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BMC Infectious Diseases
Published in: BMC Infectious Diseases 1/2003

Open Access 01-12-2003 | Research article

RIDOM: Comprehensive and public sequence database for identification of Mycobacteriumspecies

Authors: Dag Harmsen, Stefan Dostal, Andreas Roth, Stefan Niemann, Jörg Rothgänger, Michael Sammeth, Jürgen Albert, Matthias Frosch, Elvira Richter

Published in: BMC Infectious Diseases | Issue 1/2003

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Abstract

Background

Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases.

Methods

In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined.

Results

Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum / M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD ± 0.57) were present.

Conclusions

The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project http://​www.​ridom-rdna.​de), for similarity searches.
Appendix
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Literature
1.
Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH: Manual of clinical microbiology. Edited by: MurrayPR, BaronEJ, PfallerMA, TenoverFC and YolkenRH. 1999, Washinghton, D.C., American Society for Microbiology, 7
2.
Butler WR, Jost K.C.,Jr, Kilburn JO: Identification of mycobacteria by high-performance liquid chromatography. J Clin Microbiol. 1991, 29: 2468-2472.PubMedPubMedCentral
3.
Luquin M, Ausina V, Lopez Calahorra F, Belda F, Garcia Barcelo M., Celma C, Prats G: Evaluation of practical chromatographic procedures for identification of clinical isolates of mycobacteria. J Clin Microbiol. 1991, 29: 120-130.PubMedPubMedCentral
4.
Persing DH, Smith TF, Tenover FC, White TJ: Diagnostic molecular microbiology: principles and applications. Edited by: PersingDH, SmithTF, TenoverFC and WhiteTJ. 1993, Washington, D.C., American Society for Microbiology
5.
Springer B, Stockman L, Teschner K, Roberts GD, Böttger EC: Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol. 1996, 34: 296-303.PubMedPubMedCentral
6.
Patel JB, Leonard DG, Pan X, Musser JM, Berman RE, Nachamkin I: Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. J Clin Microbiol. 2000, 38: 246-251.PubMedPubMedCentral
7.
Kirschner P, Springer B, Vogel U, Meier A, Wrede A, Kiekenbeck M, Bange FC, Böttger EC: Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol. 1993, 31: 2882-2889.PubMedPubMedCentral
8.
Stahl DA, Urbance JW: The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol. 1990, 172: 116-124.PubMedPubMedCentral
9.
Rogall T, Wolters J, Flohr T, Böttger EC: Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol. 1990, 40: 323-330.CrossRefPubMed
10.
Pitulle C, Dorsch M, Kazda J, Wolters J, Stackebrandt E: Phylogeny of rapidly growing members of the genus Mycobacterium. Int J Syst Bacteriol. 1992, 42: 337-343.CrossRefPubMed
11.
Roth A, Reischl U, Streubel A, Naumann L, Kroppenstedt RM, Habicht M, Fischer M, Mauch H: Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S-23S rRNA gene spacer and restriction endonucleases. J Clin Microbiol. 2000, 38: 1094-1104.PubMedPubMedCentral
12.
Telenti A, Marchesi F, Balz M, Bally F, Böttger EC, Bodmer T: Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol. 1993, 31: 175-178.PubMedPubMedCentral
13.
Devallois A, Goh KS, Rastogi N: 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. 1997, 35: 2969-2973.PubMedPubMedCentral
14.
