Illumina MiSeq; Pacbio,139x,Unicycler v. 0.4.1,1,7,8,5923538,56.604465,6044,5864,feces,,2013-01-23,Sweden,Sweden: Gothenburg,,,,Pneumonia; Cerebral Hemorrhage,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,Pneumonia; Cerebral Hemorrhage,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.50096,Klebsiella pneumoniae SHX180,SHX180,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27028875,573,,,,,,,,2022-08-12T00:00:00Z,,PRJNA692086,GCA_024637895.1,"CP094512,CP094513,CP094514",,,PacBio Sequel; Illumina HiSeq,200.0x,Unicycler v. v0.4.8,1,2,3,5313581,57.53,5170,5025,blood,,2018,China,China,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:HX,,,,,,,Bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.50111,Klebsiella pneumoniae KPH1,KPH1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30176384,573,,,,MLST.Klebsiella_pneumoniae.16,,,,2022-08-15T00:00:00Z,,PRJNA866984,GCA_024666265.1,"CP102546,CP102547,CP102548,CP102549,CP102550,CP102551",,,Illumina NovaSeq; Oxford Nanopore,1.0x,Unicycler v. v0.4.8,1,5,6,5641225,57.13227,5676,5466,microbial,,2020,Thailand,Thailand: Bangkok,,,,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Faculty of Medicine, Chulalongkorn University",,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.50115,Klebsiella pneumoniae KPH3,KPH3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30176386,573,,,,MLST.Klebsiella_pneumoniae.340,,,,2022-08-15T00:00:00Z,,PRJNA866985,GCA_024666505.1,"CP102552,CP102553,CP102554,CP102555,CP102556,CP102557,CP102558,CP102559",,,Illumina NovaSeq; Oxford Nanopore,1.0x,Unicycler v. v0.4.8,1,7,8,5499989,57.15333,5507,5343,microbial,,2020,Thailand,Thailand: Bangkok,,,,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Faculty of Medicine, Chulalongkorn University",,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.50174,Klebsiella pneumoniae KP4863,KP4863,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30309203,573,,,,MLST.Klebsiella_pneumoniae.1027,,,,2022-08-22T00:00:00Z,,PRJNA869512,GCA_024731085.1,"CP102841,CP102842,CP102843,CP102844",,,Illumina HiSeq; PacBio,26.85x,FALCON v. 0.3; HGAP v. 4,1,3,4,5497324,57.318214,5424,5227,vaginal secretion,,2022-04,China,China: Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- HP,573.50175,Klebsiella pneumoniae KP0079,KP0079,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30309189,573,,,,MLST.Klebsiella_pneumoniae.751,,,,2022-08-22T00:00:00Z,,PRJNA869509,GCA_024730945.1,"CP102836,CP102837,CP102838,CP102839,CP102840",,,Illumina HiSeq; PacBio,45.53x,FALCON v. 0.3; HGAP v. 4,1,4,5,5842143,57.047356,5939,5705,bronchoalveolar lavage fluid,,2022-05,China,China: Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.50176,Klebsiella pneumoniae KP4962,KP4962,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30309188,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2022-08-22T00:00:00Z,,PRJNA869507,GCA_024730825.1,"CP102833,CP102834,CP102835",,,Illumina HiSeq; PacBio,76.74x,FALCON v. 0.3; HGAP v. 4,1,2,3,5566977,57.208645,5544,5352,sputum,,2022-05,China,China: Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.50183,Klebsiella pneumoniae SCAID PND1-2022 (426) strain SCAID PND1-2022 (426),SCAID PND1-2022 (426),Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30333623,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-08-24T00:00:00Z,,PRJNA754843,GCA_024734755.1,"CP102940,CP102941",,,PacBio Sequel,142x,Velvet v. 1.2.10,1,1,2,5548951,57.166897,5533,5303,purulent-necrotic detritus,,2022-04,Kazakhstan,Kazakhstan: Almaty,,,,cholecystitis,,,Resistant;Susceptible;Intermediate,Computational Method,,,,,,,,,,"collected_by:JSC Scientific Center for anti-infectious Drugs, Laboratory of Microbiology",,,,,,,cholecystitis,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Other,Urinary Tract Diseases-Lower UTI HP,573.50433,Klebsiella pneumoniae strain hvKP12,hvKP12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30403289,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-08-30T00:00:00Z,,PRJNA871048,GCA_024762135.1,"CP103315,CP103317,CP103318,CP103321,CP103322,CP103323,CP103319,CP103320,CP103316",,The First Affiliated Hospital of Chongqing Medical University,Illumina HiSeq; Oxford Nanopore,90.0x,SPAdes v. 3.5.0,1,8,9,6068182,56.72577,6237,5971,blood,,2021-03-10,China,China: Chongqing,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"the first report of tigecycline-resistant ST11-KL64 CR-hvKP bacteria co-producing blaKPC and blaNDM, causing fatal blood infection.",sample_type:Blood,,,,,,,,,,,,,,,,,,,,,100,0.25,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.50518,Klebsiella pneumoniae strain 1021,1021,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29397002,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-09-09T00:00:00Z,,PRJNA853564,GCA_025118435.1,"CP100308,CP100311,CP100310,CP100309",,Sapienza University of Rome,Illumina MiSeq; Oxford Nanopore MinION,62x,Unicycler v. 0.4.8.0,1,3,4,5497877,57.33524,5439,5255,blood,,2021-09-04,Italy,Italy: Rome,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Evolution of Klebsiella pneumoniae ST37 Genome sequencing and assembly,collected_by:Policlinico Umberto I Hospital,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.33,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.50519,Klebsiella pneumoniae strain 1020,1020,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29397001,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-09-09T00:00:00Z,,PRJNA853564,GCA_025118455.1,"CP100312,CP100315,CP100314,CP100313",,Sapienza University of Rome,Illumina MiSeq; Oxford Nanopore MinION,72x,Unicycler v. 0.4.8.0,1,3,4,5497429,57.34013,5434,5207,blood,,2021-08-23,Italy,Italy: Rome,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Evolution of Klebsiella pneumoniae ST37 Genome sequencing and assembly,collected_by:Policlinico Umberto I Hospital,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.33,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.50521,Klebsiella pneumoniae strain 10MC160002271,10MC160002271,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15813776,573,,,,MLST.Klebsiella_pneumoniae.383,,,,2022-09-12T00:00:00Z,,PRJNA656934,GCA_025144525.1,"CP091813,CP091814,CP091815,CP091816,CP091817,CP091818",,Sidra Medicine,Illumina NextSeq; Oxford Nanopore,100.0x,Unicycler v. v0.4.7,1,5,6,5806556,56.532307,5928,5635,pus,,2016-04-28,Qatar,Qatar:Doha,,,,not collected,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The project aims to use the whole genome sequencing approach to characterize antimicrobial resistance genes from ESBL and carbapenemase Producing Enterobacteriaceae in HMC, Qatar Raw sequence reads",collected_by:Hamad Medical Corporation,,,,,,,not collected,,,,,,,,,,,,,,100,0.84,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.50570,Klebsiella pneumoniae strain CHN23026,CHN23026,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30636576,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-09-17T00:00:00Z,,PRJNA832474,GCA_025244645.1,"CP104196,CP104197,CP104198,CP104199,CP104200,CP104201",,"Sir Run Run Shaw Hospital, Zhejiang University School of Medicine",Illumina; Oxford Nanopore,110.0x,Unicycler v. 0.4.8,1,5,6,5555527,57.176323,5573,5404,urine,,2018-10-01,China,China: Taiyuan,,,,infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Molecular epidemiological investigation of Klebsiella pneumoniae in China,collected_by:Huhuangdu,,,,,,,infection,,,,,,,,,,,,,,100,0.32,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.50571,Klebsiella pneumoniae strain KP8132,KP8132,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30711370,573,,,,MLST.Klebsiella_pneumoniae.751,,,,2022-09-19T00:00:00Z,,PRJNA877475,GCA_025252425.1,"CP104312,CP104313,CP104314,CP104315,CP104316",,Jinan University,Illumina HiSeq; PacBio,813.95x,HGAP v. 4; FALCON v. 0.3,1,4,5,5831033,57.05387,5946,5698,midpiece urine,,2022-04,China,China:Zhuhai,,,,severe pulmonary infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae strain KP8132 chromosome, complete genome",collected_by:Qinghuan Zhang,,,,,,,severe pulmonary infection,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.50572,Klebsiella pneumoniae strain SZS128,SZS128,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29161340,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-09-19T00:00:00Z,,PRJNA692086,GCA_025258665.1,"CP099522,CP099523,CP099524,CP099525",,Peking Union Medical College Hospital,PacBio Sequel,200.0x,Unicycler v. v0.4.8,1,3,4,5734103,56.859512,5787,5566,blood,,2018,,China,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome sequencing of BSI-Kpns,collected_by:ZS,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.11,0.48,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.50573,Klebsiella pneumoniae strain 2021CK-01815,2021CK-01815,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24523856,573,,,,MLST.Klebsiella_pneumoniae.133,,,,2022-09-19T00:00:00Z,,PRJNA812595,GCA_025259665.1,"CP104373,CP104374,CP104375,CP104376",,Utah Public Health Laboratory Infectious Disease submission group,Illumina MiSeq; Oxford Nanopore GridION,243.0x,Unicycler v. 0.5.0,1,3,4,5556516,57.301483,5448,5255,wound/abscess,,2021-12-07,,USA,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Bacteria with public health implications due to virulence or antimicrobial resistance. Many of these bacteria were associated with outbreaks or have abnormal characteristics. Unfortunately, we don't have time to write up why each of these bacterial isolates were sequenced, but we have created a bioproject where we can submit reads and assemblies. Please contact the authors for more information for isolates that require additional information.",,,,,,,,,,,,,,,,,,,,,,100,0.96,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.50832,Klebsiella pneumoniae KP5076,KP5076,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30959810,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-09-29T00:00:00Z,,PRJNA883161,GCA_025490515.1,"CP106654,CP106655,CP106656,CP106657",,,Illumina HiSeq; PacBio,589.61x,HGAP v. 4; FALCON v. 0.3; Canu v. 0.7,1,3,4,5525453,57.096043,5543,5345,secretion,,2021,China,China: Zhuhai,,,,infection,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.50836,Klebsiella pneumoniae 4680,4680,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174066,573,,,,MLST.Klebsiella_pneumoniae.29,genotype:ST29,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917255.1,"CP103567,CP103568,CP103569",,,Oxford Nanopore GridION,168x,Flye v. 2.8.3-b1695,1,2,3,5477888,57.276985,5364,5193,blood,,2019-05-04,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50837,Klebsiella pneumoniae 4014,4014,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174049,573,,,,MLST.Klebsiella_pneumoniae.2004,genotype:ST2004,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917415.1,"CP103579,CP103580,CP103581",,,Oxford Nanopore GridION,163x,Flye v. 2.8.3-b1695,1,2,3,5446111,57.331276,5362,5215,blood,,2019-03-23,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50838,Klebsiella pneumoniae 3571,3571,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174036,573,,,,,genotype:ST3293,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917495.1,"CP103614,CP103615,CP103616,CP103617",,,Oxford Nanopore GridION,168x,Flye v. 2.8.3-b1695,1,3,4,5534853,57.295235,5465,5285,blood,,2018-10-10,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50839,Klebsiella pneumoniae 1498,1498,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173994,573,,,,MLST.Klebsiella_pneumoniae.1373,genotype:ST1373,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917435.1,"CP103582,CP103583,CP103584,CP103585",,,Oxford Nanopore GridION,230x,Flye v. 2.8.3-b1695,1,3,4,5618800,57.047714,5598,5400,blood,,2019-03-09,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50840,Klebsiella pneumoniae 4737,4737,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174070,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917515.1,"CP103586,CP103587,CP103588",,,Oxford Nanopore GridION,105x,Flye v. 2.8.3-b1695,1,2,3,5676418,57.0891,5638,5460,blood,,2019-01-20,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50841,Klebsiella pneumoniae 3221,3221,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174025,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917555.1,"CP103635,CP103636,CP103637,CP103638",,,Oxford Nanopore GridION,127x,Flye v. 2.8.3-b1695,1,3,4,5634542,57.151424,5571,5392,blood,,2018-08-01,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50842,Klebsiella pneumoniae 4383,4383,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174058,573,,,,MLST.Klebsiella_pneumoniae.15,genotype:ST15,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917595.1,"CP103618,CP103619,CP103620",,,Oxford Nanopore GridION,153x,Flye v. 2.8.3-b1695,1,2,3,5640101,57.10614,5535,5361,blood,,2018-09-16,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50843,Klebsiella pneumoniae 5589,5589,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174104,573,,,,MLST.Klebsiella_pneumoniae.45,genotype:ST45,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917755.1,"CP103499,CP103500,CP103501,CP103502",,,Oxford Nanopore GridION,230x,Flye v. 2.8.3-b1695,1,3,4,5635610,57.194378,5639,5424,blood,,2019-12-03,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50844,Klebsiella pneumoniae 5547,5547,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174102,573,,,,MLST.Klebsiella_pneumoniae.14,genotype:ST14,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917835.1,"CP103503,CP103504,CP103505,CP103506,CP103507",,,Oxford Nanopore GridION,251x,Flye v. 2.8.3-b1695,1,4,5,5687024,56.804684,5697,5467,blood,,2019-11-24,USA,USA: Houston,,,,Bacteremia,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50845,Klebsiella pneumoniae 4386,4386,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174060,573,,,,MLST.Klebsiella_pneumoniae.29,genotype:ST29,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917855.1,"CP103605,CP103606,CP103607,CP103608",,,Oxford Nanopore GridION,215x,Flye v. 2.8.3-b1695,1,3,4,5483928,57.27765,5372,5207,blood,,2018-12-04,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50846,Klebsiella pneumoniae 5165,5165,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174085,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917875.1,"CP103560,CP103561",,,Oxford Nanopore GridION,145x,Flye v. 2.8.3-b1695,1,1,2,5555022,57.21288,5456,5274,blood,,2019-05-11,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50847,Klebsiella pneumoniae 5531,5531,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174100,573,,,,MLST.Klebsiella_pneumoniae.23,genotype:ST23,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917915.1,"CP103512,CP103513,CP103514",,,Oxford Nanopore GridION,111x,Flye v. 2.8.3-b1695,1,2,3,5881006,57.013172,5846,5623,blood,,2019-11-07,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50848,Klebsiella pneumoniae ST307,ST307,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173997,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917935.1,"CP103699,CP103700,CP103701,CP103702,CP103703",,,Oxford Nanopore GridION,101x,Flye v. 2.8.3-b1695,1,4,5,5622678,57.203293,5549,5380,blood,,2017-03-17,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50849,Klebsiella pneumoniae 3987,3987,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174045,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918055.1,"CP103548,CP103549",,,Oxford Nanopore GridION,43x,Flye v. 2.8.3-b1695,1,1,2,5571490,57.19653,5484,5313,same blood draw as mb8764,,2019-07-25,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50850,Klebsiella pneumoniae 2791,2791,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174007,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918075.1,"CP103550,CP103551,CP103552,CP103553",,,Oxford Nanopore GridION,262x,Flye v. 2.8.3-b1695,1,3,4,5570189,57.26057,5525,5334,blood,,2019-08-03,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50851,Klebsiella pneumoniae 2946,2946,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174011,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918095.1,"CP103676,CP103677,CP103678",,,Oxford Nanopore GridION,153x,Flye v. 2.8.3-b1695,1,2,3,5528504,57.245415,5407,5246,blood,,2017-12-04,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.9,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50852,Klebsiella pneumoniae 433,433,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173985,573,,,,MLST.Klebsiella_pneumoniae.870,genotype:ST870,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918175.1,"CP103621,CP103622",,,Oxford Nanopore GridION,176x,Flye v. 2.8.3-b1695,1,1,2,5462416,57.294502,5393,5206,blood,,2018-09-26,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50853,Klebsiella pneumoniae 1159,1159,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173992,573,,,,MLST.Klebsiella_pneumoniae.307,genotype:ST307,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918315.1,"CP103654,CP103655,CP103656",,,Oxford Nanopore GridION,133x,Flye v. 2.8.3-b1695,1,2,3,5438561,57.35006,5348,5180,blood,,2018-06-12,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50854,Klebsiella pneumoniae ST307,ST307,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173993,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918455.1,"CP103687,CP103688,CP103689",,,Oxford Nanopore GridION,134x,Flye v. 2.8.3-b1695,1,2,3,5620450,57.15409,5559,5376,blood,,2017-07-06,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50855,Klebsiella pneumoniae ST15,ST15,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174030,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918435.1,"CP103714,CP103715,CP103716,CP103717",,,Oxford Nanopore GridION,159x,Flye v. 2.8.3-b1695,1,3,4,5374117,57.241924,5246,5081,blood,,2017-01-29,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50856,Klebsiella pneumoniae ST3576,ST3576,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174003,573,,,,MLST.Klebsiella_pneumoniae.628,,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918475.1,"CP103697,CP103698",,,Oxford Nanopore GridION,159x,Flye v. 2.8.3-b1695,1,1,2,5686240,57.19609,5642,5422,blood,,2017-05-22,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.4,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50857,Klebsiella pneumoniae 2289,2289,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174000,573,,,,MLST.Klebsiella_pneumoniae.17,genotype:ST17,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918835.1,"CP103727,CP103728",,,Oxford Nanopore GridION,57x,Flye v. 2.8.3-b1695,1,1,2,5315023,57.485847,5254,5098,blood,,2016-12-18,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50858,Klebsiella pneumoniae 197,197,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173983,573,,,,MLST.Klebsiella_pneumoniae.280,genotype:ST280,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918855.1,"CP103729,CP103730",,,Oxford Nanopore GridION,36x,Flye v. 2.8.3-b1695,1,1,2,5572187,57.22288,5533,5371,blood,,2016-12-03,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50859,Klebsiella pneumoniae 913,913,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173989,573,,,,MLST.Klebsiella_pneumoniae.15,genotype:ST15,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918875.1,"CP103731,CP103732,CP103733,CP103734,CP103735,CP103736,CP103737,CP103738",,,Oxford Nanopore GridION,347x,Flye v. 2.8.3-b1695,1,7,8,5667351,57.05355,5601,5401,blood,,2016-11-25,USA,USA: Houston,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.50951,Klebsiella pneumoniae 1021,1021,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29397002,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-09-09T00:00:00Z,,PRJNA853564,GCA_025118435.1,"CP100308,CP100311,CP100310,CP100309",,,Illumina MiSeq; Oxford Nanopore MinION,62x,Unicycler v. 0.4.8.0,1,3,4,5497877,57.33524,5439,5255,blood,,2021-09-04,Italy,Italy: Rome,,,,Sepsis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Policlinico Umberto I Hospital,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.50953,Klebsiella pneumoniae 1020,1020,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29397001,573,,,,MLST.Klebsiella_pneumoniae.37,,,,2022-09-09T00:00:00Z,,PRJNA853564,GCA_025118455.1,"CP100312,CP100315,CP100314,CP100313",,,Illumina MiSeq; Oxford Nanopore MinION,72x,Unicycler v. 0.4.8.0,1,3,4,5497429,57.34013,5434,5207,blood,,2021-08-23,Italy,Italy: Rome,,,,Sepsis,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Policlinico Umberto I Hospital,,,,,,,Sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.50963,Klebsiella pneumoniae 10MC160002271,10MC160002271,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15813776,573,,,,MLST.Klebsiella_pneumoniae.383,,,,2022-09-12T00:00:00Z,,PRJNA656934,GCA_025144525.1,"CP091813,CP091814,CP091815,CP091816,CP091817,CP091818",,,Illumina NextSeq; Oxford Nanopore,100.0x,Unicycler v. v0.4.7,1,5,6,5806556,56.532307,5928,5635,pus,,2016-04-28,Qatar,Qatar:Doha,,,,not collected,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hamad Medical Corporation,,,,,,,not collected,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.50964,Klebsiella pneumoniae KP0937,KP0937,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30996806,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-10-11T00:00:00Z,,PRJNA883808,GCA_025642295.1,"CP106760,CP106761,CP106762,CP106763,CP106764",,,Illumina HiSeq; PacBio,64.23x,Hifiasm v. 0.13-r308; Canu v. 0.7; pilon,1,4,5,5896626,57.002514,6026,5797,sputum,,2022-05,China,China: Zhuhai,,,,Pulmonary infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:zhuhai hospital,,,,,,,Pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.50965,Klebsiella pneumoniae KP1161,KP1161,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30999259,573,,,,MLST.Klebsiella_pneumoniae.592,,,,2022-10-11T00:00:00Z,,PRJNA883928,GCA_025642315.1,"CP106786,CP106787,CP106788",,,Illumina HiSeq; PacBio,55.83x,Canu v. 0.7,1,2,3,5429663,57.245304,5368,5205,sputum,,2022,China,China: Zhuhai,,,,pulmonary infections,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,pulmonary infections,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.51039,Klebsiella pneumoniae CHN23026,CHN23026,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30636576,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-09-17T00:00:00Z,,PRJNA832474,GCA_025244645.1,"CP104196,CP104197,CP104198,CP104199,CP104200,CP104201",,,Illumina; Oxford Nanopore,110.0x,Unicycler v. 0.4.8,1,5,6,5555527,57.176323,5573,5404,urine,,2018-10-01,China,China: Taiyuan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Huhuangdu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.51040,Klebsiella pneumoniae KP8132,KP8132,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30711370,573,,,,MLST.Klebsiella_pneumoniae.751,,,,2022-09-19T00:00:00Z,,PRJNA877475,GCA_025252425.1,"CP104312,CP104313,CP104314,CP104315,CP104316",,,Illumina HiSeq; PacBio,813.95x,HGAP v. 4; FALCON v. 0.3,1,4,5,5831033,57.05387,5946,5698,midpiece urine,,2022-04,China,China:Zhuhai,,,,severe pulmonary infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Qinghuan Zhang,,,,,,,severe pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Urinary Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.51041,Klebsiella pneumoniae SZS128,SZS128,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29161340,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-09-19T00:00:00Z,,PRJNA692086,GCA_025258665.1,"CP099522,CP099523,CP099524,CP099525",,,PacBio Sequel,200.0x,Unicycler v. v0.4.8,1,3,4,5734103,56.859512,5787,5566,blood,,2018,China,China,,,,Bloodstream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:ZS,,,,,,,Bloodstream infection,,,,,,,,,,,,,,99.7,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.51850,Klebsiella pneumoniae HUM7199,HUM7199,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26232717,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-10-21T00:00:00Z,,PRJNA810075,GCA_025782805.1,"CP093314,CP093315,CP093316",,,Oxford Nanopore MinION; Illumina MiSeq,760X,Trycycler v. 0.4.1; Flye v. 2.8.1; Raven,1,2,3,5431736,57.028324,5404,5180,faecal sample,,2012,Botswana,Botswana: Kasane,,,,diarrhea,,,Resistant;Susceptible;Not defined;Intermediate,Computational Method,,,,,,,,,,"collected_by:Center for African Resources: Animals, Communities and Land Use (CARACAL)",,,,,,,diarrhea,,,,,,,,,,,,,,99.7,0.4,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,573.51885,Klebsiella pneumoniae WX17388,WX17388,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29490475,573,,,,MLST.Klebsiella_pneumoniae.660,genotype:K16,,,2022-10-31T00:00:00Z,,PRJNA855442,GCA_025917765.1,"CP100601,CP100602",,,Oxford Nanopore PromethION,100.0x,SOAPdenovo v. 20220601,1,1,2,5487529,57.26078,5381,5198,pus,,2017-12-21,China,China:jiangsu,,,64,Neck Abscess,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:hu renjing,,,,,,,Neck Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses NHP,573.51886,Klebsiella pneumoniae KpST17-2177,KpST17-2177,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8550523,573,,,,MLST.Klebsiella_pneumoniae.17,,,,2022-10-31T00:00:00Z,,PRJNA730998,GCA_025920785.1,"CP075591,CP075592,CP075593,CP075594",,,Illumina MiSeq; Oxford Nanopore,50.0x,SPAdes v. 3.13.0,1,3,4,5647759,57.14842,5653,5425,breast milk,,2008-11-26,Norway,Norway,,,,,,host_health_state:healthy,Susceptible;Resistant,Computational Method,,,,,,,,,,,,,,,,,,healthy,,,,,,,,,,,,,100,0.1,,,Other,- HP,573.51890,Klebsiella pneumoniae KP1650,KP1650,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31373057,573,,,,MLST.Klebsiella_pneumoniae.751,,,,2022-11-01T00:00:00Z,,PRJNA892243,GCA_025946845.1,"CP109948,CP109949,CP109950,CP109951,CP109952",,,Illumina HiSeq; PacBio,30.65x,HGAP v. 4; FALCON v. 0.3; Canu v. 0.7,1,4,5,5880971,56.972904,5988,5747,bronchoalveolar lavage fluid,,2022-04,China,China:Zhuhai,,,,severe pulmonary infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Jie Wei,,,,,,,severe pulmonary infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,573.51891,Klebsiella pneumoniae KP424,KP424,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31413558,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2022-11-01T00:00:00Z,,PRJNA893192,GCA_025946965.1,"CP109983,CP109986,CP109990,CP109984,CP109985,CP109987,CP109988,CP109989,CP109991",,,Oxford Nanopore,30.0x,SPAdes v. 1.3,1,8,9,6044973,56.38108,6096,5820,stool,,2021-10-28,China,China:Hangzhou,,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Fang He,,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Gastrointestinal,Respiratory Diseases-Pneumonia HP,573.51899,Klebsiella pneumoniae KP7626,KP7626,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31523650,573,,,,MLST.Klebsiella_pneumoniae.101,,,,2022-11-07T00:00:00Z,,PRJNA895758,GCA_026016005.1,"CP110369,CP110370",,,Illumina NovaSeq; PacBio,150.44x,Hifiasm v. 0.13-r308; Canu v. version 0.7,1,1,2,5596667,57.084976,5584,5376,puncture fluid,,2022-05,China,China: Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.52173,Klebsiella pneumoniae AUSMDU00003562,AUSMDU00003562,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07503096,573,,,,MLST.Klebsiella_pneumoniae.258,genotype:ST258,,,2017-12-06T00:00:00Z,,PRJNA397262,,"CP025005,CP025006,CP025007",,,PacBio,193.0x,Canu v. v1.5,1,2,3,5633657,57.04128,5816,5674,sacral swab,,2014-01-13,Australia,Australia: Victoria,,,,Infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Microbiological Diagnostic Unit Public Health Laboratory,,,,,,,Infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.52175,Klebsiella pneumoniae SGH10,SGH10,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06112188,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2017-12-07T00:00:00Z,,PRJNA391004,,"CP025080,CP025081",,,Illumina MiniSeq; Illumina MiSeq;,159.3x,SPAdes v. v3.11.1; Unicycler v.,1,1,2,5716697,57.13362,5556,5381,liver abscess,,,Singapore,Singapore,,,,liver abscess,,,Susceptible,Computational Method,,,,,,,,,,collected_by:National University of Singapore,,,,,,,liver abscess,,,,,,,,,,,,,,100,0.1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52176,Klebsiella pneumoniae NU-CRE047,NU-CRE047,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08111037,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2017-12-06T00:00:00Z,,PRJNA395086,,"CP025037,CP025038,CP025039,CP025040,CP025041,CP025042",,,PacBio; Illumina HiSeq,90.0x,Celera Assembler v. 8.1,1,5,6,6067344,56.856823,6331,6141,urine,,Sep-2011,USA,"USA: Chicago, IL",,,,Cystitis,,,Resistant;Susceptible,Computational Method,,,,,,,,,,,,,,,,,Cystitis,,,,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,573.52227,Klebsiella pneumoniae SCKP020049,SCKP020049,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07609113,573,,,,MLST.Klebsiella_pneumoniae.1,,,,2018-10-17T00:00:00Z,,PRJNA353728,,NWEH00000000,,,Illumina HiSeq; MinION,200.0x,Unicycler v. 0.4.4,1,3,4,5498451,57.24687,5549,5401,pus,,24-Oct-2016,China,"China: Leshan, Sichuan",,,,,,,Resistant;Susceptible,Computational Method,,,,,,,,,,sample_type:Culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.52382,Klebsiella pneumoniae LS356,LS356,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08281236,573,,,,MLST.Klebsiella_pneumoniae.485,,,,2018-01-10T00:00:00Z,,PRJNA428155,,"CP025636,CP025637,CP025638",,,Illumina MiSeq,200.0x,A5-miseq v. V20152522,1,2,3,5649218,57.128098,5697,5557,liver abscess puncture fluid,,22-Oct-2011,China,China:Shanghai,,,,Liver abscess,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Department:Huashan Hospital, Shanghai Medical College, Fudan University",,,,,,,Liver abscess,,,,,,,,,,,,,,100,0.2,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52383,Klebsiella pneumoniae LS357,LS357,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08281238,573,,,,MLST.Klebsiella_pneumoniae.23,,,,2018-01-10T00:00:00Z,,PRJNA428157,,"CP025639,CP025640",,,Illumina MiSeq,200.0x,A5-miseq v. V20152522,1,1,2,5624748,57.11826,5694,5523,liver abscess puncture fluid,,14-Mar-2012,China,China:Shanghai,,,,Liver abscess,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:Department:Huashan Hospital, Shanghai Medical College, Fudan University",,,,,,,Liver abscess,,,,,,,,,,,,,,99.9,0.1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52386,Klebsiella pneumoniae LS355,LS355,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08281242,573,,,,MLST.Klebsiella_pneumoniae.1941,,,,2018-01-10T00:00:00Z,,PRJNA428161,,"CP025641,CP025642",,,Illumina MiSeq,200.0x,A5-miseq v. V20152522,1,1,2,5540843,57.229336,5554,5388,liver abscess puncture fluid,,20-Oct-2011,China,China:Shanghai,,,,Liver abscess,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Xiaofei jiang,,,,,,,Liver abscess,,,,,,,,,,,,,,100,0.1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52387,Klebsiella pneumoniae LS359,LS359,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08281240,573,,,,MLST.Klebsiella_pneumoniae.700,,,,2018-01-10T00:00:00Z,,PRJNA428159,,CP025630,,,Illumina MiSeq,200.0x,A5-miseq v. V20152522,1,0,1,4766516,57.59314,4728,4624,liver abscess puncture fluid,,09-Apr-2013,China,China:Shanghai,,,,liver abscess,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Xiaofei Jiang,,,,,,,liver abscess,,,,,,,,,,,,,,95.8,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52388,Klebsiella pneumoniae LS358,LS358,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08281239,573,,,,MLST.Klebsiella_pneumoniae.29,,,,2018-01-10T00:00:00Z,,PRJNA428158,,CP025629,,,Illumina MiSeq,200.0x,A5-miseq v. V20152522,1,0,1,5061886,58.026707,4999,4898,liver abscess puncture fluid,,25-May-2012,China,China:Shanghai,,,,Liver abscess,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Xiaofei Jiang,,,,,,,Liver abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.52398,Klebsiella pneumoniae K201054,K201054,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31311655,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2022-11-13T00:00:00Z,,PRJNA891137,,"CP110638,CP110637,CP110639",,,Illumina MiSeq,100.0x,SOAPdenovo v. version 2.04,1,2,3,5657319,57.082302,5516,,blood,,2020-04-25,China,China: Zhejiang,,,,"sepsis, meningitis and urinary system infection",,,Susceptible,Computational Method,,,,,,,,,,collected_by:Affiliated Wuxi No.2 Peoples Hospital,,,,,,,"sepsis, meningitis and urinary system infection",,,,,,,,,,,,,,100,0.1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Blood and Circulatory System,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.52573,Klebsiella pneumoniae P1-1,P1-1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25749320,573,,,,,,,,2022-11-14T00:00:00Z,36265800,PRJNA804391,,"CP092077,CP092078",,,Nanopore; Illumina HiSeq,200.0x,Unicycler v. 0.4.8,1,1,2,5432744,57.307926,5329,5162,bloodstream,,2019,China,China: Hangzhou,,,,bloodstream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Feiteng Zhu,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.52803,Klebsiella pneumoniae BA4946,BA4946,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21529401,573,,,,MLST.Klebsiella_pneumoniae.2096,,,,2022-11-28T00:00:00Z,,PRJNA739550,,"CP083932,CP083934,CP083933,CP083937,CP083936,CP083935",,,Illumina HiSeq; Oxford Nanopore MinION,60.0x,Unicycler v. June 2021,1,5,6,5795589,56.738514,5741,5516,blood,,2020,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.52804,Klebsiella pneumoniae BA13643,BA13643,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21565548,573,,,,,,,,2022-11-28T00:00:00Z,,PRJNA765514,,"CP102490,CP102492,CP102491,CP102493",,,Illumina HiSeq,90.0x,Unicycler v. September 2021,1,3,4,5598141,57.28684,5552,5324,blood,,2020,India,India,,,,Bacteremia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College, Vellore",,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.52958,Klebsiella pneumoniae KP6870155,KP6870155,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23708555,573,,,,MLST.Klebsiella_pneumoniae.8,,,,2022-12-19T00:00:00Z,,PRJNA263680,,"CP114375,CP114376,CP114377,CP114378,CP114379,CP114380",,,"Illumina, OxfordNanopore",256x,SPAdes v. 3.14.0,1,5,6,5554356,57.348465,5458,5218,n/a,,,,,,,,lung infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,,,,,,,,lung infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Other,Respiratory Diseases-Lung Diseases HP,573.53043,Klebsiella pneumoniae R307,R307,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32129555,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-12-27T00:00:00Z,,PRJNA910533,,CP114785,,,Illumina MiSeq,87.0x,SPAdes v. v3.13.1,1,0,1,5795792,57.113983,5957,5725,rectal swab,,2012,France,France,,,,Infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Patrice Nordmann,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.53059,Klebsiella pneumoniae S245,S245,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32317434,573,,,,MLST.Klebsiella_pneumoniae.307,,,,2022-12-28T00:00:00Z,,PRJNA914077,,"CP114853,CP114854,CP114855,CP114856",,,Illumina HiSeq; PacBio,59.6x,Hifiasm v. 0.13-r308; Canu v. 0.7; pilon,1,3,4,5868291,56.709526,5859,5614,blood,,2022,China,China: Guangzhou,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Jing Chen,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.53495,Klebsiella pneumoniae S12_CRE12,S12_CRE12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387632,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074523,CP074524,CP074525,CP074526,CP074527",,,Illumina NextSeq; PacBio Sequel,299x,Unicycler v. v0.4.7,1,4,5,5825322,56.972027,5883,5687,"urine, clean catch",,2017-06-29,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.53496,Klebsiella pneumoniae S10_CRE10,S10_CRE10,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387630,573,,,,MLST.Klebsiella_pneumoniae.17,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074519,CP074520,CP074521,CP074522",,,Illumina NextSeq; PacBio Sequel,292x,Unicycler v. v0.4.7,1,3,4,5515915,57.27313,5451,5274,"urine, straight cath",,2017-05-03,USA,"USA: Durham, NC",,,,Bacterial infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.53497,Klebsiella pneumoniae S1_CRE1,S1_CRE1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387621,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074442,CP074443,CP074444,CP074445",,,Illumina NextSeq; PacBio Sequel,363x,Unicycler v. v0.4.7,1,3,4,5624921,57.20002,5622,5450,left thigh tissue,,2017-01-03,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53498,Klebsiella pneumoniae S24_CRE24,S24_CRE24,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387643,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074541,CP074542,CP074543,CP074544",,,Illumina NextSeq; PacBio Sequel,284x,Unicycler v. v0.4.7,1,3,4,5855779,56.902573,5896,5697,urine straight cath,,2017-09-04,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.53499,Klebsiella pneumoniae S20_CRE20,S20_CRE20,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387639,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074539,CP074540",,,Illumina NextSeq; PacBio Sequel,351x,Unicycler v. v0.4.7,1,1,2,5620705,57.129025,5605,5426,pelvic abscess,,2017-08-01,USA,"USA: Durham, NC",,,,Bacterial infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.53500,Klebsiella pneumoniae S14_CRE14,S14_CRE14,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387634,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074528,CP074529,CP074530,CP074531,CP074532,CP074533,CP074534",,,Illumina NextSeq; PacBio Sequel,360x,Unicycler v. v0.4.7,1,6,7,5807702,57.00871,5810,5570,blood,,2017-07-13,USA,"USA: Durham, NC",,,,Bacterial infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.53501,Klebsiella pneumoniae S16_CRE16,S16_CRE16,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387635,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074535,CP074536,CP074537,CP074538",,,Illumina NextSeq; PacBio Sequel,335x,Unicycler v. v0.4.7,1,3,4,5896689,56.999428,5889,5698,"tissue, l hip",,2017-07-18,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,573.53502,Klebsiella pneumoniae S37_CRE38,S37_CRE38,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387655,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074553,CP074554,CP074555,CP074556,CP074557",,,Illumina NextSeq; PacBio Sequel,330x,Unicycler v. v0.4.7,1,4,5,5640356,57.124638,5639,5451,bal,,2017-11-14,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53503,Klebsiella pneumoniae S39_CRE40,S39_CRE40,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387657,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074558,CP074559,CP074560",,,Illumina NextSeq; PacBio Sequel,427x,Unicycler v. v0.4.7,1,2,3,5794251,56.962185,5840,5634,urine cc,,2018-02-16,USA,"USA: Raleigh, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.53553,Klebsiella pneumoniae KPN0421,KPN0421,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32661441,573,,,,MLST.Klebsiella_pneumoniae.2004,,,,2023-01-18T00:00:00Z,,PRJNA922498,,"CP115714,CP115715,CP115716",,,PacBio,200.0x,Canu v. v2.0; Racon v. v1.4.13; Pilon v.,1,2,3,5614556,57.076515,5645,5433,blood,,2018-02,China,China: Tianjin,,,,bloodstream infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Shuangqing Liu,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,573.53570,Klebsiella pneumoniae CRKP_45,CRKP_45,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207074,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107291,CP107292,CP107293,CP107294,CP107295,CP107296",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,5,6,6016652,56.859013,6095,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53571,Klebsiella pneumoniae CRKP_44,CRKP_44,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207073,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107297,CP107298,CP107299,CP107300,CP107301,CP107302",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,5,6,6028562,56.851982,6109,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53572,Klebsiella pneumoniae CRKP_42,CRKP_42,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207071,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107308,CP107309,CP107310,CP107311",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5622748,57.295403,5567,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53573,Klebsiella pneumoniae CRKP_38,CRKP_38,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207067,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107334,CP107335,CP107336,CP107337,CP107338,CP107339,CP107340",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5985456,56.845993,6029,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53574,Klebsiella pneumoniae CRKP_40,CRKP_40,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207069,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107320,CP107321,CP107322,CP107323,CP107324,CP107325,CP107326",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5985333,56.846146,6020,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53575,Klebsiella pneumoniae CRKP_36,CRKP_36,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207065,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107345,CP107346,CP107347,CP107348,CP107349,CP107350,CP107351",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5985371,56.846115,6034,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53576,Klebsiella pneumoniae CRKP_39,CRKP_39,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207068,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107327,CP107328,CP107329,CP107330,CP107331,CP107332,CP107333",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5985334,56.846283,6022,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53577,Klebsiella pneumoniae CRKP_37,CRKP_37,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207066,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107341,CP107342,CP107343,CP107344",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5689077,57.223026,5667,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53578,Klebsiella pneumoniae CRKP_43,CRKP_43,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207072,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107303,CP107304,CP107305,CP107306,CP107307",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5633897,57.260914,5576,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53579,Klebsiella pneumoniae CRKP_41,CRKP_41,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207070,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107312,CP107313,CP107314,CP107315,CP107316,CP107317,CP107318,CP107319",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,7,8,6045520,56.786133,6125,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53580,Klebsiella pneumoniae CRKP_35,CRKP_35,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207064,573,,,,MLST.Klebsiella_pneumoniae.1049,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107352,CP107353,CP107354,CP107355,CP107356,CP107357,CP107358",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5806309,56.95248,5702,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53581,Klebsiella pneumoniae CRKP_34,CRKP_34,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207063,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107359,CP107360,CP107361,CP107362",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5628071,57.257736,5578,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53582,Klebsiella pneumoniae CRKP_32,CRKP_32,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207061,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107367,CP107368,CP107369,CP107370,CP107371",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5621243,57.296917,5566,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53583,Klebsiella pneumoniae CRKP_27,CRKP_27,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207056,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107394,CP107395,CP107396,CP107397",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5622656,57.26363,5563,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53584,Klebsiella pneumoniae CRKP_26,CRKP_26,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207055,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107398,CP107399,CP107400,CP107401,CP107402",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5734710,57.112583,5684,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,99.1,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53585,Klebsiella pneumoniae CRKP_28,CRKP_28,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207057,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107390,CP107391,CP107392,CP107393",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5624663,57.261955,5566,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53586,Klebsiella pneumoniae CRKP_30,CRKP_30,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207059,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107379,CP107380,CP107381,CP107382",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5626970,57.247383,5575,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53587,Klebsiella pneumoniae CRKP_24,CRKP_24,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207053,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107408,CP107409,CP107410,CP107411",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5714832,57.233845,5686,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53588,Klebsiella pneumoniae CRKP_25,CRKP_25,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207054,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107403,CP107404,CP107405,CP107406,CP107407",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5689998,57.21076,5639,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53589,Klebsiella pneumoniae CRKP_29,CRKP_29,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207058,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107383,CP107384,CP107385,CP107386,CP107387,CP107388,CP107389",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5984186,56.846863,6022,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53590,Klebsiella pneumoniae CRKP_31,CRKP_31,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207060,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107372,CP107373,CP107374,CP107375,CP107376,CP107377,CP107378",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,6,7,5986790,56.84517,6032,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53591,Klebsiella pneumoniae CRKP_22,CRKP_22,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207051,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107412,CP107413,CP107414,CP107415,CP107416",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5774168,57.12286,5735,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,99.1,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.53592,Klebsiella pneumoniae CRKP_21,CRKP_21,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207050,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107417,CP107418,CP107419,CP107420,CP107421",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5895132,57.051495,5882,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53593,Klebsiella pneumoniae CRKP_33,CRKP_33,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207062,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107363,CP107364,CP107365,CP107366",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5569199,57.29779,5499,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53594,Klebsiella pneumoniae CRKP_19,CRKP_19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207048,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107426,CP107427,CP107428,CP107429,CP107430,CP107431",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,5,6,5887474,57.06753,5873,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53595,Klebsiella pneumoniae CRKP_17,CRKP_17,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207046,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107436,CP107437,CP107438,CP107439,CP107440",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5844442,57.08964,5825,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53596,Klebsiella pneumoniae CRKP_18,CRKP_18,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207047,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107432,CP107433,CP107434,CP107435",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5770944,57.179466,5760,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53597,Klebsiella pneumoniae CRKP_15,CRKP_15,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207044,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107447,CP107448,CP107449,CP107450,CP107451",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5839498,57.091278,5825,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53598,Klebsiella pneumoniae CRKP_14,CRKP_14,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207043,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107452,CP107453,CP107454,CP107455,CP107456,CP107457",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,5,6,5810744,57.065464,5808,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53599,Klebsiella pneumoniae CRKP_16,CRKP_16,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207045,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107441,CP107442,CP107443,CP107444,CP107445,CP107446",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,5,6,5895613,57.0502,5881,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53600,Klebsiella pneumoniae CRKP_12,CRKP_12,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207041,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107463,CP107464,CP107465,CP107466,CP107467",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5657340,57.315117,5589,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53601,Klebsiella pneumoniae CRKP_11,CRKP_11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207040,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107468,CP107469,CP107470,CP107471,CP107472",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838006,57.096363,5818,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53602,Klebsiella pneumoniae CRKP_10,CRKP_10,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207039,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107473,CP107474,CP107475,CP107476,CP107477",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838754,57.09182,5818,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53603,Klebsiella pneumoniae CRKP_8,CRKP_8,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207037,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107483,CP107484,CP107485,CP107486,CP107487",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5840822,57.090595,5830,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53604,Klebsiella pneumoniae CRKP_7,CRKP_7,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207036,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107488,CP107489,CP107490,CP107491,CP107492",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838427,57.092037,5817,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53605,Klebsiella pneumoniae CRKP_6,CRKP_6,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207035,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107493,CP107494,CP107495,CP107496,CP107497",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838863,57.093666,5823,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53606,Klebsiella pneumoniae CRKP_9,CRKP_9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207038,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107478,CP107479,CP107480,CP107481,CP107482",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5837995,57.092445,5823,,sputum,,2018-12-04,China,China: Wuhan,,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53607,Klebsiella pneumoniae CRKP_5,CRKP_5,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207034,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107498,CP107499,CP107500,CP107501,CP107502",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5778933,57.139336,5777,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53608,Klebsiella pneumoniae CRKP_4,CRKP_4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207033,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107503,CP107504,CP107505,CP107506,CP107507",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5837354,57.09284,5817,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53609,Klebsiella pneumoniae CRKP_2,CRKP_2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207031,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107513,CP107514,CP107515,CP107516,CP107517",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5832689,57.0997,5814,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53610,Klebsiella pneumoniae CRKP_3,CRKP_3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207032,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107508,CP107509,CP107510,CP107511,CP107512",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838437,57.09206,5819,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53611,Klebsiella pneumoniae CRKP_1,CRKP_1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207030,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107518,CP107519,CP107520,CP107521,CP107522",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5838431,57.091915,5820,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53618,Klebsiella pneumoniae KP2722,KP2722,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32946429,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-02-06T00:00:00Z,,PRJNA929019,,"CP116903,CP116904,CP116905,CP116906,CP116907,CP116908",,,Illumina NovaSeq; PacBio,50.88x,Hifiasm v. 0.13-r308; Canu v. 0.7; Pilon,1,5,6,6084045,56.968597,6227,5984,sputum,,2022,China,China:Zhuhai,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Wei Jie,,,,,,,infection,,,,,,,,,,,,,,100,3.1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.53640,Klebsiella pneumoniae S40_CRE5b,S40_CRE5b,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387658,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2023-01-09T00:00:00Z,,PRJNA667445,,"CP074561,CP074562,CP074564,CP074565,CP074566,CP074567,CP074568,CP074569,CP074563",,,Illumina NextSeq; PacBio Sequel,322x,Unicycler v. v0.4.7,1,8,9,6023682,56.895332,6078,5858,urine,,2017-04-04,USA,"USA: Durham, NC",,,,Bacterial infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.54338,Klebsiella pneumoniae GN4539,GN4539,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30273448,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-03-14T00:00:00Z,,PRJNA861980,,"CP102687,CP102688,CP102689,CP102690,CP102691",,,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Unicycler v. v0.4.8,1,4,5,5657937,57.1705,5671,5477,urine,,2021-06,Jamaica,Jamaica,,,,urine tract infections,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Camille-Ann Thoms-Rodriguez,,,,,,,urine tract infections,,,,,,,,,,,,,,99.9,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.54339,Klebsiella pneumoniae GN4549,GN4549,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29935323,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-03-14T00:00:00Z,,PRJNA861980,,"CP101835,CP101836,CP101837,CP101838,CP101839,CP101840,CP101841",,,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Unicycler v. v0.4.8,1,6,7,5663795,57.16065,5670,5485,urine,,2021-06,Jamaica,Jamaica,,,,urine tract infections,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Camille-Ann Thoms-Rodriguez,,,,,,,urine tract infections,,,,,,,,,,,,,,99.9,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.54340,Klebsiella pneumoniae GN4542,GN4542,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30273449,573,,,,MLST.Klebsiella_pneumoniae.247,,,,2023-03-14T00:00:00Z,,PRJNA861980,,"CP102692,CP102693",,,Illumina MiSeq; Oxford Nanopore GridION,100.0x,Unicycler v. v0.4.8,1,1,2,5443634,57.32553,5353,5209,urine,,2021-06,Jamaica,Jamaica,,,,urine tract infections,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Camille-Ann Thoms-Rodriguez,,,,,,,urine tract infections,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.54341,Klebsiella pneumoniae CQ22WZ0036,CQ22WZ0036,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31461132,573,,,,MLST.Klebsiella_pneumoniae.11,genotype:ST11,,,2023-03-14T00:00:00Z,,PRJNA894513,,"CP119332,CP119333",,,PacBio,100.0x,SOAPdenovo v. 2.3,1,1,2,5744230,57.05553,5808,5604,sputum,,2022-03-15,China,China: Chongqing,,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Kong Linghan,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.54621,Klebsiella pneumoniae CRKP_20,CRKP_20,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207049,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107422,CP107423,CP107424,CP107425",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,3,4,5611228,57.30193,5544,,lavage fluid,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.54622,Klebsiella pneumoniae CRKP_13,CRKP_13,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31207042,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-01-30T00:00:00Z,36636376,PRJNA888051,,"CP107458,CP107459,CP107460,CP107461,CP107462",,,Oxford Nanopore PromethION,300X,unicycler v. 0.4.8,1,4,5,5921345,56.888664,5916,,sputum,,2018-12-04,China,China: Wuhan,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Fan,,,,,,,infection,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.54842,Klebsiella pneumoniae GIMC1006:Kpn-102106,GIMC1006:Kpn-102106,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31029729,573,,,,MLST.Klebsiella_pneumoniae.395,,,,2023-04-04T00:00:00Z,,PRJNA561493,,"CP120890,CP120891,CP120892,CP120893",,,Illumina,31.0x,SPAdes v. 3.13.0; CLC Genomics,1,3,4,6015127,56.20908,6234,5924,blood,,2021,Russia,Russia:Moscow,,,,Sepsis and the multiorgan failure,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Kruglov A.N.,,,,,,,Sepsis and the multiorgan failure,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,573.54868,Klebsiella pneumoniae UHD-4_PH,UHD-4_PH,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33954877,573,,,,MLST.Klebsiella_pneumoniae.628,genotype:ST628,,,2023-04-09T00:00:00Z,,PRJNA949681,,"CP121139,CP121140",,,Oxford Nanopore MinionNovaseq illumina,1480x,FlyePolypolish v. v.2.9.1v.0.5.0,1,1,2,5509834,57.341656,5411,5235,midstream specimen of urine,,2022-05-31,United Kingdom,United Kingdom,,,,Infected C-section,,host_subject_id:UHD-4,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Dr Elizabeth Sheridan,,,,,,,Infected C-section,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.55060,Klebsiella pneumoniae SCCH112:Kpn2161521,SCCH112:Kpn2161521,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31157671,573,,,,MLST.Klebsiella_pneumoniae.395,,,,2023-04-18T00:00:00Z,,PRJNA561493,,"CP122342,CP122343,CP122344,CP122345,CP122346,CP122347,CP122348,CP122349",,,Illumina,856.0x,SPAdes v. 3.13.0; CLC Genomics,1,7,8,6048975,56.34012,6250,5958,anus swab,,2021-07-29,Russia,Russia:Moscow,,,,"Spastic tetraplegia. Chronic right-sided pneumonia, exacerbation.",,host_description:P24\; 2009 year of birth,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Novikova I.E.,,,,,,,"Spastic tetraplegia. Chronic right-sided pneumonia, exacerbation.",,,P24; 2009 year of birth,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.55063,Klebsiella pneumoniae GIMC1010:Kpn-52ICU-7H,GIMC1010:Kpn-52ICU-7H,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31654606,573,,,,MLST.Klebsiella_pneumoniae.512,,,,2023-04-18T00:00:00Z,,PRJNA561493,,"CP122337,CP122338,CP122339,CP122340,CP122341",,,Illumina,249.0x,SPAdes v. 3.13.0; CLC Genomics,1,4,5,5845885,56.7567,5930,5710,tracheal aspirate,,2021-09-27,Russia,Russia:Moscow,,,,"COVID-19, extremely severe",,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Nikitenko N.A., Burmistrov E.M.",,,,,,,"COVID-19, extremely severe",,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.55064,Klebsiella pneumoniae KP9650,KP9650,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34136943,573,,,,MLST.Klebsiella_pneumoniae.866,,,,2023-04-18T00:00:00Z,,PRJNA954202,,"CP122389,CP122390,CP122391,CP122392",,,Illumina NovaSeq; PacBio Sequel,139.44x,Hifiasm v. 0.13-r308; Canu v. 1.7,1,3,4,5974356,56.527664,6041,5756,sputum,,2022,China,China: Zhuhai,,,,infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Zhuhai People's Hospital,,,,,,,infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.55089,Klebsiella pneumoniae KpBSB53,KpBSB53,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34178607,573,,,,MLST.Klebsiella_pneumoniae.105,,,,2023-04-27T00:00:00Z,,PRJNA955456,,"CP123642,CP123641",,,Oxford Nanopore MinION; BGISeq,186.0x,Flye v. 2.9,1,1,2,5373079,57.360035,5287,5131,tracheal aspiration,,2016-04-04,Brazil,"Brazil: Hospital Universitario de Brasilia, Brasilia-DF",,,,Klebsiella Infection,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:Hospital Universitario de Brasilia, HuB",,,,,,,Klebsiella Infection,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,573.55235,Klebsiella pneumoniae BAK085,BAK085,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34510231,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-16T00:00:00Z,,PRJNA965941,,"CP125088,CP125089,CP125090,CP125091,CP125092,CP125093",,,Illumina; Oxford Nanopore,150.0x,SPAdes v. v3.15.5,1,5,6,5592970,57.180855,5624,5456,urine,,,Singapore,Singapore,,,,Bacterial infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:National University of Singapore Hospital,,,,,,,Bacterial infection,,,,,,,,,,,,,,99.8,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.55255,Klebsiella pneumoniae WYKP586,WYKP586,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34436301,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-18T00:00:00Z,,PRJNA962850,,"CP125334,CP125335,CP125336,CP125337,CP125338",,,Oxford Nanopore MinION,12.0x,HGAP v. 2.3,1,4,5,5890313,57.00687,6004,5782,sputum,,2022-06-17,China,China: Shanghai,,,,severe pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Cong Zhou,,,,,,,severe pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.55256,Klebsiella pneumoniae WYKP589,WYKP589,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34436364,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-18T00:00:00Z,,PRJNA962850,,"CP125343,CP125344,CP125342,CP125341,CP125340,CP125339",,,Oxford Nanopore MinION,12.0x,HGAP v. 2.3,1,5,6,5895536,56.985897,6009,5789,sputum,,2022-06-21,China,China: Shanghai,,,,severe pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Cong Zhou,,,,,,,severe pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.55258,Klebsiella pneumoniae WYKP594,WYKP594,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34439573,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-18T00:00:00Z,,PRJNA962850,,"CP125349,CP125350,CP125348,CP125347,CP125346,CP125345",,,Oxford Nanopore MinION,12.0x,HGAP v. 2.3,1,5,6,5897553,56.98333,6021,5796,sputum,,2022-06-25,China,China: Shanghai,,,,severe pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Cong Zhou,,,,,,,severe pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.55264,Klebsiella pneumoniae VA833,VA833,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642723,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093451,CP093454,CP093455,CP093452,CP093453,CP093456,CP093457",,,Illumina; Oxford Nanopore,220X,Flye v. 2.9-b1768; Tricycler v. 0.5.0;,1,6,7,5997469,56.802563,6268,5866,isolated from blood of an 54 years old female,,2019-04-23,Chile,Chile: Metropolitan Region,,female,54,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,3.3,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.55267,Klebsiella pneumoniae VA684,VA684,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642722,573,,,,MLST.Klebsiella_pneumoniae.505,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093458,CP093460,CP093464,CP093459,CP093461,CP093463,CP093462",,,Illumina; Oxford Nanopore,195X,unicycler v. 0.4.9b; Canu v. 2.3,1,6,7,5775575,56.780426,5751,5497,isolated from catheter blood of an 15 years old female,,2019-04-25,Chile,Chile: Metropolitan Region,,female,15,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.55268,Klebsiella pneumoniae VA569,VA569,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642719,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093476,CP093478,CP093480,CP093479,CP093477",,,Illumina; Oxford Nanopore,164X,unicycler v. 0.4.9b; Canu v. 2.3,1,4,5,5710320,57.12974,5762,5572,isolated from peritoneal fluid of a 79 years old male,,2019-04-06,Chile,Chile: Metropolitan Region,,male,53,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Abdominal,Respiratory Diseases-Pneumonia HP,573.55269,Klebsiella pneumoniae VA681,VA681,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642721,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093465,CP093469,CP093466,CP093468,CP093470,CP093467",,,Illumina; Oxford Nanopore,204X,unicycler v. 0.4.9b; Canu v. 2.3,1,5,6,5554568,57.143147,5564,5377,isolated from an abscess of an 32 years old female,,2019-04-24,Chile,Chile: Metropolitan Region,,female,32,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Pneumonia,Skin and Soft Tissue,Respiratory Diseases-Pneumonia HP,573.55270,Klebsiella pneumoniae VA591,VA591,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642720,573,,,,MLST.Klebsiella_pneumoniae.45,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093471,CP093472,CP093473,CP093475,CP093474",,,Illumina; Oxford Nanopore,180X,unicycler v. 0.4.9b; Canu v. 2.3,1,4,5,5653497,57.17898,5586,5376,isolated from blood of a 29 years old male,,2019-04-11,Chile,Chile: Metropolitan Region,,male,29,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.55271,Klebsiella pneumoniae VA564,VA564,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642718,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093481,CP093482,CP093485,CP093484,CP093483",,,Illumina; Oxford Nanopore,182X,unicycler v. 0.4.9b; Canu v. 2.3,1,4,5,5718217,57.004936,5743,5512,isolated from blood of a 79 years old male,,2019-04-02,Chile,Chile: De Los Lagos Region,,male,79,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.55272,Klebsiella pneumoniae VA172,VA172,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642717,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093486,CP093488,CP093487",,,Illumina; Oxford Nanopore,198X,unicycler v. 0.4.9b; Canu v. 2.3,1,2,3,5403938,57.440277,5356,5176,isolated from bone tissue of a 71 years old male,,2019-01-25,Chile,Chile: Del Maule Region,,male,71,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Bone and Joint,Respiratory Diseases-Pneumonia HP,573.55273,Klebsiella pneumoniae VA32,VA32,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642715,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093495,CP093497,CP093496,CP093499,CP093500,CP093498",,,Illumina; Oxford Nanopore,202X,unicycler v. 0.4.9b; Canu v. 2.3,1,5,6,5730122,57.16613,5758,5548,isolated from bronchoalveolar lavage of an 81 years old female,,2019-01-04,Chile,Chile: Metropolitan Region,,female,81,Klebsiella pneumoniae infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.55274,Klebsiella pneumoniae VA04,VA04,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642714,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093501,CP093502,CP093504,CP093503,CP093505",,,Illumina; Oxford Nanopore,176X,unicycler v. 0.4.9b; Canu v. 2.3,1,4,5,5762453,56.982574,5818,5575,isolated from cerebrospinal fluid of a 36 years old male,,2018-12-05,Chile,Chile: Metropolitan Region,,male,36,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,99.9,0,Respiratory Diseases,Pneumonia,Central Nervous System,Respiratory Diseases-Pneumonia HP,573.55275,Klebsiella pneumoniae VA126,VA126,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26642716,573,,,,MLST.Klebsiella_pneumoniae.25,,,,2023-05-22T00:00:00Z,,PRJNA815754,,"CP093489,CP093494,CP093491,CP093490,CP093492,CP093493",,,Illumina; Oxford Nanopore,181X,unicycler v. 0.4.9b; Canu v. 2.3,1,5,6,5757426,56.984596,5810,5573,isolated from blood of a 33 years old male,,2019-01-16,Chile,Chile: Metropolitan Region,,male,33,Klebsiella pneumoniae infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Instituto de Salud Pblica de Chile,,,,,,,Klebsiella pneumoniae infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,573.56400,Klebsiella pneumoniae BA11088,BA11088,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27555111,573,,,,MLST.Klebsiella_pneumoniae.231,,,,2023-06-22T00:00:00Z,,PRJNA613369,,"CP095557,CP095559,CP095558,CP095561,CP095562,CP095560,CP095563,CP095564,CP095565",,,Illumina HiSeq; Oxford Nanopore MinION,50.0x,Unicycler v. June 2021,1,8,9,5555316,57.11349,5527,5316,blood,,2020,India,India,,,,bacteremia,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore",,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,573.56436,Klebsiella pneumoniae Mu1413,Mu1413,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27934724,573,,,,MLST.Klebsiella_pneumoniae.15,,,,2023-06-05T00:00:00Z,,PRJNA833050,,"CP096814,CP096815,CP096816,CP096817",,,Illumina NextSeq; Oxford Nanopore,100.0x,unicycler v. 0.4.8,1,3,4,5667507,57.03222,5585,5409,urine,,2012/2015,USA,"USA: Georgia, Atlanta",,,,,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Georgia Emerging Infections Program,,,,,,,N/A,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.56991,Klebsiella pneumoniae strain_52,strain_52,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773952,573,,,,MLST.Klebsiella_pneumoniae.405,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128441,,,Illumina,55x,SPAdes v. v3.15.5,1,0,1,5762490,56.685272,5876,5638,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.57001,Klebsiella pneumoniae strain_65,strain_65,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773953,573,,,,MLST.Klebsiella_pneumoniae.147,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128442,,,Illumina,44x,SPAdes v. v3.15.5,1,0,1,5676449,56.820633,5797,5594,urine,,2021,Gaza Strip,Gaza Strip,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.57002,Klebsiella pneumoniae strain_69,strain_69,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35773955,573,,,,MLST.Klebsiella_pneumoniae.14,,,,2023-06-30T00:00:00Z,,PRJNA984638,,CP128444,,,Illumina,43x,SPAdes v. v3.15.5,1,0,1,5428380,57.2532,5472,5324,ear,,2021,Gaza Strip,Gaza Strip,,,,infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:Nabil El Aila, Nahed Al Laham",,,,,,,infection,,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,573.57065,Klebsiella pneumoniae MAKM-3381,MAKM-3381,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35786903,573,,,,MLST.Klebsiella_pneumoniae.39,,,,2023-07-05T00:00:00Z,,PRJNA985059,,CP129122,,,Illumina NovaSeq,612.0x,SPAdes v. 3.15; Medusa v. 1.3,1,0,1,5403180,57.397842,5341,5167,rectal swab,,2022-03-02,Uganda,Uganda: Kampala,,,,Gastrointestinal infections,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Simon Sekyanzi,,,,,,,Gastrointestinal infections,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,573.57101,Klebsiella pneumoniae HMKP141603t,HMKP141603t,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35786900,573,,,,MLST.Klebsiella_pneumoniae.412,,,,2023-07-09T00:00:00Z,,PRJNA985056,,"CP129202,CP129203,CP129204,CP129205",,,Illumina; Oxford Nanopore,100.0x,Unicycler v. 0.5.0,1,3,4,5432219,57.353874,5286,5119,clinically infected patient,,2014,China,"China: Kunming, Yunnan",,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,"collected_by:School of Medicine, Kunming University",,,,,,,pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.57296,Klebsiella pneumoniae MAKM-5490,MAKM-5490,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36467616,573,,,,MLST.Klebsiella_pneumoniae.39,,,,2023-07-28T00:00:00Z,,PRJNA985213,,"CP130492,CP130493,CP130494,CP130495,CP130496",,,Illumina NovaSeq,613.0x,SPAdes v. 3.15; Medusa v. 1.3,1,4,5,5975741,56.76395,6052,5785,rectal swab,,2022-03-02,Uganda,Uganda: Kampala,,,,Gastrointestinal infections,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Simon Sekyanzi,,,,,,,Gastrointestinal infections,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,573.57365,Klebsiella pneumoniae KP9,KP9,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36621066,573,not collected,,,MLST.Klebsiella_pneumoniae.37,genotype:not collected,not collected,,2023-07-30T00:00:00Z,,PRJNA996717,,"CP130674,CP130675,CP130676,CP130677,CP130678,CP130679,CP130680",,,Illumina NovaSeq; PacBio Sequel,182.0x,SPAdes v. v3.12,1,6,7,5768427,56.730022,5813,5557,not collected,,2021-05-30,China,China,,,,,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"sample_type:Cell culture;biomaterial_provider:Pharmacological Toxicology Laboratory;collected_by:Pharmacology Toxicology Laboratory, School of Veterinary Medicine;identified_by:not collected;mating_type:not collected;specimen_voucher:not collected",he Third Affiliated Hospital of Henan University of Chinese Medicine,,,,,,,,,,,,,,,,he Third Affiliated Hospital of Henan University of Chinese Medicine,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,573.7241,Klebsiella pneumoniae strain CAV1453,CAV1453,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03733793,573,,,,MLST.Klebsiella_pneumoniae.258,,,,2016-12-13T00:00:00Z,,PRJNA246471,GCF_001902255.1,"CP018356,CP018353,CP018355,CP018354","NZ_CP018356.1,NZ_CP018353.1,NZ_CP018355.1,NZ_CP018354.1",University of Oxford,PacBio,129x,HGAP v. unspecified,1,3,4,5594981,57.24,5714,5768,perirectal,,2011-10,USA,USA:Virginia,,,,,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,not applicable,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,573.7242,Klebsiella pneumoniae strain Kp_Goe_154414,Kp_Goe_154414,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412805,573,,,,MLST.Klebsiella_pneumoniae.23,genotype:MLST ST23,,,2016-12-13T00:00:00Z,,PRJNA329409,GCF_001902335.1,"CP018337,CP018339,CP018338,CP018340,CP018341,CP018342,CP018343","NZ_CP018337.1,NZ_CP018339.1,NZ_CP018338.1,NZ_CP018340.1,NZ_CP018341.1,NZ_CP018342.1,NZ_CP018343.1",University Medical Center Goettingen,PacBio,147.0x,SMRT Analysis Software v. 2.3.0.,1,6,7,5851286,56.62,6093,6039,wound swab,,2014-07-21,Germany,Germany: Goettingen,,male,36,wound (hand),,host_description:German citizen,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,wound (hand),,,German citizen,,,,,,,,,,,100,0.1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.7243,Klebsiella pneumoniae strain Kp_Goe_62629,Kp_Goe_62629,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412811,573,,,,MLST.Klebsiella_pneumoniae.395,genotype:MLST ST395,DSM:103698,,2016-12-13T00:00:00Z,,PRJNA329409,GCF_001902355.1,"CP018364,CP018365,CP018366","NZ_CP018364.1,NZ_CP018365.1,NZ_CP018366.1",University Medical Center Goettingen,PacBio,153.0x,SMRT Analysis Software v. 2.3.0,1,2,3,5778578,57.13,5971,5998,urine,,2015-06-22,Germany,Germany: Goettingen,,male,43,urinary tract infection,,host_description:refugee from orth africa,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,urinary tract infection,,,refugee from orth africa,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.7244,Klebsiella pneumoniae strain Kp_Goe_39795,Kp_Goe_39795,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412810,573,,,,MLST.Klebsiella_pneumoniae.15,genotype:MLST ST15,DSM:103697,,2016-12-13T00:00:00Z,,PRJNA329409,GCF_001902395.1,"CP018458,CP018460,CP018461,CP018462,CP018459","NZ_CP018458.1,NZ_CP018460.1,NZ_CP018461.1,NZ_CP018462.1,NZ_CP018459.1",University Medical Center Goettingen,PacBio,139.0x,SMRT Analysis Software v. 2.3.0,1,4,5,5676522,56.97,5762,5787,tracheal secretion,,2014-09-23,Germany,Germany: Goettingen,,male,53,pneumonia,,host_description:German citizen,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,pneumonia,,,German citizen,,,,,,,,,,,100,0.7,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.7246,Klebsiella pneumoniae strain Kp_Goe_33208,Kp_Goe_33208,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412455,573,,,,MLST.Klebsiella_pneumoniae.101,genotype:MLST ST101,DSM:103696,,2016-12-13T00:00:00Z,,PRJNA329409,GCF_001902435.1,"CP018447,CP018448,CP018449","NZ_CP018447.1,NZ_CP018448.1,NZ_CP018449.1",University Medical Center Goettingen,PacBio,140.0x,SMRT Analysis Software v. 2.3.0,1,2,3,5655658,56.95,5833,5802,wound swab,,2013-04-05,Germany,Germany: Goettingen,,male,31,wound infection,,,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,wound infection,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,573.7247,Klebsiella pneumoniae strain SWU01,SWU01,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06109054,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2016-12-13T00:00:00Z,,PRJNA354663,GCF_001902475.1,"CP018454,CP018455","NZ_CP018454.1,NZ_CP018455.1",Southwest Medical University,Illumina Miseq and PacBio RS Sequencing,180.0x,SOAPdenovo v. v2.04,1,1,2,5699058,57.4,5654,,blood specimen,,2015-03,China,China,,,,infection,,,,,,,,,,,,,Molecular characteristic of a hypermucoviscous Klebsiella pneumoniae strian isolate from the Liver abscess patients,collected_by:Yingshun Zhou,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,573.7248,Klebsiella pneumoniae strain Kp_Goe_71070,Kp_Goe_71070,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412456,573,,,,MLST.Klebsiella_pneumoniae.101,genotype:MLST ST101,DSM:103699,,2016-12-13T00:00:00Z,,PRJNA329409,GCF_001902515.1,"CP018450,CP018451,CP018452,CP018453","NZ_CP018450.1,NZ_CP018451.1,NZ_CP018452.1,NZ_CP018453.1",University Medical Center Goettingen,PacBio,123.0x,SMRT Analysis Software v. 2.3.0,1,3,4,5658942,56.95,5845,5809,urine sample,,2013-04-05,Germany,Germany: Goettingen,,male,31,Urinary tract infection,,host_description:Refugee from North Africa,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,Urinary tract infection,,,Refugee from North Africa,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.7249,Klebsiella pneumoniae strain CAV1417,CAV1417,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03733765,573,,,,MLST.Klebsiella_pneumoniae.340,,,,2016-12-13T00:00:00Z,,PRJNA246471,GCA_001902535.1,"CP018352,CP018351,CP018350,CP018348,CP018349",,University of Oxford,PacBio,133x,HGAP v. unspecified,1,3,5,5513536,56.95,5731,5779,urine/genitourinary,,2011-05,USA,USA:Virginia,,,,,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,missing,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,573.7351,Klebsiella pneumoniae strain CAV1042,CAV1042,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03024576,573,,,,MLST.Klebsiella_pneumoniae.244,,,,2016-12-19T00:00:00Z,,PRJNA246471,GCF_001908515.1,"CP018671,CP018670,CP018665,CP018666,CP018667,CP018668,CP018669","NZ_CP018671.1,NZ_CP018670.1,NZ_CP018665.1,NZ_CP018666.1,NZ_CP018667.1,NZ_CP018668.1,NZ_CP018669.1",University of Oxford,PacBio,170x,HGAP v. unspecified,1,6,7,5752260,56.83,5944,5931,urine,,2008-04,USA,USA:Virginia,,,,Urinary Tract Infection,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,100,0.