Development and application of multiprobe real-time PCR method targeting the hsp65 gene for differentiation of Mycobacterium species from isolates and sputum specimens

Journal of Clinical Microbiology

Volumn 48, Issue 9, 2010, Pages 3073-3080

  Kim, Kijeong ^c   Lee, Hyungki ^a   Lee, Mi Kyung ^c   Lee, Seoung Ae ^a   Shim, Tae Sun ^d   Lim, Seong Yong ^e   Koh, Won Jung ^f   Yim, Jae Joon ^b   Munkhtsetseg, Bazarragchaa ^c   Kim, Wonyong ^c   Chung, Sang In ^c   Kook, Yoon Hoh ^a   Kim, Bum Joon ^a  

^a Seoul National University   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

^c Chung Ang University   (South Korea)

^d University of Ulsan College of Medicine   (South Korea)

^e Sungkyunkwan University School of Medicine   (South Korea)

^f Sungkyunkwan University School of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN 65;

ACID FAST BACTERIUM; ADULT; AGED; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA EXTRACTION; FEMALE; GENE SEQUENCE; GENE TARGETING; HUMAN; MALE; MOLECULAR PROBE; MYCOBACTERIUM; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM CELATUM; MYCOBACTERIUM CHELONEI; MYCOBACTERIUM FLAVESCENS; MYCOBACTERIUM FORTUITUM; MYCOBACTERIUM GASTRI; MYCOBACTERIUM GENAVENSE; MYCOBACTERIUM GORDONAE; MYCOBACTERIUM HAEMOPHILUM; MYCOBACTERIUM INTRACELLULARE; MYCOBACTERIUM KANSASII; MYCOBACTERIUM MALMOENSE; MYCOBACTERIUM MARINUM; MYCOBACTERIUM MASSILENSE; MYCOBACTERIUM PEREGRINUM; MYCOBACTERIUM PHLEI; MYCOBACTERIUM SCROFULACEUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM SZULGAI; MYCOBACTERIUM TERRAE; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM ULCERANS; MYCOBACTERIUM XENOPEI; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; SENSITIVITY AND SPECIFICITY; SPUTUM SMEAR;

BACTERIAL PROTEINS; BACTERIOLOGICAL TECHNIQUES; CHAPERONIN 60; DNA PRIMERS; DNA-DIRECTED RNA POLYMERASES; FEMALE; HUMANS; MALE; MIDDLE AGED; MYCOBACTERIUM; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SPUTUM; TUBERCULOSIS;

CORYNEBACTERINEAE; MYCOBACTERIUM; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM FORTUITUM; MYCOBACTERIUM INTRACELLULARE; MYCOBACTERIUM KANSASII; MYCOBACTERIUM MASSILIENSE; MYCOBACTERIUM TUBERCULOSIS;

EID: 77956843528     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00939-10     Document Type: Article

References (34)

