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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.


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