Ringuet H, Akoua-Koffi C, Honore S, Varnerot A, Vincent V, Berche P, Gaillard JL, Pierre-Audigier C: hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol. 1999, 37: 852-857.PubMedPubMedCentral
15.
16.
Harmsen D, Heesemann J, Brabletz T, Kirchner T, Müller-Hermelink HK: Heterogeneity among Whipple's-disease-associated bacteria. Lancet. 1994, 343: 1288.-10.1016/S0140-6736(94)92176-8.CrossRefPubMed
17.
Holberg-Petersen M, Steinbakk M, Figenschau KJ, Jantzen E, Eng J, Melby KK: Identification of clinical isolates of Mycobacterium spp. by sequence analysis of the 16S ribosomal RNA gene. Experience from a clinical laboratory. APMIS. 1999, 107: 231-239.CrossRefPubMed
18.
Maidak BL, Cole JR, Lilburn TG, Parker C.T.,Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM: The RDP-II (ribosomal database project). Nucleic Acids Res. 2001, 29: 173-174. 10.1093/nar/29.1.173.CrossRefPubMedPubMedCentral
19.
20.
Harmsen D, Rothgänger J, Singer C, Albert J, Frosch M: Intuitive hypertext-based molecular identification of micro-organisms. Lancet. 1999, 353: 291.-10.1016/S0140-6736(98)05748-1.CrossRefPubMed
21.
Harmsen D, Singer C, Rothgänger J, Tønjum T, de Hoog GS, Shah H, Albert J, Frosch M: Diagnostics of Neisseriaceae and Moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms. J Clin Microbiol. 2001, 39: 936-942. 10.1128/JCM.39.3.936-942.2001.CrossRefPubMedPubMedCentral
22.
Harmsen D, Rothgänger J, Frosch M, Albert J: RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Res. 2002, 30: 416-417. 10.1093/nar/30.1.416.CrossRefPubMedPubMedCentral
23.
van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Giquel B, Hermans P, Martin C, McAdam R, Shinnick TM, Small PM: Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol. 1993, 31: 406-409.PubMedPubMedCentral
24.
Lane DJ: 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. Edited by: StackebrandtE and GoodfellowM. 1991, Chichester, United Kingdom, John Wiley & Sons Ltd., 115-175.
25.
Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8: 186-194.CrossRefPubMed
26.
27.
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680.CrossRefPubMedPubMedCentral
28.
Frothingham R, Wilson KH: Sequence-based differentiation of strains in the Mycobacterium avium complex. J Bacteriol. 1993, 175: 2818-2825.PubMedPubMedCentral
29.
Picardeau M, Prod'Hom G, Raskine L, LePennec MP, Vincent V: Genotypic characterization of five subspecies of Mycobacterium kansasii. J Clin Microbiol. 1997, 35: 25-32.PubMedPubMedCentral
30.
Olsen GJ, Woese CR, Overbeek R: The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol. 1994, 176: 1-6.PubMedPubMedCentral
31.
Peterson EM, Lu R, Floyd C, Nakasone A, Friedly G, de la Maza LM: Direct identification of Mycobacterium tuberculosis, Mycobacterium avium, and Mycobacterium intracellulare from amplified primary cultures in BACTEC media using DNA probes. J Clin Microbiol. 1989, 27: 1543-1547.PubMedPubMedCentral
32.
Tortoli E, Nanetti A, Piersimoni C, Cichero P, Farina C, Mucignat G, Scarparo C, Bartolini L, Valentini R, Nista D, Gesu G, Tosi CP, Crovatto M, Brusarosco G: Performance assessment of new multiplex probe assay for identification of mycobacteria. J Clin Microbiol. 2001, 39: 1079-1084. 10.1128/JCM.39.3.1079-1084.2001.CrossRefPubMedPubMedCentral
33.
Turenne CY, Tschetter L, Wolfe J, Kabani A: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J Clin Microbiol. 2001, 39: 3637-3648. 10.1128/JCM.39.10.3638-3648.2001.CrossRefPubMedPubMedCentral
34.
Frothingham R, Wilson KH: Molecular phylogeny of the Mycobacterium avium complex demonstrates clinically meaningful divisions. J Infect Dis. 1994, 169: 305-312.CrossRefPubMed
