Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S-23S rRNA gene spacer and restriction endonucleases

Journal of Clinical Microbiology

Volumn 38, Issue 3, 2000, Pages 1094-1104

  Roth, Andreas ^a,d   Reischl, Udo ^b   Streubel, Anna ^a   Naumann, Ludmila ^b   Kroppenstedt, Reiner M ^c   Habicht, Marion ^a   Fischer, Marga ^a   Mauch, Harald ^a  

^a Lungenklinik Heckeshorn   (Germany)

^b UNIVERSITY OF REGENSBURG   (Germany)

^c LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^d Lungenklinik Heckeshorn Zehlendorf   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE; RNA 16S; RNA 23S;

ALGORITHM; ARTICLE; BACTERIUM IDENTIFICATION; MYCOBACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TAXONOMY;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); CORYNEBACTERINEAE; GORDONIA TERRAE; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM AVIUM COMPLEX; MYCOBACTERIUM CHELONAE; MYCOBACTERIUM FARCINOGENES; MYCOBACTERIUM FORTUITUM; MYCOBACTERIUM INTRACELLULARE; MYCOBACTERIUM KANSASII; MYCOBACTERIUM PEREGRINUM; MYCOBACTERIUM SENEGALENSE; UNCULTURED ACTINOMYCETE; UNIDENTIFIED AGENTS;

EID: 0034049470     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.38.3.1094-1104.2000     Document Type: Article

References (34)

