J Korean Med Sci.  2022 Nov;37(46):e328. 10.3346/jkms.2022.37.e328.

Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application

• Kim N
• Seok KH
• Shin S
• Kim B
• Park H
• Roh EY
• Yoon JH
• Shin S

• KMID: 2536135
• DOI: http://doi.org/10.3346/jkms.2022.37.e328

Abstract

Background
Whole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of userfriendly WGS tools in reporting resistance profiles and identifying lineages of clinical TB isolates from South Korea.
Methods
Forty clinical samples from TB patients showing discrepancies between their rapid molecular and conventional drug susceptibility tests were used in this study. Among these clinical isolates, 37 strains were successfully evaluated via WGS software, using the GenTB, TB Profiler, PhyResSE, CASTB, and Mykrobe.
Results
More accurate and faster susceptibility results could be obtained with isoniazid than with rifampin. Using the phenotypic test as the gold standard, the isoniazid concordance rate between phenotypic drug susceptibility test (DST) and WGS (GenTB: 45.9%, TB profiler: 40.5%, PhyResSE: 40.5%, CASTB: 48.6%, and Mykrobe: 43.2%) was much higher than between phenotypic DST and rapid molecular genotypic DST (18.9%) among the 37 strains. In contrast, the rifampin concordance rate between phenotypic DST and WGS and that between phenotypic DST and rapid molecular genotypic DST was similar (81.1–89.2%). We also found novel mutations associated with INH in katG and ahpC gene region, not covered by the line probe assay. In addition, lineage analysis identified 81.1% of these samples as L2 East Asian lineage strains, and 18.9% as L4 Euro-American lineage strains.
Conclusion
WGS may play a pivotal role in TB diagnosis and the detection of drug resistance, genetic diversity, and transmission dynamics in the near future because of its accuracy, speed, and extensibility.

Keyword

Mycobacterium tuberculosis; Drug-Resistant Tuberculosis; Drug Susceptibility Test; Whole Genome Sequencing

Reference

1. Centers for Disease Control and Prevention. Basic TB facts 2016. Updated 2016. Accessed April 23, 2020. https://www.cdc.gov/tb/topic/basics/default.htm .

2. Furin J, Cox H, Pai M. Tuberculosis. Lancet. 2019; 393(10181):1642–1656. PMID: 30904262.

3. World Health Organization. Tuberculosis, fact sheets 2020. Updated 2020. Accessed July 2, 2021. https://www.who.int/news-room/fact-sheets/detail/tuberculosis .

4. World Health Organization. Global tuberculosis report 2020. Updated 2020. Accessed July 2, 2021. https://www.who.int/publications/i/item/9789240013131 .

5. World Health Organization. The top 10 causes of death 2020. Updated 2020. Accessed July 2, 2021. https://www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death .

6. Kim JS, Shin JY, Kong IS. Characteristics of the notified tuberculosis - Republic of Korea, 2019. Public Health Wkly Rep. 2020; 13(14):832–850.

7. Korea Centers for Disease Control and Prevention. Annual Report on the Notified Tuberculosis in Korea 2019. Cheongju, Korea: Korea Centers for Disease Control and Prevention;2020.

8. Go U, Park M, Kim UN, Lee S, Han S, Lee J, et al. Tuberculosis prevention and care in Korea: evolution of policy and practice. J Clin Tuberc Other Mycobact Dis. 2018; 11:28–36. PMID: 31720389.

9. World Health Organization. WHO Consolidated Guidelines on Drug-Resistant Tuberculosis Treatment 2019. Geneva, Switzerland: WHO;2019.

10. Joint Committee for the Revision of Korean Guidelines for Tuberculosis and Korea Center for Disease Control and Prevention. Korean Guidelines for Tuberculosis. 4th ed. 2020.

11. World Health Organization. The Use of Next-Generation Sequencing Technologies for the Detection of Mutations Associated With Drug Resistance in Mycobacterium tuberculosis Complex: Technical Guide 2018. Geneva, Switzerland: WHO;2018.

