D-BeONE.1.2 BeONE dataset

JRP24-FBZSH9-BEONE WP1 deliverable 1.2.

WP Leader: Vítor Borges (INSA)

Other contributors: Verónica Mixão (INSA), Miguel Pinto (INSA), Holger Brendebach (BfR), Simon Tausch (BfR), Carlus Deneke (BfR), Karin Lagesen (NVI)

In order to contribute to the accomplishment of specific objectives of the BeOne project, WP1-T2 compiled an anonymized dataset (including sequencing reads and respective metadata) aiming to capture the genomic diversity within the populations of Listeria monocytogenes, Salmonella enterica, Escherichia coli (STEC) and Campylobacter jejuni. This dataset counts with data shared by the BeOne partners and comprises a total of 3,884 isolates, from which the anonymized sequencing reads were released in the European Nucleotide Archive (ENA) and the anonymized genome assemblies in the Zenodo repository [1,426 L. monocytogenes (accession: PRJEB57166 and 10.5281/zenodo.7267486); 1,540 S. enterica (accession: PRJEB57179 and 10.5281/zenodo.7267785); 308 E. coli (accession: PRJEB57098 and10.5281/zenodo.7267844); 610 C. jejuni (accession: PRJEB57119 and 10.5281/zenodo.7267879)]. 

As a complement to the BeOne dataset, additional samples were carefully selected among the WGS data publicly available at the beginning of the analysis (November 2021) in ENA or the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), in order to ensure the representativeness of the genomic diversity within public databases (assessed in terms of sequence type or serotype, depending on the species). In the end, a so-called “public dataset” with the 8,383 samples that passed the curation step was released in Zenodo repository [1,874 L. monocytogenes (accession: 10.5281/zenodo.7116878); 1,434 S. enterica (accession: 10.5281/zenodo.7119735), 1,999 E. coli (accession: 10.5281/zenodo.7120057); 3,076 C. jejuni (accession: 10.5281/zenodo.7120166)].