Identification of high-risk extended-spectrum β-lactamase-producing Escherichia coli clones harboring tet(X4) along the pork supply chain in central Thailand.

Abstract

The global dissemination of antimicrobial-resistant (AMR) bacteria along the pork supply chain is a critical concern, as pigs are significant reservoirs for multidrug-resistant (MDR) Escherichia coli, a WHO-listed priority pathogen. This study investigated the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli across the pork production chain in Central Thailand, specifically focusing on the emergence of the last-resort tigecycline resistance gene, tet(X4). ESBL-producing E. coli isolates from a slaughterhouse pig cecum (n = 14) and retail market pork (n = 26) in central Thailand were collected. Whole-genome sequencing (WGS) was employed to analyze the resistome, virulome, and phylogenomic relationships. Analysis included non-metric multidimensional scaling (NMDS) of resistance and virulence gene determinants, single-nucleotide polymorphism (SNP) phylogeny, and core genome MLST (cgMLST). Resistome, virulome, and NMDS analysis demonstrated a shared clustering of antimicrobial resistance genes (ARGs) and virulence factors (VF) genes between cecum and pork isolates. Most isolates possessed extraintestinal pathogenic E. coli (ExPEC)-associated VF genes, underscoring the widespread pathogenic risk. tet(X4) was predominantly found in the dominant ST48 clone and these tet(X4) adjacent to ISCR2, providing evidence of horizontal gene transfer (HGT). cgMLST further demonstrated that these tet(X4) isolates are genetically related to global human, animal, and environmental strains. This study provides the first genomic evidence of tet(X4) circulation in ESBL-producing E. coli population across the slaughterhouse-to-retail continuum in central Thailand. Our findings suggest that the dissemination of tet(X4) in the pork supply chain is primarily via HGT. The implementation of firm food safety policies and enhanced hygiene practices is urgently required to inhibit the transmission of these high-risk strains to consumers.