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.7352,Klebsiella pneumoniae strain Kp_Goe_149473,Kp_Goe_149473,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412458,573,,,,MLST.Klebsiella_pneumoniae.147,genotype:MLST ST147,DSM:103708,,2016-12-19T00:00:00Z,,PRJNA329409,GCF_001908595.1,"CP018686,CP018687,CP018689,CP018690,CP018691,CP018688","NZ_CP018686.1,NZ_CP018687.1,NZ_CP018689.1,NZ_CP018690.1,NZ_CP018691.1,NZ_CP018688.1",University Medical Center Goettingen,PacBio,140.0x,SMRT Analysis Software v. 2.3.0,,5,6,5916317,56.59,6082,6063,tracheal secretion,,2014-05-07,Germany,Germany: Goettingen,,male,70,pneumonia,,host_description:German citizen,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,pneumonia,,,German citizen,,,,,,,,,,,100,0.3,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,573.7353,Klebsiella pneumoniae strain Kp_Goe_827024,Kp_Goe_827024,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412797,573,,,,MLST.Klebsiella_pneumoniae.147,genotype:MLST ST147,DSM:103704,,2016-12-19T00:00:00Z,,PRJNA329409,GCF_001908625.1,"CP018701,CP018702,CP018704,CP018706,CP018705,CP018703","NZ_CP018701.1,NZ_CP018702.1,NZ_CP018704.1,NZ_CP018706.1,NZ_CP018705.1,NZ_CP018703.1",University Medical Center Goettingen,PacBio,128.0x,SMRT Analysis Software v. 2.3.0,1,5,6,5907691,56.6,6072,6061,abdominal drainage fluid,,2014-05-30,Germany,Germany: Goettingen,,male,51,peritonitis,,,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,peritonitis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,573.7355,Klebsiella pneumoniae strain Kp_Goe_152021,Kp_Goe_152021,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412803,573,,,,MLST.Klebsiella_pneumoniae.147,genotype:MLST ST147,DSM:103710,,2016-12-19T00:00:00Z,,PRJNA329409,GCF_001908675.1,"CP018713,CP018714,CP018716,CP018717,CP018718,CP018715","NZ_CP018713.1,NZ_CP018714.1,NZ_CP018716.1,NZ_CP018717.1,NZ_CP018718.1,NZ_CP018715.1",University Medical Center Goettingen,PacBio,126.0x,SMRT Analysis Software v. 2.3.0,1,5,6,5921376,56.59,6079,6063,abdominal drainage fluid,,2014-06-13,Germany,Germany: Goettingen,,female,82,peritonitis,,host_description:German citizen,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,peritonitis,,,German citizen,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,573.7357,Klebsiella pneumoniae strain CAV1217,CAV1217,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03024585,573,,,,MLST.Klebsiella_pneumoniae.340,,,,2016-12-19T00:00:00Z,,PRJNA246471,GCA_001908715.1,"CP018676,CP018674,CP018672,CP018675,CP018673",,University of Oxford,PacBio,200x,HGAP v. unspecified,1,3,5,5379063,57.11,5559,5625,urine,,2010-08,USA,USA:Virginia,,,,Urinary Tract Infection,,,,,,,,,,,,,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,Urinary Tract Infection,,,,,,,,,,,,,,99.7,0.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.7358,Klebsiella pneumoniae strain Kp_Goe_149832,Kp_Goe_149832,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412459,573,,,,MLST.Klebsiella_pneumoniae.147,genotype:MLST ST147,DSM:103709,,2016-12-19T00:00:00Z,,PRJNA329409,GCF_001908875.1,"CP018695,CP018696,CP018698,CP018700,CP018699,CP018697","NZ_CP018695.1,NZ_CP018696.1,NZ_CP018698.1,NZ_CP018700.1,NZ_CP018699.1,NZ_CP018697.1",University Medical Center Goettingen,PacBio,160.0x,SMRT Analysis Software v. 2.3.0,1,5,6,5920288,56.59,6078,6064,abdominal drain fluid,,2014-05-12,Germany,Germany: Goettingen,,male,51,peritonitis,,host_description:German citizen,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,peritonitis,,,German citizen,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Peritoneal Conditions,Abdominal,Gastrointestinal Diseases-Peritoneal Conditions HP,573.7360,Klebsiella pneumoniae strain Kp_Goe_121641,Kp_Goe_121641,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05412452,573,,,,MLST.Klebsiella_pneumoniae.101,genotype:MLST ST101,DSM:103707,,2016-12-21T00:00:00Z,,PRJNA329409,GCF_001913175.1,"CP018735,CP018737,CP018736,CP018738,CP018740,CP018739","NZ_CP018735.1,NZ_CP018737.1,NZ_CP018736.1,NZ_CP018738.1,NZ_CP018740.1,NZ_CP018739.1",University Medical Center Goettingen,PacBio,308.0x,SMRT Analysis Software v. 2.3.0,1,5,6,5627728,56.97,5612,5265,urine sample,,2013-03-12,Germany,Germany: Goettingen,,male,32,Urinary tract infection,,host_description:Refugee from North Africa,,,,,,,,,,,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",collected_by:Andreas Erich Zautner,,,,,,,Urinary tract infection,,,Refugee from North Africa,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,573.9629,Klebsiella pneumoniae strain 1756,1756,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06216564,573,,,,MLST.Klebsiella_pneumoniae.2549,,,,2017-01-17T00:00:00Z,,PRJNA360900,GCF_001952835.1,"CP019219,CP019220","NZ_CP019219.1,NZ_CP019220.1",National Yang Ming University,PacBio,173.0x,HGAP version 3.0 v. 2016-05-19,1,1,2,5269768,57.52,5268,5321,pus,,2004-10-26,Taiwan,Taiwan,,,,,,,,,,,,,,,,,K. pneumoniae strain 1756 is resistant to carbapenems,sample_type:Clinical isolate,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,573.9643,Klebsiella pneumoniae strain KP38731,KP38731,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04457965,573,,,,MLST.Klebsiella_pneumoniae.11,,,,2017-03-02T00:00:00Z,,PRJNA311034,GCA_002009075.1,"CP014294,CP014295,CP014296,CP014297,CP014298,CP014299,CP014300","NZ_CP014294.1,NZ_CP014295.1,NZ_CP014296.1,NZ_CP014297.1,NZ_CP014298.1,NZ_CP014299.1,NZ_CP014300.1",USAMRIID,PacBio,150,HGAP v. 2.3,1,6,7,5852942,57.11,6138,5802,,,2015-12-01,,,,,,pneumonia,,,Resistant,Computational Prediction,,,,,,,,,Whole genome long-read sequencing of isolates of Klebsiella and Acinetobacter,collected_by:USAMRIID,,,,,,,pneumonia,,,,,,,,,,,,,,100,3.3,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,573.9779,Klebsiella pneumoniae strain kp757,kp757,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04621179,573,,,,MLST.Klebsiella_pneumoniae.86,,,,2017-05-02T00:00:00Z,,PRJNA317547,GCA_002116885.1,CP015120,,USAMRIID,PacBio,215,HGAP v. 2.3,1,,1,5264852,57.56,5174,5106,,,2015,USA,United States,,,,pneumonia,,,,,,,,,,,,,Genomic investigation of drug-resistant isolates of Klebsiella pneumoniae,collected_by:USAMRIID,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.7,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,57706.158,Citrobacter braakii strain DY2019,DY2019,Citrobacter braakii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20511720,57706,,,,,,,,2021-08-10T00:00:00Z,,PRJNA751212,GCA_019502645.1,"CP080539,CP080540,CP080541",,"The First Affiliated Hospital, School of Medicine, Zhejiang University",Illumina NovaSeq,200X,SPAdes v. 3.9.1,1,2,3,5357557,51.933933,5273,5035,clinical,,2019-05-23,China,China: Jinhua,,,,Multiple fracture,,,,,,,,,,,,,pDY2019-NDM and pDY2019-OXA,collected_by:Hao Xu,,,,,,,Multiple fracture,,,,,,,,,,,,,,99.97,1.66,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57706.19,Citrobacter braakii strain FDAARGOS_253,FDAARGOS_253,Citrobacter braakii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04875579,57706,,,,,,FDA:FDAARGOS_253,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073755.2,CP020448,,US Food and Drug Administration,PacBio,18.43x,CA v. 8.2,1,,1,5244065,52.03,5089,4912,blood,,2014-10-24,USA,USA:DC,,male,59Y,Infection with Citrobacter braakii,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:George Washington University,,,,,,,Infection with Citrobacter braakii,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,57743.255,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_80,colony_80,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713981,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657405.1,CP067980,,Ministry of Public Health-Thailand,Illumina HiSeq,96.718x,De Bruijn Graph De Novo Assembler v.,1,0,1,5047093,52.285553,4950,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.256,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_78,colony_78,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713980,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657525.1,CP067981,,Ministry of Public Health-Thailand,Illumina HiSeq,96.71x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552507,52.61254,4360,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.58,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.257,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_77,colony_77,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713979,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657685.1,CP067982,,Ministry of Public Health-Thailand,Illumina HiSeq,96.728x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552507,52.61407,4359,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.6,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.258,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_76,colony_76,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713978,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657725.1,CP067983,,Ministry of Public Health-Thailand,Illumina HiSeq,96.725x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552574,52.61276,4351,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.61,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.259,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_75,colony_75,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713977,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657745.1,CP067984,,Ministry of Public Health-Thailand,Illumina HiSeq,96.694x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552508,52.61316,4355,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.61,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.260,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_72,colony_72,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713975,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657765.1,CP067986,,Ministry of Public Health-Thailand,Illumina HiSeq,96.731x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552478,52.610977,4369,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.72,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.261,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_69,colony_69,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713974,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657785.1,CP067987,,Ministry of Public Health-Thailand,Illumina HiSeq,96.722x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552507,52.61475,4357,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.6,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.262,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_74,colony_74,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713976,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657805.1,CP067985,,Ministry of Public Health-Thailand,Illumina HiSeq,96.758x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552508,52.614418,4368,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.6,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.263,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_68,colony_68,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713973,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657825.1,CP067988,,Ministry of Public Health-Thailand,Illumina HiSeq,96.652x,De Bruijn Graph De Novo Assembler v.,1,0,1,5047093,52.28451,4941,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.264,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_66,colony_66,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713972,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016657905.1,CP067989,,Ministry of Public Health-Thailand,Illumina HiSeq,96.695x,De Bruijn Graph De Novo Assembler v.,1,0,1,4552507,52.615135,4361,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,98.16,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57743.265,Salmonella enterica subsp. enterica serovar Weltevreden strain colony_64,colony_64,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16713971,57743,Weltevreden,,,MLST.Salmonella_enterica.365,,,,2021-01-18T00:00:00Z,,PRJNA668870,GCA_016658065.1,CP067990,,Ministry of Public Health-Thailand,Illumina HiSeq,96.72x,De Bruijn Graph De Novo Assembler v.,1,0,1,5047093,52.285397,4942,,missing,,,Thailand,Thailand: Yasothon,,,,,,,,,,,,,,,,,Establishment capacity for Whole genome Sequencing for food-borne outbreaks in Thailand,"collected_by:Department of Disease Control, Ministry of Public Health",,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,577675.3,Escherichia coli O91:H21 strain FWSEC0008,FWSEC0008,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768109,577675,O91:H21,,,MLST.Escherichia_coli_1.442,,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037775.2,NFGY00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,98.41x;82.67x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5093580,50.856236,5289,5198,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",1989,Germany,Germany,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:Laboratory for Foodborne Zoonoses: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.93,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,57975.30,Burkholderia thailandensis strain FDAARGOS_238,FDAARGOS_238,Burkholderia thailandensis,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05004747,57975,,,,"MLST.Burkholderia_cepacia_complex.544,MLST.Burkholderia_pseudomallei.101",,FDA:FDAARGOS_238,,2018-03-27T00:00:00Z,,PRJNA231221,GCA_003020185.1,"CP020392,CP020391",,US Food and Drug Administration,PacBio; Illumina,12.8898913309567x,HGAP v. 3,2,,2,6768654,67.78389,6992,6411,pleural wound,,2009,,,,male,76Y,Wound infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID,,,,,,,Wound infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,1,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,57975.47,Burkholderia thailandensis strain BPM,BPM,Burkholderia thailandensis,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN14351735,57975,,,,"MLST.Burkholderia_cepacia_complex.488,MLST.Burkholderia_pseudomallei.76",,,,2020-03-20T00:00:00Z,,PRJNA611888,GCA_011578485.1,"CP050020,CP050021",,"Daping Hospital, Army Medical University",Illumina HiSeq; PacBio Sequel,405.0x,SOAPdenovo v. V2.04,2,0,2,6601257,67.77757,6557,5661,blood from patient,,2013-10,China,China: Chongqing,,,,,,,,,,,,,,,,,The objective of this study was to reveal the molecular mechanism involved in virulence of a Burkholderia thailandensis clinical isolate BPM,sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,2.48,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,58096.69,Salmonella enterica subsp. enterica serovar Bareilly strain FC745,FC745,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16514989,58096,Bareilly,,,MLST.Salmonella_enterica.203,genotype:ST203,,,2020-11-04T00:00:00Z,,PRJNA670605,GCA_015223545.3,"CP063684,CP063685",,"Christian Medical College, Vellore",IonTorrent; Oxford Nanopore MinION,150.0x,Unicycler v. 0.4.8,1,1,2,4904654,52.185005,4978,4634,feces,,2017-07,India,India: Vellore,,male,,Gastroenteritis,,,,,,,,,,,,,Multidrug-resistant NTS isolate S. Bareilly carrying blaNDM-7 in a IncA/C2 plasmid along with characteristic pathogenicity islands and virulence factors: A public health concern,collected_by:CMC Vellore,,,,,,,Gastroenteritis,,,,,,,,,,,,,,100,0.66,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,58097.91,Salmonella enterica subsp. enterica serovar Bovismorbificans strain 2020LSAL11867,2020LSAL11867,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18747132,58097,Bovismorbificans,,,MLST.Salmonella_enterica.142,,,,2021-05-11T00:00:00Z,,PRJNA722181,GCA_018340585.1,"CP073715,CP073716,CP073717",,"French Agency for Food, Environmental and Occupational Health & Safety",Illumina NovaSeq; MinION,100.0x,Unicycler v. MARCH-2021,1,2,3,4676102,52.286156,4659,4383,pork product,isolated from a pork sausage eaten by a patient suffering from Salmonellosis,2021-02,France,France,,,,Salmonellosis,,,,,,,,,,,,,Foodborne outbreaks associated with Salmonella require thorough genomic investigation that relies on whole genome sequencing. We present the closed genome sequence of one strain of Salmonella enterica subsp. enterica serovar Bovismorbificans isolated from a pork sausage eaten by a patient suffering from Salmonellosis.,collected_by:ANSES,,,,,,,,,,,,,,,,,,,,,100,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,58101.4,Salmonella enterica subsp. enterica serovar Waycross strain RSE24,RSE24,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10638908,58101,Waycross,,,MLST.Salmonella_enterica.2460,,,,2019-01-06T00:00:00Z,,PRJNA510422,GCA_003994735.1,"CP034707,CP034708",,Pennsylvania State University,IonTorrent & Oxford Nanopore MiniION,52x,Unicycler v. 0.4.7,1,1,2,4732696,52.12287,5067,4570,hospital,,2018-03-27,Rwanda,Rwanda:Rulindo,,male,,gastroenteritis,,,,,,,,,,,,,Complete genome sequencing of Salmonella isolates from Rwanda,collected_by:Maurice Byukusenge,,,,,,,gastroenteritis,,,,,,,,,,,,,,99.37,0.23,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,582.135,Morganella morganii strain GN28,GN28,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08473461,582,,,,,,,,2018-02-14T00:00:00Z,,PRJNA433256,GCA_002946575.1,CP026651,,Beijing Institute of Microbiology and Epidemiology,Illumina MiSeq,42.0x,Newbler v. 2.6,1,,1,4091949,50.868404,4154,3865,sputum,,2015-07-31,China,China: Beijing,,,,Pneumonia,,,,,,,,,,,,,Morganella morganii GN28 chromosome;missing tRNA genes,collected_by:Beijing Institute of Microbiology and Epidemiology,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.7,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,582.219,Morganella morganii strain L241,L241,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10218950,582,,,,,,,,2018-12-19T00:00:00Z,,PRJNA495096,GCA_003955965.1,"CP033056,CP033057",,Zhejiang University,PacBio Sequel,300.0x,HGAP v. 3,1,1,2,3896605,51.041687,3939,3652,feces,,2016-01-26,China,China: Hangzhou,,,53,hepatitis,,,,,,,,,,,,,The whole genome of NDM-5 producing Morganella morganii clinical isolate,collected_by:Tao Lv,,,,,,,hepatitis,,,,,,,,,,,,,,100,1.09,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,582.559,Morganella morganii strain MM46903,MM46903,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933265,582,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939515.1,"CP070524,CP070523,CP070522,CP070521",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,4259678,50.836613,4361,3988,pressure ulcer swab,,2018-10-10,Czech Republic,Czech Republic: Praha,,,,Anoxic brain damage,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,"collected_by:SPADIA LAB, a.s.",,,,,,,Anoxic brain damage,,,,,,,,,,,,,,100,0.75,Neurological Diseases,Other Brain Infections,Skin and Soft Tissue,Neurological Diseases-Other Brain Infections HP,582.560,Morganella morganii strain MM48659,MM48659,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933275,582,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939575.1,"CP070537,CP070536,CP070535",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,2,3,4264385,50.974407,4359,3993,urine (permanent catheter),,2019-01-21,Czech Republic,Czech Republic: Hradec Krlov,,,,Liver disease,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Hradec Krlov,,,,,,,Liver disease,,,,,,,,,,,,,,100,0.03,Liver Diseases,,Urinary Tract,Liver Diseases- HP,582.561,Morganella morganii strain MM50821,MM50821,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933284,582,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939635.1,"CP070553,CP070552,CP070551,CP070550",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,4305707,50.919537,4431,4074,sputum-aspirate,,2019-05-15,Czech Republic,Czech Republic: Praha,,,,Acute respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Krlovsk Vinohrady,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,582.562,Morganella morganii strain MM51087,MM51087,Morganella morganii,Morganella,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933287,582,,,,,,,,2021-03-01T00:00:00Z,,PRJNA700516,GCA_017114545.1,JAFIQH000000000,,Charles University in Prague,PacBio Sequel,250x,Microbial Assembly v. 1.1,4,1,5,4304377,50.89482,4436,4056,pus,,2019-06-03,Czech Republic,Czech Republic: Praha,,,,Respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Fakultn nemocnice Krlovsk Vinohrady,,,,,,,Respiratory failure,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Skin and Soft Tissue,Respiratory Diseases-Other Respiratory Diseases HP,58231.6,Treponema medium strain ATCC 700293,ATCC 700293,Treponema medium,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN09721498,58231,,,,,,ATCC:700293,,2021-03-03T00:00:00Z,,PRJNA482935,GCA_017161265.1,CP031393,,University of Liverpool,454; Illumina MiSeq,1.0x,SPAdes v. 3.0.0; Newbler v. 2.0.00.20,1,0,1,2721998,44.26135,2617,2352,oral,,,,,,,,,,,,,,,,,,,,,"The complete genome of the human oral pathogen, Treponema medium.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,584.1161,Proteus mirabilis strain CRPM10,CRPM10,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12636071,584,,,,,,,,2019-09-02T00:00:00Z,,PRJNA562190,GCA_008195605.1,"CP043332,CP043333",,Zhejiang Provincial People's Hospital,Oxford Nanopore GridION; Illumina NextSeq,100.0x,Unicycler v. 0.4.7,1,1,2,4204856,38.95132,3970,3813,urine sample,,2018-05-18,China,China:Hangzhou,,,,urinary tract infection,,,,,,,,,,,,,Proteus mirabilis Genome sequencing of CRPM10,collected_by:Fang He,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.1238,Proteus mirabilis strain CRE14IB,CRE14IB,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13082492,584,,,,,,,,2019-10-31T00:00:00Z,,PRJNA578857,GCA_009429045.1,"CP045538,CP045539,CP045540",,Charles University in Prague,PacBio Sequel,152.0x,HGAP v. 4,1,2,3,4120262,38.73278,3928,3750,urine catheter,,2019-04-03,Italy,Italy: Lodi,,,,UTI,,,,,,,,,,,,,NDM-1 producing Proteus mirabilis,collected_by:S. Angelo Lodigiano hospital,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,584.1247,Proteus mirabilis strain ENT1301,ENT1301,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11567707,584,,,,,,,,2019-11-20T00:00:00Z,31725155,PRJNA540912,GCA_009684635.1,CP044135,,National University Hospital,Oxford Nanopore MiniION,1x,Unicycler v. 0.4.3,1,0,1,4107982,38.975906,3766,3478,urine,,2014-04-07,Singapore,Singapore,,,,UTI,,,,,,,,,,,,,blaOXA-23-AbaR4 Acinetobacter baumannii resistance island in Proteus mirabilis,collected_by:NPHL,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,584.1248,Proteus mirabilis strain ENT1157,ENT1157,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11567705,584,,,,,,,,2019-11-20T00:00:00Z,31725155,PRJNA540912,GCA_009684665.1,CP044136,,National University Hospital,Oxford Nanopore MiniION,1x,Unicycler v. 0.4.3,1,0,1,4105149,38.97632,3853,3702,urine,,2014-01-05,Singapore,Singapore,,,,UTI,,,,,,,,,,,,,blaOXA-23-AbaR4 Acinetobacter baumannii resistance island in Proteus mirabilis,collected_by:NPHL,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,584.1273,Proteus mirabilis strain ENT1224,ENT1224,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11567706,584,,,,,,,,2019-11-20T00:00:00Z,31725155,PRJNA540912,GCA_009684595.1,CP044134,,National University Hospital,Oxford Nanopore MiniION,1x,Unicycler v. 0.4.3,1,0,1,4105071,38.987446,3856,3700,urine,,2014-04-06,Singapore,Singapore,,,,UTI,,,,,,,,,,,,,blaOXA-23-AbaR4 Acinetobacter baumannii resistance island in Proteus mirabilis,collected_by:NPHL,,,,,,,UTI,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,584.1339,Proteus mirabilis strain PmBR607,PmBR607,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12995602,584,,,,,,,,2020-03-11T00:00:00Z,,PRJNA576511,GCA_011149675.1,"CP049753,CP049754,CP049755",,USP,Illumina MiSeq,200x,SPAdes v. 3.11,1,2,3,4087423,39.02672,3793,3644,urine,,2015,Brazil,Brazil,,,,urinary infection,,,,,,,,,,,,,Proteus mirabilis causes catheter-associated urinary tract infections (CAUTIs). We identified Integrative and Conjugative Elements (ICEs) of SXT/R391 family.,collected_by:Mario C. Noronha do Amaral,,,,,,,urinary infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.1342,Proteus mirabilis strain XH1569,XH1569,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14331403,584,,,,,,,,2020-03-17T00:00:00Z,,PRJNA611104,GCA_011383045.1,CP049942,,Zhejiang University,Illumina HiSeq; Oxford Nanopore MiniION,200.0x,Unicycler v. 0.4.8,1,0,1,3998116,38.769886,3681,3575,urine,,2020-01-10,China,China:Hangzhou,,,,urinary tract infection,,,,,,,,,,,,,The complete genome of Proteus mirabilis XH1569,collected_by:Feng Zhao,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.1605,Proteus mirabilis strain PM52808,PM52808,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933297,584,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939735.1,"CP070572,CP070573,CP070574,CP070575",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,3,4,4300807,39.528862,4137,3935,sputum,,2019-09-03,Czech Republic,Czech Republic: Nymburk,,,,Acute respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,584.1606,Proteus mirabilis strain PM52260,PM52260,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933295,584,,,,,,,,2021-02-25T00:00:00Z,,PRJNA700516,GCA_016939715.1,"CP070569,CP070570,CP070571",,Charles University in Prague,PacBio Sequel,250X,Microbial Assembly v. 1.1,1,2,3,4296295,39.51968,4140,3936,sputum,,2019-08-06,Czech Republic,Czech Republic: Nymburk,,,,Pneumonia,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,584.1607,Proteus mirabilis strain PM53415,PM53415,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933303,584,,,,,,,,2021-03-01T00:00:00Z,,PRJNA700516,GCA_017114525.1,JAFIQK000000000,,Charles University in Prague,PacBio Sequel,250x,Microbial Assembly v. 1.1,4,2,6,4449693,39.574234,4384,4157,pressure ulcer swab,,2019-10-01,Czech Republic,Czech Republic: Nymburk,,,,Acute respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Acute respiratory failure,,,,,,,,,,,,,,100,2.7,Respiratory Diseases,Other Respiratory Diseases,Skin and Soft Tissue,Respiratory Diseases-Other Respiratory Diseases HP,584.1635,Proteus mirabilis strain PM52812,PM52812,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16933299,584,,,,,,,,2021-03-01T00:00:00Z,,PRJNA700516,GCA_017309565.1,JAFIQJ000000000,,Charles University in Prague,PacBio Sequel,250x,Microbial Assembly v. 1.1,3,4,7,4410794,39.62706,4322,4093,pressure ulcer swab,,2019-09-03,Czech Republic,Czech Republic: Nymburk,,,,Chronic respiratory failure,,,,,,,,,,,,,Molecular characterization of KPC-producing Enterobacterales from Czech hospitals\; evidence of an epidemic spread,collected_by:Nemocnice Nymburk,,,,,,,Chronic respiratory failure,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Skin and Soft Tissue,Respiratory Diseases-Other Respiratory Diseases HP,584.1766,Proteus mirabilis strain XH1653,XH1653,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16824307,584,,,,,,,,2021-06-21T00:00:00Z,,PRJNA679136,GCA_018972025.1,CP065039,,Zhejiang University,Illumina HiSeq; Oxford Nanopore MinION,300.0x,Unicycler v. v0.4.8,1,0,1,4113626,39.16598,3870,3733,urine,,2015-10-25,China,China:Hangzhou,,,,urinary tract infection,,,,,,,,,,,,,the genome sequence of Proteus mirabilis XH1653,collected_by:Xiaoting Hua,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,1.08,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.1798,Proteus mirabilis strain 6Pmi283,6Pmi283,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19608370,584,,,,,,,,2021-07-11T00:00:00Z,,PRJNA736086,GCA_019192645.1,"CP077963,CP077965,CP077964",,Universidad El Bosque,PacBio RSII,206.0x,HGAP v. 2.3,1,2,3,4189249,39.24849,3924,3789,urine,,2018-09,Colombia,Colombia: Bogota,,female,,urinary tract infection,,,,,,,,,,,,,6Pmi283 is a Colombian Proteus mirabilis isolate harboring blaNDM-1,collected_by:Shaio Clinical Foundation,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.2106,Proteus mirabilis HURS-181823,HURS-181823,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27518677,584,,,,,,,,2022-05-05T00:00:00Z,,PRJNA825519,GCA_023242175.1,CP096775,,,Oxford Nanopore; Illumina,38X 50X,Unicycler v. 0.4.9,1,0,1,4278183,39.120182,4089,3937,urine,,2018,Spain,Spain,,,,Unirary tract infection,,,,,,,,,,,,,,"collected_by:University Hospital Reina Sofia, Cordoba, Spain",,,,,,,Unirary tract infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,584.217,Proteus mirabilis strain T21,T21,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05715221,584,,,,,,,,2017-09-18T00:00:00Z,,PRJNA340922,GCA_002310875.1,"CP017082,CP017083,CP017084",,Zhejiang University,Pacbio,100x,SMRT analysis v. 2.3.1,1,2,3,4286593,39.68,4164,3915,sputum,,2013,China,China: Zhejiang,,,,ventilator-associated pneumonia,,,,,,,,,,,,,Proteus mirabilis Genome sequencing,collected_by:Yunsong Yu,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,100,0.9,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,584.218,Proteus mirabilis strain T18,T18,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05715220,584,,,,,,,,2017-09-18T00:00:00Z,,PRJNA340922,GCA_002310895.1,"CP017085,CP017086",,Zhejiang University,Pacbio,100x,SMRT analysis v. 2.3.1,1,1,2,4190461,39.26,4048,3803,urine,,2014,China,China: Zhejiang,,,,ventilator-associated pneumonia,,,,,,,,,,,,,Proteus mirabilis Genome sequencing,collected_by:Yunsong Yu,,,,,,,ventilator-associated pneumonia,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Urinary Tract,Respiratory Diseases-Pneumonia HP,584.2253,Proteus mirabilis strain XH983,XH983,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09908145,584,,,,,,,,2022-09-19T00:00:00Z,,PRJNA487687,GCA_025264285.1,"CP031846,CP031847",,Zhejiang University,PacBio RSII,300.0x,Canu v. v1.5,1,1,2,4153141,39.141243,4001,3831,blood,,2014-12-10,China,China: Hangzhou,,,,septicemia,,,,,,,,,,,,,the complete genome sequence of Proteus mirabilis XH983 by pacbio,collected_by:Xiaoting Hua,,,,,,,septicemia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,584.2308,Proteus mirabilis XH983,XH983,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09908145,584,,,,,,,,2022-09-19T00:00:00Z,,PRJNA487687,GCA_025264285.1,"CP031846,CP031847",,,PacBio RSII,300.0x,Canu v. v1.5,1,1,2,4153141,39.141243,4001,3831,blood,,2014-12-10,China,China: Hangzhou,,,,septicemia,,,,,,,,,,,,,,collected_by:Xiaoting Hua,,,,,,,septicemia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,584.2362,Proteus mirabilis DP2019,DP2019,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31634663,584,,,,,,,,2022-11-14T00:00:00Z,,PRJNA898893,,CP110673,,,PacBio Sequel,1826.51x,pb_assembly_microbial v. smrtlink10; Canu,1,0,1,3817239,38.624382,3470,3369,clinical isolate,,2019-01,China,China: Guangzhou,,,,urinary tract infection,,,,,,,,,,,,,,collected_by:Xiaoyan Deng,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.301,Proteus mirabilis strain K1609,K1609,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08798891,584,,,,,,,,2018-04-15T00:00:00Z,,PRJNA445791,GCA_003051845.1,CP028522,,The Jan Kochanowski University,Illumina MiSeq,90.0x,CLC Genomic Workbench v. 5,1,,1,3817795,38.496,3554,,hospital,,2000,Poland,Poland: Kielce,,,,Urinary trakt infection,,,,,,,,,,,,,To examinate the genetic basis of mechanisms engaged in Proteus mirabilis territoriality.;missing tRNA genes,collected_by:not applicated,,,,,,,Urinary trakt infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.302,Proteus mirabilis strain K670,K670,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08798946,584,,,,,,,,2018-04-03T00:00:00Z,,PRJNA445794,GCA_003030945.1,CP028356,,The Jan Kochanowski University,Illumina MiSeq,90.0x,CLC Genomic Workbench v. 5,1,,1,3935626,38.69517,3665,,hospital,,2000,Poland,Poland: Kielce,,,,Urinary tract infection,,,,,,,,,,,,,The model organism for studying the genetic basis of mechanisms engaged in Proteus mirabilis territoriality.,collected_by:not applicated,,,,,,,Urinary tract infection,,,,,,,,,,,,,,99.5,0.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Other,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,584.430,Proteus mirabilis strain CCUG 70746,CCUG 70746,Proteus mirabilis,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07602702,584,,,,,,CCUG:70746,,2018-06-06T00:00:00Z,,PRJNA401330,GCA_003194305.1,"CP023273,CP023274",,Chalmers University of Technology,Illumina MiSeq; PacBio,107.0x,SPAdes v. v3.7.0,1,1,2,4101638,39.28708,3933,3783,feces,,2013-01-24,Sweden,Sweden: Gothenburg,,,,,,,Resistant;Intermediate;Susceptible;Not defined,AMR Panel,,,,,,,,,"In this study, we aimed to characterize the resistome of highly multi-resistant pathogens, all phenotypically resistant to at least one carbapenem antibiotic.","collected_by:Clinical Microbiology Laboratory, Sahlgrenska University Hospital",,,,,,,N/A,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,585.123,Proteus vulgaris strain CCU063,CCU063,Proteus vulgaris,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08271944,585,,,,,,,,2021-01-15T00:00:00Z,,PRJNA312015,GCA_016647575.1,CP032663,,National Chung Cheng University,Oxford Nanopore; Illumina,40.0x,Unicycler v. 0.4.7,1,0,1,4141308,37.998333,3766,3676,blood,,2015,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,Environmental and clinical isolates of Shewanella,collected_by:Ching-Lin Shy,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,585055.56,Escherichia coli 55989,55989,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196158,585055,,,,MLST.Escherichia_coli_1.131,,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028695.1,CP028304,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4989876,50.786613,4966,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,587.141,Providencia rettgeri strain Pr-15-2-50,Pr-15-2-50,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11523820,587,,,,,,,,2019-05-06T00:00:00Z,,PRJNA540114,GCA_005155965.1,CP039844,,Zhengzhou University,Illumina; PacBio,12.0x,CLC Genomeics Workbench v. 10.0,1,,1,4649193,40.29678,4402,,synovial fluid,isolated from China，for bacteria resistance,2015,China,China,,female,,synovitis,,,,,,,,,,,,,These strain were isolated from China，for bacteria resistance.,collected_by:Zhengzhou University,,,,,,,synovitis,,,,,,,,,,,,,,99.46,1.62,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,587.225,Providencia rettgeri strain P01,P01,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15576635,587,,,,,,,,2020-07-26T00:00:00Z,,PRJNA647128,GCA_013694385.1,CP059298,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,4601020,40.54173,4383,4171,urine,,2014,China,China: Shandong,,,,Fever,,,,,,,,,,,,,Complete sequence of chromosome of strain P01,collected_by:a teaching hospital,,,,,,,Fever,,,,,,,,,,,,,,100,0.54,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,587.226,Providencia rettgeri strain 2055,2055,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15576908,587,,,,,,,,2020-07-27T00:00:00Z,,PRJNA647134,GCA_013702025.1,CP059345,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,4674814,40.450657,4355,4163,urine,,2013,China,China: Gansu,,,,Fever,,,,,,,,,,,,,Complete sequence of chromosome of strain 2055,collected_by:a public hospital,,,,,,,Fever,,,,,,,,,,,,,,100,1.08,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,587.328,Providencia rettgeri strain PreM15973,PreM15973,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19573044,587,,,,,,,,2021-06-13T00:00:00Z,,PRJNA735191,GCA_018861215.1,CP076406,,"Servicio Antimicrobianos, INEI-ANLIS Dr. Carlos G. Malbran",Illumina MiSeq; Oxford Nanopore MinION,40x,SPAdes v. 3.9.0,1,0,1,4367913,40.40511,4066,3895,screening,,2013-10,Argentina,Argentina,,,,Ischemic stroke,,,,,,,,,,,,,Characterization of NDM-producing Providencia rettgeri clinical isolate form Argentina,collected_by:Hospital General de Agudos Dr. Juan A Fernandez,,,,,,,Ischemic stroke,,,,,,,,,,,,,,100,1.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,587.503,Providencia rettgeri 18004577,18004577,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN25186315,587,,,,,,,,2022-06-06T00:00:00Z,,PRJNA799674,GCA_023650895.1,"CP098040,CP098041,CP098042",,,Illumina; Nanopore,100.0x,SPAdes v. 1.0,1,2,3,5067041,41.105705,5006,4762,urine,,2018-02-11,China,China:Shandong province,,,,bacterial infectious disease,,,,,,,,,,,,,,collected_by:Yingying Hao,,,,,,,bacterial infectious disease,,,,,,,,,,,,,,99.9,2.4,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,587.514,Providencia rettgeri 12105,12105,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29990039,587,,,,,,,,2022-10-31T00:00:00Z,,PRJNA862704,GCA_025916175.1,"CP109846,CP109847",,,PacBio,128.2x,HGAP v. 2.3,1,1,2,4662952,40.287975,4486,4271,urine,,2014-11-19,Mexico,"Mexico: Nuevo Leon, Monterrey",,,,urinary tract infection,,,,,,,,,,,,,,collected_by:Instituto Nacional de Salud de Mexico,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,587.560,Providencia rettgeri 12100,12100,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29990040,587,,,,,,,,2023-05-22T00:00:00Z,,PRJNA862704,,"CP118863,CP118864,CP118865",,,PacBio RSII,260.652x,HGAP v. 2.3,1,2,3,4781198,40.846184,4560,,urine,,2013-09-30,Mexico,"Mexico: Nuevo Leon, Monterrey",,,,urinary tract infection,,,,,,,,,,,,,,collected_by:Instituto Nacional de Salud de Mexico,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,1,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,587.58,Providencia rettgeri strain FDAARGOS_330,FDAARGOS_330,Providencia rettgeri,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173343,587,,,,,,FDA:FDAARGOS_330,,2018-03-09T00:00:00Z,,PRJNA231221,GCA_002984195.1,CP027418,,US Food and Drug Administration,PacBio; Illumina,15.0368768789957x,"SMRT v. 2.3.0, HGAP v. 3.0",1,,1,4518601,40.144814,4290,4109,urine,,2015-01-24,USA,USA:DC,,female,10Y,Urinary tract infection,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Urinary tract infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,58712.101,Salmonella enterica subsp. enterica serovar Anatum strain R16.0676,R16.0676,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09373897,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2018-06-15T00:00:00Z,,PRJNA474787,GCA_003231095.1,"CP029800,CP029801,CP029802",,"Centers for Disease Control, R.O.C (Taiwan)",Illumina MiSeq; MinION,50.0x,CLC NGS Cell v. 10.1.1; Canu v. 1.7,1,2,3,4798390,52.07186,4980,4810,pus,,2016-04-25,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,antibiotic resistant research,"collected_by:Landseed Hospital, Taiwan",,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,58712.251,Salmonella enterica subsp. enterica serovar Anatum strain Sal-2097,Sal-2097,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074771,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011465815.1,CP045465,,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,0,1,4813791,52.173912,4886,4613,clinical,,2013-11-01,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.252,Salmonella enterica subsp. enterica serovar Anatum strain Sal-3973,Sal-3973,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074786,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011465945.1,"CP045466,CP045467",,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,1,2,4866577,52.13603,4953,4697,clinical,,2016-09-15,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.48,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.254,Salmonella enterica subsp. enterica serovar Anatum strain Sal-1135,Sal-1135,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074770,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011465695.1,CP045464,,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,0,1,4773013,52.182552,4814,4551,clinical,,2012-06-22,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.257,Salmonella enterica subsp. enterica serovar Anatum strain Sal-4737,Sal-4737,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074806,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011466775.1,"CP045516,CP045517",,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,1,2,4728349,52.186928,4779,4519,clinical,,2017-08-17,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.48,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.258,Salmonella enterica subsp. enterica serovar Anatum strain Sal-5091,Sal-5091,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074811,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011466815.1,"CP045518,CP045519,CP045520,CP045521",,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,3,4,4902491,52.024387,5018,4743,clinical,,2017-11-24,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.48,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.259,Salmonella enterica subsp. enterica serovar Anatum strain Sal-4295,Sal-4295,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074794,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011466595.1,CP045515,,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,0,1,4673793,52.177494,4722,4449,clinical,,2017-01-11,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,58712.260,Salmonella enterica subsp. enterica serovar Anatum strain Sal-3948,Sal-3948,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13074785,58712,Anatum,,,MLST.Salmonella_enterica.64,,,,2020-03-19T00:00:00Z,,PRJNA578814,GCA_011466455.1,"CP045513,CP045514",,Zhejiang University School of Medicine,Oxford Nanopore GridION,100.0x,Unicycler v. 0.4.6,1,1,2,4850675,52.232815,4920,4650,clinical,,2016-09-06,Taiwan,Taiwan: Linkou,,,,gastroenteritis,,,,,,,,,,,,,This project investigates the genomic characteristics of the outbreak event caused by Salmonella serovar Anatum in Taiwan in 2016-2019.,collected_by:Chang Gung Memorial Hospital,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,588.211,Providencia stuartii strain 3347685,3347685,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17736026,588,,,,,,,,2021-04-22T00:00:00Z,,PRJNA698767,GCA_018128385.1,"CP071068,CP071069",,,Illumina NovaSeq; Oxford Nanopore MiniION,252x,Unicycler v. 0.4.8,1,1,2,4664788,41.97265,4696,4299,decubitus ulcer,,2020,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,588.252,Providencia stuartii CMC-4104,CMC-4104,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27484493,588,,,,,,,,2022-05-25T00:00:00Z,,PRJNA824933,GCA_023547145.1,"CP095443,CP095444,CP095442,CP095445",,,Oxford Nanopore MinION; Illumina NextSeq,70.0x,Flye v. MARCH-2022; Geneious v. Prime,1,3,4,4837555,41.74464,4777,4471,splenic fine needle aspirate,,2021-05-12,USA,"USA: Roanoke, VA",,male,45,Intra-abdominal infection (splenic abscess),,"host_description:Previous history of necrotizing pancreatitis with multiple necrosectomies and abdominal surgeries, now with splenic abscess that grew the XDR Providencia spp. With NDM;host_disease_outcome:Death;host_disease_stage:Organism isolated early in course from a fine needle aspiration prior to decompensation (eventually required pressor support and ventilation), eventually became bacteremic with index organism with seeding to the other organ systems such as the lungs (were then identified in pulmonary isolate);host_health_state:Significant comorbidities\; alcoholic necrotizing pancreatitis (likely linked to disease state)",,,,,,,,,,,,collected_by:Carilion Roanoke Memorial Hospital,,,,,,,Intra-abdominal infection (splenic abscess),Significant comorbidities; alcoholic necrotizing pancreatitis (likely linked to disease state),Death,"Previous history of necrotizing pancreatitis with multiple necrosectomies and abdominal surgeries, now with splenic abscess that grew the XDR Providencia spp. With NDM","Organism isolated early in course from a fine needle aspiration prior to decompensation (eventually required pressor support and ventilation), eventually became bacteremic with index organism with seeding to the other organ systems such as the lungs (were then identified in pulmonary isolate)",,,,,,,,,,100,0.4,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,588.26,Providencia stuartii strain BE2467,BE2467,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05629093,588,,,,,,,,2016-12-02T00:00:00Z,27895127,PRJNA340005,GCF_001888205.1,"CP017054,CP017055,CP017056","NZ_CP017054.1,NZ_CP017055.1,NZ_CP017056.1",University of Michigan Medical School,PacBio,55.3,HGAP v. 3,1,2,3,4607493,41.78,4608,4206,urine,isolated from the urine of a female with an indwelling urinary catheter,1983-12,USA,USA: Maryland,,female,,urinary tract infection,,,,,,,,,,,,,To sequence the genome of a urease-positive and plasmid-bearing isolate of Providencia stuartii that was isolated from the urine of a female with an indwelling urinary catheter.,collected_by:Harry mobley,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,0.7,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,588.275,Providencia stuartii CAVP496,CAVP496,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33687286,588,,,,,,,,2023-03-20T00:00:00Z,,PRJNA942364,,"CP119540,CP119541,CP119545,CP119544,CP119543,CP119542",,,Illumina MiSeq + Oxford Nanopore MinION,100X,Unicycler v. v0.5.0,1,5,6,4653186,41.45624,4491,4200,human,,,USA,USA: Virginia,,,,Bacteremia,,,,,,,,,,,,,,collected_by:University of Virginia Health System,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.7,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,588.276,Providencia stuartii CAVP450,CAVP450,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33687284,588,,,,,,,,2023-03-20T00:00:00Z,,PRJNA942364,,"CP119552,CP119553,CP119558,CP119557,CP119556,CP119555,CP119554",,,Illumina MiSeq + Oxford Nanopore MinION,100X,Unicycler v. v0.5.0,1,6,7,4655992,41.46532,4500,4203,human,,,USA,USA: Virginia,,,,Bacteremia,,,,,,,,,,,,,,collected_by:University of Virginia Health System,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.6,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,588.277,Providencia stuartii CAVP490,CAVP490,Providencia stuartii,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33687285,588,,,,,,,,2023-03-20T00:00:00Z,,PRJNA942364,,"CP119546,CP119547,CP119551,CP119550,CP119549,CP119548",,,Illumina MiSeq + Oxford Nanopore MinION,100X,Unicycler v. v0.5.0,1,5,6,4622190,41.413788,4462,4171,human,,,USA,USA: Virginia,,,,Bacteremia,,,,,,,,,,,,,,collected_by:University of Virginia Health System,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.5,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,59201.2825,Salmonella enterica subsp. enterica strain LHST_2018,LHST_2018,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14691772,59201,,,,MLST.Salmonella_enterica.1,,,,2020-05-04T00:00:00Z,,PRJNA627952,GCA_012970745.1,"CP052767,CP052768",,"Christian Medical College, Vellore",IonTorrent; Oxford Nanopore MiniION,152.0x,Unicycler v. 0.4.8; Canu Correct v. 2.0,1,1,2,4855364,51.97942,5264,4696,blood,,2018-12-27,India,India: Mumbai,,,,Enteric Fever,,,,,,,,,,,,,Complete genome of cephalosporin resistant S. Typhi carrying IncX3 plasmid isolated from India,"collected_by:Lilavati Hospital & Research Centre, Mumbai",,,,,,,Enteric Fever,,,,,,,,,,,,,,99.83,0.04,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,59201.3173,Salmonella enterica subsp. enterica strain DRB_0883TJX21,DRB_0883TJX21,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19351183,59201,,,,MLST.Salmonella_enterica.40,,,,2021-12-09T00:00:00Z,,PRJNA732894,GCA_021134575.1,"CP076466,CP076467,CP076468",,Microbion SrL,Illumina MiSeq; Oxford Nanopore MinION,150.0x,CLC NGS Cell v. v7,1,2,3,4966639,52.06789,5048,4702,,,2020-10-10,,Italy,,,,,,,,,,,,,,,,,Genome assembly of a multidrug resistant Salmonella Group-B (ESBL) isolated from a patient with watery diarrhea,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,59201.3269,Salmonella enterica subsp. enterica 3018683606,3018683606,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26818630,59201,,,,MLST.Salmonella_enterica.34,genotype:ST3606,,,2022-03-31T00:00:00Z,,PRJNA818143,GCA_022760155.1,"CP094332,CP094333,CP094334,CP094335,CP094336,CP094337",,,Illumina HiSeq; PacBio,304.03x,HGAP v. 4; FALCON v. 0.3,1,5,6,5149873,52.117752,5338,4990,feces,,2021-10,China,China: Zhuhai,,,,Infectious diarrhea,,,,,,,,,,,,,,collected_by:Jie Wei,,,,,,,Infectious diarrhea,,,,,,,,,,,,,,96.3,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,59201.3771,Salmonella enterica subsp. enterica 123,123,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33038040,59201,,,,MLST.Salmonella_enterica.34,,,,2023-02-12T00:00:00Z,,PRJNA930969,,"CP117184,CP117186,CP117187,CP117185",,,Oxford Nanopore GridION; Illumina HiSeq,100.0x,Unicycler v. 0.5.0,1,3,4,5092381,52.168915,5249,4927,stool,,2019,China,China: Sanmen,,,,Infection,,,,,,,,,,,,,,collected_by:Danni Bao,,,,,,,Infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,59201.3810,Salmonella enterica subsp. enterica BC04,BC04,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35714885,59201,,,,MLST.Salmonella_enterica.1,,,,2023-07-11T00:00:00Z,,PRJNA982791,,CP129110,,,Oxford Nanopore MinION,590.0x,Unicycler v. October-2022,1,0,1,4807678,52.081005,5070,4621,blood,,2015-08-03,Tanzania,Tanzania,,,,Typhoid fever,,,,,,,,,,,,,,collected_by:Annette Onken,,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,59201.3811,Salmonella enterica subsp. enterica BC06,BC06,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35714917,59201,,,,MLST.Salmonella_enterica.1,,,,2023-07-11T00:00:00Z,,PRJNA982791,,CP129109,,,Oxford Nanopore MinION,590.0x,Unicycler v. October-2022,1,0,1,4807710,52.081013,5087,4641,blood,,2016-02-02,Tanzania,Tanzania,,,,Typhoid fever,,,,,,,,,,,,,,collected_by:Annette Onken,,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,59201.3812,Salmonella enterica subsp. enterica 4_29_19,4_29_19,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34994532,59201,,,,MLST.Salmonella_enterica.469,,,,2023-07-21T00:00:00Z,,PRJNA972423,,CP126310,,,Illumina MiSeq; Oxford Nanopore MinION,400.0x,FullForcePlasmidAssembler (FFPA.py) v.,1,0,1,4919121,52.089813,4973,4639,urinary infection,,2018,Italy,Italy,,,,,,,,,,,,,,,,,,sample_type:isolate strain,,,,,,,,,,,,,Enter-Net-Italia,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,59201.911,Salmonella enterica subsp. enterica strain NCTC6480,NCTC6480,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4012326,59201,"Florida, 1 , 6, 14, 25 : D : 1, 7",,,MLST.Salmonella_enterica.931,,NCTC:6480,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900477995.1,LS483454,,SC,,,,1,,1,4907449,51.943523,4971,4586,not available: to be reported later,,1942,,,,,,,,host_health_state:Enteritis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Enteritis,,,100,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,59201.928,Salmonella enterica subsp. enterica strain LSP 389/97,LSP 389/97,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04849646,59201,,,,MLST.Salmonella_enterica.19,,,,2018-07-31T00:00:00Z,,PRJNA318369,GCA_003347075.1,"CP018219,CP018220",,University of Oviedo,PacBio,50.0x,smrt pac bio v. 2014,1,1,2,5099344,52.16112,5393,5194,feces,,1997,Spain,Spain: Asturias,,,,Salmonella gastroenteritis,,,,,,,,,,,,,Genome sequences of Salmonella strains from Asturias,collected_by:LSP,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,59204.19,Salmonella enterica subsp. diarizonae strain HZS154,HZS154,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07633032,59204,,,,,,,,2017-11-21T00:00:00Z,,PRJNA406863,GCA_002794415.1,CP023345,,The First Affiliated Hospital College of Medicine Zhejiang University,PacBio,151.67x,SMRTanalysis v. R2.3.0,1,,1,5087369,51.36,5270,4933,stool,,2016-09,China,China: Hangzhou,,male,83,bacterial enteropathy,,,,,,,,,,,,,Genomic analysis of Salmonella enterica subsp. diarizonae isolated from pus of a patient with bacterial enteropathy,collected_by:Chen Qiong,,,,,,,bacterial enteropathy,,,,,,,,,,,,,,100,1.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,595.395,Salmonella enterica subsp. enterica serovar Infantis strain 119944,119944,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13850655,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2020-02-21T00:00:00Z,,PRJNA601150,GCA_010919335.1,"CP047881,CP047882",,Sheba medical center,Illumina GAII; Oxford Nanopore MiniION,671.0x,Unicycler v. Oct-2019,1,1,2,5011038,52.171566,5096,4734,stool sample,,2008-11,Israel,Israel,,,,Salmonella gastroenteritis,,,,,,,,,,,,,Complete genome of Salmonella enterica subsp. enterica serovar Infantis str. 119944,collected_by:The Infectious Diseases Research Laboratory,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.58,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,595.399,Salmonella enterica subsp. enterica serovar Infantis strain SBO53,SBO53,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10837496,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2020-04-09T00:00:00Z,,PRJNA521806,GCA_012223625.1,"CP040061,CP040062",,Centro de Ciencias Genomicas - UNAM,Illumina MiSeq,56X,SPAdes v. 3.13.0,1,1,2,5005995,52.140587,5188,4864,stool; hospital,,2016-07-19,Bolivia,Bolivia: Santa Cruz de la Sierra,,female,2 years,Salmonella gastroenteritis,,,,,,,,,,,,,"In the framework of the CYTED-SalmoIber network, we performed whole genome sequencing to analyze Salmonella enterica strains from diverse sources and serovars recovered in several Latin-American countries. The aim of this project is to obtain an overview of the full complement of virulence and antimicrobial resistance determinants for the most abundant Salmonella serovars in the region.",collected_by:Lorena Soleto,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.58,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,595.400,Salmonella enterica subsp. enterica serovar Infantis strain SPE102,SPE102,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10837492,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2020-04-09T00:00:00Z,,PRJNA521806,GCA_012223285.1,"CP040164,CP040165",,Centro de Ciencias Genomicas - UNAM,Illumina MiSeq,84X,SPAdes v. 3.13.0,1,1,2,4993635,52.13264,5149,4849,stool; hospital,,2016-03,Peru,Peru: Lima,,female,,Recurrent salmonellosis,,,,,,,,,,,,,"In the framework of the CYTED-SalmoIber network, we performed whole genome sequencing to analyze Salmonella enterica strains from diverse sources and serovars recovered in several Latin-American countries. The aim of this project is to obtain an overview of the full complement of virulence and antimicrobial resistance determinants for the most abundant Salmonella serovars in the region.",collected_by:Coralith Garcia,,,,,,,Recurrent salmonellosis,,,,,,,,,,,,,,100,0.58,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,595.401,Salmonella enterica subsp. enterica serovar Infantis strain SBO17,SBO17,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10837495,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2020-04-09T00:00:00Z,,PRJNA521806,GCA_012223145.1,CP040163,,Centro de Ciencias Genomicas - UNAM,Illumina MiSeq,54X,SPAdes v. 3.13.0,1,0,1,4584024,52.284424,4598,4354,stool; hospital,,2015-12-15,Bolivia,Bolivia: Santa Cruz de la Sierra,,male,1 year,Salmonella gastroenteritis,,,,,,,,,,,,,"In the framework of the CYTED-SalmoIber network, we performed whole genome sequencing to analyze Salmonella enterica strains from diverse sources and serovars recovered in several Latin-American countries. The aim of this project is to obtain an overview of the full complement of virulence and antimicrobial resistance determinants for the most abundant Salmonella serovars in the region.",collected_by:Lorena Soleto,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,595.403,Salmonella enterica subsp. enterica serovar Infantis strain SPE55,SPE55,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10837490,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2020-04-09T00:00:00Z,,PRJNA521806,GCA_012224005.1,"CP040065,CP040066",,Centro de Ciencias Genomicas - UNAM,Illumina MiSeq,59X,SPAdes v. 3.13.0,1,1,2,4965265,52.132103,5121,4814,bloodstream; hospital,,2011-02-28,Peru,Peru: Lima,,male,,Bacteremia,,,,,,,,,,,,,"In the framework of the CYTED-SalmoIber network, we performed whole genome sequencing to analyze Salmonella enterica strains from diverse sources and serovars recovered in several Latin-American countries. The aim of this project is to obtain an overview of the full complement of virulence and antimicrobial resistance determinants for the most abundant Salmonella serovars in the region.",collected_by:Coralith Garcia,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.72,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,595.829,Salmonella enterica subsp. enterica serovar Infantis 423_13,423_13,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26540071,595,Infantis,,,MLST.Salmonella_enterica.32,,,,2022-04-18T00:00:00Z,35358729,PRJNA814220,GCA_023024545.1,"CP093373,CP093374",,,Oxford Nanopore MinION; IonTorrent,50.0x,SPAdes v. Unicycler 0.4.8,1,1,2,5044286,52.1499,5249,4803,stool,,2013,Brazil,"Brazil: Sao Paulo, Sao Paulo",,male,21,Diarrhea,,,,,,,,,,,,,,collected_by:Instituto Adolfo Lutz,,,,,,,Diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases NHP,59561.31,Trueperella bernardiae UMB8254,UMB8254,Trueperella bernardiae,Trueperella,Actinomycetaceae,Actinomycetales,Actinomycetes,Actinomycetota,SAMN35366347,59561,,,,,,,,2023-06-08T00:00:00Z,,PRJNA316969,,CP127099,,,Nanopore,236x,Flye v. Flye 2.9,1,0,1,2103060,65.19101,1898,1855,urine,,2018-01-31,USA,"USA: Maywood, Loyola University Medical Center",,,,,,,,,,,,,,,,,,,human microbiome,Bladder,URINE,,,,,,,,,,,,,,human microbiome,,,,99.8,0.8,,,Urinary Tract,- HP,596.109,Salmonella enterica subsp. enterica serovar Muenchen 180135033,180135033,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN23543477,596,Muenchen,,,MLST.Salmonella_enterica.82,,,,2022-03-14T00:00:00Z,,PRJNA785151,GCA_022559825.1,"CP088901,CP088902",,,Illumina HiSeq; Oxford Nanopore MinION,2700.0x,TryCycler v. 0.5.0,1,1,2,5142025,51.888973,5269,4910,blood,,2018,Israel,"Israel: Sheba medical cneter, Tel Hashomer",,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:Sheba medical center,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.58,Gastrointestinal Diseases,Diarrheal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Diarrheal Diseases NHP,59843.9,Paenibacillus glucanolyticus strain W10507,W10507,Paenibacillus glucanolyticus,Paenibacillus,Paenibacillaceae,Bacillales,Bacilli,Bacillota,SAMN08743844,59843,,,,,,,,2018-04-04T00:00:00Z,,PRJNA282954,GCA_003033945.1,CP028366,,The Forsyth Institute,PacBio,94x,canu v. 1.6 / quiver,1,,1,6573405,48.78275,6426,5898,"subgingival plaque, gingival sulcus",,2011-09-21,United Kingdom,United Kingdom: London,env_biome:Human oral cavity,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,Healthy,,,,,,,,,Human oral cavity,,,,100,1.4,,,Oral,- HP,615.1121,Serratia marcescens strain 4201,4201,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13840998,615,,,,,,,,2020-01-21T00:00:00Z,,PRJNA595033,GCA_009909345.1,"CP047679,CP047680,CP047681",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore,320X,Unicycler v. 4.0,1,2,3,5428798,59.319042,5317,5060,sputum,,2019-02-27,China,China,,,,,,,,,,,,,,,,,"Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most associated with clinical infections, data on Serratia marcescens are inadequate and superficial. In this study, we analysed 36 carbapenem-resistant S. marcescens (CRSM) isolates that clonally disseminated in our hospital from April 2018 to March 2019 using whole genome sequencing (WGS).",sample_type:sputum,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,615.1122,Serratia marcescens strain 3024,3024,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13840997,615,,,,,,,,2020-01-21T00:00:00Z,,PRJNA595033,GCA_009909365.1,"CP047682,CP047683,CP047684",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore,287X,Unicycler v. 4.0,1,2,3,5534941,59.611782,5447,5156,blood,,2018-12-25,China,China,,,,,,,,,,,,,,,,,"Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most associated with clinical infections, data on Serratia marcescens are inadequate and superficial. In this study, we analysed 36 carbapenem-resistant S. marcescens (CRSM) isolates that clonally disseminated in our hospital from April 2018 to March 2019 using whole genome sequencing (WGS).",sample_type:blood,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,615.1123,Serratia marcescens strain 1140-,1140-,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13840995,615,,,,,,,,2020-01-21T00:00:00Z,,PRJNA595033,GCA_009909385.1,"CP047688,CP047689,CP047690",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore,311X,Unicycler v. 4.0,1,2,3,5535124,59.611816,5445,5155,body fluid,,2018-09-05,China,China,,,,,,,,,,,,,,,,,"Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most associated with clinical infections, data on Serratia marcescens are inadequate and superficial. In this study, we analysed 36 carbapenem-resistant S. marcescens (CRSM) isolates that clonally disseminated in our hospital from April 2018 to March 2019 using whole genome sequencing (WGS).",sample_type:body fluid,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,615.1124,Serratia marcescens strain 2838,2838,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13840996,615,,,,,,,,2020-01-21T00:00:00Z,,PRJNA595033,GCA_009909405.1,"CP047685,CP047686,CP047687",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore,362X,Unicycler v. 4.0,1,2,3,5522536,59.630123,5428,5143,body fluid,,2018-12-17,China,China,,,,,,,,,,,,,,,,,"Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most associated with clinical infections, data on Serratia marcescens are inadequate and superficial. In this study, we analysed 36 carbapenem-resistant S. marcescens (CRSM) isolates that clonally disseminated in our hospital from April 2018 to March 2019 using whole genome sequencing (WGS).",sample_type:body fluid,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,615.1125,Serratia marcescens strain C110,C110,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13840994,615,,,,,,,,2020-01-21T00:00:00Z,,PRJNA595033,GCA_009909425.1,"CP047691,CP047692,CP047693",,"Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University",Oxford Nanopore,316X,Unicycler v. 4.0,1,2,3,5533861,59.614147,5443,5153,sputum,,2018-06-16,China,China,,,,,,,,,,,,,,,,,"Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most associated with clinical infections, data on Serratia marcescens are inadequate and superficial. In this study, we analysed 36 carbapenem-resistant S. marcescens (CRSM) isolates that clonally disseminated in our hospital from April 2018 to March 2019 using whole genome sequencing (WGS).",sample_type:sputum,,,,,,,,,,,,,,,,,,,,,99.81,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,615.1226,Serratia marcescens strain SER00094,SER00094,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14265996,615,,,,,,,,2020-03-30T00:00:00Z,,PRJNA609916,GCA_011769885.1,CP050447,,University of Pittsburgh School of Medicine,Oxford Nanopore MinION,100x,Unicycler v. v0.4.8-beta,1,0,1,5217372,59.470917,4984,4814,sputum,,2017,USA,"USA: Pennsylvania, Pittsburgh",,,,,,,,,,,,,,,,,"Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this threat by facilitating the rapid spread of genes conferring antibiotic resistance, enhanced virulence, and environmental persistence between nosocomial pathogens. Despite recent advances in microbial genomics, studies of HGT in hospital settings remain limited in scope. The objective of this study was to identify and track the movement of MGEs within a single hospital system using unbiased methods.",collected_by:University of Pittsburgh Medical Center,,,,,,,Unknown,,,,,,,,,,,,,,99.86,1,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,615.1292,Serratia marcescens strain ICU-4,ICU-4,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15470909,615,,,,,,,,2020-07-20T00:00:00Z,,PRJNA644677,GCA_013425845.1,CP059036,,Universidade Federal de Pelotas,IonTorrent,30X,Newbler v. 2017; CLC NGS Cell v. 2017;,1,0,1,5209716,59.86702,5774,4885,blood,,2013,Brazil,Brazil:Dourados,,,,Serratia infection,,,,,,,,,,,,,"Genome sequencing and assembly of Serratia marcescens strain 02, 03 and 04",collected_by:UFGD,,,,,,,Serratia infection,,,,,,,,,,,,,,97.92,1.12,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,615.1293,Serratia marcescens strain ICU-3,ICU-3,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15470908,615,,,,,,,,2020-07-20T00:00:00Z,,PRJNA644677,GCA_013425865.1,CP059037,,Universidade Federal de Pelotas,IonTorrent,30X,Newbler v. 2017; CLC NGS Cell v. 2017;,1,0,1,5215968,59.869022,5597,4882,blood,,2013,Brazil,Brazil:Dourados,,,,Serratia infection,,,,,,,,,,,,,"Genome sequencing and assembly of Serratia marcescens strain 02, 03 and 04",collected_by:UFGD,,,,,,,Serratia infection,,,,,,,,,,,,,,97.43,1.12,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,615.1294,Serratia marcescens strain ICU-2,ICU-2,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15470907,615,,,,,,,,2020-07-20T00:00:00Z,,PRJNA644677,GCA_013425885.1,CP059038,,Universidade Federal de Pelotas,IonTorrent,30X,Newbler v. 2017; CLC NGS Cell v. 2017;,1,0,1,5226346,59.862072,5640,4911,blood,,2013,Brazil,Brazil:Dourados,,,,Serratia infection,,,,,,,,,,,,,"Genome sequencing and assembly of Serratia marcescens strain 02, 03 and 04",collected_by:UFGD,,,,,,,Serratia infection,,,,,,,,,,,,,,98.5,1.12,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,615.1295,Serratia marcescens strain 12/2010,12/2010,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14999148,615,,,,,,,,2020-07-20T00:00:00Z,21967170,PRJNA634544,GCA_013426135.1,CP053925,,University of Manitoba,PacBio RSII,30.0x,HGAP v. SMRTLink V6,1,0,1,5642069,59.389687,5596,5325,platelet concentrate,,2010,Canada,Canada: Ottawa,,,,septicemia,,,,,,,,,,,,,Serratia marcescens genome from platelet concentration,collected_by:Canadian Blood Services,,,,,,,septicemia,,,,,,,,,,,,,,99.86,0.67,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,615.1296,Serratia marcescens strain 11/2010,11/2010,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14998449,615,,,,,,,,2020-07-20T00:00:00Z,21967170,PRJNA634532,GCA_013426155.1,"CP053927,CP053926",,University of Manitoba,PacBio RSII,30.0x,HGAP v. SMRTLink V6,1,1,2,5492570,59.389904,5449,5170,platelet concentrate,,2010,Canada,Canada: Ottawa,,,,septicemia,,,,,,,,,,,,,This is a platelet concentrate bacterial contaminant Serratia marcescens CBS11 (11/2010),collected_by:Canadian Blood Services,,,,,,,septicemia,,,,,,,,,,,,,,99.86,0.45,Bloodstream Infections,Sepsis,Other,Bloodstream Infections-Sepsis HP,615.1999,Serratia marcescens strain SL267 strain Serratia marcescens SL267,Serratia marcescens SL267,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00389786,615,,,,,,,,2021-10-01T00:00:00Z,,PRJDB11945,GCA_020886895.1,"AP024916,AP024917",,"Department of Microbiology, Juntendo University",Oxford nanopore MinION; Illumina Miseq,77x,Unicycler v. 0.4.7,1,1,2,5173769,59.660336,4998,4833,,,2018-07-03,Japan,Japan:Tokyo,,,,,,,,,,,,,,,,,The aim of this project is to analyze a transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-beta-lactamase in three clinical isolates of Enterobacteriaceae from one patient.,"biomaterial_provider:St. Luke's International Hospital, Tokyo",not applicable,not applicable,Pancreatic fluid,not applicable,A transferrable IncL/M plasmid harboring IMP-1,,,Pancreatitis,,,,,,,,,not applicable,,,,99.81,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,615.516,Serratia marcescens strain UMH7,UMH7,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164061,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220715.1,"CP018919,CP018920,CP018921,CP018922",,University of Michigan,PacBio,245.67,HGAP v. 2,1,3,4,5363653,59.24,5298,5038,university of michigan health system,,2013-09,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.517,Serratia marcescens strain UMH10,UMH10,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164064,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220695.1,CP018928,,University of Michigan,PacBio,279.21,HGAP v. 2,1,,1,5221713,59.34,5024,4817,university of michigan health system,,2014-05,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.6,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.518,Serratia marcescens strain UMH6,UMH6,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164060,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220675.1,CP018926,,University of Michigan,PacBio,328.56,HGAP v. 2,1,,1,5192910,59.52,5056,4838,university of michigan health system,,2013-07,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.519,Serratia marcescens strain UMH3,UMH3,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164058,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220655.1,CP018925,,University of Michigan,PacBio,241.84,HGAP v. 2,1,,1,5300955,59.7,5174,4954,university of michigan health system,,2014-03,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.520,Serratia marcescens strain UMH5,UMH5,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164059,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220635.1,"CP018917,CP018918",,University of Michigan,PacBio,303.22,HGAP v. 2,1,1,2,5457855,59.5,5400,5134,university of michigan health system,,2014-04,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.9,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.521,Serratia marcescens strain UMH1,UMH1,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164056,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220615.1,"CP018915,CP018916",,University of Michigan,PacBio,missing,HGAP v. 2,1,1,2,5129681,59.45,4911,4726,university of michigan health system,,2013-11,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.522,Serratia marcescens strain UMH12,UMH12,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164066,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220595.1,CP018930,,University of Michigan,PacBio,319.96,HGAP v. 2,1,,1,5196805,59.33,5040,4837,university of michigan health system,,2014-08,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.523,Serratia marcescens strain UMH11,UMH11,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164065,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220575.1,CP018929,,University of Michigan,PacBio,253.84,HGAP v. 2,1,,1,5221717,59.34,5022,4816,university of michigan health system,,2014-05,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.6,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.524,Serratia marcescens strain UMH9,UMH9,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164063,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220555.1,CP018923,,University of Michigan,PacBio,284.3,HGAP v. 2,1,,1,5024591,60.16,4803,4615,university of michigan health system,,2014-08,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.525,Serratia marcescens strain UMH8,UMH8,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164062,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220535.1,CP018927,,University of Michigan,PacBio,316.97,HGAP v. 2,1,,1,5155137,59.63,5004,4798,university of michigan health system,,2013-08,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.526,Serratia marcescens strain UMH2,UMH2,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06164057,615,,,,,,,,2017-07-18T00:00:00Z,28536292,PRJNA357595,GCA_002220515.1,CP018924,,University of Michigan,PacBio,244.43,HGAP v. 2,1,,1,5308626,59.39,5181,4926,university of michigan health system,,2014-01,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"Serratia marcescens is a ubiquitous Gram-negative bacterium that causes healthcare-associated opportunistic infections that can be difficult to treat due to multi-drug resistance. In this study, we sought to determine the fitness requirements of S. marcescens during mammalian bloodstream infection by performing transposon insertion sequencing using a murine model of bacteremia. Mice were infected intravenously with a library of random transposon insertion mutants, followed by recovery of bacteria from the spleen and the identification of bacterial fitness genes.