Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy.
BMC Vet Res. 2022 Jul 7;18(1):264. doi: 10.1186/s12917-022-03341-1.
Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardinia (Italy).
Genomes were assigned into lineage clusters using PopPUNK, which found 27 distinct isolate clusters, indicating considerable genetic variability consistent with environmental isolates. Geographic trends were identified including regional linkage of several isolate clusters. Multi-locus Sequence Typing (MLST) performed poorly and provided no new insights. Genomes were then screened for antimicrobial resistance genes, which were compared to phenotypic resistance profiles. Isolates showed consistent phenotypic resistance to aminoglycosides with variable resistance to novobiocin and tetracycline. In general, identification of antimicrobial resistance genes did not correlate with phenotypic resistance profiles, indicating unknown genetic determinants. A multi-antimicrobial resistance cassette (aminoglycoside, lincosamide and streptogramin) was identified in the chromosome of three genomes, flanked by vestigial phage recombinases. This locus appears to have spread horizontally within discrete S. uberis populations within a 40 km radius (Sassari region). Genomes were screened for putative virulence factors, which identified 16 genes conserved between sheep and cow isolates, with no host-specific genes shared uniformly across all host-specific isolates. Pangenomic analysis was then performed to identify core genes which were putatively surface-exposed, for identification of potential vaccine targets. As all genomes encoded sortase, core genes were screened for the sortase cleavage motif. Of the 1445 core S. uberis genes, 64 were putative sortase substrates and were predominantly adhesins, permeases and peptidases, consistent with compounds found within ruminant milk such as xanthine, fibronectin and lactoferrin.
This study demonstrated the importance of whole genome sequencing for surveillance of S. uberis and tracking horizontal acquisition of antimicrobial resistance genes, as well as providing insight into genetic determinants of disease, which cannot be inferred from the MLST schemes. Future mastitis surveillance should be informed by genomic analysis.
无乳链球菌是绵羊乳腺炎的主要病原体之一，但人们对这种全球环境病原体及其疾病的基因组机制知之甚少。在这项研究中，我们对从撒丁岛（意大利）乳腺炎感染绵羊中收集的 46 株无乳链球菌进行了基因组分析。
使用 PopPUNK 将基因组分配到谱系群中，发现了 27 个不同的分离株群，表明存在相当大的遗传变异，与环境分离株一致。确定了地理趋势，包括几个分离株群的区域联系。多位点序列分型（MLST）表现不佳，没有提供新的见解。然后筛选基因组对抗菌药物的耐药基因，并将其与表型耐药谱进行比较。分离株对氨基糖苷类药物表现出一致的表型耐药性，对新生霉素和四环素的耐药性不同。一般来说，抗菌药物耐药基因的鉴定与表型耐药谱不相关，表明存在未知的遗传决定因素。在三个基因组的染色体中发现了一个多抗菌药物耐药盒（氨基糖苷类、林可酰胺类和链阳性菌素类），由残余噬菌体重组酶侧翼。该基因座似乎在 40 公里半径（萨萨里地区）内的离散无乳链球菌种群中水平传播。筛选基因组中可能的毒力因子，确定了 16 个在绵羊和奶牛分离株中保守的基因，没有在所有宿主特异性分离株中普遍共享的宿主特异性基因。然后进行了泛基因组分析，以鉴定核心基因，这些基因被认为是表面暴露的，用于鉴定潜在的疫苗靶点。由于所有基因组都编码了凝结酶，因此筛选了核心基因的凝结酶切割基序。在 1445 个无乳链球菌核心基因中，有 64 个是潜在的凝结酶底物，主要是黏附素、渗透酶和肽酶，与反刍动物乳中的化合物如黄嘌呤、纤维连接蛋白和乳铁蛋白一致。
这项研究表明，全基因组测序对于无乳链球菌的监测和跟踪抗菌药物耐药基因的水平获得非常重要，同时也深入了解了疾病的遗传决定因素，这是无法从 MLST 方案中推断出来的。未来的乳腺炎监测应该以基因组分析为依据。
