Prevalence and Genomic Characterization of Listeria monocytogenes in Retail Beef and Farm Samples in Korea

Listeria monocytogenes (Lm) is a major foodborne pathogen that can persist in food-processing environments and is responsible for listeriosis outbreaks. In this study, a total of 445 samples were collected from the beef supply chain, including 205 samples from cattle farms and 240 from retail markets across South Korea. Notably, 22 Lm isolates were exclusively recovered from retail beef samples, suggesting that contamination likely occurred during postfarm processing. Whole-genome sequencing revealed that the isolates belonged to lineage I (36.4%) and lineage II (63.6%), with CC9 being the most frequently identified clonal complex. Lineage I included hypervirulent clones such as CC3, CC87, and CC224, which harbored LIPI-3 or LIPI-4 and a full-length inlA gene, consistent with high virulence potential. Notably, the CC224 strains shared several molecular features with the Korean outbreak strain (sublineage, resistance gene, and a premature stop codon [PMSC] mutation in the llsX gene), although they were not closely genetically related. In contrast, all CC9 isolates harbored inlA PMSC mutations, which are associated with attenuated virulence. Virulence and stress-related genetic elements exhibited lineage-specific patterns, with SSI-2, internalin genes (inlG and inlL), and virulence factors (ami and comK) predominantly found in lineage II. All isolates remained susceptible to most antibiotics; however, tetracycline resistance was observed in a subset (n = 4, 18.2%). Our findings demonstrate the coexistence of hypervirulent and stress-adapted subtypes in beef products and underscore the need for continuous genomic surveillance and enhanced hygiene measures during meat processing and distribution to mitigate public health risks.