This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow An author's correction has been published
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Turenne, C. Y.
Right arrow Articles by Kabani, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Turenne, C. Y.
Right arrow Articles by Kabani, A.

 Previous Article  |  Next Article 

Journal of Clinical Microbiology, October 2001, p. 3637-3648, Vol. 39, No. 10
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.10.3638-3648.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Necessity of Quality-Controlled 16S rRNA Gene Sequence Databases: Identifying Nontuberculous Mycobacterium Species

Christine Y. Turenne,1,* Lorelee Tschetter,1 Joyce Wolfe,1 and Amin Kabani1,2

National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Population and Public Health Branch, Health Canada,1 and Department of Medical Microbiology, University of Manitoba,2 Winnipeg, Manitoba, Canada

Received 2 May 2001/Returned for modification 28 June 2001/Accepted 22 July 2001

The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing ~440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.

* Corresponding author. Mailing address: National Reference Centre for Mycobacteriology, Canadian Science Centre for Human and Animal Health, 1015 Arlington St., Winnipeg, Manitoba, Canada R3E 3R2. Phone: (204) 789-6081. Fax: (204) 789-2036. E-mail: cturenne{at}hc-sc.gc.ca.

Journal of Clinical Microbiology, October 2001, p. 3637-3648, Vol. 39, No. 10
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.10.3638-3648.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Tortoli, E., Baruzzo, S., Heijdra, Y., Klenk, H.-P., Lauria, S., Mariottini, A., van Ingen, J. (2009). Mycobacterium insubricum sp. nov.. Int. J. Syst. Evol. Microbiol. 59: 1518-1523 [Abstract] [Full Text]  
  • Sheng, W.-H., Huang, Y.-T., Chang, S.-C., Hsueh, P.-R. (2009). Brain Abscess Caused by Tsukamurella tyrosinosolvens in an Immunocompetent Patient. J. Clin. Microbiol. 47: 1602-1604 [Abstract] [Full Text]  
  • Heller, L. C., Jones, M., Widen, R. H. (2008). Comparison of DNA Pyrosequencing with Alternative Methods for Identification of Mycobacteria. J. Clin. Microbiol. 46: 2092-2094 [Abstract] [Full Text]  
  • Nakanaga, K., Ishii, N., Suzuki, K., Tanigawa, K., Goto, M., Okabe, T., Imada, H., Kodama, A., Iwamoto, T., Takahashi, H., Saito, H. (2007). "Mycobacterium ulcerans subsp. shinshuense" Isolated from a Skin Ulcer Lesion: Identification Based on 16S rRNA Gene Sequencing. J. Clin. Microbiol. 45: 3840-3843 [Abstract] [Full Text]  
  • Ichimura, S., Nagano, M., Ito, N., Shimojima, M., Egashira, T., Miyamoto, C., Ohkusu, K., Ezaki, T. (2007). Evaluation of the Invader Assay with the BACTEC MGIT 960 System for Prompt Isolation and Identification of Mycobacterial Species from Clinical Specimens. J. Clin. Microbiol. 45: 3316-3322 [Abstract] [Full Text]  
  • Wu, X., Zhang, J., Liang, J., Lu, Y., Li, H., Li, C., Yue, J., Zhang, L., Liu, Z. (2007). Comparison of Three Methods for Rapid Identification of Mycobacterial Clinical Isolates to the Species Level. J. Clin. Microbiol. 45: 1898-1903 [Abstract] [Full Text]  
  • Williams, K. J., Ling, C. L., Jenkins, C., Gillespie, S. H., McHugh, T. D. (2007). A paradigm for the molecular identification of Mycobacterium species in a routine diagnostic laboratory. J Med Microbiol 56: 598-602 [Abstract] [Full Text]  
  • Turenne, C. Y., Wallace, R. Jr., Behr, M. A. (2007). Mycobacterium avium in the Postgenomic Era. Clin. Microbiol. Rev. 20: 205-229 [Abstract] [Full Text]  
  • 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., Iseman, M., Olivier, K., Ruoss, S., von Reyn, C. F., Wallace, R. J. Jr., Winthrop, K., on behalf of the ATS Mycobacterial Diseases Subcom, (2007). An Official ATS/IDSA Statement: Diagnosis, Treatment, and Prevention of Nontuberculous Mycobacterial Diseases. Am. J. Respir. Crit. Care Med. 175: 367-416 [Full Text]  
