Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

This Article

	Full Text
	Full Text (PDF)
	Alert me when this article is cited
	Alert me if a correction is posted

Services

	Similar articles in this journal
	Similar articles in PubMed
	Alert me to new issues of the journal
	Download to citation manager
	Reprints and Permissions
	Copyright Information
	Books from ASM Press
	MicrobeWorld

Citing Articles

	Citing Articles via HighWire
	Citing Articles via Google Scholar

Google Scholar

	Articles by Roth, A.
	Articles by Mauch, H.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Roth, A.
	Articles by Mauch, H.

Previous Article | Next Article

Journal of Clinical Microbiology, January 1998, p. 139-147, Vol. 36, No. 1
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

Andreas Roth,¹^,^* Marga Fischer,¹ Mohamed E. Hamid,¹^,² Sabine Michalke,¹ Wolfgang Ludwig,³ and Harald Mauch¹

Institut für Mikrobiologie und Immunologie, Krankenhaus Zehlendorf, 14109 Berlin,¹ and Institut für Botanik und Mikrobiologie, Lehrstuhl für Mikrobiologie, Technische Universität München, 80290 Munich,³ Germany, and Faculty of Veterinary Science, University of Khartoum, Khartoum, Sudan²

Received 4 August 1997/Returned for modification 17 September 1997/Accepted 17 October 1997

Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNAsequences, however, do not vary greatly within a species, andthey are either indistinguishable in some species, for example,in Mycobacterium kansasii and M. gastri, or highly similar, forexample, in M. malmoense and M. szulgai. We determined 16S-23SrDNA internal transcribed spacer (ITS) sequences of 60 strainsin the genus Mycobacterium representing 13 species (M. avium,M. conspicuum, M. gastri, M. genavense, M. kansasii, M. malmoense,M. marinum, M. shimoidei, M. simiae, M. szulgai, M. triplex, M.ulcerans, and M. xenopi). An alignment of these sequences togetherwith additional sequences available in the EMBL database (forM. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis)was established according to primary- and secondary-structuresimilarities. Comparative sequence analysis applying differenttreeing methods grouped the strains into species-specific clusterswith low sequence divergence between strains belonging to thesame species (0 to 2%). The ITS-based tree topology only partiallycorrelated to that based on 16S rDNA, but the main branching orderswere preserved, notably, the division of fast-growing from slowlygrowing mycobacteria, separate branching for M. simiae, M. genavense,and M. triplex, and distinct branches for M. xenopi and M. shimoidei.Comparisons of M. gastri with M. kansasii and M. malmoense withM. szulgai revealed ITS sequence similarities of 93 and 88%, respectively.M. marinum and M. ulcerans possessed identical ITS sequences.Our results show that ITS sequencing represents a supplement to16S rRNA gene sequences for the differentiation of closely relatedspecies. Slowly growing mycobacteria show a high sequence variationin the ITS; this variation has the potential to be used for thedevelopment of probes as a rapid approach to mycobacterial identification.

^* Corresponding author. Mailing address: Institut für Mikrobiologie und Immunologie, Lungenklinik Heckeshorn-Zehlendorf, ZumHeckeshorn 33, D 14109 Berlin, Germany. Phone: 49-30-8002 2254.Fax: 49-30-8002 2299.

Journal of Clinical Microbiology, January 1998, p. 139-147, Vol. 36, No. 1
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

This article has been cited by other articles:

