Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.
Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.
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DOI：
10.1128/jcm.00227-17
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发表时间：
2017-06
影响因子：
9.4
通讯作者：
Martinez-Urtaza J
中科院分区：
文献类型：
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作者：
Gonzalez-Escalona N;Jolley KA;Reed E;Martinez-Urtaza J
副溶血弧菌是一种重要的人类食源性病原体，其传播与食用受污染的海鲜有关，近年来全球报告的感染数量不断增加。副溶血弧菌多位点序列分型 (MLST) 数据库于 2008 年创建，并已鉴定出大量克隆，导致全球范围内严重暴发（序列类型 3 [ST3]）、在某些地区反复暴发（例如 ST36）或传播到非地方性流行的其他地区（例如 ST88 或 ST189）。当前的 MLST 方案使用 7 个基因的序列来生成 ST，这成为推断该病原体群体结构的强大工具，尽管分辨率有限，特别是与脉冲场凝胶电泳 (PFGE) 相比。全基因组测序 (WGS) 的应用已成为追溯研究的常规方法，核心基因组 MLST (cgMLST) 分析是在流行病学背景下探索复杂基因组数据的最直接方法之一。因此，需要生成一种新的、便携式的、标准化的和更先进的系统，该系统使用WGS数据提供副溶血性弧菌菌株之间更高的分辨率和辨别力。我们对 92 个副溶血弧菌基因组进行了测序，并以菌株 RIMD 2210633 的基因组作为参考（总共 4,832 个基因），以确定哪些基因适合建立副溶血弧菌 cgMLST 方案。该分析确定了 2,254 个适合用于 cgMLST 方案的核心基因。为了评估该方案的性能，我们对 92 个新测序的基因组以及 NCBI 提供的基因组的另外 142 个菌株进行了 cgMLST 分析。 cgMLST 分析能够区分相关和不相关的菌株，包括具有相同 ST 的菌株，清楚地表明其比传统 MLST 分析具有更高的分辨率。它还区分了同一 ST 内的暴发相关菌株和非暴发相关菌株。从这项工作中获得的序列已被保存并可在公共数据库（http://pubmlst.org/vparahaemolyticus）中获取。应用该 cgMLST 方案来表征世界各地不同实验室提供的副溶血性弧菌菌株，将揭示该病原体的流行病学、传播和进化的全球情况，并将成为疫情调查的有力工具，从而可以对全球覆盖范围的菌株进行明确的比较。
Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008, and a large number of clones have been identified, causing severe outbreaks worldwide (sequence type 3 [ST3]), recurrent outbreaks in certain regions (e.g., ST36), or spreading to other regions where they are nonendemic (e.g., ST88 or ST189). The current MLST scheme uses sequences of 7 genes to generate an ST, which results in a powerful tool for inferring the population structure of this pathogen, although with limited resolution, especially compared to pulsed-field gel electrophoresis (PFGE). The application of whole-genome sequencing (WGS) has become routine for trace back investigations, with core genome MLST (cgMLST) analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological context. Therefore, there is a need to generate a new, portable, standardized, and more advanced system that provides higher resolution and discriminatory power among V. parahaemolyticus strains using WGS data. We sequenced 92 V. parahaemolyticus genomes and used the genome of strain RIMD 2210633 as a reference (with a total of 4,832 genes) to determine which genes were suitable for establishing a V. parahaemolyticus cgMLST scheme. This analysis resulted in the identification of 2,254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of 92 newly sequenced genomes, plus an additional 142 strains with genomes available at NCBI. cgMLST analysis was able to distinguish related and unrelated strains, including those with the same ST, clearly showing its enhanced resolution over conventional MLST analysis. It also distinguished outbreak-related from non-outbreak-related strains within the same ST. The sequences obtained from this work were deposited and are available in the public database (http://pubmlst.org/vparahaemolyticus). The application of this cgMLST scheme to the characterization of V. parahaemolyticus strains provided by different laboratories from around the world will reveal the global picture of the epidemiology, spread, and evolution of this pathogen and will become a powerful tool for outbreak investigations, allowing for the unambiguous comparison of strains with global coverage.