Standardization and evaluation of a tetraplex polymerase chain reaction to detect and differentiate Mycobacterium tuberculosis complex and nontuberculous Mycobacteria-a retrospective study on pulmonary TB patients

Diagnostic Microbiology and Infectious Disease

Volumn 72, Issue 3, 2012, Pages 239-247

  Anilkumar, A K ^a   Madhavilatha, G K ^a   Paul, Laiza K ^a   Radhakrishnan, Indulakshmi ^a   Kumar, R Ajay ^a   Mundayoor, Sathish ^a  

^a RAJIV GANDHI CENTRE FOR BIOTECHNOLOGY   (India)

Author keywords

Atypical Mycobacteria; Disease surveillance; Multiplex PCR; Mycobacterium tuberculosis complex; NTM; Taguchi's protocol

Indexed keywords

BACTERIAL DNA;

16S 23S INTERNAL TRANSCRIBED SPACER REGION GENE; ARTICLE; ATYPICAL MYCOBACTERIUM; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM ISOLATE; CLINICAL EVALUATION; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DIAGNOSTIC ACCURACY; DISEASE SURVEILLANCE; GENE TARGETING; HSP65 GENE; HUMAN; LUNG TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RESTRICTION MAPPING; RETROSPECTIVE STUDY; RPOB GENE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STANDARDIZATION; STRAIN DIFFERENCE; VALIDATION PROCESS;

GENES, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; MULTIPLEX POLYMERASE CHAIN REACTION; MYCOBACTERIUM TUBERCULOSIS; NONTUBERCULOUS MYCOBACTERIA; RETROSPECTIVE STUDIES; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; TUBERCULOSIS, PULMONARY;

EID: 84856610574     PISSN: 07328893     EISSN: 18790070     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2011.11.006     Document Type: Article

References (37)

