Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB
- 1 May 2011
- journal article
- research article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 49 (5), 1799-1809
- https://doi.org/10.1128/jcm.02350-10
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.This publication has 36 references indexed in Scilit:
- Complete Genome Sequence of Staphylococcus lugdunensis Strain HKU09-01Journal of Bacteriology, 2010
- First Report of Gordonibacter pamelaeae BacteremiaJournal of Clinical Microbiology, 2010
- Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteriaJournal of Medical Microbiology, 2009
- The Complete Genome and Proteome of Laribacter hongkongensis Reveal Potential Mechanisms for Adaptations to Different Temperatures and HabitatsPLoS Genetics, 2009
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysisNucleic Acids Research, 2008
- Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratoriesClinical Microbiology & Infection, 2008
- GenBankNucleic Acids Research, 2007
- Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical LaboratoryJournal of Clinical Microbiology, 2006
- In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteriaJournal of Clinical Pathology, 2006
- Bacteremia Caused by Solobacterium moorei in a Patient with Acute Proctitis and Carcinoma of the CervixJournal of Clinical Microbiology, 2006