The OHEJP BeONE Project – Escherichia coli genome assembly dataset

Dataset This dataset comprises the genome assemblies of 308 Escherichia coli 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/7120057), comprising genome assemblies of 1,999 E. coli 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_Ec_metadata.xlsx” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers, in-silico Multi Locus Sequence Type and Serotype. The archive “BeONE_Ec_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 E. coli genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57098. 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, 308 isolates passed the dataset curation step and were included in the final dataset. In-silico serotyping was performed with seq_typing v2.2. 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