Ko, W.-C., Lee, N.-Y., Su, S. C., Dijkshoorn, L., Vaneechoutte, M., Wang, L.-R., Yan, J.-J., Chang, T. C. (2008). Oligonucleotide Array-Based Identification of Species in the Acinetobacter calcoaceticus-A. baumannii Complex in Isolates from Blood Cultures and Antimicrobial Susceptibility Testing of the Isolates. J. Clin. Microbiol. 46: 2052-2059 [Abstract] [Full Text]
Alvarez, J., Garcia, I. G., Aranaz, A., Bezos, J., Romero, B., de Juan, L., Mateos, A., Gomez-Mampaso, E., Dominguez, L. (2008). Genetic Diversity of Mycobacterium avium Isolates Recovered from Clinical Samples and from the Environment: Molecular Characterization for Diagnostic Purposes. J. Clin. Microbiol. 46: 1246-1251 [Abstract] [Full Text]
Durnez, L., Eddyani, M., Mgode, G. F., Katakweba, A., Katholi, C. R., Machang'u, R. R., Kazwala, R. R., Portaels, F., Leirs, H. (2008). First Detection of Mycobacteria in African Rodents and Insectivores, Using Stratified Pool Screening. Appl. Environ. Microbiol. 74: 768-773 [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]
Mignard, S., Flandrois, J.-P. (2007). Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene. J Med Microbiol 56: 1033-1041 [Abstract] [Full Text]
Tung, S. K., Teng, L. J., Vaneechoutte, M., Chen, H. M., Chang, T. C. (2007). Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S-23S intergenic spacer region. J Med Microbiol 56: 504-513 [Abstract] [Full Text]
Mun, H.-S., Kim, H.-J., Oh, E.-J., Kim, H., Bai, G.-H., Yu, H.-K., Park, Y.-G., Cha, C.-Y., Kook, Y.-H., Kim, B.-J. (2007). Mycobacterium seoulense sp. nov., a slowly growing scotochromogenic species. Int. J. Syst. Evol. Microbiol. 57: 594-599 [Abstract] [Full Text]
Tung, S. K., Teng, L. J., Vaneechoutte, M., Chen, H. M., Chang, T. C. (2006). Array-Based Identification of Species of the Genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus. J. Clin. Microbiol. 44: 4414-4424 [Abstract] [Full Text]
Reischl, U., Melzl, H., Kroppenstedt, R. M., Miethke, T., Naumann, L., Mariottini, A., Mazzarelli, G., Tortoli, E. (2006). Mycobacterium monacense sp. nov.. Int. J. Syst. Evol. Microbiol. 56: 2575-2578 [Abstract] [Full Text]
Xiong, L., Kong, F., Yang, Y., Cheng, J., Gilbert, G. L. (2006). Use of PCR and Reverse Line Blot Hybridization Macroarray Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences for Rapid Identification of 34 Mycobacterium Species.. J. Clin. Microbiol. 44: 3544-3550 [Abstract] [Full Text]
Waters, W. R., Palmer, M. V., Thacker, T. C., Payeur, J. B., Harris, N. B., Minion, F. C., Greenwald, R., Esfandiari, J., Andersen, P., McNair, J., Pollock, J. M., Lyashchenko, K. P. (2006). Immune Responses to Defined Antigens of Mycobacterium bovis in Cattle Experimentally Infected with Mycobacterium kansasii. CVI 13: 611-619 [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]
Rodriguez-Nava, V., Couble, A., Devulder, G., Flandrois, J.-P., Boiron, P., Laurent, F. (2006). Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species. J. Clin. Microbiol. 44: 536-546 [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]
Palomino, J. C. (2005). Nonconventional and new methods in the diagnosis of tuberculosis: feasibility and applicability in the field. Eur Respir J 26: 339-350 [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]
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]
Lebrun, L., Weill, F.-X., Lafendi, L., Houriez, F., Casanova, F., Gutierrez, M. C., Ingrand, D., Lagrange, P., Vincent, V., Herrmann, J. L. (2005). Use of the INNO-LiPA-MYCOBACTERIA Assay (Version 2) for Identification of Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum Complex Isolates. J. Clin. Microbiol. 43: 2567-2574 [Abstract] [Full Text]
Tortoli, E., Rindi, L., Goh, K. S., Katila, M. L., Mariottini, A., Mattei, R., Mazzarelli, G., Suomalainen, S., Torkko, P., Rastogi, N. (2005). Mycobacterium florentinum sp. nov., isolated from humans. Int. J. Syst. Evol. Microbiol. 55: 1101-1106 [Abstract] [Full Text]
