Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia. Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant Mycobacterium tuberculosis in Java, Indonesia. Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared. Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS–MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33–76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population. Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.

中文翻译：

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来自印度尼西亚爪哇的耐多药结核分枝杆菌的全基因组测序分析。

介绍。耐多药结核病（MDR-TB）是包括印度尼西亚在内的全球主要的公共卫生问题。全基因组测序（WGS）分析很少用于印度尼西亚的结核病和耐多药结核病研究。目标。我们评估了WGS在药物敏感性测试（DST）中的使用，并调查了印度尼西亚爪哇的耐药结核分枝杆菌的种群结构。方法。30名疑似MDR-TB分离株接受了基于MGIT 960系统（MGIT）的DST和WGS。使用WGS数据进行了系统发育分析。比较了使用基于MGIT的DST和基于WGS的DST获得的结果。结果。 WGS和MGIT之间的一致性为利福平为93.33％，异烟肼为83.33％，链霉素为76.67％，但乙胺丁醇仅为63.33％。对于包括丁胺卡那霉素，卡那霉素和氟喹诺酮在内的二线药物，发现了中等的WGS–MGIT协议（73.33–76.67％）。耐多药结核病在东亚血统的分离株中更为常见（63.3％）。在测试人群中未发现DR-TB的克隆传播证据。结论。我们的研究证明了WGS在印度尼西亚爪哇的DST和DR-TB分子流行病学中的适用性。我们在印度尼西亚未发现DR-TB的传播。