ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Molecular Bacterial Pathogenesis
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1654546
-Population structure, resistome, and virulome of Staphylococcus chromogenes strains from milk of subclinical bovine mastitis in South Africa
Provisionally accepted
- 1Central University of Technology, Bloemfontein, South Africa
- 2North-West University, Potchefstroom, South Africa
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Staphylococcus chromogenes 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. This study presents a comparative genomic analysis of 17 S. chromogenes isolates from South Africa, including five newly sequenced bovine mastitis strains and twelve porcine-derived genomes retrieved from GenBank. In-silico analysis using multilocus sequence typing (MLST), virulence genes, antibiotic resistance genes and plasmids replicon types were used to characterise these isolates. 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., dfrC, mgrA, norA, and tet( 38), which confer resistance to trimethoprim, fluoroquinolones, and tetracyclines. In contrast, the compared porcine strains harboured a diverse set of resistance determinants, including blaZ, ermC, tet(K), and vgaALC that encode for beta-lactams, macrolides, tetracycline, and lincosamides, respectively. The five S. chromogenes isolates grouped into two 2 sequence types, namely ST138 and ST62. Pangenome reconstruction of 177 global genomes confirmed that S. chromogenes 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 nichespecific adaptation to the mammary environment in the Free State Province of South Africa. These findings advance our understanding of S. chromogenes population structure and resistance ecology. They underscore the importance of continued genomic surveillance of livestock pathogens to inform
Keywords: intramammary infection1, mastitis2, whole genome sequencing3, Pangenomics4, cattle5
Received: 27 Jun 2025; Accepted: 30 Jul 2025.
Copyright: © 2025 Khasapane, Nkhebenyane, Thekisoe, Ramatla and Lekota. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ntelekwane Khasapane, Central University of Technology, Bloemfontein, South Africa
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