ArticleJournal of clinical microbiology2011
Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB.
Article in Journal of clinical microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Detection of Microorganisms in Body Fluid Samples.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Pathogenic Role ofAntibiotics (Basel, Switzerland) · 2020Review
- Species-Level Analysis of Human Gut Microbiota With Metataxonomics.Frontiers in microbiology · 2020Article
- Parvimonas micra bacteremia in a patient with colonic carcinoma.Caspian journal of internal medicine · 2019Article
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- Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide.Computational and structural biotechnology journal · 2018Review
- First report of Sneathia sanguinegens together with Mycoplasma hominis in postpartum prosthetic valve infective endocarditis: a case report.BMC infectious diseases · 2017Article
- Rising Strengths Hong Kong SAR in Bioinformatics.Interdisciplinary sciences, computational life sciences · 2017Review
- Metataxonomics reveal vultures as a reservoir for Clostridium perfringens.Emerging microbes & infections · 2017Article
- Bacteraemia due to Parvimonas micra, a commensal pathogen, in a patient with an oesophageal tumour.BMJ case reports · 2016Article
- Article
- Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.PloS one · 2015Article
- Clinical microbiology informatics.Clinical microbiology reviews · 2014Review
- GyrB polymorphisms accurately assign invasive viridans group streptococcal species.Journal of clinical microbiology · 2014Article
- Actinomyces urogenitalis bacteremia and tubo-ovarian abscess after an in vitro fertilization (IVF) procedure.Journal of clinical microbiology · 2013Article
- Romance of the three domains: how cladistics transformed the classification of cellular organisms.Protein & cell · 2013Review
- Direct bacterial identification in positive blood cultures by use of two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems.Journal of clinical microbiology · 2013Article
- Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssGeneFinder Webserver and its application to Salmonella enterica serovar Typhi.Journal of clinical microbiology · 2012Article
- Extraction of bacterial RNA from soil: challenges and solutions.Microbes and environments · 2012Review
- Molecular characterization of a catalase-negative Staphylococcus aureus subsp. aureus Strain collected from a patient with mitral valve endocarditis and pericarditis revealed a novel nonsense mutation in the katA gene.Journal of clinical microbiology · 2011Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the "best match in 16SpathDB." For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories.
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