  • Wang, C.-Y., Chuang, Y.-M., Teng, L.-J., Lee, L.-N., Yang, P.-C., Kuo, S.-H., Hsueh, P.-R. (2006). Bacteraemic pneumonia caused by Neisseria lactamica with reduced susceptibility to penicillin and ciprofloxacin in an adult with liver cirrhosis.. J Med Microbiol 55: 1151-1152 [Abstract] [Full Text]  
  • Cloud, J. L., Meyer, J. J., Pounder, J. I., Jost, K. C. Jr, Sweeney, A., Carroll, K. C., Woods, G. L. (2006). Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens. Int. J. Syst. Evol. Microbiol. 56: 1413-1418 [Abstract] [Full Text]  
  • Brown-Elliott, B. A., Brown, J. M., Conville, P. S., Wallace, R. J. Jr (2006). Clinical and Laboratory Features of the Nocardia spp. Based on Current Molecular Taxonomy. Clin. Microbiol. Rev. 19: 259-282 [Abstract] [Full Text]  
  • Adekambi, T., Stein, A., Carvajal, J., Raoult, D., Drancourt, M. (2006). Description of Mycobacterium conceptionense sp. nov., a Mycobacterium fortuitum Group Organism Isolated from a Posttraumatic Osteitis Inflammation. J. Clin. Microbiol. 44: 1268-1273 [Abstract] [Full Text]  
  • Adekambi, T., Berger, P., Raoult, D., Drancourt, M. (2006). rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov.. Int. J. Syst. Evol. Microbiol. 56: 133-143 [Abstract] [Full Text]  
  • Wallace, R. J. Jr., Brown-Elliott, B. A., Brown, J., Steigerwalt, A. G., Hall, L., Woods, G., Cloud, J., Mann, L., Wilson, R., Crist, C., Jost, K. C. Jr., Byrer, D. E., Tang, J., Cooper, J., Stamenova, E., Campbell, B., Wolfe, J., Turenne, C. (2005). Polyphasic Characterization Reveals that the Human Pathogen Mycobacterium peregrinum Type II Belongs to the Bovine Pathogen Species Mycobacterium senegalense. J. Clin. Microbiol. 43: 5925-5935 [Abstract] [Full Text]  
  • Lai, C.-C., Lee, L.-N., Teng, L.-J., Wu, M. S., Tsai, J.-C., Hsueh, P.-R. (2005). Disseminated Nocardia farcinica infection in a uraemia patient with idiopathic thrombocytopenia purpura receiving steroid therapy. J Med Microbiol 54: 1107-1110 [Abstract] [Full Text]  
  • Han, X. Y., Tarrand, J. J., Infante, R., Jacobson, K. L., Truong, M. (2005). Clinical Significance and Epidemiologic Analyses of Mycobacterium avium and Mycobacterium intracellulare among Patients without AIDS. J. Clin. Microbiol. 43: 4407-4412 [Abstract] [Full Text]  
  • Khan, I. U. H., Selvaraju, S. B., Yadav, J. S. (2005). Method for Rapid Identification and Differentiation of the Species of the Mycobacterium chelonae Complex Based on 16S-23S rRNA Gene Internal Transcribed Spacer PCR-Restriction Analysis. J. Clin. Microbiol. 43: 4466-4472 [Abstract] [Full Text]  
  • Mohamed, A. M., Kuyper, D. J., Iwen, P. C., Ali, H. H., Bastola, D. R., Hinrichs, S. H. (2005). Computational Approach Involving Use of the Internal Transcribed Spacer 1 Region for Identification of Mycobacterium Species. J. Clin. Microbiol. 43: 3811-3817 [Abstract] [Full Text]  
  • Cloud, J. L., Hoggan, K., Belousov, E., Cohen, S., Brown-Elliott, B. A., Mann, L., Wilson, R., Aldous, W., Wallace, R. J. Jr., Woods, G. L. (2005). Use of the MGB Eclipse System and SmartCycler PCR for Differentiation of Mycobacterium chelonae and M. abscessus. J. Clin. Microbiol. 43: 4205-4207 [Abstract] [Full Text]  
  • Tortoli, E., Chianura, L., Fabbro, L., Mariottini, A., Martin-Casabona, N., Mazzarelli, G., Russo, C., Spinelli, M. (2005). Infections Due to the Newly Described Species Mycobacterium parascrofulaceum. J. Clin. Microbiol. 43: 4286-4287 [Abstract] [Full Text]  
  • Kim, H., Kim, S.-H., Shim, T.-S., Kim, M.-n., Bai, G.-H., Park, Y.-G., Lee, S.-H., Chae, G.-T., Cha, C.-Y., Kook, Y.-H., Kim, B.-J. (2005). Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65). Int. J. Syst. Evol. Microbiol. 55: 1649-1656 [Abstract] [Full Text]  
