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Article: Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB

TitleAutomated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB
Authors
Issue Date2011
PublisherAmerican Society for Microbiology.
Citation
Journal Of Clinical Microbiology, 2011, v. 49 n. 5, p. 1799-1809 How to Cite?
AbstractDespite 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. Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Persistent Identifierhttp://hdl.handle.net/10722/135263
ISSN
2015 Impact Factor: 3.631
2015 SCImago Journal Rankings: 2.151
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
HKSAR
Research Grants Council
University of Hong Kong
Funding Information:

This work is partly supported by the HKSAR Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau, Research Grants Council Grant, and University Development Fund, The University of Hong Kong.

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorTeng, JLLen_HK
dc.contributor.authorYeung, JMYen_HK
dc.contributor.authorTse, Hen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2011-07-27T01:30:52Z-
dc.date.available2011-07-27T01:30:52Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of Clinical Microbiology, 2011, v. 49 n. 5, p. 1799-1809en_HK
dc.identifier.issn0095-1137en_HK
dc.identifier.urihttp://hdl.handle.net/10722/135263-
dc.description.abstractDespite 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. Copyright © 2011, American Society for Microbiology. All Rights Reserved.en_HK
dc.languageengen_US
dc.publisherAmerican Society for Microbiology.-
dc.relation.ispartofJournal of Clinical Microbiologyen_HK
dc.rightsJournal of Clinical Microbiology. Copyright © American Society for Microbiology.-
dc.rightsCopyright © American Society for Microbiology, [Journal of Clinical Microbiology, volume 49, p. 1799-1809, 2011]-
dc.subject.meshBacteria - classification - genetics-
dc.subject.meshBacterial Infections - diagnosis - microbiology-
dc.subject.meshDNA, Bacterial - chemistry - genetics-
dc.subject.meshDNA, Ribosomal - chemistry - genetics-
dc.subject.meshDatabases, Nucleic Acid-
dc.titleAutomated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDBen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0095-1137&volume=49&issue=5&spage=1799&epage=1809&date=2011&atitle=Automated+identification+of+medically+important+bacteria+by+16S+rRNA+gene+sequencing+using+a+novel+comprehensive+database,+16SpathDB-
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailTeng, JLL:llteng@hku.hken_HK
dc.identifier.emailTse, H:herman@graduate.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.identifier.authorityTeng, JLL=rp00277en_HK
dc.identifier.authorityTse, H=rp00519en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1128/JCM.02350-10en_HK
dc.identifier.pmid21389154-
dc.identifier.pmcidPMC3122693-
dc.identifier.scopuseid_2-s2.0-79955546432en_HK
dc.identifier.hkuros187237en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79955546432&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume49en_HK
dc.identifier.issue5en_HK
dc.identifier.spage1799en_HK
dc.identifier.epage1809en_HK
dc.identifier.isiWOS:000289941000016-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridTeng, JLL=7202560229en_HK
dc.identifier.scopusauthoridYeung, JMY=55186190400en_HK
dc.identifier.scopusauthoridTse, H=7006070596en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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