1. Ahmad S., Mokaddas E., Jaber A.A. Rapid detection of ethambutol-resistant Mycobacterium tuberculosis strains by PCR-RFLP targeting embB codons 306 and 497 and iniA codon 501 mutations. Mol. Cell. Probes. 2004, 18:299-306.
2. Ajithkumar K., Madhavilatha G.K., Sulekha B., Godreuil S., Anilkumar A.K., Girija K., Mundayoor S. Do Mycobacterium marinum infections occur in India?. Indian J. Dermatol. Venereol. Leprol. 2010, 76:191-192.
3. Balasingham S.V., Davidsen T., Szpinda I., Frye S.A., Tonjum T. Molecular diagnostics in tuberculosis: basis and implications for therapy. Mol. Diagn. Ther. 2009, 13:137-151.
4. Bills N.D., Hinrichs S.H., Aden T.A., Wickert R.S., Iwen P.C. Molecular identification of Mycobacterium chimaera as a cause of infection in a patient with chronic obstructive pulmonary disease. Diagn. Microbiol. Infect. Dis. 2009, 63:292-295.
5. Blackwood K.S., He C., Gunton J., Turenne C.Y., Wolfe J., Kabani A.M. Evaluation of recA sequences for identification of Mycobacterium species. J. Clin. Microbiol. 2000, 38:2846-2852.
6. Chakravorty S., Tyagi J.S. Novel multipurpose methodology for detection of mycobacteria in pulmonary and extrapulmonary specimens by smear microscopy, culture, and PCR. J. Clin. Microbiol. 2005, 43:2697-2702.
7. Chen C.Y., Chen H.Y., Chou C.H., Huang C.T., Lai C.C., Hsueh P.R. Pulmonary infection caused by nontuberculous mycobacteria in a medical center in Taiwan, 2005-2008. Diagn. Microbiol. Infect. Dis. 2012, 72:47-51.
8. Cobb B.D., Clarkson J.M. A simple procedure for optimising the polymerase chain reaction (PCR) using modified Taguchi methods. Nucleic Acids Res. 1994, 22:3801-3805.
9. Couble A., Rodriguez-Nava V., de Montclos M.P., Boiron P., Laurent F. Direct detection of Nocardia spp. in clinical samples by a rapid molecular method. J. Clin. Microbiol. 2005, 43:1921-1924.
10. Del Giudice G., Iadevaia C., Santoro G., Moscariello E., Smeraglia R., Marzo C. Nontuberculous mycobacterial lung disease in patients without HIV infection: a retrospective analysis over 3 years. Clin. Respir. J. 2011, 5:203-210.
11. Gillespie S.H., McHugh T.D., Newport L.E. Specificity of IS6110-based amplification assays for Mycobacterium tuberculosis complex. J. Clin. Microbiol. 1997, 35:799-801.
12. Gordon S.V., Heym B., Parkhill J., Barrell B., Cole S.T. New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology 1999, 145:881-892.
13. Griffith D.E., Aksamit T., Brown-Elliott B.A., Catanzaro A., Daley C., Gordin F., Holland S.M., Horsburgh R., Huitt G., Iademarco M.F. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am. J. Respir. Crit. Care Med. 2007, 175:367.
14. Herrera E.A., Segovia M. Evaluation of mtp40 genomic fragment amplification for specific detection of Mycobacterium tuberculosis in clinical specimens. J. Clin. Microbiol. 1996, 34:1108-1113.
15. Holberg-Petersen M., Steinbakk M., Figenschau K.J., Jantzen E., Eng J., Melby K.K. Identification of clinical isolates of Mycobacterium spp. by sequence analysis of the 16S ribosomal RNA gene. Experience from a clinical laboratory. APMIS 1999, 107:231-239.
16. Joseph B.V., Soman S., Radhakrishnan I., Madhavilatha G.K., Paul L.K., Mundayoor S., Kumar R.A. Drug resistance in Mycobacterium tuberculosis isolates from tuberculosis patients in Kerala, India. Int. J. Tuberc. Lung. Dis. 2009, 13:494-499.
17. Jun H.J., Jeon K., Um S.W., Kwon O.J., Lee N.Y., Koh W.J. Nontuberculous mycobacteria isolated during the treatment of pulmonary tuberculosis. Respir. Med. 2009, 103:1936-1940.
18. Kendall B.A., Varley C.D., Hedberg K., Cassidy P.M., Winthrop K.L. Isolation of non-tuberculous mycobacteria from the sputum of patients with active tuberculosis. Int. J. Tuberc. Lung Dis. 2010, 14:654-656.
19. Koh W.J., Yu C.M., Suh G.Y., Chung M.P., Kim H., Kwon O.J., Lee N.Y., Chung M.J., Lee K.S. Pulmonary TB and NTM lung disease: comparison of characteristics in patients with AFB smear-positive sputum. Int. J. Tuberc. Lung Dis. 2006, 10:1001-1007.
20. Lee A.S., Jelfs P., Sintchenko V., Gilbert G.L. Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing. J. Med. Microbiol. 2009, 58:900-904.
21. Lok K.H., Benjamin W.H., Kimerling M.E., Pruitt V., Lathan M., Razeq J., Hooper N., Cronin W., Dunlap N.E. Molecular differentiation of Mycobacterium tuberculosis strains without IS6110 insertions. Emerg. Infect. Dis. 2002, 8:1310-1313.
22. Magdalena J., Vachee A., Supply P., Locht C. Identification of a new DNA region specific for members of Mycobacterium tuberculosis complex. J. Clin. Microbiol. 1998, 36:937-943.
23. Makinen J., Marjamaki M., Marttila H., Soini H. Evaluation of a novel strip test, GenoType Mycobacterium CM/AS, for species identification of mycobacterial cultures. Clin. Microbiol. Infect. 2006, 12:481-483.
24. McHugh T.D., Newport L.E., Gillespie S.H. IS6110 homologs are present in multiple copies in mycobacteria other than tuberculosis-causing mycobacteria. J. Clin. Microbiol. 1997, 35:1769-1771.
25. Parsons L.M., Brosch R., Cole S.T., Somoskovi A., Loder A., Bretzel G., Van Soolingen D., Hale Y.M., Salfinger M. Rapid and simple approach for identification of Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J. Clin. Microbiol. 2002, 40:2339-2345.
26. Radhakrishnan I., K M.Y., Kumar R.A., Mundayoor S. Implications of low frequency of IS6110 in fingerprinting field isolates of Mycobacterium tuberculosis from Kerala, India. J. Clin. Microbiol. 2001, 39:1683.
27. Sarojini S., Soman S., Radhakrishnan I., Mundayoor S. Identification of moaA3 gene in patient isolates of Mycobacterium tuberculosis in Kerala, which is absent in M. tuberculosis H37Rv and H37Ra. BMC Infect. Dis. 2005, 5:81.
28. Saves I., Lewis L.A., Westrelin F., Warren R., Daffe M., Masson J.M. Specificities and functions of the recA and pps1 intein genes of Mycobacterium tuberculosis and application for diagnosis of tuberculosis. J. Clin. Microbiol. 2002, 40:943-950.
29. Telenti A., Marchesi F., Balz M., Bally F., Bottger E.C., Bodmer T. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J. Clin. Microbiol. 1993, 31:175-178.
30. Thierry D., Brisson-Noel A., Vincent-Levy-Frebault V., Nguyen S., Guesdon J.L., Gicquel B. Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis. J. Clin. Microbiol. 1990, 28:2668-2673.
31. Turenne C.Y., Tschetter L., Wolfe J., Kabani A. Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J. Clin. Microbiol. 2001, 39:3637-3648.
32. van Soolingen D., Hermans P.W., de Haas P.E., Soll D.R., van Embden J.D. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 1991, 29:2578-2586.
33. Viana-Niero C., de Haas P.E., van Soolingen D., Leao S.C. Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates. Microbiology 2004, 150:967-978.
34. Walker D.A., Taylor I.K., Mitchell D.M., Shaw R.J. Comparison of polymerase chain reaction amplification of two mycobacterial DNA sequences, IS6110 and the 65kDa antigen gene, in the diagnosis of tuberculosis. Thorax 1992, 47:690-694.
35. Weil A., Plikaytis B.B., Butler W.R., Woodley C.L., Shinnick T.M. The mtp40 gene is not present in all strains of Mycobacterium tuberculosis. J. Clin. Microbiol. 1996, 34:2309-2311.
36. Weng F.Y., Chiou C.S., Lin P.H., Yang S.S. Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species. J. Appl. Microbiol. 2009, 107:452-464.
37. Winthrop K.L., McNelley E., Kendall B., Marshall-Olson A., Morris C., Cassidy M., Saulson A., Hedberg K. Pulmonary nontuberculous mycobacterial disease prevalence and clinical features: an emerging public health disease. Am. J. Respir. Crit. Care Med. 2010, 182:977-982.