UCL-TB and UCL Centre for Clinical Microbiology, Department of Infection, University College London, UK; Imperial College Healthcare NHS Trust, London, UK.
UCL-TB and UCL Respiratory, University College London, UK; Royal Free London NHS Foundation Trust, London, UK.
Clin Microbiol Infect. 2018 Jun;24(6):604-609. doi: 10.1016/j.cmi.2017.10.030. Epub 2017 Nov 3.
Nearly two decades after completion of the genome sequence of Mycobacterium tuberculosis (MTB), and with the advent of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been applied to a wide range of clinical scenarios. Starting in 2017, England is the first country in the world to pioneer its use on a national scale for the diagnosis of tuberculosis, detection of drug resistance, and typing of MTB.
This narrative review critically analyses the current applications of WGS for MTB and explains how close we are to realizing its full potential as a diagnostic, epidemiologic, and research tool.
We searched for reports (both original articles and reviews) published in English up to 31 May 2017, with combinations of the following keywords: whole-genome sequencing, Mycobacterium, and tuberculosis. MEDLINE, Embase, and Scopus were used as search engines. We included articles that covered different aspects of whole-genome sequencing in relation to MTB.
This review focuses on three main themes: the role of WGS for the prediction of drug susceptibility, MTB outbreak investigation and genetic diversity, and research applications of NGS.
Many of the original expectations have been accomplished, and we believe that with its unprecedented sensitivity and power, WGS has the potential to address many unanswered questions in the near future. However, caution is still needed when interpreting WGS data as there are some important limitations to be aware of, from correct interpretation of drug susceptibilities to the bioinformatic support needed.
在完成结核分枝杆菌（MTB）基因组序列近二十年之后，随着下一代测序技术（NGS）的出现，全基因组测序（WGS）已被广泛应用于各种临床情况。从 2017 年开始，英国是世界上第一个在全国范围内率先将其用于结核病诊断、耐药性检测和 MTB 分型的国家。
本叙述性综述批判性地分析了 WGS 在 MTB 中的当前应用，并解释了我们在实现其作为诊断、流行病学和研究工具的全部潜力方面的进展。
我们搜索了截至 2017 年 5 月 31 日以英文发表的报告（包括原始文章和综述），使用了以下关键词的组合：全基因组测序、分枝杆菌和结核病。我们使用 MEDLINE、Embase 和 Scopus 作为搜索引擎。我们纳入了涵盖 WGS 与 MTB 相关的不同方面的文章。
本综述重点关注三个主要主题：WGS 在预测药物敏感性、MTB 爆发调查和遗传多样性以及 NGS 的研究应用中的作用。
许多最初的期望已经实现，我们相信，凭借其前所未有的敏感性和强大功能，WGS 有可能在不久的将来解决许多悬而未决的问题。然而，在解释 WGS 数据时仍需谨慎，因为需要注意一些重要的局限性，从正确解释药物敏感性到所需的生物信息学支持。
