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

Abstract

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 drugresistant 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.

The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible

“…The results were broadly concordant with those found by Tania et al ( 23 ). Some small differences are likely a result of different versions of the TB-Profiler software used.…”

“…Tania et al ( 23 ) collected M. tuberculosis samples from 30 patients with confirmed pulmonary tuberculosis treated in four hospitals in the western region of the Indonesian island of Java. Phenotypic drug susceptibility testing (DST) was performed on the cultured samples, and DNA was isolated and sequenced Thirty samples were retrieved from EBI European Nucleotide Archive (ENA) and uploaded to the COMBAT-TB Workbench using the irida-uploader ( 24 ) command line tool.…”

“…5 ) allows metadata from the sequence analysis project’s sequencing store to be associated with tips (i.e., samples) in the phylogeny view. In addition to the metadata computed by the M. tuberculosis Sample Report pipeline, an Excel spreadsheet was generated associating each sample ID with the sample IDs and hospital collection sites identified in the paper by Tania et al ( 23 ). This spreadsheet was used to load additional metadata into the IRIDA project.…”

The COMBAT-TB Workbench: Making powerful TB bioinformatics accessible

“…Tania et al (22) collected M. tuberculosis samples from 30 patients with confirmed pulmonary tuberculosis treated in four hospitals in the Western region of the Indonesian island of Java. Phenotypic drug susceptibility testing (DST) was performed on the cultured samples and DNA was isolated, sequenced and deposited in the NCBI Sequence Read Archive (SRA) with BioProject access number PRJNA633244.…”

Use of Whole-Genome Sequencing to PredictMycobacterium tuberculosisComplex Drug Resistance from Early Positive Liquid Cultures

“…Compared with these other molecular biologic approaches for testing TB drug susceptibility, whole-genome sequencing (WGS) has the advantages of identifying all existing mutations and effectively identifying both synonymous and silent mutations ( 6 , 7 ). A number of studies have demonstrated that culture-based WGS can be used to detect drug resistance in MTBC, especially against rifampin and isoniazid ( 8 – 14 ). The application of WGS in predicting MTBC drug resistance directly from clinical isolates is limited, due to the small amount of MTBC and the high technical requirements for sequencing ( 15 – 17 ).…”