Chen, C. C., Teng, L. J., Kaiung, S., Chang, T. C. (2005). Identification of Clinically Relevant Viridans Streptococci by an Oligonucleotide Array. J. Clin. Microbiol. 43: 1515-1521 [Abstract] [Full Text]
Stragier, P., Ablordey, A., Meyers, W. M., Portaels, F. (2005). Genotyping Mycobacterium ulcerans and Mycobacterium marinum by Using Mycobacterial Interspersed Repetitive Units. J. Bacteriol. 187: 1639-1647 [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]
Devulder, G., de Montclos, M. P., Flandrois, J. P. (2005). A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int. J. Syst. Evol. Microbiol. 55: 293-302 [Abstract] [Full Text]
Adekambi, T., Reynaud-Gaubert, M., Greub, G., Gevaudan, M.-J., La Scola, B., Raoult, D., Drancourt, M. (2004). Amoebal Coculture of "Mycobacterium massiliense" sp. nov. from the Sputum of a Patient with Hemoptoic Pneumonia. J. Clin. Microbiol. 42: 5493-5501 [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]
Tortoli, E., Rindi, L., Garcia, M. J., Chiaradonna, P., Dei, R., Garzelli, C., Kroppenstedt, R. M., Lari, N., Mattei, R., Mariottini, A., Mazzarelli, G., Murcia, M. I., Nanetti, A., Piccoli, P., Scarparo, C. (2004). Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov.. Int. J. Syst. Evol. Microbiol. 54: 1277-1285 [Abstract] [Full Text]
Bruijnesteijn van Coppenraet, E. S., Lindeboom, J. A., Prins, J. M., Peeters, M. F., Claas, E. C. J., Kuijper, E. J. (2004). Real-Time PCR Assay Using Fine-Needle Aspirates and Tissue Biopsy Specimens for Rapid Diagnosis of Mycobacterial Lymphadenitis in Children. J. Clin. Microbiol. 42: 2644-2650 [Abstract] [Full Text]
Chen, C. C., Teng, L. J., Chang, T. C. (2004). Identification of Clinically Relevant Viridans Group Streptococci by Sequence Analysis of the 16S-23S Ribosomal DNA Spacer Region. J. Clin. Microbiol. 42: 2651-2657 [Abstract] [Full Text]
Selvarangan, R., Wu, W.-K., Nguyen, T. T., Carlson, L. D. C., Wallis, C. K., Stiglich, S. K., Chen, Y.-C., Jost, K. C. Jr., Prentice, J. L., Wallace, R. J. Jr., Barrett, S. L. R., Cookson, B. T., Coyle, M. B. (2004). Characterization of a Novel Group of Mycobacteria and Proposal of Mycobacterium sherrisii sp. nov.. J. Clin. Microbiol. 42: 52-59 [Abstract] [Full Text]
Lefmann, M., Honisch, C., Bocker, S., Storm, N., von Wintzingerode, F., Schlotelburg, C., Moter, A., van den Boom, D., Gobel, U. B. (2004). Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria. J. Clin. Microbiol. 42: 339-346 [Abstract] [Full Text]
Lee, H., Bang, H.-E., Bai, G.-H., Cho, S.-N. (2003). Novel Polymorphic Region of the rpoB Gene Containing Mycobacterium Species-Specific Sequences and Its Use in Identification of Mycobacteria. J. Clin. Microbiol. 41: 2213-2218 [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]
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]
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]
Miller, N., Cleary, T., Kraus, G., Young, A. K., Spruill, G., Hnatyszyn, H. J. (2002). Rapid and Specific Detection of Mycobacterium tuberculosis from Acid-Fast Bacillus Smear-Positive Respiratory Specimens and BacT/ALERT MP Culture Bottles by Using Fluorogenic Probes and Real-Time PCR. J. Clin. Microbiol. 40: 4143-4147 [Abstract] [Full Text]
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 [Abstract] [Full Text]
Makinen, J., Sarkola, A., Marjamaki, M., Viljanen, M. K., Soini, H. (2002). Evaluation of GenoType and LiPA MYCOBACTERIA Assays for Identification of Finnish Mycobacterial Isolates. J. Clin. Microbiol. 40: 3478-3481 [Abstract] [Full Text]
Doig, C., Muckersie, L., Watt, B., Forbes, K. J. (2002). Molecular Epidemiology of Mycobacterium malmoense Infections in Scotland. J. Clin. Microbiol. 40: 1103-1105 [Abstract] [Full Text]
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 [Abstract] [Full Text]
