Molecular approaches and biomarkers for detection of mycobacterium tuberculosis

Clinics in Laboratory Medicine

Volumn 33, Issue 3, 2013, Pages 553-566

  Luo, Robert F ^a,b   Banaei, Niaz ^a,b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Biomarkers; Molecular diagnostics; Mycobacterium tuberculosis; Nucleic acid amplification tests

Indexed keywords

BACTERIAL DNA; BETA LACTAMASE; BIOLOGICAL MARKER; DNA FRAGMENT; GAMMA INTERFERON; ISONIAZID; LIPOARABINOMANNAN; MYCOBACTERIUM ANTIGEN; NEOPTERIN; PROCALCITONIN; RIFAMPICIN; VOLATILE ORGANIC COMPOUND;

ANTIBIOTIC RESISTANCE; BACTERIUM DETECTION; BREATH ANALYSIS; DIAGNOSTIC EQUIPMENT; DIAGNOSTIC TEST; DNA EXTRACTION; ENZYME LINKED IMMUNOSORBENT ASSAY; GAS CHROMATOGRAPHY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTERFERON GAMMA RELEASE ASSAY; LATENT TUBERCULOSIS; LOOP MEDIATED ISOTHERMAL AMPLIFICATION; LUNG TUBERCULOSIS; MOLECULAR DIAGNOSIS; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEIC ACID AMPLIFICATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SENSITIVITY AND SPECIFICITY; SPUTUM CULTURE; SPUTUM SMEAR; TUBERCULIN TEST; TUBERCULOSIS;

BIOMARKERS; MOLECULAR DIAGNOSTICS; MYCOBACTERIUM TUBERCULOSIS; NUCLEIC ACID AMPLIFICATION TESTS;

BIOLOGICAL MARKERS; GENE EXPRESSION PROFILING; HUMANS; METABOLOMICS; MYCOBACTERIUM TUBERCULOSIS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PROTEOMICS; TUBERCULOSIS;

EID: 84881484942     PISSN: 02722712     EISSN: 15579832     Source Type: Journal    
DOI: 10.1016/j.cll.2013.03.012     Document Type: Review

References (78)