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,100,0.3,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,615.650,Serratia marcescens strain CAV1761,CAV1761,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09205456,615,,,,,,,,2018-05-22T00:00:00Z,,PRJNA411762,GCA_003146705.1,"CP029449,CP029448,CP029444,CP029445,CP029447,CP029446",,Oxford University,PacBio,36x,HGAP v. MAY-2015,1,5,6,5896859,58.474148,5994,5639,peri-rectal,,2014-03-01,USA,USA:Virginia,,,,,,,,,,,,,,,,,A collection of Gammaproteobacteria isolated from environmental and patient sources originating from a single hospital in the United States;genome length too large,collected_by:Clinical Microbiology University of Virginia Health System,,,,,,,Not Applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,615.652,Serratia marcescens strain 332,332,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06311524,615,,,,,,,,2018-06-05T00:00:00Z,,PRJNA278886,GCA_003186475.1,CP021164,,Brigham & Women's Hospital,PacBio,305.0x,HGAP v. v.3.0,1,,1,5059456,59.39447,4981,4764,wound,,2016,USA,USA:Boston,,female,72,,,host_subject_id:SBJ-10005,Susceptible;Resistant,AMR Panel,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,Missing,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,615.973,Serratia marcescens strain BWH-35,BWH-35,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04276915,615,,,,,,,,2018-04-03T00:00:00Z,,PRJNA278886,GCA_003031645.1,"CP020507,CP020508",,Brigham & Women's Hospital,PacBio,349.43x,HGAP v. 3,1,1,2,5513932,58.73926,5511,5202,sputum,,2012,USA,USA:Boston,,male,63,,,host_subject_id:SBJ-9934,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,missing,,,,,,,,,,,,,,99.88,0.51,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,615.974,Serratia marcescens strain BWH-23,BWH-23,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04276914,615,,,,,,,,2018-04-03T00:00:00Z,,PRJNA278886,GCA_003032415.1,"CP020501,CP020502",,Brigham & Women's Hospital,PacBio,564.56x,HGAP v. 3,1,1,2,5147407,59.342228,4975,4780,blood,,2012,USA,USA:Boston,,female,42,,,host_subject_id:SBJ-9935,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Xiaomin Zhao,,,,,,,missing,,,,,,,,,,,,,,99.86,0.11,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,615.999,Serratia marcescens strain 4928STDY7387938,4928STDY7387938,Serratia marcescens,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4623347,615,,,,,,,,2019-07-09T00:00:00Z,,PRJEB22252,GCA_902166755.1,LR607375,,SC,,,,1,,1,5046965,60.38327,4651,,faecal,"derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process",2018,United Kingdom,United Kingdom,,,,,,host_health_state:carriage,,,,,,,,,,,"The study investigates how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. Culturing efforts coupled with whole genome sequencing of the gastrointestinal bacteria can address key questions that are computationally non-trivial using shotgun metagenomics alone. This comprehensive gut microbiota-derived bacterial genome collection provides the basis to improve the taxonomic classification resolution of metagenomic analysis, and to allow subsequent in vitro and in vivo experiments on host physiology and gut colonisation process. To get a broad and comprehensive coverage of the gut microbiota, we cultivated bacterial species from human faecal samples on different selectice agar media and broth. Samples are whole-genome sequenced on Illumina X10 150bp PE. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/;Bacterial Genome",,,,,,,,,,,,,,,,,,,carriage,,,99.52,0,,,Other,- HP,61645.296,Enterobacter asburiae strain A2563,A2563,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00197875,61645,,,,MLST.Enterobacter_cloacae.484,,,,2020-02-06T00:00:00Z,,PRJDB9129,GCA_011396735.1,AP022628,,"Microbiology, Juntendo University School of Medicine",MiSeq; MinION,1.00x,Unicycler v. 0.4.4,1,0,1,4808368,55.76942,4614,4527,,,2018,Japan,Japan:Saitama,,,,,,,,,,,,,,,,,A total of 32 clinical isolates of E. cloacae complex non-susceptible to carbapenems were obtained from patients at 13 hospitals in Japan. Whole genome sequencing (WGS) was conducted using MiSeq.,,missing,missing,missing,missing,carbapenem-resistant and colistin-non-resistant Enterobacter cloacae complex in Japan,,,,,,,,,,,,missing,,,,99.97,0.57,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,61645.430,Enterobacter asburiae strain Ent261,Ent261,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMD00268104,61645,,,,MLST.Enterobacter_cloacae.484,,,,2021-09-02T00:00:00Z,,PRJDB10973,GCA_019973695.1,"AP024281,AP024282",,Rakuno Gakuen University,Illumina Miseq; Nanopore Minion,100x,Flye v. 2.6.,1,1,2,5060521,55.686893,4940,4852,clinical situations,derived from clinical situations,2019,Japan,Japan:Tokyo,,,,,,,,,,,,,,,,,The relationship between some antibiotics resistance and resistance gene in Enterobacter spp. has not been clarified. The purpose of this project is to clarify the relationship between antibiotic resistance and resistance genes using Enterobacter spp. derived from clinical situations.,,not applicable,not applicable,pleural effusion,missing,Whole genome sequence of antibiotic resistance Enterobacter spp.,,,,,,,,,,,,not applicable,,,,99.67,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,61645.530,Enterobacter asburiae 5549,5549,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN26527994,61645,,,,MLST.Enterobacter_cloacae.252,,,,2022-03-15T00:00:00Z,,PRJNA813899,GCA_022570715.1,"CP093154,CP093155,CP093156",,,Oxford Nanopore,100.0x,Unicycler v. 0.5.0,1,2,3,5031473,55.402863,4971,4798,urine,,2019-06-19,China,China:Yiwu,,,,bronchial granuloma,,,,,,,,,,,,,,collected_by:Zhu zhiqiang,,,,,,,bronchial granuloma,,,,,,,,,,,,,,99.07,1.69,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,61645.543,Enterobacter asburiae AR2284-yvys,AR2284-yvys,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21379553,61645,,,,MLST.Enterobacter_cloacae.252,,,,2022-04-18T00:00:00Z,35307563,PRJNA762162,GCA_023023145.1,"CP083830,CP083831,CP083832,CP083833",,,Oxford Nanopore MinION,10x,Unicycler v. v0.4.8,1,3,4,5379346,54.949783,5388,5160,sputum,,2019-07,China,China,,,,Pneumonia,,,,,,,,,,,,,,collected_by:Yushan Cui,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,61645.544,Enterobacter asburiae AR0468-yvys,AR0468-yvys,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21379552,61645,,,,MLST.Enterobacter_cloacae.27,,,,2022-04-18T00:00:00Z,35307563,PRJNA762162,GCA_023023265.1,"CP083834,CP083835,CP083836,CP083837,CP083838,CP083839,CP083840,CP083841",,,Oxford Nanopore MinION,10x,Unicycler v. v0.4.8,1,7,8,5385038,55.133186,5475,5243,sputum,,2018-04,China,China,,,,Pneumonia,,,,,,,,,,,,,,collected_by:Yushan Cui,,,,,,,Pneumonia,,,,,,,,,,,,,,99.9,0.4,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,61645.623,Enterobacter asburiae R_A5.MM,R_A5.MM,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29928038,61645,,,,MLST.Enterobacter_cloacae.22,,,,2022-08-09T00:00:00Z,,PRJNA861833,GCA_024599655.1,CP102247,,,PacBio Sequel,100X,HGAP v. JAN-2022,1,0,1,4838058,55.91421,4606,4471,catheter urine,,2020,South Africa,South Africa: Pretoria,,female,5 months,Infection,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,,,,,,,,,collected_by:National health Laboratory service,,,,,,,Infection,,,,,,,,,,,,,,99.9,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,61645.637,Enterobacter asburiae 2497,2497,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174002,61645,,,,,genotype:ST24,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917675.1,"CP103751,CP103752,CP103753,CP103754",,,Oxford Nanopore GridION,74x,Flye v. 2.8.3-b1695,1,3,4,5615356,54.99201,5722,5494,blood,,2016-09-05,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,61645.688,Enterobacter asburiae S3_CRE3,S3_CRE3,Enterobacter asburiae,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16387623,61645,,,,,,,,2023-01-09T00:00:00Z,,PRJNA667445,,CP074448,,,Illumina NextSeq; PacBio Sequel,755x,Unicycler v. v0.4.7,1,0,1,4509736,56.066807,4256,4164,decubitis wound fluid,,2017-01-24,USA,"USA: Durham, NC",,,,Bacterial infection,,,,,,,,,,,,,,collected_by:Rachel Addison,,,,,,,Bacterial infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,621.219,Shigella boydii strain DMB SH135,DMB SH135,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03291464,621,10,,,,,ATCC:12030,,2018-02-26T00:00:00Z,,PRJNA218110,GCA_002949895.1,"CP026867,CP026868,CP026869,CP026870",,CDC,PacBio,68.0x,HGAP v. 3,1,3,4,4842430,51.29483,5940,,,,2006,USA,USA:VA,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,100,4.8,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,621.221,Shigella boydii strain ATCC 35964,ATCC 35964,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916925,621,,,,,,ATCC: 35964,,2018-02-23T00:00:00Z,,PRJNA218110,GCA_002950035.1,"CP026877,CP026876",,CDC,PacBio,37.0x,HGAP v. 3,1,1,2,5295594,50.585297,6074,,feces of patient with dysentery,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,,,,,,,,missing,,,,,,,geographic origin listed as Indochina,,,,,Biosafety Level 2,,99.5,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,621.314,Shigella boydii strain 80,80,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821153,621,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738285.1,CP024693,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,457X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,5385859,50.982246,4816,4338,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-09,Brazil,Brazil: Manaus,,male,4 years old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,"negative motility; negative for glucose, indol, citrate, H2S, gas and ureate; lysine postive",,,,Urban,,,,94.44,0.1,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,621.315,Shigella boydii strain 192,192,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821150,621,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738345.1,CP024695,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,428X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,4753142,50.96773,4511,4282,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-10,Brazil,Brazil: Manaus,,male,9 years old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,98.18,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,621.316,Shigella boydii strain 183,183,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821151,621,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738325.1,CP024694,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,179X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,5000495,51.008183,4562,4218,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-10,Brazil,Brazil: Manaus,,female,9 years old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,92.99,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,621.321,Shigella boydii strain 600080,600080,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14145978,621,,,,,,,,2020-07-08T00:00:00Z,,PRJNA607768,GCA_013394495.1,"CP049606,CP049607",,"University of Maryland, School of Medicine",Illumina HiSeq; PacBio RSII,12.20323x,HGAP v. 3,1,1,2,4628191,50.94284,4976,,stool,,,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Shigella boydii 600080 Genome sequencing and assembly,"collected_by:University of Maryland, School of Medicine, Center for Vaccine Development",,,,,,,diarrhea,,,,,,,,,,,,,,98.5,0.31,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,621.322,Shigella boydii strain 600690,600690,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14145979,621,,,,,,,,2020-07-08T00:00:00Z,,PRJNA607767,GCA_013394515.1,"CP049278,CP049279,CP049280",,"University of Maryland, School of Medicine",Illumina HiSeq; PacBio RSII,14.37x,HGAP v. 3,1,2,3,5043708,50.45401,5398,,stool,,,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Shigella boydii 600690 Genome sequencing and assembly,"collected_by:University of Maryland, School of Medicine, Center for Vaccine Development",,,,,,,diarrhea,,,,,,,,,,,,,,99.74,0.41,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,621.323,Shigella boydii strain 600657,600657,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14145980,621,,,,,,,,2020-07-08T00:00:00Z,,PRJNA607765,GCA_013394535.1,"CP049281,CP049282,CP049284,CP049283",,"University of Maryland, School of Medicine",Illumina HiSeq; PacBio RSII,27.896x,canu v. 1.4,1,3,4,4833494,51.06273,5436,,stool,,,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Shigella boydii 600657 Genome sequencing and assembly,"collected_by:University of Maryland, School of Medicine, Center for Vaccine Development",,,,,,,diarrhea,,,,,,,,,,,,,,98.44,0.51,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,621.324,Shigella boydii strain 602068,602068,Shigella boydii,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14145981,621,,,,,,,,2020-07-08T00:00:00Z,,PRJNA607764,GCA_013394555.1,"CP049285,CP049286",,"University of Maryland, School of Medicine",Illumina HiSeq; PacBio RSII,15.67x,HGAP v. 3,1,1,2,4758031,50.91541,5180,,stool,,,Bangladesh,Bangladesh,,,,diarrhea,,,,,,,,,,,,,Shigella boydii 602068 Genome sequencing and assembly,"collected_by:University of Maryland, School of Medicine, Center for Vaccine Development",,,,,,,diarrhea,,,,,,,,,,,,,,98.99,0.79,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,622.418,Shigella dysenteriae strain E670/74,E670/74,Shigella dysenteriae,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916922,622,,,,,,ATCC:49345,,2018-02-23T00:00:00Z,,PRJNA218110,GCA_002943855.1,"CP027027,CP027028",,CDC,PacBio,164.0x,HGAP v. 3,1,1,2,5185765,50.690456,5470,,feces of patient with diarrhea,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.2,4.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,622.433,Shigella dysenteriae strain CFSAN010956,CFSAN010956,Shigella dysenteriae,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04316456,622,8,,,,,ATCC:12021,,2018-02-26T00:00:00Z,,PRJNA218110,GCA_002949935.1,"CP026827,CP026826",,CDC,PacBio,106.0x,HGAP v. 3,1,1,2,4782971,50.62184,5093,,clinical,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,98.8,1.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,622.436,Shigella dysenteriae strain ATCC 49346,ATCC 49346,Shigella dysenteriae,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916923,622,,,,,,ATCC:49346,,2018-02-23T00:00:00Z,,PRJNA218110,GCA_002950075.1,"CP026832,CP026833",,CDC,PacBio,158.0x,HGAP v. 3,1,1,2,4843745,51.076843,5586,,feces of patient with diarrhea,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.6,3.5,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,622.437,Shigella dysenteriae strain ATCC 49347,ATCC 49347,Shigella dysenteriae,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN01916924,622,,,,,,ATCC:49347,,2018-02-23T00:00:00Z,,PRJNA218110,GCA_002950095.1,"CP026834,CP026835",,CDC,PacBio,108.0x,HGAP v. 3,1,1,2,4783601,51.257534,5293,,feces of patient with diarrhea,,,,,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,,,,,,,,missing,,,,,,,,,,,,Biosafety Level 2,,99.6,0.4,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,622.521,Shigella dysenteriae strain CFSAN029786,CFSAN029786,Shigella dysenteriae,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04323531,622,Serotype 3,,,,,,,2019-11-14T00:00:00Z,,PRJNA541977,GCA_009662135.1,"CP045784,CP045785,CP045786,CP045787,CP045788",,FDA Center for Food Safety and Applied Nutrition,"Oxford Nanopore GridION, Illumina MiSeq","176, 244, 292, 244, 227x","SPAdes, CANU v. 3.12.0, 1.7",1,4,5,4949027,51.04187,5685,5016,,,,Somalia,Somalia,,,,,,,,,,,,,,,,,Whole genome sequencing using long-read nanopore technology of cultured pathogens collected for research purposes as part of the U.S. Food and Drug Administration surveillance project for the rapid detection of food contamination events.,collected_by:FDA,,,,,,,missing,,,,,,,,,,,,,,99.42,0.75,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,623.1082,Shigella flexneri strain SFL1520,SFL1520,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10106138,623,3b,,not collected,,,not applicable,,2019-02-12T00:00:00Z,,PRJNA492813,GCA_004171185.1,CP032513,,Australian National University,Oxford Nanopore MiniION; Illumina MiSeq,410.0x,SPAdes v. 3.12.0,1,,1,4575536,50.892944,5183,4725,stool,,1984,Bangladesh,Bangladesh: Dhaka,,,,Shigellosis,,host_description:not collected;host_disease_outcome:not collected;host_disease_stage:not collected;host_health_state:not collected;host_subject_id:not collected,,,,,,,,,,,We report the first complete genome analysis of S. flexneri serotype 3b strain SFL1520 using both long read MinION Flow (Oxford Nanopore Technologies) and short read MiSeq v3 300 bp (Illumina) sequencing platforms. The subsequent genome analysis aimed to provide a broader understanding of the genomic signatures of S. flexneri serotype 3b- an important serotype of developing countries.,"collected_by:International Centre for Diarrhoeal Disease Research, Bangladesh;passage_history:not collected;specimen_voucher:not applicable",,,,,,,Shigellosis,not collected,not collected,not collected,not collected,not collected,,,,,,,,,99.16,0.26,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1087,Shigella flexneri strain AUSMDU00008355,AUSMDU00008355,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5210150,623,,,,,,,,2019-02-11T00:00:00Z,,PRJEB30677,GCA_900659645.1,"LR213452,LR213453,LR213454",,UNIVERSITY OF MELBOURNE,,,,1,2,3,4615655,51.004982,4991,,feces,,2016,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Genomes of multidrug-resistant Shigella sonnei and Shigella flexneri from Australia,,,,,,,,,diseased,,,,,,,,,,,,,97.95,0.82,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,623.1088,Shigella flexneri strain AUSMDU00008332,AUSMDU00008332,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5210151,623,,,,,,,,2019-02-11T00:00:00Z,,PRJEB30677,GCA_900659665.1,"LR213455,LR213456,LR213457",,UNIVERSITY OF MELBOURNE,,,,1,2,3,4943933,50.738914,5429,,feces,,2016,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Genomes of multidrug-resistant Shigella sonnei and Shigella flexneri from Australia,,,,,,,,,diseased,,,,,,,,,,,,,98.43,0.57,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,623.1202,Shigella flexneri strain 201,201,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821154,623,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738265.1,CP024981,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,310X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,4645776,50.76914,5056,4633,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-10,Brazil,Brazil: Manaus,,male,3 month old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,97.84,0.18,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,623.1203,Shigella flexneri strain 113,113,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821152,623,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738305.1,CP024982,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,384X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,4646599,50.760952,5085,4644,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-10,Brazil,Brazil: Manaus,,male,7 month old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,98.16,0.18,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,623.1204,Shigella flexneri strain 36P,36P,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821149,623,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738365.1,CP024983,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,91X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,4643033,50.737816,5041,4635,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2007-08,Brazil,Brazil: Manaus,,female,2 years old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,98.79,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,623.1205,Shigella flexneri strain 837,837,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07821148,623,,,,,,,,2019-12-10T00:00:00Z,,PRJNA415104,GCA_009738385.1,CP024984,,Instituto Leonidas e Maria Deane - Fiocruz Amazonia,Illumina HiSeq 2500,185X,Velvet/ABACAS v. 1.2.10/1.3.1,1,0,1,4644863,50.746017,5049,4624,children of different hospitals,"isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil",2008-05,Brazil,Brazil: Manaus,,male,8 month old,Diarrheal disease,,,,,,,,,,,,,"Complete sequencing of different species of Shigella isolated from children of different hospitals in the city of Manaus, Amazonas - Brazil. The used techniq was the new generation sequencing, in order to study and understand the main mechanisms of pathogenicity of this bacteria.",,,,,"Stool samples in swabs were incubated in Luria Bertani broth at 37ᵒC, overnight. Lactose nonfermenting colonies were isolated on MacConkey lactose agar (MC), Salmonella-Shigella (SS), and xylose lysine deoxycholate (XLD) agar.",,,Diarrheal disease,,,,,,,,,,Urban,,,,98.48,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,623.1257,Shigella flexneri strain 5908.2,5908.2,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13075196,623,,,,,,,,2020-01-27T00:00:00Z,,PRJNA578858,GCA_009931475.1,"CP045522,CP045523",,University of Bern,Illumina NovaSeq and Oxford Nanopore,104.17x,Canu v. 1.7,1,1,2,4686959,50.90339,5275,4717,stool,,2015-08-27,Switzerland,Switzerland: Bern,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,Diarrhea,,,,,,,,,,,,,,99.41,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,623.1270,Shigella flexneri strain M2901,M2901,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13753499,623,2b,,,,,,,2020-07-12T00:00:00Z,,PRJNA599490,GCA_013402835.1,"CP058589,CP058590,CP058591,CP058592,CP058593",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore,50.0x,Flye v. MAY-2020,1,4,5,4995595,50.628082,5756,4956,feces,,2019,Australia,Australia: Queensland,,,,shigellosis,,,,,,,,,,,,,Shigella flexneri WGS,collected_by:Queensland Health,,,,,,,shigellosis,,,,,,,,,,,,,,99.7,0.94,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1513,Shigella flexneri strain AUSMDU00021847,AUSMDU00021847,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7060415,623,,,,,,,,2020-09-16T00:00:00Z,,PRJEB39384,GCA_903987005.1,"LR861785,LR861786,LR861787",,UNIVERSITY OF MELBOURNE,,,,1,2,3,4829585,50.6822,5494,,faecal,,2018,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Investigation of the origins of multidrug resistant Shigella flexneri in a patient,,,,,,,,,diseased,,,,,,,,,,,,,99.41,0.21,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,623.1514,Shigella flexneri strain AUSMDU00022017,AUSMDU00022017,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7060416,623,,,,,,,,2020-09-16T00:00:00Z,,PRJEB39384,GCA_903987015.1,"LR861788,LR861789,LR861790",,UNIVERSITY OF MELBOURNE,,,,1,2,3,4839307,50.704945,5533,,faecal,,2018,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Investigation of the origins of multidrug resistant Shigella flexneri in a patient,,,,,,,,,diseased,,,,,,,,,,,,,99.41,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,623.1852,Shigella flexneri 3160_NCHU22,3160_NCHU22,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN27117281,623,,,,,,,,2022-04-11T00:00:00Z,,PRJNA821625,GCA_022869845.1,"CP094987,CP094988,CP094989,CP094990",,,Illumina iSeq; Oxford Nanopore,147.0x,unicycler v. 0.4.8,1,3,4,4954324,50.663,5558,4909,stool,,2000,Taiwan,Taiwan,,,,shigellosis,,,,,,,,,,,,,,collected_by:Nien-Jen Hu,,,,,,,shigellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1943,Shigella flexneri strain E,E,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28576601,623,,,,,,,,2022-08-22T00:00:00Z,35979220,PRJNA841078,GCA_024732285.1,"CP097828,CP097829,CP097830",,,Oxford Nanopore MinION,169x,Flye v. 2.9,1,2,3,4811261,50.709846,5389,4766,stool,,2022-03-10,Singapore,Singapore: Singapre,,,,Shigellosis,,,,,,,,,,,,,,collected_by:Singapore General Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,99.7,0.3,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1944,Shigella flexneri D,D,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28576600,623,,,,,,,,2022-08-22T00:00:00Z,35979220,PRJNA841078,GCA_024732305.1,"CP097831,CP097833,CP097832",,,Oxford Nanopore MinION,173x,Flye v. 2.9,1,2,3,4811260,50.70996,5379,4762,stool,,2022-04-13,Singapore,Singapore: Singapre,,,,Shigellosis,,,,,,,,,,,,,,collected_by:Sengkang General Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,99.7,0.3,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1945,Shigella flexneri C,C,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28576599,623,,,,,,,,2022-08-22T00:00:00Z,35979220,PRJNA841078,GCA_024732325.1,"CP097834,CP097835,CP097836",,,Oxford Nanopore MinION,156x,Flye v. 2.9,1,2,3,4810430,50.709686,5384,4761,stool,,2022-04-04,Singapore,Singapore: Singapre,,,,Shigellosis,,,,,,,,,,,,,,collected_by:Singapore General Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,99.7,0.3,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1946,Shigella flexneri B,B,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28576598,623,,,,,,,,2022-08-22T00:00:00Z,35979220,PRJNA841078,GCA_024732345.1,"CP097837,CP097838,CP097839",,,Oxford Nanopore MinION,138x,Flye v. 2.9,1,2,3,4810435,50.709675,5390,4763,stool,,2022-04-01,Singapore,Singapore: Singapre,,,,Shigellosis,,,,,,,,,,,,,,collected_by:Sengkang General Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,100,4,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,623.1947,Shigella flexneri strain A,A,Shigella flexneri,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28576597,623,,,,,,,,2022-08-22T00:00:00Z,35979220,PRJNA841078,GCA_024732365.1,"CP097840,CP097841,CP097842",,,Oxford Nanopore MinION,132x,Flye v. 2.9,1,2,3,4810445,50.709633,5391,4761,stool,,2022-04-03,Singapore,Singapore: Singapre,,,,Shigellosis,,,,,,,,,,,,,,collected_by:Sengkang General Hospital,,,,,,,Shigellosis,,,,,,,,,,,,,,100,4,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,624.1184,Shigella sonnei strain 2015AM-1099,2015AM-1099,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06843643,624,,,,,,,,2017-05-16T00:00:00Z,,PRJNA218110,GCA_002142635.1,CP021144,,CDC,PacBio,78.0x,other v. 3,1,,1,4935567,51,5514,5308,,,,USA,United States,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library;many frameshifted proteins,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,100,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1185,Shigella sonnei strain 75/02,75/02,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06286561,624,,,,,,,,2017-05-19T00:00:00Z,,PRJNA369464,GCA_002150905.1,"CP019689,CP019690,CP019691,CP019692,CP019693,CP019694,CP019695,CP019696",,Seqomics Ltd.,Illumina MiSeq,140.0x,CLC Genomics Workbench v. 9.5; Geneious,1,7,8,5224048,50.64,5958,6087,feces,,2002,Hungary,Hungary: Halimba,,,,shigellosis,,,,,,,,,,,,,Shigella sonnei strain 75/02 Genome sequencing and assembly,"collected_by:National Center for Epidemiology, Budapest, Hungary",,,,,,,shigellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,624.1272,Shigella sonnei strain 2015C-3566,2015C-3566,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06843644,624,,,,,,,,2017-07-24T00:00:00Z,,PRJNA218110,GCA_002224625.1,"CP022457,CP022458",,CDC,PacBio,78x,PacBio Hierarchical Genome Assembly,1,1,2,4949228,51.02,5524,5329,,,,USA,United States,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1273,Shigella sonnei strain 2015C-3794,2015C-3794,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06843645,624,,,,,,,,2017-07-24T00:00:00Z,,PRJNA218110,GCA_002224605.1,"CP022455,CP022456",,CDC,PacBio,78x,PacBio Hierarchical Genome Assembly,1,1,2,4906574,51,5458,5276,,,,USA,United States,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1274,Shigella sonnei strain 2015C-3807,2015C-3807,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06843646,624,,,,,,,,2017-07-24T00:00:00Z,,PRJNA218110,GCA_002224465.1,"CP022459,CP022460,CP022461",,CDC,PacBio,78x,PacBio Hierarchical Genome Assembly,1,2,3,4929151,50.93,5691,5345,,,,USA,United States,,,,,,,,,,,,,,,,,PulseNet STEC genome reference library,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,100,3.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1285,Shigella sonnei strain CFSAN030807,CFSAN030807,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN03612247,624,Serotype group D,,,,,,,2017-10-04T00:00:00Z,,PRJNA273284,GCA_002442535.1,"CP023645,CP023646,CP023647,CP023648,CP023649,CP023650,CP023651,CP023652,CP023653",,FDA Center for Food Safety and Applied Nutrition,PacBio,700.0x,HGAP v. v.3.0,1,8,9,5062953,50.77,5712,5482,missing,,,Somalia,Somalia,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Shigella as part of FDA/CFSAN's surveillance project for rapid source tracking of foodborne illness outbreaks.,,,,,,,,none,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1348,Shigella sonnei strain 866,866,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07423557,624,,,,,,,,2018-06-26T00:00:00Z,,PRJNA396190,GCA_003265245.1,"CP022672,CP022673",,University of Texas at San Antonio,PacBio; Illumina MiSeq,107.0x,RS_HGAP.3 v. JULY-2016; Pilon v.,1,1,2,4962707,51.049397,5540,5325,feces,,2000-09-20,Spain,Spain: Barcelona,,,,Gastroenteritis,,,,,,,,,,,,,Comparative genomics of Shigella spp;many frameshifted proteins,collected_by:Hospital de la Santa Creu i Sant Pau,,,,,,,Gastroenteritis,,,,,,,,,,,,,,100,1.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.1850,Shigella sonnei strain LC1477/18,LC1477/18,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10519737,624,,,,,,,,2019-03-06T00:00:00Z,,PRJNA508357,GCA_004328985.1,"CP035008,CP035009,CP035010,CP035011",,University of Bern,Oxford Nanopore MiniION; Illumina HiSeq,40.0x,Canu v. 1.7.1,1,3,4,4905980,50.993748,5433,4911,stools,,2018-08,Italy,Italy: Lecco,,female,10 year-old,Bloody diarrhea,,host_disease_outcome:recovery,,,,,,,,,,,Whole genome sequencing of Shigella sonnei ESBL-producer from Italy,"collected_by:A. Manzoni Hospital, Lecco, Italy",,,,,,,Bloody diarrhea,,recovery,,,,,,,,,,,,99.6,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.1855,Shigella sonnei strain AUSMDU00008333,AUSMDU00008333,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5210148,624,,,,,,,,2019-02-11T00:00:00Z,,PRJEB30677,GCA_900659655.1,"LR213458,LR213459,LR213460,LR213461",,UNIVERSITY OF MELBOURNE,,,,1,3,4,5006011,50.992336,5207,,feces,,2016,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Genomes of multidrug-resistant Shigella sonnei and Shigella flexneri from Australia,,,,,,,,,diseased,,,,,,,,,,,,,96.82,1.83,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,624.1856,Shigella sonnei strain AUSMDU00008361,AUSMDU00008361,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA5210149,624,,,,,,,,2019-02-11T00:00:00Z,,PRJEB30677,GCA_900659675.1,"LR213449,LR213450,LR213451",,UNIVERSITY OF MELBOURNE,,,,1,2,3,5028685,50.907307,5350,,feces,,2016,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,Genomes of multidrug-resistant Shigella sonnei and Shigella flexneri from Australia,,,,,,,,,diseased,,,,,,,,,,,,,99.6,0.91,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,624.1858,Shigella sonnei strain FC1428,FC1428,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12139103,624,,,,,,,,2019-07-08T00:00:00Z,,PRJNA551099,GCA_006843305.1,CP041322,,Christian Medical College,IonTorrent; MinION,30.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,,1,4908612,51.041046,5563,4924,feces,,2018,India,India: Vellore,,,,Gastroenteritis,,,,,,,,,,,,,Multi-drug resistant Shigella sonnei carrying multiple antimicrobial resistant genes,collected_by:Christian Medical College,,,,,,,Gastroenteritis,,,,,,,,,,,,,,99.49,0.57,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.1865,Shigella sonnei strain AUSMDU00010534,AUSMDU00010534,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191651,624,g,,,,mlst:ST152,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664515.1,"CP045932,CP045933,CP045934,CP045935,CP045936,CP045937,CP045938,CP045939,CP045940",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,103x,de novo,1,8,9,5107412,50.80681,5449,5006,missing,,2017,Australia,Australia,,,,,,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,99.6,1.06,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.1867,Shigella sonnei strain 6904.27,6904.27,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13075195,624,,,,,,,,2020-01-27T00:00:00Z,,PRJNA578858,,"CP045524,CP045525",,University of Bern,Illumina NovaSeq and Oxford Nanopore,104.16x,Canu v. 1.7,1,1,2,4867691,51.023678,5179,4847,stool,,2018-06-27,Switzerland,Switzerland: Bern,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2208,Shigella sonnei strain 6607.69,6607.69,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13075194,624,,,,,,,,2020-01-27T00:00:00Z,,PRJNA578858,GCA_009931515.1,"CP045526,CP045527",,University of Bern,Illumina NovaSeq and Oxford Nanopore,104.16x,Canu v. 1.7,1,1,2,4912494,51.02966,5257,4906,stool,,2017-09-22,Switzerland,Switzerland: Bern,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2210,Shigella sonnei strain 3123885,3123885,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133047,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013146725.1,"CP049163,CP049164",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4636384,50.995193,4945,4591,stool,,2019-11-19,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,Diarrhea,,,,,,,,,,,,,,91.74,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2211,Shigella sonnei strain 09163633,09163633,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133045,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013146765.1,"CP049167,CP049168",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4942870,50.99873,5260,4875,stool,,2019,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Labormedizinisches Zentrum Dr Risch AG,,,,,,,Diarrhea,,,,,,,,,,,,,,99.13,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2213,Shigella sonnei strain 19.1125.3493,19.1125.3493,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133048,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013146785.1,"CP049169,CP049170",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4873610,51.022793,5149,4781,stool,,2019,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Labormedizinisches Zentrum Dr Risch AG,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2214,Shigella sonnei strain 19.0821.3486,19.0821.3486,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133038,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013146845.1,"CP049185,CP049186",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4934123,51.009754,5240,4877,stool,,2019,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Labormedizinisches Zentrum Dr Risch AG,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2215,Shigella sonnei strain 19.0820.1561,19.0820.1561,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133037,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013147065.1,"CP049173,CP049174",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4881506,51.031178,5168,4803,stool,,2019,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Labormedizinisches Zentrum Dr Risch AG,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.26,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2216,Shigella sonnei strain 7111.69,7111.69,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133046,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013147165.1,"CP049175,CP049176",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4940233,50.994354,5276,4867,stool,,2019-01-27,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,Diarrhea,,,,,,,,,,,,,,98.36,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2217,Shigella sonnei strain 509.1022,509.1022,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133040,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013147225.1,"CP049181,CP049182",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4892993,50.984478,5170,4799,,,2019,Switzerland,Switzerland,,,,,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Institute for Infectious Diseases,,,,,,,,,,,,,,,,,,,,,99.6,0.17,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,624.2220,Shigella sonnei strain 19.0822.3296,19.0822.3296,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14133039,624,,,,,,,,2020-05-22T00:00:00Z,,PRJNA578858,GCA_013147245.1,"CP049183,CP049184",,University of Bern,Illumina NovaSeq; Oxford Nanopore MiniION,40x,Canu v. 1.7,1,1,2,4893041,50.984634,5179,4802,stool,,2019,Switzerland,Switzerland,,,,Diarrhea,,,,,,,,,,,,,"In this study we aimed to characterize third-generation cephalosporins-resistant plasmids of Shigella spp., circulating in Switzerland and collected in Bern, by mean of whole-genome sequencing.",collected_by:Labormedizinisches Zentrum Dr Risch AG,,,,,,,Diarrhea,,,,,,,,,,,,,,99.6,0.17,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,624.2247,Shigella sonnei strain 506,506,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07663113,624,,,,,,,,2020-06-01T00:00:00Z,,PRJNA278886,GCA_013201485.1,"CP053751,CP053752,CP053753,CP053754,CP053755,CP053756,CP053757,CP053758,CP053759,CP053760,CP053761,CP053762",,Brigham & Women's Hospital,PacBio RSII,445.0x,HGAP v. 3.0,1,12,13,5344107,50.66697,5768,5307,stool,,2017,USA,USA:Boston,,male,51,,,host_subject_id:SBJ-9962,,,,,,,,,,,The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.,collected_by:Brigham and Women's Hospital,,,,,,,Missing,,,,,,,,,,,,,,99.6,1.02,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,624.2257,Shigella sonnei strain UKMCC_1015,UKMCC_1015,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15437744,624,,,,,,,,2020-08-17T00:00:00Z,,PRJNA643901,GCA_014217935.1,"CP060117,CP060118,CP060119",,Monash University Malaysia,Oxford Nanopore; Illumina MiSeq,49.0x,Flye v. v 2.6; Pilon v. v 1.23,1,2,3,4935775,51.03233,5202,4808,,,2018-06,Malaysia,Malaysia,,,,Shigellosis,,,,,,,,,,,,,"This study presents the complete genome of a Malaysian S. sonnei strain named UKMCC 1015, providing a potential reference genome for the South East Asia area",collected_by:UKM culture collection,,,,,,,Shigellosis,,,,,,,,,,,,,,99.56,0.11,Specific Bacterial Infections,Shigellosis,Other,Specific Bacterial Infections-Shigellosis HP,624.2637,Shigella sonnei strain 6207,6207,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16084720,624,,,,,,,,2020-09-24T00:00:00Z,,PRJNA599490,GCA_014725795.1,"CP061367,CP061363,CP061364,CP061365,CP061366",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,50.0x,Unicycler v. AUG-2020; Flye v. AUG-2020,1,4,5,5015190,51.02074,5290,4920,feces,,2020,Australia,Australia,,,,Shigellosis,,,,,,,,,,,,,Shigella flexneri WGS,collected_by:Queensland Health,,,,,,,Shigellosis,,,,,,,,,,,,,,99.6,0.57,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis HP,624.2641,Shigella sonnei strain 893916,893916,Shigella sonnei,Shigella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17152229,624,,,,,,,,2021-01-10T00:00:00Z,,PRJNA687669,GCA_016598715.1,CP066810,,University of Bath,Oxford Nanopore MinION; Illumina HiSeq,26.0x,Flye v. 2.7.1,1,0,1,4813904,51.026485,5302,4668,stool,,2020-02,United Kingdom,United Kingdom: London,,male,,shigellosis,,,,,,,,,,,,,Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. This study aimed to look at the location of AMR determinants in CTX-M-27-positive Shigella isolates spread through MSM in England and their relation to known plasmids in Shigella,collected_by:Public Health England,,,,,,,shigellosis,,,,,,,,,,,,,,99.6,0.11,Specific Bacterial Infections,Shigellosis,Gastrointestinal,Specific Bacterial Infections-Shigellosis NHP,626932.184,Alistipes indistinctus strain 2BBH45,2BBH45,Alistipes indistinctus,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00216626,626932,,,,,,,,2020-08-01T00:00:00Z,,PRJDB9565,GCA_014163495.1,"AP023049,AP023050",,"Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN",Illumina MiSeq; PacBio Sequel,196x,Unicycler v. 0.4.6,1,1,2,3095585,54.59682,2740,2463,feces of healthy japanese,,,Japan,Japan,,,,,,,,,,,,,,,,,The complete sequence of Alistipes indistinctus strain 2BBH45 harboring a plasmid p2BBH45 assembled using Unicycler,,missing,missing,feces,missing,The complete sequence of Alistipes indistinctus strain 2BBH45,,,,,,,,,,,,missing,,,,100,0,,,Gastrointestinal,- HP,632.705,Yersinia pestis strain S19960127,S19960127,Yersinia pestis,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13021983,632,,,,MLST.Yersinia_spp.79,,,,2020-11-02T00:00:00Z,,PRJNA577233,GCA_015190655.1,"CP045640,CP045636,CP045637,CP045638,CP045639",,National institute for communicable disease control and prevention,PacBio RSII,30.0x,SOAPdenovo v. 2.3,1,4,5,4852443,47.670277,4763,4575,tibetan,,1996-08-26,China,China:Tibet,,,,plague,,,,,,,,,,,,,genome sequence of Yersinia S19960127,collected_by:Center for Disease Control and Prevention,,,,,,,plague,,,,,,,,,,,,,,99.82,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,632.861,Yersinia pestis strain R,R,Yersinia pestis,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN21848823,632,,,,MLST.Yersinia_spp.79,,,,2022-08-01T00:00:00Z,35787155,PRJNA766482,GCA_024498375.1,"CP084336,CP084337,CP084338",,,PacBio Sequel,100.0x,HGAP v. 4.0,1,2,3,4848095,47.652863,4707,4308,,,2019,China,"China: Gansu, Aksay",,,,,,,,,,,,,,,,,,sample_type:Blood,,,,,,,,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,633.316,Yersinia pseudotuberculosis strain 598,598,Yersinia pseudotuberculosis,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16418511,633,,,,MLST.Yersinia_pseudotuberculosis.2,,,,2021-11-19T00:00:00Z,,PRJNA622482,GCA_020889805.1,"CP071944,CP071945,CP071946",,N.F.Gamaleya National Research Center for Epidemiology and Microbiology,Illumina MiSeq; Oxford Nanopore,67.0x,CLC Genomics Workbench v. 20; SPAdes,1,2,3,4949806,47.284294,4672,4521,"sick person, russian far east",,,Russia,Russia:The Fare East,,,,Far East scarlet-like fever,,,,,,,,,,,,,Clarifying the mechanisms of adaptation of bacteria to extreme conditions.,"collected_by:Timchenko N.F.;lab_host:Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia\; Institute of Epidemiology and Microbiology named after G.P. Somov, Vladivostok, Russia",,,,,,,Far East scarlet-like fever,,,,,,,,,,,,,,99.87,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,633.88,Yersinia pseudotuberculosis strain NZYP4713,NZYP4713,Yersinia pseudotuberculosis,Yersinia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA3988158,633,,,,MLST.Yersinia_pseudotuberculosis.42,,,,2017-01-02T00:00:00Z,,PRJEB14046,GCF_900092345.1,"LT596221,LT596222","NZ_LT596221.1,NZ_LT596222.1",UNIVERSITY OF MELBOURNE,,,,1,1,2,4794091,47.51,4514,,faeces; feces,,2014,,,,,,,,,,,,,,,,,,,This study performed comparative genomics a large temporal and geographically diverse collection of isolates belonging to the Y. pseudotuberculosis complex to explore the genomic epidemiology of a sustained outbreak of yersiniosis in New Zealand.,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,638301.55,Granulicatella adiacens ATCC 49175,ATCC 49175,Granulicatella adiacens,Granulicatella,Carnobacteriaceae,Lactobacillales,Bacilli,Bacillota,SAMN20222693,638301,,,,,,ATCC:49175,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150565.1,CP102283,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,1965422,37.781097,1913,1867,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.45,0.18,,,Other,- HP,644.199,Aeromonas hydrophila strain ZYAH75,ZYAH75,Aeromonas hydrophila,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN05589911,644,,,,,,,,2018-09-07T00:00:00Z,,PRJNA339336,GCA_003491245.1,CP016990,,HuaZhong Agricultural University,Illumina,missing,SMRT Analysis v. v2.3.0,1,,1,4955171,61.337257,4597,4311,wound secretion,,2015,China,China,,,,sorfttissue infection,,,,,,,,,,,,,For the health of mankind,collected_by:Jinquan Li,,,,,,,sorfttissue infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,644.622,Aeromonas hydrophila strain RIMD111065,Aeromonas hydrophila,Aeromonas hydrophila,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMD00261012,644,,,,MLST.Aeromonas_spp.179,,,,2020-12-18T00:00:00Z,,PRJDB10897,GCA_016592295.1,AP024234,,"Veterinary Public Health Veterinary Medicine, Kitasato University",MinION,30x,Unicycler v. 0.4.0,1,0,1,4962727,61.003094,4596,4406,human blood was performed for study on the virulence factors of the causative agent of nsti and sepsis,isolated from human blood was performed for study on the virulence factors of the causative agent of NSTI and sepsis,2015,Japan,Japan,,,,,,,,,,,,,,,,,Genome analysis of Aeromonas hydrophila isolated from human blood was performed for study on the virulence factors of the causative agent of NSTI and sepsis.,,ENVO:00002030,ENVO:00000873,ENVO_01000253?,not provided,Genome analysis of Aeromonas hydrophila,,,,,,,,,,,,ENVO:00002030,,,,99.97,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,644.733,Aeromonas hydrophila strain 71339,71339,Aeromonas hydrophila,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168048,644,,,,,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,GCA_020405365.1,CP084352,,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,0,1,4793727,61.408295,4415,4230,urine,,2020-06-15,China,China:Ningbo,,male,85,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,99.97,0,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,644.734,Aeromonas hydrophila strain 71317,71317,Aeromonas hydrophila,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168046,644,,,,MLST.Aeromonas_spp.134,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,GCA_020405385.1,CP084353,,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,0,1,4695915,61.693962,4279,4123,blood,,2020-06-05,China,China:Ningbo,,male,73,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,99.97,0,Urinary Tract Diseases,Lower UTI,Blood and Circulatory System,Urinary Tract Diseases-Lower UTI HP,644.996,Aeromonas hydrophila YURI 17,YURI 17,Aeromonas hydrophila,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901113,644,,,,MLST.Aeromonas_spp.326,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121798,CP121797,CP121796",,,Oxford Nanopore,30x,flye v. 2.9.2,1,2,3,5325528,60.60195,5042,,plasma,,2021-01-06,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,645463.109,Clostridioides difficile R20291,R20291,Clostridioides difficile,Clostridioides,Peptostreptococcaceae,Eubacteriales,Clostridia,Bacillota,SAMN32411337,645463,,,,,,,,2023-01-10T00:00:00Z,,PRJNA530817,,CP115183,,,Oxford Nanopore MinION; DNBSEQ,116.0x,Unicycler hybrid assembly v. ver.0.4.8,1,0,1,4204886,28.871746,3819,3725,feces,,2006,United Kingdom,United Kingdom,,,,C. difficile infection,,,,,,,,,,,,,,collected_by:Stoke Mandeville Hospital,,,,,,,C. difficile infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,648.237,Aeromonas caviae strain 1607-10029,1607-10029,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN13871641,648,,,,MLST.Aeromonas_spp.141,,,,2020-07-23T00:00:00Z,,PRJNA601658,GCA_013487965.1,CP047981,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v 3.0,1,0,1,4520672,61.589317,4286,4086,shunt fluid,,2016,China,China: Beijing,,,,cholangitis,,,,,,,,,,,,,Complete sequence of chromosome of strain of 1607-10029,collected_by:a public hospital,,,,,,,cholangitis,,,,,,,,,,,,,,99.38,0,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,648.445,Aeromonas caviae strain K433,K433,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21545965,648,,,,MLST.Aeromonas_spp.141,,,,2021-09-30T00:00:00Z,,PRJNA765169,GCA_020181575.1,CP084031,,Municipal Hospital Affiliated to Taizhou University,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,4682417,61.41337,4447,4229,sputum,,2020,China,China: Zhejiang,,,,pneumonia,,,,,,,,,,,,,Complete sequence of chromosome of strain K433,collected_by:a teaching hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.97,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,648.446,Aeromonas caviae strain 71442,71442,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168050,648,,,,,,not collected,,2021-10-10T00:00:00Z,,PRJNA759416,GCA_020405325.1,CP084350,,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,0,1,4444683,61.739925,4134,3961,bile,,2020-10-03,China,China:Ningbo,,male,55,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,99.97,0,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,648.500,Aeromonas caviae strain 71485,71485,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168053,648,,,,,,not collected,,2021-10-27T00:00:00Z,,PRJNA759416,GCA_020640975.1,"CP085468,CP085469",,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,1,2,4607215,61.175156,4397,4168,bile,,2020-12-09,China,China:Ningbo,,female,72,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,99.97,0,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,648.610,Aeromonas caviae 211703,211703,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN25872065,648,,,,MLST.Aeromonas_spp.264,,,,2022-02-20T00:00:00Z,,PRJNA806340,GCA_022343945.1,CP092181,,,nanopore,100.0x,Unicycler v. v0.4.5,1,0,1,4783384,61.81492,4591,4383,cerebrospinal fluid,,2021,China,China: Zhejiang,,,,Cerebral infection,,,,,,,,,,,,,,collected_by:a teaching hospital,,,,,,,Cerebral infection,,,,,,,,,,,,,,99.82,0,Neurological Diseases,Other Brain Infections,Central Nervous System,Neurological Diseases-Other Brain Infections HP,648.938,Aeromonas caviae SVJ23,SVJ23,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN31409143,648,,,,,,,,2022-11-05T00:00:00Z,,PRJNA893029,GCA_026013215.1,CP110176,,,Illumina NovaSeq,443.0x,Unicycler v0.4.8.12 v. AUGUST-2022,1,0,1,4558055,61.537895,4433,4239,stool,,2022-03-14,India,India,,male,3 days,Hemorrhagic gastroenteritis,,host_disease_outcome:Recovery;host_subject_id:SUHRC0226962,,,,,,,,,,,,collected_by:Dr. Savita Jadhav,,,,,,,Hemorrhagic gastroenteritis,,Recovery,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,648.973,Aeromonas caviae AC1520,AC1520,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33867246,648,,,,MLST.Aeromonas_spp.298,,,,2023-04-05T00:00:00Z,,PRJNA947818,,"CP120942,CP120943",,,Illumina NovaSeq; PacBio,24.81x,Hifiasm v. 0.13-r308; Canu v. 1.7,1,1,2,4737988,61.14756,4559,4324,urine,,2022-11,China,China: Zhuhai,,,,infection,,,,,,,,,,,,,,collected_by:Qinghuan Zhang,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,648.979,Aeromonas caviae FIONA 16800,FIONA 16800,Aeromonas caviae,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901114,648,,,,MLST.Aeromonas_spp.196,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121794,CP121793,CP121792",,,Oxford Nanopore,30x,flye v. 2.9.2,1,2,3,5317260,60.36513,5252,,plasma,,2020-12-08,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,649756.2867,Anaerostipes hadrus KR001_HIC_0005,KR001_HIC_0005,Anaerostipes hadrus,Anaerostipes,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100367,649756,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757705.1,CP107212,,,PacBio Sequel II,24x,HiCanu v. 2.1.1,1,0,1,2870332,37.278545,2759,2678,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,99.9,0.4,,,Gastrointestinal,- HP,650.44,Aeromonas jandaei strain JUNP479,JUNP479,Aeromonas jandaei,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMD00276024,650,,,,,,,,2021-02-02T00:00:00Z,,PRJDB11115,GCA_016865345.1,"AP024466,AP024467",,"Department of Microbiology, Juntendo University Graduate School of Medicine",Illuminia MiSeq; Oxford nanopore MinION,600x,Unicycler v. 0.4.8,1,1,2,4541146,59.024265,4257,4148,,,2019,Nepal,Nepal,,,,,,,,,,,,,,,,,Clinical isolates of colistin-resistant Aeromonas spp. was emerging in Nepal. These isolates harbored genes encoding phosphoethanolamine transferases in the chromosomes.,,missing,missing,missing,missing,Colistin-resistant Aeromonas jandaei in Nepal,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,65058.242,Corynebacterium ulcerans strain 0211,0211,Corynebacterium ulcerans,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00168433,65058,,,,,,,,2019-09-05T00:00:00Z,,PRJDB8202,GCA_008995395.1,AP019662,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Illumina GAII; ABI 3730xl,885x,ABySS v. 1.2.0,1,,1,2579078,53.35705,2422,2307,pharyngeal pseudomembrane,isolated in Japan,2002,Japan,Japan:Chiba,,,,,,,,,,,,,,,,,The purpose of this project is related to genomic epidemiology analysis and comparative genomic analysis of Corynebacterium ulcerans strains isolated in Japan.,,missing,missing,pharyngeal pseudomembrane,missing,whole genome sequencing of Corynebacterium ulcerans str. 0211,diphtheria-like symptoms,,,,,,,,,,,missing,,,,99.78,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,65058.243,Corynebacterium ulcerans strain FH2016-1,FH2016-1,Corynebacterium ulcerans,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00168434,65058,,,,,,,,2019-09-05T00:00:00Z,,PRJDB8202,GCA_009002285.1,AP019663,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Sequel; NextSeq500,1526x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,,1,2579134,53.3595,2422,2302,tracheal pseudomembrane,isolated in Japan,2016,Japan,Japan:Fukuoka,,,,,,,,,,,,,,,,,The purpose of this project is related to genomic epidemiology analysis and comparative genomic analysis of Corynebacterium ulcerans strains isolated in Japan.,,missing,missing,tracheal pseudomembrane,missing,whole genome sequencing of Corynebacterium ulcerans str. FH2016-1,diphtheria-like symptoms,,,,,,,,,,,missing,,,,99.78,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,65058.522,Corynebacterium ulcerans FRC0011,FRC0011,Corynebacterium ulcerans,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMEA112465938,65058,,,,,,,,2023-03-09T00:00:00Z,,PRJEB22103,,OX444692,,,,,,1,0,1,2442837,53.348503,2260,,human,,2008,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,65058.525,Corynebacterium ulcerans TSU-28,TSU-28,Corynebacterium ulcerans,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00567576,65058,,,,,,,,2023-02-03T00:00:00Z,,PRJDB14999,,AP027140,,,Illumina iSeq; Nanopore MK1C,496x,CLC genomic workbench v. 21. 0. 5; Pilon,1,0,1,2522327,53.422176,2368,2276,tracheal pseudomembrane; human,,2019-12-25,Japan,Japan:Shimane,,,,Diphtheria-like disease,,,,,,,,,,,,,,collected_by:not applicable,,,,,,,Diphtheria-like disease,,,,,,,,,,,,,,99.9,0.2,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,652611.49,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953208,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490375.1,CP104983,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537580,66.29263,6127,5963,clinical,,,,,,,,,,,Susceptible,Computational Method,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,99,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,652611.50,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953210,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490395.1,CP104981,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537578,66.29272,6131,5962,clinical,,Not collected,,Not applicable,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Glycerol stock,,,,,,,,,,,,,,,,,,,,,99,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,652611.51,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953206,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490415.1,CP104985,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537583,66.29375,6130,5962,clinical,,Not collected,,Not applicable,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Glycerol stock,,,,,,,,,,,,,,,,,,,,,99.1,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,652611.52,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953211,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490435.1,CP104980,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537585,66.29419,6131,5964,clinical,,Not collected,,Not applicable,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Glycerol stock,,,,,,,,,,,,,,,,,,,,,99.1,1.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,652611.53,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953207,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490455.1,CP104984,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537586,66.29417,6127,5963,clinical,,Not collected,,Not applicable,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Glycerol stock,,,,,,,,,,,,,,,,,,,,,99.1,1.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,652611.54,Pseudomonas aeruginosa PA14,PA14,Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMN30953209,652611,,,,MLST.Pseudomonas_aeruginosa.253,,,,2022-09-29T00:00:00Z,,PRJNA882857,GCA_025490475.1,CP104982,,,Illumina NovaSeq,2x,Geneious v. July-2022,1,0,1,6537581,66.29274,6129,5961,clinical,,Not collected,,Not applicable,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:Glycerol stock,,,,,,,,,,,,,,,,,,,,,99,1.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,654.653,Aeromonas veronii strain 71506,71506,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN21168054,654,,,,,,not collected,,2021-10-27T00:00:00Z,,PRJNA759416,GCA_020640955.1,"CP085465,CP085466,CP085467",,Ningbo First Hospital,Oxford Nanopore,320x,ABySS v. 2021-02-01T00:00:00,1,2,3,4692576,58.420067,4331,4122,bile,,2020-12-24,China,China:Ningbo,,male,72,cholecystitis,,host_disease_outcome:recovery,,,,,,,,,,,Antibiotic Resistance Determinants and Virulence Factors of Aeromonas in Ningbo,collected_by:Xing-bei Weng,,,,,,,cholecystitis,,recovery,,,,,,,,,,,,100,0,Urinary Tract Diseases,Lower UTI,Gastrointestinal,Urinary Tract Diseases-Lower UTI HP,654.668,Aeromonas veronii A29V,A29V,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN20667377,654,,,,,,,,2022-01-25T00:00:00Z,,PRJNA749892,GCA_021586915.1,"CP080630,CP080632,CP080631",,,Oxford Nanopore,111.0x,Unicycler v. 0.4.7,1,2,3,4535069,58.6704,4200,4012,feces,,2019,Australia,Australia,,,,gastroenteritis,,,,,,,,,,,,,,collected_by:Douglass Hanly Moir Pathology,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,654.785,Aeromonas veronii FC951,FC951,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN08281233,654,,,,,,,,2018-10-16T00:00:00Z,,PRJNA428153,,PKSR00000000,,,Oxford Nanopore MiniION; IonTorrent,94.0x,Unicycler v. 0.4.6,1,1,2,4863185,58.714073,4841,4428,feces,,2017,India,India: Vellore,,,,diarrhea,,,,,,,,,,,,,,"collected_by:Christian Medical College, Vellore",,,,,,,diarrhea,,,,,,,,,,,,,,99.7,0.3,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,654.875,Aeromonas veronii ANYA 18644,ANYA 18644,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901099,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121833,CP121834",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4535906,58.665874,4354,,plasma,,2021-08-09,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,1.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.876,Aeromonas veronii ANYA 16549,ANYA 16549,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901093,654,,,,MLST.Aeromonas_spp.170,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121843,CP121844",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4577382,58.533676,4363,,plasma,,2020-11-06,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.877,Aeromonas veronii ANYA 18661,ANYA 18661,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901100,654,,,,MLST.Aeromonas_spp.170,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121832,CP121830,CP121831",,,Oxford Nanopore,30x,flye v. 2.9.2,1,2,3,4685416,58.69564,4436,,plasma,,2021-08-10,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.878,Aeromonas veronii ANYA 14430,ANYA 14430,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901090,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121848,CP121847",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4578595,58.803627,4373,,plasma,,2020-02-18,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.879,Aeromonas veronii ANYA 19953,ANYA 19953,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901104,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121816,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4510909,58.776424,4236,,plasma,,2022-01-29,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.880,Aeromonas veronii ANYA 16702,ANYA 16702,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901094,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121842,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4447248,58.90229,4128,,plasma,,2020-11-24,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.881,Aeromonas veronii LOID 15995,LOID 15995,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901085,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121859,CP121858,CP121860",,,Oxford Nanopore,30x,flye v. 2.9.2,1,2,3,4629322,58.557926,4384,,plasma,,2020-08-04,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,99.7,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.882,Aeromonas veronii ANYA 19170,ANYA 19170,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901103,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121817,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4601947,58.819473,4352,,plasma,,2021-10-19,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.883,Aeromonas veronii ANYA 14386,ANYA 14386,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901089,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121849,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4583999,58.797634,4337,,plasma,,2020-02-10,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.884,Aeromonas veronii ANYA 15110,ANYA 15110,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901091,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121846,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4536836,58.59317,4267,,plasma,,2020-05-26,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.885,Aeromonas veronii ANYA 18462,ANYA 18462,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901098,654,,,,MLST.Aeromonas_spp.161,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121835,CP121836",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4590379,58.704674,4285,,plasma,,2021-07-14,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.886,Aeromonas veronii ANYA 18263,ANYA 18263,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901097,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121837,CP121838",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4696697,58.62043,4446,,plasma,,2021-06-21,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.887,Aeromonas veronii ANYA 18196,ANYA 18196,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901095,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121841,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4480764,58.906025,4111,,plasma,,2021-06-12,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.888,Aeromonas veronii ANYA 15694,ANYA 15694,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901092,654,,,,MLST.Aeromonas_spp.170,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121845,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4755234,58.540756,4650,,plasma,,2020-09-04,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.889,Aeromonas veronii ANYA 18197,ANYA 18197,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901096,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121840,CP121839",,,Oxford Nanopore,30x,flye v. 2.9.2,1,1,2,4532047,58.843895,4193,,plasma,,2021-06-12,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.890,Aeromonas veronii ANYA 14022,ANYA 14022,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901088,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121851,CP121850,CP121852,CP121853",,,Oxford Nanopore,30x,flye v. 2.9.2,1,3,4,4634898,58.61611,4402,,plasma,,2019-12-18,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.891,Aeromonas veronii LOID 16013,LOID 16013,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901086,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,"CP121856,CP121857,CP121855",,,Oxford Nanopore,30x,flye v. 2.9.2,1,2,3,4629037,58.55933,4392,,plasma,,2020-09-07,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,654.892,Aeromonas veronii ANYA 13997,ANYA 13997,Aeromonas veronii,Aeromonas,Aeromonadaceae,Aeromonadales,Gammaproteobacteria,Pseudomonadota,SAMN33901087,654,,,,,,,,2023-04-17T00:00:00Z,,PRJNA948391,,CP121854,,,Oxford Nanopore,30x,flye v. 2.9.2,1,0,1,4593380,58.660442,4392,,plasma,,2019-12-14,Taiwan,Taiwan: Hospital,,,,infection,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,infection,,,,,,,,,,,,,,100,1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,664662.50,Borreliella bavariensis strain A104S,A104S,Borreliella bavariensis,Borreliella,Borreliaceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN05328446,664662,,,,,,,,2021-06-10T00:00:00Z,33032522,PRJNA327303,GCA_018831565.1,"CP058812,CP058813,CP058825,CP058822,CP058823,CP058817,CP058824,CP058816,CP058818,CP058819,CP058820,CP058821",,Bavarian Health and Food Safety Authority,Illumina MiSeq; PacBio,22.0x,SPAdes v. 3.10.1; HGAP v. 3,1,13,14,1315446,27.7505,1468,,missing,,1996,Netherlands,Netherlands,,,,Lyme disease,,,,,,,,,,,,,"To understand the evolutionary history of the Borrelia burgdorferi sensu lato species complex, we used NGS sequencing to obtain a strongly supported phylogeny of many genospecies belonging to this bacterial species complex. We associated host and vector associations to this phylogeny which provides an understanding of their impact on diversification of the bacteria.",collected_by:German National Reference Centre for Borrelia,,,,,,,Lyme disease,,,,,,,,,,,,,,97.98,0,Specific Bacterial Infections,Lyme Disease,Other,Specific Bacterial Infections-Lyme Disease HP,666.3112,Vibrio cholerae strain FDAARGOS_223,FDAARGOS_223,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN04875560,666,,,,MLST.Vibrio_cholerae.69,,FDA:FDAARGOS_223,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073335.2,"CP020408,CP020407",,US Food and Drug Administration,PacBio,15.4328048373434x,HGAP v. 3,2,,2,4042138,47.49,3881,3745,blood,,,USA,USA:MD,,,,Infection with Vibrio cholerae,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:USAMRIID,,,,,,,Infection with Vibrio cholerae,Missing,Missing,Missing,Missing,,,,,,,,,,100,0.4,Specific Bacterial Infections,Cholera,Blood and Circulatory System,Specific Bacterial Infections-Cholera HP,666.3394,Vibrio cholerae strain ICDC-VC661,ICDC-VC661,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN04045282,666,,,,MLST.Vibrio_cholerae.69,,,,2017-09-19T00:00:00Z,,PRJNA295270,GCA_002313005.1,"CP012666,CP012667,CP012668",,"National Institute for Communicable Disease Control and Prevention, China CDC",,,,2,1,3,4264715,47.66,4128,3738,patient,,2006-06,China,China:Jiangxi,,,,gastroenteritis,,,,,,,,,C,,,,,"collected_by:Center for Disease Control and Prevention, Jiangxi",,,,,,,gastroenteritis,,,,,,,,,,,,,,100,3.6,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,666.3404,Vibrio cholerae strain E7946,E7946,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN07821484,666,,,,MLST.Vibrio_cholerae.69,,,,2017-11-03T00:00:00Z,,PRJNA415313,GCA_002749635.1,"CP024162,CP024163",,Tufts University,Illumina HiSeq,600.0x,CLC Genomics Workbench de novo v. 10.0,2,,2,4063073,47.5,3876,3805,stool,,1978,Bahrain,Bahrain,,,,cholera,,,,,,,,,,,,,Complete genome sequence of a laboratory strain of Vibrio cholerae O1 El Tor,collected_by:Myron Levine,,,,,,,cholera,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Cholera,Gastrointestinal,Specific Bacterial Infections-Cholera HP,666.3607,Vibrio cholerae strain A1552,A1552,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08323859,666,El Tor,,,MLST.Vibrio_cholerae.69,,,,2018-01-19T00:00:00Z,,PRJNA428893,GCA_002892855.1,"CP025936,CP025937",,University of Texas at San Antonio,Oxford Nanopore MinION; Illumina MiSeq,121.0x,SPAdes v. 3.10.1,2,,2,4085463,47.459713,3897,3825,fecal sample,,1992,USA,USA: CA,,,,Cholera,,,,,,,,,,,,,Sequencing and assembly of Vibrio cholerae genomes for comparative genomics and evolution studies,collected_by:California Department of Public Health (CDPH),,,,,,,Cholera,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Cholera,Gastrointestinal,Specific Bacterial Infections-Cholera HP,666.3619,Vibrio cholerae strain Vibrio cholerae str. BC1071,Vibrio cholerae str. BC1071,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMEA104115281,666,,,,MLST.Vibrio_cholerae.514,,,,2017-12-20T00:00:00Z,,PRJEB20589,GCA_900185995.1,"LT897797,LT897798",,Leibniz-Institut DSMZ-Deutsche Sammlung von Mikro,,,,2,,2,4194576,47.516125,3874,3689,patient blood,,2016,Germany,Germany,,,,,,host_health_state:diseased,,,,,,,,,,,Genome sequencing of Vibrio cholerae strain BK1071-16,,,,,,,,,diseased,,,,,,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,666.3624,Vibrio cholerae strain A1552,A1552,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08896638,666,El Tor,,,MLST.Vibrio_cholerae.69,"genotype:Rifampicin resistant, streptomycin sensitive",,,2018-05-08T00:00:00Z,,PRJNA447902,GCA_003097695.1,"CP028894,CP028895",,EPFL/Melanie Blokesch,PacBio,170.0x,HGAP v. 3,2,,2,4085468,47.4598,3778,3610,human sample,,1992,USA,USA: CA,,,,cholera,,host_description:Traveler from South America to California,,,,,,,,,,,Whole genome sequence data and de novo assembly of diverse Vibrio cholerae strains (Blokesch laboratory),collected_by:California Department of Public Health (CDPH),,,,,,,cholera,,,Traveler from South America to California,,,,,,,,,,"Cold seafood salad served between Lima, Peru and Los Angeles, USA was vehicle of infection",100,0,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,666.3625,Vibrio cholerae strain N16961,N16961,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08822914,666,O1 El Tor,,,MLST.Vibrio_cholerae.69,genotype:Streptomycin resistant,,,2018-04-23T00:00:00Z,,PRJNA447902,GCA_003063785.1,"CP028827,CP028828",,EPFL/Melanie Blokesch,PacBio,351.11x,HGAP v. 3,2,,2,4047835,47.495415,3734,3554,patient sample,,1975,Bangladesh,Bangladesh,,,,Cholera,,,,,,,,,,,,,Whole genome sequence data and de novo assembly of diverse Vibrio cholerae strains (Blokesch laboratory),,,,,,,,Cholera,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,666.3826,Vibrio cholerae strain V060002,V060002,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMD00118470,666,,biovar El,,MLST.Vibrio_cholerae.69,,,,2018-08-03T00:00:00Z,29930068,PRJDB7008,GCA_003574155.1,AP018677,,"Bacteriology I, National Institute of Infectious Diseases",PacBio RS II,196.55x,HGAP v. 3,1,,1,4057041,47.5011,3711,3560,patient traveled to indonesia and has been used as a model strain for studying regulatory mechanisms of chitin-induced natural transformation,isolated in 1997 from a patient traveled to Indonesia and has been used as a model strain for studying regulatory mechanisms of chitin-induced natural transformation,1997,,,,,,,,,,,Negative,Vibrios,Yes,Mesophilic,37,Anaerobic,Aquatic,cholera,The O1 biovar El Tor Ogawa Vibrio cholerae strain V060002 was isolated in 1997 from a patient traveled to Indonesia and has been used as a model strain for studying regulatory mechanisms of chitin-induced natural transformation. The genome data demonstrated that this clinical strain has a single chromosome instead of the two chromosomes usually found in V. cholerae and other Vibrio species.,,missing,missing,missing,missing,genome sequencing of V060002,,,,,,,,,,,,missing,,,,100,1.