Molecular Tests in the Diagnosis of Tuberculosis

Adem YAŞARa , Özge YILMAZa

aManisa Celal Bayar University Faculty of Medicine, Department of Pediatric Immunology and Allergy Diseases, Manisa, Türkiye

ABSTRACT
Molecular diagnosis has emerged as a crucial tool in the accurate and rapid detection of tuberculosis infections. Traditional methods for tuberculosis diagnosis often suffer from limitations such as slow turnaround time, low sensitivity, and the need for specialized infrastructure. In contrast, molecular diagnostic techniques, particularly polymerase chain reaction and nucleic acid amplification tests, have revolutionized tuberculosis diagnosis by enabling the direct detection of Mycobacterium tuberculosis DNA in clinical samples. The advantages of molecular tests in the diagnosis of tuberculosis are rapid and precise diagnosis, detection of drug resistance and monitoring of treatment efficacy. The integration of these techniques into routine clinical practice holds great promise for improving tuberculosis control strategies and reducing the burden of this infectious disease on a global scale.
Keywords: Tuberculosis; child health; molecular diagnostic techniques

Referanslar

  1. Azadi D, Motallebirad T, Ghaffari K, Shojaei H. Mycobacteriosis and Tuberculosis: Laboratory Diagnosis. Open Microbiol J. 2018;12:41-58. [Crossref]  [PubMed]  [PMC]
  2. World Health Organization [Internet]. Global tuberculosis report 2018 [cited Aug 8 2023]. Available from: [Link]
  3. World Health Organization [Internet]. Global Tuberculosis Report 2022. [cited Aug 8 2023]. Available from: [Link]
  4. Walzl G, McNerney R, du Plessis N, Bates M, McHugh TD, Chegou NN, Zumla A. Tuberculosis: advances and challenges in development of new diagnostics and biomarkers. Lancet Infect Dis. 2018;18(7):e199-e210. [Crossref]  [PubMed]
  5. World Health Organization [Internet]. WHO standard: universal access to rapid tuberculosis diagnostics. [cited 8 Aug 2023 ]. Available from: [Link]
  6. Wang CH, Chang JR, Hung SC, Dou HY, Lee G Bin. Rapid molecular diagnosis of live Mycobacterium tuberculosis on an integrated microfluidic system. Sens Actuators B Chem. 2022;365:131968. [Crossref]
  7. Lee HJ, Kim NH, Lee EH, Yoon YS, Jeong YJ, Lee BC, et al. Multicenter Testing of a Simple Molecular Diagnostic System for the Diagnosis of Mycobacterium Tuberculosis. Biosensors (Basel). 2023;13(2):259. [Crossref]  [PubMed]  [PMC]
  8. Vilchèze C, Kremer L. Acid-Fast Positive and Acid-Fast Negative Mycobacterium tuberculosis: The Koch Paradox. Microbiol Spectr. 2017;5(2). [Crossref]  [PubMed]
  9. Engström A. Fighting an old disease with modern tools: characteristics and molecular detection methods of drug-resistant Mycobacterium tuberculosis. Infect Dis (Lond). 2016;48(1):1-17. [Crossref]  [PubMed]
  10. Cho WH, Won EJ, Choi HJ, Kee SJ, Shin JH, Ryang DW, Suh SP. Comparison of AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR for Detection of Mycobacterium tuberculosis Complex in Routine Clinical Practice. Ann Lab Med. 2015;35(3):356-61. [Crossref]  [PubMed]  [PMC]
  11. Balasingham SV, Davidsen T, Szpinda I, Frye SA, Tønjum T. Molecular diagnostics in tuberculosis: basis and implications for therapy. Mol Diagn Ther. 2009;13(3):137-51. [Crossref]  [PubMed]
  12. Chin KL, Sarmiento ME, Norazmi MN, Acosta A. DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb). 2018;113:139-52. [Crossref]  [PubMed]
  13. Jagielski T, van Ingen J, Rastogi N, Dziadek J, Mazur PK, Bielecki J. Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. Biomed Res Int. 2014;2014:645802. [Crossref]  [PubMed]  [PMC]
