Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).

中文翻译：

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霍乱弧菌核心基因组多位点序列分型方案促进霍乱流行病学研究。

近年来，核心基因组多位点序列分型（cgMLST）在流行病学研究和亚种级分类中越来越受欢迎。cgMLST 保留了传统 MLST 的直观性质，但通过利用更大的基因组部分提供了更高的分辨率。在这里，我们介绍了针对霍乱弧菌的 cgMLST 方案，霍乱弧菌是一种在海洋和淡水环境中丰富的细菌，也是霍乱的病原体。本研究使用霍乱弧菌中普遍存在的一组 2,443 个核心基因来分析从 52 个国家收集的 1,262 个临床和环境菌株的综合数据集，其中包括 65 个新测序的基因组。我们基于 133 个等位基因差异建立了一个亚谱系阈值，该阈值创建了与传统 MLST 类型几乎相同的簇，从而为新的 cgMLST 分类提供了向后兼容性。我们还根据七个等位基因差异定义了爆发阈值，该阈值能够识别来自同一爆发的菌株以及密切相关的分离株，从而提供有关爆发起源的线索。使用 cgMLST，我们确认了现代流行病的南亚起源，并确定了来自同一地理起源的环境分离株亚系之间的聚类亲和力。通过与现有分类方法（例如 MLST 和基于单核苷酸多态性的方法）的直接比较，突显了该方法的优点。cgMLST 在分辨率、标准化和易用性方面优于所有现有方法。我们预计该计划将成为未来霍乱弧菌研究和流行病学监测的普遍适用的标准化分类系统的基础。此 cgMLST 方案可在 PubMLST (https://pubmlst.org/vcholerae/) 上公开获取。