One Health EJP

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Published October 31, 2022 | Version v1
Dataset Open

The OHEJP BeONE Project – Campylobacter jejuni genome assembly dataset

Creators

  • 1. National Institute of Health Doutor Ricardo Jorge (INSA), Portugal
  • 2. German Federal Institute for Risk Assessment (BfR), Germany
  • 3. Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Italy
  • 4. National Institute of Public Health and the Environment (RIVM), Netherlands
  • 5. National Veterinary Research Institute of Poland (PIWET), Poland
  • 6. Friedrich Loeffler Institute (FLI), Germany
  • 7. Norwegian Veterinary Institute (NVI), Norway
  • 8. Animal and Plant Health Agency (APHA), United Kingdom
  • 9. Norwegian Institute of Public Health (NIPH), Norway
  • 10. Technical University of Denmark (DTU), Denmark
  • 11. Robert Koch Institute (RKI), Germany
  • 12. Statens Serum Institut (SSI), Denmark

Contributors

  • 1. National Institute of Health Doutor Ricardo Jorge (INSA), Portugal
  • 2. German Federal Institute for Risk Assessment (BfR), Germany
  • 3. Animal and Plant Health Agency (APHA), United Kingdom
  • 4. Technical University of Denmark (DTU), Denmark
  • 5. Friedrich Loeffler Institute (FLI), Germany
  • 6. Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Italy
  • 7. Norwegian Institute of Public Health (NIPH), Norway
  • 8. Norwegian Veterinary Institute (NVI), Norway
  • 9. National Veterinary Research Institute of Poland (PIWET), Poland
  • 10. National Institute of Public Health and the Environment (RIVM), Netherlands
  • 11. Robert Koch Institute (RKI), Germany
  • 12. Statens Serum Institut (SSI), Denmark

Description

Dataset

This dataset comprises the genome assemblies of 610 Campylobacter jejuni samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (https://onehealthejp.eu/jrp-beone/). Additionally, a complementary dataset is also made available (https://zenodo.org/record/7120166), comprising genome assemblies of 3,076 C. jejuni samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).

File “BeONE_Cj_metadata.xlsx” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers and in-silico Multi Locus Sequence Type.

The archive “BeONE_Cj_assemblies.zip” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file.

 

Dataset selection and curation

This anonymized dataset of C. jejuni genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57119. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (Deneke et al. 2021) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 610 isolates passed the dataset curation step and were included in the final dataset.

 

Funding

This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. 

Files

BeONE_Cj_assemblies.zip

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Additional details

Funding

One Health EJP – Promoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards. 773830
European Commission