Comparative genomics reveals polyphyletic emergence of methicillin-resistant Staphylococcus aureus ST152 from a diverse methicillin-susceptible population in ghana

Abstract

BACKGROUND: Staphylococcus aureus is a major public health threat in Ghana, with the Sequence Type 152 (ST152) lineage emerging as a dominant, Panton-Valentine leukocidin toxin (PVL)-positive lineage. This study investigates the evolutionary dynamics and emergence of methicillin resistance within the ST152 population in Ghana. METHODS: We analyzed 285 publicly available S. aureus whole-genome sequences (WGS) from Ghana, encompassing isolates of human and animal origin. Comprehensive genomic characterization was performed using the StaphScope pipeline, followed by detailed pangenome and phylogenetic analyses of 80 ST152 isolates. RESULTS: ST152 was the most prevalent lineage (28.1%). Phylogenetic analysis revealed patterns consistent with polyphyletic emergence of methicillin-resistant S. aureus (MRSA) ST152 through multiple independent acquisitions of the staphylococcal cassette chromosome mec (SCCmec). Despite these multiple origins, a single MRSA-enriched sublineage has become dominant. This successful clade is characterized by the significant enrichment of additional resistance genes (catA, tet(K)), a specific plasmid replicon (rep7a_5_repD(pTZ4)), and the collagen adhesin gene (cna), which may enhance host colonization and transmission. Interestingly, methicillin-susceptible S. aureus (MSSA) isolates were found phylogenetically embedded within MRSA clusters, indicating a highly dynamic resistance landscape. CONCLUSIONS: The emergence of MRSA ST152 in Ghana is a complex, multi-origin process. The dominance of a specific sublineage harboring enhanced virulence and resistance markers suggests a specialized adaptation that facilitates its epidemiological success. These findings underscore the critical need for sustained genomic surveillance to monitor the evolution and spread of high-risk MRSA lineages in West Africa.