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Abstract：
Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97 %) isolates used and differentiated the associated sequences into 932 discrete core genome sequence types (cgSTs). Analysis of the phylogenetic relationships of cgSTs revealed no clear clustering of isolates based on metadata such as disease status or year of isolation. Geographical clustering of cgSTs was limited to identification of a UK-centric clade, but cgSTs from UK isolates were also dispersed with those originating from other geographical regions across the entire phylogenetic topology. The cgMLST scheme offers a new tool for the detailed analysis of this globally important pathogen of dairy cattle. Initial analysis has re-emphasized and exemplified the genetically diverse nature of the global population of this opportunistic pathogen.
摘要：
乳房链球菌是牛乳腺炎的全球特有且控制不佳的原因，影响了现代乳制品行业的可持续性。核心基因组来自579个新测序的S.uberis分离株，以及从全球11个国家分离的305个公开可用的S.uberis基因组序列，用于开发核心基因组多位点序列分型（cgMLST）方案。S.uberis核心基因组包含1475个基因，这些被用来识别1447个被筛选的基因座，这些基因座被索引到cgMLST方案中。这能够对使用的1037个(>97%)分离株中的1012个进行分型,并将相关序列分化成932个离散核心基因组序列类型(cgST)。对cgSTs的系统发育关系的分析显示，根据疾病状况或分离年份等元数据，分离株没有明确的聚类。cgST的地理聚类仅限于以英国为中心的进化枝的识别，但是来自英国分离株的cgSTs也与来自其他地理区域的cgSTs分散在整个系统发育拓扑中。cgMLST方案为详细分析这种全球重要的奶牛病原体提供了新工具。初步分析再次强调并举例说明了这种机会性病原体的全球种群的遗传多样性。