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,666.3842,Vibrio cholerae strain FORC_073 strain National Culture Collection for Pathogens,National Culture Collection for Pathogens,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN07684567,666,,,,MLST.Vibrio_cholerae.289,,,,2018-09-24T00:00:00Z,,PRJNA408321,GCA_003591575.1,"CP024082,CP024083",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,310.47x,PacBio SMRT Analysis v. 2.3.0,2,,2,4026094,47.60244,3726,3522,clinical isolation,,2017-01-01,South Korea,South Korea: Seoul,,,,food poisoning,,,,,,,,,,,,,Vibrio cholerae is one of the well-known food-borne pathogen. It is a clinical isolate in South Korea.,collected_by:National Culture Collection for Pathogens,,,,,,,food poisoning,,,,,,,,,,,,,,100,1.6,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,666.4178,Vibrio cholerae strain FORC_076,FORC_076,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08384473,666,,,,,,,,2019-01-29T00:00:00Z,,PRJNA431150,GCA_004117115.1,"CP026531,CP026532",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,144x,PacBio SMRT Analysis v. 2.3.0,2,,2,4021495,47.257725,3784,3623,human,isolated from human in South Korea,,South Korea,South Korea,,,,watery diarrhea,,,,,,,,,,,,,Vibrio cholerae is one of the well-known food-borne pathogen. It was isolated from human in South Korea.,,,,,,,,watery diarrhea,,,,,,,,,,,,,,98.91,0.7,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,666.4722,Vibrio cholerae strain CTMA_1441,CTMA_1441,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13613314,666,,,,MLST.Vibrio_cholerae.69,,,,2019-12-25T00:00:00Z,,PRJNA596117,GCA_009799825.1,"CP047059,CP047060",,Universite catholique de Louvain,Oxford Nanopore; Illumina MiSeq,350.0x,SPAdes v. 3.13.1,2,0,2,4042783,47.58242,3765,3656,fecal sample,,2015,Democratic Republic of the Congo,Democratic Republic of the Congo,,,,cholera,,,,,,,,,,,,,"Whole-Genome Sequence of a pathogenic Vibrio cholerae O1 El Tor strain isolated in eastern Democratic Republic of the Congo, defective for the entire Vibrio pathogenicity island-1 (VPI-1)",collected_by:Leonid Irenge Mwana Wa Bene,,,,,,,cholera,,,,,,,,,,,,,,100,0.03,Specific Bacterial Infections,Cholera,Gastrointestinal,Specific Bacterial Infections-Cholera HP,666.5228,Vibrio cholerae strain VC1374,VC1374,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN11604374,666,,,,MLST.Vibrio_cholerae.69,,,,2020-07-22T00:00:00Z,,PRJNA541899,GCA_013462495.1,"CP040172,CP040173,CP040171",,ICDC,Illumina HiSeq; PacBio Sequel,100.0x,HGAP v. 4,2,1,3,4236364,47.68337,4105,3973,missing,,2001-01-01,China,China,,,,Diarrhea,,,,,,,,,,,,,Co-existence of CTXΦ prophage and Pre-CTXΦ prophage,"collected_by:ICDC, China CDC",,,,,,,Diarrhea,,,,,,,,,,,,,,99.68,0.03,Gastrointestinal Diseases,Diarrheal Diseases,Other,Gastrointestinal Diseases-Diarrheal Diseases HP,666.6203,Vibrio cholerae N1252,N1252,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN30329103,666,,,,MLST.Vibrio_cholerae.69,,,,2022-08-24T00:00:00Z,,PRJNA869863,GCA_024734685.1,"CP102927,CP102928",,,Oxford Nanopore GridION; Illumina NextSeq,107.33x,Unicycler v. 0.4.8,2,0,2,4095848,47.512043,3750,,feces,,2022-06,Australia,Australia: New South Wales,,,,cholera,,,,,,,,,,,,,,collected_by:New South Wales Health Pathology,,,,,,,cholera,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Cholera,Gastrointestinal,Specific Bacterial Infections-Cholera HP,666.6286,Vibrio cholerae CNRVC190243,CNRVC190243,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMEA9995373,666,Inaba,,,MLST.Vibrio_cholerae.69,,CNRVC:190243,,2022-09-21T00:00:00Z,,PRJEB52123,GCA_937000105.1,"OW443147,OW443148,OW443149",,,,,,2,1,3,4235033,47.62213,3933,3758,stool,,2019-03-22,Yemen,Yemen,,,,,,host_health_state:diseased,,,,,,,,,,,,"identified_by:Abdulelah Al-Harazi, ML Quilici",,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,666.6714,Vibrio cholerae MS84A,MS84A,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN18296291,666,Ogawa,,,MLST.Vibrio_cholerae.69,,,,2023-05-22T00:00:00Z,,PRJNA714234,,"CP077060,CP077061",,,Illumina MiSeq; Oxford Nanopore MinION,825.0x,Unicyler v. v0.4.8,2,0,2,4007146,47.5239,3720,3573,stool,,2010,Thailand,Thailand: Tak,,,,diarrhea,,,,,,,,,,,,,,collected_by:DMSc/RCC,,,,,,,diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,666.6774,Vibrio cholerae man9,man9,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMD00515067,666,,,,MLST.Vibrio_cholerae.73,genotype:O1,,,2023-04-04T00:00:00Z,,PRJDB13952,,"AP026558,AP026559",,,PacBio RS II,276x,Canu v. 2.0.,2,0,2,3996015,47.494118,4058,,human feces,,1946,Japan,Japan,,,,Cholera,,,,,,,,,,,,,,collected_by:Nagasaki University Hospital,,,,,,,Cholera,,,,,,,,,,,,,,98,2.4,Specific Bacterial Infections,Cholera,Gastrointestinal,Specific Bacterial Infections-Cholera HP,670.1110,Vibrio parahaemolyticus strain FDAARGOS_191,FDAARGOS_191,Vibrio parahaemolyticus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN04875528,670,,,,MLST.Vibrio_parahaemolyticus.3,,FDA:FDAARGOS_191,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073775.2,"CP020427,CP020428",,US Food and Drug Administration,PacBio,15.6746298491941x,HGAP v. 3,2,,2,5173060,45.39,4952,4791,human,,1996,India,India,,female,,Vibrio infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:CFSAN,,,,,,,Vibrio infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,3.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,670.1228,Vibrio parahaemolyticus strain MAVP-R,MAVP-R,Vibrio parahaemolyticus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN06042545,670,,,,MLST.Vibrio_parahaemolyticus.631,,,,2017-08-01T00:00:00Z,28687650,PRJNA263814,GCA_002220985.2,"CP022552,CP022553,CP022554,CP022555",,University of New Hampshire,PacBio,56.0x,other v. 2.3.0,2,2,4,5376691,45.17,5184,4998,stool,,2011,,,,,,gastroenteritis,,,,,,,,,,,,,To study population structure of Vibrio parahaemolyticus in Northeast New England regions,collected_by:MAPDH,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,3.5,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,670.6329,Vibrio parahaemolyticus VP20210406,VP20210406,Vibrio parahaemolyticus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN29674618,670,,,,MLST.Vibrio_parahaemolyticus.3,,,,2022-10-23T00:00:00Z,,PRJNA858205,GCA_025792495.1,"CP107279,CP107280",,,Illumina NextSeq,20.0x,SPAdes v. v3.15.3,2,0,2,5165770,45.337204,4776,4538,feces,,2021-08-04,China,"China: Zhejiang, Huzhou",,,,gastroenteritis,,,,,,,,,,,,,,collected_by:Huzhou CDC,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,670.6485,Vibrio parahaemolyticus RMDVP1,RMDVP1,Vibrio parahaemolyticus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN30158696,670,O10:K4,,,MLST.Vibrio_parahaemolyticus.3,,,,2023-01-30T00:00:00Z,36689335,PRJNA866285,,"CP102434,CP102433",,,Illumina MiSeq; Oxford Nanopore,416.0x,Unicycler v. 0.4.8,2,0,2,5174465,45.37623,4787,4587,stool,,2021-11,Thailand,Thailand,,,,acute diarrhea,,,,,,,,,,,,,,collected_by:DDC/DMSc/RCC,,,,,,,acute diarrhea,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,672.1173,Vibrio vulnificus strain Vv180806,Vv180806,Vibrio vulnificus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN12816916,672,,,,MLST.Vibrio_vulnificus.303,,,,2020-08-07T00:00:00Z,,PRJNA573548,GCA_014107515.1,"CP044206,CP044207,CP044208",,Guangdong Institute of Microbiology,PacBio Sequel,529.0x,HGAP v. 4,2,1,3,5356494,46.5837,5216,4955,blood,"isolated from a mortality case, and revealed a high level of cefoxitin resistance exhibited by this bacterium",2018-08-06,China,China: Guangzhou,,,,necrotizing fasciitis,,,,,,,,,,,,,"Here, we provide the complete genome sequence of V. vulnificus Vv180806, a strain isolated from a mortality case, and revealed a high level of cefoxitin resistance exhibited by this bacterium.",collected_by:The first affiliated hospital of sun yat-sen university,,,,,,,necrotizing fasciitis,,,,,,,,,,,,,,100,0.14,Skin and Soft Tissue Infections,Necrotizing fasciitis,Blood and Circulatory System,Skin and Soft Tissue Infections-Necrotizing fasciitis HP,672.2012,Vibrio vulnificus VV2014DJH,VV2014DJH,Vibrio vulnificus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN06237111,672,,,,MLST.Vibrio_vulnificus.289,,,,2018-01-03T00:00:00Z,,PRJNA362267,,"CP019320,CP019321",,,PacBio,50.0x,SOAPdenovo v. MAY-2016,2,0,2,5074562,46.81344,4849,4623,blood,,2014-07-17,China,China: Taizhou,,,,Vibrio gastroenteritis,,,,,,,,,,,,,,collected_by:Zhejiang Provincial Center for Disease Control and Prevention,,,,,,,Vibrio gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Diarrheal Diseases HP,672.2166,Vibrio vulnificus VV2018,VV2018,Vibrio vulnificus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN35548064,672,,,,,,,,2023-06-07T00:00:00Z,,PRJNA978255,,"CP126698,CP126699",,,PacBio; Illumina HiSeq,100.0x,Celera Assembler v. Canu v2.2; GS De Novo,2,0,2,5080799,46.8112,4737,4489,blood specimen,,2018,China,China,,,,hepatitis B virus cirrhosis,,,,,,,,,,,,,,"collected_by:Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University",,,,,,,hepatitis B virus cirrhosis,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,672.848,Vibrio vulnificus strain FORC_077,FORC_077,Vibrio vulnificus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08563567,672,,,,,,,,2019-02-28T00:00:00Z,,PRJNA434522,GCA_004319645.1,"CP027030,CP027031",,"Food-borne Pathogen Omics Research Center, FORC",PacBio,163x,Pacbio SMRT analysis v. 2.3.0,2,,2,5018260,46.882744,4654,4460,human,isolated from human in South Korea,2017,South Korea,South Korea,,,,Food poisoning,,,,,,,,,,,,,Vibrio vulnificus FORC_077 Complete genome sequencing.Vibrio vulnificus is one of the well-known food-borne pathogen. It was isolated from human in South Korea.,collected_by:NCCP,,,,,,,Food poisoning,,,,,,,,,,,,,,100,0.33,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,672.849,Vibrio vulnificus strain CMCP6,CMCP6,Vibrio vulnificus,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN10360789,672,,,,,,,,2019-03-19T00:00:00Z,,PRJNA503483,GCA_004355205.1,"CP037931,CP037932",,University of South Florida,PacBio RSII,216.0x,HGAP v. NOV-2016,2,,2,5199428,46.752056,4975,4704,"chonnam national university hospital, korea, 2003",,2016-09,USA,"USA: Tampa, FL",temperature:30,,,,,,,,,,,,,,,,"Vibrio vulnificus strain CMCP6 methylome was sequenced in bacteria grown in sterile natural seawater and human serum amended with iron to mimic hemochromatosis. This was done to 1) establish the methylome of V. vulnificus, 2) determine if the methylome changes in response to the environment, and 3) identify changes in methylation that may contribute to a virulent phenotype during the transition from free living to an infectious state.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.72,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,673.18,Grimontia hollisae FDAARGOS_111,FDAARGOS_111,Grimontia hollisae,Grimontia,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN03996327,673,,,,,,FDA:FDAARGOS_111,,2019-09-30T00:00:00Z,,PRJNA231221,GCA_001558255.2,"CP014056,CP014055",,,Pacbio; Illumina,23.958x,HGAP3 v. Nov 2014,2,0,2,3998439,49.51017,3751,3552,human,,,USA,USA: MD,,,,Vibrio infection,,,,,,,,,,,,,,collected_by:FDA CFSAN,,,,,,,Vibrio infection,Missing,Missing,Missing,Missing,,,,,,,,,,93.1,0.4,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,674529.279,Bacteroides faecis strain BFG-108,BFG-108,Bacteroides faecis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547144,674529,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091505.1,"CP081916,CP081914,CP081915",,National Institute of Allergy and Infectious Disease,PacBio Sequel,288x,HGAP/FALCON v. v. 6.0,1,2,3,6352228,42.55384,5422,4931,missing,,1986,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.14,0.54,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,674529.358,Bacteroides faecis WAL8736,WAL8736,Bacteroides faecis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663845,674529,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914295.1,CP083678,,,Illumina HiSeq,205x,A5ud v. v1,1,0,1,5913648,42.148144,5005,4597,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0.2,,,Gastrointestinal,- HP,676.30,Vibrio fluvialis strain 12605,12605,Vibrio fluvialis,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN06209376,676,,,,,,,,2017-01-17T00:00:00Z,,PRJNA360363,GCF_001952955.1,"CP019118,CP019119","NZ_CP019118.1,NZ_CP019119.1",Zhejiang University,PacBio,300.0x,SmrtPipe v. 1.87,2,,2,4851664,50.12,4510,,bile,isolated from a patient,2013,China,China:Hangzhou,,,,,,,,,,,,,,,,,"This is the genome sequence of vibrio fluvialis 12605, which was isolated from a patient. Study of the genome will give us a better understanding of its pathogeny.",sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,676.305,Vibrio fluvialis strain 19-VB00936,19-VB00936,Vibrio fluvialis,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN18795813,676,,,,,,,,2021-04-26T00:00:00Z,,PRJNA722921,GCA_018140575.1,"CP073273,CP073274",,German Federal Institute for Risk Assessment,Illumina; Oxford Nanopore MinION,100.0x,Unicycler v. v0.4.8,2,0,2,4808142,50.140594,4488,4325,foot,,2019,,Baltic Sea,,,,wound infection,,,,,,,,,,,,,Vibrio fluvialis 19-VB00936 isolated from a wound infection,collected_by:Helios Hanseklinikum Stralsund,,,,,,,wound infection,,,,,,,,,,,,,,99.93,0.62,Skin and Soft Tissue Infections,Wounds and Abscesses,Other,Skin and Soft Tissue Infections-Wounds and Abscesses HP,676.375,Vibrio fluvialis ATCC 33809,ATCC 33809,Vibrio fluvialis,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN03996321,676,,,,MLST.Vibrio_spp.144,,FDA:FDAARGOS_104,,2021-07-29T00:00:00Z,,PRJNA231221,GCA_001558415.2,"CP014034,CP014035",,,PacBio; Illumina,493.223x,HGAP3 v. Sep 2014,2,0,2,4827733,49.92573,4542,4402,missing,,,Bangladesh,Bangladesh:Dacca,,,,Vibrio infection,,,,,,,,,,,,,,collected_by:FDA CFSAN,,,,,,,Vibrio infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,676.398,Vibrio fluvialis IDH05335,IDH05335,Vibrio fluvialis,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMD00603157,676,,,,,,,,2023-05-25T00:00:00Z,,PRJDB15820,,"AP028128,AP028129,AP028130,AP028131,AP028132",,,Illumina NovaSeq6000; Nanopore GridION X5,144x,Flye v. 2.9; Unicycler v. 0.4.8,2,3,5,5386988,49.35242,5213,5017,stool sample from a patient with diarrhea,,2013-05-25,India,India,,,,Diarrhea,,,,,,,,,,,,,,"collected_by:Goutam Chowdhurry, Thandavarayan Ramamurthy, Shanta Dutta and Asish Mukopadhyay",,,,,,,Diarrhea,,,,,,,,,,,,,,100,0.7,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,67824.3,Citrobacter farmeri strain AUSMDU00008141,AUSMDU00008141,Citrobacter farmeri,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07452765,67824,,,,,,,,2017-08-14T00:00:00Z,,PRJNA397262,GCA_002249995.1,"CP022695,CP022696,CP022697,CP022698",,Doherty Applied Microbial Genomics,PacBio; Illumina NextSeq,501.0x,Canu v. 1.5,1,3,4,5715629,53.06,5759,5629,rectal swab,,2015-07-05,Australia,Australia: Victoria,,,,Colonisation,,,,,,,,,,,,,"Whole-genome sequencing of KPC-producing Enterobacteriaceae from an outbreak in Victoria, Australia",collected_by:Doherty Applied Microbial Genomics,,,,,,,Colonisation,,,,,,,,,,,,,,99.7,0.7,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,67826.48,Citrobacter sedlakii strain 3347089II,3347089II,Citrobacter sedlakii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17736025,67826,,,,,,,,2021-04-22T00:00:00Z,,PRJNA698767,GCA_018128425.1,"CP071070,CP071071,CP071072",,,Illumina NovaSeq; Oxford Nanopore MiniION,170x,Unicycler v. 0.4.8,1,2,3,4967243,54.34697,4860,4624,outer malleolus,,2020,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,collected_by:Institute for Infectious Diseases Bern,,,,,,,missing,,,,,,,,,,,,,,100,0.99,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,67827.18,Citrobacter werkmanii strain UMH18,UMH18,Citrobacter werkmanii,Citrobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07729550,67827,,,,MLST.Citrobacter_freundii.31,,,,2018-10-17T00:00:00Z,30087402,PRJNA412823,GCA_003665555.1,CP024675,,University of Michigan,PacBio,166x,HGAP v. 2,1,,1,5062051,52.173794,4947,4847,,,2013-10,USA,USA: Michigan,,,,bacteremia,,,,,,,,,,,,,"The goal of this study was to identify bacterial genes that contribute to the survival and fitness of an opportunistic pathogen, Citrobacter freundii, during bacteremia. Bacterial isolates were obtained from University of Michigan Hospital System patients with Citrobacter bloodstream infections and the genomic sequences of each were determined de novo. From these isolates, a single C. freundii strain was selected for use in INSeq experiments to identify fitness genes in a murine model of bacteremia.",collected_by:University of Michigan,,,,,,,bacteremia,,,,,,,,,,,,,,99.87,1.27,Bloodstream Infections,Bacteremia,Other,Bloodstream Infections-Bacteremia HP,678932.16,Auritidibacter ignavus BABAE-5,BABAE-5,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960637,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122565,,,Illumina MiSeq; Oxford Nanopore GridION,112.4x,Unicycler v. 0.5.0,1,0,1,2649892,59.3897,2505,2354,ear,,2022-09-10,Germany,Germany: Bochum,,male,34,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.17,Auritidibacter ignavus BABAE-2,BABAE-2,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960634,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122562,,,Illumina MiSeq; Oxford Nanopore GridION,87.2x,Unicycler v. 0.5.0,1,0,1,2698227,59.536095,2513,2365,ear,,2022-04-20,Germany,Germany: Bochum,,female,27,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,2,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.18,Auritidibacter ignavus BABAE-4,BABAE-4,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960636,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122564,,,Illumina MiSeq; Oxford Nanopore GridION,77.6x,Unicycler v. 0.5.0,1,0,1,2642502,59.542244,2472,2345,ear,,2022-08-08,Germany,Germany: Bochum,,male,58,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.19,Auritidibacter ignavus BABAE-3,BABAE-3,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960635,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122563,,,Illumina MiSeq; Oxford Nanopore GridION,78.5x,Unicycler v. 0.5.0,1,0,1,2642042,59.54277,2478,2345,ear,,2022-08-08,Germany,Germany: Bochum,,male,74,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.20,Auritidibacter ignavus BABAE-1,BABAE-1,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960633,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122561,,,Illumina MiSeq; Oxford Nanopore GridION,83.6x,Unicycler v. 0.5.0,1,0,1,2776501,59.44316,2626,2470,ear,,2021-12-24,Germany,Germany: Bochum,,female,38,mastoiditis,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,mastoiditis,,,,,,,,,,,,,,99.2,1.3,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,678932.21,Auritidibacter ignavus BABAE-8,BABAE-8,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN35037159,678932,,,,,,,,2023-05-23T00:00:00Z,,PRJNA949825,,CP125879,,,Illumina MiSeq; Oxford Nanopore GridION,87.9x,Unicycler v. v. 0.5.0,1,0,1,2770414,59.658195,2635,2482,ear,,2022-01-04,Germany,Germany: Bochum,,female,32,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1.8,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.22,Auritidibacter ignavus BABAE-7,BABAE-7,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN35037158,678932,,,,,,,,2023-05-23T00:00:00Z,,PRJNA949825,,CP125880,,,Illumina MiSeq; Oxford Nanopore GridION,91.6x,Unicycler v. v. 0.5.0,1,0,1,2645303,59.581116,2461,2349,ear,,2022-09-28,Germany,Germany: Bochum,,female,50,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1.3,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,678932.23,Auritidibacter ignavus BABAE-6,BABAE-6,Auritidibacter ignavus,Auritidibacter,Micrococcaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN33960638,678932,,,,,,,,2023-04-22T00:00:00Z,,PRJNA949825,,CP122566,,,Illumina MiSeq; Oxford Nanopore GridION,116.7x,Unicycler v. 0.5.0,1,0,1,2882973,59.464725,2754,2607,ear,,2022-09-12,Germany,Germany: Bochum,,male,68,otitis media,,,Not defined,AMR Panel,,,,,,,,,,collected_by:IML Bochum GmbH,,,,,,,otitis media,,,,,,,,,,,,,,99.2,1.5,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis NHP,679190.26,Prevotella buccalis ATCC 35310,ATCC 35310,Hoylesella buccalis,Hoylesella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222704,679190,,,,,,ATCC:35310,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025151385.1,CP102287,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3307707,45.298813,3078,2642,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.29,0.83,,,Other,- HP,686.36,Vibrio cholerae O1 biovar El Tor strain HC1037,HC1037,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN08472240,686,Ogawa,,,MLST.Vibrio_cholerae.69,genotype:O1 Serogroup,,,2018-02-22T00:00:00Z,,PRJNA433212,GCA_002946655.1,"CP026647,CP026648",,Tufts University,Illumina,86.0x,CLC NGS Cell v. 7,2,,2,4061419,47.525238,3848,3769,clinical isolate from adult patient,,2014-01-08,Haiti,Haiti: Jacmel,,,Adult,Cholera,,,,,,,,,,,,,"The long-term goals of the research program are to enhance understanding of the virulence and transmission of mucosal pathogens, specifically the Gram-negative intestinal pathogen Vibrio cholerae.",collected_by:Cholera Treatment Center,,,,,,,Cholera,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,686.90,Vibrio cholerae O1 biovar El Tor strain E7946,E7946,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13734989,686,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,GCA_013085165.1,"CP047303,CP047304",,EPFL,PacBio,344.0x,HGAP v. 3,2,0,2,4082461,47.499855,3845,3665,missing,,1978,Bahrain,Bahrain,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Camilli lab,,,,,,,cholera,,,,,,,,,,,,,,100,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,686.91,Vibrio cholerae O1 biovar El Tor strain P27459,P27459,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13734999,686,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,GCA_013085125.1,"CP047299,CP047300",,EPFL,PacBio,375.0x,HGAP v. 3,2,0,2,4036513,47.487732,3772,3611,missing,,1976,Bangladesh,Bangladesh,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Reidl lab,,,,,,,cholera,,,,,,,,,,,,,,100,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,686.92,Vibrio cholerae O1 biovar El Tor strain DRC-193A,DRC-193A,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13735001,686,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,GCA_013085145.1,"CP047301,CP047302",,EPFL,PacBio,390.0x,HGAP v. 3,2,0,2,4104155,47.503517,3817,3655,missing,,2011,Democratic Republic of the Congo,Democratic Republic of the Congo,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Institut National de Recherche Biomedicale in the Democratic Republic of Congo,,,,,,,cholera,,,,,,,,,,,,,,100,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,686.93,Vibrio cholerae O1 biovar El Tor strain C6709,C6709,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13734988,686,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,GCA_013085105.1,"CP047297,CP047298",,EPFL,PacBio,343.0x,HGAP v. 3,2,0,2,4090614,47.437805,3841,3666,missing,,1991,Peru,Peru,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Reidl lab,,,,,,,cholera,,,,,,,,,,,,,,99.98,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,69710.20,Treponema vincentii OMZ 804,OMZ 804,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253843,69710,,,,,,ATCC:700766,,2020-02-10T00:00:00Z,,PRJNA602574,GCA_010365865.1,CP048020,,,Illumina HiSeq; Oxford Nanopore MiniION,260.0x,Canu v. 1.8,1,0,1,2980180,44.319202,3149,2778,subgingival plaque,,1994,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,69710.22,Treponema vincentii OMZ 861,OMZ 861,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253847,69710,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181105.1,CP051148,,,Illumina HiSeq; Oxford Nanopore MiniION,1201.0x,Canu v. 1.8; pilon v. 1.22,1,0,1,2641120,45.567184,2528,2346,subgingival plaque,,1998-03,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,69710.23,Treponema vincentii OMZ 862,OMZ 862,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253848,69710,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181125.1,CP051153,,,Illumina HiSeq; Oxford Nanopore MiniION,1115.0x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2717368,45.51592,2640,2447,subgingival plaque,,1998-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,69710.24,Treponema vincentii OMZ 802,OMZ 802,Treponema vincentii,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253845,69710,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181205.1,CP051197,,,Illumina HiSeq; Oxford Nanopore MiniION,955.0x,Canu v. 1.8; pilon v. 1.22,1,0,1,2594485,45.67658,2442,2259,subgingival plaque,,1997-07,Switzerland,Switzerland,,,,Periodontitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Periodontitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,69823.18,Selenomonas sputigena KCOM 20461,KCOM 20461,Selenomonas sputigena,Selenomonas,Selenomonadaceae,Selenomonadales,Negativicutes,Bacillota,SAMN31475584,69823,,,,,,,,2022-11-06T00:00:00Z,,PRJNA894823,GCA_026013845.1,CP110231,,,PacBio RSII,370.0x,RS HGAP v. 3.0,1,0,1,2740586,57.175034,2625,2463,"subgingival dental plaque, gingivitis",,2001-11-23,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,97.9,1.7,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,69823.19,Selenomonas sputigena KCOM 1787,KCOM 1787,Selenomonas sputigena,Selenomonas,Selenomonadaceae,Selenomonadales,Negativicutes,Bacillota,SAMN31475128,69823,,,,,,,,2022-11-07T00:00:00Z,,PRJNA894812,GCA_026015965.1,CP110383,,,Illumina HiSeq,1083.0x,SPAdes v. 3.8.2,1,0,1,2614080,56.883522,2590,2418,mandibular osteomyelitis,,2002-04-22,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,sample_type:cell culture;biomaterial_provider:KCOM;collected_by:KCOM,,,,,,,,,,,,,,,,,,,,,97.9,1.7,Miscellaneous or Unspecified Infections,,Bone and Joint,Miscellaneous or Unspecified Infections- HP,69968.12,Macrococcus bovicus LI0213,LI0213,Macrococcus bovicus,Macrococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN35742781,69968,,,,,,,,2023-06-30T00:00:00Z,,PRJNA984185,,"CP128470,CP128469,CP128468,CP128467",,,Oxford Nanopore; Illumina,187.0x,unicycler v. 0.4.8,1,3,4,2157095,44.26838,2241,2197,skin infection,,2019-05-17,Switzerland,Switzerland,,,,,,,,,,,,,,,,,,sample_type:skin swab;collected_by:Dianalabs,,,,,,,,,,,,,,,,,,,,,97.2,0.4,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,702439.159,Prevotella nigrescens F0103,F0103,Prevotella nigrescens,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352178,702439,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127865.1,"CP072341,CP072342,CP072340",,The Forsyth Institute,PacBio Sequel,561x,Pacbio MA v. 9.0.0.92188,2,1,3,3069220,42.74757,3033,2575,human oral cavity,,1988-10,USA,"USA: Blacksberg, Virginia",,male,14,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02183;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.31,0,,,Oral,- HP,70255.15,Staphylococcus condimenti strain StO 2014-01,StO 2014-01,Staphylococcus condimenti,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN06159561,70255,,,,,,,,2016-12-27T00:00:00Z,,PRJNA357697,GCF_001922405.1,"CP018776,CP018777","NZ_CP018776.1,NZ_CP018777.1",St. Olavs University Hospital,Illumina; MinION,100.0x,SPAdes v. 3.5.0,1,1,2,2700886,34.57,2585,2519,missing,,2014,Norway,Norway,,,,Soft tissue infection,,,,,,,,,,,,,Staphylococcus condimenti Genome sequencing and assembly,collected_by:St. Olavs University Hospital,,,,,,,Soft tissue infection,,,,,,,,,,,,,,97.1,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Other,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,70346.7,Acinetobacter variabilis strain RYU24,RYU24,Acinetobacter variabilis,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMD00246909,70346,,,,,,,,2021-03-30T00:00:00Z,,PRJDB10565,GCA_018409485.1,AP024524,,"Department of Microbiology, Juntendo University School of Medicine",Illumina MiSeq; Oxford Nanopore MinION,160x,Unicycler v. 0.4.6,1,0,1,3198423,42.381603,3103,3025,human fecal,isolated in various countries and regions worldwide,2012,Japan,"Japan:Okinawa, Naha",,,,,,,,,,,,,,,,,"The emergence and dissemination of drug-resistant Acinetobacter species have been recognized as a serious health concern worldwide. Drug-resistant Acinetobacter baumannii has been one of the most important nosocomial pathogens with the highest incidence rate of isolation among Acinetobacter species. The genus Acinetobacter composes 62 distinct species with validly published names and several species with effectively published names awaiting validation. Acinetobacter variabilis was originally classified as Acinetobacter DNA group 15 TU using DNA-DNA hybridization by Tjernberg and Ursing in 1989. Later, Acinetobacter DNA group 15 TU was proposed as Acinetobacter variabilis sp. nov. in 2015 by Krizova L., et al. Since NDM-1 metallo-beta-lactamase (MBL) producing Klebsiella pneumoniae and Escherichia coli was initially detected in 2008 in Sweden, NDM-type MBL producers have become endemic in the India, and these organisms were isolated in various countries and regions worldwide. Although NDM-type MBL producers seem to be not yet spreading in Japan, there is at least four reports of NDM producing clinical isolates, including an isolate of E. coli producing NDM-1 MBL obtained from a patient traveling India for business in March 2009, and two isolates of NDM-5 MBL producing E. coli and NDM-1 MBL producing K. pneumoniae obtained from two foreigners from Bangladesh and Indonesia, respectively, and an isolate of E. coli producing NDM-7 obtained from a patient with history of admission in India. In Acinetobacter species, an isolate of NDM-1 MBL producing A. baumannii was obtained from a patient in Japan. The methylation of 16S rRNA confers high resistance to all clinically important aminoglycosides in Gram-negative organism. Clinical isolates of Klebsiella pneumoniae harboring the armA, a 16S rRNA methylase, and Pseudomonas aeruginosa harboring the rmtA, another one, were identified in 2003 in France, Japan, and the other countries since 2003. To date, 10 plasmid-associated 16S rRNA methylase genes, armA, rmtA-H and npmA, have been identified in human and animal. In this study, we analysis a clinical isolate of A. variabilis producing both NDM-1 MBL and OXA-420 carbapenemases, and ArmA 16S rRNA methylase obtained from a patient in Japan.",,Humind subtropical climate,city,human fecal sample,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346588/,Whole genome sequence of Acinetobacter variabilis,,,,,,,,,,,,Humind subtropical climate,,,,99.73,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,70348.3,Acinetobacter dispersus strain NCCP 16014,NCCP 16014,Acinetobacter dispersus,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN12340932,70348,,,,,,NCCP:16014,,2020-01-15T00:00:00Z,,PRJNA556123,GCA_009884975.1,CP041970,,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,315.0x,SPAdes v. 3.1,1,0,1,4024840,40.726562,3810,3682,sputum,,2014-01-01,South Korea,South Korea: Incheon,,,,,,,,,,,,,,,,,A clinical isolate of the genus Acinetobacter,collected_by:Korea National Institute of Health,,,,,,,unknown,,,,,,,,,,,,,,100,0.28,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,712710.42,Tannerella sp. oral taxon HOT-286 strain W11666,W11666,Tannerella serpentiformis,Tannerella,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN08743846,712710,,,,,,,,2018-04-04T00:00:00Z,,PRJNA282954,GCA_003033925.1,CP028365,,The Forsyth Institute,PacBio,223x,canu v. 1.6 / quiver,1,,1,3013600,56.429035,2870,2493,subgingival dental plaque,,2015-02,United Kingdom,United Kingdom: London,env_biome:Human oral cavity,female,50,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,"Blood Agar Base No. 2 (Lab M, UK), 5% horse blood",,,,periodontitis,,,,,,,,,Human oral cavity,,,,100,1.3,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,714.596,Aggregatibacter actinomycetemcomitans strain HK_907,HK_907,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12492049,714,a,,,,,,,2019-08-26T00:00:00Z,,PRJNA560478,GCA_008086365.1,CP043003,,Aarhus University Hospital,Illumina,86x,SPAdes v. 3.13.0,1,,1,2316234,44.015026,2503,2312,bacteremia,,1994,Netherlands,Netherlands,,,,Aggressive periodontitis,,,,,,,,,,,,,Whole genome sequencing of Aggregatibacter actinomycetemcomitans cultured from blood stream infections in Denmark reveals a novel phylogenetic lineage expressing serotype a membrane O polysaccharide,collected_by:Nedergaard,,,,,,,Aggressive periodontitis,,,,,,,,,,,,,,99.89,0.45,Oral and Dental Diseases,Periodontal Diseases,Blood and Circulatory System,Oral and Dental Diseases-Periodontal Diseases HP,714.597,Aggregatibacter actinomycetemcomitans strain HK_973,HK_973,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12492050,714,nt,,,,,,,2019-08-26T00:00:00Z,,PRJNA560478,GCA_008086385.1,CP043004,,Aarhus University Hospital,Illumina,88x,SPAdes v. 3.13.0,1,,1,2298901,44.09168,2531,2324,bacteremia,,1991,Denmark,Denmark,,,,Aggressive periodontitis,,,,,,,,,,,,,Whole genome sequencing of Aggregatibacter actinomycetemcomitans cultured from blood stream infections in Denmark reveals a novel phylogenetic lineage expressing serotype a membrane O polysaccharide,collected_by:Nedergaard,,,,,,,Aggressive periodontitis,,,,,,,,,,,,,,99.55,0.23,Oral and Dental Diseases,Periodontal Diseases,Blood and Circulatory System,Oral and Dental Diseases-Periodontal Diseases HP,714.598,Aggregatibacter actinomycetemcomitans strain PN_696,PN_696,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12492048,714,a,,,,,,,2019-08-26T00:00:00Z,,PRJNA560478,GCA_008086405.1,CP043005,,Aarhus University Hospital,Illumina,88x,SPAdes v. 3.13.0,1,,1,2284248,43.999996,2473,2270,bacteremia,,2010,Denmark,Denmark,,,,Aggressive periodontitis,,,,,,,,,,,,,Whole genome sequencing of Aggregatibacter actinomycetemcomitans cultured from blood stream infections in Denmark reveals a novel phylogenetic lineage expressing serotype a membrane O polysaccharide,collected_by:Nedergaard,,,,,,,Aggressive periodontitis,,,,,,,,,,,,,,99.66,0.23,Oral and Dental Diseases,Periodontal Diseases,Blood and Circulatory System,Oral and Dental Diseases-Periodontal Diseases HP,714.686,Aggregatibacter actinomycetemcomitans strain CU1000N,CU1000N,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN19594576,714,,,,,,,,2021-11-09T00:00:00Z,,PRJNA735719,GCA_020809485.1,CP076449,,Rutgers School of Dental Medicine,PacBio Sequel,892.023412x,FALCON v. October 2020,1,0,1,2331529,44.239597,2393,2191,,,1992,USA,USA: New York City,,,,,,,,,,,,,,,,,"We report here the complete genomic sequence of Aggregatibacter actinomycetemcomitans strain CU1000N. This rough strain is used extensively as a model organism to characterize localized aggressive periodontitis pathogenesis, the basic biology and oral cavity colonization of A. actinomycetemcomitans, and its interactions with other members of the oral microbiome.",sample_type:Whole organism,,,,,,,,,,,,,,,,,,,,,99.89,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,714.774,Aggregatibacter actinomycetemcomitans 30R,30R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895065,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517875.1,CP085092,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2120195,44.384266,2125,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0.2,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.775,Aggregatibacter actinomycetemcomitans 30S,30S,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895066,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517855.1,CP085091,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2120195,44.38422,2123,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0.2,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.776,Aggregatibacter actinomycetemcomitans 31R,31R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895067,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517835.1,CP085090,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2110934,44.358944,2110,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.777,Aggregatibacter actinomycetemcomitans 31S,31S,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895068,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517815.1,CP085089,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2102524,44.39312,2098,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.778,Aggregatibacter actinomycetemcomitans 23S,23S,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895064,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517895.1,CP085093,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2173202,44.3228,2221,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.779,Aggregatibacter actinomycetemcomitans 5S,5S,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895062,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517915.1,CP085094,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2158238,44.37671,2196,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0.2,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.780,Aggregatibacter actinomycetemcomitans 4S,4S,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895060,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023518055.1,CP085096,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2109143,44.488876,2113,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.781,Aggregatibacter actinomycetemcomitans 5R,5R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21895061,714,,,,,,,,2022-05-23T00:00:00Z,,PRJNA767258,GCA_023517935.1,CP085095,,,Illumina MiSeq + Oxford Nanopore MinION,80x,SPAdes v. 3.11,1,0,1,2158228,44.37645,2199,,missing,,2018,Netherlands,Netherlands,,,,periodontitis,,,,,,,,,,,,,,collected_by:A.J. van Winkelhoff,,,,,,,periodontitis,,,,,,clinical,,,,,,,,100,0.2,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.792,Aggregatibacter actinomycetemcomitans 27R,27R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN23845307,714,c,,,,,,,2022-08-22T00:00:00Z,,PRJNA787784,GCA_024730685.1,CP093910,,,Illumina MiSeq +Oxford Nanopore,132.62x,SPAdes v. 3.11,1,0,1,2075531,44.49459,2064,,"dept of medical microbiology, university medical center groningen",,2018,Netherlands,Netherlands,,,,Periodontitis,,,,,,,,,,,,,,collected_by:A. J. van Winkelhoff,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.793,Aggregatibacter actinomycetemcomitans 16R,16R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN23845304,714,c,,,,,,,2022-08-22T00:00:00Z,,PRJNA787784,GCA_024730705.1,CP093911,,,Illumina MiSeq +Oxford Nanopore,121.95x,SPAdes v. 3.11,1,0,1,2077859,44.484634,2072,,"dept of medical microbiology, university medical center groningen",,2018,Netherlands,Netherlands,,,,Periodontitis,,,,,,,,,,,,,,collected_by:A. J. van Winkelhoff,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0.2,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.794,Aggregatibacter actinomycetemcomitans 14R,14R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN23845303,714,a,,,,,,,2022-08-22T00:00:00Z,,PRJNA787784,GCA_024730725.1,CP093912,,,Illumina MiSeq +Oxford Nanopore,115.86x,SPAdes v. 3.11,1,0,1,2361401,44.25068,2428,,"dept of medical microbiology, university medical center groningen",,2018,Netherlands,Netherlands,,,,Periodontitis,,,,,,,,,,,,,,collected_by:A. J. van Winkelhoff,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0.6,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,714.795,Aggregatibacter actinomycetemcomitans 9R,9R,Aggregatibacter actinomycetemcomitans,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN23845302,714,c,,,,,,,2022-08-22T00:00:00Z,,PRJNA787784,GCA_024730745.1,CP093913,,,Illumina MiSeq +Oxford Nanopore,130.61x,SPAdes v. 3.11,1,0,1,2116158,44.450035,2133,,"dept of medical microbiology, university medical center groningen",,2018,Netherlands,Netherlands,,,,Periodontitis,,,,,,,,,,,,,,collected_by:A. J. van Winkelhoff,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0.6,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,71452.45,Enterococcus raffinosus strain CX012922,CX012922,Enterococcus raffinosus,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN20857173,71452,,,,,,,,2021-08-30T00:00:00Z,,PRJNA756165,GCA_019797905.1,"CP081846,CP081847",,Shenzhen University,Oxford Nanopore PromethION; Illumina,300.0x,unicycler v. v0.4.9b,1,1,2,3811651,39.574844,3800,3663,feces,,2021-01-22,China,China:Guangzhou,,,,Crohn disease,,,,,,,,,,,,,Complete genome of Enterococcus raffinosus,collected_by:Zhao Hailan,,,,,,,Crohn disease,,,,,,,,,,,,,,98.94,3.53,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,71452.61,Enterococcus raffinosus Er676,Er676,Enterococcus raffinosus,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN30844987,71452,,,,,,,,2022-09-26T00:00:00Z,,PRJNA880513,GCA_025402795.1,"CP104764,CP104765",,,"Illumina NextSeq, ONT MinION","224x, 98x",Unicycler v. v.0.4.8,1,1,2,4345239,39.444206,4404,4224,urine,,2018-09,USA,"USA: Dallas, Texas",,female,,Chronic Cystitis,,host_description:Postmenopausal,,,,,,,,,,,,collected_by:UT Southwestern Medical Center/ UT Dallas,,,,,,,Chronic Cystitis,,,Postmenopausal,,,,,,,,,,,99.8,1.6,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI NHP,717959.412,Alistipes shahii WAL 8301,WAL 8301,Alistipes shahii,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222638,717959,,,,,,DSM:19121,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025145845.1,CP102253,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3809618,57.319,3626,3179,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- HP,72407.1131,Klebsiella pneumoniae subsp. pneumoniae strain SC-7,SC-7,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09487268,72407,,,,MLST.Klebsiella_pneumoniae.1660,,,,2018-07-03T00:00:00Z,,PRJNA477912,GCA_003286995.1,"CP030269,CP030268,CP030267,CP030270",,The Hong Kong Polytechnic University,Nanopore MinION; illumina,50.0x,unicycler v. v0.4.4,1,3,4,5768926,57.029125,5802,5623,missing,,2015,China,China,env_biome:Homo sapiens,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Emergence of ST1660 carbapenem-resistant hypervirulent Klebsiella penumoniae,,,,,No,,,,,,,,,,,,,Homo sapiens,,,,100,0.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,72407.1149,Klebsiella pneumoniae subsp. pneumoniae strain ARLG-3135,ARLG-3135,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10432823,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2018-11-29T00:00:00Z,,PRJNA433394,GCA_003850165.1,"CP033946,CP033947,CP033948,CP033949,CP033950,CP033951,CP033952",,JCVI,Illumina NextSeq; Oxford Nanopore,87.5729x,Unicycler v. 0.4.7,1,6,7,5562458,57.114265,5644,5472,unknown,,,,,,,,,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,These isolates constitute part 2 part series of isolates in partial fulfillment of the aims from an R21 proposal with Drs. Bonomo and VanDuin from the ARLG. ~200 isolates total when both runs are completed.Specific Aim 1: To discover molecular characteristics that are associated with poor clinical outcomes in patients infected with ST258 strains of CRKP.Specific Aim 2: To study the mechanisms and clinical impact of tigecycline and colistin resistance in CRKP strains.,,,,,,,,Unknown,,,,,,,,,,,,,,100,0.62,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,72407.1370,Klebsiella pneumoniae subsp. pneumoniae strain KpvST15_NDM,KpvST15_NDM,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11793565,72407,,,,MLST.Klebsiella_pneumoniae.15,genotype:ST15,,,2019-05-29T00:00:00Z,,PRJNA483246,GCA_005885775.1,"CP040593,CP040595,CP040598,CP040594,CP040596,CP040597,CP040599",,Public Health England,Oxford Nanopore MiniION; Illumina HiSeq,200.0x,miniasm v. 0.2-r168-dirty; racon,1,6,7,5897213,56.765186,6052,5718,throat,,2016-12-19,United Kingdom,United Kingdom,,,38,screen,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Klebsiella pneumoniae is known for its antibiotic resistance and for its virulence (referred to as hypervirulence), but until recently these two traits were not combined in the same organism. This project looks at 'high-risk clones' for antibiotic resistance that also carry a virulence plasmid, even having antibiotic resistance genes in that virulence plasmid. This is of serious public health concern.",collected_by:Hospital in London,,,,,,,screen,,,,,,,,,,,,,,100,1.8,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,72407.1417,Klebsiella pneumoniae subsp. pneumoniae strain KUH-KPNHVF1,KUH-KPNHVF1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13503956,72407,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-01-21T00:00:00Z,,PRJNA594107,GCA_009909305.1,"CP047677,CP047678",,Korea University,Illumina HiSeq,116.05x,HGAP v. 2.3.0,1,1,2,5611260,57.225452,5454,5183,stool,,2017-07-24,South Korea,South Korea: Seoul,,,,Liver abscess,,,Susceptible,Computational Prediction,,,,,,,,,Klebsiella pneumoniae isolated from fecal sample of the hypervirulent Klebsiella pneumoniae liver abscess patient,collected_by:Jong Hun Kim,,,,,,,Liver abscess,,,,,,,,,,,,,,100,1.18,Skin and Soft Tissue Infections,Wounds and Abscesses,Gastrointestinal,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1418,Klebsiella pneumoniae subsp. pneumoniae strain KUH-KPNHVL1,KUH-KPNHVL1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13503954,72407,,,,MLST.Klebsiella_pneumoniae.23,,,,2020-01-21T00:00:00Z,,PRJNA594105,GCA_009909325.1,"CP047675,CP047676",,Korea University,Illumina HiSeq,116.05x,HGAP v. 2.3.0,1,1,2,5606998,57.23298,5456,5177,liver abscess,,2017-07-20,South Korea,South Korea: Seoul,,,,Liver abscess,,,Susceptible,Computational Prediction,,,,,,,,,Hypervirulent Klebsiella pneumoniae isolated from liver abscess,collected_by:Jong Hun Kim,,,,,,,Liver abscess,,,,,,,,,,,,,,100,1.18,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1497,Klebsiella pneumoniae subsp. pneumoniae strain RJBSI76,RJBSI76,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17349264,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2021-01-31T00:00:00Z,,PRJNA681750,GCA_016774435.1,"CP068689,CP068690,CP068691,CP068692,CP068693",,Shanghai Jiao Tong University School of Medicine,Illumina NovaSeq; PacBio Sequel,490.0x,SPAdes v. v3.14,1,4,5,6109711,56.54467,6302,6008,blood,,2018-12-16,China,China:Shanghai,,,,"blood-stream infection, septic shock, and severe pneumonia",,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Klebsiella pneumoniae subsp. pneumoniae strain:RJBSI76 Genome sequencing and assembly,"collected_by:Department of Pulmonary and Critical Care Medicine, Ruijin Hospital Affiliated with Shanghai Jiao Tong University",,,,,,,"blood-stream infection, septic shock, and severe pneumonia",,,,,,,,,,,,,,99.11,0.27,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia HP,72407.1506,Klebsiella pneumoniae subsp. pneumoniae strain SA-KpST14,SA-KpST14,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18096031,72407,,,,MLST.Klebsiella_pneumoniae.14,genotype:ST14,,,2021-03-08T00:00:00Z,,PRJNA705688,GCA_017301375.1,"CP071279,CP071282,CP071283,CP071284,CP071280,CP071281",,King Abdullah International Medical Research Center (KAIMRC),Illumina MiSeq; Oxford Nanopore MinION,60.0x,Unicycler v. 0.4.8; EToKi pipeline v. 1.0,1,5,6,5906615,56.69418,5878,5622,blood,,2019-02,Saudi Arabia,Saudi Arabia,,female,40,Right-Sided Infective Endocarditis,,host_disease_outcome:Recovery,Resistant;Susceptible,Computational Prediction,,,,,,,,,"Complete Genome Sequencing of Klebsiella pneumoniae co-producing OXA-48 and NDM-1 Carbapenemases in Riaydh, Saudi Arabia",collected_by:Moayad Alqurashi,,,,,,,Right-Sided Infective Endocarditis,,Recovery,,,,,,,,,,,,100,0.31,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,72407.1601,Klebsiella pneumoniae subsp. pneumoniae strain MRSN752165,MRSN752165,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18913859,72407,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-05-09T00:00:00Z,,PRJNA725484,GCA_018310495.1,"CP074087,CP074088,CP074090,CP074089,CP074091",,Walter Reed Army Institute of Research,Illumina MiSeq; Oxford Nanopore MinION,200.0x,Unicycler v. v0.4.8,1,4,5,5878206,56.601963,5896,5631,surveillance,,2019-08-01,Italy,Italy: Siena,,,,not collected,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"Investigation of a suspected multi-facility outbreak of ST147 Klebsiella pneumoniae that was detected in Sienna, Italy beginning in November 2018.",collected_by:University of Siena,,,,,,,not collected,,,,,,,,,,,,,,100,1.39,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,72407.1605,Klebsiella pneumoniae subsp. pneumoniae strain WGR351,WGR351,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN18317431,72407,,,,MLST.Klebsiella_pneumoniae.147,,,,2021-06-02T00:00:00Z,,PRJNA714772,GCA_018623335.1,"CP076008,CP076009,CP076010,CP076011,CP076012,CP076013,CP076014,CP076015,CP076016",,Christian Medical College,Illumina HiSeq; Oxford Nanopore MinION,133.0x,CANU v. v.1.7; UNICYCLER HYBRID v.,1,8,9,5763681,56.934586,5749,5530,pus,,2017,India,India,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Klebsiella pneumoniae_WGR351,collected_by:Wockhardt Research Centre,,,,,,,Abscess,,,,,,,,,,,,,,100,1.33,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1637,Klebsiella pneumoniae subsp. pneumoniae strain WRC01_S465PC,WRC01_S465PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115014,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-20T00:00:00Z,,PRJNA744713,GCA_019286375.1,"CP079115,CP079116,CP079117,CP079118,CP079119",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,5723743,56.902256,5762,5515,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC01_S465PC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.79,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1638,Klebsiella pneumoniae subsp. pneumoniae strain WRC04_AI1235MC,WRC04_AI1235MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115068,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744723,GCA_019286515.1,"CP079131,CP079132,CP079133,CP079134,CP079135,CP079136,CP079137",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5863691,56.94635,5838,5627,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC04_AI1235MC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.54,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1639,Klebsiella pneumoniae subsp. pneumoniae strain WRC03_AI1235PC,WRC03_AI1235PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115067,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744722,GCA_019286455.1,"CP079120,CP079121,CP079130,CP079122,CP079123,CP079124,CP079125,CP079126,CP079127,CP079128,CP079129",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,10,11,5861122,56.955067,5823,5623,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC03_AI1235PC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.54,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1640,Klebsiella pneumoniae subsp. pneumoniae strain WRC05_CMC387PC,WRC05_CMC387PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115179,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744726,GCA_019286635.1,"CP079138,CP079139,CP079140,CP079141,CP079142,CP079143,CP079144",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5925924,56.62663,5908,5648,blood,,2018,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC05_CMC387PC,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,99.7,0.94,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,72407.1641,Klebsiella pneumoniae subsp. pneumoniae strain WRC07_CMC432PC,WRC07_CMC432PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115184,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744729,GCA_019286755.1,"CP079150,CP079151,CP079152,CP079153,CP079154",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,5965598,56.64262,5944,5682,endotracheal aspirate,,2018,India,India,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC07_CMC432PC,collected_by:Christian medical college,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.94,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1642,Klebsiella pneumoniae subsp. pneumoniae strain WRC11_S471PC,WRC11_S471PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115539,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-20T00:00:00Z,,PRJNA744734,GCA_019287035.1,"CP079172,CP079173,CP079174,CP079175,CP079176,CP079177,CP079178",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,50.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5884616,56.78017,5960,5702,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC11_S471PC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,1.44,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1643,Klebsiella pneumoniae subsp. pneumoniae strain WRC06_CMC387MC,WRC06_CMC387MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115183,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744728,GCA_019286695.1,"CP079145,CP079146,CP079147,CP079148,CP079149",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,5962191,56.643658,5944,5679,blood,,2018,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC06_CMC387MC,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.94,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,72407.1644,Klebsiella pneumoniae subsp. pneumoniae strain WRC09_CMC309PC,WRC09_CMC309PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115187,72407,,,,MLST.Klebsiella_pneumoniae.2096,,,,2021-07-20T00:00:00Z,,PRJNA744732,GCA_019286955.1,"CP079164,CP079165,CP079166,CP079167,CP079168,CP079169,CP079170,CP079171",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,7,8,5590939,57.236343,5454,5269,endotracheal aspirate,,2018,India,India,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC09_CMC309PC,collected_by:Christian medical college,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1645,Klebsiella pneumoniae subsp. pneumoniae strain WRC08_CMC432MC,WRC08_CMC432MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115186,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-20T00:00:00Z,,PRJNA744731,GCA_019286855.1,"CP079155,CP079156,CP079157,CP079158,CP079159,CP079160,CP079161,CP079162,CP079163",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,8,9,5959485,56.646843,5931,5675,endotracheal aspirate,,2018,India,India,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC08_CMC432MC,collected_by:Christian medical college,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.94,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1646,Klebsiella pneumoniae subsp. pneumoniae strain WRC14_AI2040MC,WRC14_AI2040MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115570,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-20T00:00:00Z,,PRJNA744740,GCA_019287195.1,"CP079186,CP079187,CP079188,CP079189,CP079190,CP079191,CP079192",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5676438,57.03214,5667,5437,urine,,2016,India,India,,,,Urinary tract infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC14_AI2040MC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.65,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1647,Klebsiella pneumoniae subsp. pneumoniae strain WRC13_AI2040PC,WRC13_AI2040PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115569,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-20T00:00:00Z,,PRJNA744738,GCA_019287095.1,"CP079179,CP079180,CP079181,CP079182,CP079183,CP079184,CP079185",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,85.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5674415,57.03342,5666,5434,urine,,2016,India,India,,,,Urinary tract infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC13_AI2040PC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.62,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1648,Klebsiella pneumoniae subsp. pneumoniae strain WRC10_CMC309MC,WRC10_CMC309MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115188,72407,,,,MLST.Klebsiella_pneumoniae.2096,,,,2021-07-22T00:00:00Z,,PRJNA744733,GCA_019317005.1,"CP079599,CP079600,CP079601,CP079602,CP079603,CP079604,CP079605",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,70.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5590819,57.239628,5458,5270,endotracheal aspirate,,2018,India,India,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC10_CMC309MC,collected_by:Christian medical college,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1649,Klebsiella pneumoniae subsp. pneumoniae strain WRC16_AI1547MC,WRC16_AI1547MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130505,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745013,GCA_019317065.1,"CP079617,CP079618,CP079619,CP079620,CP079621,CP079622,CP079623",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,6,7,5846744,56.80666,5916,5661,pus,,2016,India,India,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC16_AI1547MC,collected_by:Christian medical college,,,,,,,Abscess,,,,,,,,,,,,,,100,1.44,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1650,Klebsiella pneumoniae subsp. pneumoniae strain WRC18_CMC307MC,WRC18_CMC307MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130509,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-22T00:00:00Z,,PRJNA745017,GCA_019317085.1,"CP079629,CP079630,CP079631,CP079632,CP079633",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,67.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,6009380,56.870777,5995,5782,endotracheal aspirate,,2018,India,India,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_ WRC18_CMC307MC,collected_by:Christian medical college,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.53,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1651,Klebsiella pneumoniae subsp. pneumoniae strain WRC19_AI1572C,WRC19_AI1572C,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130519,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745018,GCA_019317105.1,"CP079634,CP079635",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,1,2,5561835,57.066074,5535,5319,pus,,2016,India,India,,,,Abscess,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC19_AI1572C,collected_by:Christian medical college,,,,,,,Abscess,,,,,,,,,,,,,,100,0.56,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1652,Klebsiella pneumoniae subsp. pneumoniae strain WRC15_AI1547PC,WRC15_AI1547PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130504,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745012,GCA_019317025.1,"CP079606,CP079607,CP079616,CP079608,CP079609,CP079610,CP079611,CP079612,CP079613,CP079614,CP079615",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,10,11,5593370,57.086746,5569,5347,pus,,2016,India,India,,,,Abscess,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC15_AI1547PC,collected_by:Christian medical college,,,,,,,Abscess,,,,,,,,,,,,,,100,0.62,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1653,Klebsiella pneumoniae subsp. pneumoniae strain WRC21_AI1646PC,WRC21_AI1646PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130521,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745020,GCA_019317125.1,"CP079636,CP079637,CP079638,CP079639,CP079640,CP079641",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,58.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,5,6,5656208,56.999638,5654,5437,laryngeal suction,,2016,India,India,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC21_AI1646PC,collected_by:Christian medical college,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.65,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,72407.1654,Klebsiella pneumoniae subsp. pneumoniae strain WRC27_S471MPC,WRC27_S471MPC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130620,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745023,GCA_019317185.1,"CP079655,CP079656,CP079665,CP079666,CP079667,CP079657,CP079658,CP079659,CP079660,CP079661,CP079662,CP079663",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,72.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,12,13,5888667,56.768944,5962,5704,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC27_S471MPC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,1.44,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1655,Klebsiella pneumoniae subsp. pneumoniae strain WRC24_S468MC,WRC24_S468MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130528,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745022,GCA_019317165.1,"CP079645,CP079646,CP079647,CP079648,CP079649,CP079650,CP079651,CP079652,CP079653,CP079654",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,65.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,9,10,5690255,56.926834,5730,5486,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC24_S468MC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.79,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1656,Klebsiella pneumoniae subsp. pneumoniae strain WRC22_AI1646MC,WRC22_AI1646MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130522,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745021,GCA_019317145.1,"CP079642,CP079643,CP079644",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,58.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,2,3,5641336,57.0236,5648,5419,laryngeal suction,,2016,India,India,,,,Pneumonia,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC22_AI1646MC,collected_by:Christian medical college,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.62,Respiratory Diseases,Pneumonia,Other,Respiratory Diseases-Pneumonia HP,72407.1657,Klebsiella pneumoniae subsp. pneumoniae strain WRC30_AI1547MPCH,WRC30_AI1547MPCH,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130732,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745031,GCA_019317245.1,"CP079683,CP079684,CP079685,CP079686,CP079687,CP079688,CP079689,CP079690,CP079691",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,8,9,5593291,57.08705,5579,5348,pus,,2016,India,India,,,,Abscess,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC30_AI1547MPCH,collected_by:Christian medical college,,,,,,,Abscess,,,,,,,,,,,,,,100,0.62,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.1658,Klebsiella pneumoniae subsp. pneumoniae strain WRC28_CMC387MPCH,WRC28_CMC387MPCH,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130675,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-22T00:00:00Z,,PRJNA745024,GCA_019317205.1,"CP079668,CP079669,CP079670,CP079671,CP079672",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,62.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,5963390,56.642933,5941,5680,blood,,2018,India,India,,,,Sepsis,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC28_CMC387MPCH,collected_by:Christian medical college,,,,,,,Sepsis,,,,,,,,,,,,,,100,0.94,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,72407.1659,Klebsiella pneumoniae subsp. pneumoniae strain WRC29_CMC309MPCH,WRC29_CMC309MPCH,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130677,72407,,,,MLST.Klebsiella_pneumoniae.2096,,,,2021-07-22T00:00:00Z,,PRJNA745030,GCA_019317225.1,"CP079673,CP079674,CP079675,CP079676,CP079677,CP079678,CP079679,CP079680,CP079681,CP079682",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,64.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,9,10,5591551,57.23539,5463,5269,endotracheal aspirate,,2018,India,India,,,,Pneumonia,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC29_CMC309MPCH,collected_by:Christian medical college,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1660,Klebsiella pneumoniae subsp. pneumoniae strain WRC31_S468MPCH,WRC31_S468MPCH,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130733,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-22T00:00:00Z,,PRJNA745032,GCA_019317265.1,"CP079692,CP079693,CP079694,CP079695,CP079696,CP079697",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,5,6,5735332,56.882164,5758,5526,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC31_S468MPCH,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.79,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1661,Klebsiella pneumoniae subsp. pneumoniae strain WRC17_CMC307PC,WRC17_CMC307PC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20130506,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2021-07-22T00:00:00Z,,PRJNA745014,GCA_019317045.1,"CP079624,CP079625,CP079626,CP079627,CP079628",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,4,5,6009334,56.87046,6000,5781,endotracheal aspirate,,2018,India,India,,,,Pneumoniae,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC17_CMC307PC,collected_by:Christian medical college,,,,,,,Pneumoniae,,,,,,,,,,,,,,100,0.53,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.1662,Klebsiella pneumoniae subsp. pneumoniae strain WRC02_S465MC,WRC02_S465MC,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20115065,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-07-25T00:00:00Z,,PRJNA744719,GCA_019334705.1,"CP079807,CP079808,CP079817,CP079809,CP079810,CP079811,CP079812,CP079813,CP079814,CP079815,CP079816",,Christian Medical College,Illumina MiSeq; Oxford Nanopore MinION,91.0x,UNICYCLER v. V.0.4.8; CANU v. V.2.1.1,1,10,11,5741516,56.87465,5778,5533,urine,,2014,India,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Complete genome of Carbapenem resistant Klebsiella pneumoniae_WRC02_S465MC,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.79,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1695,Klebsiella pneumoniae subsp. pneumoniae strain WRC12_S471M,WRC12_S471M,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20114092,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2021-10-02T00:00:00Z,,PRJNA744650,GCA_020215625.1,"CP084044,CP084045,CP084054,CP084046,CP084047,CP084048,CP084049,CP084050,CP084051,CP084052,CP084053",,Christian Medical College,Illumina MiSeq,126.43x,UNICYCLER v. V.0.4.8,1,10,11,5528540,57.146786,5496,5298,urine,,2014,,India,,,,Urinary tract infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Carbapenem resistant Klebsiella pneumoniae_WRC12_S471M,collected_by:Christian medical college,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.56,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.1717,Klebsiella pneumoniae subsp. pneumoniae KPN857,KPN857,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN24571286,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-01-12T00:00:00Z,,PRJNA793626,GCA_021442005.1,"CP090432,CP090433,CP090434,CP090435,CP090436,CP090437",,,PacBio,203.0x,SOAPdenovo v. v2.04,1,5,6,5868295,57.028286,5983,5743,blood,,2021-05-01,China,China: dongguan,,,,COPD,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,,collected_by:dongguan donghua hospital,,,,,,,COPD,,,,,,,,,,,,,,100,0.02,Respiratory Diseases,COPD/Emphysema/Bronchitis,Blood and Circulatory System,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,72407.1758,Klebsiella pneumoniae subsp. pneumoniae KP21,KP21,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN19931439,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2022-07-25T00:00:00Z,,PRJNA858218,,"CP101542,CP101543,CP101544,CP101545",,,Oxford Nanopore,250x,HGAP v. 4,1,3,4,5620607,57.347366,5644,5471,urine,,2013-04,China,China:Kunming,,,,Klebsiella infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Hu Ying,,,,,,,Klebsiella infection,,,,,,,,,,,,,,100,1.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,72407.1939,Klebsiella pneumoniae subsp. pneumoniae CRKP18622,CRKP18622,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08714644,72407,,,,MLST.Klebsiella_pneumoniae.23,,,,2022-10-31T00:00:00Z,,PRJNA438392,GCA_025920085.1,"CP027863,CP027864,CP027865,CP027866,CP027867",,,PacBio,133x,SMRT Link v. 5.0.1,1,4,5,6050320,56.84894,6242,6047,sputum,,16-Oct-2017,China,China:Qingdao,,,,pneumonia,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Weiqi Su,,,,,,,pneumonia,,,,,,,,,,,,,,100,0.1,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.2031,Klebsiella pneumoniae subsp. pneumoniae LC-1736/18,LC-1736/18,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934016,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110936,CP110940,CP110938,CP110937,CP110939",,,Illumina NovaSeq,85x,SPAdes v. 3.14.1,1,4,5,5840772,56.980038,5895,5700,bronchoaspirate,,2018-10-26,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,72407.2032,Klebsiella pneumoniae subsp. pneumoniae LC-1873/18,LC-1873/18,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934015,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110941,CP110946,CP110942,CP110943,CP110945,CP110944",,,Illumina NovaSeq,100x,SPAdes v. 3.14.1,1,5,6,5843910,56.98132,5891,5699,bronchoaspirate,,2018-11-05,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,72407.2033,Klebsiella pneumoniae subsp. pneumoniae LC-79/19,LC-79/19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934020,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110947,CP110951,CP110948,CP110949,CP110950",,,Illumina NovaSeq,105x,SPAdes v. 3.14.1,1,4,5,5723966,57.05979,5766,5589,urine,,2019-01-21,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,72407.2034,Klebsiella pneumoniae subsp. pneumoniae LC-394/19,LC-394/19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934021,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110952,CP110956,CP110954,CP110953,CP110955",,,Illumina NovaSeq,115x,SPAdes v. 3.14.1,1,4,5,5614524,57.11679,5643,5482,urine,,2019-02-25,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,72407.2035,Klebsiella pneumoniae subsp. pneumoniae LC-395/19,LC-395/19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934022,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110957,CP110961,CP110958,CP110959,CP110960",,,Illumina NovaSeq,70x,SPAdes v. 3.14.1,1,4,5,5724692,57.05846,5756,5593,urine,,2019-03-01,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,72407.2036,Klebsiella pneumoniae subsp. pneumoniae LC-424/19,LC-424/19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934025,72407,,,,MLST.Klebsiella_pneumoniae.1519,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110967,CP110969,CP110971,CP110970,CP110968",,,Illumina NovaSeq,70x,SPAdes v. 3.14.1,1,4,5,5826656,56.979183,5873,5683,urine,,2019-03-01,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,72407.2037,Klebsiella pneumoniae subsp. pneumoniae LC-422/19,LC-422/19,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29934023,72407,,,,MLST.Klebsiella_pneumoniae.512,,,,2022-11-21T00:00:00Z,,PRJNA590644,,"CP110962,CP110966,CP110963,CP110964,CP110965",,,Illumina NovaSeq,80x,SPAdes v. 3.14.1,1,4,5,5721890,57.05931,5760,5587,rectal swab,,2019-03-07,Italy,Italy: Lecco,,,,not applicable,,,Resistant;Susceptible,Computational Method,,,,,,,,,,"collected_by:Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy",,,,,,,not applicable,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,72407.2062,Klebsiella pneumoniae subsp. pneumoniae 342/9261261,342/9261261,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30382023,72407,,,,MLST.Klebsiella_pneumoniae.20,,,,2023-03-20T00:00:00Z,,PRJNA870688,,CP119527,,,Illumina NovaSeq,10.0x,BUSCO v. JANUARY-2022,1,0,1,5371871,57.529354,5168,,pleural effusion,,2019-11-28,India,"India: Maharashtra, Pune",,male,64,Necrotizing pancreatis,,host_description:Male;host_disease_outcome:recovery;host_subject_id:F-2261,Susceptible,Computational Method,,,,,,,,,,collected_by:Deepali Desai,,,,,,,Necrotizing pancreatis,,recovery,Male,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Necrotizing fasciitis,Other,Skin and Soft Tissue Infections-Necrotizing fasciitis HP,72407.2065,Klebsiella pneumoniae subsp. pneumoniae P-61,P-61,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30167957,72407,,,,MLST.Klebsiella_pneumoniae.231,,,,2023-04-12T00:00:00Z,,PRJNA866521,,CP121466,,,Illumina NovaSeq,10.0x,BUSCO v. JANUARY-2022,1,0,1,5371977,57.35908,5176,,pus,,2020-01-07,India,"India: Maharashtra, Pune",,female,75,Breast abscess,,host_health_state:Recovery;host_subject_id:11,Susceptible,Computational Method,,,,,,,,,,collected_by:Deepali Desai,,,,,,,Breast abscess,Recovery,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,72407.2080,Klebsiella pneumoniae subsp. pneumoniae HVKP1,HVKP1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34258006,72407,,,,MLST.Klebsiella_pneumoniae.380,,,,2023-05-16T00:00:00Z,,PRJNA957586,,"CP125083,CP125081,CP125084,CP125082",,,Illumina iSeq; Oxford Nanopore MinION,19.1x,Flye v. v2.8.3-b1695,1,3,4,5547821,57.215725,5377,,aerobic blood culture bottle,,2022,United Kingdom,United Kingdom: Liverpool,,female,,Lung abscess,,,Susceptible,Computational Method,,,,,,,,,,collected_by:Hugh Adler,,,,,,,Lung abscess,,,,,,,,,,,,,,100,0.2,Respiratory Diseases,Lung Diseases,Blood and Circulatory System,Respiratory Diseases-Lung Diseases HP,72407.2083,Klebsiella pneumoniae subsp. pneumoniae HVKP2,HVKP2,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34258171,72407,,,,MLST.Klebsiella_pneumoniae.23,,,,2023-05-16T00:00:00Z,,PRJNA957593,,"CP125086,CP125085",,,Illumina HiSeq; Oxford Nanopore MinION,51.3x,Flye v. v2.8.3-b1695,1,1,2,5731170,57.16679,5551,,aerobic blood culture bottle,,2022,United Kingdom,United Kingdom: Liverpool,,,,,,,Susceptible,Computational Method,,,,,,,,,,sample_type:clinical isolate,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,72407.2101,Klebsiella pneumoniae subsp. pneumoniae T1,T1,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35562370,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-06-13T00:00:00Z,,PRJNA978940,,"CP127153,CP127154,CP127155,CP127156,CP127157,CP127158",,,Illumina HiSeq,30.0x,Unicycler v. 0.4.5,1,5,6,5947914,56.93544,6110,5880,shanghai east hospital,,2021,China,China:Shanghai,,,,"epilepsy, coma, and pulmonary infection",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Shangai East Hospital,,,,,,,"epilepsy, coma, and pulmonary infection",,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,72407.2103,Klebsiella pneumoniae subsp. pneumoniae T3,T3,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35562460,72407,,,,MLST.Klebsiella_pneumoniae.147,,,,2023-06-11T00:00:00Z,,PRJNA978945,,"CP126987,CP126988,CP126989,CP126990,CP126991",,,Illumina HiSeq,30.0x,Unicycler v. 0.4.5,1,4,5,5610171,57.183693,5539,5339,shanghai east hospital,,2021,China,China:Shanghai,,,,"epilepsy, coma, and pulmonary infection",,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Shangai East Hospital,,,,,,,"epilepsy, coma, and pulmonary infection",,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,72407.2106,Klebsiella pneumoniae subsp. pneumoniae KPN-68,KPN-68,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN34122257,72407,,,,MLST.Klebsiella_pneumoniae.14,,,,2023-07-03T00:00:00Z,,PRJNA953676,,"CP122381,CP122382,CP122383,CP122384,CP122385,CP122386,CP122387,CP122388",,,Oxford Nanopore MinION; MGI DNBseq,30.0x,SPAdes v. 2023-04-08; Unicycler v.,1,7,8,5789401,56.770622,5770,5526,clinical,,2021-03-14,United Arab Emirates,United Arab Emirates: Al Ain,,,,Respiratory tract infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:UAEU,,,,,,,Respiratory tract infection,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,72407.2107,Klebsiella pneumoniae subsp. pneumoniae Kp3412_LBHALD,Kp3412_LBHALD,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35977329,72407,,,,MLST.Klebsiella_pneumoniae.39,,,,2023-07-10T00:00:00Z,,PRJNA987341,,"CP129219,CP129220",,,Illumina,70.0x,SPAdes v. 3.15.4,1,1,2,5551901,57.182163,5547,5347,leg pus,,2018-02-25,Senegal,Senegal: Dakar,,,,Hospital-acquired infection after orthopedic intervention,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Bacteriology laboratory of Aristide Le Dantec National University teaching hospital in Dakar Senegal,,,,,,,Hospital-acquired infection after orthopedic intervention,,,,,,,,,,,,,,100,0,Nosocomial Infections,Other Nosocomial Infections,Skin and Soft Tissue,Nosocomial Infections-Other Nosocomial Infections HP,72407.2109,Klebsiella pneumoniae subsp. pneumoniae Kp3739_LBHALD,Kp3739_LBHALD,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN35998437,72407,,,,MLST.Klebsiella_pneumoniae.133,,,,2023-07-12T00:00:00Z,,PRJNA988069,,"CP129403,CP129404",,,Illumina,70.0x,SPAdes v. 3.15.4,1,1,2,5613036,57.098244,5633,5481,urine,,2018-01-30,Senegal,Senegal: Dakar,,,,community-acquired urinary tract infection,,,Susceptible;Resistant,Computational Method,,,,,,,,,,collected_by:Bacteriology laboratory of Aristide Le Dantec National University teaching hospital in Dakar Senegal,,,,,,,community-acquired urinary tract infection,,,,,,,,,,,,,,100,1.