  14. MacLean E, Kohli M, Weber SF, Suresh A, Schumacher SG, Denkinger CM, Pai M. Advances in Molecular Diagnosis of Tuberculosis. J Clin Microbiol. 2020;58(10):e01582-19. [Crossref]  [PubMed]  [PMC]
  15. Shingadia D. The diagnosis of tuberculosis. Pediatr Infect Dis J. 2012;31 (3):302-5. [Crossref]  [PubMed]
  16. Nicol MP, Zar HJ. New specimens and laboratory diagnostics for childhood pulmonary TB: progress and prospects. Paediatr Respir Rev. 2011;12(1):16-21. [Crossref]  [PubMed]  [PMC]
  17. Lawn SD, Mwaba P, Bates M, Piatek A, Alexander H, Marais BJ, et al. Advances in tuberculosis diagnostics: the Xpert MTB/RIF assay and future prospects for a point-of-care test. Lancet Infect Dis. 2013;13(4):349-61. [Crossref]  [PubMed]
  18. Lawn SD, Nicol MP. Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol. 2011;6(9):1067-82. [Crossref]  [PubMed]  [PMC]
  19. Maynard-Smith L, Larke N, Peters JA, Lawn SD. Diagnostic accuracy of the Xpert MTB/RIF assay for extrapulmonary and pulmonary tuberculosis when testing non-respiratory samples: a systematic review. BMC Infect Dis. 2014;14:709. [Crossref]  [PubMed]  [PMC]
  20. Rahman A, Sahrin M, Afrin S, Earley K, Ahmed S, Rahman SM, et al. Comparison of Xpert MTB/RIF Assay and GenoType MTBDRplus DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis. PLoS One. 2016;11(4):e0152694. [Crossref]  [PubMed]  [PMC]
  21. World Health Organization [Internet]. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF system: policy statement. [cited 8 Aug 2023]. Available from: [Link]
  22. Kay AW, González Fernández L, Takwoingi Y, Eisenhut M, Detjen AK, Steingart KR, Mandalakas AM. Xpert MTB/RIF and Xpert MTB/RIF Ultra assays for active tuberculosis and rifampicin resistance in children. Cochrane Database Syst Rev. 2020;8(8):CD013359. [Crossref]  [PubMed]  [PMC]
  23. World Health Organization [Internet]. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF assay for the diagnosis of pulmonary and extrapulmonary TB in adults and children: policy update. [cited 9 Aug 2023]. Available from: [Link]
  24. World Health Organization [Internet]. Guidance for national tuberculosis programmes on the management of tuberculosis in children, 2nd ed. [cited 9 Aug 2023]. Available from: [Link]
  25. Yusoof KA, García JI, Schami A, Garcia-Vilanova A, Kelley HV, Wang SH, Rendon A, Restrepo BI, Yotebieng M, Torrelles JB. Tuberculosis Phenotypic and Genotypic Drug Susceptibility Testing and Immunodiagnostics: A Review. Front Immunol. 2022;13:870768. [Crossref]  [PubMed]  [PMC]
  26. World Health Organization [Internet]. WHO consolidated guidelines on tuberculosis: module 3: diagnosis: rapid diagnostics for tuberculosis detection, 2021 update. [cited 9 Aug 2023]. Available from: [Link]
  27. Horne DJ, Kohli M, Zifodya JS, Schiller I, Dendukuri N, Tollefson D, Set al. Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2019;6(6):CD009593. [Crossref]  [PubMed]  [PMC]
  28. Malherbe ST, Shenai S, Ronacher K, Loxton AG, Dolganov G, Kriel M, et al. Persisting PET-CT lesion activity and M. tuberculosis mRNA after pulmonary tuberculosis cure. Nat Med. 2016;22(10):1094. [Crossref]  [PubMed]  [PMC]
  29. Arend SM, van Soolingen D. Performance of Xpert MTB/RIF Ultra: a matter of dead or alive. Lancet Infect Dis. 2018;18(1):8-10. [Crossref]  [PubMed]
  30. Zhang M, Xue M, He JQ. Diagnostic accuracy of the new Xpert MTB/RIF Ultra for tuberculosis disease: A preliminary systematic review and meta-analysis. Int J Infect Dis. 2020;90:35-45. [Crossref]  [PubMed]
