1887

Abstract

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.

We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant in Java, Indonesia.

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.

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.

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.

Funding
This study was supported by the:
  • National Research Council of Thailand (Award Grant No. 60-057 and 62-003)
    • Principle Award Recipient: Kiatichai Faksri
  • Fogarty International Center (Award No. 5D43TW009522)
    • Principle Award Recipient: Angkana Chaiprasert
  • Universitas Indonesia (Award PITTA 2018)
    • Principle Award Recipient: Pratiwi Sudarmono
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001221
2020-06-24
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/jmm/69/7/1013.html?itemId=/content/journal/jmm/10.1099/jmm.0.001221&mimeType=html&fmt=ahah

References

  1. Annabel B, Anna D, Hannah M. Global Tuberculosis Report 2019 Geneva: World Health Organization; 2019
    [Google Scholar]
  2. Papaventsis D, Casali N, Kontsevaya I, Drobniewski F, Cirillo DM et al. Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review. Clinical Microbiology and Infection 2017; 23:61–68 [View Article]
    [Google Scholar]
  3. Oudghiri A, Karimi H, Chetioui F, Zakham F, Bourkadi JE et al. Molecular characterization of mutations associated with resistance to second-line tuberculosis drug among multidrug-resistant tuberculosis patients from high prevalence tuberculosis City in Morocco. BMC Infect Dis 2018; 18:1–8 [View Article]
    [Google Scholar]
  4. Faksri K, Tan JH, Chaiprasert A, Teo Y-Y, Ong RT-H. Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis . Infect Genet Evol 2016a; 45:359–368 [View Article][PubMed]
    [Google Scholar]
  5. Ali A, Hasan Z, McNerney R, Mallard K, Hill-Cawthorne G et al. Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from pakistan. PLoS One 2015; 10:e0117771–17 [View Article]
    [Google Scholar]
  6. Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A et al. Use of whole genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. J Glob Antimicrob Re 2018
    [Google Scholar]
  7. CRyPTIC C, Allix-Beguec C, Arandjelovic I, Bi L, Beckert P et al. Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing. N Engl J Med 2018; 379:1403–1415
    [Google Scholar]
  8. Brown AC, Bryant JM, Einer-Jensen K, Holdstock J, Houniet DT et al. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol 2015; 53:2230–2237 [View Article]
    [Google Scholar]
  9. McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther 2018; 16:433–442 [View Article]
    [Google Scholar]
  10. Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C et al. Whole-Genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis 2015; 15:1193–1202 [View Article]
    [Google Scholar]
  11. Witney AA, Cosgrove CA, Arnold A, Hinds J, Stoker NG et al. Clinical use of whole genome sequencing for Mycobacterium tuberculosis . BMC Med 2016; 14:1–7 [View Article]
    [Google Scholar]
  12. World Health Organization Technical manual for drug susceptibility testing of medicines used in the treatment of tuberculosis.; 2018
  13. Healey A, Furtado A, Cooper T, Henry RJ. Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 2014; 10:21–28 [View Article]
    [Google Scholar]
  14. Macedo R, Nunes A, Portugal I, Duarte S, Vieira L et al. Dissecting whole-genome sequencing-based online tools for predicting resistance in Mycobacterium tuberculosis : can we use them for clinical decision guidance?. Tuberculosis 2018; 110:44–51 [View Article]
    [Google Scholar]
  15. Jandrasits C, Kröger S, Haas W, Renard BY. Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. PLoS Comput Biol 2019; 15:e1007527 [View Article]
    [Google Scholar]
  16. Global Laboratory Intitiative Advancing TBD Line probe assays for drug-resistant tuberculosis detection - Interpretation and reporting guide for laboratory staff and clinicians; 2018
