Genomic driver underlies clonal shift of methicillin-resistant <i>Staphylococcus aureus</i> in the healthcare setting

The epidemiology of healthcare-associated methicillin-resistant <i>Staphylococcus aureus</i> (HA-MRSA) has shifted in recent decades, with a notable decline in the lineage ST239 and continued dominance of ST5. The evolutionary mechanisms underlying these contrasting trends remain unclear. We conducted a longitudinal analysis of 3,410 clinical HA-MRSA isolates collected between 2005 and 2020 to assess clonal prevalence and genomic changes. Further phenotypic characteristics were evaluated through in vitro and in vivo experiments, including biofilm formation assays, antibiotic susceptibility testing, polymorphonuclear neutrophil leukocyte (PMN) killing assays, and mouse catheter infection models. The prevalence of ST239 declined markedly from 34.85% in 2005 to 0.52% in 2020, accompanied by reduced biofilm formation and increased susceptibility to vancomycin. Genomic analyses revealed a temporal accumulation of mutations in ST239 lineage, notably a specific <i>tarJ'</i> point mutation (C665T; Thr222Ile), whose detection frequency increased as ST239 prevalence declined, becoming fixed in 100% of ST239 isolates by 2020. This <i>tarJ'</i> mutation led to cell wall defects, decreased survival in acidic environments, reduction in biofilm formation, and attenuated persistence in mouse catheter models. In contrast, ST5 exhibited no comparable genomic deterioration and maintained phenotypic stability throughout the same period. The decline of ST239 HA-MRSA is driven by mutation-induced fitness trade-offs, particularly affecting cell wall integrity and persistent infection capacity. These findings highlight how evolutionary constraints and adaptive costs shape the population structure of bacterial pathogens.