1. Adékambi, T., P. Colson, and M. Drancourt. 2003. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J. Clin. Microbiol. 41:5699-5708.
2. Barnes, P. F., A. B. Bloch, P. T. Davison, and D. E. Sneider, Jr. 1991. Tuberculosis in patients with human immunodeficiency virus infection. N. Engl. J. Med. 324:1644-1649.
3. Bloom, B. R. 1992. Back to a frightening future. Nature 358:538-539.
4. Bloom, B. R., and C. J. L. Murray. 1992. Tuberculosis: commentary on a reemergent killer. Science 257:1055-1064.
5. Cloud, J. L., H. Neal, R. Rosenberry, C. Y. Turenne, M. JAMA, D. R. Hillyard, and K. C. Carroll. 2002. Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J. Clin. Microbiol. 40:400-406.
6. Coll, P., M. Garrigo, C. Moreno, and N. Marti. 2003. Routine use of Gen- Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test for detection of Mycobacterium tuberculosis with smear-positive and smear-negative specimens. Int. J. Tuber. Lung Dis. 7:886-891.
7. Dye, C., S. Scheele, P. Dolin, V. Pathania, and M. C. Raviglione. 1999. Global burden of tuberculosis. Estimated incidence, prevalence, and mortality by country. JAMA 282:677-686.
8. Espy, M. J., J. R. Uhl, L. M. Sloan, S. P. Buckwalter, M. F. Jones, E. A. Vetter, J. D. Yao, N. L. Wengenack, J. E. Rosenblatt, F. R. Cockerill, III, and T. F. Smith. 2006. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin. Microbiol. Rev. 19:165-256.
9. Foongladda, S., S. Pholwat, B. Eampokalap, P. Kiratisin, and R. Sutthent. 2009. Multi-probe real-time PCR identification of common Mycobacterium species in blood culture broth. J. Mol. Diagn. 11:42-48.
10. Gopinath, K., and S. Singh. 2009. Multiplex PCR assay for simultaneous detection and differentiation of Mycobacterium tuberculosis, Mycobacterium avium complexes and other mycobacterial species directly from clinical specimens. J. Appl. Microbiol. 107:425-435.
11. Halse, T. A., J. Edwards, P. L. Cunningham, W. J. Wolfgang, N. B. Dumas, V. E. Escuyer, and K. A. Musser. 2010. Combined real-time PCR and rpoB gene pyrosequencing for rapid identification of Mycobacterium tuberculosis and determination of rifampin resistance directly in clinical specimens. J. Clin. Microbiol. 48:1182-1188.
12. Huminer, D., S. Dux, Z. Samra, L. Kaufman, A. Lavy, C. S. Block, and S. D. Pitlik. 1993. Mycobacterium simiae infection in Israeli patients with AIDS. Clin. Infect. Dis. 17:508-509.
13. Joh, J. S., C. H. Lee, J. E. Lee, Y. K. Park, G. H. Bai, E. C. Kim, S. K. Han, Y. S. Shim, and J. J. Yim. 2007. The interval between initiation of antituberculosis treatment in patients with culture-positive pulmonary tuberculosis and receipt of drug-susceptibility test results. J. Korean Med. Sci. 22:26-29.
14. Kent, P., and G. Kubica. 1985. Public health mycobacteriology - a guide for the level III laboratory. Centers for Disease Control and Prevention, Atlanta, GA.
15. Kim, B. J., J. H. Park, S. A. Lee, H. Kim, C. Y. Cha, Y. H. Kook, E. C. Kim, S. I. Joo, J. S. Lee, and J. J. Yim. 2008. Differentiation of mycobacteria in sputa by duplex polymerase chain reaction for mycobacterial hsp65 gene. Diagn. Microbiol. Infect. Dis. 62:193-198.
16. Kim, B. J., S. H. Lee, M. A. Lyu, S. J. Kim, G. H. Bai, G. T. Chae, E. C. Kim, C. Y. Cha, and Y. H. Kook. 1999. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J. Clin. Microbiol. 37:1714-1720.
17. Kim, H., S. H. Kim, T. S. Shim, M. N. Kim, G. H. Bai, Y. G. Park, S. H. Lee, G. T. Chae, C. Y. Cha, Y. H. Kook, and B. J. Kim. 2005. Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65). Int. J. Syst. Evol. Microbiol. 55:1649-1656.
18. Kim, H. Y., Y. Kook, Y. J. Yun, C. G. Park, N. Y. Lee, T. S. Shim, B. J. Kim, and Y. H. Kook. 2008. Proportions of Mycobacterium massiliense and Mycobacterium bolletii strains among Korean Mycobacterium chelonae-Mycobacterium abscessus group isolates. J. Clin. Microbiol. 46:3384-3890.
