Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia

Tryna Tania, Pratiwi Sudarmono, R. Lia Kusumawati, Andriansjah Rukmana, Wahyu Agung Pratama, Sanjib Mani Regmi, Orawee Kaewprasert, Angkana Chaiprasert, Virasakdi Chongsuvivatwong, Kiatichai Faksri

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9 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1013-1019
Number of pages7
JournalJournal of Medical Microbiology
Issue number7
Publication statusPublished - 1 Jul 2020


  • Indonesia
  • MDR-TB
  • Mycobacterium tuberculosis
  • whole-genome sequencing


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