ArticleBMC infectious diseases2003
RIDOM: comprehensive and public sequence database for identification of Mycobacterium species.
Article in BMC infectious diseases, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
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- Mycobacteriosis in slaughter pigs from South Africa from 1991 to 2002:Frontiers in microbiology · 2023Article
- Mechanism underlying painful radiculopathy in patients with lumbar disc herniation.European journal of pain (London, England) · 2022Article
- Genetic diversity of oral streptococci in the guinea pig as assessed by sequence analysis of the 16S rRNA and groEL genes.Folia microbiologica · 2022Article
- Laboratory Diagnosis of 37 Cases ofJournal of clinical microbiology · 2021Article
- Applicability of using 15 MIRU-VNTR loci for genotyping of Mycobacterium avium subsp. paratuberculosis from two cattle farms in Egypt.Molecular biology reports · 2019Article
- Efficacy of MALDI-TOF mass spectrometry as well as genotypic and phenotypic methods in identification of staphylococci other thanJournal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2019Article
- A New Single Gene Differential Biomarker forFrontiers in microbiology · 2019Article
- Non-tuberculous Mycobacterium species causing mycobacteriosis in farmed aquatic animals of South Africa.BMC microbiology · 2018Article
- Improved performance of the artus Mycobacterium tuberculosis RG PCR kit in a low incidence setting: a retrospective monocentric study.Scientific reports · 2017Article
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- Dynamics of mono- and dual-species biofilm formation and interactions between Staphylococcus aureus and Gram-negative bacteria.Microbial biotechnology · 2017Article
- Non-tuberculous Mycobacteria in South African Wildlife: Neglected Pathogens and Potential Impediments for Bovine Tuberculosis Diagnosis.Frontiers in cellular and infection microbiology · 2017Article
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- Complicated sea urchin-induced wound infection caused byJMM case reports · 2016Article
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- Avian Mycobacteriosis: Still Existing Threat to Humans.BioMed research international · 2016Review
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMolecular 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.
methodsIn 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.
resultsUsing 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.
conclusionsThe 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.
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