Comparative Genomic and Epidemiologic Analysis of Methicillin-Resistant Staphylococcus aureus Isolates in Republic of Korea

<b>Background/Objectives</b>: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is a major causative pathogen in Republic of Korea. While numerous variants exist, the long-term evolutionary history of indigenous lineages remains unclear. Therefore, this study aimed to reconstruct the high-resolution population structure of Korean MRSA. <b>Methods</b>: A total of 191 MRSA clinical isolates collected between 1999 and 2025 were obtained from four Korean biobanks. Whole-genome sequencing was conducted and international MRSA genomes from the National Center for Bioinformatics were used as a control group. A genome-wide association study, including single-nucleotide polymorphism (SNP)-based phylogenomic analysis, principal component analysis (PCA), and ADMIXTURE, was performed for distribution analysis. A time-scale epidemiological analysis was conducted using SNP-based phylogenetic data. Additional profiling was performed via core genome multilocus sequence typing (cgMLST) for comparison with the SNP-based phylogenomic results. Finally, antimicrobial resistance and virulence factor genes were annotated using the ResFinder and VirulenceFinder databases. <b>Results</b>: Phylogenetic analysis identified five major clades: 1 (ST5), 2 (ST6), 3 (ST72), 4 (ST1/ST188), and 5 (ST8/ST239/ST254). Time-scaled analysis estimated that these major clades began to diverge in the early 20th century (e.g., Clade 1 around 1918). Notably, Korean ST5 isolates formed a sublineage distinct from North American strains, characterized by unique AMR profiles and divergence in the 1960s. ST72 formed an independent clade that was phylogenetically closer to clade 4 (ST1/ST188) than to the canonical CC8 group (clade 5). Furthermore, the ST1 isolates showed a temporal split into an older lineage and a recent sublineage, with expanded AMR pro-files. <b>Conclusions</b>: By integrating time-scale phylogenetics with cgMLST, we elucidated the evolutionary history and transmission dynamics of Korean MRSA.