Progress in molecular diagnosis of <i>Mycobacterium tuberculosis</i>_West China Medical Journal

Authors：

JIAO Lin , LI Jing ,  YING Binwu

Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China;

Corresponding author：

YING Binwu, Email: binwuying@126.com

Keywords：

Tuberculosis; Drug-resistant tuberculosis; Molecular diagnosis; Xpert

DOI：

10.7507/1002-0179.201907093

Video：

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Delay in diagnosis of tuberculosis and the presence of drug-resistant tuberculosis are huge threats to global tuberculosis disease control. Early detection of active tuberculosis, especially the detection of drug-resistant Mycobacterium tuberculosis strains, is necessary. This paper emphasizes on the application of the molecular diagnostic techniques in the field of rapid detection of Mycobacterium tuberculosis and drug-resistant Mycobacterium tuberculosis, and discusses the performance of current molecular diagnostic techniques in solving clinical detection difficulties. The paper aims to provide the theoretical thinking for the diagnosis of tuberculosis in the future.

Citation： JIAO Lin, LI Jing, YING Binwu. Progress in molecular diagnosis of Mycobacterium tuberculosis. West China Medical Journal, 2019, 34(8): 839-843. doi: 10.7507/1002-0179.201907093 Copy

1.	World Health Organization. Global tuberculosis report 2018: WHO/CDS/TB/2018.20. Geneva: World Health Organization, 2018. https://www.who.int/tb/publications/global_report/en/.
2.	David HL. Bacteriology of the mycobacterioses. Atlanta: US Dept of Health, Education, and Welfare, Public Health Service, Center for Disease Control, Bureau of Laboratories, Bacteriology Division, Mycobacteriology Branch, 1976.
3.	Steingart KR, Henry M, Ng V, et al. Fluorescence versus conventional sputum smear microscopy for tuberculosis: a systematic review. Lancet Infect Dis, 2006, 6(9): 570-581.
4.	Steingart KR, Ramsay A, Pai M. Optimizing sputum smear microscopy for the diagnosis of pulmonary tuberculosis. Expert Rev Anti Infect Ther, 2007, 5(3): 327-331.
5.	Parsons LM, Somoskövi A, Gutierrez C, et al. Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities. Clin Microbiol Rev, 2011, 24(2): 314-350.
6.	Drobniewski F, Nikolayevskyy V, Balabanova Y, et al. Diagnosis of tuberculosis and drug resistance: what can new tools bring us?. Int J Tuberc Lung Dis, 2012, 16(7): 860-870.
7.	World Health Organization. Molecular line probe assays for rapid screening of patients at risk of multi-drug resistant tuberculosis (MDR-TB). Expert group report. Geneva: World Health Organization, 2008.
8.	Hillemann D, Weizenegger M, Kubica T, et al. Use of the genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2005, 43(8): 3699-3703.
9.	Migliori GB, Matteelli A, Cirillo D, et al. Diagnosis of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis: Current standards and challenges. Can J Infect Dis Med Microbiol, 2008, 19(2): 169-172.
10.	Tagliani E, Cabibbe AM, Miotto P, et al. Diagnostic performance of the new version (v2. 0) of GenoType MTBDRsl assay for detection of resistance to fluoroquinolones and second-line injectable drugs: a multicenter study. J Clin Microbiol, 2015, 53(9): 2961-2969.
11.	Brossier F, Guindo D, Pham A, et al. Performance of the new version (v2.0) of the GenoType MTBDRsl test for detection of resistance to second-line drugs in multidrug-resistant Mycobacterium tuberculosis complex strains. J Clin Microbiol, 2016, 54(6): 1573-1580.
12.	Gardee Y, Dreyer AW, Koornhof HJ, et al. Evaluation of the GenoType MTBDRsl version 2. 0 assay for second-line drug resistance detection of Mycobacterium tuberculosis isolates in South Africa. J Clin Microbiol, 2017, 55(3): 791-800.
13.	Cepheid. Xpert MTB/RIF package insert. 2009. http://tbevidence.org/documents/rescentre/sop/XpertMTB_Broch_R9_EU.pdf.
14.	Boehme CC, Nabeta P, Hillemann D, et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med, 2010, 363(11): 1005-1015.