1. World Health Organization Global tuberculosis report 2012, World Health Organization, Geneva (Switzerland).
2. Steingart K.R., 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.
3. Hepple P., Ford N., McNerney R. Microscopy compared to culture for the diagnosis of tuberculosis in induced sputum samples: a systematic review. Int J Tuberc Lung Dis 2012, 16(5):579-588.
4. Storla D.G., Yimer S., Bjune G.A. Asystematic review of delay in the diagnosis and treatment of tuberculosis. BMC Public Health 2008, 8:15.
5. McNerney R., Maeurer M., Abubakar I., et al. Tuberculosis diagnostics and biomarkers: needs, challenges, recent advances, and opportunities. JInfect Dis 2012, 205(Suppl 2):S147-S158.
6. Weyer K., Carai S., Nunn P. Viewpoint TB diagnostics: what does the world really need?. JInfect Dis 2011, 204(Suppl 4):S1196-S1202.
7. Greco S., Girardi E., Navarra A., et al. Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis. Thorax 2006, 61(9):783-790.
8. Centers for Disease Control and Prevention Nucleic acid amplification tests for tuberculosis. MMWR Morb Mortal Wkly Rep 1996, 45(43):950-952.
9. Piersimoni C., Callegaro A., Nista D., et al. Comparative evaluation of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. JClin Microbiol 1997, 35(1):193-196.
10. Guerra R.L., Hooper N.M., Baker J.F., et al. Use of the amplified mycobacterium tuberculosis direct test in a public health laboratory: test performance and impact on clinical care. Chest 2007, 132(3):946-951.
11. Rapid diagnostic tests for tuberculosis: what is the appropriate use? American Thoracic Society Workshop. Am J Respir Crit Care Med 1997, 155(5):1804-1814.
12. Centers for Disease Control and Prevention Updated guidelines for the use of nucleic acid amplification tests in the diagnosis of tuberculosis. MMWR Morb Mortal Wkly Rep 2009, 58(1):7-10.
13. McHugh T.D., Pope C.F., Ling C.L., et al. Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. JMed Microbiol 2004, 53(Pt 12):1215-1219.
14. Jouveshomme S., Cambau E., Trystram D., et al. Clinical utility of an amplification test based on ligase chain reaction in pulmonary tuberculosis. Am J Respir Crit Care Med 1998, 158(4):1096-1101.
15. Parsons L.M., 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.
16. Ling D.I., Flores L.L., Riley L.W., et al. Commercial nucleic-acid amplification tests for diagnosis of pulmonary tuberculosis in respiratory specimens: meta-analysis and meta-regression. PLoS One 2008, 3(2):e1536.
17. Pai M., Flores L.L., Pai N., et al. Diagnostic accuracy of nucleic acid amplification tests for tuberculous meningitis: a systematic review and meta-analysis. Lancet Infect Dis 2003, 3(10):633-643.
18. Pai M., Flores L.L., Hubbard A., et al. Nucleic acid amplification tests in the diagnosis of tuberculous pleuritis: a systematic review and meta-analysis. BMC Infect Dis 2004, 4:6.
19. Clinical and Laboratory Standards Institute Document EP12-A2. User protocol for evaluation of qualitative test performance 2008, CLSI, Wayne (PA).
20. Flores L.L., Pai M., Colford J.M., et al. In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression. BMC Microbiol 2005, 5:55.
21. Greco S., Rulli M., Girardi E., et al. Diagnostic accuracy of in-house PCR for pulmonary tuberculosis in smear-positive patients: meta-analysis and metaregression. JClin Microbiol 2009, 47(3):569-576.
22. Luo R.F., Scahill M.D., Banaei N. Comparison of single-copy and multicopy real-time PCR targets for detection of Mycobacterium tuberculosis in paraffin-embedded tissue. JClin Microbiol 2010, 48(7):2569-2570.
23. Caminero J.A. Multidrug-resistant tuberculosis: epidemiology, risk factors and case finding. Int J Tuberc Lung Dis 2010, 14(4):382-390.
24. World Health Organization Molecular line probe assays for rapid screening of patients at risk of multidrug-resistant tuberculosis 2008, World Health Organization, Geneva (Switzerland).
25. Ignatyeva O., Kontsevaya I., Kovalyov A., et al. Detection of resistance to second-line antituberculosis drugs by use of the genotype MTBDRsl assay: a multicenter evaluation and feasibility study. JClin Microbiol 2012, 50(5):1593-1597.
26. Morgan M., Kalantri S., Flores L., et al. Acommercial line probe assay for the rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a systematic review and meta-analysis. BMC Infect Dis 2005, 5:62.
27. Bwanga F., Hoffner S., Haile M., et al. Direct susceptibility testing for multi drug resistant tuberculosis: a meta-analysis. BMC Infect Dis 2009, 9:67.