35.
Böddinghaus B, Wolters J, Heikens W, Böttger EC: Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level. FEMS Microbiol Lett. 1990, 70: 197-203.CrossRef
36.
De Smet KA, Hellyer TJ, Khan AW, Brown IN, Ivanyi J: Genetic and serovar typing of clinical isolates of the Mycobacterium avium-intracellulare complex. Tuber Lung Dis. 1996, 77: 71-76.CrossRefPubMed
37.
De Smet KA, Brown IN, Yates M, Ivanyi J: Ribosomal internal transcribed spacer sequences are identical among Mycobacterium avium-intracellulare complex isolates from AIDS patients, but vary among isolates from elderly pulmonary disease patients. Microbiology. 1995, 141: 2739-2747.CrossRefPubMed
38.
Springer B, Böttger EC, Kirschner P, Wallace RJ: Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacteriummucogenicum sp. nov. Int J Syst Bacteriol. 1995, 45: 262-267.CrossRefPubMed
39.
Kirschner P, Böttger EC: Microheterogeneity within rRNA of Mycobacterium gordonae. J Clin Microbiol. 1992, 30: 1049-1050.PubMedPubMedCentral
40.
Richter E, Niemann S, Rüsch-Gerdes S, Hoffner S: Identification of Mycobacterium kansasii by using a DNA probe (AccuProbe) and molecular techniques. J Clin Microbiol. 1999, 37: 964-970.PubMedPubMedCentral
41.
Alcaide F, Richter I, Bernasconi C, Springer B, Hagenau C, Schulze-Röbbecke R, Tortoli E, Martin R, Böttger EC, Telenti A: Heterogeneity and clonality among isolates of Mycobacterium kansasii: implications for epidemiological and pathogenicity studies. J Clin Microbiol. 1997, 35: 1959-1964.PubMedPubMedCentral
42.
Springer B, Wu W-K, Bodmer T, Haase G, Pfyffer GE, Kroppenstedt RM, Schröder K-H, Emler S, Kilburn JO, Kirschner P, Telenti A, Coyle MB, Böttger EC: Isolation and characterization of a unique group of slowly growing mycobacteria: description of Mycobacterium lentiflavum sp. nov. J Clin Microbiol. 1996, 34: 1100-1107.PubMedPubMedCentral
43.
Roth A, Fischer M, Hamid ME, Michalke S, Ludwig W, Mauch H: Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol. 1998, 36: 139-147.PubMedPubMedCentral
44.
Torkko P, Suutari M, Suomalainen S, Paulin L, Larsson L, Katila ML: Separation among species of Mycobacterium terrae complex by lipid analyses: comparison with biochemical tests and 16S rRNA sequencing. J Clin Microbiol. 1998, 36: 499-505.PubMedPubMedCentral
45.
Portaels F, Fonteyne P-A, de Beenhouwer H, de Rijk P, Guedenon A, Hayman J, Meyers WM: Variability in 3' end of 16S rRNA sequence of Mycobacterium ulcerans is related to geographic origin of isolates. J Clin Microbiol. 1996, 34: 962-965.PubMedPubMedCentral
46.
Kasai H, Ezaki T, Harayama S: Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol. 2000, 38: 301-308.PubMedPubMedCentral
47.
Niemann S, Harmsen D, Rüsch-Gerdes S, Richter E: Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis. J Clin Microbiol. 2000, 38: 3231-3234.PubMedPubMedCentral
48.
Talbot EA, Williams DL, Frothingham R: PCR identification of Mycobacterium bovis BCG. J Clin Microbiol. 1997, 35: 566-569.PubMedPubMedCentral
49.
Stinear T, Ross BC, Davies JK, Marino L, Robins-Browne RM, Oppedisano F, Sievers A, Johnson PD: Identification and characterization of IS2404 and IS2606: two distinct repeated sequences for detection of Mycobacterium ulcerans by PCR. J Clin Microbiol. 1999, 37: 1018-1023.PubMedPubMedCentral
50.