15.	Boehme CC, Nicol MP, Nabeta P, et al. Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet, 2011, 377(9776): 1495-1505.
16.	Helb D, Jones M, Story E, et al. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J Clin Microbiol, 2010, 48(1): 229-237.
17.	Denkinger C. The TB diagnostic pipeline: a realistic view. Union Meeting, Liverpool, 2016. (2016-10-26)[2019-06-01]. http://www.finddx.org/wp-content/uploads/2016/10/9th-Symposium-2016-01_Denkinger.pdf.
18.	Steingart KR, Schiller I, Horne DJ, et al. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev, 2014(1): CD009593.
19.	World Health Organization. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF System. Policy statement: WHO/HTM/TB/2011.4. Geneva: World Health Organization, 2013.
20.	Foundation for Innovative New Diagnostic. Report for WHO: a multicentre noninferiority diagnostic accuracy study of the ultra assay compared to the Xpert MTB/RIF assay. Geneva: Foundation for Innovative New Diagnostic, 2017. https://www.finddx.org/wp-content/uploads/2017/03/Ultra-WHO-report_24MAR2017_FINAL.pdf.
21.	World Health Organization. WHO meeting report of a technical expert consultation: non-inferiority analysis of Xpert MTB /RIF Ultra compared to Xpert MTB/RIF: WHO/HTM/TB/2017.04. Geneva: World Health Organization, 2017.
22.	Chakravorty S, Simmons AM, Rowneki M, et al. The new Xpert MTB/RIF Ultra: improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing. MBio, 2017, 8(4): e00812-17.
23.	Dorman SE, Schumacher SG, Alland D, et al. Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy study. Lancet Infect Dis, 2018, 18(1): 76-84.
24.	Nicol MP, Workman L, Prins M, et al. Accuracy of Xpert MTB/RIF Ultra for the diagnosis of pulmonary tuberculosis in children. Pediatr Infect Dis J, 2018, 37(10): e261-e263.
25.	Nagai K, Horita N, Yamamoto M, et al. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep, 2016, 6: 39090.
26.	World Health Organization. The use of a commercial LOOP-mediated isothermal amplification assay (TB-Lamp) for the detection of tuberculosis: WHO/HTM/TB/2013.05. Geneva: World Health Organization, 2013.
27.	Sanchez JA, Pierce KE, Rice JE, et al. Linear-After-The-Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci USA, 2004, 101(7): 1933-1938.
28.	Hillemann D, Haasis C, Andres S, et al. Validation of the FluoroType MTBDR assay for detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2018, 56(6): e00072-18.
29.	Kostera J, Leckie G, Abravaya K, et al. Performance of the Abbott RealTime MTB RIF/INH resistance assay when used to test Mycobacterium tuberculosis specimens from Bangladesh. Infect Drug Resist, 2018, 11: 695-699.
30.	Ruiz P, Causse M, Vaquero M, et al. Evaluation of a new automated Abbott RealTime MTB RIF/INH assay for qualitative detection of rifampicin/isoniazid resistance in pulmonary and extra-pulmonary clinical samples of Mycobacterium tuberculosis. Infect Drug Resist, 2017, 10: 463-467.
31.	Scott L, David A, Noble L, et al. Performance of the Abbott RealTime MTB and MTB RIF/INH assays in a setting of high tuberculosis and HIV coinfection in South Africa. J Clin Microbiol, 2017, 55(8): 2491-2501.
32.	Horita N, Yamamoto M, Sato T, et al. Sensitivity and specificity of Cobas TaqMan MTB real-time polymerase chain reaction for culture-proven Mycobacterium tuberculosis: meta-analysis of 26999 specimens from 17 Studies. Sci Rep, 2015, 5: 18113.
33.	Coll F, McNerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med, 2015, 7(1): 51.
34.	Miotto P, Tessema B, Tagliani E, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J, 2017, 50(6): 1701354.
35.	McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther, 2018, 16(5): 433-442.
36.	Satta G, Atzeni A, Mchugh TD. Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist. Clin Microbiol Infect, 2017, 23(2): 69-72.
37.	Walker TM, Merker M, Kohl TA, et al. Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing. Clin Microbiol Infect, 2017, 23(3): 161-166.

