Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
Brief Bioinform. 2020 Mar 23;21(2):741-750. doi: 10.1093/bib/bbz010.
Whole genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. Traditional genomic epidemiology often uses WGS as a verification tool, namely, when a common source or epidemiological link is suspected, the collected isolates are sequenced for the determination of clonal relationships. However, increasingly frequent international travel and food transportation, and the associated potential for the cross-border transmission of bacterial pathogens, often lead to an absence of information on bacterial transmission routes. Here we introduce the concept of 'reverse genomic epidemiology', i.e. when isolates are inspected by genome comparisons to be sufficiently similar to one another, they are assumed to be a consequence of infection from a common source. Through BacWGSTdb (http://bacdb.org/BacWGSTdb/), a database we have developed for bacterial genome typing and source tracking, we have found that almost the entire analyzed 20 bacterial species exhibit the phenomenon of cross-border clonal dissemination. Five networks were further identified in which isolates sharing nearly identical genomes were collected from at least five different countries. Three of these have been documented as real infectious disease outbreaks, therefore demonstrating the feasibility and authority of reverse genomic epidemiology. Our survey and proposed strategy would be of potential value in establishing a global surveillance system for tracing bacterial transmissions and outbreaks; the related database and techniques require urgent standardization.
全基因组测序（WGS）彻底改变了细菌病原体的基因分型，有望成为用于追踪细菌传染病传播的新金标准。传统的基因组流行病学通常将 WGS 用作验证工具，即在怀疑存在共同来源或流行病学联系时，对收集的分离物进行测序以确定克隆关系。然而，越来越频繁的国际旅行和食物运输，以及由此带来的细菌病原体跨境传播的潜在风险，往往导致缺乏有关细菌传播途径的信息。在这里，我们介绍了“反向基因组流行病学”的概念，即当通过基因组比较发现分离物彼此足够相似时，它们被假定是来自共同来源的感染的结果。通过我们为细菌基因组分型和溯源开发的数据库 BacWGSTdb（http://bacdb.org/BacWGSTdb/），我们发现几乎所有分析的 20 种细菌物种都表现出跨境克隆传播的现象。进一步鉴定了五个网络，其中至少有五个不同国家收集了具有几乎相同基因组的分离物。其中三个已被记录为真实的传染病暴发，因此证明了反向基因组流行病学的可行性和权威性。我们的调查和提出的策略对于建立用于追踪细菌传播和暴发的全球监测系统可能具有潜在价值；相关数据库和技术需要紧急标准化。