Moss MT, Sanderson JD, Tizard MLV, Hermon-Taylor J, El-Zaatari FAK, Markesich DC, Graham DY: Polymerase chain reaction detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum in long term cultures from Crohn's disease and control tissues. Gut. 1992, 33: 1209-1213.CrossRefPubMedPubMedCentral
51.
52.
Ahrens P, Giese SB, Klausen J, Inglis NF: Two markers, IS901-IS902 and p40, identified by PCR and by using monoclonal antibodies in Mycobacterium avium strains. J Clin Microbiol. 1995, 33: 1049-1053.PubMedPubMedCentral
53.
Niemann S, Richter E, Rüsch-Gerdes S: 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. 2000, 38: 152-157.PubMedPubMedCentral
54.
Cloud JL, Neal H, Rosenberry R, Turenne CY, Jama M, Hillyard DR, Carroll KC: Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol. 2002, 40: 400-406. 10.1128/JCM.40.2.400-406.2002.CrossRefPubMedPubMedCentral
55.
Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE, Persing DH: Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol. 1998, 36: 3674-3679.PubMedPubMedCentral
56.
Stackebrandt E, Goebel BM: Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994, 44: 846-849.CrossRef
57.
Shojaei H, Magee JG, Freeman R, Yates M, Horadagoda NU, Goodfellow M: Mycobacterium elephantis sp. nov., a rapidly growing non-chromogenic Mycobacterium isolated from an elephant. Int J Syst Evol Microbiol. 2000, 50: 1817-1820.CrossRefPubMed
58.
Clayton RA, Sutton G, Hinkle P.S.,Jr, Bult C, Fields C: Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol. 1995, 45: 595-599.CrossRefPubMed
59.
Cook VJ, Turenne CY, Wolfe J, Pauls R, Kabani A: Conventional methods versus 16S ribosomal DNA sequencing for identification of nontuberculous mycobacteria: cost analysis. J Clin Microbiol. 2003, 41: 1010-1015. 10.1128/JCM.41.3.1010-1015.2003.CrossRefPubMedPubMedCentral
60.
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2001, 29: 11-16. 10.1093/nar/29.1.11.CrossRefPubMedPubMedCentral
61.
Roth A, Reischl U, Schonfeld N, Naumann L, Emler S, Fischer M, Mauch H, Loddenkemper R, Kroppenstedt RM: Mycobacterium heckeshornense sp. nov., a new pathogenic slowly growing Mycobacterium sp. causing cavitary lung disease in an immunocompetent patient. J Clin Microbiol. 2000, 38: 4102-4107.PubMedPubMedCentral
62.
Tortoli E, Piersimoni C, Kroppenstedt RM, Montoya-Burgos JI, Reischl U, Giacometti A, Emler S: Mycobacterium doricum sp. nov. Int J Syst Evol Microbiol. 2001, 51: 2007-2012.CrossRefPubMed
63.
Wilson RW, Steingrube VA, Böttger EC, Springer B, Brown-Elliott BA, Vincent V, Jost K.C.,Jr, Zhang Y, Garcia MJ, Chiu SH, Onyi GO, Rossmoore H, Nash DR, Wallace RJ: Mycobacterium immunogenum sp. nov., a novel species related to Mycobacteriumabscessus and associated with clinical disease, pseudo-outbreaks and contaminated metalworking fluids: an international cooperative study on mycobacterial taxonomy. Int J Syst Evol Microbiol. 2001, 51: 1751-1764.CrossRefPubMed
64.
Floyd MM, Gross WM, Bonato DA, Silcox VA, Smithwick RW, Metchock B, Crawford JT, Butler WR: Mycobacterium kubicae sp. nov., a slowly growing, scotochromogenic Mycobacterium. Int J Syst Evol Microbiol. 2000, 50: 1811-1816.CrossRefPubMed
Metadata
Title
RIDOM: Comprehensive and public sequence database for identification of Mycobacteriumspecies
Authors
Dag Harmsen
Stefan Dostal
Andreas Roth
Stefan Niemann
Jörg Rothgänger
Michael Sammeth
Jürgen Albert
Matthias Frosch
Elvira Richter
Publication date
01-12-2003
Publisher
BioMed Central
Published in
BMC Infectious Diseases / Issue 1/2003
Electronic ISSN: 1471-2334
DOI
https://doi.org/10.1186/1471-2334-3-26

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