1. World Health Organization. Global tuberculosis report 2018: WHO/CDS/TB/2018.20. Geneva: World Health Organization, 2018. https://www.who.int/tb/publications/global_report/en/.
2. David HL. Bacteriology of the mycobacterioses. Atlanta: US Dept of Health, Education, and Welfare, Public Health Service, Center for Disease Control, Bureau of Laboratories, Bacteriology Division, Mycobacteriology Branch, 1976.
3. Steingart KR, Henry M, Ng V, et al. Fluorescence versus conventional sputum smear microscopy for tuberculosis: a systematic review. Lancet Infect Dis, 2006, 6(9): 570-581.
4. Steingart KR, Ramsay A, Pai M. Optimizing sputum smear microscopy for the diagnosis of pulmonary tuberculosis. Expert Rev Anti Infect Ther, 2007, 5(3): 327-331.
5. Parsons LM, Somoskövi A, Gutierrez C, et al. Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities. Clin Microbiol Rev, 2011, 24(2): 314-350.
6. Drobniewski F, Nikolayevskyy V, Balabanova Y, et al. Diagnosis of tuberculosis and drug resistance: what can new tools bring us?. Int J Tuberc Lung Dis, 2012, 16(7): 860-870.
7. World Health Organization. Molecular line probe assays for rapid screening of patients at risk of multi-drug resistant tuberculosis (MDR-TB). Expert group report. Geneva: World Health Organization, 2008.
8. Hillemann D, Weizenegger M, Kubica T, et al. Use of the genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2005, 43(8): 3699-3703.
9. Migliori GB, Matteelli A, Cirillo D, et al. Diagnosis of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis: Current standards and challenges. Can J Infect Dis Med Microbiol, 2008, 19(2): 169-172.
10. Tagliani E, Cabibbe AM, Miotto P, et al. Diagnostic performance of the new version (v2. 0) of GenoType MTBDRsl assay for detection of resistance to fluoroquinolones and second-line injectable drugs: a multicenter study. J Clin Microbiol, 2015, 53(9): 2961-2969.
11. Brossier F, Guindo D, Pham A, et al. Performance of the new version (v2.0) of the GenoType MTBDRsl test for detection of resistance to second-line drugs in multidrug-resistant Mycobacterium tuberculosis complex strains. J Clin Microbiol, 2016, 54(6): 1573-1580.
12. Gardee Y, Dreyer AW, Koornhof HJ, et al. Evaluation of the GenoType MTBDRsl version 2. 0 assay for second-line drug resistance detection of Mycobacterium tuberculosis isolates in South Africa. J Clin Microbiol, 2017, 55(3): 791-800.
13. Cepheid. Xpert MTB/RIF package insert. 2009. http://tbevidence.org/documents/rescentre/sop/XpertMTB_Broch_R9_EU.pdf.
14. Boehme CC, Nabeta P, Hillemann D, et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med, 2010, 363(11): 1005-1015.
15. Boehme CC, Nicol MP, Nabeta P, et al. Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet, 2011, 377(9776): 1495-1505.
16. Helb D, Jones M, Story E, et al. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J Clin Microbiol, 2010, 48(1): 229-237.
17. Denkinger C. The TB diagnostic pipeline: a realistic view. Union Meeting, Liverpool, 2016. (2016-10-26)[2019-06-01]. http://www.finddx.org/wp-content/uploads/2016/10/9th-Symposium-2016-01_Denkinger.pdf.
18. Steingart KR, Schiller I, Horne DJ, et al. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev, 2014(1): CD009593.
19. World Health Organization. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF System. Policy statement: WHO/HTM/TB/2011.4. Geneva: World Health Organization, 2013.
