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Article: Then and now: Use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

TitleThen and now: Use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories
Authors
Keywords16S rDNA gene
Bacteria
Discovery
Identification
Review
Sequencing
Issue Date2008
PublisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/CLM
Citation
Clinical Microbiology And Infection, 2008, v. 14 n. 10, p. 908-934 How to Cite?
AbstractIn the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7.years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However, studies on the accuracy of the software packages have given highly varied results, and interpretation of results remains difficult for most technicians, and even for clinical microbiologists. To fully utilize 16S rDNA sequencing in clinical microbiology, better guidelines are needed for interpretation of the identification results, and additional/supplementary methods are necessary for bacterial species that cannot be identified confidently by 16S rDNA sequencing alone. © 2008 The Authors Journal compilation © 2008 European Society of Clinical Microbiology and Infectious Diseases.
Persistent Identifierhttp://hdl.handle.net/10722/59423
ISSN
2015 Impact Factor: 4.575
2015 SCImago Journal Rankings: 2.530
ISI Accession Number ID
Funding AgencyGrant Number
Research Grant Council
University Development Fund
Outstanding Young Researcher Award
HKU Special Research Achievement Award
The Croucher Senior Medical Research
The University of Hong Kong
Funding Information:

This work was partly supported by the Research Grant Council Grant, University Development Fund, Outstanding Young Researcher Award, HKU Special Research Achievement Award and The Croucher Senior Medical Research Fellowship, The University of Hong Kong. The authors declare no competing interests.

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorTeng, JLLen_HK
dc.contributor.authorTse, Hen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2010-05-31T03:49:47Z-
dc.date.available2010-05-31T03:49:47Z-
dc.date.issued2008en_HK
dc.identifier.citationClinical Microbiology And Infection, 2008, v. 14 n. 10, p. 908-934en_HK
dc.identifier.issn1198-743Xen_HK
dc.identifier.urihttp://hdl.handle.net/10722/59423-
dc.description.abstractIn the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7.years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However, studies on the accuracy of the software packages have given highly varied results, and interpretation of results remains difficult for most technicians, and even for clinical microbiologists. To fully utilize 16S rDNA sequencing in clinical microbiology, better guidelines are needed for interpretation of the identification results, and additional/supplementary methods are necessary for bacterial species that cannot be identified confidently by 16S rDNA sequencing alone. © 2008 The Authors Journal compilation © 2008 European Society of Clinical Microbiology and Infectious Diseases.en_HK
dc.languageengen_HK
dc.publisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/CLMen_HK
dc.relation.ispartofClinical Microbiology and Infectionen_HK
dc.rightsClinical Microbiology and Infection. Copyright © Blackwell Publishing Ltd.en_HK
dc.subject16S rDNA geneen_HK
dc.subjectBacteriaen_HK
dc.subjectDiscoveryen_HK
dc.subjectIdentificationen_HK
dc.subjectReviewen_HK
dc.subjectSequencingen_HK
dc.subject.meshBacteria - classification - genetics - isolation & purificationen_HK
dc.subject.meshBacterial Infections - microbiologyen_HK
dc.subject.meshBacteriological Techniquesen_HK
dc.subject.meshDNA, Bacterial - chemistry - geneticsen_HK
dc.subject.meshDNA, Ribosomal - chemistry - geneticsen_HK
dc.subject.meshGenes, rRNAen_HK
dc.subject.meshHumansen_HK
dc.subject.meshRNA, Bacterial - geneticsen_HK
dc.subject.meshRNA, Ribosomal, 16S - geneticsen_HK
dc.subject.meshSequence Analysis, DNA - standardsen_HK
dc.titleThen and now: Use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratoriesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1198-743X&volume=14&spage=908&epage=34&date=2008&atitle=Then+and+now:+use+of+16S+rDNA+gene+sequencing+for+bacterial+identification+and+discovery+of+novel+bacteria+in+clinical+microbiology+laboratoriesen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailTeng, JLL:llteng@hku.hken_HK
dc.identifier.emailTse, H:hftse@hkucc.hku.hken_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityTeng, JLL=rp00277en_HK
dc.identifier.authorityTse, H=rp00428en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1111/j.1469-0691.2008.02070.xen_HK
dc.identifier.pmid18828852-
dc.identifier.scopuseid_2-s2.0-52449129099en_HK
dc.identifier.hkuros160604en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-52449129099&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume14en_HK
dc.identifier.issue10en_HK
dc.identifier.spage908en_HK
dc.identifier.epage934en_HK
dc.identifier.isiWOS:000259236200004-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridTeng, JLL=7202560229en_HK
dc.identifier.scopusauthoridTse, H=7006070805en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.citeulike3305684-

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