  31. World Health Organization [Internet]. Line probe assays for detection of drug-resistant tuberculosis: interpretation and reporting manual for laboratory staff and clinicians. [cited 9 Aug 2023]. Available from: [Link]
  32. Desikan P, Panwalkar N, Mirza SB, Chaturvedi A, Ansari K, Varathe R, et al. Line probe assay for detection of Mycobacterium tuberculosis complex: An experience from Central India. Indian J Med Res. 2017;145(1):70-3. [Crossref]  [PubMed]  [PMC]
  33. Sinha P, Srivastava GN, Tripathi R, Mishra MN, Anupurba S. Detection of mutations in the rpoB gene of rifampicin-resistant Mycobacterium tuberculosis strains inhibiting wild type probe hybridization in the MTBDR plus assay by DNA sequencing directly from clinical specimens. BMC Microbiol. 2020;20(1):284. [Crossref]  [PubMed]  [PMC]
  34. Ninan MM, Gowri M, Christopher DJ, Rupali P, Michael JS. The diagnostic utility of line probe assays for multidrug-resistant tuberculosis. Pathog Glob Health. 2016;110(4-5):194-9. [Crossref]  [PubMed]  [PMC]
  35. World Health Organization [Internet]. Molecular line probe assays for rapid screening of patients at risk of multidrug-resistant tuberculosis (MDR-TB). [cited 9 Aug 2023]. Available from: [Link]
  36. World Health Organization [Internet]. The use of molecular line probe assays for the detection of resistance to second-line anti-tuberculosis drugs: policy guidance. [cited 8 Aug 2023]. Available from: [Link]
  37. Mitarai S, Okumura M, Toyota E, Yoshiyama T, Aono A, Sejimo A, et al. Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis. Int J Tuberc Lung Dis. 2011;15(9):1211-7. [Crossref]  [PubMed]
  38. World Health Organization [Internet]. The use of loop-mediated isothermal amplification (‎TB-LAMP)‎ for the diagnosis of pulmonary tuberculosis: policy guidance. [cited 8 Aug 2023]. Available from: [Link]
  39. Nagai K, Horita N, Yamamoto M, Tsukahara T, Nagakura H, Tashiro K, et al. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep. 2016;6:39090. [Crossref]  [PubMed]  [PMC]
  40. Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13 (2):137-46. [Crossref]  [PubMed]
  41. Nurwidya F, Handayani D, Burhan E, Yunus F. Molecular Diagnosis of Tuberculosis. Chonnam Med J. 2018;54(1):1-9. [Crossref]  [PubMed]  [PMC]
  42. Metzker ML. Emerging technologies in DNA sequencing. Genome Res. 2005;15(12):1767-76. [Crossref]  [PubMed]
  43. Strausberg RL, Levy S, Rogers YH. Emerging DNA sequencing technologies for human genomic medicine. Drug Discov Today. 2008;13(13-14):569-77. [Crossref]  [PubMed]
  44. Rizzo JM, Buck MJ. Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prev Res (Phila). 2012;5(7):887-900. [Crossref]  [PubMed]
  45. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31-46. [Crossref]  [PubMed]
  46. Witney AA, Cosgrove CA, Arnold A, Hinds J, Stoker NG, Butcher PD. Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med. 2016;14:46. [Crossref]  [PubMed]  [PMC]
  47. Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med. 2013;369(3):290-2. [Crossref]  [PubMed]  [PMC]
  48. Witney AA, Gould KA, Arnold A, Coleman D, Delgado R, Dhillon J, et al. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J Clin Microbiol. 2015;53(5):1473-83. [Crossref]  [PubMed]  [PMC]
  49. McAlister AJ, Driscoll J, Metchock B. DNA Sequencing for Confirmation of Rifampin Resistance Detected by Cepheid Xpert MTB/RIF Assay. J Clin Microbiol. 2015;53(5):1752. [Crossref]  [PubMed]  [PMC]