Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA.
J Clin Microbiol. 2019 Apr 26;57(5). doi: 10.1128/JCM.01816-18. Print 2019 May.
Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agencies, both nationally and internationally. This impedes collaborative public health efforts, so national and international efforts are underway to enable direct comparison of these different analysis methods. Ultimately, the harmonization efforts will allow the (mutually trusted and understood) production and analysis of WGS data by labs and agencies worldwide, thus improving outbreak response capabilities globally. This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance can be readily validated. The tools for doing this will ensure that the results produced are sound, reproducible, and comparable across different analytic approaches.
美国的食源性病原体监测正在从使用限制性消化技术（脉冲场凝胶电泳 [PFGE]）进行菌株鉴定转变为对整个基因组进行鸟枪法测序（全基因组测序 [WGS]）。WGS 需要一套新的分析工具，其中一些在学术界已有悠久的历史，但对于公共卫生和监管决策领域来说却是新的。虽然用于疾病监测的 WGS 数据的收集和分析的一般工作流程相当标准，但在全国和国际范围内，公共卫生机构在数据的收集和分析方面存在许多差异。这阻碍了协作性的公共卫生工作，因此正在进行国家和国际努力，以实现对这些不同分析方法的直接比较。最终，协调努力将使世界各地的实验室和机构能够（相互信任和理解）生成和分析 WGS 数据，从而提高全球的疫情应对能力。本综述提供了 WGS 在病原体追踪方面的使用的历史视角，并总结了正在进行的工作，以确保用于病原体疾病监测的系统发育管道的主要步骤可以得到方便验证。这些工具将确保生成的结果在不同分析方法中是可靠、可重复和可比较的。