20. Foundation for Innovative New Diagnostic. Report for WHO: a multicentre noninferiority diagnostic accuracy study of the ultra assay compared to the Xpert MTB/RIF assay. Geneva: Foundation for Innovative New Diagnostic, 2017. https://www.finddx.org/wp-content/uploads/2017/03/Ultra-WHO-report_24MAR2017_FINAL.pdf.
21. World Health Organization. WHO meeting report of a technical expert consultation: non-inferiority analysis of Xpert MTB /RIF Ultra compared to Xpert MTB/RIF: WHO/HTM/TB/2017.04. Geneva: World Health Organization, 2017.
22. Chakravorty S, Simmons AM, Rowneki M, et al. The new Xpert MTB/RIF Ultra: improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing. MBio, 2017, 8(4): e00812-17.
23. Dorman SE, Schumacher SG, Alland D, et al. Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy study. Lancet Infect Dis, 2018, 18(1): 76-84.
24. Nicol MP, Workman L, Prins M, et al. Accuracy of Xpert MTB/RIF Ultra for the diagnosis of pulmonary tuberculosis in children. Pediatr Infect Dis J, 2018, 37(10): e261-e263.
25. Nagai K, Horita N, Yamamoto M, et al. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep, 2016, 6: 39090.
26. World Health Organization. The use of a commercial LOOP-mediated isothermal amplification assay (TB-Lamp) for the detection of tuberculosis: WHO/HTM/TB/2013.05. Geneva: World Health Organization, 2013.
27. Sanchez JA, Pierce KE, Rice JE, et al. Linear-After-The-Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci USA, 2004, 101(7): 1933-1938.
28. Hillemann D, Haasis C, Andres S, et al. Validation of the FluoroType MTBDR assay for detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2018, 56(6): e00072-18.
29. Kostera J, Leckie G, Abravaya K, et al. Performance of the Abbott RealTime MTB RIF/INH resistance assay when used to test Mycobacterium tuberculosis specimens from Bangladesh. Infect Drug Resist, 2018, 11: 695-699.
30. Ruiz P, Causse M, Vaquero M, et al. Evaluation of a new automated Abbott RealTime MTB RIF/INH assay for qualitative detection of rifampicin/isoniazid resistance in pulmonary and extra-pulmonary clinical samples of Mycobacterium tuberculosis. Infect Drug Resist, 2017, 10: 463-467.
31. Scott L, David A, Noble L, et al. Performance of the Abbott RealTime MTB and MTB RIF/INH assays in a setting of high tuberculosis and HIV coinfection in South Africa. J Clin Microbiol, 2017, 55(8): 2491-2501.
32. Horita N, Yamamoto M, Sato T, et al. Sensitivity and specificity of Cobas TaqMan MTB real-time polymerase chain reaction for culture-proven Mycobacterium tuberculosis: meta-analysis of 26999 specimens from 17 Studies. Sci Rep, 2015, 5: 18113.
33. Coll F, McNerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med, 2015, 7(1): 51.
34. Miotto P, Tessema B, Tagliani E, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J, 2017, 50(6): 1701354.
35. McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther, 2018, 16(5): 433-442.
36. Satta G, Atzeni A, Mchugh TD. Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist. Clin Microbiol Infect, 2017, 23(2): 69-72.
37. Walker TM, Merker M, Kohl TA, et al. Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing. Clin Microbiol Infect, 2017, 23(3): 161-166.

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