Merker Matthias, Kohl Thomas A, Niemann Stefan, Supply Philip
Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Parkallee 1, 23845, Borstel, Germany.
German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany.
Adv Exp Med Biol. 2017;1019:43-78. doi: 10.1007/978-3-319-64371-7_3.
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
结核病（TB）是一种具有复杂流行病学特征的传染病。因此，结核分枝杆菌复合群（MTBC）菌株的分子分型（基因分型）对于有效指导疫情调查、确定传播动态以及协助全球疾病流行病学监测至关重要。大规模基因分型对于深入了解病原体的生物多样性和进化也很有必要。由于其周转时间较短且命名系统简单，基于24个标准化位点加4个高变位点的分枝杆菌散布重复单位可变数目串联重复序列（MIRU-VNTR）分型，可选择与间隔寡核苷酸分型（spoligotyping）相结合，在过去十年中已取代IS6110 DNA指纹图谱，成为许多应用中经典菌株分型方法的金标准。随着下一代测序（NGS）技术的不断进步和成本降低，基于全基因组测序（WGS）的分型现在越来越多地用于充分利用可用的遗传信息。然而，仍然存在一些重要挑战，例如WGS分析流程缺乏标准化、需要在全球范围内共享WGS数据的数据库，以及在不同流行病学背景下更好地理解用于定义近期结核病传播集群的相关基因组距离。本章概述了过去三十年基因分型方法的演变，最终发展为基于WGS的方法。它阐述了这些技术的相对优势和局限性，指出了当前的挑战以及促进基于WGS分型标准化的潜在方向，并根据具体研究问题就使用何种方法提供了建议。
