Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
Eur J Clin Microbiol Infect Dis. 2017 Nov;36(11):2007-2020. doi: 10.1007/s10096-017-3024-6. Epub 2017 Jun 21.
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
近年来，全基因组测序（WGS）被认为是一项具有颠覆临床微生物学潜力的技术。本文综述了 WGS 在临床微生物学实验室中最常见病原体的应用文献：大肠埃希菌和其他肠杆菌科、金黄色葡萄球菌和凝固酶阴性葡萄球菌、链球菌和肠球菌、分枝杆菌和沙眼衣原体。对于每个病原体组，我们重点关注五个不同方面：基因组特征、最常见的基因组方法以及 WGS 在（i）分型和暴发分析、（ii）毒力研究和（iii）体外药敏试验中的临床应用。在所有临床应用中，最常见和直接的用途是对细菌进行分型并追踪暴发源头。由于基于 WGS 数据的几个新的全基因组多位点序列分型系统的开发，朝着标准化迈出了下一步。虽然毒力特征分析有助于各种特定的临床环境，但主要是为了描述暴发菌株。越来越多的研究将基因型与表型抗生素药敏试验进行比较，结果大多有前景。然而，常规实施将优先在特定病原体（如分枝杆菌）的工作流程中进行，而不是作为广泛适用的通用工具。总体而言，WGS 在常规临床微生物学或感染控制实验室中的具体应用已经完成，但下一个重大挑战将是标准化和验证程序和生物信息学管道，以达到临床标准。
