Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium.
Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium.
Implement Sci. 2019 Aug 13;14(1):79. doi: 10.1186/s13012-019-0930-2.
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.
下一代测序（NGS）技术越来越多地应用于常规公共卫生实践，影响了许多病原体的监测和控制。本范围综述的目的是确定和描述最近有关细菌病原体基因组学在公共卫生实践中的应用的文献，并从流行病学家的角度评估其实施的附加值、挑战和需求。
在本次范围综述中，我们对 2015 年 1 月至 2018 年 9 月期间以英文发表的文献进行了系统的 PubMed 搜索，并进行了正向和反向的雪球搜索，以确定公共卫生环境中细菌分离物的 NGS 应用的研究。纳入的研究必须描述 NGS 在公共卫生环境中对细菌分离物的应用。从每项研究中提取研究病原体、发表年份、国家、分离株数量、抽样比例、环境、公共卫生应用、研究目的、实施水平、NGS 分析的时间方向以及关键发现。由于研究环境、应用、病原体和研究措施存在很大的异质性，因此对合格研究进行了描述性叙事综合。
在 275 篇纳入的文章中，164 篇为暴发调查，70 篇侧重于策略导向监测，41 篇侧重于控制导向监测。主要应用包括全基因组测序（WGS）数据的使用，用于（1）来源追踪，（2）早期暴发检测，（3）揭示传播动态，（4）监测药物耐药性，（5）检测跨境传播事件，（6）识别具有增强毒力或人畜共患病潜力的菌株的出现，以及（7）评估预防和控制计划的影响。与传统的分型方法相比，推断传播途径的分辨率更高被认为是一个附加值，同时还能够同时描述研究病原体的耐药组和毒力组。然而，病原体基因组学的全部潜力只能通过将其与高质量的背景数据相结合来实现。
对于一些病原体来说，现在是从概念验证研究转向在暴发调查和监测活动中常规使用 WGS 的时候了。然而，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、背景数据的质量、抽样策略和有意义的解释。跨学科、跨部门和国际合作是进行适当的基于基因组学的监测的关键。
