Yersinia enterocolitica is a psychrotrophic foodborne bacterium that can proliferate at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns about food safety and public health. However, genomic data on Y. enterocolitica isolates from South Korea are limited, despite the increasing use of whole-genome sequencing (WGS) in bacterial surveillance. Herein, 91 Y. enterocolitica isolates recovered from chicken, pork, beef, and duck samples collected nationwide in 2024 were analyzed using WGS to elucidate their genomic diversity and genomic features. Phylogenomic analysis predicted all isolates as biotype 1A (sub-biotype 1Aa) and revealed substantial genetic diversity, comprising 27 sequence types and 43 core-genome types. Pan-genome analysis identified 11,230 gene clusters, revealing an open pan-genome in which accessory and unique gene clusters were assigned to predicted functional categories associated with metabolism, defense mechanisms, and stress responses. Although the canonical virulence plasmid pYV was absent, conserved chromosomal virulence-associated genes involved in adhesion (yapE), invasion (inv), secretion, and enterotoxicity (ystB) were detected. Antimicrobial resistance genes were predominantly intrinsic, particularly blaA and vat(F), whereas acquired resistance genes were identified sporadically. These findings provide a genomic baseline for biotype 1A Y. enterocolitica isolates recovered from animal-source foods in South Korea. The functional and public health significance of the detected virulence-associated loci requires further phenotypic investigation.

Clostridium perfringens is a major foodborne pathogen in which the genomic localization of the enterotoxin gene, cpe, plays an important epidemiological role. In this study, four isolates associated with independent foodborne outbreaks in South Korea were analyzed using complete genome sequencing. All isolates were cpe-positive, including three strains carrying chromosomal cpe (c-cpe) and one strain carrying plasmid-borne cpe (p-cpe). To provide a broader genomic context, complete genomes retrieved from the National Center for Biotechnology Information database were also analyzed. Most cpe-positive strains carried p-cpe, whereas c-cpe strains were relatively uncommon. Whole-genome analysis revealed a distinct separation between c-cpe and p-cpe strains based on conserved core-genome features and virulence gene profiles. In c-cpe strains, the cpe gene was consistently located between the nadA–C operon and a downstream nucleobase transporter gene and was flanked by IS1470 family transposases, suggesting a conserved chromosomal structure and a possible vertical inheritance. Conversely, p-cpe strains carried cpe on conserved pCW3-like plasmids, indicating that horizontal gene transfer mediated by a specific plasmid lineage contributes to cpe dissemination across diverse genetic backgrounds. Overall, these findings show that cpe localization is associated with distinct genomic patterns in C. perfringens.