Population structure, resistome, and virulome of Staphylococcus chromogenes strains from milk of subclinical bovine mastitis in South Africa
1
Life Sciences, Central University of Technology, Bloemfontein, South Africa
2
Unit for Environmental Sciences and Management, North West University, Potchefstroom, South Africa
Popul. Med. 2026;8(Supplement Supplement 1):
ABSTRACT
INTRODUCTION:
Staphylococcus chromogenes is a frequent cause of intramammary infections associated with bovine subclinical mastitis, yet its genomic diversity and antimicrobial resistance (AMR) patterns are poorly understood, particularly in Africa.
METHODS:
This study conducted a comparative genomic analysis of 17 S. chromogenes isolates, comprising five newly sequenced bovine mastitis strains from South Africa and twelve porcine-derived genomes obtained from GenBank. In silico analyses included multilocus sequence typing (MLST), profiling of virulence factors, antimicrobial resistance genes (ARGs), plasmid replicon types, average nucleotide identity (ANI), and whole-genome SNP (wgSNP) analysis.
RESULTS:
ANI and wgSNP analyses demonstrated that three bovine isolates (SC21, SC28, and SC33) are highly related (ANI >99.7%) and form a clonal lineage corresponding to the bovine-adapted ST138 sequence type. In contrast, two bovine isolates (SC12 and SC14) were genetically distinct and showed closer similarity to porcine-derived strains (ANI >91%), indicating greater population heterogeneity. Overall, bovine isolates exhibited a more clonal structure compared with the genetically diverse porcine strains. Resistome analysis revealed limited AMR content in bovine isolates, with only four core ARGs detected (dfrC, mgrA, norA, and tet(38)), conferring resistance to trimethoprim, fluoroquinolones, and tetracyclines. Conversely, porcine isolates harboured a broader array of resistance genes, including blaZ, ermC, tet(K), and vgaALC, associated with resistance to beta-lactams, macrolides, tetracyclines, and lincosamides. The five bovine isolates belonged to two sequence types, ST138 and ST62. Pangenome analysis of 177 global genomes confirmed that S. chromogenes has an open pangenome, with only 17.5% of genes classified as core or soft-core. Notably, ST138 bovine isolates possessed unique genes linked to trehalose metabolism, suggesting niche-specific adaptation to the bovine mammary environment in South Africa.
CONCLUSIONS:
These findings highlight the population structure, adaptive potential, and resistance ecology of S. chromogenes, underscoring the need for ongoing genomic surveillance to guide effective mastitis control and antimicrobial stewardship.
Staphylococcus chromogenes is a frequent cause of intramammary infections associated with bovine subclinical mastitis, yet its genomic diversity and antimicrobial resistance (AMR) patterns are poorly understood, particularly in Africa.
METHODS:
This study conducted a comparative genomic analysis of 17 S. chromogenes isolates, comprising five newly sequenced bovine mastitis strains from South Africa and twelve porcine-derived genomes obtained from GenBank. In silico analyses included multilocus sequence typing (MLST), profiling of virulence factors, antimicrobial resistance genes (ARGs), plasmid replicon types, average nucleotide identity (ANI), and whole-genome SNP (wgSNP) analysis.
RESULTS:
ANI and wgSNP analyses demonstrated that three bovine isolates (SC21, SC28, and SC33) are highly related (ANI >99.7%) and form a clonal lineage corresponding to the bovine-adapted ST138 sequence type. In contrast, two bovine isolates (SC12 and SC14) were genetically distinct and showed closer similarity to porcine-derived strains (ANI >91%), indicating greater population heterogeneity. Overall, bovine isolates exhibited a more clonal structure compared with the genetically diverse porcine strains. Resistome analysis revealed limited AMR content in bovine isolates, with only four core ARGs detected (dfrC, mgrA, norA, and tet(38)), conferring resistance to trimethoprim, fluoroquinolones, and tetracyclines. Conversely, porcine isolates harboured a broader array of resistance genes, including blaZ, ermC, tet(K), and vgaALC, associated with resistance to beta-lactams, macrolides, tetracyclines, and lincosamides. The five bovine isolates belonged to two sequence types, ST138 and ST62. Pangenome analysis of 177 global genomes confirmed that S. chromogenes has an open pangenome, with only 17.5% of genes classified as core or soft-core. Notably, ST138 bovine isolates possessed unique genes linked to trehalose metabolism, suggesting niche-specific adaptation to the bovine mammary environment in South Africa.
CONCLUSIONS:
These findings highlight the population structure, adaptive potential, and resistance ecology of S. chromogenes, underscoring the need for ongoing genomic surveillance to guide effective mastitis control and antimicrobial stewardship.
| eISSN: | 2654-1459 |
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