Genomic Surveillance Reveals Distinct Clonal Lineages and Antibiotic Resistance Patterns in Staphylococcus aureus from Retail Pork in Beijing Versus Copenhagen

The global rise of multidrug resistance (MDR) across bacterial pathogens poses a severe threat to public health, with the food chain serving as a critical reservoir and transmission route for resistant clones. This study investigated the genomic epidemiology of Staphylococcus aureus in retail pork from Beijing, China, and Copenhagen, Denmark, with a focus on MDR patterns and associated genetic elements. Among 134 isolates, the livestock-associated clonal complex CC398 was the dominant lineage (24.63%) and exhibited a high burden of MDR (48.48%), carrying resistance genes to β-lactams (blaZ and mecA), tetracyclines (tetM and tetK), and aminoglycosides. Notably, MRSA isolates displayed a significantly higher MDR prevalence (73.53%) compared to MSSA isolates (18.00%), underscoring methicillin resistance as a key marker for broader resistance phenotypes. Phylogenetic analysis revealed the segregation of CC398 into distinct sub-lineages, with the livestock-associated branch consistently linked to a characteristic tetracycline–β-lactam MDR profile. Furthermore, high frequencies of mobile genetic elements, such as the rep16 plasmid, were associated with MDR dissemination in CC398. These findings highlight retail meat as an important reservoir for MDR S. aureus and illustrate how livestock-adapted clones contribute to the environmental burden of antimicrobial resistance. This study underscores the need for integrated One Health surveillance that connects veterinary, food safety, and human health sectors to monitor and contain the spread of MDR bacteria across ecological niches.