A cross-sectorial platform for the integration of genomics in surveillance of food-borne pathogens
Published July 30, 2018 | Version 1.0
Dataset Open

INNUENDO whole genome and core genome MLST schemas and datasets for Yersinia enterocolitica

Creators

  • 1. University of Helsinki
  • 2. University of Lisbon
  • 3. Instituto Nacional de Saúde Dr. Ricardo Jorge
  • 4. Terveyden ja hyvinvoinnin laitos
  • 5. Elintarviketurvallisuusvirasto
  • 6. University of the Basque Country
  • 7. University of Veterinary Medicine, Vienna

Description

Dataset

All the raw reads deposited in the European Nucleotide Archive (ENA) or in the NCBI Sequence Read Archive (SRA) as Y. enterocolitica at the time of the analysis (August 2018) were retrieved using getSeqENA. A total of 252 genomes were successfully assembled using INNUca v3.1. In addition to public available genomes, the database includes 79 novel Y. enterocolitica strains which belong to the INNUENDO Sequence Dataset (PRJEB27020). 

File 'Metadata/Yenterocolitica_metadata.txt' contains metadata information for each strain including country and year of isolation, source classification, taxon of the host, serotype, biotype, pathotype (according to patho_typing software) and classical pubMLST 7 genes ST according to Hall et al., 2005. 

The directory 'Genomes' contains all the 331 INNUca V3.1 assemblies of the strains listed in 'Metadata/Yenterocolitica_metadata.txt'.

Schema creation and validation

All the 331 genomes were used for creating the schema using chewBBACA suite. The quality of the loci have been assessed using chewBBACA Schema Evaluation and loci with single alleles, those with high length variability (i.e. if more than 1 allele is outside the mode +/- 0.05 size) and those present in less than 1% of the genomes have been removed. The wgMLST schema have been further curated, excluding all those loci detected as “Repeated Loci” and loci annotated as “non-informative paralogous hit (NIPH/ NIPHEM)” or “Allele Larger/ Smaller than length mode (ALM/ ASM)” by the chewBBACA Allele Calling in more than 1% of a dataset.

File 'Schema/Yenterocolitica_wgMLST_ 6344_schema.tar.gz' contains the wgMLST schema formatted for chewBBACA and includes a total of  6,344 loci.

File 'Schema/Yenterocolitica_cgMLST_ 2406_listGenes.txt' contains the list of genes from the wgMLST schema which defines the cgMLST schema. The cgMLST schema consists of  2,406 loci and has been defined as the loci present in at least the 99% of the 331 Y. enterocolitica genomes. Genomes have no more than 2% of missing loci.

File 'Allele_Profles/Yenterocolitica_wgMLST_alleleProfiles.tsv' contains the wgMLST allelic profile of the 331 Y. enterocolitica genomes of the dataset. Please note that missing loci follow the annotation of chewBBACA Allele Calling software.

File 'Allele_Profles/Yenterocolitica_cgMLST_alleleProfiles.tsv' contains the cgMLST allelic profile of the 331 Y. enterocolitica genomes of the dataset. Please note that missing loci are indicated with a zero.

Additional citation

The schema are prepared to be used with chewBBACA. When using the schema in this repository please cite also:

Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. 15/03/2018. M Gen 4(3): doi:10.1099/mgen.0.000166 http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166

Notes

The isolates' genomes raw sequence data produced within the activity of the INNUENDO project were submitted to the European Nucleotide Archive (ENA) database and are publicly available under the project accession number PRJEB27020. When using the schemas, the assemblies or the allele profiles please include the project number in your publication. The research from the INNUENDO project has received funding from European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 (New approaches in identifying and characterizing microbial and chemical hazards) and from the Government of the Basque Country. The conclusions, findings, and opinions expressed in this repository reflect only the view of the INNUENDO consortium members and not the official position of EFSA nor of the Government of the Basque Country. EFSA and the Government of the Basque Country are not responsible for any use that may be made of the information included in this repository. The INNUENDO consortium thanks the Austrian Agency for Health and Food Safety Limited for participating in the project by providing strains. The consortium thanks all the researchers and the authorities worldwide which are contributing by submitting the raw sequences of the bacterial strains in public repositories. The project was possible thanks to the support of CSC- Tieteen tietotekniikan keskus Oy (https://www.csc.fi/) and of INCD (http://www.incd.pt/, funded by FCT and FEDER under the project 22153-01/SAICT/2016) for providing access to cloud computing resources.

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YersiniaEnterocolitica.zip

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