Last-line antimicrobial resistance genes in food-chain Enterococcus faecium sensu stricto: a 2,090-genome public-archive audit with whole-genome species validation

The extent to which food-chain bacteria carry last-line antimicrobial resistance genes (ARGs) is poorly quantified. We screened 2,090 NCBI genomes whose BioSample metadata indicated food-chain association. Mash-based validation against type strains reassigned 663 genomes (31.7%) to Enterococcus lactis (former clade B) and exposed one misidentified record; a standardized minimap2/ResFinder re-screen removed three annotation-based false-positive calls. The primary estimand was the proportion of last-line ARG (vanA, optrA, poxtA, cfr)-positive genomes within this predefined sampling frame, not population prevalence. After excluding apparent clinical admixture, 140/1,283 E. faecium sensu stricto genomes (10.91%; 95% CI 9.32–12.74) carried a last-line ARG, versus 4/646 E. lactis (0.62%; 0.24–1.58). vanA carriage concentrated in clonal complex CC17 (59/83 observed carriers), whereas optrA/poxtA carriage did not (20–28% CC17). Carriage rose from 4.8% (2013–16) to 13.1% (2021–26) among dated genomes while multi-ARG carriage declined. No carrier had measured susceptibility data; findings are genomic and archive-bound.