Diagnostic application of genotypic identification of mycobacteria

Journal of Medical Microbiology

Volumn 55, Issue 5, 2006, Pages 529-536

  Yam, Wing Cheong ^a   Yuen, Kwok Yung ^a   Kam, Sin Yee ^a   Yiu, Lap San ^b   Chan, Kin Sang ^b   Leung, Chi Chiu ^c   Tam, Cheuk Ming ^c   Ho, Po On ^a   Yew, Wing Wai ^d   Seto, Wing Hong ^a   Ho, Pak Leung ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b Haven of Hope Hospital   (Hong Kong)

^c DEPARTMENT OF HEALTH   (Hong Kong)

^d GRANTHAM HOSPITAL   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIUM GROUP; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; BIOCHEMISTRY; CLINICAL LABORATORY; DIAGNOSTIC TEST; DNA HYBRIDIZATION; GAS LIQUID CHROMATOGRAPHY; GENE SEQUENCE; GENOTYPE; INFRASPECIFIC RANK; MORPHOLOGICAL TRAIT; MYCOBACTERIUM; MYCOBACTERIUM INTRACELLULARE AVIUM; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS COMPLEX; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA GENE; SCREENING; SPECIES; TURNAROUND TIME;

ALGORITHMS; DNA, BACTERIAL; FATTY ACIDS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENES, RRNA; GENOTYPE; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MYCOBACTERIUM AVIUM COMPLEX; MYCOBACTERIUM AVIUM-INTRACELLULARE INFECTION; MYCOBACTERIUM TUBERCULOSIS; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TIME FACTORS; TUBERCULOSIS;

EID: 33646250433     PISSN: 00222615     EISSN: None     Source Type: Journal    
DOI: 10.1099/jmm.0.46298-0     Document Type: Article

References (31)

