FoodGenVir database

Abstract

The foodGenVir database contains those MAGs obtained from food and food-related environments samples that were collected in the MASTER project and that harbored antimicrobial resistance (AMR) genes. In total, 1828 samples from food and food-producing environments that were successfully sequenced in MASTER and included in the analyses, which lead to 14,815 high-quality MAGs. The high-quality MAGs were recovered from the metagenomic samples by following the assembly-based pipeline described in Pasolli et al. (2019). The taxonomic assignment of these MAGs was performed by using phylophlan_metagenomics against the MetaRefSGB. The resulting MAGs were screened for AMR genes using the TORMES pipeline (Quijada et al., 2019) against the ResFinder database (Zankari et al., 2012; downloaded at version from 24/10/2022). In total, 928 MAGs harbored AMR genes. The current release contains the assembled-genome FASTA files from the AMR-carrying MAGs and a MASTER_MAGs_FGV.tsv table, that contains the taxonomic information of each MAG as well as the different AMR genes found in its genome and the antimicrobial compounds that those genes confer resistance to according to the ResFinder database.