A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model

International Journal of Systematic and Evolutionary Microbiology

Volumn 55, Issue 1, 2005, Pages 293-302

  Devulder, G ^a   de Montclos, M Pérouse ^b   Flandrois, J P ^a,b  

^a LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

^b CENTRE HOSPITALIER LYON SUD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; HEAT SHOCK PROTEIN 65; RNA 16S; RNA POLYMERASE BETA SUBUNIT; SUPEROXIDE DISMUTASE;

ACCURACY; ARTICLE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DISCRIMINANT ANALYSIS; DNA SEQUENCE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; MYCOBACTERIUM; NONHUMAN; PRIORITY JOURNAL; SEQUENCE DATABASE;

ANIMALS; BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; CHAPERONINS; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; GENES, RRNA; HUMANS; MYCOBACTERIUM; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SUPEROXIDE DISMUTASE;

ANIMALIA; BACTERIA (MICROORGANISMS); MYCOBACTERIUM;

EID: 13244273719     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63222-0     Document Type: Article

References (39)

1. Afghani, B. & Stutman, H. R. (1996). Polymerase chain reaction for diagnosis of M. tuberculosis: comparison of simple boiling and a conventional method for DNA extraction. Biochem Mol Med 57, 14-18.
2. Blackwood, K. S., He, C., Gunton, J., Turenne, C. Y., Wolfe, J. & Kabani, A. M. (2000). Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38, 2846-2852.
3. Brunello, F., Ligozzi, M., Cristelli, E., Bonora, S., Tortoli, E. & Fontana, R. (2001). Identification of 54 mycobacterial species by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. J Clin Microbiol 39, 2799-2806.
4. 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.
5. Daubin, V., Gouy, M. & Perrière, G. (2002). A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12, 1080-1090.
6. De Beenhouwer, H., Liang, Z., De Rijk, P., Van Eekeren, C. & Portaels, F. (1995). Detection and identification of mycobacteria by DNA amplification and oligonucleotide-specific capture plate hybridization. J Clin Microbiol 33, 2994-2998.
7. Devallois, A., Goh, K. S. & Rastogi, N. (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.
8. Domenech, P., Menendez, M. C. & Garcia, M. J. (1994). Restriction fragment length polymorphisms of 16S rRNA genes in the differentiation of fast-growing mycobacterial species. FEMS Microbiol Lett 116, 19-24.
9. Galtier, N., Gouy, M. & Gautier, C. (1996). SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12, 543-548.
10. Gingeras, T. R., Ghandour, G., Wang, E. & 7 other authors (1998). Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res 8, 435-448.
11. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
12. Hamid, M. E., Roth, A., Landt, O., Kroppenstedt, R. M., Goodfellow, M. & Mauch, H. (2002). Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense strains based on 16S-23S ribosomal DNA internal transcribed spacer sequences. J Clin Microbiol 40, 707-711.
13. Harmsen, D., Rothganger, J., Frosch, M. & Albert, J. (2002). RIDOM: ribosomal differentiation of medical micro-organisms database. Nucleic Acids Res 30, 416-417.
14. Ji, Y., Colston, M. J. & Cox, R. A. (1994). The ribosomal RNA (rrn) operons of fast-growing mycobacteria: primary and secondary structures and their relation to rrn operons of pathogenic slow-growers. Microbiology 140, 2829-2840.
15. Kasai, H., Ezaki, T. & Harayama, S. (2000). Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38, 301-308.
16. Kim, B. J., Lee, S. H., Lyu, M. A., Kim, S. J., Bal, G. H., Chae, G. T., Kim, E. C., Cha, C. Y. & Kook, Y. H. (1999). Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37, 1714-1720.
17. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
18. Kirschner, P. & Bottger, E. C. (1998). Species identification of mycobacteria using rDNA sequencing. Methods Mol Biol 101, 349-361.
19. Kolbert, C. P. & Persing, D. H. (1999). Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr Opin Microbiol 2, 299-305.
20. Menendez, M. C., Garcia, M. J., Navarro, M. C., Gonzalez-y-Merchand, J. A., Rivera-Gutierrez, S., Garcia-Sanchez, L. & Cox, R. A. (2002). Characterization of an rRNA operon (rrnB) of Mycobacterium fortuitum and other mycobacterial species: implications for the classification of mycobacteria. J Bacteriol 184, 1078-1088.
21. Niemann, S., Harmsen, D., Rusch-Gerdes, S. & Richter, E. (2000). Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis. J Clin Microbiol 38, 3231-3234.
22. Perrière, G. & Gouy, M. (1996). WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364-369.
23. Richter, E., Niemann, S., Gloeckner, F. O., Pfyffer, G. E. & Rüsch-Gerdes, S. (2002). Mycobacterium holsaticum sp. nov. Int J Syst Evol Microbiol 52, 1991-1996.
24. Ringuet, H., Akoua-Koffi, C., Honore, S., Varnerot, A., Vincent, V., Berche, P., Gaillard, J. L. & Pierre-Audigier, C. (1999 . hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37, 852-857.
25. Robinson-Rechavi, M. & Huchon, D. (2000). RRTree: relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16, 296-297.
26. Rogall, T., Flohr, T. & Böttger, E. C. (1990). Differentiation of Mycobacterium species by direct sequencing of amplified DNA. J Gen Microbiol 136, 1915-1920.
27. Roth, A., Fischer, M., Hamid, M. E., Michalke, S., Ludwig, W. & Mauch, H. (1998). Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol 36, 139-147.
28. Shinnick, T. M. (1987). The 65-kilodalton of Mycobacterium tuberculosis. J Bacteriol 169, 1080-1088.
29. Springer, B., Stockman, L., Teschner, K., Roberts, G. D. & Bottger, E. C. (1996). Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol 34, 296-303.
30. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
31. Stackebrandt, E., Frederiksen, W., Garrity, G. M. & 10 other authors (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
32. Stahl, D. A. & Urbance, J. W. (1990). The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol 172, 116-124.
33. Stinear, T. P., Jenkin, G. A., Johnson, P. D. & Davies, J. K. (2000). Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium marinum reveals evidence of recent divergence. J Bacteriol 182, 6322-6330.
34. Suzuki, M. T., Beja, O., Taylor, L. T. & Delong, E. F. (2001). Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3, 323-331.
35. Teichmann, S. A. & Mitchison, G. (1999). Is there a phylogenetic signal in prokaryote proteins? J Mol Evol 49, 98-107.
36. Telenti, A., Marchesi, F., Balz, M., Bally, F., Bottger, E. C. & Bodmer, T. (1993). Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31, 175-178.
37. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
38. Tortoli, E. (2003). Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16, 319-354.
39. Zolg, J. W. & Philippi-Schulz, S. (1994). The superoxide dismutase gene, a target for detection and identification of mycobacteria by PCR. J Clin Microbiol 32, 2801-2812.