The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.

中文翻译：

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全基因组测序和结核分枝杆菌：样品制备和测序数据分析的挑战

由耐药菌株引起的结核病 (TB) 患者的数量仍然令人震惊。因此，与目前使用的表型和基因型方法相比，有必要更快、更准确地确定耐药性。近年来，随着技术的进步，全基因组测序 (WGS) 方法已被引入作为临床实验室常规诊断的一部分。将范围广泛的分枝杆菌基因组变异与参考基因组进行比较，可以对结核分枝杆菌 (M.tuberculosis) 的分子流行病学和耐药性进行一致的评估，以应对多种抗结核药物。获得的测序数据的质量与样本的类型以及用于 DNA 提取和测序文库制备的方法密切相关。而且，结果的正确解释也受到生物信息学数据处理的影响。目前有大量的生物信息学管道，其敏感性因包含相关突变的数据库大小不同而异。本综述重点关注测序工作流程中包含的各个步骤以及可能影响最终结果解释的因素。