1. Alcaide, F., I. Richter, C. Bernasconi, B. Springer, C. Hagenau, R. Schulze-Röbbecke, E. Tortoli, R. Martin, E. Böttger, and A. Telenti. 1997. Heterogeneity and clonality among isolates of Mycobacterium kansasii: implications for epidemiological and pathogenicity studies. J. Clin. Microbiol. 35:1959-1964.
2. Anz, W., and K.-H. Schröder. 1970. Photochromogenic strains of Mycobacterium gastri? Zentrabl. Bakteriol. 214:553-554.
3. De Beenhouwer, H., Z. Liang, P. de Rijk, C. van Eekeren, and F. Portaels. 1995. Detection and identification of mycobacteria by DNA amplification and oligonucleotide-specific capture plate hybridization. J. Clin. Microbiol. 33:2994-2998.
4. De Smet, A. L., I. N. Brown, M. Yates, and J. Ivanyi. 1995. Ribosomal internal transcribed spacers are identical among Mycobacterium avium-intracellulare complex isolates from AIDS patients, but vary among isolates from elderly pulmonary disease patients. Microbiology 141:2739-2747.
5. Devallois, A., K. S. Goh, and N. Rastogi. 1997. Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J. Clin. Microbiol. 35:2969-2973.
6. Emler, S., B. Ninet, P. Rohner, R. Auckenthaler, D. Jäger, and B. Hirschel. 1995. Molecular basis for cross-reactivity between a strain of Mycobacterium terrae and DNA probes for Mycobacterium tuberculosis complex. Eur. J. Microbiol. Infect. Dis. 14:627-629.
7. Falkinham, J. O. 1996. Epidemiology of infection by nontuberculous mycobacteria. Clin. Microbiol. Rev. 9:177-215.
8. Frothingham, R., and K. H. Wilson. 1993. Sequence-based differentiation of strains in the Mycobacterium avium complex. J. Bacterial. 175:2818-2825.
9. Frothingham, R., and K. H. Wilson. 1994. Molecular phylogeny of the Mycobacterium avium complex demonstrates clinically meaningful divisions. J. Infect. Dis. 169:305-312.
10. Good, R. C. 1985. Opportunistic pathogens in the genus Mycobacterium. Annu. Rev. Microbiol. 39:347-369.
11. Gürtler, V., and V. A. Stanisch. 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142:3-16.
12. Kent, P. T., and G. P. Kubica. 1985. Public health mycobacteriology - a guide for the level III laboratory. U.S. Department of Health and Human Services publication (CDC) 86-8230. Centers for Disease Control, Atlanta, Ga.
13. Kim, B.-J., S.-H. Lee, M.-A. Lyu, S.-J. Kim, G.-H. Bai, S.-J. Kim, 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.
14. Kirschner, P., B. Springer, U. Vogel, A. Meier, A. Wrede, M. Kiekenbeck, F. C. Bange, and E. C. Böttger. 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.
15. Kox, L. F. F., J. van Leeuwen, S. Knijper, H. M. Jansen, and A. H. Kolk. 1995. PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples. J. Clin. Microbiol. 33: 3225-3233.
16. Lappayawichit, P., S. Rienthong, D. Rienthong, C. Chuchottaworn, A. Chaiprasert, W. Panbangred, H. Saringcarinkul, and P. Palittapongarnpim. 1996. Differentiation of Mycobacterium species by restriction enzyme analysis of amplified 16S-23S ribosomal DNA spacer sequences. Tubercle Lung Dis. 77:257-263.
17. Müller, K.-D., E. N. Schmid, and R. M. Kroppenstedt. 1998. Improved identification of mycobacteria by using the Microbial Identification System in combination with additional trimethylsulfonium hydroxide pyrolysis. J. Clin. Microbiol. 36:2477-2480.
18. Picardeau, M., G. Prod'Hom, L. Raskine, M. P. LePennec, and V. Vincent. 1997. Genotypic characterization of five subspecies of M. kansasii. J. Clin. Microbiol. 35:25-32.
19. Portaeles, F., P. de Rijk, G. Jannes, R. Lemans, W. Mijs, L. Riqouts, and R. Rossau. 1996. The 16S-23S rRNA spacer, a useful tool for taxonomical and epidemiological studies of the M. chelonae complex. Tubercle Lung Dis. 77(Suppl. 2):17-18.
20. Richter, E., S. Niemann, S. Rüsch-Gerdes, and S. Hoffner. 1999. Identification of M. kansasii by using a DNA probe (AccuProbe) and molecular techniques. J. Clin. Microbiol. 37:964-970.
21. Ringuet, H., C. Akoua-Koffi, S. Honore, A. Varnerot, V. Vincent, P. Berche, J. L. Gaillard, and C. Pierre-Audigier. 1999. hsp65 sequencing for identification of rapidly growing mycobacteria. J. Clin. Microbiol. 37:852-857.
22. Roth, A., M. Fischer, H. E. Hamid, W. Ludwig, S. Michalke, and H. Mauch. 1998. Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J. Clin. Microbiol. 36:139-147.
23. Sanguinetti, M., B. Pasteraro, F. Ardito, S. Zanetti, A. Cingolani, L. Sechi, A. De Luca, L. Ortona, and G. Fadda. 1998. Routine use of PCR-reverse cross-blot hybridization assay for rapid identification of Mycobacterium species growing in liquid media. J. Clin. Microbiol. 36:1530-1533.
24. Schröder, K.-H., L. Naumann, R. M. Kroppenstedt, and U. Reischl. 1997. Mycobacterium hassiacum sp. nov., a new rapidly growing thermophilic mycobacterium. Int. J. Syst. Bacteriol. 47:86-91.
25. Shinnick, T. M., and R. C. Good. 1994. Mycobacterial taxonomy. Eur. J. Clin. Microbiol. Infect. Dis. 13:884-901.
26. Springer, B., L. Stockman, K. Teschner, G. D. Roberts, and E. C. Böttger. 1996. Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J. Clin. Microbiol. 34:296-303.
27. Steingrube, A. V., J. L. Gibson, B. A. Brown, Y. Zhang, R. W. Wilson, M. Rajagopalan, and R. J. Wallace. 1995. PCR amplification and restriction endonuclease analysis of a 65-kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria. J. Clin. Microbiol. 33:149-153.
28. Steingrube, V. A., R. W. Wilson, B. A. Brown, K. C. Jost, Z. Blacklock, J. L. Gibson, and R. J. Wallace. 1997. Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordonia, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J. Clin. Microbiol. 35:817-822.
29. Taylor, T. B., C. Patterson, Y. Hlae, and W. W. Safranek. 1997. Routine use of PCR-restriction fragment length polymorphism analysis for identification of mycobacteria growing in liquid media. J. Clin. Microbiol. 35:79-85.
30. Telenti, A., F. Marchesi, M. Balz, F. Bally, E. C. Böttger, and T. Bodmer. 1993. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J. Clin. Microbiol. 31:175-178.
31. Troesch, A., H. Nguyen, C. G. Miyada, S. Desvarenne, T. R. Gingeras, P. M. Kaplan, P. Cros, and C. Mabilat. 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37:49-55.
32. Torkko, P., M. Suutari, S. Suomalainen, L. Paulin, L. Larsson, and M.-L. Katila. 1998. Separation among species of Mycobacterium terrae complex by lipid analysis: comparison with biochemical tests and 16S rRNA sequencing. J. Clin. Microbiol. 36:499-505.
33. Wallace, R. J. 1994. Recent changes in taxonomy and disease manifestations of the rapidly growing mycobacteria. Eur. J. Clin. Microbiol. Infect. Dis. 13:953-960.
34. Wilson, R. W., V. A. Steingrube, B. A. Brown, and R. J. Wallace. 1998. Clinical application of PCR-restriction enzyme pattern analysis for rapid identification of aerobic actinomycete isolates. J. Clin. Microbiol. 36:148-152.