Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea

Background Yersinia enterocolitica is a psychrotrophic foodborne bacterium capable of growing at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns for food safety and public health. Despite its relevance and the increasing use of whole-genome sequencing (WGS) for bacterial surveillance, genomic studies on Y. enterocolitica isolates from South Korea are limited. In this study, we analyzed 157 Y. enterocolitica isolates obtained from pork, beef, chicken, and duck collected nationwide using WGS to elucidate their genomic diversity and adaptive features. Results Phylogenomic analysis classified all isolates as biotype 1A (sub-biotype 1Aa) and revealed considerable genetic heterogeneity, comprising 40 sequence types (STs) and 66 core-genome types (CTs). No clear segregation by source was observed, suggesting cross-source circulation within livestock production and processing environments. Pan-genome analysis identified 23,110 gene clusters, revealing an open pan-genome enriched in genes associated with metabolism, defense mechanisms, and stress responses, reflecting high genomic flexibility. Although the canonical virulence plasmid pYV was absent, we identified a conserved set of chromosomal virulence-associated genes linked to adhesion ( inv , yapE ), secretion, and enterotoxicity ( ystB ), suggesting enhanced potential for persistence rather than pronounced pathogenicity. Antimicrobial resistance (AMR) genes were predominantly intrinsic, including blaA (β-lactamase) and vat(F) (streptogramin resistance), which were universally detected, whereas acquired AMR genes such as tet(C) and ant(3'')-Ia were sporadically observed. Furthermore, approximately one-third of isolates harbored Col- and Inc-type plasmid replicons, supporting the occurrence of horizontal gene exchange and environmental adaptation. Conclusions Y. enterocolitica from animal-source foods in South Korea represents a genetically diverse and environmentally resilient population with limited virulence and predominantly intrinsic AMR determinants. These findings establish a genomic framework for understanding the ecology of Y. enterocolitica in animal-source foods and underscore the need for ongoing genomic surveillance to detect emerging variants that may influence food safety and public health.