Population structure, resistome, and virulome of strains from milk of subclinical bovine mastitis in South Africa.

INTRODUCTION

are commonly found in intramammary infections associated with bovine subclinical mastitis in dairy cattle, yet their genomic diversity and antimicrobial resistance dynamics remain poorly characterized, particularly in African settings.

METHODS

This study presents a comparative genomic analysis of 17 isolates from South Africa, including five newly sequenced bovine mastitis strains and twelve porcine-derived genomes retrieved from GenBank. analysis using multilocus sequence typing (MLST), virulence genes, antibiotic resistance genes and plasmids replicon types were used to characterise these isolates.

RESULTS AND DISCUSSION

Pairwise average nucleotide identity (ANI) analysis revealed that bovine isolates SC21, SC28, and SC33 are closely related and likely clonal members of the bovine-adapted ST138 lineage (ANI >99.7%), while SC12 and SC14 are more genetically distinct and show closer similarity (ANI >91%) to porcine-derived strains. This was supported by whole-genome SNP (wgSNP) analysis, whereby the ST138 bovine-derived isolates formed a clonal lineage and displayed a diverse population structure compared to porcine strains. Resistome profiling uncovered antimicrobial resistance gene (ARG) content, bovine isolates reflecting only four core ARGs i.e., , and , which confer resistance to trimethoprim, fluoroquinolones, and tetracyclines. In contrast, the compared porcine strains harboured a diverse set of resistance determinants, including , and that encode for beta-lactams, macrolides, tetracycline, and lincosamides, respectively. The five isolates grouped into two 2 sequence types, namely ST138 and ST62. Pangenome reconstruction of 177 global genomes confirmed that possesses an open pangenome, with only ~17.5% of genes conserved as core or soft-core elements. Notably, unique strain-specific genes of the ST138 were determined to be associated with trehalose metabolism identified in bovine isolates, potentially reflecting niche-specific adaptation to the mammary environment in the Free State Province of South Africa.

CONCLUSION

These findings advance our understanding of population structure and resistance ecology. They underscore the importance of continued genomic surveillance of livestock pathogens to inform targeted intervention strategies and improve animal health in diverse production settings, and further clarify the implications for future antibiotic therapy and prevention of infections associated with this species.