  • Zelazny, A. M., Calhoun, L. B., Li, L., Shea, Y. R., Fischer, S. H. (2005). Identification of Mycobacterium Species by secA1 Sequences. J. Clin. Microbiol. 43: 1051-1058 [Abstract] [Full Text]  
  • Naughton, J. F., Mealey, K. L., Wardrop, K. J., Oaks, J. L., Bradway, D. S. (2005). Systemic Mycobacterium avium Infection in a Dog Diagnosed by Polymerase Chain Reaction Analysis of Buffy Coat. Journal of the American Animal Hospital Association 41: 128-132 [Abstract] [Full Text]  
  • Zhang, Y., Yakrus, M. A., Graviss, E. A., Williams-Bouyer, N., Turenne, C., Kabani, A., Wallace, R. J. Jr. (2004). Pulsed-Field Gel Electrophoresis Study of Mycobacterium abscessus Isolates Previously Affected by DNA Degradation. J. Clin. Microbiol. 42: 5582-5587 [Abstract] [Full Text]  
  • Wallace, R. J. Jr., Brown-Elliott, B. A., Wilson, R. W., Mann, L., Hall, L., Zhang, Y., Jost, K. C. Jr., Brown, J. M., Kabani, A., Schinsky, M. F., Steigerwalt, A. G., Crist, C. J., Roberts, G. D., Blacklock, Z., Tsukamura, M., Silcox, V., Turenne, C. (2004). Clinical and Laboratory Features of Mycobacterium porcinum. J. Clin. Microbiol. 42: 5689-5697 [Abstract] [Full Text]  
  • Mohamed, A. M., Iwen, P. C., Tarantolo, S., Hinrichs, S. H. (2004). Mycobacterium nebraskense sp. nov., a novel slowly growing scotochromogenic species. Int. J. Syst. Evol. Microbiol. 54: 2057-2060 [Abstract] [Full Text]  
  • Lee, S. A., Raad, I. I., Adachi, J. A., Han, X. Y. (2004). Catheter-Related Bloodstream Infection Caused by Mycobacterium brumae. J. Clin. Microbiol. 42: 5429-5431 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • Turenne, C. Y., Cook, V. J., Burdz, T. V., Pauls, R. J., Thibert, L., Wolfe, J. N., Kabani, A. (2004). Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae. Int. J. Syst. Evol. Microbiol. 54: 1543-1551 [Abstract] [Full Text]  
  • Schinsky, M. F., Morey, R. E., Steigerwalt, A. G., Douglas, M. P., Wilson, R. W., Floyd, M. M., Butler, W. R., Daneshvar, M. I., Brown-Elliott, B. A., Wallace, R. J. Jr, McNeil, M. M., Brenner, D. J., Brown, J. M. (2004). Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates. Int. J. Syst. Evol. Microbiol. 54: 1653-1667 [Abstract] [Full Text]  
  • McNabb, A., Eisler, D., Adie, K., Amos, M., Rodrigues, M., Stephens, G., Black, W. A., Isaac-Renton, J. (2004). Assessment of Partial Sequencing of the 65-Kilodalton Heat Shock Protein Gene (hsp65) for Routine Identification of Mycobacterium Species Isolated from Clinical Sources. J. Clin. Microbiol. 42: 3000-3011 [Abstract] [Full Text]  
  • Patel, J. B., Wallace, R. J. Jr., Brown-Elliott, B. A., Taylor, T., Imperatrice, C., Leonard, D. G. B., Wilson, R. W., Mann, L., Jost, K. C., Nachamkin, I. (2004). Sequence-Based Identification of Aerobic Actinomycetes. J. Clin. Microbiol. 42: 2530-2540 [Abstract] [Full Text]  
  • Kiska, D. L., Turenne, C. Y., Dubansky, A. S., Domachowske, Joseph. B. (2004). First Case Report of Catheter-Related Bacteremia Due to "Mycobacterium lacticola". J. Clin. Microbiol. 42: 2855-2857 [Abstract] [Full Text]  
  • Turenne, C. Y., Thibert, L., Williams, K., Burdz, T. V., Cook, V. J., Wolfe, J. N., Cockcroft, D. W., Kabani, A. (2004). Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex. Int. J. Syst. Evol. Microbiol. 54: 659-667 [Abstract] [Full Text]  
  • Blackwood, K. S., Turenne, C. Y., Harmsen, D., Kabani, A. M. (2004). Reassessment of Sequence-Based Targets for Identification of Bacillus Species. J. Clin. Microbiol. 42: 1626-1630 [Abstract] [Full Text]  