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.2111,Klebsiella pneumoniae subsp. pneumoniae SM117,SM117,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN36664845,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2023-07-30T00:00:00Z,,PRJNA997112,,"CP130662,CP130659,CP130661,CP130663,CP130664,CP130666,CP130660,CP130665",,,Oxford Nanopore GridION; Illumina HiSeq,100.0x,Unicycler v. 0.5.0,1,7,8,6104486,56.792675,6406,6101,sputum,,2023-01-19,China,China: Sanmen,,,,Infection,,,Resistant;Susceptible,Computational Method,,,,,,,,,,collected_by:Danni Bao,,,,,,,Infection,,,,,,,,,,,,,,99.9,0.8,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,72407.626,Klebsiella pneumoniae subsp. pneumoniae strain RJA166,RJA166,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06200334,72407,,,,MLST.Klebsiella_pneumoniae.23,,,,2017-06-02T00:00:00Z,,PRJNA360094,GCA_002163895.1,"CP019047,CP019048,CP019049,CP019050",,Shanghai Ruijin Hospital Affiliated with Jiaotong University,Illumina MiSeq; PacBio,400.0x,SPAdes v. 3.9,1,3,4,5918670,56.68,6049,6014,sputum,,2015-05-04,China,China: Shanghai,,,,heart disease,,,Susceptible,Computational Prediction,,,,,,,,,comparative genomic analysis,"collected_by:Department of Critical Care Medicine and Respiratory Intensive Care Unit, Shanghai Ruijin Hospital Affiliated with Jiaotong University",,,,,,,heart disease,,,,,,,,,,,,,,100,0.3,Cardiovascular Diseases,Other Cardiovascular Diseases,Respiratory Tract,Cardiovascular Diseases-Other Cardiovascular Diseases HP,72407.693,Klebsiella pneumoniae subsp. pneumoniae strain AUSMDU00008079,AUSMDU00008079,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07452764,72407,KL106:O2v2,,,MLST.Klebsiella_pneumoniae.258,mlst:ST258,,,2017-08-14T00:00:00Z,33180013,PRJNA397262,GCA_002249975.1,"CP022691,CP022692,CP022693,CP022694",,Doherty Applied Microbial Genomics,llumina NextSeq500/550 or MiSeq,85.0x,de novo,1,3,4,5814263,57.02,5998,5835,patient urine,,2012-09-26,Australia,Australia: Victoria,,,,Urinary tract infection,,,Resistant,AMR Panel,,,,,,,,,"Whole-genome sequencing of KPC-producing Enterobacteriaceae from an outbreak in Victoria, Australia",collected_by:Doherty Applied Microbial Genomics,,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,72407.733,Klebsiella pneumoniae subsp. pneumoniae strain H11,H11,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN04244588,72407,,,,MLST.Klebsiella_pneumoniae.659,,,,2017-11-07T00:00:00Z,,PRJNA301380,GCA_002761515.1,CP018056,,Peking University People's Hospital,PacBio,100.0x,HGAP v. 2.0,1,,1,5316818,57.43,5186,5121,separated from patient's sputum,,2010-07-08,China,China:Beijing,,male,65,pneumonia,,,Susceptible,Computational Prediction,,,,Mesophilic,37 C,Aerobic,HostAssociated,pneumonia,study of the complete genome sequence of the strian of Klebsiella pneumoniae H11,"collected_by:Laboratory Medicine, Peking University People's Hospital",,,,,,,pneumonia,,,,,,,,,,,,,,100,0.4,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,72407.900,Klebsiella pneumoniae subsp. pneumoniae strain GD4,GD4,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08166690,72407,,,,MLST.Klebsiella_pneumoniae.11,,,,2018-01-21T00:00:00Z,,PRJNA422171,GCA_002893825.1,"CP025951,CP025952",,The Hong Kong Polytechnic University,PacBio,30.0x,SPAdes v. 3.9.1,1,1,2,5537629,57.362274,5668,5580,missing,,2015,China,China,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China,"collected_by:Ning Dong, Sheng Chen, Rong Zhang",,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,72407.977,Klebsiella pneumoniae subsp. pneumoniae strain BR7,BR7,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173548,72407,,,,MLST.Klebsiella_pneumoniae.437,,,,2018-02-02T00:00:00Z,,PRJNA358426,GCA_002951555.1,"CP018883,CP018884",,University of California,PacBio,100.0x,PacBio v. HGAP.2,1,1,2,5431353,57.391666,5537,5607,blood,,2009,Brazil,Brazil: Rio de Janeiro,,,,bloodstream infection,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,High-level carbapenem resistance in KPC-producing Klebsiella pneumoniae emerges from subpopulations that undergo distinct stepwise transcriptional programs from a population exposed to a lethal carbapenem dose.,collected_by:Federal University of Rio de Janeiro,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,2,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,72407.978,Klebsiella pneumoniae subsp. pneumoniae strain BR21,BR21,Klebsiella pneumoniae,Klebsiella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06173549,72407,,,,MLST.Klebsiella_pneumoniae.437,,,,2018-02-02T00:00:00Z,,PRJNA358426,GCA_002951595.1,"CP018885,CP018886,CP018887",,University of California,PacBio,100.0x,PacBio v. HGAP.2,1,2,3,5708729,57.192398,5887,5951,urine,,2009,Brazil,Brazil: Rio de Janeiro,,,,urinary tract infection,,,Resistant;Susceptible,Computational Prediction,,,,,,,,,High-level carbapenem resistance in KPC-producing Klebsiella pneumoniae emerges from subpopulations that undergo distinct stepwise transcriptional programs from a population exposed to a lethal carbapenem dose.,collected_by:Federal University of Rio de Janeiro,,,,,,,urinary tract infection,,,,,,,,,,,,,,99.7,0.3,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,725.17,Haemophilus influenzae biotype aegyptius strain HE7/F1946,HE7/F1946,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12687934,725,,,,MLST.Haemophilus_influenzae.65,,,,2019-09-19T00:00:00Z,,PRJNA563784,GCA_008586745.1,CP043770,,Griffith University,PacBio Sequel,128.4x,HGAP v. 4,1,,1,1985844,38.224857,2036,1947,skin (petechiae),,1988,Brazil,Brazil: Promissao,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,"Closed annotated genomes of five strains of Haemophilus influenzae biogroup aegyptius, responsible for purelent conjunctivitis and Brazilian Purpuric fever",,,,,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,725.19,Haemophilus influenzae biotype aegyptius strain HE37/F3052,HE37/F3052,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12687937,725,,,,MLST.Haemophilus_influenzae.71,,,,2019-09-19T00:00:00Z,,PRJNA563784,GCA_008586785.1,CP043810,,Griffith University,PacBio Sequel,138.2x,HGAP v. 4,1,,1,1877864,38.118683,2127,1822,conjunctiva,,1988,Brazil,Brazil: So Paulo,,,,Conjunctivitis,,,,,,,,,,,,,"Closed annotated genomes of five strains of Haemophilus influenzae biogroup aegyptius, responsible for purelent conjunctivitis and Brazilian Purpuric fever",,,,,,,,Conjunctivitis,,,,,,,,,,,,,,95.25,0.44,Miscellaneous or Unspecified Infections,,Eye,Miscellaneous or Unspecified Infections- HP,725.20,Haemophilus influenzae biotype aegyptius strain HE24/F3037,HE24/F3037,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12687936,725,,,,MLST.Haemophilus_influenzae.65,,,,2019-09-19T00:00:00Z,,PRJNA563784,GCA_008586805.1,CP043772,,Griffith University,PacBio Sequel,161.9x,HGAP v. 4,1,,1,1987687,38.21688,2051,1946,blood,,1988,Brazil,Brazil: Guatapar,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,"Closed annotated genomes of five strains of Haemophilus influenzae biogroup aegyptius, responsible for purelent conjunctivitis and Brazilian Purpuric fever",,,,,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,725.21,Haemophilus influenzae biotype aegyptius strain HE15/F3028,HE15/F3028,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12687935,725,,,,MLST.Haemophilus_influenzae.65,,,,2019-09-19T00:00:00Z,,PRJNA563784,GCA_008586825.1,CP043771,,Griffith University,PacBio Sequel,245.6x,HGAP v. 4,1,,1,1984979,38.220154,2035,1941,csf,,1988,Brazil,Brazil: Fartura,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,"Closed annotated genomes of five strains of Haemophilus influenzae biogroup aegyptius, responsible for purelent conjunctivitis and Brazilian Purpuric fever",,,,,,,,Brazilian Purpuric Fever (BPF),,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Central Nervous System,Miscellaneous or Unspecified Infections- HP,727.1050,Haemophilus influenzae strain FDAARGOS_199,FDAARGOS_199,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN04875536,727,,,,MLST.Haemophilus_influenzae.47,,FDA:FDAARGOS_199,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073475.2,CP020411,,US Food and Drug Administration,PacBio,26.57x,CA v. 8.2,1,,1,1830602,38.14,1826,1742,human,,,USA,USA:VA,,,,Infection with Haemophilus infleunzae,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:ATCC < HO Smith < K.W. Wilcox KW20,,,,,,,Infection with Haemophilus infleunzae,Missing,Missing,Missing,Missing,,,,,,,,,,100,2.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.1720,Haemophilus influenzae strain P621-7028,P621-7028,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421898,727,Non Typable,,,MLST.Haemophilus_influenzae.1025,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425445.1,CP031689,,Institute of Agrobiotechnology,PacBio RSII,188x,HGAP v. 2.3.0,1,,1,1838740,38.20143,1798,1752,sputum,,2010-09-23,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_6,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,1.9,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1721,Haemophilus influenzae strain P650-8603,P650-8603,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421927,727,Non Typable,,,MLST.Haemophilus_influenzae.2022,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425465.1,CP031685,,Institute of Agrobiotechnology,PacBio RSII,147x,HGAP v. 2.3.0,1,,1,1833710,38.072105,1799,1753,sputum,,2013-01-18,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_9,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1722,Haemophilus influenzae strain P652-8881,P652-8881,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421929,727,Non Typable,,,MLST.Haemophilus_influenzae.485,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425485.1,CP031684,,Institute of Agrobiotechnology,PacBio RSII,168x,HGAP v. 2.3.0,1,,1,1811303,38.03908,1759,1702,sputum,,2013-05-18,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_9,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1723,Haemophilus influenzae strain P669-6977,P669-6977,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421944,727,Non Typable,,,MLST.Haemophilus_influenzae.3,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425505.1,CP031681,,Institute of Agrobiotechnology,PacBio RSII,141x,HGAP v. 2.3.0,1,,1,2013003,38.424286,2045,1985,sputum,,2010-08-16,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_12,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,1.3,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1724,Haemophilus influenzae strain P642-4396,P642-4396,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421919,727,Non Typable,,,MLST.Haemophilus_influenzae.145,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425525.1,CP031686,,Institute of Agrobiotechnology,PacBio RSII,156x,HGAP v. 2.3.0,1,,1,1897311,38.16712,1892,1827,sputum,,2010-01-19,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_9,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1725,Haemophilus influenzae strain P679-2791,P679-2791,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421955,727,Non Typable,,,MLST.Haemophilus_influenzae.1069,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425565.1,CP031678,,Institute of Agrobiotechnology,PacBio RSII,168x,HGAP v. 2.3.0,1,,1,1858634,38.146725,1818,1767,sputum,,2003-05-09,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_13,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1726,Haemophilus influenzae strain P636-8296,P636-8296,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421913,727,Non Typable,,,MLST.Haemophilus_influenzae.12,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425585.1,CP031688,,Institute of Agrobiotechnology,PacBio RSII,199x,HGAP v. 2.3.0,1,,1,1840498,38.148914,1791,1740,sputum,,2012-06-05,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_8,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1727,Haemophilus influenzae strain P676-2514,P676-2514,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421951,727,Non Typable,,,MLST.Haemophilus_influenzae.1069,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425605.1,CP031679,,Institute of Agrobiotechnology,PacBio RSII,83x,HGAP v. 2.3.0,1,,1,1858630,38.14659,1819,1766,sputum,,2002-10-16,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_13,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1728,Haemophilus influenzae strain P672-7661,P672-7661,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421947,727,Non Typable,,,MLST.Haemophilus_influenzae.1789,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425625.1,CP031680,,Institute of Agrobiotechnology,PacBio RSII,129x,HGAP v. 2.3.0,1,,1,1833305,38.120335,1783,1735,sputum,,2011-05-07,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_12,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,1.9,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1729,Haemophilus influenzae strain P665-7858,P665-7858,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421940,727,Non Typable,,,MLST.Haemophilus_influenzae.474,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425645.1,CP031682,,Institute of Agrobiotechnology,PacBio RSII,114x,HGAP v. 2.3.0,1,,1,1908143,38.108624,1928,1864,sputum,,2011-10-15,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_11,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1730,Haemophilus influenzae strain P617-9224,P617-9224,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421894,727,Non Typable,,,MLST.Haemophilus_influenzae.12,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425715.1,CP031690,,Institute of Agrobiotechnology,PacBio RSII,181x,HGAP v. 2.3.0,1,,1,1848210,38.15281,1814,1755,sputum,,2013-11-13,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_5,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1731,Haemophilus influenzae strain P595-8370,P595-8370,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421872,727,Non Typable,,,MLST.Haemophilus_influenzae.2022,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425765.1,CP031692,,Institute of Agrobiotechnology,PacBio RSII,134x,HGAP v. 2.3.0,1,,1,1833864,38.07267,1798,1754,sputum,,2012-07-19,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_2,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1732,Haemophilus influenzae strain P615-8618,P615-8618,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421892,727,Non Typable,,,MLST.Haemophilus_influenzae.1025,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425815.1,CP031691,,Institute of Agrobiotechnology,PacBio RSII,146x,HGAP v. 2.3.0,1,,1,1840062,38.1948,1799,1756,sputum,,2013-01-25,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_5,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,1.9,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1733,Haemophilus influenzae strain P641-4342,P641-4342,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421918,727,Non Typable,,,MLST.Haemophilus_influenzae.145,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425935.1,CP031687,,Institute of Agrobiotechnology,PacBio RSII,125x,HGAP v. 2.3.0,1,,1,1849483,38.0907,1822,1758,sputum,,2009-12-28,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_9,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1734,Haemophilus influenzae strain P662-7189,P662-7189,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421937,727,Non Typable,,,MLST.Haemophilus_influenzae.46,,,,2018-08-23T00:00:00Z,,PRJNA282520,GCA_003425955.1,CP031683,,Institute of Agrobiotechnology,PacBio RSII,142x,HGAP v. 2.3.0,1,,1,1904311,38.134842,1895,1833,sputum,,2010-12-30,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:Patient_11,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,100,0.6,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1805,Haemophilus influenzae strain P602-8883,P602-8883,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421879,727,Non Typable,,,MLST.Haemophilus_influenzae.1025,,,,2018-10-29T00:00:00Z,,PRJNA282520,GCA_003691635.1,CP033168,,Institute of Agrobiotechnology,PacBio RSII,115x,HGAP v. 2.3.0,1,,1,1843353,38.212387,1803,1756,sputum,,2013-05-16,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:4,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,99.67,0.8,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.1806,Haemophilus influenzae strain P657-8759,P657-8759,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07421933,727,Non Typable,,,MLST.Haemophilus_influenzae.670,,,,2018-10-29T00:00:00Z,,PRJNA282520,GCA_003691655.1,CP033167,,Institute of Agrobiotechnology,PacBio RSII,171x,HGAP v. 2.3.0,1,,1,1849398,38.12014,1814,1764,sputum,,2013-03-26,Spain,Spain:Catalunya,,male,,COPD,,host_subject_id:11,,,,,,,C,,,Severe COPD,"Sequenced whole genomes, serial isolates recovered from distinct patients suffering severe COPD",collected_by:Dra. Jose Fina Linares,,,,,,,COPD,,,,,,,,,,,,,,99.56,0.58,Respiratory Diseases,COPD/Emphysema/Bronchitis,Respiratory Tract,Respiratory Diseases-COPD/Emphysema/Bronchitis HP,727.2381,Haemophilus influenzae strain PittGG,PittGG,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN12877006,727,nontypeable,,,MLST.Haemophilus_influenzae.43,,,,2019-10-07T00:00:00Z,,PRJNA575052,GCA_008831525.1,CP044497,,Drexel,PacBio RSII,214.0x,HGAP v. 2.3.0,1,,1,1887343,38.012962,1885,1810,middle ear fluid,,2000,USA,"USA: Pittsburgh, PA",,,child,otitis media,,host_health_state:sick,,,,,,,,,,,"This project provides a closed circular genome for the PittGG strain of Haemophilus influenzae. Previously, we sequenced this genome using 454 sequencing technology and submitted it as PRJNA16401. That assembly has been suppressed from RefSeq due to frameshift errors. Here we provide an assembly of PIttGG created using PacBio's RSII sequencer.",collected_by:Children's Hospital of Pittsburgh,,,,,,,otitis media,sick,,,,,,,,,,,,,99.67,0.07,Ear Conditions,Otitis,Ear,Ear Conditions-Otitis HP,727.2641,Haemophilus influenzae strain 2018-Y40,2018-Y40,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00210359,727,,,,MLST.Haemophilus_influenzae.422,,,,2020-07-09T00:00:00Z,,PRJDB9463,GCA_013394405.1,AP022867,,Tokyo University of Pharmacy and Life Sciences,PacBioRSII,386x,RS HGAP assembly v. 3.0,1,0,1,1957393,38.24168,1988,1926,pediatric patient,isolated from a pediatric patient,2018,,,,,,,,,,,Negative,Bacilli,No,,,,,,Characterization of quinolone low-susceptible Haemophilus influenzae outbreak clone isolated from a pediatric patient.,,not applicable,not applicable,not applicable,aerobic,quinolone low-sesceptible H. influenzae,,,,,,,,,,,,not applicable,,,,99.43,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.2899,Haemophilus influenzae strain TAMBA230,TAMBA230,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00204789,727,serovar A,,,,,,,2020-09-16T00:00:00Z,,PRJDB9304,GCA_014701215.1,AP022846,,"Department of Bacteriology II, National Institute of Infectious Diseases",illumina MiSeq; Nanopore GridION,951x,Unicycler v. 0.4.8,1,0,1,1809645,38.03188,1740,1694,blood,isolated from 72-years old male accompany with pyogenic arthritis at Hyogo Prefectural Tamba Medical Center as a secondary emergency medical institutions,2019-09,Japan,"Japan:Hyogo, Tamba, Hikami",,male,72,,,,,,Negative,Bacilli,,,,,,pyogenic arthritis,"Almost of invasive infection of Haemophilus influenzae in adult is caused by non-typeable Haemophisu influenzae so called NTHI. In the case of child, invasive infection of Haemophilus influenzae caused meningitides had been occurred by type b Haemophilus influenzae. However after introduction of Hib vaccine (The Haemophilus influenzae type B vaccine) for child as a regular vaccination in 2013, meningitides under 5 years old was decreased drastically. Serotype A Haemophilus influenzae is first report as an invasive infection by Haemophilus influenzae in both children and adults in Japan. There is no vaccine for adults to prevent invasive Haemophilus influenzae in Japan and around the world. For that purpose, it is necessary to accumulate biologically detailed data including the genome analysis of the causative bacteria causing invasive Haemophilus influenzae infection. The Haemophilus influenzae serotype A was isolated from 72-years old male accompany with pyogenic arthritis at Hyogo Prefectural Tamba Medical Center as a secondary emergency medical institutions. This bacterium was relatively susceptible to many antibiotics. In MLST analysis, it was ST1511, the same as Haemophilus influenzae serotype A isolated from the blood of a 65-year-old man in Australia in 2014.",biomaterial_provider:Hyogo Prefectural Tamba Medical Center,human body,blood,not applicable,not applicable,Whole genome sequence of Haemophilus influenzae serotype A in Japan.,,,pyogenic arthriti,,,,,,,,,human body,,,,99.67,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,727.2976,Haemophilus influenzae strain M1C112_1,M1C112_1,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409221,727,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931495.1,CP063127,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,177x,Unicycler v. 0.4.7,1,0,1,1894676,38.00523,1860,1797,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-06-28,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.67,0.07,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,727.3002,Haemophilus influenzae strain CHBN-II-5,CHBN-II-5,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119529,727,,,,MLST.Haemophilus_influenzae.14,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703455.1,AP018768,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1805925,38.075226,1740,1691,,,2012,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 5,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.63,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3003,Haemophilus influenzae strain CHBN-II-4,CHBN-II-4,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119528,727,,,,MLST.Haemophilus_influenzae.436,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703425.1,AP018767,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1832515,38.07134,1780,1727,,,2010,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 4,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.67,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3004,Haemophilus influenzae strain CHBN-II-1,CHBN-II-1,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119525,727,,,,MLST.Haemophilus_influenzae.3,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703365.1,AP018764,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1979718,38.36516,1971,1924,,,2010,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 1,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3005,Haemophilus influenzae strain CHBN-II-3,CHBN-II-3,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119527,727,,,,,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703405.1,AP018766,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1853393,38.093433,1801,1746,,,2012,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 3,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.72,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3006,Haemophilus influenzae strain CHBN-II-7,CHBN-II-7,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119531,727,,,,MLST.Haemophilus_influenzae.1017,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703525.1,AP018770,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1886480,38.162716,1851,1804,,,2010,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 7,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3007,Haemophilus influenzae strain CHBN-II-2,CHBN-II-2,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119526,727,,,,MLST.Haemophilus_influenzae.3,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703385.1,AP018765,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1979786,38.365864,1970,1924,,,2012,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 2,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3008,Haemophilus influenzae strain CHBN-III-1,CHBN-III-1,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119533,727,,,,MLST.Haemophilus_influenzae.155,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703575.1,AP018772,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1816076,38.01113,1732,1683,,,2014,Japan,Japan:Shizuoka,,,,,,host_subject_id:Japanese infants\; 1,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3009,Haemophilus influenzae strain CHBN-III-3,CHBN-III-3,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119535,727,,,,MLST.Haemophilus_influenzae.107,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703615.1,AP018774,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1810977,38.04819,1728,1675,,,2012,Japan,Japan:Okinawa,,,,,,host_subject_id:Japanese infants\; 3,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3010,Haemophilus influenzae strain CHBN-II-6,CHBN-II-6,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119530,727,,,,MLST.Haemophilus_influenzae.160,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703495.1,AP018769,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1819364,38.056484,1754,1703,,,2011,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 6,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3011,Haemophilus influenzae strain CHBN-III-2,CHBN-III-2,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119534,727,,,,MLST.Haemophilus_influenzae.159,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703595.1,AP018773,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1914722,38.161205,1866,1820,,,2012,Japan,Japan:Fukuoka,,,,,,host_subject_id:Japanese infants\; 2,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3012,Haemophilus influenzae strain CHBN-III-4,CHBN-III-4,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119536,727,,,,MLST.Haemophilus_influenzae.396,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703635.1,AP018775,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1818266,38.01666,1756,1703,,,2012,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 4,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3013,Haemophilus influenzae strain CHBN-III-5,CHBN-III-5,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119537,727,,,,MLST.Haemophilus_influenzae.156,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703655.1,AP018776,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1822115,38.053143,1750,1702,,,2012,Japan,Japan:Nagasaki,,,,,,host_subject_id:Japanese infants\; 5,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.77,0.23,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3014,Haemophilus influenzae strain CHBN-II-8,CHBN-II-8,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119532,727,,,,MLST.Haemophilus_influenzae.1431,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703545.1,AP018771,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1902536,38.134575,1880,1831,,,2010,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 8,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.67,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3015,Haemophilus influenzae strain CHBN-III-8,CHBN-III-8,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119540,727,,,,MLST.Haemophilus_influenzae.393,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703715.1,AP018779,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1791343,38.002884,1714,1672,,,2010,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 8,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.56,0.58,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3016,Haemophilus influenzae strain CHBN-III-6,CHBN-III-6,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119538,727,,,,,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703675.1,AP018777,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1884503,37.97447,1836,1802,,,2008,Japan,Japan:Kagoshima,,,,,,host_subject_id:Japanese infants\; 6,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.66,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3017,Haemophilus influenzae strain CHBN-III-7,CHBN-III-7,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119539,727,,,,MLST.Haemophilus_influenzae.1444,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703695.1,AP018778,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1911890,38.223328,1894,1850,,,2015,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 7,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.67,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3018,Haemophilus influenzae strain CHBN-V-2,CHBN-V-2,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119543,727,,,,MLST.Haemophilus_influenzae.584,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703775.1,AP018782,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1790924,37.965153,1744,1700,,,2012,Japan,Japan:Kagoshima,,,,,,host_subject_id:Japanese infants\; 2,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,97.26,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3019,Haemophilus influenzae strain CHBN-IV-1,CHBN-IV-1,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119541,727,,,,,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703735.1,AP018780,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1882642,38.10082,1832,1787,,,2011,Japan,Japan:Kagoshima,,,,,,host_subject_id:Japanese infants\; 1,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.56,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3020,Haemophilus influenzae strain CHBN-V-3,CHBN-V-3,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119544,727,,,,MLST.Haemophilus_influenzae.187,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703795.1,AP018783,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1936686,38.138966,1910,1862,,,2015,Japan,Japan:Chiba,,,,,,host_subject_id:Japanese infants\; 3,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.64,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3021,Haemophilus influenzae strain CHBN-V-1,CHBN-V-1,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMD00119542,727,,,,MLST.Haemophilus_influenzae.1434,,,,2021-05-22T00:00:00Z,,PRJDB7052,GCA_019703755.1,AP018781,,Chiba University,PacBio RS II,100x,HGAP v. 2,1,0,1,1953394,38.09467,1923,1871,,,2012,Japan,Japan:Okinawa,,,,,,host_subject_id:Japanese infants\; 1,,,,,,,,,,,"We reveal the relationship between the variation of the genes detected by whole genome sequences and the phenotypes like invasiveness, pathogenic, toxicity and antimicrobial susceptibility.",,not applicable,not applicable,blood and spinal fluid,not provided,Analysis of sequences from invasive NTHi,,,,,,,,,,,,not applicable,,,,99.07,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,727.3051,Haemophilus influenzae strain KR271,KR271,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMEA10987108,727,,,,MLST.Haemophilus_influenzae.14,,,,2021-12-03T00:00:00Z,,PRJEB48813,GCA_919946725.1,OV040584,,LUND UNIVERSITY,,,,1,0,1,1805497,38.06664,1723,1680,blood,isolated from the blood sample of 75-years old patient with bacteremia,2007,,Sweden,,,75 years,bacteremia,,host_health_state:diseased,,,,,,,,,,,"Nontypeable Haemophilus influenzae KR271 (NTHi KR271) was isolated from the blood sample of 75-years old patient with bacteremia. The strain is non-capsulated hence is denoted as “nontypeable (NTHi)”. NTHi KR271 has been included in several studies of host-pathogen interactions in our research group. We showed that KR271 interacts with human complement regulators for serum resistance, and bind to human extracellular matrix proteins for enhanced adherence to the host epithelial cells. The strain sequence will be used for our genomic/transcriptomic/proteomics comparative analysis.",,,,,,,,,diseased,,,,,,,,,,,,,99.66,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,727.3052,Haemophilus influenzae strain 3655,3655,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMEA10982446,727,,,,MLST.Haemophilus_influenzae.411,,,,2021-12-03T00:00:00Z,,PRJEB48794,GCA_919949215.1,OV040719,,LUND UNIVERSITY,,,,1,0,1,1917048,38.167587,1895,1823,middle ear,isolated from the middle ear effusion of a child in Missouri (USA) with acute otitis media,,,USA,,,,,,host_health_state:diseased,,,,,,,,,,,"Nontypeable Haemophilus influenzae 3655 (NTHi 3655\; also known as NTHi 3655KR in our lab collection), was isolated from the middle ear effusion of a child in Missouri (USA) with acute otitis media. This strain is non-capsulated hence is noted as “nontypeable”. This strain has been widely used in the our study of host-pathogen interaction of NTHi\; the strain uses host complement regulators and ECM proteins for serum resistance and enhanced adherence, respectively. The genome sequence of this strain was initially sequenced, assembled and deposited as 23 contigs in GenBank. Here we re-sequence the strain for a complete whole genome sequence with full annotation. The strain sequence will be used for our genomic/transcriptomic/proteomics comparative analysis.",,,,,,,,,diseased,,,,,,,,,,,,,99.67,0,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,727.3409,Haemophilus influenzae NRCH180079,NRCH180079,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN33859267,727,NT,,,,,,,2023-04-08T00:00:00Z,,PRJNA947565,,CP121103,,,Illumina,"1,991,786x",SPAdes v. 1,1,0,1,1991786,38.158085,2056,1993,sputum,,2018-03-27,Belgium,Belgium,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,collected_by:NRC for H. influenzae Belgium,,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,727.3410,Haemophilus influenzae NRCH190002,NRCH190002,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN33859269,727,NT,,,,,,,2023-04-08T00:00:00Z,,PRJNA947565,,CP121105,,,Illumina,"1,991,325x",SPAdes v. 1,1,0,1,1991363,38.15573,2062,2000,sputum,,2019-01-03,Belgium,Belgium,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,collected_by:NRC for H. influenzae Belgium,,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,727.3411,Haemophilus influenzae NRCH180136,NRCH180136,Haemophilus influenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN33859268,727,NT,,,,,,,2023-04-08T00:00:00Z,,PRJNA947565,,CP121104,,,Illumina,"1,991,321x",SPAdes v. 1,1,0,1,1991359,38.1557,2055,1994,sputum,,2018-06-21,Belgium,Belgium,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,collected_by:NRC for H. influenzae Belgium,,,,,,,chronic obstructive pulmonary disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Other Respiratory Diseases,Respiratory Tract,Respiratory Diseases-Other Respiratory Diseases HP,72758.23,Staphylococcus capitis subsp. capitis strain DSM 20326,DSM 20326,Staphylococcus capitis,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN29053769,72758,,,,,,DSM:20326,,2022-09-19T00:00:00Z,,PRJNA849394,GCA_025272975.1,"CP103049,CP103050,CP103051,CP103052,CP103053",,German Aerospace Center (DLR),Illumina MiSeq; Oxford Nanopore MinION,120.0x,Unicycler v. 0.4.9,1,4,5,2486324,32.881275,2435,,skin,,1975-04-24,,,,,,,,,,,,,,,,,,,Comparative genomics study of four Staphylococcus capitis subsp. capitis strains with space flight relevance,sample_type:bacterial culture,,,,,,,,,,,,,,,,,,,,,99.81,0.06,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,72759.16,Staphylococcus aureus subsp. anaerobius strain Zhenghai,Zhenghai,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN10227280,1280,Not applicable,,,MLST.Staphylococcus_aureus.5,genotype:ST5,Not applicable,,2019-11-04T00:00:00Z,,PRJNA494949,GCA_009497915.1,CP033117,,"Ningbo Municipal Centre for Disease Control and Prevention, Ningbo, Zhejiang Province, China",Illumina MiSeq,60.0x,SPAdes v. 3.12.0,1,,1,2744906,32.87197,2757,2773,pus,,2017-10-10,China,China: Zhejiang province,temperature:39 degree Celsius,,,,,,Susceptible,Computational Prediction,,,,,,,,,Staphylococcal foodborne intoxication is caused by various staphylococcal enterotoxins (SEs). SED is one of such enterotoxins. This project was aimed to investigate an food poisoning outbreak caused by a SED-positive strain.,sample_type:Whole organism;biomaterial_provider:Not applicable;collected_by:Qifa Song;identified_by:Qifa song;lab_host:Not applicable;mating_type:Not applicable;passage_history:Not applicable;specimen_voucher:Not applicable,,,,,,,,,,,,,,,,,Not applicable,,,,99.4,0.08,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,729.1543,Haemophilus parainfluenzae strain LC_1315_18,LC_1315_18,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN10774168,729,,,,,,,,2019-01-24T00:00:00Z,,PRJNA515889,GCA_004104465.1,CP035368,,University of Bern,Oxford Nanopore MiniION,40.0x,CANU v. 1.7,1,,1,2067358,39.574085,2046,1992,urethral swab,,2018,Italy,Italy: Lecco,,male,,Infection,,,,,,,,,,,,,We report the first Italian case of urethritis caused by H. parainfluenzae resistant to third-generation cephalosporins,collected_by:A. Manzoni Hospital,,,,,,,Infection,,,,,,,,,,,,,,99.66,0.44,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,729.2130,Haemophilus parainfluenzae strain M1C160_1,M1C160_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409282,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931275.1,CP063110,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,120x,Unicycler v. 0.4.7,1,0,1,2018144,39.56774,1890,1863,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-06-24,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.3,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2131,Haemophilus parainfluenzae strain M1C149_1,M1C149_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409271,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931315.1,CP063112,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,344x,Unicycler v. 0.4.7,1,0,1,2015253,39.706825,1886,1851,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-03-11,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.66,0,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2133,Haemophilus parainfluenzae strain M1C147_1,M1C147_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409268,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931335.1,"CP063113,CP063114,CP063115",,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,286x,Unicycler v. 0.4.7,1,2,3,1981608,39.632206,1885,1841,bronchoalveolar lavage,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-03-24,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,729.2134,Haemophilus parainfluenzae strain M1C142_1,M1C142_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409259,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931375.1,"CP063117,CP063118,CP063119",,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,120x,Unicycler v. 0.4.7,1,2,3,2037540,39.601185,1939,1884,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-03-18,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2135,Haemophilus parainfluenzae strain M1C146_1,M1C146_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409265,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931355.1,CP063116,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,546x,Unicycler v. 0.4.7,1,0,1,1926530,39.664837,1827,1787,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-06-16,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.08,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2136,Haemophilus parainfluenzae strain M1C130_2,M1C130_2,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409239,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931415.1,CP063121,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,481x,Unicycler v. 0.4.7,1,0,1,1994590,39.646294,1887,1853,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-04-21,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.08,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2137,Haemophilus parainfluenzae strain M1C137_2,M1C137_2,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409249,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931395.1,CP063120,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,278x,Unicycler v. 0.4.7,1,0,1,2177054,39.487675,2122,2071,bronchoalveolar lavage,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-03-09,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.11,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,729.2138,Haemophilus parainfluenzae strain M1C125_4,M1C125_4,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409233,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931435.1,CP063122,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,494x,Unicycler v. 0.4.7,1,0,1,1953198,39.601208,1823,1791,sputum,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-10-06,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.08,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,729.2139,Haemophilus parainfluenzae strain M1C120_2,M1C120_2,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409231,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931455.1,CP063123,,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,329x,Unicycler v. 0.4.7,1,0,1,2000745,39.56761,1903,1860,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-10-05,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.89,0.08,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis HP,729.2140,Haemophilus parainfluenzae strain M1C113_1,M1C113_1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN16409224,729,,,,,,,,2020-10-26T00:00:00Z,,PRJNA668428,GCA_014931475.1,"CP063124,CP063125,CP063126",,Monash University,Illumina MiniSeq; Oxford Nanopore MiniION,252x,Unicycler v. 0.4.7,1,2,3,2089461,39.470657,2079,1962,cough swab,isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms,2016-03-07,Australia,Australia: Melbourne,,,,Cystic fibrosis,,,,,,,,,,,,,"Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF during periods of exacerbated respiratory symptoms. However, little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples collected during quarterly clinic visits from 147 participants aged less than 12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program.",collected_by:MCRI,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.66,1.5,Respiratory Diseases,Cystic Fibrosis,Other,Respiratory Diseases-Cystic Fibrosis NHP,729.2290,Haemophilus parainfluenzae EL1,EL1,Haemophilus parainfluenzae,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN34140652,729,,,,,,,,2023-06-01T00:00:00Z,,PRJNA954350,,CP125087,,,Illumina NextSeq and Oxford Nanopore,555.0x,Prokka v. Jully-2021,1,0,1,2153240,39.406475,2042,2005,,,2019-05-22,USA,USA: Rhode Island,,,,,,,,,,,,,,,,,,,Oral cavity,Supragingival plaque,not applicable,https://github.com/thpalma,,commensal,,,,,,,,,,commensal,Oral cavity,,,,100,0.2,,,Other,- NHP,742725.163,Alistipes indistinctus YIT 12060,YIT 12060,Alistipes indistinctus,Alistipes,Rikenellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222634,742725,,,,,,DSM:22520,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025144995.1,CP102250,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2857445,54.75829,2530,2301,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- NHP,74426.1538,Collinsella aerofaciens strain P10wA7,P10wA7,Collinsella aerofaciens,Collinsella,Coriobacteriaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMN11637225,74426,,,,,,,,2019-05-22T00:00:00Z,,PRJNA542677,GCA_005576555.1,CP040348,,Columbia University,Illumina NextSeq; PacBio Sequel,200.0x,SPAdes v. 3.13.0,1,,1,2264854,60.015877,1968,,feces,,2017-10-30,USA,USA: New York City,,,,,,,,,,,,,,,,,"Bacterial RNA-seq is a powerful methodology to quantitatively understand the physiology and functionality of diverse microbial species. Depletion of ribosomal RNA (rRNA) is required to enable cost-effective sequencing of resulting libraries at appropriate coverage. However, current methodology for efficient rRNA depletion of diverse and non-model bacterial species is limited. Here we develop a new probe and RNase H based strategy for bacterial rRNA depletion. We validate the technique on 3 novel gut microbiota isolates representing three distinct phyla, show compatibility with chemically synthesized oligo or amplicon-based ssDNA probes, and demonstrate that probe sets can be successfully utilized on closely related species. A detailed protocol and online tool to generate probe libraries and predict performance on related species is available, and lays the groundwork for large-scale bacterial transcriptomics studies.",,Homo sapiens,gastrointestinal tract,feces,25163406,,,,,,,,,,,,,Homo sapiens,,,,100,0.81,,,Gastrointestinal,- NHP,74426.1748,Collinsella aerofaciens strain NBRC 114504,NBRC 114504,Collinsella aerofaciens,Collinsella,Coriobacteriaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMN21163594,74426,,,,,,,,2021-09-30T00:00:00Z,,PRJNA747117,GCA_020181355.1,"CP084004,CP084005,CP084006",,"National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute",Illumina MiSeq; Oxford Nanopore GridION,477.0x,Flye v. v. 2.8.3; Unicycler v. v. 0.4.7,1,2,3,2278612,60.28003,2011,1919,human feces,,2018,,Japan,,,,,,,,,,,,,,,,,This work develops defined microbial mock communities to serve as control reagents for human fecal microbiota measurements by metagenome or amplicon (targeted loci) sequencing.,sample_type:pure culture,,,,,,,,,,,,,,,,,,,,,100,0.81,,,Gastrointestinal,- NHP,74426.49,Collinsella aerofaciens strain indica,indica,Collinsella aerofaciens,Collinsella,Coriobacteriaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMN07821249,74426,,,,,,,,2017-10-30T00:00:00Z,,PRJNA415274,GCA_002736145.1,CP024160,,Translational Health Science and Technology Institute,Illumina HiSeq; Nanpore,225.0x,SPAdes v. SEP-2017,1,,1,2306349,60.12,1981,1920,stool,,2017-05-23,India,India: Faridabad,,,,,,,,,,,,,,,,,"Collinsella aerofaciens, a rod-shaped non-motile obligate anaerobe, is the mostabundant Actinobacteria in the gastrointestinal tract of healthy humans. Altered abundance of C. aerofaciens may be linked with several health disorders including irritable bowel syndrome. In the present study, we report the complete genome sequence of C. aerofaciens strain Indica.",sample_type:stool sample,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- HP,747.530,Pasteurella multocida strain FDAARGOS_384,FDAARGOS_384,Pasteurella multocida,Pasteurella,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN07312428,747,,,,MLST.Pasteurella_multocida_1.25,,FDA:FDAARGOS_384,,2017-09-28T00:00:00Z,,PRJNA231221,GCA_002393385.1,CP023516,,US Food and Drug Administration,PacBio; Illumina,24.04x,Celera v. 8.2,1,,1,2346722,40.45,2214,2172,abscess,,2015-05-19,USA,USA:DC,,female,5Y,Cellullitis,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Cellullitis,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,747.738,Pasteurella multocida strain 161215033201-1,161215033201-1,Pasteurella multocida,Pasteurella,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN08498425,747,,,,MLST.Pasteurella_multocida_1.39,,ATCC 43137,,2018-02-19T00:00:00Z,,PRJNA433487,GCA_002948995.1,CP026744,,Regional Laboratory for Medical Microbiology and Public Health,Illumina MiSeq,230.0x,other v. 7.0.1,1,,1,2126408,40.747547,1996,,"lung, right",,2016-12-14,Netherlands,Netherlands: Hoofddorp,,female,,bilateral pneumonia,,,,,,,,,,,,,"To elucidate the origin of a patient’s P. multocida, the genome of the isolate was sequenced by Illumina Nextera XT whole-genome sequencing to determine a whole-genome contig using Genbank sequence CP008918.1 (P. multocida ATCC43137) as alignment reference sequence.",collected_by:Mooij-Kalverda,,,,,,,bilateral pneumonia,,,,,,,,,,,,,,98.5,0.5,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,747.813,Pasteurella multocida strain NCTC10382,NCTC10382,Pasteurella multocida,Pasteurella,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMEA2822166,747,,,,"MLST.Pasteurella_multocida_1.130,MLST.Pasteurella_multocida_2.14",,NCTC:10382,,2018-06-17T00:00:00Z,,PRJEB6403,GCA_900478175.1,LS483473,,SC,,,,1,,1,2314214,40.31805,2189,2138,infected finger,,1964,,,,,,,,host_health_state:Infected,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Infected,,,100,0.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,753.13,Pasteurella canis strain HL268,HL268,Pasteurella canis,Pasteurella,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21032957,753,,,,,,,,2021-09-18T00:00:00Z,,PRJNA758714,GCA_020034555.1,CP083262,,Hallym University,Illumina MiSeq; Oxford Nanopore MinION,322.0x,Unicycler v. 0.4.8,1,0,1,2301094,36.827267,2134,2114,pus,,2004,South Korea,South Korea,,,,Inflammation,,,,,,,,,,,,,"Pasteurella canis HL268, clinical isolate",collected_by:Kangdong Sacred Hospital,,,,,,,Inflammation,,,,,,,,,,,,,,99.89,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,753.14,Pasteurella canis strain HL1500,HL1500,Pasteurella canis,Pasteurella,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN21032959,753,,,,,,,,2021-09-20T00:00:00Z,,PRJNA758715,GCA_020042685.1,"CP083396,CP083397",,Hallym University,Oxford Nanopore MinION; Illumina MiSeq,416.0x,Unicycler v. 0.4.8,1,1,2,2188044,36.77417,2008,1975,pus,,2017,South Korea,South Korea,,,,Inflammation,,,,,,,,,,,,,"Pasteurella canis HL1500, clinical isolate",collected_by:Kangdong Sacred Hospital,,,,,,,Inflammation,,,,,,,,,,,,,,99.89,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,758802.13,Mycolicibacterium litorale strain NIIDNTM18,NIIDNTM18,Mycolicibacterium litorale,Mycolicibacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMD00200502,758802,,,,,,,,2020-07-11T00:00:00Z,,PRJDB9155,GCA_014218295.1,AP023287,,"Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases - Japan",MinION; Illumina HiSeq X,61x,Unicycler v. 0.4.8.0,1,0,1,5634149,68.88141,5514,5480,pacemaker device infection,isolated from pacemaker device infection,2018,Japan,Japan:Tokyo,,,,,,,,,,,,,,,,,"Mycolicibacterium litorale is rapid growing, scotochromogenic nontuberculous mycobacteria. This is the WGS study of Mycolicibacterium litorale firstly isolated from pacemaker device infection.",,not applicable,not applicable,not applicable,10.1099/ijs.0.033449-0,WGS study of Mycolicibacterium litorale infection,,,pace maker infection,,,,,,,,,not applicable,,,,99.44,0.09,Miscellaneous or Unspecified Infections,,Medical Device,Miscellaneous or Unspecified Infections- HP,76832.95,Myroides odoratimimus 31,31,Myroides odoratimimus,Myroides,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN34590097,76832,,,,,,,,2023-06-01T00:00:00Z,,PRJNA967385,,"CP125987,CP125988",,,Illumina Novaseq 6000,300.0x,Bowtie2 v. 2.5.1,1,1,2,3938562,34.202255,3575,3457,urinary,,2021-11-11,Turkey,Turkey,,,,,,,,,,,,,,,,,,,,,,,,,UTI,,,,,,,,,,,,,,99.7,1.6,Urinary Tract Diseases,Lower UTI,Urinary Tract,Urinary Tract Diseases-Lower UTI HP,76856.5,Fusobacterium nucleatum subsp. nucleatum strain ChDC F317,ChDC F317,Fusobacterium nucleatum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN03263083,76856,,,,,,KCOM:1323,,2017-06-30T00:00:00Z,,PRJNA270127,GCA_002211605.1,CP022122,,Chosun University,Illumina HiSeq,1769.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,,1,2233010,27.08,2174,2113,subgingival dental plaque,,2005-03-01,South Korea,South Korea: Gwangju,"env_biome:Subgingival dental plaque,periodontitis",,,,,,,,Negative,Filamentous,No,,,,,,Analyzing virulence factors of Fusobacterium nucleatum subsp. nucleatum KCOM 1323,,,,,Non,,,,,,,,,strain coidentity: ChDC F317=KCOM 1323,,,,"Subgingival dental plaque,periodontitis",,,,100,0.5,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,76857.43,Fusobacterium nucleatum subsp. polymorphum strain KCOM 1275,KCOM 1275,Fusobacterium polymorphum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07125867,76857,,,,,,,,2017-06-30T00:00:00Z,,PRJNA386738,GCA_002211625.1,CP022123,,Chosun University,Illumina HiSeq,348.0x,AllPaths_LG v. 47944; SSPACE v. 2.3.1;,1,,1,2521394,26.83,2479,2420,subgingival plaque,,2005-03-01,South Korea,South Korea: Gwangju,,,,normal,,,,,,,,,,,,,Genome sequencing of Fusobacterium nucleatum subsp. polymorphum KCOM 1275 (=ChDC F310),collected_by:Korean Collection for Oral Microbiology,,,,,,,normal,,,,,,strain coidentity: KCOM 1275=ChDC F310,,,,,,,,100,0,,,Oral,- HP,76860.44,Streptococcus constellatus TCV107,TCV107,Streptococcus constellatus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN09005831,76860,,,,,,,,2022-07-25T00:00:00Z,,PRJNA454548,GCA_024399395.1,CP029207,,,Oxford Nanopore,125.0x,Canu v. 1.5,1,0,1,1980997,38.11071,2048,1934,abscess,,2017-10-17,Taiwan,Taiwan,,,,Abscess,,,,,,,,,,,,,,collected_by:Po-Yu Liu,,,,,,,Abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses HP,777.185,Coxiella burnetii strain Henzerling,Henzerling,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN04500797,777,,,,,,,,2017-10-23T00:00:00Z,28848533,PRJNA312577,GCA_002634025.1,"CP014559,CP014560",,Central Veterinary Institute part of Wageningen UR,Illumina,239.3x,SPAdes v. 3.6.2,1,1,2,2000126,42.4,2353,2064,,isolated during the outbreak period (2007-2010) in Netherlands are compared in this project,1945,Italy,Italy,,,,,,,,,,,,,C,,,,Several Coxiella burnetii strains along with strains isolated during the outbreak period (2007-2010) in Netherlands are compared in this project.,sample_type:Cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.186,Coxiella burnetii strain Heizberg,Heizberg,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN04500798,777,,,,,,,,2017-10-23T00:00:00Z,28848533,PRJNA312578,GCA_002634045.1,"CP014561,CP014562",,Central Veterinary Institute part of Wageningen UR,Illumina,228.25x,SPAdes v. 3.6.2,1,1,2,1999884,42.4,2361,2062,,isolated during the outbreak period (2007-2010) in Netherlands are compared in this project,,Greece,Greece,,,,,,,,,,,,,C,,,,Several Coxiella burnetii strains along with strains isolated during the outbreak period (2007-2010) in Netherlands are compared in this project.,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.303,Coxiella burnetii strain CB132,CB132,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429672,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918495.1,CP103432,,IHU mediterranee infection,SOLiD,152x,CLC NGS Cell v. 7,1,0,1,1996301,42.60446,2172,,,,2014,,Belgium,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.305,Coxiella burnetii strain CB80,CB80,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429678,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918535.1,CP103426,,IHU mediterranee infection,SOLiD,162x,CLC NGS Cell v. 7,1,0,1,1995939,42.62636,2184,,,,2014,,France,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.307,Coxiella burnetii strain CB155,CB155,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429674,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918575.1,CP103430,,IHU mediterranee infection,SOLiD,158x,CLC NGS Cell v. 7,1,0,1,1996133,42.648163,2114,,,,2014,,United Kingdom,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.308,Coxiella burnetii strain CB121,CB121,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429670,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918595.1,CP103434,,IHU mediterranee infection,SOLiD,163x,CLC NGS Cell v. 7,1,0,1,1995888,42.617474,2195,,,,2014,,Switzerland,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.309,Coxiella burnetii strain CB13,CB13,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429671,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918615.1,CP103433,,IHU mediterranee infection,SOLiD,174x,CLC NGS Cell v. 7,1,0,1,1996299,42.608513,2198,,,,2014,,France,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.310,Coxiella burnetii strain BRASOV,BRASOV,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429669,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918635.1,CP103435,,IHU mediterranee infection,SOLiD,156x,CLC NGS Cell v. 7,1,0,1,1996222,42.66036,2115,,,,2013,,Romania,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.312,Coxiella burnetii strain CB170,CB170,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429675,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918675.1,CP103429,,IHU mediterranee infection,SOLiD,161x,CLC NGS Cell v. 7,1,0,1,1996109,42.63147,2125,,,,2014,,USA,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,777.313,Coxiella burnetii strain CB180,CB180,Coxiella burnetii,Coxiella,Coxiellaceae,Legionellales,Gammaproteobacteria,Pseudomonadota,SAMN30429676,777,,,,,,,,2022-09-04T00:00:00Z,,PRJNA871194,GCA_024918695.1,CP103428,,IHU mediterranee infection,SOLiD,162x,CLC NGS Cell v. 7,1,0,1,1995665,42.585606,2167,,,,2013,,France,,,,,,,,,,,,,,,,,"We performed a pangenomic analysis of C. burnetii using the genomes from 75 C. burnetii strains including 63 novel genomes, in order to evaluate the genetic diversity, evolution, antibiotic resistance, and disease-specific characteristics of this pathogen. The comparative genomics enabled us to understand more the genomic dynamics of C. burnetii, its evolution, host adaptation, epidemiology and clinical profiles. In this study we showed that C. burnetii has a high genome plasticity, gene transfer, and that genomic features, including genotypes are correlated to the clinical outcome and geographic distribution. This large genomic analysis will bring new insights into the world of this intracellular bacterium and its relatives. To our knowledge, the present work is the largest study on the association of C. burnetii strains and clinical presentation. Future analysis with more animal and human infecting strains from different MST genotypes and from multiple geographical locations will be an added value to the Coxiella burnetii evolutional and in depth studies.",sample_type:Tissus,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,783.32,Rickettsia rickettsii RMSPvaccine,RMSPvaccine,Rickettsia rickettsii,Rickettsia,Rickettsiaceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN30852922,783,,,,,,,,2022-12-22T00:00:00Z,,PRJNA880551,,CP114277,,,Illumina NextSeq,1022.0x,Bowtie2 aligned to reference genome,1,0,1,1268254,32.45502,1577,,crushed rocky mountain wood ticks,,1944,USA,"USA: Hamilton, Montana",,,,Rocky Mountain spotted fever,,,,,,,,,,,,,,collected_by:Rocky Mountain Laboratories,,,,,,,Rocky Mountain spotted fever,,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,803.12,Bartonella quintana CO21_0024,CO21_0024,Bartonella quintana,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN19611717,803,,,,,,,,2022-08-22T00:00:00Z,,PRJNA736168,GCA_024731485.1,CP076598,,,Illumina MiSeq,707x,SPAdes v. 3.15.0,1,0,1,1581130,38.805527,1658,,blood,,2021-02-03,USA,USA: Colorado,,,,Bartonella quintana,,,,,,,,,,,,,,"collected_by:UC Health, CDPHE, CDC",,,,,,,Bartonella quintana,,,,,,PatientD,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,803.13,Bartonella quintana CO20_0321,CO20_0321,Bartonella quintana,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN19611716,803,,,,,,,,2022-08-22T00:00:00Z,,PRJNA736168,GCA_024731605.1,CP076599,,,Illumina MiSeq,1031x,SPAdes v. 3.15.0,1,0,1,1580604,38.814644,1654,,blood,,2020-07-23,USA,USA: Colorado,,,,Bartonella quintana,,,,,,,,,,,,,,"collected_by:UC Health, CDPHE, CDC",,,,,,,Bartonella quintana,,,,,,PatientC,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,803.14,Bartonella quintana CO20_0257,CO20_0257,Bartonella quintana,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN19611714,803,,,,,,,,2022-08-22T00:00:00Z,,PRJNA736168,GCA_024731645.1,CP076601,,,Illumina MiSeq,225x,SPAdes v. 3.15.0,1,0,1,1581053,38.805897,1662,,blood,,2020-05-29,USA,USA: Colorado,,,,Bartonella quintana,,,,,,,,,,,,,,"collected_by:UC Health, CDPHE, CDC",,,,,,,Bartonella quintana,,,,,,PatientA,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,803.15,Bartonella quintana CO20_0297,CO20_0297,Bartonella quintana,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN19611715,803,,,,,,,,2022-08-22T00:00:00Z,,PRJNA736168,GCA_024731625.1,CP076600,,,Illumina MiSeq,884x,SPAdes v. 3.15.0,1,0,1,1581324,38.803295,1662,,blood,,2020-05-31,USA,USA: Colorado,,,,Bartonella quintana,,,,,,,,,,,,,,"collected_by:UC Health, CDPHE, CDC",,,,,,,Bartonella quintana,,,,,,PatientB,,,,,,,,100,0.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,803.16,Bartonella quintana CO20_0256,CO20_0256,Bartonella quintana,Bartonella,Bartonellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN19611713,803,,,,,,,,2022-08-22T00:00:00Z,,PRJNA736168,GCA_024731665.1,CP076602,,,Illumina MiSeq,1130x,SPAdes v. 3.15.0,1,0,1,1579572,38.796425,1674,,blood,,2020-05-01,USA,USA: Colorado,,,,Bartonella quintana,,,,,,,,,,,,,,"collected_by:UC Health, CDPHE, CDC",,,,,,,Bartonella quintana,,,,,,PatientA,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,813.135,Chlamydia trachomatis strain SQ32,SQ32,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870231,813,D-,,,MLST.Chlamydiales_spp.4,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776745.1,CP017730,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1047716,41.3,968,916,epithelial cells,,1995,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 1,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.136,Chlamydia trachomatis strain SQ29,SQ29,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870230,813,D-,,,MLST.Chlamydiales_spp.4,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776795.1,CP017731,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1047716,41.3,967,917,epithelial cells,,1991-10,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 1,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.137,Chlamydia trachomatis strain SQ20,SQ20,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870245,813,H,,,MLST.Chlamydiales_spp.13,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776845.1,CP017732,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048530,41.3,955,916,epithelial cells,,1991-06,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 7,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.138,Chlamydia trachomatis strain SQ24,SQ24,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870246,813,H,,,MLST.Chlamydiales_spp.13,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776885.1,CP017733,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048538,41.3,954,917,epithelial cells,,1993,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 7,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.139,Chlamydia trachomatis strain SQ09,SQ09,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870239,813,Ia,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776955.1,CP017736,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1042567,41.31,957,909,epithelial cells,,1992-07,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 5,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.140,Chlamydia trachomatis strain SQ10,SQ10,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870240,813,Ia,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776975.1,CP017737,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1042575,41.31,960,911,epithelial cells,,1993,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 5,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.141,Chlamydia trachomatis strain SQ12,SQ12,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870241,813,Ia,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002776995.1,CP017738,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1042577,41.3,965,912,epithelial cells,,1995,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 5,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.142,Chlamydia trachomatis strain SQ14,SQ14,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870242,813,Ia,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777015.1,CP017739,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1042578,41.31,962,911,epithelial cells,,1996,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 5,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.143,Chlamydia trachomatis strain SQ01,SQ01,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870232,813,J,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777035.1,CP017740,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048696,41.31,950,917,epithelial cells,,1995-04,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 2,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.144,Chlamydia trachomatis strain SQ02,SQ02,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870233,813,J,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777055.1,CP017741,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048696,41.3,951,917,epithelial cells,,1996,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 2,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.145,Chlamydia trachomatis strain SQ05,SQ05,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870234,813,J,,,MLST.Chlamydiales_spp.9,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777075.1,CP017742,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048696,41.31,950,917,epithelial cells,,1998,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 2,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.146,Chlamydia trachomatis strain SQ25,SQ25,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870235,813,Ja,,,MLST.Chlamydiales_spp.12,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777095.1,CP017743,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1043246,41.31,959,911,epithelial cells,,1992-02,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 3,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.147,Chlamydia trachomatis strain SQ15,SQ15,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870243,813,K,,,,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777135.1,CP017745,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048307,41.3,949,916,epithelial cells,,1986-12,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 6,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.148,Chlamydia trachomatis strain SQ19,SQ19,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN05870244,813,K,,,,,,,2017-11-16T00:00:00Z,,PRJNA338746,GCA_002777155.1,CP017746,,Oregon State University,Illumina Hiseq 2000,missing,Geneious v. 7.1.7,1,,1,1048306,41.3,949,915,epithelial cells,,1989,USA,"USA: Seattle, WA",env_biome:Human genital epithelium,female,,,,host_subject_id:Patient 6,,,,,,,,,,,"This project was designed to examine whether different same-serovar strains from single patients were most likely persistent or repeat infections. As long-term or repeated exposure to C. trachomatis is considered important in serious disease of the genital tract, understanding the nature of these infections is important.",,,,,missing,,,,,,,,,,,,,Human genital epithelium,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,813.351,Chlamydia trachomatis L2f,L2f,Chlamydia trachomatis,Chlamydia,Chlamydiaceae,Chlamydiales,Chlamydiia,Chlamydiota,SAMN31133397,813,,,,MLST.Chlamydiales_spp.44,,,,2022-11-14T00:00:00Z,,PRJNA886480,GCA_025723025.1,"CP106985,CP106986",,,Illumina iSeq; Oxford Nanopore MinION,200.0x,Unicycler v. 0.5.0,1,1,2,1045668,41.289394,952,907,rectal swab,,2017-05-01,Italy,Italy,,,,Chlamydia infection,,,,,,,,,,,,,,collected_by:Policlinico Sant'Orsola-Malpighi,,,,,,,Chlamydia infection,,,,,,,,,,,,,,100,0,Sexually Transmitted Infections (STIs),Chlamydia,Gastrointestinal,Sexually Transmitted Infections (STIs)-Chlamydia HP,817.1270,Bacteroides fragilis strain CCUG4856T,CCUG4856T,Bacteroides fragilis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN11040710,817,,,,,,CCUG:4856T,,2019-05-23T00:00:00Z,,PRJNA525024,GCA_005706655.1,"CP036555,CP036556",,Odense University Hospital,Illumina MiSeq; Oxford Nanopore MiniION,200.0x,Unicycler v. v0.4.7,1,1,2,5241693,43.114296,4788,4580,appendix abscess,,1955,United Kingdom,United Kingdom:London,,,,appendicitis,,,,,,,,,,,,,Complete genome assembly of Bacteroides fragilis CCUG4856T (=ATCC25285=NCTC9343) for selection of optimal assembly pipepline for Bacteroides fragilis and comparison to existing assemblies. Isolate purchased from https://www.ccug.se/strain?id=4856 on 2012-11-12.,collected_by:L.P.Garrod,,,,,,,appendicitis,,,,,,,,,,,,,,99.26,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,817.1742,Bacteroides fragilis strain DK1985,DK1985,Bacteroides fragilis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN12869706,817,,,,,,,,2021-02-11T00:00:00Z,,PRJNA574815,GCA_016864615.1,CP044428,,Odense University Hospital,Oxford Nanopore MiniION; Illumina MiSeq,100.0x,Unicycler v. 0.4.7,1,0,1,5380874,43.3269,4957,4589,blood,isolated in 1985,1985,Denmark,Denmark,,,,,,,,,,,,,,,,,Complete genome assembly of B. fragilis DK_1985. A clinical blood isolate isolated in 1985. doi:10.1016/j.ijantimicag.2017.05.007,collected_by:Justesen,,,,,,,unknown,,,,,,,,,,,,,,99.26,0.87,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,817.1883,Bacteroides fragilis strain BFG-1,BFG-1,Bacteroides fragilis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546948,817,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091565.1,"CP081922,CP081921",,National Institute of Allergy and Infectious Disease,PacBio Sequel,148x,Canu v. v. 1.6,1,1,2,5223334,43.26482,4645,4172,blood,,1985,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.26,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,817.2297,Bacteroides fragilis DH4096B,DH4096B,Bacteroides fragilis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663831,817,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916355.1,CP083688,,,Illumina HiSeq,224x,A5ud v. v1,1,0,1,4950652,43.2264,4364,3985,feces,,not collected,USA,USA: Maywood,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11472924,,,,,,,,,,,,,human gut microbiome,,,,100,0.1,,,Gastrointestinal,- NHP,818.1561,Bacteroides thetaiotaomicron strain CL11T00C24,CL11T00C24,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451195,818,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289275.1,"CP072224,CP072225,CP072226",,Brigham & Women's Hospital,PacBio Sequel,324x,FALCON-Unzip v. 1.2.0,1,2,3,6776017,42.859146,5784,5359,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.41,0.4,,,Gastrointestinal,- NHP,818.1562,Bacteroides thetaiotaomicron strain CL06T03C18,CL06T03C18,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451188,818,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018291825.1,CP072242,,Brigham & Women's Hospital,PacBio Sequel,331x,FALCON-Unzip v. 1.2.0,1,0,1,5830764,42.80465,4583,4330,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.35,0.08,,,Gastrointestinal,- HP,818.1650,Bacteroides thetaiotaomicron strain BFG-55,BFG-55,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547032,818,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091305.1,CP081898,,National Institute of Allergy and Infectious Disease,PacBio Sequel,269x,Canu v. v. 1.6,1,0,1,6337561,42.837585,5185,4791,peritoneal fluid,,1986,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.46,0.08,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- NHP,818.2205,Bacteroides thetaiotaomicron KR001_HAM_0006,KR001_HAM_0006,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100331,818,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757925.1,CP107194,,,PacBio Sequel II,5x,hifiasm_meta v. 0.2-r040,1,0,1,6310637,42.55559,5095,4732,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2206,Bacteroides thetaiotaomicron WAL8713,WAL8713,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663844,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914215.1,CP083679,,,Illumina HiSeq,136x,A5ud v. v1,1,0,1,6611797,42.812267,5567,5109,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2207,Bacteroides thetaiotaomicron WAL8669,WAL8669,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663843,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914235.1,CP083680,,,Illumina HiSeq,238x,A5ud