RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species

<p>Abstract</p> <p>Background</p> <p>Molecular identification of <it>Mycobacterium </it>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...

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Main Authors: Albert Jürgen, Sammeth Michael, Rothgänger Jörg, Niemann Stefan, Roth Andreas, Dostal Stefan, Harmsen Dag, Frosch Matthias, Richter Elvira
Format: Article
Language:English
Published: BMC 2003-11-01
Series:BMC Infectious Diseases
Online Access:http://www.biomedcentral.com/1471-2334/3/26
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spelling doaj-f2377d8e7ada408ca5e5d17b7df737c52020-11-25T03:13:34ZengBMCBMC Infectious Diseases1471-23342003-11-01312610.1186/1471-2334-3-26RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>speciesAlbert JürgenSammeth MichaelRothgänger JörgNiemann StefanRoth AndreasDostal StefanHarmsen DagFrosch MatthiasRichter Elvira<p>Abstract</p> <p>Background</p> <p>Molecular identification of <it>Mycobacterium </it>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.</p> <p>Methods</p> <p>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 (<it>Escherichia coli </it>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.</p> <p>Results</p> <p>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 <it>Mycobacterium tuberculosis </it>complex species, <it>M. marinum </it>/ <it>M. ulcerans </it>and the <it>M. avium </it>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.</p> <p>Conclusions</p> <p>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 <url>http://www.ridom-rdna.de</url>), for similarity searches.</p> http://www.biomedcentral.com/1471-2334/3/26
collection DOAJ
language English
format Article
sources DOAJ
author Albert Jürgen
Sammeth Michael
Rothgänger Jörg
Niemann Stefan
Roth Andreas
Dostal Stefan
Harmsen Dag
Frosch Matthias
Richter Elvira
spellingShingle Albert Jürgen
Sammeth Michael
Rothgänger Jörg
Niemann Stefan
Roth Andreas
Dostal Stefan
Harmsen Dag
Frosch Matthias
Richter Elvira
RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
BMC Infectious Diseases
author_facet Albert Jürgen
Sammeth Michael
Rothgänger Jörg
Niemann Stefan
Roth Andreas
Dostal Stefan
Harmsen Dag
Frosch Matthias
Richter Elvira
author_sort Albert Jürgen
title RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
title_short RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
title_full RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
title_fullStr RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
title_full_unstemmed RIDOM: Comprehensive and public sequence database for identification of <it>Mycobacterium </it>species
title_sort ridom: comprehensive and public sequence database for identification of <it>mycobacterium </it>species
publisher BMC
series BMC Infectious Diseases
issn 1471-2334
publishDate 2003-11-01
description <p>Abstract</p> <p>Background</p> <p>Molecular identification of <it>Mycobacterium </it>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.</p> <p>Methods</p> <p>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 (<it>Escherichia coli </it>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.</p> <p>Results</p> <p>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 <it>Mycobacterium tuberculosis </it>complex species, <it>M. marinum </it>/ <it>M. ulcerans </it>and the <it>M. avium </it>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.</p> <p>Conclusions</p> <p>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 <url>http://www.ridom-rdna.de</url>), for similarity searches.</p>
url http://www.biomedcentral.com/1471-2334/3/26
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