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

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ID: 332236
2026
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Abstract
Abstract 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.
Reference Key
openalex_W7221649830 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors sheng song, Yu Liu, Li Yan, BaiYu Li, Lanxin Xu
Journal letters in applied microbiology
Year 2026
DOI
10.1093/lambio/ovag087
URL
https://doi.org/10.1093/lambio/ovag087
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