v. v1,1,0,1,6410115,42.60516,5238,4859,feces,,not collected,USA,USA: Los Angeles,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2208,Bacteroides thetaiotaomicron VPI-BT8702,VPI-BT8702,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663839,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914275.1,CP083682,,,Illumina HiSeq,215x,A5ud v. v1,1,0,1,6730461,42.841503,5609,5171,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2209,Bacteroides thetaiotaomicron VPI-BTDOT2,VPI-BTDOT2,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663840,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914255.1,CP083681,,,Illumina HiSeq,162x,A5ud v. v1,1,0,1,6467639,43.12923,5367,4989,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0.7,,,Gastrointestinal,- NHP,818.2210,Bacteroides thetaiotaomicron VPI-BT7853,VPI-BT7853,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663838,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916255.1,CP083683,,,Illumina HiSeq,174x,A5ud v. v1,1,0,1,6319080,42.601223,5249,4833,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,11157217,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2211,Bacteroides thetaiotaomicron VPI-5482A,VPI-5482A,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663837,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916275.1,CP083684,,,Illumina HiSeq,239x,A5ud v. v1,1,0,1,6254757,42.867973,5179,4755,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,https://doi.org/10.1099/00207713-28-2-245,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2212,Bacteroides thetaiotaomicron VPI-3164,VPI-3164,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663835,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916315.1,CP083686,,,Illumina HiSeq,212x,A5ud v. v1,1,0,1,6521709,42.50582,5401,5018,rectal abcess,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,rectal abcess,rectal abcess,https://doi.org/10.1099/00207713-28-2-245,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2213,Bacteroides thetaiotaomicron VPI-3443,VPI-3443,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663836,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916295.1,CP083685,,,Illumina HiSeq,224x,A5ud v. v1,1,0,1,6301124,42.76517,5221,4853,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,https://doi.org/10.1099/00207713-28-2-245,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,818.2214,Bacteroides thetaiotaomicron VPI-2808B,VPI-2808B,Bacteroides thetaiotaomicron,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663834,818,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025916335.1,CP083687,,,Illumina HiSeq,165x,A5ud v. v1,1,0,1,6225667,42.8355,5191,4765,rectal abcess,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,rectal abcess,rectal abcess,https://doi.org/10.1099/00207713-28-2-245,,,,,,,,,,,,,human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,820.5428,Bacteroides uniformis strain CL11T00C07,CL11T00C07,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451196,820,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289175.1,"CP072220,CP072221,CP072222,CP072223",,Brigham & Women's Hospital,PacBio Sequel,271x,FALCON-Unzip v. 1.2.0,1,3,4,5339045,46.57653,4907,4588,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.26,0,,,Gastrointestinal,- NHP,820.5429,Bacteroides uniformis strain CL06T06C18,CL06T06C18,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451190,820,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289375.1,"CP072236,CP072237,CP072238",,Brigham & Women's Hospital,PacBio Sequel,282x,FALCON-Unzip v. 1.2.0,1,2,3,5069972,46.279327,4492,4177,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.26,0.19,,,Gastrointestinal,- NHP,820.5430,Bacteroides uniformis strain CL06T03C05,CL06T03C05,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451189,820,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018291785.1,"CP072239,CP072240,CP072241",,Brigham & Women's Hospital,PacBio Sequel,282x,FALCON-Unzip v. 1.2.0,1,2,3,5471617,46.39091,5055,4674,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.26,0,,,Gastrointestinal,- NHP,820.5953,Bacteroides uniformis strain ATCC 8492,ATCC 8492,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222662,820,,,,,,ATCC:8492,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147485.1,CP102263,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,4629452,46.549007,3950,3686,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:ATCC,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,98.88,0,,,Other,- NHP,820.5971,Bacteroides uniformis VPI-3537,VPI-3537,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN19663846,820,,,,,,,,2022-10-31T00:00:00Z,,PRJNA736687,GCA_025914195.1,CP083677,,,Illumina HiSeq,439x,A5ud v. v1,1,0,1,4716350,46.320503,4113,3830,feces,,not collected,,not collected,,,,,,,,,,,,,,,,,,,human gut microbiome,feces,feces,https://doi.org/10.1099/00207713-28-2-245,,,,,,,,,,,,,human gut microbiome,,,,100,0.2,,,Gastrointestinal,- NHP,821.4312,Phocaeicola vulgatus strain CL06T03C24,CL06T03C24,Phocaeicola vulgatus,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451191,821,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289355.1,"CP072234,CP072235",,Brigham & Women's Hospital,PacBio Sequel,77x,FALCON-Unzip v. 1.2.0,1,1,2,5306031,42.38441,4733,4347,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.25,0,,,Gastrointestinal,- HP,821.4572,Phocaeicola vulgatus strain BFG-191,BFG-191,Phocaeicola vulgatus,Phocaeicola,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15547037,821,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091465.1,"CP081912,CP081909,CP081910,CP081911",,National Institute of Allergy and Infectious Disease,PacBio Sequel,502x,HGAP/FALCON v. v. 6.0,1,3,4,5293332,42.42683,4803,4344,peritoneal fluid,,1987,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.25,0,Miscellaneous or Unspecified Infections,,Abdominal,Miscellaneous or Unspecified Infections- HP,823.3064,Parabacteroides distasonis strain CavFT-hAR46,CavFT-hAR46,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN11642307,823,,,,,,,,2019-06-07T00:00:00Z,,PRJNA542869,GCA_006149185.1,CP040468,,Case Western Reserve University School of Medicine,PacBio RSII,168.0x,HGAP v. FEB-2018,1,,1,4952323,45.2021,4339,4104,intramural gut wall,,2017-01-10,USA,USA: Cleveland,,,,Crohn's Disease,,,,,,,,,,,,,The aim of the study is to explore the pathogenic bacteria that contribute to Crohn's disease (CD),,digestive tract environment,intestine environment,gut wall,TSA with 5% blood,,,Crohn's Disease,,,,,,,,,,digestive tract environment,,,,99.42,0,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Other,Gastrointestinal Diseases-Inflammatory Bowel Diseases NHP,823.3160,Parabacteroides distasonis strain NBRC 113806,NBRC 113806,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMD00169831,823,,,,,,NBRC:113806,,2019-06-12T00:00:00Z,,PRJDB8042,GCA_006739545.1,AP019729,,"Biological Resource Center, National Institute of Technology and Evaluation (NBRC)",Illumina MiSeq; ONT GridION,378x,Unicycler v. 0.4.4,1,,1,5179960,45.009712,4447,4171,,,2018-03-22,,,,,,,,,,,,,,,,,,,"The NBRC Whole Genome sequencing Project aims to provide reference genomes of NBRC culture collection strains for identifying useful genes for taxonomic classification, risk/safety assessment, and industrial application, and for understanding the structure and evolution of microbial genomes. One of our goals is to sequence 2,000 representative strains in the NBRC culture collection. The sequence information will be released to the society through the NBRC web site (http://www.nite.go.jp/en/nbrc/genome/index.html) and DDBJ/EMBL/GenBank databases.",,Human,missing,feces,missing,Parabacteroides distasonis NBRC 113806 genome sequencing project,,,healthy,,,,,,,,free living,Human,,,,99.42,0.71,,,Other,- NHP,823.3406,Parabacteroides distasonis strain FDAARGOS_759 strain Not applicable,Not applicable,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN11056474,823,,,,,,FDA:FDAARGOS_759,,2020-06-04T00:00:00Z,,PRJNA231221,GCA_013267615.1,CP054012,,US Food and Drug Administration,Pacbio; Illumina,614.09x,Canu v. 1.7,1,0,1,4926033,45.174427,4243,3980,human fecal sample,,,USA,USA:VA,,,,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.42,0,,,Gastrointestinal,- NHP,823.3648,Parabacteroides distasonis strain CL11T00C22,CL11T00C22,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451200,823,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018288975.1,"CP072210,CP072211",,Brigham & Women's Hospital,PacBio Sequel,341x,FALCON-Unzip v. 1.2.0,1,1,2,5328687,45.122505,4697,4405,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.42,0,,,Gastrointestinal,- NHP,823.3649,Parabacteroides distasonis strain CL06T03C10,CL06T03C10,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451192,823,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018289335.1,"CP072231,CP072233,CP072232",,Brigham & Women's Hospital,PacBio Sequel,366x,FALCON-Unzip v. 1.2.0,1,2,3,5311305,45.237545,4732,4464,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.42,0.77,,,Gastrointestinal,- HP,823.3733,Parabacteroides distasonis strain BFG-238,BFG-238,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN15546933,823,,,,,,,,2021-09-22T00:00:00Z,,PRJNA646575,GCA_020091445.1,"CP081908,CP081907",,National Institute of Allergy and Infectious Disease,PacBio Sequel,448x,HGAP/FALCON v. v. 6.0,1,1,2,5562109,45.104744,4940,4650,biopsy,,1987,USA,USA:Bethesda,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,"Isolates underwent genomic sequencing with a combination of Illumina, PacBio and Oxford Nanopore Technologies sequencing approaches.",collected_by:Department of Laboratory Medicine - NIH Clinical Center,,,,,,,BACTEROIDES INFECTIONS,,,,,,,,,,,,,,99.23,1.35,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,823.3972,Parabacteroides distasonis KR001_HAM_0055,KR001_HAM_0055,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN31100333,823,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757725.1,CP107196,,,PacBio Sequel II,11x,hifiasm_meta v. 0.2-r040,1,0,1,4848511,45.07724,4141,3910,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.6,,,Gastrointestinal,- HP,827.94,Campylobacter ureolyticus strain FDAARGOS_673,FDAARGOS_673,Campylobacter ureolyticus,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11056388,827,,,,,,ATCC:43606D-5,,2020-04-12T00:00:00Z,,PRJNA231221,GCA_012273175.1,CP050963,,US Food and Drug Administration,Pacbio; Illumina,2657.06x,canu v. 1.4,1,0,1,1559279,29.242184,1589,1529,urethra of man with non-gonococcal urethritis.,,,USA,USA:VA,,male,,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:ATCC,,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,98.95,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,83333.442,Escherichia coli K-12 strain MG655,MG655,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196156,83333,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028735.1,CP028306,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4736591,50.777607,4665,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,100,0.4,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,83334.221,Escherichia coli O157:H7,B6-914ARS,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07369154,83334,O157:H7,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.822",,,,2017-08-18T00:00:00Z,,PRJNA395316,GCA_002259555.1,NOKN00000000,,U.S. Department of Agriculture,PacBio,20.0x,Celera Assembler v. March-2016,3,1,4,5652987,50.28,6192,5952,fecal sample,,,USA,USA: Washington (state),,,,,,,,,,,,,,,,,"Escherichia coli serotype O157:H7 strain B6-914 is a human fecal isolate that was submitted to the Centers for Disease Control and Prevention and later deposited with the American Type Culture Collection (ATCC) as strain ATCC 43888. Its virulence is attenuated due to the lack of stx1, stx2, or stx variants, which resulted in its widespread use in applied microbiology studies for safety reasons. A B6-914 isolate in one USDA culture collection (designated B6-914ARS) has been shown to have unique properties with regard to biofilm formation and persistence on processing surfaces that likely stem from variations in genomic regions that carry bacteriophage insertions. Therefore, it would be valuable to determine the entire genomic sequence of strain B6-914 for use in comparative studies with sequences of deposited serotype O157:H7 strains.",,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,83334.250,Escherichia coli O157:H7 strain Sakai,Sakai,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07196155,83334,,,,"MLST.Escherichia_coli_1.453,MLST.Escherichia_coli_2.86",,,,2018-04-02T00:00:00Z,,PRJNA389368,GCA_003028755.1,CP028307,,Rehman Medical Institute,Illumina MiSeq,30X,SPAdes v. 3.10.1,1,,1,4709905,50.763325,4637,,urine,,2016-12-06,Pakistan,"Pakistan: Sheikh Zaid Hospital, Lahore",,,,Urinary tract infection,,,,,,,,,,,,,"To find out antibiotic resistant genes, De novo mutations, presence of bacteriophage in genome, phylogenetic tree of uropathogens and correlation b/w different phylogentic groups and antibiotic resistance of clinical isolates. Investigating the potential of Lactic acid bacteria to replace antibiotic for treatment of UTI;missing ribosomal protein genes;missing tRNA genes","collected_by:Asma Manzoor, Nabila Ishaq",,,,,,,Urinary tract infection,,,,,,,,,,,,,,96.8,1.5,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,83334.292,Escherichia coli O157:H7 strain FWSEC0004,FWSEC0004,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768105,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037735.2,NEWF00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,130.71x;172.42x,Unicycler;Canu v. 0.4.4.0;1.7,1,2,3,5505679,50.446655,5890,5726,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",1987,Canada,"Canada:Ontario,Toronto",,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.293,Escherichia coli O157:H7 strain ECP17-1298,ECP17-1298,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11787763,83334,serovar Typhimurium,,,MLST.Escherichia_coli_1.11,,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885915.1,"CP040570,CP040571",,FDA Center for Food Safety and Applied Nutrition,PacBio,270x,HGAP v. 3,1,1,2,5550459,50.465195,5840,5521,missing,,,USA,USA:NY,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.294,Escherichia coli O157:H7 strain ECP17-46,ECP17-46,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11786966,83334,serovar Typhimurium,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885955.1,"CP040572,CP040573",,FDA Center for Food Safety and Applied Nutrition,PacBio,490x,HGAP v. 3,1,1,2,5569576,50.441723,5877,5530,missing,,,,,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:CDC,,,,,,,missing,,,,,,,,,,,,,,99.87,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.296,Escherichia coli O157:H7 strain COPRO21317,COPRO21317,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10873602,83334,O157:H7,,Escherichia coli - STEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2019-06-28T00:00:00Z,,PRJNA521017,GCA_006514375.1,"CP035706,CP035705",,Ezequiel Dias Foundation,IonTorrent,33.0x,Geneious v. 11.1.5,1,1,2,5522685,50.516335,5906,5437,stools,,2017-09-26,Brazil,"Brazil: Belo Horizonte, Minas Gerais",,,,Hemolytic uremic syndrome,,,,,,,,,,,,,"We sequenced E. coli 213/17 to provide a more accurate view of the molecular epidemiology and genetic diversity of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in Minas Gerais State, Brazil.",collected_by:Epidemiological surveillance,,,,,,,Hemolytic uremic syndrome,,,,,Escherichia coli - STEC,,,,,,,,,99.82,0.09,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,83334.297,Escherichia coli O157:H7 strain ATCC 43888,ATCC 43888,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12261986,83334,O157:H7,,,MLST.Escherichia_coli_1.11,genotype:Stx-minus,ATCC:43888,,2019-08-08T00:00:00Z,,PRJNA294158,GCA_007922655.1,"CP041623,CP041625,CP041624",,USDA/ARS/Eastern Regional Research Center,PacBio,90.0x,HGAP v. 4,1,2,3,5503522,50.37198,5790,5425,feces,,1986,USA,USA,,,,,,,,,,,,,C,,,,"The project goals are to study DNA sequence, transcriptomic, and phenotypic variations among strains of Shiga toxin producing Escherichia coli in reference to biofilm formation and surface adhesion.",collected_by:US CDC,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,83334.298,Escherichia coli O157:H7 strain TT12B strain not applicable,not applicable,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11310481,83334,O157:H7,,EHEC,MLST.Escherichia_coli_1.11,,,,2019-11-08T00:00:00Z,,PRJNA530317,GCA_009627495.1,"CP038494,CP038495",,University of Texas at San Antonio,PacBio RSII,142x,HGAP v. v2.3,1,1,2,5428573,50.462894,5654,5335,feces,,1994-10-25,Japan,Japan: Yokosuka,,,,Hemorrhagic colitis,,,,,,,,,,,,,The goal of this study is to comprehensively analyze the genomes and transcriptomes of Enterohemorrhagic Escherichia coli of the O157:H7 serotype and derived atypical non-shigatoxigenic strains,collected_by:National Children's Medical Research Center,,,,,,,Hemorrhagic colitis,,,,,EHEC,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,83334.299,Escherichia coli O157:H7 strain CFSAN076619,CFSAN076619,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10574722,83334,,,,MLST.Escherichia_coli_1.11,,ATCC:43890,,2019-11-12T00:00:00Z,,PRJNA541972,GCA_009650175.1,"CP045863,CP045864,CP045865",,FDA Center for Food Safety and Applied Nutrition,Illumina MiSeq; Oxford Nanopore GridION,30.0x,SPAdes v. 3.12.0; CANU v. 1.7,1,2,3,5438085,50.499947,5608,5214,human feces,,1987,USA,USA:CA,,,,,,,,,,,,,,,,,Whole genome sequencing using long-read nanopore technology of cultured STECs as part of the U.S. Food and Drug Administration surveillance project for the rapid detection of food contamination events.;R. Binet et al (2017) Construction of stable fluorescent laboratory control strains for several food safety relevant Enterobacteriaceae- Food Microbiology (accepted),collected_by:CDC,,,,,,,missing,,,,,,,,R. Binet et al (2017) Construction of stable fluorescent laboratory control strains for several food safety relevant Enterobacteriaceae- Food Microbiology (accepted),,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,83334.340,Escherichia coli O157:H7 strain TB182A,TB182A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229499,83334,O157:H7,,STEC,"MLST.Escherichia_coli_2.553,MLST.Escherichia_coli_1.335",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167255.1,"CP038295,CP038296,CP038297,CP038298,CP038299",,United State Department of Agriculture,PacBio RSII,441x,HGAP v. 3,1,4,5,5367819,50.46025,5494,5219,missing,,1991,USA,USA:Washington,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.346,Escherichia coli O157:H7 strain OK1,OK1,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229501,83334,O157:H7,,STEC,MLST.Escherichia_coli_1.11,,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167355.1,"CP038313,CP038314,CP038315",,United State Department of Agriculture,PacBio RSII,272x,HGAP v. 3,1,2,3,5560677,50.47112,5833,5543,missing,,1996,Japan,Japan:Okayama,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.354,Escherichia coli O157:H7 strain H6437,H6437,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229492,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167515.1,"CP038339,CP038341,CP038340",,United State Department of Agriculture,PacBio RSII,259x,HGAP v. 3,1,2,3,5626776,50.361576,5937,5618,missing,,,USA,USA,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.87,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.358,Escherichia coli O157:H7 strain H2495,H2495,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229491,83334,O157:H7,,STEC,MLST.Escherichia_coli_1.11,,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167535.1,"CP038342,CP038343",,United State Department of Agriculture,PacBio RSII,490x,HGAP v. 3,1,1,2,5588988,50.48508,5875,5593,missing,,,USA,USA,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.369,Escherichia coli O157:H7 strain E32511,E32511,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229498,83334,O157:H7,,STEC,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167875.1,"CP038380,CP038382,CP038381",,United State Department of Agriculture,PacBio RSII,239x,HGAP v. 3,1,2,3,5621861,50.345196,5950,5611,missing,,,,,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.370,Escherichia coli O157:H7 strain DEC5E,DEC5E,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229486,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.61,MLST.Escherichia_coli_2.553",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167935.1,"CP038383,CP038385,CP038384",,United State Department of Agriculture,PacBio RSII,238x,HGAP v. 3,1,2,3,5721525,50.56325,5981,5673,missing,,1963,Iran,Iran,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.89,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.371,Escherichia coli O157:H7 strain DEC5D,DEC5D,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229485,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.335,MLST.Escherichia_coli_2.553",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167975.1,"CP038386,CP038387,CP038388",,United State Department of Agriculture,PacBio RSII,307x,HGAP v. 3,1,2,3,5259579,50.43238,5327,5063,missing,,1965,Sri Lanka,Sri Lanka,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.372,Escherichia coli O157:H7 strain DEC5B,DEC5B,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229484,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.335,MLST.Escherichia_coli_2.553",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013167995.1,"CP038389,CP038390,CP038391,CP038392,CP038393",,United State Department of Agriculture,PacBio RSII,120x,HGAP v. 3,1,4,5,5484204,50.461163,5724,5398,missing,,1979,USA,USA:Florida,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.06,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.373,Escherichia coli O157:H7 strain DEC4E,DEC4E,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229482,83334,O157:H7,,STEC,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013168035.1,"CP038398,CP038401,CP038399,CP038400",,United State Department of Agriculture,PacBio RSII,217x,HGAP v. 3,1,3,4,5466350,50.45533,5674,5393,missing,,1988,Denmark,Denmark,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.374,Escherichia coli O157:H7 strain DEC5A,DEC5A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229483,83334,O157:H7,,STEC,"MLST.Escherichia_coli_2.553,MLST.Escherichia_coli_1.335",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013168015.1,"CP038394,CP038395,CP038396,CP038397",,United State Department of Agriculture,PacBio RSII,275x,HGAP v. 3,1,3,4,5380215,50.40468,5517,5242,missing,,1950,USA,USA:New York,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.67,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.376,Escherichia coli O157:H7 strain ATCC 35150,ATCC 35150,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229481,83334,O157:H7,,STEC,MLST.Escherichia_coli_1.11,,ATCC:35150,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013168075.1,"CP038405,CP038406,CP038407",,United State Department of Agriculture,PacBio RSII,249x,HGAP v. 3,1,2,3,5555348,50.46006,5838,5540,missing,,,USA,USA,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.377,Escherichia coli O157:H7 strain 493/89,493/89,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229500,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.523",,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013168115.1,"CP038412,CP038413",,United State Department of Agriculture,PacBio RSII,320x,HGAP v. 3,1,1,2,5606577,50.466873,5847,5573,missing,,1989,Germany,Germany,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.379,Escherichia coli O157:H7 strain 86-24,86-24,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11229497,83334,O157:H7,,STEC,MLST.Escherichia_coli_1.11,,,,2020-05-26T00:00:00Z,,PRJNA528413,GCA_013168095.1,"CP038408,CP038410,CP038409,CP038411",,United State Department of Agriculture,PacBio RSII,380x,HGAP v. 3,1,3,4,5594122,50.36939,5888,5577,missing,,1986,USA,USA:Washington,,,,,,,,,,,,,,,,,"The goal of this study is to compare complete genomes from Shiga toxin-containing Escherichia coli O157:H7 strains. Many studies have used short-read sequencing technologies to obtain draft genomes for comparison. However, this study uses long-read sequencing to generate complete closed genomes for comparison. This study will provide additional information about the architecture of the chromosome along with describing the different mobile genetic elements.",,,,,,,,missing,,,,,STEC,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.476,Escherichia coli O157:H7 strain Z1812,Z1812,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16327603,83334,O157:H7,,STEC,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2021-03-04T00:00:00Z,,PRJNA666790,GCA_017165015.1,"CP062727,CP062728",,United State Department of Agriculture,PacBio RSII,118.41984524773561x,HGAP v. 3,1,1,2,5606380,50.48186,5825,5418,feces,,2002,United Kingdom,United Kingdom,,,,Gastroenteritis Escherichia coli,,,,,,,,,,,,,"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.",collected_by:Socttish E. coli Reference Laboratory (SERL),,,,,,,Gastroenteritis Escherichia coli,,,,,STEC,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,83334.477,Escherichia coli O157:H7 strain Z1813,Z1813,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16327604,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2021-03-04T00:00:00Z,,PRJNA666790,GCA_017164995.1,"CP062725,CP062726",,United State Department of Agriculture,PacBio RSII,205.9768441748391x,HGAP v. 3,1,1,2,5684358,50.52548,5932,5531,feces,,2002,United Kingdom,United Kingdom,,,,Gastroenteritis Escherichia coli,,,,,,,,,,,,,"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.",collected_by:Socttish E. coli Reference Laboratory (SERL),,,,,,,Gastroenteritis Escherichia coli,,,,,STEC,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,83334.490,Escherichia coli O157:H7 strain Z1626,Z1626,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16327596,83334,O157:H7,,STEC,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,,,2021-03-04T00:00:00Z,,PRJNA666790,GCA_017165155.1,"CP062742,CP062743",,United State Department of Agriculture,PacBio RSII,92.30691037488617x,HGAP v. 3,1,1,2,5609276,50.484306,5841,5422,feces,,2014,United Kingdom,United Kingdom,,,,Gastroenteritis Escherichia coli,,,,,,,,,,,,,"While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.",collected_by:Socttish E. coli Reference Laboratory (SERL),,,,,,,Gastroenteritis Escherichia coli,,,,,STEC,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,83334.515,Escherichia coli O157:H7 strain TT12A strain not applicable,not applicable,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11310480,83334,O157:H7,,EHEC,MLST.Escherichia_coli_1.11,,,,2021-03-16T00:00:00Z,,PRJNA530317,GCA_017357545.1,"CP038496,CP038497",,University of Texas at San Antonio,PacBio RSII,154x,HGAP v. v2.3,1,1,2,5593719,50.44313,5893,5586,feces,,1994-10-25,Japan,Japan: Yokosuka,,,,Hemorrhagic colitis,,,,,,,,,,,,,The goal of this study is to comprehensively analyze the genomes and transcriptomes of Enterohemorrhagic Escherichia coli of the O157:H7 serotype and derived atypical non-shigatoxigenic strains,collected_by:National Children's Medical Research Center,,,,,,,Hemorrhagic colitis,,,,,EHEC,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Inflammatory Bowel Diseases,Gastrointestinal,Gastrointestinal Diseases-Inflammatory Bowel Diseases HP,83334.614,Escherichia coli O157:H7 strain 6535WT,6535WT,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20437362,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2021-12-12T00:00:00Z,,PRJNA750123,GCA_021166395.1,"CP089032,CP089033",,University of Texas at San Antonio,"PacBio, IlluminaMiSeq",117x,HGAP v. 2.3.0,1,1,2,5741710,50.499382,6076,5642,fecal sample,,2006,USA,USA: Minnesota,,,,STEC infection,,,,,,,,,,,,,Strains associated with an EHEC O157:H7 laboratory co-infection,,,,,,,,STEC infection,,,,,,,,,,,,,,99.97,0.63,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,83334.615,Escherichia coli O157:H7 strain 6535NalR,6535NalR,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20437390,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2021-12-12T00:00:00Z,,PRJNA750123,GCA_021166415.1,"CP089034,CP089035",,University of Texas at San Antonio,"PacBio, IlluminaMiSeq",154x,HGAP v. 2.3.0,1,1,2,5737031,50.494514,6063,5644,laboratory mutant of 6535,,2013,USA,USA: Minnesota,,,,STEC infection,,,,,,,,,,,,,Strains associated with an EHEC O157:H7 laboratory co-infection,,,,,,,,STEC infection,,,,,,,,,,,,,,99.97,0.33,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Other,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,83334.626,Escherichia coli O157:H7 M1300706002,M1300706002,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20437425,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2021-12-15T00:00:00Z,,PRJNA750123,GCA_021184105.1,"CP089270,CP089271",,,PacBioRSII,345x,HGAP v. 3,1,1,2,5738515,50.491566,6067,5643,fecal sample from patient,,2013,USA,USA: Minnesota,,,,STEC infection,,,,,,,,,,,,,,,,,,,,,STEC infection,,,,,,,,,,,,,,99.97,0.93,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,83334.627,Escherichia coli O157:H7 M1300706001A,M1300706001A,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20437332,83334,O157:H7,,,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,,,2021-12-15T00:00:00Z,,PRJNA750123,GCA_021184125.1,"CP089272,CP089273",,,PacBioRSII,143x,HGAP v. 3,1,1,2,5620975,50.420166,5907,5498,fecal sample from patient,,2013,USA,USA: Washington State,,,,STEC infection,,,,,,,,,,,,,,,,,,,,,STEC infection,,,,,,,,,,,,,,99.97,0.53,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,83334.637,Escherichia coli O157:H7 strain 380-94,380-94,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30166759,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2022-09-19T00:00:00Z,,PRJNA294158,GCA_025252445.1,"CP104309,CP104310",,USDA/ARS/Eastern Regional Research Center,PacBio Sequel,109.0x,flye v. 2.9.1,1,1,2,5535488,50.480175,5744,5379,clinical isolate,,1994,,USA,,,,,,,,,,,,,C,,,,"The project goals are to study DNA sequence, transcriptomic, and phenotypic variations among strains of Shiga toxin producing Escherichia coli in reference to biofilm formation and surface adhesion.",sample_type:bacteria;collected_by:CDC,,,,,,,,,,,,,,,,,,,,,99.97,0.33,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83334.639,Escherichia coli O157:H7 380-94,380-94,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN30166759,83334,O157:H7,,,MLST.Escherichia_coli_1.11,,,,2022-09-19T00:00:00Z,,PRJNA294158,GCA_025252445.1,"CP104309,CP104310",,,PacBio Sequel,109.0x,flye v. 2.9.1,1,1,2,5535488,50.480175,5744,5379,clinical isolate,,1994,USA,USA,,,,,,,,,,,,,,,,,,sample_type:bacteria;collected_by:CDC,,,,,,,,,,,,,,,,,,,,,100,0.2,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,83655.105,Leclercia adecarboxylata strain 16008513 strain 16005813,16005813,Leclercia adecarboxylata,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10923138,83655,,,,,,,,2019-02-25T00:00:00Z,,PRJNA522028,GCA_004295325.1,CP036199,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,177.0x,HGAP v. 3.0,1,,1,4815267,55.704845,4636,4508,sputum,isolated from sputum samples from patients in department of respiratory medicine in a Chinese teaching hospital in 2016,2016-05,China,China,,,,pneumonia,,,,,,,,,,,,,Leclercia adecarboxylata 16005813 was isolated from sputum samples from patients in department of respiratory medicine in a Chinese teaching hospital in 2016.,collected_by:Yin Zhe,,,,,,,pneumonia,,,,,,,,,,,,,,99.6,0.42,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,83655.113,Leclercia adecarboxylata strain J656,J656,Leclercia adecarboxylata,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12530229,83655,,,,,,,,2019-10-03T00:00:00Z,,PRJNA559240,GCA_008807335.1,CP042930,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,,1,4835321,55.60634,4630,4459,secretion,,2018,China,China: Guangdong,,,,osteomyelitis,,,,,,,,,,,,,identiy plasmid and chromosome-mediated colistin resistance gene in Leclercia adecarboxylata,collected_by:Zhujiang Hospital,,,,,,,osteomyelitis,,,,,,,,,,,,,,99.6,0.91,Bone and Joint Infections,Osteomyelitis,Other,Bone and Joint Infections-Osteomyelitis HP,83655.124,Leclercia adecarboxylata strain 707804,707804,Leclercia adecarboxylata,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14260873,83655,,,,,,,,2020-03-17T00:00:00Z,,PRJNA609890,GCA_011387015.1,CP049980,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. 3.0,1,0,1,4773926,55.786015,4523,4378,blood,,2015,China,China,,,,pancreatitis,,,,,,,,,,,,,Complete sequence of chromosome of strain 707804,collected_by:a public hospital,,,,,,,pancreatitis,,,,,,,,,,,,,,99.6,0.46,Gastrointestinal Diseases,Pancreatic Disorders,Blood and Circulatory System,Gastrointestinal Diseases-Pancreatic Disorders HP,83655.130,Leclercia adecarboxylata strain 16400,16400,Leclercia adecarboxylata,Leclercia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15902828,83655,,,,,,,,2020-09-06T00:00:00Z,,PRJNA659272,GCA_014489435.1,CP060824,,Instituto Nacional de Salud Publica,Illumina MiSeq,110.0x,SPAdes v. 3.12.0,1,0,1,5299968,55.098484,5232,5000,blood,,2019-05-30,Mexico,Mexico,,,,sepsis,,,,,,,,,,,,,Leclercia adecarboxylata carbapenemase producing isolate,collected_by:Hospital Civil de Guadalajara,,,,,,,sepsis,,,,,,,,,,,,,,99.6,1.93,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,837.119,Porphyromonas gingivalis strain KCOM 3131,KCOM 3131,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840095,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416024,GCA_002753935.1,CP024596,,Korean Collection for Oral Microbiology,PacBio,167.1x,RS HGAP v. 3.0,1,,1,2359159,48.22,2311,2031,subgingival dental plaque,,2017-02-22,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 3131,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.120,Porphyromonas gingivalis strain KCOM 2799,KCOM 2799,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07836928,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA415884,GCA_002753955.1,CP024601,,Korean Collection for Oral Microbiology,PacBio,355.2x,RS HGAP v. 3.0,1,,1,2469365,48.42,2463,2183,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2799,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.121,Porphyromonas gingivalis strain KCOM 2801,KCOM 2801,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840081,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416018,GCA_002753975.1,CP024600,,Korean Collection for Oral Microbiology,PacBio,419.2x,RS HGAP v. 3.0,1,,1,2478317,48.27,2501,2193,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2801,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.122,Porphyromonas gingivalis strain KCOM 2802,KCOM 2802,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840090,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416019,GCA_002754015.1,CP024591,,Korean Collection for Oral Microbiology,PacBio,381.1x,RS HGAP v. 3.0,1,,1,2374087,48.53,2346,2065,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2802,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.123,Porphyromonas gingivalis strain KCOM 2803,KCOM 2803,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840091,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416020,GCA_002754035.1,CP024592,,Korean Collection for Oral Microbiology,PacBio,216.9x,RS HGAP v. 3.0,1,,1,2353912,48.42,2343,2058,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2803,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.124,Porphyromonas gingivalis strain KCOM 2804,KCOM 2804,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840092,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416021,GCA_002754055.1,CP024593,,Korean Collection for Oral Microbiology,PacBio,382.1x,RS HGAP v. 3.0,1,,1,2463791,48.25,2444,2170,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2804,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.125,Porphyromonas gingivalis strain KCOM 3001,KCOM 3001,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840097,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416025,GCA_002754095.1,CP024595,,Korean Collection for Oral Microbiology,PacBio,558.9x,RS HGAP v. 3.0,1,,1,2353520,48.36,2323,1998,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 3001,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,837.126,Porphyromonas gingivalis strain KCOM 2805,KCOM 2805,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07840094,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA416023,GCA_002754075.1,CP024594,,Korean Collection for Oral Microbiology,PacBio,362.7x,RS HGAP v. 3.0,1,,1,2482917,48.24,2462,2184,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2805,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.127,Porphyromonas gingivalis strain KCOM 2796,KCOM 2796,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07831761,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA415687,GCA_002754115.1,CP024597,,Korean Collection for Oral Microbiology,PacBio,393.1x,RS HGAP v. 3.0,1,,1,2476166,48.15,2430,2146,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2796,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,99.3,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.128,Porphyromonas gingivalis strain KCOM 2798,KCOM 2798,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07836904,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA415867,GCA_002754135.1,CP024598,,Korean Collection for Oral Microbiology,PacBio,374.2x,RS HGAP v. 3.0,1,,1,2410673,48.32,2408,2110,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2798,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.129,Porphyromonas gingivalis strain KCOM 2800,KCOM 2800,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07836934,837,,,,,,,,2017-11-06T00:00:00Z,,PRJNA415885,GCA_002754155.1,CP024599,,Korean Collection for Oral Microbiology,PacBio,186.1x,RS HGAP v. 3.0,1,,1,2254720,48.44,2215,1938,subgingival dental plaque,,2013-11-03,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Porphyromonas gingivalis KCOM 2800,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.133,Porphyromonas gingivalis strain TDC 60,TDC 60,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07315161,837,,,,,,JCM:19600,,2018-01-19T00:00:00Z,29338683,PRJNA393092,GCA_002892555.1,CP025931,,CNRS - Universite de Rennes 1,PacBio,30.4x,canu v. 1.3,1,,1,2334880,48.35178,2233,1759,severe periodontal lesion,,,,,,,,Periodontitis,,,,,,,,,,,,,"Resequencing, Reassembly and Reannotation of Porphyromonas gingivalis strains ATCC 33277, TDC60 and W83.",collected_by:JCM collection;passage_history:less than 10,,,,,,,Periodontitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases HP,837.134,Porphyromonas gingivalis strain W83,W83,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN07315163,837,,,,MLST.Porphyromonas_gingivalis.24,,ATCC 33277,,2018-01-19T00:00:00Z,29338683,PRJNA393092,GCA_002892595.1,CP025932,,CNRS - Universite de Rennes 1,PacBio,29.7x,canu v. 1.3,1,,1,2343999,48.28526,2246,1721,human clinical specimen,,,,,,,,Periodontitis,,,,,,,,,,,,,"Resequencing, Reassembly and Reannotation of Porphyromonas gingivalis strains ATCC 33277, TDC60 and W83.",collected_by:ATCC collection;passage_history:less than 20,,,,,,,Periodontitis,,,,,,,also known as BAA-308,,,,,,,100,0,Oral and Dental Diseases,Periodontal Diseases,Other,Oral and Dental Diseases-Periodontal Diseases HP,837.203,Porphyromonas gingivalis strain GMU202011,GMU202011,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18753385,837,,,,,,,,2021-04-28T00:00:00Z,,PRJNA722373,GCA_018141805.1,CP073348,,Guangzhou Medical University,PacBio,975.51x,HGAP v. 4,1,0,1,2375739,48.357964,2231,,pus,"isolated from pus from a patient with pulmonary infection, it was confirmed as the pathogenic bacteria",2020-11-23,China,China: Guangzhou,,,,Pneumonia,,,,,,,,,,,,,"Porphyromonas gingivalis GMU202011 was isolated from pus from a patient with pulmonary infection, it was confirmed as the pathogenic bacteria.",collected_by:Liang Peng,,,,,,,Pneumonia,,,,,,,,,,,,,,99.92,0,Respiratory Diseases,Pneumonia,Skin and Soft Tissue,Respiratory Diseases-Pneumonia HP,837.278,Porphyromonas gingivalis grey,grey,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN28956759,837,,,,,,,,2023-07-12T00:00:00Z,,PRJNA847540,,CP098925,,,Illumina MiSeq,76x,CLC NGS Cell v. 12,1,0,1,2515721,48.041695,2464,2121,patient with periodontitis,,2011-03-15,Netherlands,Netherlands,,,,,,,,,,,,,,,,,,sample_type:oral cavity;collected_by:M. J. D. Smit,,,,,,,,,,,,,,,,,,,,,99.9,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,837.279,Porphyromonas gingivalis yellow,yellow,Porphyromonas gingivalis,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN28956760,837,,,,,,,,2023-07-12T00:00:00Z,,PRJNA847540,,CP098924,,,Illumina MiSeq,72x,CLC NGS Cell v. 12,1,0,1,2515718,48.0433,2464,2120,patient with periodontitis,,2011-03-15,Netherlands,Netherlands,,,,,,,,,,,,,,,,,,sample_type:oral cavity;collected_by:M. J. D. Smit,,,,,,,,,,,,,,,,,,,,,99.9,0.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,847.8,Oxalobacter formigenes strain HC-1,HC-1,Oxalobacter formigenes,Oxalobacter,Oxalobacteraceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN06036219,847,,,,,,,,2017-05-11T00:00:00Z,,PRJNA353993,GCA_002127965.1,CP018787,,UNIVERSITY OF FLORIDA,PacBio,250.0x,RS_HGPA v. 3.0,1,,1,2468871,49.58,2549,2244,feces,isolated from rumen contents by Dr M. Allison at Iowa State University (1),1985-06-25,USA,"USA: National Animal Disease Center at Ames, Iowa",,,,,,,,,,,,,,,,,"In the 80s, an anaerobic bacterium, with a substrate-specificity for oxalate, was isolated from rumen contents by Dr M. Allison at Iowa State University (1). Later, when it was isolated from feces of humans and other animals, a new genus and species Oxalobacter formigenes, was established to include these microorganisms. Human patients forming oxalate kidney stones who are Oxalobacter-negative have significantly higher urinary oxalate excretion and recurrent kidney stone episodes appear to correlate with the lack of Oxalobacter colonization (2). Animal studies have shown that urinary oxalate excretion is significantly reduced when animals are colonized with Oxalobacter sp. compared to animals not colonized and this is partly due to a reduction in the intraluminal oxalate load available for absorption across the intestine because of this oxalate-degrading action (3, 4). Interestingly, however, studies in the Hatch lab have demonstrated that Oxalobacter has a dual action of deriving oxalate from systemic sources by initiating or enhancing intestinal oxalate secretion (i.e. enteric excretion) in addition to intraluminal degradation. This was initially substantiated in our laboratory using rats (4) and later in studies using mice (5,6). Remarkably, colonization of a mouse model of the genetic disease Primary Hyperoxaluria, type 1 (PH1) with Oxalobacter resulted in a normalization of both hyperoxaluria and hyperoxalemia exhibited in non-colonized counterparts (5). This was attributed to a physiological interaction between the bacteria and the enterocyte which induced active transmural oxalate excretion across the caecum and distal colon. Later studies confirmed that the human strain, HC-1, produced the same result in both the small and large intestine of wild type mice (6). This study was undertaken to determine and compare the genome sequence of HC-1 and OXCC13 which are both human strains of Oxalobacter formigenes isolated from two different individuals.1. Allison et al. (1985) Arch Microbiol, 141: 1-72. Hatch, M. and Freel, R.W. (2008) Sem in Neph, 28:143-1503. Sidhu et al. (1999) JASN. 10 Suppl 14: S334-404. Hatch et al. (2006) Kidney Int. 69: 691-6985. Hatch et al. (2011) Am J Physiol. 300 (3): 461-4696. Hatch, M. and Freel, R.W. (2013) Urolithiasis 41 (5):379-384",sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- NHP,853.172,Faecalibacterium prausnitzii strain Indica,Indica,Faecalibacterium prausnitzii,Faecalibacterium,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN07764380,853,,,,,,,,2017-10-18T00:00:00Z,,PRJNA413728,GCA_002586945.1,CP023819,,Translational Health Science and Technology Institute,Illumina HiSeq; Nanopore,500.0x,SPAdes v. SEP-2017,1,,1,2868932,56.95,2887,2638,,,2017-06-22,India,India: Faridabad,,,,,,,,,,,,,,,,,"Faecalibacterium prausnitzii is the most abundant (~4%) member of Firmicutes in the colon of healthy humans. It is a strictly anaerobes and plays important role in the intestinal homeostasis. In the present study, we report the complete genome sequence of F. prausnitzii strain “Indica”.",sample_type:stool,,,,,,,,,,,,,,,,,,,,,99.3,2.6,,,Other,- NHP,853.8512,Faecalibacterium prausnitzii KR001_HIC_0004,KR001_HIC_0004,Faecalibacterium prausnitzii,Faecalibacterium,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100368,853,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757765.1,CP107213,,,PacBio Sequel II,30x,HiCanu v. 2.1.1,1,0,1,2858485,57.719105,2944,2685,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.3,,,Gastrointestinal,- HP,856.11,Fusobacterium varium strain Fv113-g1,Fv113-g1,Fusobacterium varium,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMD00073606,856,,,,,,,,2017-09-16T00:00:00Z,,PRJDB5491,GCA_002356455.1,"AP017968,AP017969,AP017970",,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",MiSeq; PacBioRS II; ABI 3730xl,200x,PacBio assembler HGAP v. 3; A5 MiSeq v.,3,,3,4122841,29.09,3826,3693,patient with ulcerative colitis,isolated from a patient with ulcerative colitis,,Japan,Japan,,,,ulcerative colitis,,,,,Negative,,No,,,Anaerobic,,,Fusobacterium varium str. Fv113-g1 was isolated from a patient with ulcerative colitis. This isolate was sequenced using Illumina MiSeq and PacBio RSII.,,missing,missing,missing,missing,missing,,,,,,,,,,,,missing,,,,100,0,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- NHP,856.123,Fusobacterium varium KR001_HAM_0062,KR001_HAM_0062,Fusobacterium varium,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN31100349,856,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757605.1,CP107203,,,PacBio Sequel II,4x,hifiasm_meta v. 0.2-r040,1,0,1,3425653,29.307755,3242,3125,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,2,,,Gastrointestinal,- HP,85698.171,Achromobacter xylosoxidans strain AX1,AX1,Achromobacter xylosoxidans,Achromobacter,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN12683688,85698,,,,,,,,2019-09-17T00:00:00Z,,PRJNA563576,GCA_008432465.1,CP043820,,Laboratory for Diagnosis and Treatment of Infectious Diseases,PacBio Sequel,200.0x,SPAdes v. 3.10.2,1,,1,6402982,67.70925,5890,5736,alveolar lavage fluid,,2018-12,China,China,,,,lung infection,,,,,,,,,,,,,Characteristics of isolated from alveolar lavage fluid,collected_by:shuangLi,,,,,,,lung infection,,,,,,,,,,,,,,99.53,0.47,Respiratory Diseases,Lung Diseases,Other,Respiratory Diseases-Lung Diseases HP,85698.183,Achromobacter xylosoxidans strain R4,R4,Achromobacter xylosoxidans,Achromobacter,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA3614068,85698,,,,MLST.Achromobacter_spp.183,,,,2019-11-14T00:00:00Z,,PRJEB11387,GCA_900009125.1,LN890476,,UNIVERSITY OF LIVERPOOL,,,,1,0,1,6626924,67.65976,6133,5981,urine,,2012-04-02,Thailand,Thailand,,,,,,host_health_state:diseased,,,,,,,,,,,Genomic DNA of mulidrug-resistant isolates of Achromobacter xylosoxidans was sequenced to reveal genes associated with multiple antibiotic resistance and relevant mechanisms.,,,,,,,,,diseased,,,,,,,,,,,,,99.53,1.4,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,85698.184,Achromobacter xylosoxidans strain R8,R8,Achromobacter xylosoxidans,Achromobacter,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMEA3614070,85698,,,,MLST.Achromobacter_spp.185,,,,2019-11-14T00:00:00Z,,PRJEB11392,GCA_900010105.1,LN890477,,UNIVERSITY OF LIVERPOOL,,,,1,0,1,6690584,67.558754,6271,6104,peripheral blood,,2010-12-21,Thailand,Thailand,,,,,,host_health_state:diseased,,,,,,,,,,,Genomic DNA of mulidrug-resistant isolates of Achromobacter xylosoxidans was sequenced to reveal genes associated with multiple antibiotic resistance and relevant mechanisms.,,,,,,,,,diseased,,,,,,,,,,,,,99.53,1.4,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,85698.242,Achromobacter xylosoxidans strain GN008 strain not applicable,not applicable,Achromobacter xylosoxidans,Achromobacter,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13961775,85698,,,,,,,,2020-06-05T00:00:00Z,32366575,PRJNA604252,GCA_013282255.1,CP053618,,Medical College of Wisconsin,PacBio RSII,500x,Celera Assembler v. Canu v1.6,1,0,1,6608203,67.608986,6159,6021,cystic fibrosis lung sputum,,2010-06-29,USA,USA: Wisconsin,,,,,,,,,,,,,,,,,Sequencing clinical isolates of A. xylosoxidans for the purpose of determining pathogenic determinants,sample_type:Mixed Culture,,,,,,,,,,,,,,,,,,,,,99.53,0.47,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,85698.243,Achromobacter xylosoxidans strain GN050 strain not applicable,not applicable,Achromobacter xylosoxidans,Achromobacter,Alcaligenaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13961776,85698,,,,,,,,2020-06-05T00:00:00Z,32366575,PRJNA604252,GCA_013282235.1,CP053617,,Medical College of Wisconsin,PacBio RSII,500x,Celera Assembler v. Canu v1.6,1,0,1,6452474,67.72043,5966,5828,ear effusion,,2010-07-12,USA,USA: Wisconsin,,,,,,,,,,,,,,,,,Sequencing clinical isolates of A. xylosoxidans for the purpose of determining pathogenic determinants,sample_type:Mixed Culture,,,,,,,,,,,,,,,,,,,,,99.53,0.47,Miscellaneous or Unspecified Infections,,Ear,Miscellaneous or Unspecified Infections- HP,860.10,Fusobacterium periodonticum strain KCOM 1283,KCOM 1283,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956182,860,,,,,,KCOM:1283,,2017-11-13T00:00:00Z,,PRJNA416417,GCA_002763595.1,CP024698,,Korean Collection for Oral Microbiology,PacBio,260.3x,RS HGAP v. 3.0,1,,1,2222370,28.2,2168,2132,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,periodontitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1283,collected_by:Korean Collection for Oral Microbiology,,,,,,,periodontitis,,,,,,,,,,,,,,100,0.9,Oral and Dental Diseases,Periodontal Diseases,Oral,Oral and Dental Diseases-Periodontal Diseases NHP,860.11,Fusobacterium periodonticum strain KCOM 1261,KCOM 1261,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956185,860,,,,,,KCOM:1261,,2017-11-13T00:00:00Z,,PRJNA416420,GCA_002763625.1,CP024699,,Korean Collection for Oral Microbiology,PacBio,280.0x,RS HGAP v. 3.0,1,,1,2372880,28.04,2282,2256,tongue,,2005-03-01,South Korea,South Korea: Gwangju,,,,normal,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1261,collected_by:Korean Collection for Oral Microbiology,,,,,,,normal,,,,,,,,,,,,,,100,0,,,Oral,- HP,860.12,Fusobacterium periodonticum strain KCOM 1263,KCOM 1263,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956207,860,,,,,,KCOM:1263,,2017-11-13T00:00:00Z,,PRJNA416422,GCA_002763695.1,CP024700,,Korean Collection for Oral Microbiology,PacBio,433.5x,RS HGAP v. 3.0,1,,1,2651118,27.96,2760,2694,subgingival dental plaque,,2005-03-01,South Korea,South Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1263,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,1.1,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,860.13,Fusobacterium periodonticum strain KCOM 1277,KCOM 1277,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956209,860,,,,,,KCOM:1277,,2017-11-13T00:00:00Z,,PRJNA416424,GCA_002763735.1,CP024701,,Korean Collection for Oral Microbiology,PacBio,433.9x,RS HGAP v. 3.0,1,,1,2324076,28.07,2334,2303,subgingival dental plaque,,2005-03-01,South Korea,South Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1277,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,0,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,860.14,Fusobacterium periodonticum strain KCOM 1282,KCOM 1282,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956210,860,,,,,,KCOM:1282,,2017-11-13T00:00:00Z,,PRJNA416425,GCA_002763775.1,CP024702,,Korean Collection for Oral Microbiology,PacBio,465.0x,RS HGAP v. 3.0,1,,1,2216236,28.31,2150,2116,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1282,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,0.9,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,860.15,Fusobacterium periodonticum strain KCOM 2305,KCOM 2305,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956241,860,,,,,,KCOM:2305,,2017-11-13T00:00:00Z,,PRJNA416427,GCA_002763815.1,CP024703,,Korean Collection for Oral Microbiology,PacBio,337.5x,RS HGAP v. 3.0,1,,1,2273832,28.14,2229,2199,subgingival dental plaque,,2005-03-01,Korea,Korea: Gwangju,,,,gingivitis,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 2305,collected_by:Korean Collection for Oral Microbiology,,,,,,,gingivitis,,,,,,,,,,,,,,100,0.5,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis NHP,860.16,Fusobacterium periodonticum strain KCOM 2555,KCOM 2555,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956248,860,,,,,,KCOM:2555,,2017-11-13T00:00:00Z,,PRJNA416428,GCA_002763875.1,CP024704,,Korean Collection for Oral Microbiology,PacBio,441.6x,RS HGAP v. 3.0,1,,1,2477385,28.06,2432,2389,dental plaque,,2005-03-01,South Korea,South Korea: Gwangju,,,,normal,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 2555,collected_by:Korean Collection for Oral Microbiology,,,,,,,normal,,,,,,,,,,,,,,100,0.2,,,Oral,- NHP,860.17,Fusobacterium periodonticum strain KCOM 1262,KCOM 1262,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956033,860,,,,,,KCOM:1262,,2017-11-13T00:00:00Z,,PRJNA416413,GCA_002763915.1,CP024731,,Korean Collection for Oral Microbiology,PacBio,372.6x,RS HGAP v. 3.0,1,,1,2643576,27.98,2748,2700,tongue,,2005-03-01,South Korea,South Korea: Gwangju,,,,normal,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 1262,collected_by:Korean Collection for Oral Microbiology,,,,,,,normal,,,,,,,,,,,,,,100,1.1,,,Oral,- NHP,860.18,Fusobacterium periodonticum strain KCOM 2653,KCOM 2653,Fusobacterium periodonticum,Fusobacterium,Fusobacteriaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN07956258,860,,,,,,KCOM:2653,,2017-11-13T00:00:00Z,,PRJNA416430,GCA_002763925.1,CP024705,,Korean Collection for Oral Microbiology,PacBio,408.6x,RS HGAP v. 3.0,1,,1,2291059,28.21,2256,2212,tongue,,2005-03-01,South Korea,South Korea: Gwangju,,,,normal,,,,,,,,,,,,,Genome sequencing of Fusobacterium periodonticum KCOM 2653,collected_by:Korean Collection for Oral Microbiology,,,,,,,normal,,,,,,,,,,,,,,100,0,,,Oral,- HP,867914.5,Staphylococcus aureus LAC,LAC,Staphylococcus aureus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN15239172,867914,,,,MLST.Staphylococcus_aureus.8,,,,2020-11-13T00:00:00Z,,PRJNA639565,GCA_015475575.1,"CP055225,CP055226",,University of Arkansas for Medical Sciences,Illumina; Oxford Nanopore MiniION,1129.0x,Unicycler v. v0.4.4,1,1,2,2877525,32.7798,2837,2803,not applicable,,,,,,,,,,,Susceptible;Resistant,Computational Prediction,,,,,,,,,"The genome sequence presented here was generated using the USA300 LAC strain used by Dr Anthony R. Richardson at the University of Pittsburgh to generate a TnSeq library (Grosser et al., PLOS Pathogens, 2018). This library, and the parent strain, were obtained by the laboratory of Dr Mark S. Smeltzer at the University of Arkansas for Medical Sciences (UAMS). The genome of the parent strain was subsequently sequenced, assembled and polished at UAMS by Dr Piroon Jenjaroenpun and Ms. Duah Alkam.",sample_type:isolate,,,,,,,,,,,,,,,,,,,,,99.51,0.08,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,87883.148,Burkholderia multivorans strain FDAARGOS_246,FDAARGOS_246,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05004755,87883,,,,MLST.Burkholderia_cepacia_complex.650,,FDA:FDAARGOS_246,,2018-03-27T00:00:00Z,,PRJNA231221,GCA_003019965.1,"CP020397,CP020398,CP020399",,US Food and Drug Administration,PacBio; Illumina,12.0306940149552x,HGAP v. 3,2,1,3,6322859,67.242035,6323,5952,cystic fibrosis patient,,2013,,,,,,Infection with Burkholderia multivorans,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:USAMRIID < LMG Belgium < S. Lauwers,,,,,,,Infection with Burkholderia multivorans,Missing,Missing,Missing,Missing,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,87883.366,Burkholderia multivorans strain P1Bm2015,P1Bm2015,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876243,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165195.1,"CP048445,CP048446,CP048447",,KU Leuven,Hybrid nanopore and illumina,81x,Unicycler v. v0.4.7,3,0,3,6499180,67.24948,6381,5833,sputum,,2015-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.367,Burkholderia multivorans strain P2Bm2011a,P2Bm2011a,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876244,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165175.1,"CP048441,CP048442,CP048443,CP048444",,KU Leuven,Hybrid nanopore and illumina,63x,Unicycler v. v0.4.7,3,1,4,6705051,67.03837,6557,5982,sputum,,2011-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.9,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.368,Burkholderia multivorans strain P1Bm2011b,P1Bm2011b,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876238,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165515.1,"CP048454,CP048455,CP048456",,KU Leuven,Hybrid nanopore and illumina,81x,Unicycler v. v0.4.7,3,0,3,6496880,67.25169,6372,5829,sputum,,2011-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.369,Burkholderia multivorans strain P1Bm2009,P1Bm2009,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876236,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165555.1,"CP048460,CP048461,CP048462,CP048463",,KU Leuven,Hybrid nanopore and illumina,77x,Unicycler v. v0.4.7,3,1,4,6569085,67.186005,6480,5917,sputum,,2009-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.370,Burkholderia multivorans strain P1Bm2011a,P1Bm2011a,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876237,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165535.1,"CP048457,CP048458,CP048459",,KU Leuven,Hybrid nanopore and illumina,84x,Unicycler v. v0.4.7,3,0,3,6498339,67.2506,6394,5830,sputum,,2011-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,99.46,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.371,Burkholderia multivorans strain P1Bm2012b,P1Bm2012b,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876240,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165495.1,"CP048451,CP048452,CP048453",,KU Leuven,Hybrid nanopore and illumina,82x,Unicycler v. v0.4.7,3,0,3,6495911,67.25221,6370,5828,sputum,,2012-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.372,Burkholderia multivorans strain P1Bm2014,P1Bm2014,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876242,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-04T00:00:00Z,,PRJNA601875,GCA_017165475.1,"CP048448,CP048449,CP048450",,KU Leuven,Hybrid nanopore and illumina,83x,Unicycler v. v0.4.7,3,0,3,6497010,67.25015,6372,5831,sputum,,2014-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.376,Burkholderia multivorans strain P1Bm2013,P1Bm2013,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876241,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-08T00:00:00Z,,PRJNA601875,GCA_017301875.1,JAAEEE000000000,,KU Leuven,Nanopore; Illumina,82x,Unicycler v. 0.4.7,10,0,10,6495877,67.25129,6390,5814,sputum,,2013-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.377,Burkholderia multivorans strain P1Bm2012a,P1Bm2012a,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876239,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-08T00:00:00Z,,PRJNA601875,GCA_017301895.1,JAAEEF000000000,,KU Leuven,Nanopore; Illumina,79x,Unicycler v. 0.4.7,6,0,6,6496445,67.25126,6384,5812,sputum,,2012-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,87883.378,Burkholderia multivorans strain P3Bm2015,P3Bm2015,Burkholderia multivorans,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN13876246,87883,,,,MLST.Burkholderia_cepacia_complex.742,,,,2021-03-08T00:00:00Z,,PRJNA601875,GCA_017301905.1,JAAEEC000000000,,KU Leuven,Nanopore; Illumina,68x,Unicycler v. 0.4.7,4,1,5,6725592,67.0604,6663,6048,sputum,,2015-01-01,Belgium,Belgium,,,,Cystic fibrosis,,,,,,,,,,,,,"In this study, we looked at the genomes of multiple isolates of an epidemic Burkholderia multivorans strain with sequence type ST-742.",collected_by:LMG,,,,,,,Cystic fibrosis,,,,,,,,,,,,,,100,0.04,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,881260.24,Enterobacter bugandensis strain 1367,1367,Enterobacter bugandensis,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11349925,881260,,,,,,,,2019-04-23T00:00:00Z,,PRJNA531146,GCA_004804395.1,CP039452,,Justus-Liebig University,Illumina NextSeq; Oxford Nanopore MiniION,391.0x,Unicycler v. v0.4.8-beta,1,,1,4750456,55.971237,4568,4471,blood,,2011-01-01,Germany,Germany: North Rhine-Westphalia,,,,blood-stream infection,,,,,,,,,,,,,Enterobacter bugandensis from Germany,collected_by:R-Net,,,,,,,blood-stream infection,,,,,,,,,,,,,,99.97,0.04,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections HP,881260.9,Enterobacter bugandensis strain EB-247,EB-247,Enterobacter bugandensis,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104711314,881260,,,,MLST.Enterobacter_cloacae.495,,DSM 29888T,,2018-03-31T00:00:00Z,,PRJEB11452,GCA_900324475.1,LT992502,,JUSTUS LIEBIG UNIVERSITY,,,,1,,1,4717613,55.99728,4435,,blood,"isolated from an outbreak in a neonatal unit, Tanzania, could not be assigned to any known species and was further investigated",2010-01-05,Tanzania,Tanzania,,,,,,host_health_state:diseased,,,,,,,,,,,"An ‘Enterobacter-like’ bacterium (EB-247T) isolated from an outbreak in a neonatal unit, Tanzania, could not be assigned to any known species and was further investigated. We used fermentation characteristics, biochemical assays and fatty acid profiles for taxonomic analysis of EB-247T, and supplemented this with information derived from sub-genome- and genome- based analysis. Phenotypic and morphological tests revealed that the isolate is a Gram-negative, rod-shaped, highly motile and facultatively anaerobic. Whole cell analysis showed that most of the fatty acids, with the exception of C17:0 Cyclo and C16:1ω6c/C16:1ω7c that were present in altered ratios, were typical for the Enterobacter species. We performed whole genome sequencing of EB-247T to perform subgenome-based phylogenetic analysis i.e. 16S rRNA, multi-locus sequence analysis (MLSA) and whole-genome-based taxonomic analysis. The draft genome of EB-247T was approximately 4.9 Mb in size with a G+C content of 56.0%. The 16S rDNA sequence of EB-247T showed > 97% similarity to all the Enterobacter species, while MLSA clustered EB-247T within Enterobacter but classified it as a separate species. Analysis using in silico DNA-DNA hybridization showed it had less than 70% sequence similarity with other Enterobacter species. The average nucleotide identity of EB-247T exhibited less than 95% sequence similarity to all the compared Enterobacter species supporting it’s a new species. From these results, we conclude that EB-247T possesses sufficient characteristics that are different from known Enterobacter species, and should be considered to be a novel species. The name Enterobacter bugandensis sp. nov. is proposed for isolate EB-247T (=DSM 29888T=NCCB 100573T).",,,,,,,,,diseased,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,88431.1235,Dorea longicatena strain DSM 13814,DSM 13814,Dorea longicatena,Dorea,Lachnospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN20222689,88431,,,,,,DSM:13814,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025150085.1,CP102280,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,2919963,41.490116,2846,2727,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:DSMZ,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.42,0,,,Other,- HP,888061.5,Desulfomicrobium orale DSM 12838,DSM 12838,Desulfomicrobium orale,Desulfomicrobium,Desulfomicrobiaceae,Desulfovibrionales,Desulfovibrionia,Thermodesulfobacteriota,SAMN04435861,888061,,,,,,DSM:12838,,2016-02-18T00:00:00Z,,PRJNA282954,GCA_001553625.1,CP014230,,The Forsyth Institute,PacBio,313x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2783374,58.925606,2883,2551,subgingival dental plaque,,,Netherlands,Netherlands,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,unknown,,,,periodontitis,,,,,,,,,Human oral cavity,,,,98.51,1.19,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,888727.210,Eubacterium sulci ATCC 35585,ATCC 35585,[Eubacterium] sulci,-,Eubacteriales Family XIII. Incertae Sedis,Eubacteriales,Clostridia,Bacillota,SAMN03704030,888727,,,,,,ATCC:35585,,2015-08-07T00:00:00Z,,PRJNA282954,GCA_001189495.1,CP012068,,The Forsyth Institute,PacBio,382x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,1739380,39.920433,1619,1475,"subgingival plaque, gingival sulcus",,,USA,"USA: Blacksberg, VA",,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,Gingivitis or periodontitis,,,,,,,,,Human oral cavity,,,,100,0.71,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,89586.3,Candidatus Neoehrlichia mikurensis strain SE20,SE20,Neoehrlichia mikurensis,Candidatus Neoehrlichia,Anaplasmataceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN15143484,89586,,,,,,,,2021-07-09T00:00:00Z,,PRJNA630882,GCA_019186745.1,CP054597,,University of Gothenburg,Illumina HiSeq,4800.0x,Supernova assembler v. 22.0,1,0,1,1112315,26.838503,919,859,blood,,2019-02-20,Sweden,Sweden:Kungalv,,,,,,,,,,,,,,,,,Whole genome sequencing of a tick-borne human pathogen directly from a clinical sample,sample_type:whole organsim,,,,,,,,,,,,,,,,,,,,,93.59,1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,89586.4,Candidatus Neoehrlichia mikurensis strain SE26,SE26,Neoehrlichia mikurensis,Candidatus Neoehrlichia,Anaplasmataceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN15921915,89586,,,,,,,,2021-07-09T00:00:00Z,,PRJNA630882,GCA_019186765.1,CP060793,,University of Gothenburg,Illumina HiSeq,4000.0x,Supernova assembler v. 2.0,1,0,1,1112271,26.837227,915,860,blood,,2018-04-17,Sweden,Sweden: Kungalv,,,,,,,,,,,,,,,,,Whole genome sequencing of a tick-borne human pathogen directly from a clinical sample,sample_type:Blood,,,,,,,,,,,,,,,,,,,,,93.59,1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,89586.5,Candidatus Neoehrlichia mikurensis strain SE24,SE24,Neoehrlichia mikurensis,Candidatus Neoehrlichia,Anaplasmataceae,Rickettsiales,Alphaproteobacteria,Pseudomonadota,SAMN14847427,89586,,,,,,,,2021-07-09T00:00:00Z,,PRJNA630882,GCA_019186785.1,CP066557,,University of Gothenburg,Illumina HiSeq; 10X Chromium,4890.0x,10X Assembler supernova v. 2.0,1,0,1,1112301,26.8383,922,860,blood,,2017-10-10,Sweden,Sweden: Eskilstuna,,,,,,,,,,,,,,,,,Whole genome sequencing of a tick-borne human pathogen directly from a clinical sample,sample_type:Bacteria,,,,,,,,,,,,,,,,,,,,,93.59,1,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,90105.187,Salmonella enterica subsp. enterica serovar Saintpaul strain AUSMDU00010531,AUSMDU00010531,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191645,90105,Saintpaul,,,MLST.Salmonella_enterica.50,mlst:ST50,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664655.1,CP045954,,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,105x,de novo,1,0,1,4731476,52.266735,4714,4413,missing,,2016,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90105.254,Salmonella enterica subsp. enterica serovar Saintpaul strain S25,S25,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22488162,90105,Saintpaul,,,MLST.Salmonella_enterica.27,,,,2021-11-01T00:00:00Z,,PRJNA773584,GCA_020691705.1,"CP085696,CP085698,CP085697",,Guangzhou Medical University,Oxford Nanopore PromethION; Illumina,110.0x,SPAdes v. 3.13.1; unicycler v. 0.4.8,1,2,3,5103835,51.877285,5244,4907,stool,"isolated from a tertiary hospital in Guangzhou, which contains an IncHI2 plasmid carrying CTX-M-55 gene",2014-06-26,China,"China: Guangzhou, Guangdong",,,,Salmonella gastroenteritis,,,,,,,,,,,,,"S25 is a Salmonella Saintpaul isolated from a tertiary hospital in Guangzhou, which contains an IncHI2 plasmid carrying CTX-M-55 gene.",collected_by:a patient in a tertiary hospital,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90105.85,Salmonella enterica subsp. enterica serovar Saintpaul strain CFSAN004173,CFSAN004173,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05915913,90105,Saintpaul,,,MLST.Salmonella_enterica.50,,,,2017-01-18T00:00:00Z,,PRJNA186035,GCA_001953675.1,"CP019204,CP019205",,Center for Food Safety and Applied Nutrition,PacBio,157,HGAP v. v. 3.0,1,1,2,4858999,52.17,4999,4773,stool,,2013-02-15,USA,USA:CA,,,,,,,,,,,,,,,,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,collected_by:CA,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90105.86,Salmonella enterica subsp. enterica serovar Saintpaul strain CFSAN004174,CFSAN004174,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN05915912,90105,Saintpaul,,,MLST.Salmonella_enterica.50,,,,2017-01-18T00:00:00Z,,PRJNA186035,GCA_001953695.1,"CP019206,CP019207",,Center for Food Safety and Applied Nutrition,PacBio,140,HGAP v. v. 3.0,1,1,2,4859001,52.17,5006,4774,stool,,2013-02-25,USA,USA:CA,,,,,,,,,,,,,,,,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,collected_by:CA,,,,,,,missing,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90370.2206,Salmonella enterica subsp. enterica serovar Typhi strain BL60006,BL60006,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104109193,90370,Typhi,,,,,,,2017-06-03T00:00:00Z,,PRJEB21155,GCA_900185485.1,"LT882486,LT882487",,WTSI,,,,1,1,2,4812943,52.04,5028,,blood,,2017,,,,,,,,host_health_state:diseased,,,,,,,,,,,Outbreak of Ceftriaxone resistant H58 Salmonella Typhi in Pakistan,,,,,,,,,diseased,,,,,,,,,,,,,98.9,0.3,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,90370.2473,Salmonella enterica subsp. enterica serovar Typhi strain 311189_221186,311189_221186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320528,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003716995.1,"CP029923,CP029924",,LNCC,Illumina-HiSeq 4000,111.0x,Newbler v. 3,1,1,2,5000268,51.85886,5280,4436,missing,,1999,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2474,Salmonella enterica subsp. enterica serovar Typhi strain 311189_219186,311189_219186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320526,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717035.1,"CP029911,CP029910",,LNCC,Illumina-HiSeq 4000,114.0x,Newbler v. 3,1,1,2,5001453,51.85603,5281,4429,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2475,Salmonella enterica subsp. enterica serovar Typhi strain 311189_220186,311189_220186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320527,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717015.1,"CP029886,CP029887",,LNCC,Illumina-HiSeq 4000,116.0x,Newbler v. 3,1,1,2,5000436,51.8589,5272,4427,missing,,2005,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2476,Salmonella enterica subsp. enterica serovar Typhi strain 311189_217103,311189_217103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320523,90370,Typhi,,,MLST.Salmonella_enterica.2209,mlst:2209,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717055.1,CP029927,,LNCC,Illumina-HiSeq 4000,95.0x,Newbler v. 3,1,,1,4778473,52.106415,4975,4195,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2477,Salmonella enterica subsp. enterica serovar Typhi strain 311189_216103,311189_216103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320522,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717075.1,"CP029928,CP029929",,LNCC,Illumina-HiSeq 4000,131.0x,Newbler v. 3,1,1,2,4906132,52.0838,5153,4356,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2478,Salmonella enterica subsp. enterica serovar Typhi strain 311189_215186,311189_215186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320521,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717095.1,"CP029930,CP029931",,LNCC,Illumina-HiSeq 4000,122.0x,Newbler v. 3,1,1,2,4999523,51.857468,5277,4435,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2479,Salmonella enterica subsp. enterica serovar Typhi strain 311189_214186,311189_214186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320520,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717115.1,"CP029933,CP029934",,LNCC,Illumina-HiSeq 4000,120.0x,Newbler v. 3,1,1,2,4999937,51.860615,5276,4437,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2480,Salmonella enterica subsp. enterica serovar Typhi strain 311189_213186,311189_213186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320519,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717135.1,"CP029936,CP029935",,LNCC,Illumina-HiSeq 4000,130.0x,Newbler v. 3,1,1,2,4999942,51.8577,5272,4428,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2481,Salmonella enterica subsp. enterica serovar Typhi strain 311189_212186,311189_212186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320518,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717215.1,"CP029944,CP029943",,LNCC,Illumina-HiSeq 4000,100.0x,Newbler v. 3,1,1,2,5001887,51.85611,5279,4442,missing,,1999,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2482,Salmonella enterica subsp. enterica serovar Typhi strain 311189_211186,311189_211186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320517,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717285.1,CP029945,,LNCC,Illumina-HiSeq 4000,107.0x,Newbler v. 3,1,,1,4786194,52.04384,4986,4214,missing,,1999,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2483,Salmonella enterica subsp. enterica serovar Typhi strain 