  • Cloud, J. L., Conville, P. S., Croft, A., Harmsen, D., Witebsky, F. G., Carroll, K. C. (2004). Evaluation of Partial 16S Ribosomal DNA Sequencing for Identification of Nocardia Species by Using the MicroSeq 500 System with an Expanded Database. J. Clin. Microbiol. 42: 578-584 [Abstract] [Full Text]  
  • Adekambi, T., Colson, P., Drancourt, M. (2003). rpoB-Based Identification of Nonpigmented and Late-Pigmenting Rapidly Growing Mycobacteria. J. Clin. Microbiol. 41: 5699-5708 [Abstract] [Full Text]  
  • Yang, S.-C., Hsueh, P.-R., Lai, H.-C., Teng, L.-J., Huang, L.-M., Chen, J.-M., Wang, S.-K., Shie, D.-C., Ho, S.-W., Luh, K.-T. (2003). High Prevalence of Antimicrobial Resistance in Rapidly Growing Mycobacteria in Taiwan. Antimicrob. Agents Chemother. 47: 1958-1962 [Abstract] [Full Text]  
  • Conville, P. S., Brown, J. M., Steigerwalt, A. G., Lee, J. W., Byrer, D. E., Anderson, V. L., Dorman, S. E., Holland, S. M., Cahill, B., Carroll, K. C., Witebsky, F. G. (2003). Nocardia veterana as a Pathogen in North American Patients. J. Clin. Microbiol. 41: 2560-2568 [Abstract] [Full Text]  
  • Turenne, C. Y., Suchak, A. A., Wolfe, J. N., Kabani, A., Nicolle, L. E. (2003). Soft Tissue Infection Caused by a Novel Pigmented, Rapidly Growing Mycobacterium Species. J. Clin. Microbiol. 41: 2779-2782 [Abstract] [Full Text]  
  • Tortoli, E. (2003). Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s. Clin. Microbiol. Rev. 16: 319-354 [Abstract] [Full Text]  
  • Song, Y., Liu, C., McTeague, M., Finegold, S. M. (2003). 16S Ribosomal DNA Sequence-Based Analysis of Clinically Significant Gram-Positive Anaerobic Cocci. J. Clin. Microbiol. 41: 1363-1369 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • Huard, R. C., de Oliveira Lazzarini, L. C., Butler, W. R., van Soolingen, D., Ho, J. L. (2003). PCR-Based Method To Differentiate the Subspecies of the Mycobacterium tuberculosis Complex on the Basis of Genomic Deletions. J. Clin. Microbiol. 41: 1637-1650 [Abstract] [Full Text]  
  • Devulder, G., Perriere, G., Baty, F., Flandrois, J. P. (2003). BIBI, a Bioinformatics Bacterial Identification Tool. J. Clin. Microbiol. 41: 1785-1787 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • Cook, V. J., Turenne, C. Y., Wolfe, J., Pauls, R., Kabani, A. (2003). Conventional Methods versus 16S Ribosomal DNA Sequencing for Identification of Nontuberculous Mycobacteria: Cost Analysis. J. Clin. Microbiol. 41: 1010-1015 [Abstract] [Full Text]  
  • Dauendorffer, J.-N., Guillemin, I., Aubry, A., Truffot-Pernot, C., Sougakoff, W., Jarlier, V., Cambau, E. (2003). Identification of Mycobacterial Species by PCR Sequencing of Quinolone Resistance-Determining Regions of DNA Gyrase Genes. J. Clin. Microbiol. 41: 1311-1315 [Abstract] [Full Text]  
  • Roth, A., Andrees, S., Kroppenstedt, R. M., Harmsen, D., Mauch, H. (2003). Phylogeny of the Genus Nocardia Based on Reassessed 16S rRNA Gene Sequences Reveals Underspeciation and Division of Strains Classified as Nocardia asteroides into Three Established Species and Two Unnamed Taxons. J. Clin. Microbiol. 41: 851-856 [Abstract] [Full Text]  
  • Garcia-Quintanilla, A., Gonzalez-Martin, J., Tudo, G., Espasa, M., Jimenez de Anta, M. T. (2002). Simultaneous Identification of Mycobacterium Genus and Mycobacterium tuberculosis Complex in Clinical Samples by 5'-Exonuclease Fluorogenic PCR. J. Clin. Microbiol. 40: 4646-4651 [Abstract] [Full Text]  
  • Ucko, M., Colorni, A., Kvitt, H., Diamant, A., Zlotkin, A., Knibb, W. R. (2002). Strain Variation in Mycobacteriummarinum Fish Isolates. Appl. Environ. Microbiol. 68: 5281-5287 [Abstract] [Full Text]  
  • Turenne, C., Chedore, P., Wolfe, J., Jamieson, F., May, K., Kabani, A. (2002). Phenotypic and Molecular Characterization of Clinical Isolates of Mycobacterium elephantis from Human Specimens. J. Clin. Microbiol. 40: 1230-1236 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»