1. Arnold, L. J., Jr, Hammond, P. W., Wiese, W. A. & Nelson, N. C. (1989). Assay formats involving acridinium-ester-labeled DNA probes. Clin Chem 35, 1588-1594.
2. Brown-Elliott, B. A. & Wallace, R. J., Jr (2002). Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria. Clin Microbiol Rev 15, 716-746.
3. Brown-Elliott, B. A., Griffith, D. E. & Wallace, R. J., Jr (2002). Newly described or emerging human species of nontuberculous mycobacteria. Infect Dis Clin North Am 16, 187-220.
4. Chan, C. M., Yuen, K. Y., Chan, K. S., Yam, W. C., Yim, K. H., Ng, W. F. & Ng, M. H. (1996). Single-tube nested PCR in the diagnosis of tuberculosis. J Clin Pathol 49, 290-294.
5. Chou, S., Chedore, P. & Kasatiya, S. (1998). Use of gas chromatographic fatty acid and mycolic acid cleavage product determination to differentiate among Mycobacterium genavense, Mycobacterium fortuitum, Mycobacterium simiae, and Mycobacterium tuberculosis. J Clin Microbiol 36, 577-579.
6. Clarridge, J. E., III (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17, 840-862.
7. Cloud, J. L., Neal, H., Rosenberry, R., Turenne, C. Y., Jama, M., Hillyard, D. R. & Carroll, K. C. (2002). Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol 40, 400-406.
8. Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J. P. & Raoult, D. (2000). 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38, 3623-3630.
9. El Amin, N. M., Hanson, H. S., Pettersson, B., Petrini, B. & Von Stedingk, L. V. (2000). Identification of non-tuberculous mycobacteria: 16S rRNA gene sequence analysis vs. conventional methods. Scand J Infect Dis 32, 47-50.
10. Goto, M., Oka, S., Okuzumi, K., Kimura, S. & Shimada, K. (1991). Evaluation of acridinium-ester-labeled DNA probes for identification of Mycobacterium tuberculosis and Mycobacterium avium-Mycobacterium intracellulare complex in culture. J Clin Microbiol 29, 2473-2476.
11. Hall, L., Doerr, K. A., Wohlfiel, S. L. & Roberts, G. D. (2003). Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J Clin Microbiol 41, 1447-1453.
12. Holberg-Petersen, M., Steinbakk, M., Figenschau, K. J., Jantzen, E., Eng, J. & Melby, K. K. (1999). Identification of clinical isolates of Mycobacterium spp. by sequence analysis of the 16S ribosomal RNA gene. Experience from a clinical laboratory. Acta Pathol Microbiol Immunol Scand 107, 231-239.
13. Kirschner, P., Springer, B., Vogel, U., Meier, A., Wrede, A., Kiekenbeck, M., Bange, F. C. & Bottger, E. C. (1993). Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol 31, 2882-2889.
14. Larsson, L., Jantzen, E. & Johnsson, J. (1985). Gas Chromatographic fatty acid profiles for characterisation of mycobacteria: an interlaboratory methodological evaluation. Eur J Clin Microbiol 4, 483-487.
15. Lebrun, L., Espinasse, F., Poveda, J. D. & Vincent-Levy-Frebault, V. (1992). Evaluation of nonradioactive DNA probes for identification of mycobacteria. J Clin Microbiol 30, 2476-2478.
16. Li, Z., Bai, G. H., von Reyn, C. F., Marino, P., Brennan, M. J., Gine, N. & Morris, S. L. (1996). Rapid detection of Mycobacterium avium in stool samples from AIDS patients by immunomagnetic PCR. J Clin Microbiol 34, 1903-1907.
17. Padilla, E., Gonzalez, V., Manterola, J. M. & 8 other authors (2004). Comparative evaluation of the new version of the INNO-LiPA Mycobacteria and GenoType Mycobacterium assays for identification of Mycobacterium species from MB/BacT liquid cultures artificially inoculated with mycobacterial strains. J Clin Microbiol 42, 3083-3088.
18. Park, Y. K., Bai, G. H. & Kim, S. J. (2000). Restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolated from countries in the western Pacific region. J Clin Microbiol 38, 191-197.
19. Patel, S., Yates, M. & Saunders, N. A. (1997). PCR-enzyme-linked immunosorbent assay and partial rRNA gene sequencing: a rational approach to identifying mycobacteria. J Clin Microbiol 35, 2375-2380.
20. Patel, J. B., Leonard, D. G., Pan, X., Musser, J. M., Berman, R. E. & Nachamkin, I. (2000). Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. J Clin Microbiol 38, 246-251.
21. Pfyffer, G. E., Brown-Elliott, B. A. & Wallace, R. J. (2003). Mycobacterium: general characteristics, isolation, and staining procedures. In Manual of Clinical Microbiology, pp. 532-559. Edited by P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller & R. H. Yolken. Washington, DC: American Society for Microbiology.
22. Richter, E., Weizenegger, M., Fahr, A. M. & Rusch-Gerdes, S. (2004). Usefulness of the GenoType MTBC assay for differentiating species of the Mycobacierium tuberculosis complex in cultures obtained from clinical specimens. J Clin Microbiol 42, 4303-4306.
23. Sarkola, A., Makinen, J., Marjamaki, M., Marttila, H. J., Viljanen, M. K. & Soini, H. (2004). Prospective evaluation of the GenoType assay for routine identification of mycobacteria. Eur J Clin Microbiol Inject Dis 23, 642-645.
24. Torkko, P., Katila, M. L. & Kontro, M. (2003). Gas-chromatographic lipid profiles in identification of currently known slowly growing environmental mycobacteria. J Med Microbiol 52, 315-323.
25. Vincent, V., Brown-Elliott, B. A., Jost, K. C., Jr & Wallace, R. J. (2003). Mycobacterium: phenotypic and genotypic identification. In Manual of Clinical Microbiology, pp. 560-587. Edited by P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller & R. H. Yolken. Washington, DC: American Society for Microbiology.
26. Witebsky, F. G. & Kruczak-Filipov, P. (1996). Identification of mycobacteria by conventional methods. Clin Lab Med 16, 569-601.
27. Woo, P. C., Ng, K. H., Lau, S. K., Yip, K. T., Fung, A. M., Leung, K. W., Tam, D. M., Que, T. L. & Yuen, K. Y. (2003). Usefulness of the MicroSeq 500 16S rihosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J Clin Microbiol 41, 1996-2001.
28. Yakrus, M. A., Hernandez, S. M., Floyd, M. M., Sikes, D., Butler, W. R. & Metchock, B. (2001). Comparison of methods for identification of Mycobacterium abscessus and M. chelonae isolates. J Clin Microbiol 39, 4103-4110.
29. Yam, W. C., Yuen, K. Y. & Seto, W. H. (1998). Direct detection of Mycobacterium tuberculosis in respiratory specimens using an automated DNA amplification assay and a single tube nested polymerase chain reaction. Clin Chem Lab Med 36, 597-599.
30. Yam, W. C., Tam, C. M., Leung, C. C. & 8 other authors (2004). Direct detection of rifampin-resistant Mycobacterium tuberculosis in respiratory specimens by PCR-DNA sequencing. J Clin Microbiol 42, 4438-4443.
31. Yuen, K. Y., Yam, W. C., Wong, L. P. & Seto, W. H. (1997). Comparison of two automated DNA amplification systems with a manual one-tube nested PCR assay for diagnosis of pulmonary tuberculosis. J Clin Microbiol 35, 1385-1389.