Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans. Here, we therefore developed a cgMLST scheme for S. mutans. We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans. This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.

中文翻译：

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变形链球菌的核心基因组多位点序列分型方案。

变形链球菌是导致龋齿发展的主要病原体之一。最近基于全基因组测序 (WGS) 的核心基因组多位点序列分型 (cgMLST) 方法已用于特定人类病原体的流行病学研究。然而，这种方法尚未在变形链球菌的研究中报道。在这里，我们因此开发了一个用于变形链球菌的 cgMLST 方案。我们调查了 199 个可用的变形链球菌基因组，作为识别 cgMLST 目标的一种手段，开发了一个方案，其中包含来自变形链球菌UA159 参考基因组的594 个目标。在该 cgMLST 方案 (cgSTs) 中，在 80 种变异链球菌中鉴定了 68 种序列类型 (STs)与通过多位点序列分型 (MLST) 鉴定的 35 个 ST 相比，本研究中对 40 名儿童进行了测序。根据我们的 cgMLST 方案，56 个 cgST (82.35%) 与单个分离株相关，明显高于 MLST 方案 (11.43%)。此外，我们的 cgMLST 方案进一步区分了 58.06% 具有 ≥ 2 个分离株的所有 MLST 谱。最大似然系统发育树的拓扑分析表明，我们的 cgMLST 方案比 MLST 方案更可靠。基于 cgMLST 方案开发的来自 10 个国家的 145株变形链球菌的最小生成树突出了变形链球菌的多样化种群结构. 因此，cgMLST 方案提供了一种新的分子分型方法，适用于评估这种病原体的流行病学分布，并有可能成为未来全球龋齿流行病学研究的基准。