19. Kim, H. J., H. S. Mun, H. Kim, E. J. Oh, Y. Ha, G. H. Bai, Y. G. Park, C. Y. Cha, Y. H. Kook, and B. J. Kim. 2006. Differentiation of mycobacterial species by hsp65 duplex PCR followed by duplex-PCR-based restriction analysis and direct sequencing. J. Clin. Microbiol. 44:3855-3862.
20. Koh, W. J., O. J. Kwon, and K. S. Lee. 2005. Diagnosis and treatment of nontuberculous mycobacterial pulmonary diseases: a Korean perspective. J. Korean Med. Sci. 20:913-925.
21. Lee, H., H. J. Park, S. N. Cho, G. H. Bai, and S. J. Kim. 2000. Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J. Clin. Microbiol. 38:2966-2971.
22. Leung, K. L., C. W. Yip, W. F. Cheung, A. C. Lo, W. M. Ko, and K. M. Kam. 2009. Development of a simple and low-cost real-time PCR method for the identification of commonly encountered mycobacteria in a high throughput laboratory. J. Appl. Microbiol. 107:1433-1439.
23. Lim, S. Y., B. J. Kim, M. K. Lee, and K. Kim. 2008. Development of a real-time PCR-based method for rapid differential identification of Mycobacterium species. Lett. Appl. Microbiol. 46:101-106.
24. Massenkeil, G., M. Opravil, M. Salfinger, A. von Graevenitz, and R. Lüthy. 1992. Disseminated coinfection with Mycobacterium avium complex and Mycobacterium kansasii in a patient with AIDS and liver abscess. Clin. Infect. Dis. 14:618-619.
25. McNabb, A., K. Adie, M. Rodrigues, W. A. Black, and J. Isaac-Renton. 2006. Direct identification of mycobacteria in primary liquid detection media by partial sequencing of the 65-kilodalton heat shock protein gene. J. Clin. Microbiol. 44:60-66.
26. Miller, N., T. Cleary, G. Kraus, A. K. Young, G. Spruill, and H. J. Hnatyszyn. 2002. Rapid and specific detection of Mycobacterium tuberculosis from acid-fast bacillus smear-positive respiratory specimens and BacT/ALERT MP culture bottles by using fluorogenic probes and real-time PCR. J. Clin. Microbiol. 40:4143-4147.
27. Mun, H. S., H. J. Kim, E. J. Oh, H. Kim, Y. G. Park, G. H. Bai, J. Do, C. Y. Cha, Y. H. Kook, and B. J. Kim. 2007. Direct application of AvaII PCR restriction fragment length polymorphism analysis (AvaII PRA) targeting 644 bp heat shock protein 65 (hsp65) gene to sputum samples. Microbiol. Immunol. 51:105-110.
28. Nakanaga, K., N. Ishii, K. Suzuki, K. Tanigawa, M. Goto, T. Okabe, H. Imada, A. Kodama, T. Iwamoto, H. Takahashi, and H. Saito. 2007. "Mycobacterium ulcerans subsp. shinshuense" isolated from a skin ulcer lesion: identification based on 16S rRNA gene sequencing. J. Clin. Microbiol. 45:3840-3843.
29. Pinsky, B. A., and N. Banaei. 2008. Multiplex real-time PCR assay for rapid identification of Mycobacterium tuberculosis complex members to the species level. J. Clin. Microbiol. 46:2241-2246.
30. Rosenzweig, D. Y. 1996. Nontuberculous mycobacterial disease in the immunocompetent adult. Semin. Respir. Infect. 11:252-261.
31. Simmon, K. E., J. I. Pounder, J. N. Greene, F. Walsh, C. M. Anderson, S. Cohen, and C. A. Petti. 2007. Identification of an emerging pathogen, Mycobacterium massiliense, by rpoB sequencing of clinical isolates collected in the United States. J. Clin. Microbiol. 45:1978-1980.
32. Taylor, Z., C. M. Nolan, and H. M. Blumberg. 2005. Controlling tuberculosis in the United States. Recommendations from the American Thoracic Society, CDC, and the Infectious Diseases Society of America. MMWR Recommend. Rep. 54(RR-12):1-81.
33. Wagner, D., and L. S. Young. 2004. Nontuberculous mycobacterial infections: a clinical review. Infection 32:257-270.
34. Wolinsky, E. 1992. Mycobacterial diseases other than tuberculosis Clin. Infect. Dis. 15:1-10.