311189_210186,311189_210186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320516,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717355.1,"CP029946,CP029947",,LNCC,Illumina-HiSeq 4000,2.9x,Newbler v. 3,1,1,2,5004332,51.852436,5282,4441,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2484,Salmonella enterica subsp. enterica serovar Typhi strain 311189_208186,311189_208186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320514,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717395.1,"CP029949,CP029948",,LNCC,Illumina-HiSeq 4000,137.0x,Newbler v. 3,1,1,2,5000621,51.85722,5271,4429,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2485,Salmonella enterica subsp. enterica serovar Typhi strain 311189_208103,311189_208103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320513,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717435.1,CP029932,,LNCC,Illumina-HiSeq 4000,106.0x,Newbler v. 3,1,,1,4783092,52.05085,4981,4210,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2486,Salmonella enterica subsp. enterica serovar Typhi strain 311189_207186,311189_207186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320512,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717455.1,"CP029938,CP029937",,LNCC,Illumina-HiSeq 4000,137.0x,Newbler v. 3,1,1,2,5001425,51.85482,5279,4441,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2487,Salmonella enterica subsp. enterica serovar Typhi strain 311189_206186,311189_206186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320511,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717475.1,"CP029940,CP029939",,LNCC,Illumina-HiSeq 4000,102.0x,Newbler v. 3,1,1,2,5002279,51.859264,5275,4444,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2488,Salmonella enterica subsp. enterica serovar Typhi strain 311189_205186,311189_205186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320510,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717515.1,"CP029950,CP029951",,LNCC,Illumina-HiSeq 4000,113.0x,Newbler v. 3,1,1,2,4928027,52.093525,5183,4377,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2489,Salmonella enterica subsp. enterica serovar Typhi strain 311189_204186,311189_204186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320509,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717535.1,"CP029954,CP029953",,LNCC,Illumina-HiSeq 4000,110.0x,Newbler v. 3,1,1,2,5002162,51.85386,5280,4429,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2490,Salmonella enterica subsp. enterica serovar Typhi strain 311189_202186,311189_202186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320507,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717575.1,"CP029956,CP029955",,LNCC,Illumina-HiSeq 4000,28.0x,Newbler v. 3,1,1,2,5017285,51.921967,5294,4468,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2491,Salmonella enterica subsp. enterica serovar Typhi strain 343077_260153,343077_260153,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320564,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717615.1,"CP029861,CP029860",,LNCC,Illumina-HiSeq 4000,138.0x,Newbler v. 3,1,1,2,4875582,52.03961,5098,4291,missing,,,Bangladesh,Dhaka,,Female,9 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2492,Salmonella enterica subsp. enterica serovar Typhi strain 343077_228157,343077_228157,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320562,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717655.1,"CP029864,CP029865",,LNCC,Illumina-HiSeq 4000,113.0x,Newbler v. 3,1,1,2,4914114,52.05311,5165,4366,missing,,2012,Bangladesh,Dhaka,,Female,28 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2493,Salmonella enterica subsp. enterica serovar Typhi strain 343077_255118,343077_255118,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320563,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717635.1,CP029907,,LNCC,Illumina-HiSeq 4000,143.0x,Newbler v. 3,1,,1,4774500,52.09915,4987,4219,missing,,2013,Bangladesh,Dhaka,,Female,6 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2494,Salmonella enterica subsp. enterica serovar Typhi strain 343077_228140,343077_228140,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320561,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717675.1,"CP029866,CP029867",,LNCC,Illumina-HiSeq 4000,90.0x,Newbler v. 3,1,1,2,4897299,52.079605,5138,4358,missing,,2012,Bangladesh,Dhaka,,Male,56 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2495,Salmonella enterica subsp. enterica serovar Typhi strain 343077_215174,343077_215174,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320560,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717695.1,"CP029868,CP029869",,LNCC,Illumina-HiSeq 4000,109.0x,Newbler v. 3,1,1,2,4877556,52.040447,5098,4293,missing,,2011,Bangladesh,Dhaka,,Male,69 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2496,Salmonella enterica subsp. enterica serovar Typhi strain 343077_214162,343077_214162,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,ERS2579438,90370,Typhi,,,1,,,,2018-11-07T00:00:00Z,30425150,PRJNA474465,GCA_003717715.1,CP029862,,LNCC,Illumina HiSeq 4000,107.0x,Newbler v. 3,1,,1,4814028,52.035946,5038,4247,,,2010,Bangladesh,Dhaka,,Female,83,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,typhoid fever,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospital,,,,,,,,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2497,Salmonella enterica subsp. enterica serovar Typhi strain 343077_214135,343077_214135,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320558,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717735.1,"CP029872,CP029871",,LNCC,Illumina-HiSeq 4000,102.0x,Newbler v. 3,1,1,2,4875052,52.04002,5096,4291,missing,,2010,Bangladesh,Dhaka,,Male,60 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2498,Salmonella enterica subsp. enterica serovar Typhi strain 343077_212159,343077_212159,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320556,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717775.1,CP029870,,LNCC,Illumina-HiSeq 4000,106.0x,Newbler v. 3,1,,1,4795465,52.096283,5010,4231,missing,,2012,Bangladesh,Dhaka,,Male,27 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2499,Salmonella enterica subsp. enterica serovar Typhi strain 343077_213147,343077_213147,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320557,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717755.1,"CP029897,CP029898",,LNCC,Illumina-HiSeq 4000,120.0x,Newbler v. 3,1,1,2,5004298,52.0282,5281,4482,missing,,2011,Bangladesh,Dhaka,,Female,60 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2500,Salmonella enterica subsp. enterica serovar Typhi strain 343077_212138,343077_212138,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320555,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717795.1,CP029919,,LNCC,Illumina-HiSeq 4000,96.0x,Newbler v. 3,1,,1,4774558,52.099274,4989,4219,missing,,2012,Bangladesh,Dhaka,,Female,66 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2501,Salmonella enterica subsp. enterica serovar Typhi strain 343077_211171,343077_211171,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320554,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717815.1,"CP029873,CP029874",,LNCC,Illumina-HiSeq 4000,103.0x,Newbler v. 3,1,1,2,4874717,52.040253,5100,4292,missing,,2012,Bangladesh,Dhaka,,Female,34 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2502,Salmonella enterica subsp. enterica serovar Typhi strain 343076_294172,343076_294172,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320553,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717835.1,"CP029888,CP029889",,LNCC,Illumina-HiSeq 4000,131.0x,Newbler v. 3,1,1,2,4915877,52.049065,5158,4362,missing,,2009,Bangladesh,Dhaka,,Male,49 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2503,Salmonella enterica subsp. enterica serovar Typhi strain 343076_269157,343076_269157,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320552,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717855.1,CP029881,,LNCC,Illumina-HiSeq 4000,119.0x,Newbler v. 3,1,,1,4791108,52.113186,4993,4232,missing,,2009,Bangladesh,Dhaka,,Male,84 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2504,Salmonella enterica subsp. enterica serovar Typhi strain 343076_253155,343076_253155,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320551,90370,Typhi,,,,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717875.1,"CP029890,CP029891",,LNCC,Illumina-HiSeq 4000,124.0x,Newbler v. 3,1,1,2,4898293,52.080265,5140,4355,missing,,2013,Bangladesh,Dhaka,,Male,72 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2505,Salmonella enterica subsp. enterica serovar Typhi strain 343076_252143,343076_252143,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320550,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717895.1,"CP029892,CP029893",,LNCC,Illumina-HiSeq 4000,129.0x,Newbler v. 3,1,1,2,4914991,52.048622,5156,4357,missing,,2012,Bangladesh,Dhaka,,Male,204 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2506,Salmonella enterica subsp. enterica serovar Typhi strain 343076_248190,343076_248190,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320548,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717935.1,CP029882,,LNCC,Illumina-HiSeq 4000,122.0x,Newbler v. 3,1,,1,4773823,52.097908,4988,4221,missing,,2007,Bangladesh,Dhaka,,Female,50 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2507,Salmonella enterica subsp. enterica serovar Typhi strain 343076_249107,343076_249107,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320549,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717915.1,"CP029913,CP029912",,LNCC,Illumina-HiSeq 4000,143.0x,Newbler v. 3,1,1,2,4875739,52.04052,5099,4291,missing,,2013,Bangladesh,Dhaka,,Male,54 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2508,Salmonella enterica subsp. enterica serovar Typhi strain 343076_241106,343076_241106,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320547,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717955.1,CP029899,,LNCC,Illumina-HiSeq 4000,115.0x,Newbler v. 3,1,,1,4775702,52.098225,4990,4219,missing,,2009,Bangladesh,Dhaka,,Female,13 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2509,Salmonella enterica subsp. enterica serovar Typhi strain 343076_232188,343076_232188,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320546,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717975.1,"CP029900,CP029901",,LNCC,Illumina-HiSeq 4000,116.0x,Newbler v. 3,1,1,2,4907327,52.042793,5140,4356,missing,,2009,Bangladesh,Dhaka,,Male,24 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2510,Salmonella enterica subsp. enterica serovar Typhi strain 343076_227128,343076_227128,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320545,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003717995.1,"CP029875,CP029876",,LNCC,Illumina-HiSeq 4000,102.0x,Newbler v. 3,1,1,2,4906905,52.042988,5145,4348,missing,,2009,Bangladesh,Dhaka,,Female,42 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2511,Salmonella enterica subsp. enterica serovar Typhi strain 343076_217103,343076_217103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320544,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718015.1,CP029914,,LNCC,Illumina-HiSeq 4000,83.0x,Newbler v. 3,1,,1,4775784,52.098167,4986,4219,missing,,2008,Bangladesh,Dhaka,,Male,48 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2512,Salmonella enterica subsp. enterica serovar Typhi strain 343076_202113,343076_202113,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320543,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718035.1,"CP029915,CP029916",,LNCC,Illumina-HiSeq 4000,88.0x,Newbler v. 3,1,1,2,4905975,52.04356,5141,4348,missing,,2008,Bangladesh,Dhaka,,Male,168 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2513,Salmonella enterica subsp. enterica serovar Typhi strain 311189_282186,311189_282186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320541,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718075.1,"CP029920,CP029921",,LNCC,Illumina-HiSeq 4000,96.0x,Newbler v. 3,1,1,2,4906662,52.04308,5144,4347,missing,,2008,Bangladesh,Dhaka,,Male,192 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2514,Salmonella enterica subsp. enterica serovar Typhi strain 311189_291186,311189_291186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320542,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718055.1,CP029894,,LNCC,Illumina-HiSeq 4000,116.0x,Newbler v. 3,1,,1,4806999,52.080166,5020,4239,missing,,2008,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2515,Salmonella enterica subsp. enterica serovar Typhi strain 311189_269186,311189_269186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320540,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718095.1,CP029922,,LNCC,Illumina-HiSeq 4000,111.0x,Newbler v. 3,1,,1,4782083,52.049934,4981,4200,missing,,2008,Bangladesh,Dhaka,,Male,108 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2516,Salmonella enterica subsp. enterica serovar Typhi strain 311189_268186,311189_268186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320539,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718115.1,"CP029883,CP029884",,LNCC,Illumina-HiSeq 4000,125.0x,Newbler v. 3,1,1,2,4914387,52.047955,5153,4364,missing,,2007,Bangladesh,Dhaka,,Male,54 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2517,Salmonella enterica subsp. enterica serovar Typhi strain 311189_268103,311189_268103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320538,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718135.1,"CP029902,CP029903",,LNCC,Illumina-HiSeq 4000,128.0x,Newbler v. 3,1,1,2,4892630,52.069275,5121,4335,missing,,2007,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2518,Salmonella enterica subsp. enterica serovar Typhi strain 311189_256186,311189_256186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320537,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718155.1,CP029917,,LNCC,Illumina-HiSeq 4000,138.0x,Newbler v. 3,1,,1,4800376,52.07359,5010,4222,missing,,2007,Bangladesh,Dhaka,,Female,48 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2519,Salmonella enterica subsp. enterica serovar Typhi strain 311189_255186,311189_255186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320536,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718175.1,CP029885,,LNCC,Illumina-HiSeq 4000,102.0x,Newbler v. 3,1,,1,4808675,52.080544,5022,4238,missing,,,Bangladesh,Dhaka,,Female,168 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2520,Salmonella enterica subsp. enterica serovar Typhi strain 311189_252186,311189_252186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320535,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718195.1,"CP029896,CP029895",,LNCC,Illumina-HiSeq 4000,112.0x,Newbler v. 3,1,1,2,4999085,51.86209,5276,4427,missing,,2006,Bangladesh,Dhaka,,Male,360 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2521,Salmonella enterica subsp. enterica serovar Typhi strain 311189_232103,311189_232103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320533,90370,Typhi,,,MLST.Salmonella_enterica.2209,mlst:2209,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718235.1,CP029918,,LNCC,Illumina-HiSeq 4000,115.0x,Newbler v. 3,1,,1,4778368,52.10532,4982,4194,missing,,2000,Bangladesh,Dhaka,,,,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2522,Salmonella enterica subsp. enterica serovar Typhi strain 311189_231186,311189_231186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320532,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718255.1,"CP029904,CP029905",,LNCC,Illumina-HiSeq 4000,122.0x,Newbler v. 3,1,1,2,4914136,52.04856,5153,4358,missing,,2006,Bangladesh,Dhaka,,Male,57 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2523,Salmonella enterica subsp. enterica serovar Typhi strain 311189_224186,311189_224186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320531,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718275.1,"CP029878,CP029877",,LNCC,Illumina-HiSeq 4000,161.0x,Newbler v. 3,1,1,2,4999748,51.858234,5281,4438,missing,,2006,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2524,Salmonella enterica subsp. enterica serovar Typhi strain 311189_222186,311189_222186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320529,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718315.1,CP029909,,LNCC,Illumina-HiSeq 4000,113.0x,Newbler v. 3,1,,1,4842715,52.103004,5073,4294,missing,,1999,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2525,Salmonella enterica subsp. enterica serovar Typhi strain 311189_223186,311189_223186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320530,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718295.1,"CP029880,CP029879",,LNCC,Illumina-HiSeq 4000,118.0x,Newbler v. 3,1,1,2,4998358,51.85895,5273,4435,missing,,2005,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2526,Salmonella enterica subsp. enterica serovar Typhi strain 343078_273110,343078_273110,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320578,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718355.1,"CP029846,CP029847",,LNCC,Illumina-HiSeq 4000,139.0x,Newbler v. 3,1,1,2,4907851,52.04015,5144,4351,missing,,,Bangladesh,Dhaka,,Male,32 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2527,Salmonella enterica subsp. enterica serovar Typhi strain 343078_256191,343078_256191,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320577,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718375.1,CP029959,,LNCC,Illumina-HiSeq 4000,111.0x,Newbler v. 3,1,,1,4795890,52.09757,5016,4221,missing,,,Bangladesh,Dhaka,,Female,59 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2528,Salmonella enterica subsp. enterica serovar Typhi strain 343078_251131,343078_251131,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320576,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718395.1,"CP029960,CP029961",,LNCC,Illumina-HiSeq 4000,134.0x,Newbler v. 3,1,1,2,4906452,52.047955,5145,4360,missing,,,Bangladesh,Dhaka,,Female,9 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2529,Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140,343078_228140,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320575,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718415.1,"CP029962,CP029963",,LNCC,Illumina-HiSeq 4000,116.0x,Newbler v. 3,1,1,2,4876601,52.04262,5103,4292,missing,,,Bangladesh,Dhaka,,Male,55 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2530,Salmonella enterica subsp. enterica serovar Typhi strain 343078_223175,343078_223175,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320574,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718435.1,"CP029964,CP029965",,LNCC,Illumina-HiSeq 4000,87.0x,Newbler v. 3,1,1,2,4874555,52.04071,5094,4302,missing,,,Bangladesh,Dhaka,,Female,36 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2531,Salmonella enterica subsp. enterica serovar Typhi strain 343078_211126,343078_211126,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320573,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718455.1,"CP029848,CP029849",,LNCC,Illumina-HiSeq 4000,92.0x,Newbler v. 3,1,1,2,4906454,52.042675,5142,4346,missing,,2012,Bangladesh,Dhaka,,Male,43 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2532,Salmonella enterica subsp. enterica serovar Typhi strain 343078_203125,343078_203125,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320572,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718475.1,"CP029850,CP029851",,LNCC,Illumina-HiSeq 4000,135.0x,Newbler v. 3,1,1,2,4908524,52.04041,5140,4357,missing,,2011,Bangladesh,Dhaka,,Male,52 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2533,Salmonella enterica subsp. enterica serovar Typhi strain 343078_201101,343078_201101,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320571,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718495.1,CP029852,,LNCC,Illumina-HiSeq 4000,74.0x,Newbler v. 3,1,,1,4782235,52.050224,4981,4210,missing,,2011,Bangladesh,Dhaka,,Female,24 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2534,Salmonella enterica subsp. enterica serovar Typhi strain 343077_292148,343077_292148,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320570,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718515.1,CP029855,,LNCC,Illumina-HiSeq 4000,93.0x,Newbler v. 3,1,,1,4800586,52.073895,5014,4222,missing,,2009,Bangladesh,Dhaka,,Female,35 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2535,Salmonella enterica subsp. enterica serovar Typhi strain 343077_286126,343077_286126,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320569,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718535.1,"CP029856,CP029857",,LNCC,Illumina-HiSeq 4000,151.0x,Newbler v. 3,1,1,2,4904334,52.03942,5149,4353,missing,,2009,Bangladesh,Dhaka,,Male,16 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2536,Salmonella enterica subsp. enterica serovar Typhi strain 343077_285138,343077_285138,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320568,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718555.1,"CP029858,CP029859",,LNCC,Illumina-HiSeq 4000,128.0x,Newbler v. 3,1,1,2,4907634,52.046017,5140,4352,missing,,,Bangladesh,Dhaka,,Female,41 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2537,Salmonella enterica subsp. enterica serovar Typhi strain 343077_281186,343077_281186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320567,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718575.1,"CP029853,CP029854",,LNCC,Illumina-HiSeq 4000,159.0x,Newbler v. 3,1,1,2,4872916,52.006683,5137,4327,missing,,2008,Bangladesh,Dhaka,,Female,34 months,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2538,Salmonella enterica subsp. enterica serovar Typhi strain 343077_278127,343077_278127,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320566,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718595.1,CP029863,,LNCC,Illumina-HiSeq 4000,151.0x,Newbler v. 3,1,,1,4807245,52.078957,5017,4230,missing,,2006,Bangladesh,Dhaka,,Male,16 months,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2539,Salmonella enterica subsp. enterica serovar Typhi strain 343077_267164,343077_267164,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320565,90370,Typhi,,,MLST.Salmonella_enterica.2,mlst:2,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718615.1,CP029906,,LNCC,Illumina-HiSeq 4000,119.0x,Newbler v. 3,1,,1,4775386,52.099014,4984,4220,missing,,2013,Bangladesh,Dhaka,,Male,45 months,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Hospitalized,,,,,,,missing,,,,,,,,,,,,,,99.88,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2540,Salmonella enterica subsp. enterica serovar Typhi strain 311189_218186,311189_218186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320525,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718635.1,"CP029925,CP029926",,LNCC,Illumina-HiSeq 4000,106.0x,Newbler v. 3,1,1,2,5003831,51.85089,5279,4441,missing,,2002,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2541,Salmonella enterica subsp. enterica serovar Typhi strain 311189_201186,311189_201186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320506,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003718655.1,"CP029958,CP029957",,LNCC,Illumina-HiSeq 4000,109.0x,Newbler v. 3,1,1,2,5000389,51.857285,5272,4428,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2542,Salmonella enterica subsp. enterica serovar Typhi strain 311189_239103,311189_239103,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320534,90370,Typhi,,,MLST.Salmonella_enterica.2209,mlst:2209,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003719215.1,CP029908,,LNCC,Illumina-HiSeq 4000,107.0x,Newbler v. 3,1,,1,4778864,52.104496,4979,4194,missing,,2006,Bangladesh,Dhaka,,,,,blood,,Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2543,Salmonella enterica subsp. enterica serovar Typhi strain 311189_203186,311189_203186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320508,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003719235.1,"CP029942,CP029941",,LNCC,Illumina-HiSeq 4000,120.0x,Newbler v. 3,1,1,2,5003407,51.85201,5279,4446,missing,,1999,Bangladesh,Dhaka,,,,,blood,,Resistant;Susceptible,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2544,Salmonella enterica subsp. enterica serovar Typhi strain 311189_209186,311189_209186,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09320515,90370,Typhi,,,MLST.Salmonella_enterica.1,mlst:1,,,2018-11-07T00:00:00Z,31253105,PRJNA474465,GCA_003719255.1,CP029952,,LNCC,Illumina-HiSeq 4000,113.0x,Newbler v. 3,1,,1,4782252,52.05071,4981,4201,missing,,2001,Bangladesh,Dhaka,,,,,blood,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Typhoid fever is a endemic disease of Bangladesh, affecting affects children and adolescents. Although of low mortality, bacterial resistance to the antibiotics usually used for treatment have been reported, with large spreading in the country. Characterizations of Salmonella serovar Typhi genomes are essential for a better understanding of propagation and resistance bacterial and for the development of prophylactic measures for this disease, which is a public health problem.",setting:Outpatient,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2576,Salmonella enterica subsp. enterica serovar Typhi strain LXYSH,LXYSH,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09630442,90370,Typhi,,,MLST.Salmonella_enterica.1,,,,2019-02-04T00:00:00Z,,PRJNA480202,GCA_004136335.1,CP030936,,Institute of Microbiology,PacBio,174.49x,HGAP v. 2.0,1,,1,4780894,52.08417,5176,4868,missing,,2018-03-26,China,China: Zhejiang,,,,Infectious shock,,,,,,,,,,,,,To submit the whole genome sequence in NCBI,collected_by:Yanjun Zhang,,,,,,,Infectious shock,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90370.2584,Salmonella enterica subsp. enterica serovar Typhi strain WGS1146,WGS1146,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11792777,90370,Typhi,,,MLST.Salmonella_enterica.1,,,,2019-05-29T00:00:00Z,,PRJNA543969,GCA_005885835.1,"CP040575,CP040574",,Copenhagen University Hospital Hvidovre,Illumina MiSeq; Oxford Nanopore MiniION,33.0x,Unicycler v. v0.4.7,1,1,2,4897615,52.05548,5121,,blood,isolated from blood in a pregnant woman returning from Pakistan,2019-04-24,Denmark,Denmark,,,,Typhoid fever,,,,,,,,,,,,,Whole genome sequencing of a ceftriaxone resistant Salmonella Typhi isolated from blood in a pregnant woman returning from Pakistan.,collected_by:Copenhagen University Hospital Hvidovre,,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0.04,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,90370.4136,Salmonella enterica subsp. enterica serovar Typhi strain ISP2825,ISP2825,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20695325,90370,Typhi,,,MLST.Salmonella_enterica.2,,,,2021-08-17T00:00:00Z,,PRJNA753482,GCA_019645915.1,CP080960,,Cornell University,Oxford Nanopore MinION,511.0x,Flye v. v2.8.3-b1695; Racon v. v1.4.22;,1,0,1,4774014,52.100914,5022,4577,chilean patient is one of the major s; n/a,"isolated in 1983 from a Chilean patient is one of the major S. Typhi strains used for research, along with strains Ty2, CT18, and H58",1983,Chile,Chile,,,,Typhoid fever,,,,,,,,,,,,,"Salmonella enterica serovar Typhi ISP2825 isolated in 1983 from a Chilean patient is one of the major S. Typhi strains used for research, along with strains Ty2, CT18, and H58. The complete genome sequence of ISP2825 will help understand typhoid pathogenesis and evolution.",,,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0.04,Specific Bacterial Infections,Typhoid Fever,Other,Specific Bacterial Infections-Typhoid Fever HP,90370.5790,Salmonella enterica subsp. enterica serovar Typhi 1521-2017_CI,1521-2017_CI,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33313064,90370,Typhi,,,MLST.Salmonella_enterica.2,,,,2023-06-12T00:00:00Z,,PRJNA935358,,CP120397,,,Illumina NextSeq 500 and Oxford Nanopore,772x,SPAdes v. 3.1.4,1,0,1,4832976,52.069965,5125,4665,blood,,2017-06-02,Chile,Chile: Santiago,,female,21 years old,Typhoid fever,,,,,,,,,,,,,,collected_by:Centro para Vacunas en Desarollo (CVD-Chile),,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,90370.5792,Salmonella enterica subsp. enterica serovar Typhi 1698-2017_CI,1698-2017_CI,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33313050,90370,Typhi,,,MLST.Salmonella_enterica.2,,,,2023-06-12T00:00:00Z,,PRJNA935358,,CP120395,,,Illumina NextSeq 500 and Oxford Nanopore,963x,SPAdes v. 3.1.4,1,0,1,4777908,52.10132,5046,4617,joint fluid,,2017-06-29,Chile,Chile: Santiago,,female,9 months old,Typhoid fever,,,,,,,,,,,,,,collected_by:Centro para Vacunas en Desarollo (CVD-Chile),,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Bone and Joint,Specific Bacterial Infections-Typhoid Fever HP,90370.5794,Salmonella enterica subsp. enterica serovar Typhi 2027-2019_CI,2027-2019_CI,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33313061,90370,Typhi,,,MLST.Salmonella_enterica.1,,,,2023-06-12T00:00:00Z,,PRJNA935358,,CP120394,,,Illumina NextSeq 500 and Oxford Nanopore,724xx,SPAdes v. 3.1.4,1,0,1,4780244,52.055187,5050,4606,blood,,2019-07-19,Chile,Chile: Santiago,,female,6 years old,Typhoid fever,,,,,,,,,,,,,,collected_by:Centro para Vacunas en Desarollo (CVD-Chile),,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,90370.5795,Salmonella enterica subsp. enterica serovar Typhi 424-2019_CI,424-2019_CI,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN33313052,90370,Typhi,,,MLST.Salmonella_enterica.2,,,,2023-06-12T00:00:00Z,,PRJNA935358,,CP120398,,,Illumina NextSeq 500 and Oxford Nanopore,791x,SPAdes v. 3.1.4,1,0,1,4777787,52.101234,5034,4599,blood,,2019-02-02,Chile,Chile: Santiago,,male,13 years old,Typhoid fever,,,,,,,,,,,,,,collected_by:Centro para Vacunas en Desarollo (CVD-Chile),,,,,,,Typhoid fever,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Typhoid Fever,Blood and Circulatory System,Specific Bacterial Infections-Typhoid Fever HP,90371.2143,Salmonella enterica subsp. enterica serovar Typhimurium strain 81741,81741,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06185755,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2017-02-07T00:00:00Z,,PRJNA358799,GCF_001989635.1,"CP019442,CP019443,CP019444","NZ_CP019442.1,NZ_CP019443.1,NZ_CP019444.1",The forth affiliated hospital of Guangzhou medical university,PacBio,134.09,HGAP v. 2.0,1,2,3,5293223,51.86,5614,5336,stool,,2015-08-15,China,China:Guangdong,,,,diarrhea,,,,,,,,,,,,,study on the mechanism of antibiotic resistance of this strain,collected_by:The Clinical Laboratory of the first people's Hospital of Foshan,,,,,,,diarrhea,,,,,,,,,,,,,,100,0.2,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.2827,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC50,FORC50,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06161238,90371,Typhimurium,,,MLST.Salmonella_enterica.11,,,,2017-12-07T00:00:00Z,,PRJNA357860,GCA_002813935.1,CP019383,,Seoul National University,PacBio,265.58x,SMRT Analysis v. 2.3.0,1,,1,4673894,52.18,4694,4713,stool,"isolated from the blood of a food-poisoned patient in Seoul, Korea",2016-01-01,South Korea,South Korea: Seoul,,,,Salmonella gastroenteritis,,,,,,,,,,,,,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activates with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",collected_by:Samsung Seoul Hospital,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,99,0.2,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.2957,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC58,FORC58,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN06660623,90371,Typhimurium,,,MLST.Salmonella_enterica.27,,,,2018-04-03T00:00:00Z,,PRJNA380989,GCA_003031835.1,CP020565,,Seoul National University,PacBio,282.39x,SMRT Analysis v. 2.3.0,1,,1,4698556,52.249565,4672,4691,human stool,isolated from the human stool in Korea,2009-12-09,South Korea,"South Korea: Jeollabuk-do, jeonju",,,,Salmonella gastrienteritis,,,,,,,,,,,,,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activities with high prevalence, every year. This sample was isolated from the human stool in Korea.",collected_by:KCDC,,,,,,,Salmonella gastrienteritis,,,,,,,,,,,,,,100,1.4,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.2972,Salmonella enterica subsp. enterica serovar Typhimurium strain UGA14,UGA14,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN07159261,90371,Typhimurium,,,MLST.Salmonella_enterica.313,,,,2018-06-06T00:00:00Z,,PRJNA387603,GCA_003194225.1,"CP021462,CP021463,CP021464,CP021465,CP021466",,Los Alamos National Laboratory,Illumina HiSeq; PacBio,389.0x,Velvet v. 1.2.08; IDBA v. 1.1.0; Phrap v.,1,4,5,5352626,51.864506,5693,5435,blood,,2003,Kenya,Kenya,,,,gastroenteritis,,,,,,,,,,,,,"The significant problems of emerging invasiveness and AMR are exemplified by NTS in high disease burden environments such as Siaya, Kenya. We bring together clinically and epidemiologically relevant samples, systematic phenotypic comparison, and comparative genomic analysis of four evolutionary mechanisms to shed light on a variety of evolutionary processes that shape the emergence of invasive and AMR phenotypes for NTS.",collected_by:DJ Perkins,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.5,Gastrointestinal Diseases,Diarrheal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3031,Salmonella enterica subsp. enterica serovar Typhimurium strain D23580,D23580,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA4886686,90371,serovar Typhimurium,,,MLST.Salmonella_enterica.313,,,,2018-09-09T00:00:00Z,,PRJEB28511,GCA_900538085.1,"LS997973,LS997975,LS997976,LS997977,LS997974",,UNIVERSITY OF LIVERPOOL,,,,1,4,5,5085051,52.06994,5156,,blood of 26-month child with malaria and anemia,,2004-01,Malawi,Malawi,,,,,,host_health_state:diseased,,,,,,,,,,,"In order to perform transcriptomic comparison of D23580 and 4/74 strains of Salmonella enterica serovar Typhimurium, we have assembled and carefully annotated both genomes.",,,,,,,,,diseased,,,,,,,,,,,,,100,0.7,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,90371.3072,Salmonella enterica subsp. enterica serovar Typhimurium strain B3589,B3589,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN10716141,90371,Typhimurium,,,MLST.Salmonella_enterica.313,genotype:ST313,,,2019-01-15T00:00:00Z,,PRJNA513917,GCA_004022525.1,"CP034968,CP034969",,Christian Medical College,IonTorrent; Oxford Nanopore MiniION,54.0x,Canu v. 1.7; Unicycler hybrid v. 0.4.6,1,1,2,4917945,52.187813,5241,4839,blood,,2014-02-03,India,India: Vellore,,,,Extra-intestinal infection,,,,,,,,,,,,,"Salmonella enterica serovar Typhimurium is one of the most prevalent serotypes associated with foodborne infections worldwide . Interestingly S. Typhimurium strains within multi-locus sequence type (MLST) ST313 have been identified as the major cause of invasive diseases in many Sub-Saharan African countries. Previously S. Typhimurium ST313 was rarely reported from regions other than sub-Saharan Africa. Although S. Typhimurium ST313 had previously been isolated from India, the genomics and diversity of this important sequence type were limited Genotypic characterisation of S. Typhimurium ST313 isolates circulating in India has been discussed in this study",collected_by:Christian Medical College and Hospital Vellore,,,,,,,Extra-intestinal infection,,,,,,,,,,,,,,99.55,0.64,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,90371.3189,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC88,FORC88,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08944422,90371,Typhimurium,,,MLST.Salmonella_enterica.23,,,,2019-05-06T00:00:00Z,,PRJNA450526,GCA_005166225.1,CP029029,,Seoul National University,PacBio,350x,SMRT Analysis v. 2. 3. 0,1,,1,4634278,52.134075,4616,4650,human blood,"isolated from the blood of a food-poisoned patient in Seoul, Korea",2015-02-01,South Korea,South Korea: Seoul,,,,Salmonella gastroenteritis,,,,,,,,,,,,,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activities with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",collected_by:Samsung Seoul Hospital,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Blood and Circulatory System,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3196,Salmonella enterica subsp. enterica serovar Typhimurium strain SAP17-7399,SAP17-7399,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11787767,90371,Typhimurium,,,MLST.Salmonella_enterica.2210,,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885855.1,"CP040562,CP040563",,FDA Center for Food Safety and Applied Nutrition,PacBio,456x,HGAP v. 3,1,1,2,4905613,52.143883,5024,4712,stool,,,USA,USA:WA,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:WA,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3197,Salmonella enterica subsp. enterica serovar Typhimurium strain SAP17-7699,SAP17-7699,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11787765,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885875.1,"CP040564,CP040565",,FDA Center for Food Safety and Applied Nutrition,PacBio,230x,HGAP v. 3,1,1,2,4977610,52.140385,5126,4791,stool,,,USA,USA:WA,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:WA,,,,,,,missing,,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3198,Salmonella enterica subsp. enterica serovar Typhimurium strain SAP17-7299,SAP17-7299,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11787766,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885895.1,"CP040566,CP040567",,FDA Center for Food Safety and Applied Nutrition,PacBio,264x,HGAP v. 3,1,1,2,4963459,52.12903,5110,4784,stool,,,USA,USA:WA,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:WA,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3199,Salmonella enterica subsp. enterica serovar Typhimurium strain SAP17-8290,SAP17-8290,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN11786967,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2019-05-29T00:00:00Z,,PRJNA507262,GCA_005885935.1,"CP040568,CP040569",,FDA Center for Food Safety and Applied Nutrition,PacBio,256x,HGAP v. 3,1,1,2,5059269,52.122433,5254,4917,stool,,,USA,USA:NM,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured foodborne bacterial pathogens collected from the 2017 GenomeTrakr/PulseNet proficiency testing exercise. Six isolates were distributed for sequencing: 4 Salmonella enterica subsp. enterica serovar Typhimurium and 2 E.coli O157:H7 isolates.,collected_by:NM,,,,,,,missing,,,,,,,,,,,,,,100,0.37,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3596,Salmonella enterica subsp. enterica serovar Typhimurium strain 10ST07093,10ST07093,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09302771,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2019-06-20T00:00:00Z,,PRJNA474402,GCA_006384195.1,"CP029839,CP029837,CP029838",,Queensland Department of Health,PacBio,176.0x,HGAP v. 3,1,2,3,5052667,52.14179,5323,5111,feces,,2010,Australia,Australia,,,,Salmonella gastroenteritis,,,,,,,,,,,,,Sequencing of Salmonella Typhimurium pSLT and IncI1 like plasmids,collected_by:QLD department of Health,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3597,Salmonella enterica subsp. enterica serovar Typhimurium strain 01ST04081,01ST04081,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN09302772,90371,Typhimurium,,,,,,,2019-06-20T00:00:00Z,,PRJNA474402,GCA_006384995.1,"CP029840,CP029841,CP029842",,Queensland Department of Health,PacBio,200.0x,HGAP v. 3,1,2,3,5125257,52.03339,5411,5206,feces,,2001,Australia,Australia,,,,Salmonella gastroenteritis,,,,,,,,,,,,,Sequencing of Salmonella Typhimurium pSLT and IncI1 like plasmids,collected_by:QLD department of Health,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.33,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3755,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010530,AUSMDU00010530,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191648,90371,Typhimurium,,,MLST.Salmonella_enterica.34,mlst:ST34,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664575.1,"CP045947,CP045948",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,370x,de novo,1,1,2,4969000,52.188972,5053,4729,missing,,2017,Australia,Australia,,,,,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90371.3756,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529,AUSMDU00010529,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191647,90371,Typhimurium,,,MLST.Salmonella_enterica.19,mlst:ST19,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664595.1,"CP045949,CP045950,CP045951",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,316x,de novo,1,2,3,5053299,52.141125,5166,4798,missing,,2015,Australia,Australia,,,,,,,Susceptible,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90371.3757,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00008979,AUSMDU00008979,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN13191646,90371,Typhimurium,,,MLST.Salmonella_enterica.34,mlst:ST34,,,2019-11-17T00:00:00Z,33180013,PRJNA556438,GCA_009664635.1,"CP045952,CP045953",,Microbiological Diagnostic Unit,llumina NextSeq500/550 or MiSeq,99x,de novo,1,1,2,5166907,52.19393,5456,5062,missing,,2012,Australia,Australia,,,,,,,Susceptible;Resistant,AMR Panel,,,,,,,,,"Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.",,,,,,,,missing,,,,,,,,,,,,,,100,0.22,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,90371.3763,Salmonella enterica subsp. enterica serovar Typhimurium strain RM13672,RM13672,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08775946,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2020-01-12T00:00:00Z,,PRJNA445323,GCA_009857075.1,"CP047323,CP047324",,"United States Department of Agriculture, Agricultural Research Service",Illumina MiSeq,43.0x,Geneious Reference Assembly v. 2019-01,1,1,2,4964098,52.213875,5064,4702,feces,"isolated from environmental, food and clinical sources in five different states across the United States, which all have the same traditional subtyping profiles and identical to common laboratory strain 14028s",2009-08,USA,USA: Oregon,,,,gastroenteritis,,,,,,,,,,,,,"Between 2002 and 2011, several strains of Salmonella enterica subsp. enterica serovar Typhimurium were isolated from environmental, food and clinical sources in five different states across the United States, which all have the same traditional subtyping profiles and identical to common laboratory strain 14028s. These S. Typhimurium strains were sequenced on an Illumina MiSeq and used for whole genome SNP analysis, using strain 14028s as a reference, in order to establish the phylogenetic relationship of these strains to each other, and also provide additional scientific-based data for creating appropriate SNP analysis cutoff values for source tracking S. Typhimurium outbreaks.",collected_by:Oregon State Public Health Laboratory,,,,,,,gastroenteritis,,,,,,,,,,,,,,100,0.04,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3764,Salmonella enterica subsp. enterica serovar Typhimurium strain NCCP 16207,NCCP 16207,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12340931,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,NCCP:16207,,2020-01-15T00:00:00Z,,PRJNA556122,GCA_009884375.1,"CP041976,CP041974,CP041975",,Korea Centers for Disease Control & Prevention (KCDC),IonTorrent; PacBio,324.0x,SPAdes v. 3.1,1,2,3,5091224,52.153175,5385,4975,stool,,2011,South Korea,South Korea: Daejeon,,,,diarrhea,,,,,,,,,,,,,Pathogen genome project of Salmonella Typhimurium,collected_by:Korea National Institute of Health,,,,,,,diarrhea,,,,,,,,,,,,,,99.71,0.37,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.3944,Salmonella enterica subsp. enterica serovar Typhimurium strain ST53,ST53,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450163,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012049605.1,"CP050745,CP050746,CP050747,CP050748,CP050749",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,76x,Unicycler v. 0.4.8,1,4,5,5185065,52.148525,5347,4959,diarrheal patient,,2011-07-14,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3945,Salmonella enterica subsp. enterica serovar Typhimurium strain ST46,ST46,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450162,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012050025.1,"CP050750,CP050751,CP050752",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,33x,Unicycler v. 0.4.8,1,2,3,5259011,51.949234,5432,5033,diarrheal patient,,2011-05-26,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3946,Salmonella enterica subsp. enterica serovar Typhimurium strain ST113,ST113,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450168,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012051085.1,"CP050726,CP050727",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,51x,Unicycler v. 0.4.8,1,1,2,5121995,52.1832,5259,4912,diarrheal patient,,2013-11-04,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.26,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3947,Salmonella enterica subsp. enterica serovar Typhimurium strain ST106,ST106,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450167,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012051245.1,"CP050728,CP050729,CP050730",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,89x,Unicycler v. 0.4.8,1,2,3,5195418,51.85814,5349,4963,diarrheal patient,,2013-10-02,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3948,Salmonella enterica subsp. enterica serovar Typhimurium strain ST101,ST101,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450166,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012051385.1,"CP050731,CP050732,CP050733",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,19x,Unicycler v. 0.4.8,1,2,3,5225110,52.15272,5430,5057,diarrheal patient,,2013-09-12,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.51,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3950,Salmonella enterica subsp. enterica serovar Typhimurium strain ST56,ST56,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450164,90371,Typhimurium,,,,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012051825.1,"CP050739,CP050740,CP050741,CP050742,CP050743,CP050744",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,113x,Unicycler v. 0.4.8,1,5,6,5210197,52.24146,5421,5043,diarrheal patient,,2011-07-21,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.24,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.3951,Salmonella enterica subsp. enterica serovar Typhimurium strain ST45,ST45,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN14450161,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-04-06T00:00:00Z,,PRJNA615288,GCA_012052225.1,"CP050753,CP050754,CP050755",,University of Maryland,Illumina MiSeq; Oxford Nanopore MiniION,40x,Unicycler v. 0.4.8,1,2,3,5259999,51.944782,5428,5033,diarrheal patient,,2011-05-25,China,China:Shanghai,,,,,,,,,,,,,,,,,"Some multidrug-resistant isolates of S. Indiana, Typhimurium, and Enteritidis were sequenced using MinION and MiSeq sequencing technologies, both individually and in combination. The qualities of MinION, MiSeq, and hybrid genome assemblies were then compared in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome.",collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,,,,missing,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.4557,Salmonella enterica subsp. enterica serovar Typhimurium strain BKQZM9,BKQZM9,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15796617,90371,Typhimurium,,,MLST.Salmonella_enterica.313,,,,2020-08-19T00:00:00Z,,PRJNA656707,GCA_014250355.1,"CP060169,CP060171,CP060170",,University of Liverpool,Illumina HiSeq 4000; Oxford Nanopore,200.0x,Unicycler v. v0.4.4,1,2,3,4973766,52.18812,5070,,blood,,2018,Malawi,Malawi,,,,iNTS,,,,,,,,,,,,,"Bloodstream infections caused by invasive non-Typhoidal Salmonella (iNTS) have emerged as a major public health concern in Africa, resulting in ~66,500 deaths every year. The iNTS epidemic has largely been driven by variants of the S. Typhimurium serovar which belong to the sequence type ST313. Two tightly clustered lineages of ST313 exist in Africa (ST313 L1 and ST313 L2), and a more diverse range of ST313 isolates were found in the United Kingdom and Latin America. It has been proposed that antimicrobial resistance (AMR) and genome degradation have contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes has not been described.Here, we assembled a large and up-to date collection of ST313 isolates from Africa to analyse the stepwise evolution of S. Typhimurium causing BSI. We uncovered an epidemiologically emerging pan-susceptible ST313 lineage (ST313 L3) in Malawi, reflecting the value of changing treatment recommendations in response to AMR. ST313 L3 emerged in Malawi in 2016 and is genetically similar to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Despite its recent emergence, ST313 L3 represents an evolutionary intermediate between ST313 L1 and the epidemic multidrug resistant ST313 L2. Our in-depth genotypic and phenotypic characterisation identified the crucial loss-of-function genetic events that occurred along the evolutionary pathway of invasive S. Typhimurium across Africa.Together, our data provide an expanded insight into the dynamics of a pathogen responsible for an ongoing epidemic of bloodstream infections and highlights the positive consequence of improved antibiotic stewardship in driving epidemiological shifts in the circulation of Salmonella lineages.","collected_by:College of Medicine, University of Malawi",,,,,,,iNTS,,,,,,,,,,,,,,100,0.04,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,90371.4793,Salmonella enterica subsp. enterica serovar Typhimurium strain NCTC 74,NCTC 74,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN16707726,90371,Typhimurium,,,MLST.Salmonella_enterica.504,,,,2020-11-18T00:00:00Z,,PRJNA675428,GCA_015565735.1,CP064709,,Pharmacology and Toxicology Laboratory,PacBio,120.0x,HGAP v. 3,1,0,1,4638880,52.047928,4639,4344,food poisoning; feces,,1911,,,,,,,,,,,,,,,,,,,"Using this Salmonella typhimurium as a model strain, its genome was sequenced to provide a reference genome for the authors' subsequent bacterial drug resistance studies.",sample_type:whole organism;collected_by:American Type Culture Collection,,,,,,,,,,,,,,,,,,,,,100,0.07,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.4798,Salmonella enterica subsp. enterica serovar Typhimurium strain S585,S585,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962528,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015697745.1,"CP061115,CP061116,CP061117",,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,2,3,5314704,51.858334,5519,5108,stool,,2018-12,China,China:Hangzhou,,,,Gastrointestinal disorders,,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,Gastrointestinal disorders,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,90371.4799,Salmonella enterica subsp. enterica serovar Typhimurium strain S441,S441,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962525,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015697785.1,"CP061122,CP061123",,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,1,2,5205476,51.906876,5342,4965,stool,,2017-03,China,China:Hangzhou,,,,Infectious diarrhea,,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,Infectious diarrhea,,,,,,,,,,,,,,99.41,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.4800,Salmonella enterica subsp. enterica serovar Typhimurium strain S438,S438,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962524,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015697805.1,"CP061124,CP061125",,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,1,2,5225758,51.939854,5411,5017,stool,,2016-12,China,China:Hangzhou,,,,Enteritis,,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,Enteritis,,,,,,,,,,,,,,99.71,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.4801,Salmonella enterica subsp. enterica serovar Typhimurium strain S304,S304,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962523,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015697825.1,"CP061126,CP061127,CP061128,CP061129,CP061130",,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,4,5,5263346,51.824677,5436,5031,stool,,2015-05,China,China:Hangzhou,,,,Acute enteritis,,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,Acute enteritis,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.4802,Salmonella enterica subsp. enterica serovar Typhimurium strain S520,S520,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN15962526,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2020-11-30T00:00:00Z,,PRJNA660858,GCA_015732575.1,"CP061119,CP061120,CP061121",,Zhejiang University,Illumina HiSeq,300x,other: Unicycler v. 0.4.8,1,2,3,5294294,51.8865,5476,5075,stool,,2017-09,China,China:Hangzhou,,,,Diarrhea,,,,,,,,,,,,,MCR-1 positive Salmonella Clinical isolate in China,collected_by:Xiaoting Hua,,,,,,,Diarrhea,,,,,,,,,,,,,,100,0.15,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.5036,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00027944,AUSMDU00027944,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8520469,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163145.1,"OU015340,OU015341",,UNIVERSITY OF MELBOURNE,,,,1,1,2,5237669,52.22172,5412,,feces,,2012,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,99.71,0.22,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5037,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00027951,AUSMDU00027951,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8520471,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163195.1,"OU015328,OU015329,OU015330,OU015331,OU015332,OU015333",,UNIVERSITY OF MELBOURNE,,,,1,5,6,5232853,51.880856,5325,,feces,,2012,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,100,0.29,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5038,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00005182,AUSMDU00005182,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7503125,90371,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163165.1,"OU015325,OU015326,OU015327",,UNIVERSITY OF MELBOURNE,,,,1,2,3,5312318,51.890247,5425,,feces,,2016,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,100,0.15,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5039,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00018340,AUSMDU00018340,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA7503126,90371,"4,[5],12:i:-",,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163185.1,"OU015337,OU015338,OU015339",,UNIVERSITY OF MELBOURNE,,,,1,2,3,5301194,51.87486,5410,,feces,,2014,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,100,0.15,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5040,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00004549,AUSMDU00004549,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8520468,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163175.1,"OU015323,OU015324",,UNIVERSITY OF MELBOURNE,,,,1,1,2,5231618,52.20077,5381,,feces,,2015,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,99.71,0.22,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5041,Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00007171,AUSMDU00007171,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA8520470,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-05-12T00:00:00Z,,PRJEB41036,GCA_907163245.1,"OU015342,OU015343,OU015344",,UNIVERSITY OF MELBOURNE,,,,1,2,3,5004181,52.17567,5018,,feces,,2017,Australia,Australia,,,,,,host_health_state:diseased,,,,,,,,,,,"Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:-",,,,,,,,,diseased,,,,,,,,,,,,,100,0.11,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,90371.5143,Salmonella enterica subsp. enterica serovar Typhimurium strain S34,S34,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22814778,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-11-07T00:00:00Z,,PRJNA776703,GCA_020783475.1,CP086118,,Guangzhou Medical University,Oxford Nanopore PromethION,110.0x,Unicycler v. 0.4.8,1,0,1,4983099,52.178955,5070,4746,stool,,2014-07-05,China,"China: Guangzhou, Guangdong",,,,Salmonella gastroenteritis,,,,,,,,,,,,,Salmonella Typhimurium S34 carrying CTX-M-55 in Guangzhou,collected_by:a patient in a tertiary hospital,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.07,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.5155,Salmonella enterica subsp. enterica serovar Typhimurium strain S29,S29,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN22488165,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2021-11-01T00:00:00Z,,PRJNA773587,GCA_020691725.1,"CP085699,CP085701,CP085702,CP085703,CP085700",,Guangzhou Medical University,Illumina NovaSeq; Oxford Nanopore,110.0x,SPAdes v. 3.13.1; unicycler v. 0.4.8,1,4,5,5106141,52.122593,5226,4899,stool,"isolated from a tertiary hospital in Guangzhou, which contains an IncI1 plasmid carrying CTX-M-55 gene",2014-07-02,China,"China: Guangzhou, Guangdong",,,,Salmonella gastroenteritis,,,,,,,,,,,,,"S29 is a Salmonella Typhimurium isolated from a tertiary hospital in Guangzhou, which contains an IncI1 plasmid carrying CTX-M-55 gene.",collected_by:a patient in a tertiary hospital,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0.11,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.5194,Salmonella enterica subsp. enterica serovar Typhimurium NCCP16345,NCCP16345,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN17319566,90371,Typhimurium,,,MLST.Salmonella_enterica.19,,,,2022-01-19T00:00:00Z,,PRJNA692263,GCA_021513315.1,"CP068696,CP068697",,,PacBio RSII; IonTorrent,341.0x,HGAP v. 3,1,1,2,4998898,52.16406,5113,4756,pus,,2012-06-08,South Korea,South Korea: Gwangju,,,,,,,,,,,,,,,,,,collected_by:KNIH,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,90371.6050,Salmonella enterica subsp. enterica serovar Typhimurium 1104-75,1104-75,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31055796,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2022-11-05T00:00:00Z,,PRJNA884865,GCA_026013295.1,"CP110198,CP110199,CP110200",,,Oxford Nanopore PromethION,110.0x,unicycler v. 0.4.8,1,2,3,5059623,52.191635,5165,4838,stool,,2021-11-27,China,China: Guangzhou,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:a patient in a tertiary hospital in Guangzhou.,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,90371.6051,Salmonella enterica subsp. enterica serovar Typhimurium 1104-65,1104-65,Salmonella enterica,Salmonella,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN31056807,90371,Typhimurium,,,MLST.Salmonella_enterica.34,,,,2022-11-05T00:00:00Z,,PRJNA884869,GCA_026013315.1,CP110201,,,Oxford Nanopore PromethION,110.0x,unicycler v. 0.4.8,1,0,1,4975504,52.181225,5052,4736,stool,,2021-11-17,China,China: Guangzhou,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,collected_by:a patient in a tertiary hospital in Guangzhou.,,,,,,,Salmonella gastroenteritis,,,,,,,,,,,,,,100,0,Gastrointestinal Diseases,Diarrheal Diseases,Gastrointestinal,Gastrointestinal Diseases-Diarrheal Diseases HP,903895.5,Acinetobacter baumannii Canada BC-5,Canada BC-5,Acinetobacter baumannii,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN32805326,903895,,,,MLST.Acinetobacter_baumannii_2.1,,NIAID:NR-17783,,2023-02-01T00:00:00Z,,PRJNA565663,,"CP116680,CP116681",,,Illumina HiSeq; Oxford Nanopore MinION,330.0x,Unicycler v. Galaxy version 0.4.6.0,1,1,2,4018824,39.193157,3866,3777,nosocomial spread of war-related mdr-abc in a canadian civilian hospital with origin from soldier evacuated via landstuhl regional medical center,,2007,Canada,Canada: British Columbia,,,,Nosocomial infection,,,Susceptible,Computational Method,,,,,,,,,,"collected_by:The following reagent was obtained through BEI Resources, NIAID, NIH: Acinetobacter baumannii, Strain BC-5, NR-17783.",,,,,,,Nosocomial infection,,,,,,,,,,,,,,99.8,0,Nosocomial Infections,Other Nosocomial Infections,Other,Nosocomial Infections-Other Nosocomial Infections HP,910265.3,Pseudomonas aeruginosa C-NN2 strain early isolate NN2 (clone C),early isolate NN2 (clone C),Pseudomonas aeruginosa,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota,SAMEA104083446,910265,,,,MLST.Pseudomonas_aeruginosa.17,,,,2017-06-09T00:00:00Z,,PRJEB5222,GCA_900185255.1,LT883143,,MHH,,,,1,,1,6902967,66.12,6586,6601,cystic fibrosis lung,,1985-12-05,,,,,,,,host_health_state:diseased,Susceptible,Computational Prediction,,,,,,,,,In this study we closed the contig of the most common Pseudomonas aerugiosa clone C followed by an annotation step. In addition RNA-seq was performed to identify transcriptional start sites (TSS) und small RNA.,,,,,,,,,diseased,,,,,,,,,,,,,100,0.6,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,93221.13,Pandoraea pulmonicola DSM 16583,DSM 16583,Pandoraea pulmonicola,Pandoraea,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03263587,93221,,,,,,DSM:16583,,2016-11-17T00:00:00Z,,PRJNA270151,GCA_000815105.2,CP010310,,,PacBio RSII,110.5x,HGAP v. 3,1,0,1,5867621,64.295105,5400,4938,sputum,,,Canada,Canada,,,,lung infection,,,,,,,,,,,,,,collected_by:DSMZ,,,,,,,lung infection,,,,,,,,,,,,,,97.9,3.5,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,941322.177,Escherichia coli O25b:H4-ST131 4993,4993,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174077,941322,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917335.1,"CP103557,CP103558",,,Oxford Nanopore GridION,158x,Flye v. 2.8.3-b1695,1,1,2,5466654,50.65435,5656,5331,blood,,2019-06-02,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.178,Escherichia coli O25b:H4-ST131 4224,4224,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174053,941322,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917455.1,"CP103592,CP103593,CP103594,CP103595",,,Oxford Nanopore GridION,41x,Flye v. 2.8.3-b1695,1,3,4,5331778,50.840546,5440,5154,blood,,2019-01-10,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.179,Escherichia coli O25b:H4-ST131 5506,5506,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174099,941322,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917895.1,"CP103508,CP103509,CP103510,CP103511",,,Oxford Nanopore GridION,225x,Flye v. 2.8.3-b1695,1,3,4,5179171,50.807262,5276,4989,blood,,2019-11-13,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.2,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.180,Escherichia coli O25b:H4-ST131 751,751,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28173988,941322,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024917975.1,"CP103562,CP103563,CP103564,CP103565,CP103566",,,Oxford Nanopore GridION,273x,Flye v. 2.8.3-b1695,1,4,5,5494413,50.680756,5673,5349,blood,,2019-05-06,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.181,Escherichia coli O25b:H4-ST131 5392,5392,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174092,941322,,,,"MLST.Escherichia_coli_2.567,MLST.Escherichia_coli_1.131",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918115.1,"CP103465,CP103466,CP103467",,,Oxford Nanopore GridION,119x,Flye v. 2.8.3-b1695,1,2,3,4950240,50.775276,4968,4713,blood,,2020-02-13,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,99.8,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.182,Escherichia coli O25b:H4-ST131,ST131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174028,941322,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918235.1,"CP103710,CP103711,CP103712,CP103713",,,Oxford Nanopore GridION,161x,Flye v. 2.8.3-b1695,1,3,4,5212621,50.89687,5332,5080,blood,,2017-02-03,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.183,Escherichia coli O25b:H4-ST131 2822,2822,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174008,941322,,,,"MLST.Escherichia_coli_2.567,MLST.Escherichia_coli_1.131",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918395.1,"CP103742,CP103743,CP103744",,,Oxford Nanopore GridION,262x,Flye v. 2.8.3-b1695,1,2,3,5099400,50.849434,5159,4892,blood,,2016-11-06,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0.1,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.184,Escherichia coli O25b:H4-ST131 4433,4433,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN28174062,941322,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",genotype:ST131,,,2022-09-04T00:00:00Z,,PRJNA836696,GCA_024918415.1,CP103672,,,Oxford Nanopore GridION,259x,Flye v. 2.8.3-b1695,1,0,1,5386924,50.562267,5529,5230,blood,,2018-03-15,USA,USA: Houston,,,,Bacteremia,,,,,,,,,,,,,,collected_by:MDACC,,,,,,,Bacteremia,,,,,,,,,,,,,,100,0,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,941322.195,Escherichia coli O25b:H4-ST131,ST131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA112356746,941322,,,,MLST.Escherichia_coli_1.131,,,,2023-06-23T00:00:00Z,,PRJEB51925,,"OY019088,OY019089,OY019090",,,,,,1,2,3,5428674,50.754456,5461,,urinary tract,,2019-04-15,Armenia,Armenia,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0.1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,941322.196,Escherichia coli O25b:H4-ST131,ST131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA112356748,941322,,,,MLST.Escherichia_coli_1.131,,,,2023-06-01T00:00:00Z,,PRJEB51925,,"OX637961,OX637962,OX637963",,,,,,1,2,3,5143242,50.754505,5088,,urinary tract,,2019-01-09,Armenia,Armenia,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,941322.197,Escherichia coli O25b:H4-ST131,ST131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA112356747,941322,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,,,2023-06-01T00:00:00Z,,PRJEB51925,,"OX637964,OX637965,OX637966,OX637967",,,,,,1,3,4,5386170,50.776062,5430,,urinary tract,,2019-03-11,Armenia,Armenia,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,941322.198,Escherichia coli O25b:H4-ST131,ST131,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA112356745,941322,,,,MLST.Escherichia_coli_1.131,,,,2023-06-01T00:00:00Z,,PRJEB51925,,"OX637959,OX637960",,,,,,1,1,2,5085034,50.735195,5007,,urinary tract,,2019-03-07,Armenia,Armenia,,,,,,host_health_state:diseased,,,,,,,,,,,,,,,,,,,,diseased,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,948564.7,Vibrio cholerae C6706,C6706,Vibrio cholerae,Vibrio,Vibrionaceae,Vibrionales,Gammaproteobacteria,Pseudomonadota,SAMN13734987,948564,El Tor,,,MLST.Vibrio_cholerae.69,,,,2020-05-13T00:00:00Z,,PRJNA598947,GCA_013085075.1,"CP047295,CP047296",,EPFL,PacBio,329.0x,HGAP v. 3,2,0,2,4085431,47.460316,3856,3661,missing,,1991,Peru,Peru,,,,cholera,,,,,,,,,,,,,The goal of this study was to de novo assemble diverse pandemic V. cholerae strains and compare their closed genomes.,passage_history:provided by Mekalanos lab,,,,,,,cholera,,,,,,StrepS,,,,,,,,99.73,0.03,Specific Bacterial Infections,Cholera,Other,Specific Bacterial Infections-Cholera HP,95486.299,Burkholderia cenocepacia strain VC7848,VC7848,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05001925,95486,,,,MLST.Burkholderia_cepacia_complex.224,genotype:RAPD44,,,2017-02-15T00:00:00Z,,PRJNA289138,GCF_001999785.1,CP019668,NZ_CP019668.1,University of British Columbia,PacBio,64.8x,HGAP v. 2.0,1,,1,7499459,66.92,7394,6925,sputum,,1996-09-10,Canada,Canada: Vancouver,,,,Cystic Fibrosis,,host_subject_id:Patient 9,,,,,,,C,,HostAssociated,,"Cystic fibrosis (CF) is the most common fatal genetic disorder in children and young adults in Canada. The primary cause of CF-related deaths is chronic microbial infection in the lungs of affected patients. In particular, bacterial pathogens from the Burkholderia cepacia complex (Bcc) are a serious health concern for CF patients, because Bcc can establish persistent infections in the lungs and are highly resistant to antibiotics. Complicating the clinical picture is the fact that CF patients infected with the “same” Burkholderia strains, as identified by the lower-resolution genotyping methods, can have drastically different clinical outcomes. In this study, we sequenced over 200 clinical isolates of B. cenocepacia using Illumina paired-end and PacBio long-read sequencing. Our goal is to capture the genomic diversity and changes that are found in clinical B. cenocepacia isolates.",collected_by:Canadian Burkholderia cepacia Complex Research and Referral Repository (CBCCRRR),,,,,,,Cystic Fibrosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,95486.300,Burkholderia cenocepacia strain VC2307,VC2307,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05001798,95486,,,,MLST.Burkholderia_cepacia_complex.210,genotype:RAPD06,,,2017-02-15T00:00:00Z,,PRJNA289138,GCF_001999805.1,"CP019666,CP019664,CP019667,CP019665",,University of British Columbia,PacBio,100x,HGAP v. 2.0,3,1,4,7915879,66.94,7851,7421,sputum,,1987-04-04,Canada,Canada: Vancouver,,,,Cystic Fibrosis,,host_subject_id:Patient 1,,,,,,,C,,HostAssociated,,"Cystic fibrosis (CF) is the most common fatal genetic disorder in children and young adults in Canada. The primary cause of CF-related deaths is chronic microbial infection in the lungs of affected patients. In particular, bacterial pathogens from the Burkholderia cepacia complex (Bcc) are a serious health concern for CF patients, because Bcc can establish persistent infections in the lungs and are highly resistant to antibiotics. Complicating the clinical picture is the fact that CF patients infected with the “same” Burkholderia strains, as identified by the lower-resolution genotyping methods, can have drastically different clinical outcomes. In this study, we sequenced over 200 clinical isolates of B. cenocepacia using Illumina paired-end and PacBio long-read sequencing. Our goal is to capture the genomic diversity and changes that are found in clinical B. cenocepacia isolates.",collected_by:Canadian Burkholderia cepacia Complex Research and Referral Repository (CBCCRRR),,,,,,,Cystic Fibrosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,95486.301,Burkholderia cenocepacia strain VC12802,VC12802,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05001933,95486,,,,MLST.Burkholderia_cepacia_complex.267,genotype:RAPD15,,,2017-02-15T00:00:00Z,,PRJNA289138,GCF_001999825.1,"CP019670,CP019669","NZ_CP019670.1,NZ_CP019669.1",University of British Columbia,PacBio,138.9x,HGAP v. 2.0,2,,2,7394909,67.05,7188,6782,sputum,,2005-03-27,Canada,Canada: Vancouver,,,,Cystic Fibrosis,,host_subject_id:Patient 9,,,,,,,C,,HostAssociated,,"Cystic fibrosis (CF) is the most common fatal genetic disorder in children and young adults in Canada. The primary cause of CF-related deaths is chronic microbial infection in the lungs of affected patients. In particular, bacterial pathogens from the Burkholderia cepacia complex (Bcc) are a serious health concern for CF patients, because Bcc can establish persistent infections in the lungs and are highly resistant to antibiotics. Complicating the clinical picture is the fact that CF patients infected with the “same” Burkholderia strains, as identified by the lower-resolution genotyping methods, can have drastically different clinical outcomes. In this study, we sequenced over 200 clinical isolates of B. cenocepacia using Illumina paired-end and PacBio long-read sequencing. Our goal is to capture the genomic diversity and changes that are found in clinical B. cenocepacia isolates.",collected_by:Canadian Burkholderia cepacia Complex Research and Referral Repository (CBCCRRR),,,,,,,Cystic Fibrosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,95486.302,Burkholderia cenocepacia strain VC12308,VC12308,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05001912,95486,,,,MLST.Burkholderia_cepacia_complex.306,genotype:RAPD09,,,2017-02-15T00:00:00Z,,PRJNA289138,GCF_001999885.1,"CP019674,CP019672,CP019673,CP019671","NZ_CP019674.1,NZ_CP019672.1,NZ_CP019673.1,NZ_CP019671.1",University of British Columbia,PacBio,96.9x,HGAP v. 2.0,3,1,4,7634498,67.15,7466,7041,sputum,,2004-03-23,Canada,Canada: Vancouver,,,,Cystic Fibrosis,,host_subject_id:Patient 8,,,,,,,C,,HostAssociated,,"Cystic fibrosis (CF) is the most common fatal genetic disorder in children and young adults in Canada. The primary cause of CF-related deaths is chronic microbial infection in the lungs of affected patients. In particular, bacterial pathogens from the Burkholderia cepacia complex (Bcc) are a serious health concern for CF patients, because Bcc can establish persistent infections in the lungs and are highly resistant to antibiotics. Complicating the clinical picture is the fact that CF patients infected with the “same” Burkholderia strains, as identified by the lower-resolution genotyping methods, can have drastically different clinical outcomes. In this study, we sequenced over 200 clinical isolates of B. cenocepacia using Illumina paired-end and PacBio long-read sequencing. Our goal is to capture the genomic diversity and changes that are found in clinical B. cenocepacia isolates.",collected_by:Canadian Burkholderia cepacia Complex Research and Referral Repository (CBCCRRR),,,,,,,Cystic Fibrosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,95486.303,Burkholderia cenocepacia strain VC1254,VC1254,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN05001969,95486,,,,MLST.Burkholderia_cepacia_complex.32,genotype:RAPD01,,,2017-02-15T00:00:00Z,,PRJNA289138,GCF_001999925.1,"CP019678,CP019676,CP019675,CP019677",,University of British Columbia,PacBio,73.5x,HGAP v. 2.0,3,1,4,8177367,66.96,8045,7606,sputum,,1985-02-21,Canada,Canada: Vancouver,,,,Cystic Fibrosis,,host_subject_id:Patient 13,,,,,,,C,,HostAssociated,,"Cystic fibrosis (CF) is the most common fatal genetic disorder in children and young adults in Canada. The primary cause of CF-related deaths is chronic microbial infection in the lungs of affected patients. In particular, bacterial pathogens from the Burkholderia cepacia complex (Bcc) are a serious health concern for CF patients, because Bcc can establish persistent infections in the lungs and are highly resistant to antibiotics. Complicating the clinical picture is the fact that CF patients infected with the “same” Burkholderia strains, as identified by the lower-resolution genotyping methods, can have drastically different clinical outcomes. In this study, we