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

Authors

Sheng Song, Yu Liu, Li Yan, BaiYu Li, LanXin Xu

Published in

Letters in applied microbiology. Oct 13, 2026. Epub Oct 13, 2026.

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.

PMID:
42867221
Bibliographic data and abstract were imported from PubMed on 14 Oct 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.