Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Diseases, Atlanta, Georgia.
Foodborne Pathog Dis. 2019 Jul;16(7):504-512. doi: 10.1089/fpd.2019.2650. Epub 2019 Jun 27.
The routine use of whole-genome sequencing (WGS) as part of enteric disease surveillance is substantially enhancing our ability to detect and investigate outbreaks and to monitor disease trends. At the same time, it is revealing as never before the vast complexity of microbial and human interactions that contribute to outbreak ecology. Since WGS analysis is primarily used to characterize and compare microbial genomes with the goal of addressing epidemiological questions, it must be interpreted in an epidemiological context. In this article, we identify common challenges and pitfalls encountered when interpreting sequence data in an enteric disease surveillance and investigation context, and explain how to address them.
常规使用全基因组测序（WGS）作为肠道疾病监测的一部分，极大地提高了我们检测和调查疫情以及监测疾病趋势的能力。与此同时，它前所未有地揭示了微生物和人类相互作用的巨大复杂性，这些相互作用有助于疫情的发生。由于 WGS 分析主要用于对微生物基因组进行特征描述和比较，目的是解决流行病学问题，因此必须在流行病学背景下进行解释。在本文中，我们确定了在肠道疾病监测和调查背景下解释序列数据时常见的挑战和陷阱，并解释了如何解决这些问题。
