Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.

中文翻译：

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细菌基因组学在公共卫生实践中的现状和潜力：范围回顾

下一代测序（NGS）越来越多地被转化为常规的公共卫生实践，从而影响了许多病原体的监测和控制。范围界定审查的目的是确定和表征有关细菌病原体基因组学在公共卫生实践中的应用的最新文献，并从流行病学家的角度评估与其实施相关的附加价值，挑战和需求。在此范围界定的审查中，进行了具有向前和向后滚雪球的系统性PubMed搜索，以识别2015年1月至2018年9月之间发布的英文手稿。所包括的研究必须描述NGS在公共卫生环境中在细菌分离物中的应用。研究的病原体，出版年份，国家/地区，分离株数量，采样分数，设置，从每项研究中提取了公共卫生应用，研究目的，实施水平，NGS分析的时间方向以及主要发现。由于设置，应用，病原体和研究测量的异质性很大，因此对符合条件的研究进行了描述性叙述综合。在275篇文章中，有164篇是疫情调查，有70篇是针对策略性监视的，而41篇是针对控制性监视的。主要应用包括将全基因组测序（WGS）数据用于（1）溯源，（2）早期暴发检测，（3）揭示传播动力学，（4）监测耐药性，（5）检测跨境传播事件，（6）确认毒力或人畜共患病潜力增强的菌株的出现，（7）评估预防和控制计划的影响。据报道，与传统的分型方法相比，它具有更高的分辨率，可以推断出传播途径，并且具有同时表征所研究病原体的抗药性和毒理学特性的能力。但是，只有将病原体基因组学与高质量的背景数据相结合，才能充分发挥其潜力。对于几种病原体，现在是在爆发调查和监视活动期间从概念验证研究转向常规使用WGS的时候了。但是，从流行病学家的角度来看，仍然存在一些实施方面的挑战，例如数据集成，上下文数据的质量，采样策略和有意义的解释。跨学科，跨部门，