28. Ling D.I., Zwerling A.A., Pai M. GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis. Eur Respir J 2008, 32(5):1165-1174.
29. World Health Organization Rapid implementation of the Xpert MTB/RIF diagnostic test 2011, World Health Organization, Geneva (Switzerland).
30. Boehme C.C., Nabeta P., Hillemann D., et al. Rapid molecular detection of tuberculosis and rifampin resistance. NEngl J Med 2010, 363(11):1005-1015.
31. Boehme C.C., Nicol M.P., 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.
32. Scott L.E., McCarthy K., Gous N., et al. Comparison of Xpert MTB/RIF with other nucleic acid technologies for diagnosing pulmonary tuberculosis in a high HIV prevalence setting: a prospective study. PLoS Med 2011, 8(7):e1001061.
33. Banada P.P., Sivasubramani S.K., Blakemore R., et al. Containment of bioaerosol infection risk by the Xpert MTB/RIF assay and its applicability to point-of-care settings. JClin Microbiol 2010, 48(10):3551-3557.
34. Andrews J.R., Lawn S.D., Rusu C., et al. The cost-effectiveness of routine tuberculosis screening with Xpert MTB/RIF prior to initiation of antiretroviral therapy: a model-based analysis. AIDS 2012, 26(8):987-995.
35. Vassall A., van Kampen S., Sohn H., et al. Rapid diagnosis of tuberculosis with the Xpert MTB/RIF assay in high burden countries: a cost-effectiveness analysis. PLoS Med 2011, 8(11):e1001120.
36. Boehme C.C., Nabeta P., Henostroza G., et al. Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries. JClin Microbiol 2007, 45(6):1936-1940.
37. Geojith G., Dhanasekaran S., Chandran S.P., et al. Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting. JMicrobiol Methods 2011, 84(1):71-73.
38. Mitarai S., Okumura M., Toyota E., 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):1211-1217. i.
39. Pai N.P., Pai M. Point-of-care diagnostics for HIV and tuberculosis: landscape, pipeline, and unmet needs. Discov Med 2012, 13(68):35-45.
40. Fang X., Chen H., Xu L., et al. Aportable and integrated nucleic acid amplification microfluidic chip for identifying bacteria. Lab Chip 2012, 12(8):1495-1499.
41. Köser C.U., Ellington M.J., Cartwright E.J., et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012, 8(8):e1002824.
42. Gardy J.L., Johnston J.C., Ho Sui S.J., et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. NEngl J Med 2011, 364(8):730-739.
43. Wallis R.S., Pai M., Menzies D., et al. Biomarkers and diagnostics for tuberculosis: progress, needs, and translation into practice. Lancet 2010, 375(9729):1920-1937.
44. Vesenbeckh S.M., Schönfeld N., Mauch H., et al. The use of interferon gamma release assays in the diagnosis of active tuberculosis. Tuberc Res Treat 2012, 2012:768723.
45. Metcalfe J.Z., Everett C.K., Steingart K.R., et al. Interferon-γ release assays for active pulmonary tuberculosis diagnosis in adults in low- and middle-income countries: systematic review and meta-analysis. JInfect Dis 2011, 204(Suppl 4):S1120-S1129.
46. Rangaka M.X., Wilkinson K.A., Glynn J.R., et al. Predictive value of interferon-γ release assays for incident active tuberculosis: a systematic review and meta-analysis. Lancet Infect Dis 2012, 12(1):45-55.
47. Sester M., Sotgiu G., Lange C., et al. Interferon-γ release assays for the diagnosis of active tuberculosis: a systematic review and meta-analysis. Eur Respir J 2011, 37(1):100-111.
48. Turtle L., Kemp T., Davies G.R., et al. In routine UK hospital practice T-SPOT.TB™ is useful in some patients with a modest pre-test probability of active tuberculosis. Eur J Intern Med 2012, 23(4):363-367.
49. Steingart K.R., Flores L.L., Dendukuri N., et al. Commercial serological tests for the diagnosis of active pulmonary and extrapulmonary tuberculosis: an updated systematic review and meta-analysis. PLoS Med 2011, 8(8):e1001062.
50. World Health Organization Commercial serodiagnostic tests for the diagnosis of tuberculosis: policy statement 2011, World Health Organization, Geneva (Switzerland).
51. Grenier J., Pinto L., Nair D., et al. Widespread use of serological tests for tuberculosis: data from 22 high-burden countries. Eur Respir J 2012, 39(2):502-505.
52. Cannas A., Goletti D., Girardi E., et al. Mycobacterium tuberculosis DNA detection in soluble fraction of urine from pulmonary tuberculosis patients. Int J Tuberc Lung Dis 2008, 12(2):146-151.
53. Chan J., Fan X.D., Hunter S.W., et al. Lipoarabinomannan, a possible virulence factor involved in persistence of Mycobacterium tuberculosis within macrophages. Infect Immun 1991, 59(5):1755-1761.