12. Casali N, Broda A, Harris SR, Parkhill J, Brown T, Drobniewski F. Whole genome sequence analysis of a large isoniazid-resistant tuberculosis outbreak in London: a retrospective observational study. PLoS Med. 2016; 13(10):e1002137. PMID: 27701423.

13. Napier G, Campino S, Merid Y, Abebe M, Woldeamanuel Y, Aseffa A, et al. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med. 2020; 12(1):114. PMID: 33317631.

14. Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P, et al. Evaluation of whole-genome sequencing for mycobacterial species identification and drug susceptibility testing in a clinical setting: a large-scale prospective assessment of performance against line probe assays and phenotyping. J Clin Microbiol. 2018; 56(2):e01480-17. PMID: 29167290.

15. GOV.UK. England world leaders in the use of whole genome sequencing to diagnose TB. Updated 2017. Accessed July 2, 2021. https://www.gov.uk/government/news/england-world-leaders-in-the-use-of-whole-genome-sequencing-to-diagnose-tb .

16. Cabibbe AM, Walker TM, Niemann S, Cirillo DM. Whole genome sequencing of Mycobacterium tuberculosis. Eur Respir J. 2018; 52(5):1801163. PMID: 30209198.

17. Genestet C, Hodille E, Berland JL, Ginevra C, Bryant JE, Ader F, et al. Whole-genome sequencing in drug susceptibility testing of Mycobacterium tuberculosis in routine practice in Lyon, France. Int J Antimicrob Agents. 2020; 55(4):105912. PMID: 31991222.

18. Goig GA, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Navarro D, Borrás R, et al. Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study. Lancet Microbe. 2020; 1(4):e175–e183. PMID: 35544271.

19. Wu X, Gao R, Shen X, Guo Y, Yang J, Wu Z, et al. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis. 2020; 96:48–53. PMID: 32339720.

20. Vogel M, Utpatel C, Corbett C, Kohl TA, Iskakova A, Ahmedov S, et al. Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country. Sci Rep. 2021; 11(1):15333. PMID: 34321545.

21. Nathavitharana RR, Cudahy PG, Schumacher SG, Steingart KR, Pai M, Denkinger CM. Accuracy of line probe assays for the diagnosis of pulmonary and multidrug-resistant tuberculosis: a systematic review and meta-analysis. Eur Respir J. 2017; 49(1):1601075. PMID: 28100546.

22. Takii T, Seki K, Wakabayashi Y, Morishige Y, Sekizuka T, Yamashita A, et al. Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: application of the genome research for Asian tuberculosis (GReAT) database. Sci Rep. 2019; 9(1):12823. PMID: 31492902.

23. Cox HS, Kubica T, Doshetov D, Kebede Y, Rüsch-Gerdess S, Niemann S. The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia. Respir Res. 2005; 6(1):134. PMID: 16277659.

24. European Concerted Action on New Generation Genetic Markers and Techniques for the Epidemiology and Control of Tuberculosis. Beijing/W genotype Mycobacterium tuberculosis and drug resistance. Emerg Infect Dis. 2006; 12(5):736–743. PMID: 16704829.

25. Hakamata M, Takihara H, Iwamoto T, Tamaru A, Hashimoto A, Tanaka T, et al. Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection. Sci Rep. 2020; 10(1):17997. PMID: 33093577.

26. Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015; 7(1):51. PMID: 26019726.

27. Nguyen TN, Anton-Le Berre V, Bañuls AL, Nguyen TV. Molecular diagnosis of drug-resistant tuberculosis; a literature review. Front Microbiol. 2019; 10:794. PMID: 31057511.

28. World Health Organization. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance 2021. Updated 2021. Accessed October 17, 2021. https://www.who.int/publications/i/item/9789240028173 .

29. Ruhwald M, Carmona S, Pai M. Learning from COVID-19 to reimagine tuberculosis diagnosis. Lancet Microbe. 2021; 2(5):e169–e170. PMID: 33778790.

30. The Lancet Public Health. Renewing the fight to end tuberculosis. Lancet Public Health. 2021; 6(5):e260. PMID: 33780658.