Khasapane N G, Nkhebenyane S J, Thekisoe O, Ramatla T, Lekota K E
Center for Applied Food Safety and Biotechnology, Department of Life Sciences, Central University of Technology, Bloemfontein, South Africa.
Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
Front Cell Infect Microbiol. 2025 Aug 22;15:1654546. doi: 10.3389/fcimb.2025.1654546. eCollection 2025.
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 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.
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.
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.
常见于与奶牛亚临床乳腺炎相关的乳腺内感染中，但其基因组多样性和抗菌药物耐药性动态仍未得到充分表征，尤其是在非洲地区。
本研究对来自南非的17株分离株进行了比较基因组分析，包括5株新测序的牛乳腺炎菌株和从GenBank中检索到的12株猪源基因组。使用多位点序列分型（MLST）、毒力基因、抗生素耐药基因和质粒复制子类型分析来表征这些分离株。
成对平均核苷酸同一性（ANI）分析表明，牛分离株SC21、SC28和SC33密切相关，可能是牛适应型ST138谱系的克隆成员（ANI>99.7%），而SC12和SC14在遗传上更具差异，与猪源菌株显示出更高的相似性（ANI>91%）。全基因组SNP（wgSNP）分析支持了这一点，即ST138牛源分离株形成了一个克隆谱系，与猪源菌株相比显示出不同的群体结构。耐药基因组分析揭示了抗菌药物耐药基因（ARG）含量，牛分离株仅反映了四个核心ARG，即 、 和 ，它们分别赋予对甲氧苄啶、氟喹诺酮类和四环素的耐药性。相比之下，所比较的猪源菌株含有多种耐药决定因素，包括 、 和 ，它们分别编码β-内酰胺类、大环内酯类、四环素类和林可酰胺类。这5株 分离株分为两种序列类型，即ST138和ST62。对177个全球基因组进行泛基因组重建证实 具有开放的泛基因组，只有约17.5%的基因作为核心或软核心元件保守。值得注意的是，ST138的独特菌株特异性基因被确定与在牛分离株中鉴定出的海藻糖代谢相关，这可能反映了在南非自由邦省对乳腺环境的生态位特异性适应。
这些发现推进了我们对 群体结构和耐药生态学的理解。它们强调了对家畜病原体持续进行基因组监测的重要性，以便为有针对性的干预策略提供信息并改善不同生产环境中的动物健康，并进一步阐明对未来抗生素治疗和预防与该物种相关感染的影响。