54. Minion J., Leung E., Talbot E., et al. Diagnosing tuberculosis with urine lipoarabinomannan: systematic review and meta-analysis. Eur Respir J 2011, 38(6):1398-1405.
55. Lawn S.D., Edwards D.J., Kranzer K., et al. Urine lipoarabinomannan assay for tuberculosis screening before antiretroviral therapy diagnostic yield and association with immune reconstitution disease. AIDS 2009, 23(14):1875-1880.
56. Lawn S.D., Kerkhoff A.D., Vogt M., et al. Diagnostic accuracy of a low-cost, urine antigen, point-of-care screening assay for HIV-associated pulmonary tuberculosis before antiretroviral therapy: a descriptive study. Lancet Infect Dis 2012, 12(3):201-209.
57. Phillips M., Basa-Dalay V., Bothamley G., et al. Breath biomarkers of active pulmonary tuberculosis. Tuberculosis (Edinb) 2010, 90(2):145-151.
58. Kolk A., Hoelscher M., Maboko L., et al. Electronic-nose technology using sputum samples in diagnosis of patients with tuberculosis. JClin Microbiol 2010, 48(11):4235-4238.
59. Phillips M., Basa-Dalay V., Blais J., et al. Point-of-care breath test for biomarkers of active pulmonary tuberculosis. Tuberculosis (Edinb) 2012, 92(4):314-320.
60. Bruins M., Rahim Z., Bos A., et al. Diagnosis of active tuberculosis by e-nose analysis of exhaled air. Tuberculosis (Edinb) 2012, 93(2):232-238.
61. Kolk A.H., van Berkel J.J., Claassens M.M., et al. Breath analysis as a potential diagnostic tool for tuberculosis. Int J Tuberc Lung Dis 2012, 16(6):777-782.
62. Qin L., Zheng R., Ma Z., et al. The selection and application of ssDNA aptamers against MPT64 protein in Mycobacterium tuberculosis. Clin Chem Lab Med 2009, 47(4):405-411.
63. Rotherham L.S., Maserumule C., Dheda K., et al. Selection and application of ssDNA aptamers to detect active TB from sputum samples. PLoS One 2012, 7(10):e46862.
64. Flores L.L., Steingart K.R., Dendukuri N., et al. Systematic review and meta-analysis of antigen detection tests for the diagnosis of tuberculosis. Clin Vaccine Immunol 2011, 18(10):1616-1627.
65. Xie H., Mire J., Kong Y., et al. Rapid point-of-care detection of the tuberculosis pathogen using a BlaC-specific fluorogenic probe. Nat Chem 2012, 4(10):802-809.
66. Li H., Yang L., Zheng C.Y., et al. Use of bronchoalveolar lavage enzyme-linked immunospot for diagnosis of smear-negative pulmonary tuberculosis. Int J Tuberc Lung Dis 2012, 16(12):1668-1673.
67. Cattamanchi A., Ssewenyana I., Nabatanzi R., et al. Bronchoalveolar lavage enzyme-linked immunospot for diagnosis of smear-negative tuberculosis in HIV-infected patients. PLoS One 2012, 7(6):e39838.
68. Greco S., Girardi E., Masciangelo R., et al. Adenosine deaminase and interferon gamma measurements for the diagnosis of tuberculous pleurisy: a meta-analysis. Int J Tuberc Lung Dis 2003, 7(8):777-786.
69. Jiang J., Shi H.Z., Liang Q.L., et al. Diagnostic value of interferon-gamma in tuberculous pleurisy: a metaanalysis. Chest 2007, 131(4):1133-1141.
70. Juan R.S., Sánchez-Suárez C., Rebollo M.J., et al. Interferon gamma quantification in cerebrospinal fluid compared with PCR for the diagnosis of tuberculous meningitis. JNeurol 2006, 253(10):1323-1330.
71. Liang Q.L., Shi H.Z., Wang K., et al. Diagnostic accuracy of adenosine deaminase in tuberculous pleurisy: a meta-analysis. Respir Med 2008, 102(5):744-754.
72. Xu H.B., Jiang R.H., Li L., et al. Diagnostic value of adenosine deaminase in cerebrospinal fluid for tuberculous meningitis: a meta-analysis. Int J Tuberc Lung Dis 2010, 14(11):1382-1387.
73. Jadhav A.A., Jain A. Sputum adenosine deaminase and alkaline phosphatase activity in pulmonary tuberculosis. Arch Physiol Biochem 2012, 118(1):6-9.
74. Maertzdorf J., Weiner J., Kaufmann S.H. Enabling biomarkers for tuberculosis control. Int J Tuberc Lung Dis 2012, 16(9):1140-1148.
75. Wang C., Yang S., Sun G., et al. Comparative miRNA expression profiles in individuals with latent and active tuberculosis. PLoS One 2011, 6(10):e25832.
76. Kumar S.G., Venugopal A.K., Mahadevan A., et al. Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clin Proteomics 2012, 9(1):12.
77. Fu Y.R., Yi Z.J., Guan S.Z., et al. Proteomic analysis of sputum in patients with active pulmonary tuberculosis. Clin Microbiol Infect 2012, 18(12):1241-1247.
78. Zhang L., Wang Q., Wang W., et al. Identification of putative biomarkers for the serodiagnosis of drug-resistant Mycobacterium tuberculosis. Proteome Sci 2012, 10:12.