Turenne, C. Y., Tschetter, L., Wolfe, J., Kabani, A. (2001). Necessity of Quality-Controlled 16S rRNA Gene Sequence Databases: Identifying Nontuberculous Mycobacterium Species. J. Clin. Microbiol. 39: 3637-3648 [Abstract] [Full Text]
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 [Abstract] [Full Text]
Dutly, F., Altwegg, M. (2001). Whipple's Disease and ""Tropheryma whippelii"". Clin. Microbiol. Rev. 14: 561-583 [Abstract] [Full Text]
Suomalainen, S., Koukila-Kahkola, P., Brander, E., Katila, M.-L., Piilonen, A., Paulin, L., Mattson, K. (2001). Pulmonary Infection Caused by an Unusual, Slowly Growing Nontuberculous Mycobacterium. J. Clin. Microbiol. 39: 2668-2671 [Abstract] [Full Text]
Niobe, S. N., Bebear, C. M., Clerc, M., Pellegrin, J.-L., Bebear, C., Maugein, J. (2001). Disseminated Mycobacterium lentiflavum Infection in a Human Immunodeficiency Virus-Infected Patient. J. Clin. Microbiol. 39: 2030-2032 [Abstract] [Full Text]
Soini, H., Musser, J. M. (2001). Molecular Diagnosis of Mycobacteria. Clin. Chem. 47: 809-814 [Abstract] [Full Text]
Hazra, R., Floyd, M. M., Sloutsky, A., Husson, R. N. (2001). Novel Mycobacterium Related to Mycobacterium triplex as a Cause of Cervical Lymphadenitis. J. Clin. Microbiol. 39: 1227-1230 [Abstract] [Full Text]
Park, H., Jang, H., Kim, C., Chung, B., Chang, C. L., Park, S. K., Song, S. (2000). Detection and Identification of Mycobacteria by Amplification of the Internal Transcribed Spacer Regions with Genus- and Species-Specific PCR Primers. J. Clin. Microbiol. 38: 4080-4085 [Abstract] [Full Text]
Roth, A., Reischl, U., Schönfeld, N., Naumann, L., Emler, S., Fischer, M., Mauch, H., Loddenkemper, R., Kroppenstedt, R. M. (2000). Mycobacterium heckeshornense sp. nov., a New Pathogenic Slowly Growing Mycobacterium sp. Causing Cavitary Lung Disease in an Immunocompetent Patient. J. Clin. Microbiol. 38: 4102-4107 [Abstract] [Full Text]
KOUKILA-KAHKOLA, P., PAULIN, L., BRANDER, E., JANTZEN, E., EHO-REMES, M., KATILA, M.-L. (2000). Characterisation of a new isolate of Mycobacterium shimoidei from Finland. J Med Microbiol 49: 937-940 [Abstract] [Full Text]
Morgenegg, S., Dutly, F., Altwegg, M. (2000). Cloning and Sequencing of a Part of the Heat Shock Protein 65 Gene (hsp65) of "Tropheryma whippelii" and Its Use for Detection of "T. whippelii" in Clinical Specimens by PCR. J. Clin. Microbiol. 38: 2248-2253 [Abstract] [Full Text]
Roth, A., Reischl, U., Streubel, A., Naumann, L., Kroppenstedt, R. M., Habicht, M., Fischer, M., Mauch, H. (2000). Novel Diagnostic Algorithm for Identification of Mycobacteria Using Genus-Specific Amplification of the 16S-23S rRNA Gene Spacer and Restriction Endonucleases. J. Clin. Microbiol. 38: 1094-1104 [Abstract] [Full Text]
Niemann, S., Richter, E., Rüsch-Gerdes, S. (2000). Differentiation among Members of the Mycobacterium tuberculosis Complex by Molecular and Biochemical Features: Evidence for Two Pyrazinamide-Susceptible Subtypes of M. bovis. J. Clin. Microbiol. 38: 152-157 [Abstract] [Full Text]
Kasai, H., Ezaki, T., Harayama, S. (2000). Differentiation of Phylogenetically Related Slowly Growing Mycobacteria by Their gyrB Sequences. J. Clin. Microbiol. 38: 301-308 [Abstract] [Full Text]
Kim, B.-J., Lee, S.-H., Lyu, M.-A., Kim, S.-J., Bai, G.-H., Kim, S.-J., 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 [Abstract] [Full Text]
Chun, J., Huq, A., Colwell, R. R. (1999). Analysis of 16S-23S rRNA Intergenic Spacer Regions of Vibrio cholerae and Vibrio mimicus. Appl. Environ. Microbiol. 65: 2202-2208 [Abstract] [Full Text]
Richter, E., Niemann, S., Rüsch-Gerdes, S., Hoffner, S. (1999). Identification of Mycobacterium kansasii by Using a DNA Probe (AccuProbe) and Molecular Techniques. J. Clin. Microbiol. 37: 964-970 [Abstract] [Full Text]
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 [Abstract] [Full Text]

Antimicrob. Agents Chemother.	Clin. Microbiol. Rev.

Clin. Vaccine Immunol.	ALL ASM JOURNALS