Comparative genomics of bovine mastitis Staphylococcus aureus reveals a conserved CC97 lineage and first detection of ST7012 in South Africa

Staphylococcus aureus is a causative agent of bovine mastitis, posing significant challenges to animal health and dairy productivity due to its genomic adaptability, diverse virulence, and antimicrobial resistance. This study investigated the genomic diversity, virulence potential, antimicrobial resistance determinants, and plasmid replicon types of eight S. aureus isolates associated with subclinical bovine mastitis in 50 cows on a single farm in South Africa’s Dr Kenneth Kaunda District. Whole-genome sequencing of eight bovine milk isolates was performed and compared with global bovine genomes ( n = 209). Average Nucleotide Identity (ANI) analysis revealed high genomic relatedness (≥ 99.8%) among the eight South African isolates sequenced from this study, indicating a shared clonal background within clonal complex CC97 (spa type t189). Comparative genomic analysis showed that these isolates form a tightly conserved subclade of ST7012 within the global CC97 lineage, with limited genomic diversification compared with global strains. Pangenome analysis identified an open pangenome (γ = 0.224), indicating ongoing but constrained gene acquisition, with reduced accessory genome variability. Beta diversity showed detection of rare resistance determinants divergent in strain 43LFONT, including blaZ and plasmid-associated adK , highlighting emerging resistance potential. Whole-genome SNP phylogeny further demonstrated that the South African isolates cluster with the sequenced bovine isolates from the Free State Province, defined by 72 SNPs; despite belonging to different sequence types (ST8501), they share the same CC97 lineage. A conserved core resistome comprising mepA , mepR , norA , mgrA , and tet(38) was observed across compared genomes, while the plasmid-borne tet(K) gene was restricted to strains 44LF2 and 45RF2. These isolates constitute a genomically conserved lineage within a globally distributed lineage, representing the first report of ST7012 in bovine-derived samples from South Africa and highlighting the emergence of resistance determinants with potential clinical significance. These findings indicate a clonally structured S. aureus population within CC97, with evidence of local expansion across provinces despite sequence type variation, underscoring the importance of continued genomic surveillance within a One Health framework.