Department of Health Security, National Institute for Health and Welfare (THL), Helsinki, Finland; European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.
Department of Health Security, National Institute for Health and Welfare (THL), Helsinki, Finland.
Clin Microbiol Infect. 2019 Jan;25(1):82-86. doi: 10.1016/j.cmi.2018.03.041. Epub 2018 Apr 11.
Culture-based assays are currently the reference standard for drug susceptibility testing for Mycobacterium tuberculosis. They provide good sensitivity and specificity but are time consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture-based assays for drug susceptibility testing of M. tuberculosis.
M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n = 211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first-line drug susceptibilities. WGS was performed for all isolates using the Illumina MiSeq system, and data were analysed using five software tools (PhyResSE, Mykrobe Predictor, TB Profiler, TGS-TB and KvarQ). Diagnostic time and reagent costs were estimated for both methods.
The sensitivity of the five software tools to predict any resistance among strains was almost identical, ranging from 74% to 80%, and specificity was more than 95% for all software tools except for TGS-TB. The sensitivity and specificity to predict resistance to individual drugs varied considerably among the software tools. Reagent costs for MGIT and WGS were €26 and €143 per isolate respectively. Turnaround time for MGIT was 19 days (range 10-50 days) for first-line drugs, and turnaround time for WGS was estimated to be 5 days (range 3-7 days).
WGS could be used as a prescreening assay for drug susceptibility testing with confirmation of resistant strains by MGIT. The functionality and ease of use of the software tools need to be improved.
基于培养的检测方法是目前分枝杆菌药物敏感性检测的参考标准。它们具有良好的敏感性和特异性，但耗时较长。本研究的目的是评估全基因组测序（WGS）结合数据分析软件工具是否可以替代常规培养法用于分枝杆菌的药物敏感性检测。
2014 年，将送往芬兰分枝杆菌参考实验室的分枝杆菌培养物（n=211）通过分枝杆菌生长指示管（MGIT）进行一线药物敏感性表型检测。所有分离株均使用 Illumina MiSeq 系统进行 WGS 检测，并使用五种软件工具（PhyResSE、Mykrobe Predictor、TB Profiler、TGS-TB 和 KvarQ）进行数据分析。估计了两种方法的诊断时间和试剂成本。
五种软件工具预测耐药菌株的敏感性几乎相同，范围在 74%至 80%之间，除 TGS-TB 外，所有软件工具的特异性均超过 95%。预测耐药的个别药物的敏感性和特异性因软件工具而异。MGIT 和 WGS 的试剂成本分别为每个分离物 26 欧元和 143 欧元。MGIT 用于一线药物的周转时间为 19 天（范围 10-50 天），WGS 的周转时间估计为 5 天（范围 3-7 天）。
WGS 可作为药物敏感性检测的预筛选检测方法，通过 MGIT 对耐药菌株进行确认。需要改进软件工具的功能和易用性。
