Screening of AMR-related genes in the genomes of Vibrio parahaemolyticus strains isolated in Europe from clinical, environmental and other sources

The distribution of antimicrobial resistance (AMR) genes for the EU and European Free Trade Association (EFTA) countries data was obtained from the global Vibrio parahaemolyticus genomes based on a collection of nearly 10,000 genomes. Some of the strains are from the collection of prof. Jaime Martinez-Urtaza (Department of Genetics and Microbiology, Universitat Autònoma de Barcelona) or are part of ongoing studies to expand the genome collection; other genomes were retrieved from the European Nucleotide Archive (ENA at https://www.ebi.ac.uk/ena/browser/home) and the National Center for Biotechnology Information (NCBI) [GenBank at https://www.ncbi.nlm.nih.gov/genbank/;  RefSeq at https://www.ncbi.nlm.nih.gov/refseq/; SRA at https://www.ncbi.nlm.nih.gov/sra]. For detection of AMR genes, a resistance genes detection pipeline based on one of the standard databases (CARD database at https://card.mcmaster.ca/) was used. The phylogenetic tree was prepared and includes the reference genome from Japan "Osaka" as reference. The RIMD 2210633 strain has been added as the global reference strain which has been historically used for all the phylogenetic analysis of V. parahaemolyticus. The metadata includes the source of the strain, i.e., country, origin (clinical, environmental or unclear), date of isolation, and subtype. The antibiotic-resistant genes are shown as present, absent or not applicable. To build the ARGs European V. parahaemolyticus tree, the Parsnp tool, a fast core-genome multi-aligner and SNP detector, from the Harvest suite was used (Treangen et al., 2014). Parsnp calculates the MUMi distances between the reference genome (RIMD_2210633) and each one of the 152 genomes used in this study. The resulting Newick formatted core genome SNP tree was then uploaded onto the webtool I-Tol (Letunic and Bork, 2021), midpoint rooted and the metadata of the samples was incorporated.

The accession IDs for the genomes included in the metadata are accessible in the following databases according to the first characters:* GCA: GenBank (https://www.ncbi.nlm.nih.gov/genbank/)* GCF: RefSeq (https://www.ncbi.nlm.nih.gov/refseq/)* ERR: ENA (https://www.ebi.ac.uk/ena/browser/home)* SRR: SRA (https://www.ncbi.nlm.nih.gov/sra)

References

Letunic I and Bork P, 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res, 49:W293-w296. doi: 10.1093/nar/gkab301

Treangen TJ, Ondov BD, Koren S and Phillippy AM, 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol, 15:524. doi: 10.1186/s13059-014-0524-x