sequenced over 200 clinical isolates of B. cenocepacia using Illumina paired-end and PacBio long-read sequencing. Our goal is to capture the genomic diversity and changes that are found in clinical B. cenocepacia isolates.",collected_by:Canadian Burkholderia cepacia Complex Research and Referral Repository (CBCCRRR),,,,,,,Cystic Fibrosis,,,,,,,,,,,,,,100,0,Respiratory Diseases,Cystic Fibrosis,Respiratory Tract,Respiratory Diseases-Cystic Fibrosis HP,95486.802,Burkholderia cenocepacia C6433,C6433,Burkholderia cenocepacia,Burkholderia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN28745300,95486,,,,MLST.Burkholderia_cepacia_complex.278,,,,2022-06-13T00:00:00Z,,PRJNA843523,GCA_023704255.1,"CP098497,CP098498,CP098499",,,Illumina,22.0x,SPAdes v. v3.13.0,2,1,3,7785917,67.33967,7884,7309,respiratory isolate,,2020,Canada,Canada: Edmonton,,,,bacterial infection,,,,,,,,,,,,,,collected_by:University of Alberta,,,,,,,bacterial infection,,,,,,,,,,,,,,100,0.8,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,964.22,Herbaspirillum seropedicae strain AU13965,AU13965,Herbaspirillum seropedicae,Herbaspirillum,Oxalobacteraceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN10532542,964,,,,,,,,2019-06-19T00:00:00Z,,PRJNA508889,GCA_006378125.1,"CP034395,CP034394",,UFPR - Universidade Federal do Parana,IonTorrent; Illumina MiSeq,160.0x,SPAdes v. 3.10.0; MIRA v. 4.0.2; CLC NGS,1,1,2,5392975,63.12117,4976,4729,sputum,,2008,USA,"USA:Ann Arbor, MI",,,,Cystic fibosis associated infection,,,,,,,,,,,,,A clinical Herbaspirillum seropedicae strain isolated from sputum of cystic fibrosis patients,"collected_by:Division of Infectious Diseases, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI",,,,,,,Cystic fibosis associated infection,,,,,,,,,,,,,,99.87,0.8,Miscellaneous or Unspecified Infections,,Respiratory Tract,Miscellaneous or Unspecified Infections- HP,985002.188,Staphylococcus argenteus strain XNO106,XNO106,Staphylococcus argenteus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07510742,985002,,,,,,,,2017-12-06T00:00:00Z,,PRJNA400109,GCA_002812345.1,CP025023,,Third Military Medical University,PacBio,50.0x,SMRT portal v. Version 3.2.0,1,,1,2744502,32.42,2637,2614,tissue obtained from patient with prosthetic joint infection,,2015-01-05,China,China: Chongqing,,,,prosthetic joint infection,,,,,,,,,,,,,The Genome Sequence of Staphylococcus argenteus XNO106,"collected_by:Jiang Bei,Hu Xiaomei",,,,,,,prosthetic joint infection,,,,,,,,,,,,,,100,0,Bone and Joint Infections,Other Joint Infections,Bone and Joint,Bone and Joint Infections-Other Joint Infections HP,985002.198,Staphylococcus argenteus strain XNO62,XNO62,Staphylococcus argenteus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN07510741,985002,,,,,,,,2017-11-30T00:00:00Z,,PRJNA398564,GCA_003595345.1,CP023076,,Third Military Medical University,PacBio,not specified,SMRT portal v. 3.2.0,1,,1,2744503,32.41924,2630,2617,joint fluid,,2014-09-29,China,China: Chongqing,,,,prosthetic joint infection,,,,,,,,,,,,,Staphylococcus argenteus obtained from joint fluid of a patient with prosthetic joint infection,"collected_by:Jiang Bei,Hu Xiaomei",,,,,,,prosthetic joint infection,,,,,,,,,,,,,,99.37,0.36,Bone and Joint Infections,Other Joint Infections,Bone and Joint,Bone and Joint Infections-Other Joint Infections HP,985002.328,Staphylococcus argenteus strain Tokyo13064,Tokyo13064,Staphylococcus argenteus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMD00071154,985002,,,,,,,,2020-12-25T00:00:00Z,,PRJDB5453,GCA_016756355.1,AP024200,,"Microbiology, Tokyo Metropolitan Institute of Public Health",Illumina MiSeq; Oxford Nanopore MinION,1007.6X,Unicycler v. 0.4.2,1,0,1,2750811,32.38543,2572,2543,feces,,2010-08,Japan,Japan,,,,,,,,,,,,,,,,,The main objective of this project is to identify genome polymorphism among staphylococcal food poisoning isolates and study its genetic contents. The genomic data of staphylococcal isolates were obtained using the MiSeq platform. Detailed genomic analyses and comparative studies with other genomes will give further information and insight into the enterotoxigenic activities of staphylococcus species.,,not applicable,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,not applicable,,,,99.65,0.36,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,985002.426,Staphylococcus argenteus MRSA-139-14-168,MRSA-139-14-168,Staphylococcus argenteus,Staphylococcus,Staphylococcaceae,Bacillales,Bacilli,Bacillota,SAMN27652595,985002,,,,,,,,2022-04-27T00:00:00Z,,PRJNA817299,GCA_023158915.1,"CP096114,CP096113",,,Illumina NextSeq; Oxford Nanopore MinION,366.0x,Flye v. 2.7.1; pilon v. 1.23; racon v.,1,1,2,2818859,32.395164,2682,2630,skin,,2014,Australia,Australia: Perth,,,,skin infection,,,,,,,,,,,,,,collected_by:Pathwest laboratories,,,,,,,skin infection,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Other Skin and Soft Tissue Infections,Skin and Soft Tissue,Skin and Soft Tissue Infections-Other Skin and Soft Tissue Infections HP,991915.7,Escherichia coli O121:H19 strain FWSEC0006,FWSEC0006,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768107,991915,O121:H19,,,MLST.Escherichia_coli_1.655,,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037715.2,NETR00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,103.62x;127.66x,Unicycler;Canu v. 0.4.4.0;1.7,1,1,2,5479551,50.62349,5904,5698,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2003,Canada,Canada:Alberta,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.91,0.36,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,991919.15,Escherichia coli O145:NM strain FWSEC0002,FWSEC0002,Escherichia coli,Escherichia,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08768103,991919,O145:NM,,,"MLST.Escherichia_coli_1.32,MLST.Escherichia_coli_2.436",,,,2019-05-03T00:00:00Z,,PRJNA287560,GCA_005037815.2,NJGT00000000,,National Microbiology Laboratory,Illumina MiSeq;Oxford Nanopore MinION,78.00x;124.40x,Unicycler;Canu v. 0.4.4.0;1.7,1,2,3,5790057,50.641365,6315,6056,clinical: human (homo sapiens),"is from Environmental, animal husbandry, food samples, and medical isolates",2003,Canada,Canada:Alberta,,,,,,,,,,,,Mesophilic,37 C,Facultative,Multiple,,"The food and water safety pilot project is a comprehensive strategy that integrates multidisciplinary components from diverse federal science sources to address two main goals. The first is to enhance food and water safety by developing genomics-based methods for pathogen isolation, detection and characterisation. The second goal is to develop a federally integrated system to manage, store and provide open access to genomic data related to food and water borne pathogens. The model organisms for this study are Shiga-toxin Producing Escherchia coli (STEC) and Salmonella Enteritidis from Environmental, animal husbandry, food samples, and medical isolates.",collected_by:National Microbiology Laboratory: Public Health Agency of Canada,,,,,,,missing,,,,,,,,,,,,,,99.82,0.64,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,997873.77,Bacteroides caccae CL03T12C61,CL03T12C61,Bacteroides caccae,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451178,997873,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292205.1,"CP072258,CP072259,CP072260,CP072261",,Brigham & Women's Hospital,PacBio Sequel,164x,FALCON-Unzip v. 1.2.0,1,3,4,5499725,42.83378,4904,4473,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.3,0.08,,,Gastrointestinal,- NHP,997879.7,Bacteroides fragilis CL03T12C07,CL03T12C07,Bacteroides fragilis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451179,997879,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292185.1,CP072257,,Brigham & Women's Hospital,PacBio Sequel,380x,FALCON-Unzip v. 1.2.0,1,0,1,5224217,43.464294,4613,4258,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.26,0.07,,,Gastrointestinal,- NHP,997890.6,Bacteroides uniformis CL03T12C37,CL03T12C37,Bacteroides uniformis,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451181,997890,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292165.1,"CP072255,CP072256",,Brigham & Women's Hospital,PacBio Sequel,334x,FALCON-Unzip v. 1.2.0,1,1,2,4920161,46.203995,4345,4031,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.26,0.74,,,Gastrointestinal,- HP,99822.25,Streptococcus dysgalactiae subsp. dysgalactiae strain NCTC4669,NCTC4669,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMEA3539719,99822,Lancefield Group C,,,MLST.Streptococcus_dysgalactiae_equisimilis.300,,NCTC:4669,,2018-12-20T00:00:00Z,,PRJEB6403,GCA_900635345.1,LR134094,,SC,,,,1,,1,2201894,39.20016,2266,2188,not available: to be reported later,,1900-1935,United Kingdom,United Kingdom: London,,,,,,host_health_state:Mastitis,,,,,,,,,,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,,,,,,,,,,,,,,,,,,,Mastitis,,,99.81,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,99822.26,Streptococcus dysgalactiae subsp. dysgalactiae strain DB49998-05,DB49998-05,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08943320,99822,,,,,,,,2019-11-12T00:00:00Z,,PRJNA450511,GCA_009650235.1,CP033163,,Singapore General Hospital,PacBio RSII,200X,Celera Assembler v. JAN-2017,1,,1,2171413,39.430798,2186,2040,blood,,2005,Singapore,Singapore,,,,Septicaemia,,,,,,,,,,,,,Comparative Genomic Analysis of the Streptococcus dysgalactiae subspecies dysgalactiae,collected_by:SGH,,,,,,,Septicaemia,,,,,,,,,,,,,,99.62,0.75,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,99822.27,Streptococcus dysgalactiae subsp. dysgalactiae strain DB31752-13,DB31752-13,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08943321,99822,,,,,,,,2019-11-12T00:00:00Z,,PRJNA450511,GCA_009650255.1,CP033164,,Singapore General Hospital,PacBio RSII,150X,Celera Assembler v. JAN-2017,1,,1,2319570,39.28656,2389,2226,blood,,2013,Singapore,Singapore,,,,Septicaemia,,,,,,,,,,,,,Comparative Genomic Analysis of the Streptococcus dysgalactiae subspecies dysgalactiae,collected_by:SGH,,,,,,,Septicaemia,,,,,,,,,,,,,,98.76,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis HP,99822.28,Streptococcus dysgalactiae subsp. dysgalactiae strain DB60705-15,DB60705-15,Streptococcus dysgalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN08943322,99822,,,,,,,,2019-11-12T00:00:00Z,,PRJNA450511,GCA_009650275.1,CP033165,,Singapore General Hospital,PacBio RSII,120X,Celera Assembler v. JAN-2017,1,,1,2190656,39.72991,2214,2080,blood,,2015,Singapore,Singapore,,,,Septicaemia,,,,,,,,,,,,,Comparative Genomic Analysis of the Streptococcus dysgalactiae subspecies dysgalactiae,collected_by:SGH,,,,,,,Septicaemia,,,,,,,,,,,,,,99.25,0,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis NHP,999416.50,Parabacteroides distasonis CL03T12C09,CL03T12C09,Parabacteroides distasonis,Parabacteroides,Tannerellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN16451183,999416,,,,,,,,2021-05-06T00:00:00Z,33901198,PRJNA669351,GCA_018292145.1,CP072254,,Brigham & Women's Hospital,PacBio Sequel,321x,FALCON-Unzip v. 1.2.0,1,0,1,5062790,45.130787,4358,4132,feces,,2009-05,USA,USA: Boston,,,,,,,,,,,,,,,,,Several fecal isolates from each of three individuals are examined via PacBio sequencing and assembly for the propensity of integrative and conjugative elements (ICE) carrying Type VI secretion system (T6SS) loci to propagate or sweep through communities of Bacteroides and Parabacteroides co-resident in the human gut microbiota.,"sample_type:cultured bacterial isolate;biomaterial_provider:Dr. Lauire Comstock, Brigham & Women's Hospital, 181 Longwood Avenue, Boston, MA 02115 USA",,,,,,,,,,,,,,,,,,,,,99.42,0.38,,,Gastrointestinal,- HP,2798861.3,Acinetobacter sp. CS-2,CS-2,Acinetobacter sp. CS-2,Acinetobacter,Moraxellaceae,Moraxellales,Gammaproteobacteria,Pseudomonadota,SAMN17142163,2798861,,,,,,,,2021-01-11T00:00:00Z,,PRJNA687053,GCA_016599715.1,"CP067019,CP067020,CP067021",,East China University of Science and Technology,Illumina NovaSeq,350.0x,HGAP v. v4,1,2,3,3567654,41.48673,3585,3379,hospital wastewater,,2020-08-05,China,China,,,,Acinetobacter blood infections,,,,,,,,,,,,,Acinetobacter sp. CS-2 Genome sequencing,collected_by:Yao shijie,,,,,,,Acinetobacter blood infections,,,,,,,,,,,,,,99.66,0.82,Bloodstream Infections,Other Bloodstream Infections,Other,Bloodstream Infections-Other Bloodstream Infections HP,2820817.3,Aggregatibacter sp. 2125159857,2125159857,Aggregatibacter sp. 2125159857,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN18435607,2820817,,,,,,,,2021-04-06T00:00:00Z,,PRJNA716419,GCA_017798005.1,CP072548,,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,183.0x,Unicycler v. v0.4.9b,1,0,1,1999512,43.015297,1951,1859,blood culture,,2021,Australia,Australia,,,,Sepsis,,,,,,,,,,,,,Aggregatibacter WGS,collected_by:Queensland Health,,,,,,,Sepsis,,,,,,,,,,,,,,99.66,0.45,Bloodstream Infections,Sepsis,Blood and Circulatory System,Bloodstream Infections-Sepsis NHP,712150.3,Aggregatibacter sp. oral taxon 513 strain W11186,W11186,Aggregatibacter sp. oral taxon 513,Aggregatibacter,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN18352203,712150,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128305.1,"CP072381,CP072382,CP072383",,The Forsyth Institute,PacBio Sequel,300x,Pacbio MA v. 9.0.0.92188,1,2,3,1939696,42.717518,1895,1820,human oral cavity,,2012-01,United Kingdom,United Kingdom: London,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02155;collected_by:William Wade, King's College London",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,99.89,0.45,,,Oral,- NHP,2810513.3,Agrococcus sp. Marseille-Q4369,Marseille-Q4369,Agrococcus sp. Marseille-Q4369,Agrococcus,Microbacteriaceae,Micrococcales,Actinomycetes,Actinomycetota,SAMN17833046,2810513,,,,,,,,2021-05-07T00:00:00Z,,PRJNA700510,GCA_018308945.1,CP070501,,IHU - Mediterannee Infection,Illumina; Oxford Nanopore,9.211749x,SPAdes v. 3.10,1,0,1,2737735,72.26996,2760,2691,,,2021,France,France: Marseille,,,,,,,,,,,,,,,,,Agrococcus sp nov strain Marseille-Q4369 was isolated from a human healthy skin swab as part of a culturomics project,sample_type:Skin swab,,,,,,,,,,,,,,,,,,,,,100,0.67,,,Other,- HP,1839798.3,Bacillus sp. FDAARGOS_235 strain FDAARGOS_235,FDAARGOS_235,Bacillus sp. FDAARGOS_235,Bacillus,Bacillaceae,Bacillales,Bacilli,Bacillota,SAMN04875572,1839798,,,,,,FDA:FDAARGOS_235,,2017-03-29T00:00:00Z,,PRJNA231221,GCA_002073415.2,"CP020437,CP020434,CP020436,CP020435",,US Food and Drug Administration,PacBio,14.0110509265725x,HGAP v. 3,1,3,4,5608141,35.28,6019,5799,blood,,2014-09-15,USA,USA:DC,,male,4Y,CVL infection,,,,,,,,,,,,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences\; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers\; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",collected_by:Children's National Hospital,,,,,,,CVL infection,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.2,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,556259.32,Bacteroides sp. D2,D2,Bacteroides sp. D2,Bacteroides,Bacteroidaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN20222658,556259,,,,,,,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147085.1,CP102261,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,6955292,41.722244,5419,5148,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:BEI,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.14,0.43,,,Other,- NHP,2291324.18,Bifidobacteriaceae bacterium KR001_MFL_0031,KR001_MFL_0031,Bifidobacteriaceae bacterium,Unclassified Bifidobacteriaceae,Bifidobacteriaceae,Bifidobacteriales,Actinomycetes,Actinomycetota,SAMN31100400,2291324,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757825.1,CP107219,,,PacBio Sequel II,8x,metaFlye v. 2.8.3-b1695,1,0,1,2290421,59.966488,1973,1870,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,1.1,,,Gastrointestinal,- NHP,2860051.3,Blautia sp. KLE_1732_HM_1032,KLE_1732_HM_1032,Blautia sp. KLE_1732_HM_1032,Blautia,Lachnospiraceae,Lachnospirales,Clostridia,Bacillota,SAMN20222667,2860051,,,,,,,,2022-09-12T00:00:00Z,,PRJNA746600,GCA_025147905.1,CP102266,,Stanford University,Illumina HiSeq; Oxford Nanopore,100x,Unicycler v. 0.4.8,1,0,1,3732965,44.27012,3716,3430,,,not applicable,,not applicable,,,,,,,,,,,,,,,,,"We construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2.",biomaterial_provider:BEI,not applicable,not applicable,not applicable,not applicable,,,,,,,,,,,,,not applicable,,,,99.24,0.03,,,Other,- HP,2592625.4,Brucella sp. 2280,2280,Brucella sp. 2280,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN12091575,2592625,,,,,,,,2019-11-06T00:00:00Z,,PRJNA549556,GCA_009601725.1,"CP045697,CP045698",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,12.0x,Unicycler v. v0.4.8,2,0,2,3584454,57.02958,3648,3442,lymph node,,2019,Australia,Australia: Queensland,,,,Brucellosis,,,,,,,,,,,,,Brucella WGS,collected_by:Queensland Health,,,,,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,2769351.3,Brucella sp. 6810,6810,Brucella sp. 6810,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN15962648,2769351,,,,,,,,2020-09-09T00:00:00Z,,PRJNA549556,GCA_014495905.1,"CP061088,CP061089,CP061090",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,100.0x,Unicycler v. AUG-2020,2,1,3,3522910,57.009518,3606,3351,blood culture,,2020,Australia,Australia,,,,Brucellosis,,,,,,,,,,,,,Brucella WGS,collected_by:Queensland Health,,,,,,,Brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Blood and Circulatory System,Specific Bacterial Infections-Brucellosis HP,693750.17,Brucella sp. BO2,BO2,Brucella sp. BO2,Brucella,Brucellaceae,Hyphomicrobiales,Alphaproteobacteria,Pseudomonadota,SAMN16909640,693750,,,,,,,,2020-12-08T00:00:00Z,,PRJNA549556,GCA_015832115.1,"CP065399,CP065400",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,53.0x,Unicycler v. NOV-2020,2,0,2,3290672,57.1978,3196,3023,lung biopsy,,2007,Australia,Australia,,,,Pneumonia,,,,,,,,,,,,,Brucella WGS,collected_by:Queensland Health,,,,,,,Pneumonia,,,,,,,,,,,,,,100,0,Respiratory Diseases,Pneumonia,Respiratory Tract,Respiratory Diseases-Pneumonia HP,2691913.3,Brucella sp. BO3,BO3,Brucella sp. BO3,Brucella sp. BO3,Brucella sp. BO3,Brucella sp. BO3,Brucella sp. BO3,Brucella sp. BO3,SAMN13656845,2691913,,,,,,,,2020-08-06T00:00:00Z,32719850,PRJNA597040,GCA_014084005.1,"CP047232,CP047233",,Northern Arizona University,Oxford Nanopore MiniION; Illumina MiSeq,85.0x,Unicycler v. 1.5.5,2,0,2,3378310,57.112225,3343,3135,lymph node,,2019-01,France,France: Lorient,,,,brucellosis,,,,,,,,,,,,,Whole genome sequencing and assembly of Brucella sp,"collected_by:Centre National de Reference des Brucella, Nimes",,,,,,,brucellosis,,,,,,,,,,,,,,100,0,Specific Bacterial Infections,Brucellosis,Other,Specific Bacterial Infections-Brucellosis HP,2814653.3,Caballeronia sp. M1242,M1242,Caballeronia sp. M1242,Caballeronia,Burkholderiaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN18042977,2814653,,,,,,,,2021-03-06T00:00:00Z,,PRJNA704483,GCA_017220215.1,"CP071129,CP071130,CP071131,CP071132",,Queensland Health Forensic and Scientific Services,Illumina NextSeq; Oxford Nanopore GridION,123.0x,Unicycler v. V0.4.8,1,3,4,5755538,63.87599,5563,5164,eta,,2021,Australia,Australia,,,,Respiratory Tract Infections,,,,,,,,,,,,,Caballeronia WGS,collected_by:Queensland Health,,,,,,,Respiratory Tract Infections,,,,,,,,,,,,,,99.6,0.8,Respiratory Diseases,Other Respiratory Diseases,Other,Respiratory Diseases-Other Respiratory Diseases HP,2572074.3,Campylobacter sp. CFSAN093224,CFSAN093224,Campylobacter sp. CFSAN093224,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487378,2572074,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012897395.1,CP040607,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",88x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1625593,30.563494,1690,1632,,,2017-11-07,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.57,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572065.3,Campylobacter sp. CFSAN093226,CFSAN093226,Campylobacter sp. CFSAN093226,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487369,2572065,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012897595.1,"CP040608,CP040609",,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",71x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,1,2,1720916,30.468367,1797,1746,,,2017-11-15,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.38,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572069.3,Campylobacter sp. CFSAN093227,CFSAN093227,Campylobacter sp. CFSAN093227,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487373,2572069,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012897855.1,CP040610,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",66x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1824459,30.160393,1959,1861,,,2018-05-01,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.5,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572084.3,Campylobacter sp. CFSAN093238,CFSAN093238,Campylobacter sp. CFSAN093238,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487388,2572084,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012898015.1,CP040611,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",76x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1745502,30.35018,1847,1762,,,2018-02-24,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.57,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572059.3,Campylobacter sp. CFSAN093241,CFSAN093241,Campylobacter sp. CFSAN093241,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487363,2572059,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012889595.1,CP040612,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",66x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1662100,30.507792,1707,1655,,,2018-01-03,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.84,0.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572050.3,Campylobacter sp. CFSAN093246,CFSAN093246,Campylobacter sp. CFSAN093246,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487354,2572050,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012889415.1,"CP040613,CP040614",,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",73x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,1,2,1752737,30.354868,1851,1772,,,2018-02-28,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.38,0.15,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572082.3,Campylobacter sp. CFSAN093256,CFSAN093256,Campylobacter sp. CFSAN093256,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487386,2572082,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012889735.1,CP040615,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",84x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1653603,30.530787,1701,1652,,,2018-03-06,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.56,0.16,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572083.3,Campylobacter sp. CFSAN093259,CFSAN093259,Campylobacter sp. CFSAN093259,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487387,2572083,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012889985.1,CP040617,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",64x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1688111,30.512508,1758,1714,,,2018-04-22,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.53,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2572085.3,Campylobacter sp. CFSAN093260,CFSAN093260,Campylobacter sp. CFSAN093260,Campylobacter,Campylobacteraceae,Campylobacterales,Epsilonproteobacteria,Campylobacterota,SAMN11487389,2572085,,,,,,,,2020-04-27T00:00:00Z,,PRJNA258022,GCA_012890095.1,CP040618,,FDA/CFSAN,"Oxford Nanopore GridION, Illumina MiSeq",70x,SPAdes; CANU v. SPAdes v3.1.1; Canu v1.7,1,0,1,1627779,30.555193,1674,1617,,,2017-10-18,Chile,Chile,,,,,,,,,,,,,,,,,Whole genome sequencing of cultured Campylobacter from FDA-CFSAN (Center for Food Safety and Applied Nutrition) for surveillance of foodborne pathogens.,"collected_by:Carlos Blondel lab, Universidad Autonoma",,,,,,,missing,,,,,,,,,,,,,,99.52,0.11,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,209053.3,Capnocytophaga sp. ChDC OS43 strain ChDC OS43,ChDC OS43,Capnocytophaga sp. ChDC OS43,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN07125685,209053,,,,,,KCOM:1579,,2017-06-27T00:00:00Z,,PRJNA386716,GCA_002209445.1,CP022022,,Chosun University,Illumina HiSeq,323.0x,SPAdes v. 3.8.2,1,,1,3412686,38.24,3230,3075,abscess,,2005,South Korea,South Korea: Gwangju,,,,refractory periapical abscess,,,,,,,,,,,,,Genome sequence of Capnocytophaga sp.,collected_by:Korean Collection for Oral Microbiology,,,,,,,refractory periapical abscess,,,,,,,,,,,,,,100,0,Skin and Soft Tissue Infections,Wounds and Abscesses,Skin and Soft Tissue,Skin and Soft Tissue Infections-Wounds and Abscesses NHP,2545799.3,Capnocytophaga sp. FDAARGOS_737 strain Not applicable,Not applicable,Capnocytophaga sp. FDAARGOS_737,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN11056452,2545799,,,,,,FDA:FDAARGOS_737,,2019-12-05T00:00:00Z,,PRJNA231221,GCA_009730375.1,CP046316,,US Food and Drug Administration,Pacbio; Illumina,1442.04x,"SMRT v. 2.3.0, HGAP v. 3",1,0,1,2652717,40.065037,2424,2319,human oral cavity,,,USA,USA:VA,,,,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.05,0.24,,,Oral,- NHP,1316593.3,Capnocytophaga sp. oral taxon 864 strain F0512,F0512,Capnocytophaga sp. oral taxon 864,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN08439036,1316593,,,,,,,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002998835.1,"CP027232,CP027233",,The Forsyth Institute,PacBio,119x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,1,2,2682541,39.467506,2465,2325,coronal/gingival,,2007,USA,"USA: Cambridge, MA",env_biome:Human oral cavity,male,5,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,Blood agar,,,,Healthy,,,,,,,,,Human oral cavity,,,,100,2.7,,,Oral,- NHP,1316596.3,Capnocytophaga sp. oral taxon 878 strain F0545,F0545,Capnocytophaga sp. oral taxon 878,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN08472925,1316596,,,,,,,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002999135.1,"CP027229,CP027230",,The Forsyth Institute,PacBio,307x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,1,2,2990835,37.947296,2836,2663,coronal/gingival,,2007,USA,"USA: Cambridge, MA",env_biome:Human oral cavity,male,4,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,Blood agar,,,,Healthy,,,,,,,,,Human oral cavity,,,,100,0,,,Oral,- NHP,2748316.3,Capnocytophaga sp. oral taxon 902 strain W10638,W10638,Capnocytophaga sp. oral taxon 902,Capnocytophaga,Flavobacteriaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN15360087,2748316,,,,,,,,2020-07-08T00:00:00Z,,PRJNA282954,GCA_013394735.1,CP058261,,The Forsyth Institute,PacBio RS II,161.0x,HGAP v. 2,1,0,1,2837214,39.263836,2617,2385,sub-gingival plaque oral cavity,,2011-12-01,United Kingdom,United Kingdom: London,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:whole organism;collected_by:Forsyth Institute,,,,,,,,periodontally healthy,,,,,,,,,,,,,99.29,0.71,,,Oral,- HP,2039166.3,Chryseobacterium sp. 6424,6424,Chryseobacterium sp. 6424,Chryseobacterium,Weeksellaceae,Flavobacteriales,Flavobacteriia,Bacteroidota,SAMN07672384,2039166,,,,,,,,2018-10-29T00:00:00Z,,PRJNA407992,GCA_003692615.1,CP023540,,Korea Centers for Disease Control and Prevention,PacBio; IonTorrent,300.0x,SPAdes v. v3.1,1,,1,2586303,42.402534,2546,2368,blood,,2014-05-25,South Korea,South Korea: Chonbuk,,,,Systemic lupus erythematosus,,,,,,,,,,,,,A novel species of the genus Chryseobacterium,collected_by:Chonbuk National University Medical School,,,,,,,Systemic lupus erythematosus,,,,,,,,,,,,,,99.51,1.47,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- NHP,1898204.361,Clostridiaceae bacterium KR001_HAM_0047,KR001_HAM_0047,Clostridiaceae bacterium ,unclassified Clostridiaceae,Eubacteriales ,Eubacteriales ,Clostridia ,Bacillota ,SAMN31100354,1898204,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757965.1,CP107207,,,PacBio Sequel II,5x,hifiasm_meta v. 0.2-r040,1,0,1,3220732,53.656033,3228,2964,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,99,0,,,Gastrointestinal,- NHP,1898207.5059,Clostridiales bacterium KR001_HIC_0007,KR001_HIC_0007,Clostridiales bacterium,unclassified Clostridiaceae,Eubacteriales ,Eubacteriales ,Clostridia ,Bacillota ,SAMN31100388,1898207,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757645.1,CP107216,,,PacBio Sequel II,18x,HiCanu v. 2.1.1,1,0,1,2378857,60.55244,2417,2282,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,97.4,1.3,,,Gastrointestinal,- NHP,2011094.224,Coriobacteriaceae bacterium KR001_HIC_0047,KR001_HIC_0047,Coriobacteriaceae bacterium,Unclassified Coriobacteriaceae,Coriobacteriaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMN31100390,2011094,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757745.1,CP107217,,,PacBio Sequel II,14x,HiCanu v. 2.1.1,1,0,1,2323157,59.68232,2027,1948,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,99.7,1.2,,,Gastrointestinal,- HP,169292.173,Corynebacterium aurimucosum DSM 44532,DSM 44532,Corynebacterium aurimucosum,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13404510,169292,,,,,,DSM:44532,,2023-07-05T00:00:00Z,,PRJNA433401,,"CP047048,CP047049",,,Illumina MiSeq,90.7x,Newbler v. 2.8,1,1,2,2740104,60.296616,2570,2526,clinical material,,,Germany,Germany,,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 44532,,,,,,,,,,,,,,,,,,,,,98.9,2.1,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,679663.4,Corynebacterium canis DSM 45402,DSM 45402,Corynebacterium canis,Corynebacterium,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN13404513,679663,,,,,,DSM:45402,,2023-07-05T00:00:00Z,,PRJNA454028,,CP047080,,,Illumina MiSeq; Oxford Nanopore GridION,75.9x,Newbler v. 2.8; canu v. 1.8,1,0,1,3045310,60.06367,2929,2682,infected wound from a dog bite,,2009,Germany,Germany: Freiburg,,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 45402,,,,,,,,,,,,,,,,,,,,,99.5,1.1,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,394964.3,Corynebacterium hansenii DSM 45109,DSM 45109,Corynebacterium hansenii,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,Corynebacteriaceae,SAMN06041734,394964,,,,,,DSM:45109,,2023-07-05T00:00:00Z,,PRJNA354159,,CP047211,,,Illumina MiSeq,31.3x,Newbler v. 2.8,1,0,1,3098017,70.13696,2778,2671,human liposarcoma pus,,,France,France,,,,,,,,,,,,,,,,,,sample_type:pure culture;biomaterial_provider:DSM 45109,,,,,,,,,,,,,,,,,,,,,98,1.1,Miscellaneous or Unspecified Infections,,Skin and Soft Tissue,Miscellaneous or Unspecified Infections- HP,2815361.3,Corynebacterium sp. CNCTC7651,CNCTC7651,Corynebacterium sp. CNCTC7651,Corynebacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,Corynebacteriaceae,SAMN18092215,2815361,,,,,,,,2022-01-18T00:00:00Z,,PRJNA705566,GCA_021496665.1,CP071246,,,Oxford Nanopore; Illumina MiSeq,40.0x,CANU v. 2021; Pilon v. 2021,1,0,1,2453109,64.89679,2346,2252,blood,,2019,Czech Republic,Czech Republic,,,,bacteremia,,,,,,,,,,,,,,collected_by:P Jezek,,,,,,,bacteremia,,,,,,,,,,,,,,97.65,3.35,Bloodstream Infections,Bacteremia,Blood and Circulatory System,Bloodstream Infections-Bacteremia HP,2027919.18,Enterobacter cloacae complex bacterium strain C45 strain C45-chromosome,C45-chromosome,Enterobacter cloacae complex sp.,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMEA104700141,2027919,,,,MLST.Enterobacter_cloacae.873,,,,2018-03-22T00:00:00Z,,PRJEB25613,GCA_900322725.1,"LT991957,LT991958,LT991959,LT991960",,CHU Clermont-ferrand,,,,1,3,4,5290194,55.195045,5204,,hospital,isolated over a one-year period and originating from hospital environment,2014,France,France,,,,,,host_health_state:diseased,,,,,,,,,,,"We investigated nosocomial infections involving unusual carbapenemase-producing Enterobacter cloacae complex (ECC) strains isolated over a one-year period and originating from hospital environment. Whole-genome sequence typing revealed the predominance of epidemic isolates belonging to the novel sequence type ST873 , which produced the carbapenemase VIM-4. The mechanism underlying the one-year outbreak involved the emergence of a new phylogenetic lineage within the ECC, which should be closely monitored in the context of nosocomial infections",,,,,,,,,diseased,,,,,,,,,,,,,99.4,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2969431.4,Enterobacter cloacae complex sp. R_G8,R_G8,Enterobacter cloacae complex sp. R_G8,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN29928042,2969431,,,,,,,,2022-08-09T00:00:00Z,,PRJNA861833,GCA_024599795.1,CP102246,,Univeristy of Pretoria and National Health Laboratory Services,PacBio Sequel,100X,HGAP v. JAN-2022,1,0,1,4952526,55.17655,4652,4553,rectal swab,,2020,South Africa,South Africa: Pretoria,,female,42,Infection,,,Susceptible;Resistant;Not defined,AMR Panel,,,,,,,,,"Both carbapenem and colistin-resistance mechanisms are seen in Klebsiella pneumoniae. Carbapenem and colistin resistance mechanisms pose a significant threat to public and clinical health because carbapenem and colistin are last-line antibiotics for ESBL-positive Enterobacteriaceae. The aim of the study, therefore, is to study the resistance mechanisms of both carbapenem and colistin-resistant K. pneumoniae strains using genomics, and transcriptomics, and clustered-regularly interspaced short palindromic repeats (CRISPR). It will highlight the differentially expressed genes (DEGs) in the presence of the antibiotics. Clustered-regularly interspaced short palindromic repeats (CRISPR) associated proteins (Cas) will be used to knock out these genes to identify their function in antibiotic resistance.",collected_by:National health Laboratory service,,,,,,,Infection,,,,,,,,,,,,,,97.61,4.53,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,2027919.295,Enterobacter cloacae complex sp. strain ECL42,ECL42,Enterobacter cloacae complex sp.,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20834670,2027919,,,,,,,,2021-09-02T00:00:00Z,,PRJNA757181,GCA_019856235.1,"CP082147,CP082148,CP082149,CP082150,CP082151,CP082152",,Yongchuan Hospital of Chongqing Medical University,Oxford Nanopore PromethION,338.0x,canu v. 1.6,1,5,6,5483197,54.34762,5491,5269,blood,,2016-09-23,China,"China: Jiamusi, Heilongjiang Province",,,,,,,,,,,,,,,,,"Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, the objectives of our study were the following: (i) to describe the prevalence of clinical CRE isolates, (ii) to identify the mechanisms and clonal relatedness among these CRE strains, (iii) to examine the genetic context of IMP-4.",sample_type:Pure culture,,,,,,,,,,,,,,,,,,,,,99.7,2.19,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2027919.296,Enterobacter cloacae complex sp. strain ECL60,ECL60,Enterobacter cloacae complex sp.,Enterobacter,Enterobacteriaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN20825299,2027919,,,,,,,,2021-09-15T00:00:00Z,,PRJNA757181,GCA_019998725.1,"CP083234,CP083235,CP083236",,Yongchuan Hospital of Chongqing Medical University,Oxford Nanopore PromethION,500.0x,canu v. 1.6,1,2,3,4954601,54.794724,4826,4650,blood,,2017-09-22,China,"China: Jiamusi, Heilongjiang Province",,,,,,,,,,,,,,,,,"Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, the objectives of our study were the following: (i) to describe the prevalence of clinical CRE isolates, (ii) to identify the mechanisms and clonal relatedness among these CRE strains, (iii) to examine the genetic context of IMP-4.",sample_type:Pure culture,,,,,,,,,,,,,,,,,,,,,99.97,0.92,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2582830.3,Enterococcus sp. M190262,M190262,Enterococcus sp. M190262,Enterococcus,Enterococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN11660479,2582830,,,,,,,,2019-05-26T00:00:00Z,,PRJNA543310,GCA_005843965.1,"CP040461,CP040462",,New York Medical College,Illumina,not specified,SPAdes v. 3.9.0,1,1,2,3550287,40.231705,3472,3276,missing,,2019-02-20,USA,USA:Valhalla,,,,,,,,,,,,,,,,,Enterococcus sp. M190262 is a clinical isolate with vancomycin-resistant.,sample_type:whole organism,,,,,,,,,,,,,,,,,,,,,99.25,0.19,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2109692.3,Erysipelotrichaceae bacterium GAM147,GAM147,Erysipelotrichaceae bacterium GAM147,Unclassified Erysipelotrichaceae,Erysipelotrichaceae,Erysipelotrichales,Erysipelotrichia,Bacillota,SAMD00113753,2109692,,,,,,JCM:32526,,2018-06-02T00:00:00Z,,PRJDB6815,GCA_003573995.1,AP018537,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",PacBio RSII; MiSeq,157x,HGAP Assembly v. 3.0; Pilon v. 1.18,1,,1,2753585,29.818872,2867,,,,2016,Japan,Japan,env_biome:not applicable,,,,,,,,,,,,,,,,"Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media.",,not applicable,not applicable,feces,not applicable,Whole genome sequencing of novel bacterial isolates from feces of a healthy Japanese individual,,,,,,,,,,,,not applicable,,,,96.4,3.3,,,Other,- NHP,2841037.3,Eubacterium sp. c-25,c-25,Eubacterium sp. c-25,Eubacterium,Eubacteriaceae,Eubacteriales,Clostridia,Bacillota,SAMD00327613,2841037,,,,,,,,2021-11-03T00:00:00Z,,PRJDB11774,GCA_020892095.1,AP024845,,"Research Faculty of Agriculture, Hokkaido University",Illumina MiSeq; Oxford Nanopore MinION,200x,unicycler v. 0.4.7,1,0,1,3042110,44.50832,3038,2893,,,,,not applicable,,,,,,,,,Positive,ARRAY(0x731a9e0),No,Mesophilic,37,Anaerobic,HostAssociated,,Genome sequencing of secondary bile acid-producing bacteria and characterization of the gene functions relevant for the production.,"biomaterial_provider:Dr. Hiroshi Oda, Department of Bacteriology, Faculty of Medicine, Kagoshima University, Kagoshima, Japan",human-associated habitat,intestine environment,feces,7224633,Eubacterium sp. c-25 Genome sequencing and assembly,,,,,,,,,,,commensal,human-associated habitat,,,,98.25,0.88,,,Other,- NHP,712310.3,Haemophilus sp. oral taxon 036 strain F0629,F0629,Haemophilus sp. oral taxon 036,Haemophilus,Pasteurellaceae,Pasteurellales,Gammaproteobacteria,Pseudomonadota,SAMN08439034,712310,,,,,,,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002998595.1,CP027235,,The Forsyth Institute,PacBio,98x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,1805716,38.400723,1671,1646,nylon brush,,2015-05-18,USA,"USA: Boston, MA",env_biome:Human oral cavity,female,33,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,"Fastidious Anaerobe Agar (FAA) supplemented with 5g/L yeast extract, 5% sheep blood, 1 ug/ml 2, 4-Dihydroxy naphthoate (DHNA), 10 ug/ml Hemin and nicotinamide adenine dinucleotide (NAD), 1 ug/mL",,,,Healthy,,,,,,,,,Human oral cavity,,,,100,0,,,Other,- HP,2855441.3,Halomonas sp. 18071143,18071143,Halomonas sp. 18071143,Halomonas,Halomonadaceae,Oceanospirillales,Gammaproteobacteria,Pseudomonadota,SAMN20058479,2855441,,,,,,,,2021-07-14T00:00:00Z,,PRJNA743705,GCA_019211725.1,CP078120,,Chengdu Medical College,Oxford Nanopore PromethION,474.51x,Canu v. 1.5,1,0,1,3863061,60.38072,3689,,blood,,2018-07-11,China,China: Chengdu,,,,bloodstream infection,,,,,,,,,,,,,Halomonas sp. strain 18071143 from the blood of a neonatal patient,collected_by:Chengbin Xie;sample_type:blood,,,,,,,bloodstream infection,,,,,,,,,,,,,,100,1.19,Bloodstream Infections,Other Bloodstream Infections,Blood and Circulatory System,Bloodstream Infections-Other Bloodstream Infections NHP,2109690.3,Lachnospiraceae bacterium Choco86,Choco86,Lachnospiraceae bacterium Choco86,Unclassified Lachnospiraceae,Lachnospiraceae,Lachnospirales,Clostridia,Bacillota,SAMD00113752,2109690,,,,,,JCM:32527,,2018-06-02T00:00:00Z,,PRJDB6815,GCA_003584665.1,AP018535,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Sequel; NextSeq 500,210x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,,1,2785030,44.030693,2686,,,,2016,Japan,Japan,env_biome:not applicable,,,,,,,,,,,,,,,,"Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media.",,not applicable,not applicable,feces,not applicable,Whole genome sequencing of novel bacterial isolates from feces of a healthy Japanese individual,,,,,,,,,,,,not applicable,,,,100,1.9,,,Other,- NHP,2109691.3,Lachnospiraceae bacterium GAM79,GAM79,Lachnospiraceae bacterium GAM79,Unclassified Lachnospiraceae,Lachnospiraceae,Lachnospirales,Clostridia,Bacillota,SAMD00113756,2109691,,,,,,JCM:32525,,2018-06-02T00:00:00Z,,PRJDB6815,GCA_003584705.1,AP018536,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",PacBio RSII; MiSeq,124x,HGAP Assembly v. 3.0; Pilon v. 1.18,1,,1,4078671,46.233173,3939,,,,2016,Japan,Japan,env_biome:not applicable,,,,,,,,,,,,,,,,"Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media.",,not applicable,not applicable,feces,not applicable,Whole genome sequencing of novel bacterial isolates from feces of a healthy Japanese individual,,,,,,,,,,,,not applicable,,,,100,4.4,,,Other,- NHP,2594789.3,Lachnospiraceae bacterium KGMB03038,KGMB03038,Lachnospiraceae bacterium KGMB03038,Unclassified Lachnospiraceae,Lachnospiraceae,Lachnospirales,Clostridia,Bacillota,SAMN12234500,2594789,,,,,,,,2019-07-24T00:00:00Z,,PRJNA553314,GCA_007361935.1,CP041667,,Korean Research Institute of Bioscience and Biotechnology,PacBio Sequel,382.92x,HGAP v. 4.0,1,,1,3334474,47.828594,3323,,feces from healthy person,,2017-08-18,South Korea,South Korea: Seoul National University Bundang Hospital,,,,,,,,,,,,,,,,,To functional study of human gut microbiome,sample_type:cultured single cell,,,,,,,,,,,,,,,,,,,,,98.83,1.17,,,Gastrointestinal,- NHP,1898203.4013,Lachnospiraceae bacterium KR001_HAM_0003,KR001_HAM_0003,Lachnospiraceae bacterium ,Unclassified Lachnospiraceae ,Lachnospiraceae ,Lachnospirales ,Clostridia ,Bacillota ,SAMN31100341,1898203,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757865.1,CP107200,,,PacBio Sequel II,8x,hifiasm_meta v. 0.2-r040,1,0,1,3727648,48.063255,3744,3413,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,97.3,3.3,,,Gastrointestinal,- NHP,1898203.4015,Lachnospiraceae bacterium KR001_HIC_0035,KR001_HIC_0035,Lachnospiraceae bacterium ,Unclassified Lachnospiraceae ,Lachnospiraceae ,Lachnospirales ,Clostridia ,Bacillota ,SAMN31100338,1898203,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025758065.1,CP107199,,,PacBio Sequel II,32x,HiCanu v. 2.1.1,1,0,1,3954180,43.237686,3822,3589,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,98.2,1.8,,,Gastrointestinal,- NHP,1898203.4014,Lachnospiraceae bacterium KR001_MFL_0129,KR001_MFL_0129,Lachnospiraceae bacterium ,Unclassified Lachnospiraceae ,Lachnospiraceae ,Lachnospirales ,Clostridia ,Bacillota ,SAMN31100350,1898203,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025758025.1,CP107204,,,PacBio Sequel II,14x,metaFlye v. 2.8.3-b1695,1,0,1,3398993,36.568947,3042,2849,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- HP,712982.61,Lachnospiraceae bacterium oral taxon 096 strain F0428,F0428,Lachnospiraceae bacterium oral taxon 096,Unclassified Lachnospiraceae ,Lachnospiraceae ,Lachnospirales ,Clostridia ,Bacillota ,SAMN18352199,712982,,,,,,,,2021-04-28T00:00:00Z,,PRJNA282954,GCA_018141845.1,CP073340,,The Forsyth Institute,PacBio Sequel,560x,Pacbio MA v. 9.0.0.92188,1,0,1,2241976,39.68828,2124,2072,human oral cavity,,2008-04-10,USA,"USA: Boston, Massachusetts",,female,3.9,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02161;collected_by:Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,Severe early childhood dental caries,,,,,,,,,human oral cavity,,,,97.15,0.42,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,712991.3,Lachnospiraceae bacterium oral taxon 500 strain W11650,W11650,Lachnospiraceae bacterium oral taxon 500,Unclassified Lachnospiraceae ,Lachnospiraceae ,Lachnospirales ,Clostridia ,Bacillota ,SAMN08439028,712991,,,,,,,,2018-03-16T00:00:00Z,,PRJNA282954,GCA_002999035.1,CP027241,,The Forsyth Institute,PacBio,107x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,3201383,45.333534,3216,2871,periodontal pocket,,2013-05-03,United Kingdom,United Kingdom: London,env_biome:Human oral cavity,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,Periodontitis,,,,,,,,,Human oral cavity,,,,96.1,1.3,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- NHP,2816909.3,Lactococcus sp. LG1074,LG1074,Lactococcus sp. LG1074,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086912,2816909,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309525.1,"CP071293,CP071294",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,1,2,2082475,38.151142,2088,2009,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0,,,Gastrointestinal,- NHP,2816910.3,Lactococcus sp. LG1267,LG1267,Lactococcus sp. LG1267,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086946,2816910,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309545.1,"CP071295,CP071296,CP071297,CP071298",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,3,4,2181478,37.953945,2121,2059,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.62,0,,,Gastrointestinal,- NHP,2816911.3,Lactococcus sp. LG592,LG592,Lactococcus sp. LG592,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086908,2816911,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309625.1,"CP071300,CP071299",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,1,2,2162438,37.971123,2137,2061,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,99.62,0,,,Gastrointestinal,- NHP,2816912.3,Lactococcus sp. LG606,LG606,Lactococcus sp. LG606,Lactococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN18086909,2816912,,,,,,,,2021-03-09T00:00:00Z,,PRJNA705383,GCA_017309645.1,"CP071301,CP071302,CP071303,CP071304",,The Second Affiliated Hospital of Zhejiang University,Illumina NovaSeq 6000; Nanopore,200.0x,Unicycler v. v.0.4.3,1,3,4,2318463,37.839294,2303,2222,human feces,isolated from faecal samples of healthy humans,2019,China,China:Hangzhou,,,,,,,,,,,,,,,,,"To characterize the linezolid resistance gene optrA identified in Lactococcus garvieae, which were isolated from faecal samples of healthy humans.",sample_type:mixed culture,,,,,,,,,,,,,,,,,,,,,100,0.57,,,Gastrointestinal,- NHP,712361.3,Leptotrichia sp. oral taxon 218 strain F0707,F0707,Leptotrichia sp. oral taxon 218,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN18352197,712361,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128225.1,CP072377,,The Forsyth Institute,PacBio Sequel,208x,Flye v. 2.8,1,0,1,2172496,28.955496,2098,2004,human oral cavity,,2017-05-12,USA,"USA: Cambridge, Massachusetts",,female,51,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02163;collected_by:Sowmya Balasubramanian, Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,98.88,1.12,,,Oral,- NHP,712362.3,Leptotrichia sp. oral taxon 221 strain F0705,F0705,Leptotrichia sp. oral taxon 221,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN18352196,712362,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018128245.1,"CP072378,CP072379",,The Forsyth Institute,PacBio Sequel,637x,Pacbio MA v. 9.0.0.92188,1,1,2,2076334,29.22762,1843,1798,human oral cavity,,2017-05-12,USA,"USA: Cambridge, Massachusetts",,female,51,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02162;collected_by:Sowmya Balasubramanian, Forsyth Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,100,1.12,,,Oral,- NHP,712368.3,Leptotrichia sp. oral taxon 498,F0590,Leptotrichia sp. oral taxon 498,Leptotrichia,Leptotrichiaceae,Fusobacteriales,Fusobacteriia,Fusobacteriota,SAMN05413925,712368,,,,,,,,2017-08-02T00:00:00Z,,PRJNA282954,GCA_002240055.1,CP016753,,The Forsyth Institute,PacBio,98x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2152181,29.62,2134,2010,"curette; supragingival dental plaque, molar tooth",,2008-08-05,USA,"USA: Boston, MA",env_biome:Human oral cavity,male,4.3 years,,,,,,,,,,C,,,,Forsyth oral bacterial genomes,,,,,TSBY,,,,"Medially healthy, severe/advance early childhood dental caries",,,,,,,,,Human oral cavity,,,,100,1.7,,,Oral,- HP,180434.89,Morganella morganii subsp. morganii QLYYMMQL588,QLYYMMQL588,Morganella morganii,Morganella,Morganellaceae ,Enterobacterales,Gammaproteobacteria,Pseudomonadota ,SAMN35741046,180434,,,ESBL,,,,,2023-06-28T00:00:00Z,,PRJNA983965,,"CP128435,CP128436,CP128437",,,Illumina HiSeq; PacBio,99.34x,SOAPdenovo2 v. v1.2.9,1,2,3,3978273,51.151817,3997,,urine,,2023-01-19,China,China,,female,53,urinary tract infection,,host_disease_stage:fever;host_health_state:fever,,,,,,,,,,,,collected_by:Qilu Hospital of Shandong University,,,,,,,,,,,,,,,,,,,,,99.1,1,Miscellaneous or Unspecified Infections,,Urinary Tract,Miscellaneous or Unspecified Infections- HP,2857058.3,Mycobacterium sp. SMC-2,SMC-2,Mycobacterium sp. SMC-2,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN20167550,2857058,,,,,,,,2022-09-19T00:00:00Z,,PRJNA745498,GCA_025263485.1,"CP079863,CP079864",,Samsung Medical Center,Illumina HiSeq X Ten; Oxford Nanopore,100.0x,Canu v. MAY-2021,1,1,2,6027766,67.573425,5814,5614,sputum,,2018-05-19,South Korea,South Korea: Seoul,,,,Lung disease,,,,,,,,,,,,,Report of novel Mycobacterium species,collected_by:Tae Yeul Kim,,,,,,,Lung disease,,,,,,,,,,,,,,99.94,0.61,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,2857059.3,Mycobacterium sp. SMC-4,SMC-4,Mycobacterium sp. SMC-4,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN20167676,2857059,,,,,,,,2022-09-19T00:00:00Z,,PRJNA745503,GCA_025263265.1,"CP079869,CP079870,CP079879,CP079873,CP079871,CP079872,CP079874,CP079875,CP079876,CP079877,CP079878",,Samsung Medical Center,Illumina HiSeq X Ten; Oxford Nanopore,100.0x,Unicycler v. MAY-2021,1,10,11,5936685,66.64014,5741,5594,sputum,,2019-04-04,South Korea,South Korea: Seoul,,,,Lung disease,,,,,,,,,,,,,Report of novel Mycobacterium species,collected_by:Tae Yeul Kim,,,,,,,Lung disease,,,,,,,,,,,,,,100,0,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases HP,2857060.3,Mycobacterium sp. SMC-8,SMC-8,Mycobacterium sp. SMC-8,Mycobacterium,Mycobacteriaceae,Mycobacteriales,Actinomycetes,Actinomycetota,SAMN20167551,2857060,,,,,,,,2022-09-19T00:00:00Z,,PRJNA745500,GCA_025263565.1,"CP079865,CP079866,CP079867,CP079868",,Samsung Medical Center,Illumina HiSeq X Ten; Oxford Nanopore,100.0x,NextDenovo v. MAY-2021,1,3,4,6882089,67.434654,6837,6499,sputum,,2020-07-11,South Korea,South Korea: Seoul,,,,Lung disease,,,,,,,,,,,,,Report of novel Mycobacterium species,collected_by:Tae Yeul Kim,,,,,,,Lung disease,,,,,,,,,,,,,,99.96,1.67,Respiratory Diseases,Lung Diseases,Respiratory Tract,Respiratory Diseases-Lung Diseases NHP,2109685.3,Olsenella sp. GAM18,GAM18,Olsenella sp. GAM18,Olsenella,Atopobiaceae,Coriobacteriales,Coriobacteriia,Actinomycetota,SAMD00113754,2109685,,,,,,JCM:32523,,2018-06-02T00:00:00Z,,PRJDB6815,GCA_003609875.1,AP018530,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",PacBio RSII; MiSeq,240x,HGAP Assembly v. 3.0; Pilon v. 1.18,1,,1,2100540,65.60237,1924,,,,2016,Japan,Japan,,,,,,,,,,,,,,,,,"Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media.",,not applicable,not applicable,feces,not applicable,Whole genome sequencing of novel bacterial isolates from feces of a healthy Japanese individual,,,,,,,,,,,,not applicable,,,,100,0,,,Other,- NHP,2109687.3,Oscillibacter sp. PEA192,PEA192,Oscillibacter sp. PEA192,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMD00113757,2109687,,,,,,JCM:32522,,2018-06-02T00:00:00Z,,PRJDB6815,GCA_003574015.1,AP018532,,"Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases",Sequel; NextSeq 500,370x,Canu v. 1.4; minimap v. 0.2-r124; racon v.,1,,1,3320462,59.27865,3577,,,,2016,Japan,Japan,env_biome:not applicable,,,,,,,,,,,,,,,,"Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media.",,not applicable,not applicable,feces,not applicable,Whole genome sequencing of novel bacterial isolates from feces of a healthy Japanese individual,,,,,,,,,,,,not applicable,,,,98.7,1.3,,,Other,- NHP,2485925.2112,Oscillospiraceae bacterium KR001_HAM_0005,KR001_HAM_0005,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100353,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757945.1,CP107206,,,PacBio Sequel II,4x,hifiasm_meta v. 0.2-r040,1,0,1,3279038,42.1527,3210,3023,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,99.8,0,,,Gastrointestinal,- NHP,2485925.2108,Oscillospiraceae bacterium KR001_HAM_0045,KR001_HAM_0045,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100345,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757625.1,CP107201,,,PacBio Sequel II,5x,hifiasm_meta v. 0.2-r040,1,0,1,3532120,57.36954,3464,3148,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,2485925.2114,Oscillospiraceae bacterium KR001_HAM_0051,KR001_HAM_0051,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100346,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025758005.1,CP107202,,,PacBio Sequel II,5x,hifiasm_meta v. 0.2-r040,1,0,1,3530461,40.89854,3392,3235,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,2485925.2109,Oscillospiraceae bacterium KR001_HAM_0053,KR001_HAM_0053,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100412,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757685.1,CP107220,,,PacBio Sequel II,8x,hifiasm_meta v. 0.2-r040,1,0,1,1986203,53.302658,1894,1812,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,91.6,2.8,,,Gastrointestinal,- NHP,2485925.2111,Oscillospiraceae bacterium KR001_HAM_0066,KR001_HAM_0066,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100365,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757845.1,CP107211,,,PacBio Sequel II,4x,hifiasm_meta v. 0.2-r040,1,0,1,2914266,58.080627,2996,2732,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,99.7,0.3,,,Gastrointestinal,- NHP,2485925.2113,Oscillospiraceae bacterium KR001_HAM_0071,KR001_HAM_0071,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100361,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757985.1,CP107210,,,PacBio Sequel II,4x,hifiasm_meta v. 0.2-r040,1,0,1,3072273,56.926548,3094,2843,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,2485925.2107,Oscillospiraceae bacterium KR001_HIC_0038,KR001_HIC_0038,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100360,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757565.1,CP107209,,,PacBio Sequel II,51x,HiCanu v. 2.1.1,1,0,1,3089280,56.010494,3219,2926,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,2485925.2115,Oscillospiraceae bacterium KR001_HIC_0042,KR001_HIC_0042,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100358,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025758045.1,CP107208,,,PacBio Sequel II,20x,HiCanu v. 2.1.1,1,0,1,3159018,56.862007,3127,2894,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0,,,Gastrointestinal,- NHP,2485925.211,Oscillospiraceae bacterium KR001_HIC_0044,KR001_HIC_0044,Oscillospiraceae bacterium,Oscillibacter,Oscillospiraceae,Eubacteriales,Clostridia,Bacillota,SAMN31100370,2485925,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757805.1,CP107214,,,PacBio Sequel II,23x,HiCanu v. 2.1.1,1,0,1,2819195,56.231018,2833,2588,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.5,,,Gastrointestinal,- NHP,1658672.29,Ottowia sp. oral taxon 894 strain W10237,W10237,Ottowia sp. oral taxon 894,Ottowia,Comamonadaceae,Burkholderiales,Betaproteobacteria,Pseudomonadota,SAMN03704033,1658672,,,,,,,,2015-08-07T00:00:00Z,,PRJNA282954,GCA_001262075.1,CP012073,,The Forsyth Institute,PacBio,105x,SMRT Analysis RS_HGAP_Assembly.2 v.,1,,1,2925783,63.592583,3295,2284,"subgingival plaque, gingival sulcus",,2011-09-21,United Kingdom,United Kingdom: London,,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:pure culture,,,,TSBY,,,,"Supragingival plaque, healthy",,,,,,,,,Human oral cavity,,,,99.02,1.17,,,Oral,- HP,2806263.3,Paludibacterium sp. B53371,B53371,Paludibacterium sp. B53371,Paludibacterium ,Chromobacteriaceae,Neisseriales,Betaproteobacteria,Pseudomonadota,SAMN17600831,2806263,,,,,,,,2021-06-09T00:00:00Z,,PRJNA695077,GCA_018802765.1,CP069163,,National Cheng Kung University Hospital,PacBio,480.0x,PacBio subreads Flye v. 2.5,1,0,1,3626872,61.205856,3421,,blood,,2018-09-07,Taiwan,Taiwan: Tainan,,,,pneumonia,,,,,,,,,,,,,A clinical Paludibacteria strain isolated from one patient with severe pneumonia,collected_by:National Cheng Kung University Hospital,,,,,,,pneumonia,,,,,,,,,,,,,,99.57,0.45,Respiratory Diseases,Pneumonia,Blood and Circulatory System,Respiratory Diseases-Pneumonia NHP,712435.3,Porphyromonas sp. oral taxon 275 strain W7780,W7780,Porphyromonas sp. oral taxon 275,Porphyromonas,Porphyromonadaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352206,712435,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127745.1,CP072333,,The Forsyth Institute,PacBio Sequel,242x,Pacbio MA v. 9.0.0.92188,1,0,1,2180921,60.637318,1827,1699,human oral cavity,,1992-01-02,Finland,Finland:Helsinki,,male,2,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02164;collected_by:Eija Kononen, University of Turku",human oral cavity,,,,Genome analysis of human oral bacteria,,,healthy,,,,,,,,,human oral cavity,,,,97.08,0.47,,,Oral,- HP,712471.3,Prevotella sp. oral taxon 475 strain F0059,F0059,Prevotella sp. oral taxon 475,Prevotella,Prevotellaceae,Bacteroidales,Bacteroidia,Bacteroidota,SAMN18352175,712471,,,,,,,,2021-04-22T00:00:00Z,,PRJNA282954,GCA_018127805.1,CP072334,,The Forsyth Institute,PacBio Sequel,563x,Pacbio MA v. 9.0.0.92188,1,0,1,2560308,50.02406,2272,1959,human oral cavity,,1988-01,USA,"USA: Blacksberg, Virginia",,female,adult,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,"sample_type:whole organism;biomaterial_provider:Floyd E. Dewhirst, The Forsyth Institute, 245 First Street, Cambridge, Massachusetts, 02187;collected_by:Moores, Virginia Polytechnic Institute",human oral cavity,,,,Genome analysis of human oral bacteria,,,moderate periodontitis,,,,,,,,,human oral cavity,,,,98.81,0,Miscellaneous or Unspecified Infections,,Oral,Miscellaneous or Unspecified Infections- HP,2490996.3,Proteus sp. GOKU,GOKU,Proteus sp. GOKU,Proteus,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN08166470,2490996,,,,,,,,2020-11-13T00:00:00Z,,PRJNA505956,GCA_015475555.1,CP034105,,National Chung Cheng University,Illumina; Oxford Nanopore,101.0x,Unicycler v. 0.4.7,1,0,1,4141308,37.998333,3766,3676,tissue,,2015,Taiwan,Taiwan,,,,infection,,,,,,,,,,,,,Analysis of the genome in order to understand the genetic factors leading to virulence and antibiotic resistance,collected_by:Ching-Lin Shy,,,,,,,infection,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2603246.3,Providencia sp. 1709051003,1709051003,Providencia sp. 1709051003,Providencia,Morganellaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN12560326,2603246,,,,,,,,2020-03-02T00:00:00Z,,PRJNA559816,GCA_011045655.1,CP042861,,Beijing Institute of Microbiology and Epidemiology,PacBio RSII,100.0x,HGAP v. v3.0,1,0,1,4649235,40.297382,4412,4202,urine,,2017,China,China: zhengzhou,,,,urinary tract infection,,,,,,,,,,,,,Complete sequence of chromosome of strain 1709051003,,,,,,,,urinary tract infection,,,,,,,,,,,,,,100,1.08,Urinary Tract Diseases,Unspecified Urinary Tract Diseases,Urinary Tract,Urinary Tract Diseases-Unspecified Urinary Tract Diseases HP,2056231.21,Pseudomonas qingdaonensis L1712hy,L1712hy,Pseudomonas qingdaonensis ,Pseudomonadas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria ,Pseudomonadota,SAMN36375298,2056231,,,,,,,,2023-07-19T00:00:00Z,,PRJNA390758,,CP129981,,,Oxford Nanopore,200X,Unicycler v. 0.4.9,1,0,1,6054743,63.904465,5637,5531,stool,,2019-10-14,China,China:Hangzhou,,,,Diarrhea,,,,,,,,,,,,,,collected_by:Hao Xu,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Gastrointestinal,Miscellaneous or Unspecified Infections- HP,2018067.3,Pseudomonas sp. FDAARGOS_380,FDAARGOS_380,Pseudomonas sp. FDAARGOS_380,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota ,SAMN07312424,2018067,,,,,,FDA:FDAARGOS_380,,2017-10-18T00:00:00Z,,PRJNA231221,GCA_002591235.1,CP023969,,US Food and Drug Administration,PacBio; Illumina,14.44x,"SMRT v. 2.3.0, HGAP v. 3",1,,1,6499364,59.73,6203,5963,g tube,,2015-04-27,USA,USA:DC,,male,8M,,,,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:Children's National Hospital,,,,,,,Missing,Missing,Missing,Missing,Missing,,,,,,,,,,100,1.3,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2545800.3,Pseudomonas sp. FDAARGOS_761 strain Not applicable,Not applicable,Pseudomonas sp. FDAARGOS_761,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota ,SAMN11056476,2545800,,,,MLST.Pseudomonas_aeruginosa.971,,FDA:FDAARGOS_761,,2020-06-15T00:00:00Z,,PRJNA231221,GCA_013343155.1,CP054572,,US Food and Drug Administration,Pacbio; Illumina,616.89x,"SMRT v. 2.3.0, HGAP v. 3",1,0,1,6384852,66.415596,6009,5847,"healthy biopsy tissue taken from the rectum; healthy biopsy tissue, rectum",,,USA,USA:VA,,male,59Y,,,host_description:Not applicable,,,,,,,,,,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",collected_by:BEI Resources/American Type and Culture Collection (ATCC),,,,,,,Unknown,Unknown,Unknown,Not applicable,Unknown,,,,,,,,,,99.68,0.14,,,Gastrointestinal,- NHP,3019098.3,Pseudomonas sp. TUM22785,TUM22785,Pseudomonas sp. TUM22785,Pseudomonas,Pseudomonadaceae,Pseudomonadales,Gammaproteobacteria,Pseudomonadota ,SAMN32406711,3019098,,,,,,,,2023-01-28T00:00:00Z,,PRJDB14962,,CP116239,,,Illumina MiSeq; Oxford Nanopore MinION,377.0x,Unicycler v. NOV-2022,1,0,1,7016867,66.01659,6377,6202,urine,,2022,Japan,Japan,,,,,,,,,,,,,,,,,,,missing,missing,missing,normal,,,,,,,,,,,,,missing,,,,100,2.6,,,Urinary Tract,- HP,2204208.3,Salmonella sp. FORC89,FORC89,Salmonella sp. FORC89,Salmonella,Enterobacteriaceae,Enterobacteriales,Gammaproteobacteria,Pseudomonadota,SAMN09258664,2204208,,,,MLST.Salmonella_enterica.11,,,,2022-09-16T00:00:00Z,,PRJNA473048,GCA_025232695.1,"CP029682,CP029683",,Seoul National University,PacBio,,SMRT Analysis v. 2.3.0,1,1,2,4766465,52.122276,4842,4833,stool,,2016-01-01,South Korea,South Korea: Seoul,,,,Food-poisoning,,,,,,,,,,,,,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activities with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea",collected_by:Samsung Seoul Hospital,,,,,,,Food-poisoning,,,,,,,,,,,,,,100,0.13,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,2204208.4,Salmonella sp. FORC89,FORC89,Salmonella sp. FORC89,Salmonella,Enterobacteriaceae,Enterobacteriales,Gammaproteobacteria,Pseudomonadota,SAMN09258664,2204208,,,,MLST.Salmonella_enterica.11,,,,2022-09-16T00:00:00Z,,PRJNA473048,GCA_025232695.1,"CP029682,CP029683",,,PacBio,,SMRT Analysis v. 2.3.0,1,1,2,4766465,52.122276,4842,4833,stool,,01-Jan-2016,South Korea,South Korea: Seoul,,,,Food-poisoning,,,,,,,,,,,,,,collected_by:Samsung Seoul Hospital,,,,,,,Food-poisoning,,,,,,,,,,,,,,100,1.2,Gastrointestinal Diseases,Other Gastrointestinal Diseases,Gastrointestinal,Gastrointestinal Diseases-Other Gastrointestinal Diseases HP,2816952.3,Salmonella sp. SAL-007,SAL-007,Salmonella sp. SAL-007,Salmonella,Enterobacteriaceae,Enterobacteriales,Gammaproteobacteria,Pseudomonadota,SAMN18175052,2816952,,,,MLST.Salmonella_enterica.11,,,,2021-03-17T00:00:00Z,,PRJNA707124,GCA_017372375.1,"CP071686,CP071687,CP071688,CP071689",,Wuhan Polytechnic University,Oxford Nanopore PromethION; Illumina,100.0x,SPAdes v. December-2020,1,3,4,4776778,52.143055,4862,4531,,,2020-11,China,China:WuHan,,,,,,,,,,,,,,,,,Multi-drug resistant Salmonella clinical strain,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2816953.3,Salmonella sp. SAL-020,SAL-020,Salmonella sp. SAL-020,Salmonella,Enterobacteriaceae,Enterobacteriales,Gammaproteobacteria,Pseudomonadota,SAMN18175061,2816953,,,,MLST.Salmonella_enterica.11,,,,2021-03-17T00:00:00Z,,PRJNA707128,GCA_017372215.1,"CP071690,CP071691,CP071692",,Wuhan Polytechnic University,Oxford Nanopore PromethION; Illumina,100.0x,SPAdes v. December-2020,1,2,3,4768808,52.133385,4850,4517,,,2020-11,China,China:WuHan,,,,,,,,,,,,,,,,,Multi-drug resistant Salmonella clinical strain,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,2816951.3,Salmonella sp. SAL-045,SAL-045,Salmonella sp. SAL-045,Salmonella,Enterobacteriaceae,Enterobacteriales,Gammaproteobacteria,Pseudomonadota,SAMN18175062,2816951,,,,MLST.Salmonella_enterica.11,,,,2021-03-17T00:00:00Z,,PRJNA707129,GCA_017372255.1,"CP071693,CP071694,CP071695",,Wuhan Polytechnic University,Oxford Nanopore PromethION; Illumina,100.0x,SPAdes v. December-2020,1,2,3,5021852,51.866802,5177,4784,,,2020-11,China,China:WuHan,,,,,,,,,,,,,,,,,Multi-drug resistant Salmonella clinical strain,sample_type:cell culture,,,,,,,,,,,,,,,,,,,,,100,0.17,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,3021405.3,Serratia sp. K-E0102,K-E0102,Serratia sp. K-E0102,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32762131,3021405,,,,,,,,2023-05-10T00:00:00Z,,PRJNA924557,,CP124754,,,Oxford Nanopore GridION; Illumina MiSeq,169.1x,flye v. 2.9; Newbler v. 2.8,1,0,1,5160726,59.94674,4955,4747,peritoneal wash fluid,,2021-11-07,Germany,"Germany: Ev. Klinikum Bielefeld, Bielefeld",,,,bacterial sepsis,,,,,,,,,,,,,,collected_by:Ev. Klinikum Bielefeld,,,,,,,bacterial sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Abdominal,Bloodstream Infections-Sepsis HP,3020826.3,Serratia sp. K-M0706,K-M0706,Serratia sp. K-M0706,Serratia,Yersiniaceae,Enterobacterales,Gammaproteobacteria,Pseudomonadota,SAMN32727621,3020826,,,,,,,,2023-05-10T00:00:00Z,,PRJNA923618,,"CP124750,CP124751,CP124752,CP124753",,,Oxford Nanopore GridION; Illumina MiSeq,110.5x,flye v. 2.9; Newbler v. 2.8,1,3,4,5185617,59.862865,5013,4793,wound swab,,2022-06-18,Germany,"Germany: Klinikum Bielefeld - Mitte, Bielefeld",,,,bacterial sepsis,,,,,,,,,,,,,,collected_by:Klinikum Bielefeld - Mitte,,,,,,,bacterial sepsis,,,,,,,,,,,,,,100,0,Bloodstream Infections,Sepsis,Skin and Soft Tissue,Bloodstream Infections-Sepsis HP,2795738.3,Sphingobacterium sp. UDSM-2020,UDSM-2020,Sphingobacterium sp. UDSM-2020,Sphingobacterium,Sphingobacteriaceae,Sphingobacteriales,Sphingobacteriia,Bacteroidota,SAMN17058658,2795738,,,,,,,,2020-12-21T00:00:00Z,,PRJNA684507,GCA_016132525.1,CP066166,,University of Dar es Salaam,Illumina NovaSeq,431.9x,SPAdes v. 3.14.1,1,0,1,6101723,36.34193,5465,5106,vagina,isolated several strains and deployed whole genome sequencing of Sphingobacterium species along with one fungal species from which we can deduce relevant clinical information,2020-02-06,Tanzania,Tanzania,,,,Not applicable,,,,,,,,,,,,,Our project focuses on vaginal bacterial and fungal species associated with vaginal infections. We isolated several strains and deployed whole genome sequencing of Sphingobacterium species along with one fungal species from which we can deduce relevant clinical information. Our ultimate goal is to eventually link their genomic features with pathogenicity and/or drug resistance in order to gain insight into their clinical importance and suggest possible interventions.,collected_by:Yustin Chaula,,,,,,,Not applicable,,,,,,,,,,,,,,100,1.43,Miscellaneous or Unspecified Infections,,Genitourinary,Miscellaneous or Unspecified Infections- NHP,2810514.3,Sporosarcina sp. Marseille-Q4063,Marseille-Q4063,Sporosarcina sp. Marseille-Q4063,Sporosarcina,Planococcaceae,Bacillales,Bacilli,Bacillota,SAMN17833048,2810514,,,,,,,,2021-05-07T00:00:00Z,,PRJNA700513,GCA_018309085.1,CP070502,,IHU - Mediterannee Infection,Illumina; Oxford Nanopore,53.7493x,SPAdes v. 3.10,1,0,1,3978257,39.791473,4107,3898,skin,,2020-07,France,France: Marseille,,,,,,,,,,,,,,,,,Sporosarcina sp nov strain Marseille-Q4063 was isolated from a human healthy skin swab as part of a culturomics project,sample_type:Human healthy skin swab,,,,,,,,,,,,,,,,,,,,,97.35,0,,,Skin and Soft Tissue,- HP,342616.21,Streptococcus agalactiae COH1,COH1,Streptococcus agalactiae,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN35521427,342616,III,,,MLST.Streptococcus_agalactiae.17,,,,2023-07-17T00:00:00Z,,PRJNA977207,,CP129875,,,PacBio,1223x,SMRTLink v. 1,1,0,1,2065074,35.400864,2039,,blood from neonate,,,USA,USA,,,,Invasive disease,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,100,0,Miscellaneous or Unspecified Infections,,Blood and Circulatory System,Miscellaneous or Unspecified Infections- HP,2576376.3,Streptococcus sp. 1643,1643,Streptococcus sp. 1643,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Bacillota,SAMN06040852,2576376,,,,,,,,2019-06-11T00:00:00Z,,PRJNA542100,GCA_006228325.1,CP040231,,The University of Texas at Dallas,Illumina HiSeq; PacBio RSII,100.0x,Unicycler v. 0.4.7,1,,1,1898954,41.23349,1913,1882,infective endocarditits,,1999-2003,USA,USA,,,,,,,,,,,,,,,,,Whole genome sequencing associated with phosphatidylcholine biosynthesis in Mitis Group Streptococci,sample_type:Hospital Isolate,,,,,,,,,,,,,,,,,,,,,99.87,1.13,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1902136.3,Streptococcus sp. NPS 308,NPS 308,Streptococcus sp. NPS 308,Streptococcus,Streptococcaceae,Lactobacillales ,Bacilli,Bacillota,SAMD00061134,1902136,,,,,,,,2016-10-14T00:00:00Z,,PRJDB5166,GCA_002355895.1,AP017652,,"Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences",PacBio RS II,314X,HGAP v.3,1,,1,1924728,41.09,1872,1828,"8-years-old girl diagnosed ie, was performed to elucidate the pathogenic factors","isolated from an 8-years-old girl diagnosed IE, was performed to elucidate the pathogenic factors",2008-03-25,Japan,Japan: Nagasaki,,female,8-years-old,infective endocarditis,,,,,,,,,,,,,"The genus Streptococcus encompasses a broad range of Gram-positive catalase-negative chain-forming coccus-shaped organisms. Streptococci are widely present in the oral cavity and are established part of commensal flora. Infective endocarditis (IE) is characterized by a formation of septic masses of platelets on the surfaces of heart valves and oral viridans streptococci are one of the major pathogen of IE. In this project, whole genome sequence from a strain of Streptococcus sp., isolated from an 8-years-old girl diagnosed IE, was performed to elucidate the pathogenic factors. This genome sequence may provide fundamental molecular information on the genetic characteristics and pathogenesis of Streptococcus sp. NPS308.","biomaterial_provider:Department of Pediatric Dentistry, Nagasaki University Graduated School of Biomedical Sciences",missing,missing,missing,missing,whole genome sequencing of Streptococcus sp. NPS 308,,infective endocarditis,,,,,,,,,,missing,,,,100,0.3,Bloodstream Infections,Other Bloodstream Infections,Ear,Bloodstream Infections-Other Bloodstream Infections NHP,712623.3,Streptococcus sp. oral taxon 061 strain F0704,F0704,Streptococcus sp. oral taxon 061,Streptococcus,Streptococcaceae,Lactobacillales ,Bacilli,Bacillota,SAMN15358107,712623,,,,,,,,2020-07-08T00:00:00Z,,PRJNA282954,GCA_013394695.1,CP058258,,The Forsyth Institute,PacBio RS II,628.0x,HGAP v. 2,1,0,1,1765730,39.521614,1710,1668,tongue oral cavity,,2017-07-06,USA,"USA: Cambridge, Massachusetts",,,,,,,,,,,,,C,,,,Forsyth oral bacterial genomes isolated in pure culture from human oral samples,sample_type:whole organism;collected_by:Forsyth Institute,,,,,,,,healthy,,,,,,,,,,,,,100,2.37,,,Oral,- HP,2898276.3,Streptomyces sp. MRC013,MRC013,Streptomyces sp. MRC013,Streptomyces,Streptomycetaceae,Kitasatosporales,Actinomycetes,Actinomycetota,SAMN23388489,2898276,,,,,,,,2022-05-31T00:00:00Z,,PRJNA782605,GCA_023614235.1,CP094264,,,Oxford Nanopore MinION; Illumina iSeq,204x,Flye v. 2.8.2; Medaka v. 1.2.1; pilon v.,1,0,1,5331980,74.1114,5385,4755,mycetoma lesion,,2019-06-23,Sudan,Sudan,,,,Actinomycetoma,,,,,,,,,,,,,,collected_by:Mycetoma Research Centre,,,,,,,Actinomycetoma,,,,,,,,,,,,,,95.9,2.5,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- HP,1643512.3,Treponema sp. OMZ 855,OMZ 855,Treponema sp. OMZ 855,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253840,1643512,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181145.1,CP051194,,,Illumina HiSeq; Oxford Nanopore MiniION,1046x,SPAdes v. 3.12.0; Unicycler v. 0.4.5;,1,0,1,2689385,44.50356,2592,2381,subgingival plaque,,1998-05,China,China,,,,Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Oral and Dental Diseases,Gingivitis,Oral,Oral and Dental Diseases-Gingivitis HP,1643513.3,Treponema sp. OMZ 857,OMZ 857,Treponema sp. OMZ 857,Treponema,Treponemataceae,Spirochaetales,Spirochaetia,Spirochaetota,SAMN11253841,1643513,,,,,,,,2022-07-07T00:00:00Z,,PRJNA284866,GCA_024181085.1,CP051147,,,Illumina HiSeq; Oxford Nanopore MiniION,620.0x,Canu v. 1.8; pilon v. 1.22,1,0,1,2842704,44.25424,2760,2539,subgingival plaque,,1998-04,China,China,,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],periodontium [UBERON_0001758],subgingival plaque,27864174,,,Acute Necrotizing Ulcerative Gingivitis,,,,,,,,,,Oral cavity; mouth[UBERON_0000165],,,,100,0,Gastrointestinal Diseases,Gastritis and Ulcers,Oral,Gastrointestinal Diseases-Gastritis and Ulcers HP,2682455.3,Veillonella sp. S12025-13,S12025-13,Veillonella sp. S12025-13,Veillonella,Veillonellaceae,Veillonellales,Negativicutes,Bacillota,SAMD00199104,2682455,,,,,,,,2021-04-02T00:00:00Z,,PRJDB3830,GCA_018406505.1,AP022322,,Health Sciences University of Hokkaido,Illumina MiSeq; GridION X5,150x,Unicycler v. 0.4.8,1,0,1,2072807,38.611263,1898,1884,,,2015-03-25,Thailand,Thailand:Bangkok,,,,,,,,,Negative,Cocci,No,,,,,,It is already reported that Veillonella has important roles to form oral biofilms at early stage. The goal of this study is set as the development of novel method to control the biofilm formation at early stage to clarify the roles of Veillonella. Whole genome sequence has important parts of this project.,,not applicable,not applicable,not applicable,29458564,"Whole genome sequences of oral Veillonella, Analyzing roles of Veillonella in oral biofilm.",,,,,,,,,,,,not applicable,,,,100,0,Miscellaneous or Unspecified Infections,,Other,Miscellaneous or Unspecified Infections- NHP,2049049.53,Veillonellaceae bacterium KR001_HIC_0043,KR001_HIC_0043,Veillonellaceae bacterium,Unclassified Veillonella,Veillonellaceae,Veillonellales,Negativicutes,Bacillota ,SAMN31100397,2049049,,,,,,,,2022-10-19T00:00:00Z,,PRJNA798244,GCA_025757885.1,CP107218,,,PacBio Sequel II,98x,HiCanu v. 2.1.1,1,0,1,2308176,48.36568,2307,2106,feces,,2021,South Korea,South Korea:Seoul,,,,,,,,,,,,,,,,,,sample_type:metagenomic assembly,Human gut microbiome,Human feces,missing,,,,,,,,,,,,,,Human gut microbiome,,,,100,0.3,,,Gastrointestinal,-