  17. Maningi NE, Malinga LA, Antiabong JF, Lekalakala RM, Mbelle NM. Comparison of line probe assay to BACTEC MGIT 960 system for susceptibility testing of first and second-line anti-tuberculosis drugs in a referral laboratory in South Africa. BMC Infect Dis 2017; 17:1–8 [View Article]
    [Google Scholar]
  18. Christianson S, Voth D, Wolfe J, Sharma MK. Re-Evaluation of the critical concentration for ethambutol antimicrobial sensitivity testing on the MGIT 960. PLoS One 2014; 9:e108911–11 [View Article]
    [Google Scholar]
  19. Frederick A, Robin M, Elizabeth M, Thomas C, Helden V et al. Susceptibility in Mycobacterium tuberculosis embB 306 Mutations as Molecular Indicators to Predict Ethambutol Susceptibility in Mycobacterium tuberculosis . Chemotherapy 2012; 58:358–363
    [Google Scholar]
  20. Arjomandzadegan M, Titov L, Farnia P, Owlia P, Ranjbar R et al. Molecular detection of fluoroquinolone resistance-associated gyrA mutations in ofloxacin-resistant clinical isolates of Mycobacterium tuberculosis from Iran and Belarus. Int J Mycobacteriol 2016; 5:299–305 [View Article]
    [Google Scholar]
  21. Gardee Y, Dreyer AW, Koornhof HJ, Omar SV, Silva P et al. Evaluation of the GenoType MTBDRsl tuberculosis Isolates in South Africa. J Clin Microbiol 2017; 55:791–800
    [Google Scholar]
  22. Lacoma A, García-Sierra N, Prat C, Maldonado J, Ruiz-Manzano J et al. GenoType MTBDR sl for Molecular Detection of Second-Line-Drug and Ethambutol Resistance in Mycobacterium tuberculosis Strains and Clinical Samples. J Clin Microbiol 2012; 50:30–36 [View Article]
    [Google Scholar]
  23. Brossier F, Guindo D, Pham A, Reibel F, Sougakoff W et al. Performance of the New Version (v2.0) of the GenoType MTBDR sl Test for Detection of Resistance to Second-Line Drugs in Multidrug-Resistant Mycobacterium tuberculosis Complex Strains. J Clin Microbiol 2016; 54:1573–1580 [View Article]
    [Google Scholar]
  24. Jian J, Yang X, Yange J, Chen L. Evaluation of the GenoType MTBDR plus and MTBDR sl for the detection of drug-resistant Mycobacterium tuberculosis on isolates from Beijing, China Jiyong Jian. Infection and Drug Resistance 2018; 11:1–29
    [Google Scholar]
  25. Bae AS, Ku KS, Miller MD, Mo H, Svarovskaia ES. Allele-Specific real-time PCR system for detection of subpopulations of genotype 1A and 1b hepatitis C NS5B Y448H mutant viruses in clinical samples. J Clin Microbiol 2011; 49:3168–3174 [View Article]
    [Google Scholar]
  26. Yimer SA, Norheim G, Namouchi A, Zegeye ED, Kinander W et al. Mycobacterium tuberculosis Lineage 7 Strains Are Associated with Prolonged Patient Delay in Seeking Treatment for Pulmonary Tuberculosis in Amhara Region, Ethiopia. J Clin Microbiol 2015; 53:1301–1309 [View Article]
    [Google Scholar]
  27. Chaidir L, Sengstake S, Beer JD, Oktavian A, Krismawati H et al. Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura, Indonesia Papua. MEEGID. 2016
    [Google Scholar]
  28. Parwati I, Crevel RV, Sudiro M, Alisjahbana B, Pakasi T. Mycobacterium tuberculosis Population Structures Differ Significantly on Mycobacterium tuberculosis Population Structures Differ Significantly on Two Indonesian Islands. Journal of Clinical Microbiology 2008
    [Google Scholar]
  29. Faksri K, Tan JH, Disratthakit A, Xia E, Prammananan T et al. Whole-genome sequencing analysis of serially isolated multi-drug and extensively drug resistant Mycobacterium tuberculosis from Thai patients. PLoS One 2016b; 11:e0160992–16 [View Article]
    [Google Scholar]
  30. Ballif M, Harino P, Ley S, Coscolla M, Niemann S et al. Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea. BMC Microbiol 2012; 12:191 [View Article][PubMed]
    [Google Scholar]
  31. Chaidir L, Sengstake S, Beer JD, Krismawati H, Lestari FD et al. Mycobacterium tuberculosis genotypic drug resistance patterns and clustering in Jayapura, Papua, Indonesia; 2015; 19428–433
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001221
Loading
/content/journal/jmm/10.1099/jmm.0.001221
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error