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Article: Usefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles

TitleUsefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles
Authors
Issue Date2003
PublisherAmerican Society for Microbiology.
Citation
Journal Of Clinical Microbiology, 2003, v. 41 n. 5, p. 1996-2001 How to Cite?
AbstractDue to the inadequate automation in the amplification and sequencing procedures, the use of 16S rRNA gene sequence-based methods in clinical microbiology laboratories is largely limited to identification of strains that are difficult to identify by phenotypic methods. In this study, using conventional full-sequence 16S rRNA gene sequencing as the "gold standard," we evaluated the usefulness of the MicroSeq 500 16S ribosomal DNA (rDNA)-based bacterial identification system, which involves amplification and sequencing of the first 527-bp fragment of the 16S rRNA genes of bacterial strains and analysis of the sequences using the database of the system, for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. Among 37 clinically significant bacterial strains that showed ambiguous biochemical profiles, representing 37 nonduplicating aerobic gram-positive and gram-negative, anaerobic, and Mycobacterium species, the MicroSeq 500 16S rDNA-based bacterial identification system was successful in identifying 30 (81.1%) of them. Five (13.5%) isolates were misidentified at the genus level (Granulicatella adiacens was misidentified as Abiotrophia defectiva, Helcococcus kunzii was misidentified as Clostridium hastiforme, Olsenella uli was misidentified as Atopobium rimae, Leptotrichia buccalis was misidentified as Fusobacterium mortiferum, and Bergeyella zoohelcum was misidentified as Rimerella anatipestifer), and two (5.4%) were misidentified at the species level (Actinomyces odontolyticus was misidentified as Actinomyces meyeri and Arcobacter cryaerophilus was misidentified as Arcobacter butzleri). When the same 527-bp DNA sequences of these seven isolates were compared to the known 16S rRNA gene sequences in the GenBank, five yielded the correct identity, with good discrimination between the best and second best match sequences, meaning that the reason for misidentification in these five isolates was due to a lack of the 16S rRNA gene sequences of these bacteria in the database of the MicroSeq 500 16S rDNA-based bacterial identification system. In conclusion, the MicroSeq 500 16S rDNA-based bacterial identification system is useful for identification of most clinically important bacterial strains with ambiguous biochemical profiles, but the database of the MicroSeq 500 16S rDNA-based bacterial identification system has to be expanded in order to encompass the rarely encountered bacterial species and achieve better accuracy in bacterial identification.
Persistent Identifierhttp://hdl.handle.net/10722/49230
ISSN
2015 Impact Factor: 3.631
2015 SCImago Journal Rankings: 2.151
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorNg, KHLen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYip, KTen_HK
dc.contributor.authorFung, AMYen_HK
dc.contributor.authorLeung, KWen_HK
dc.contributor.authorTam, DMWen_HK
dc.contributor.authorQue, TLen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2008-06-12T06:37:12Z-
dc.date.available2008-06-12T06:37:12Z-
dc.date.issued2003en_HK
dc.identifier.citationJournal Of Clinical Microbiology, 2003, v. 41 n. 5, p. 1996-2001en_HK
dc.identifier.issn0095-1137en_HK
dc.identifier.urihttp://hdl.handle.net/10722/49230-
dc.description.abstractDue to the inadequate automation in the amplification and sequencing procedures, the use of 16S rRNA gene sequence-based methods in clinical microbiology laboratories is largely limited to identification of strains that are difficult to identify by phenotypic methods. In this study, using conventional full-sequence 16S rRNA gene sequencing as the "gold standard," we evaluated the usefulness of the MicroSeq 500 16S ribosomal DNA (rDNA)-based bacterial identification system, which involves amplification and sequencing of the first 527-bp fragment of the 16S rRNA genes of bacterial strains and analysis of the sequences using the database of the system, for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. Among 37 clinically significant bacterial strains that showed ambiguous biochemical profiles, representing 37 nonduplicating aerobic gram-positive and gram-negative, anaerobic, and Mycobacterium species, the MicroSeq 500 16S rDNA-based bacterial identification system was successful in identifying 30 (81.1%) of them. Five (13.5%) isolates were misidentified at the genus level (Granulicatella adiacens was misidentified as Abiotrophia defectiva, Helcococcus kunzii was misidentified as Clostridium hastiforme, Olsenella uli was misidentified as Atopobium rimae, Leptotrichia buccalis was misidentified as Fusobacterium mortiferum, and Bergeyella zoohelcum was misidentified as Rimerella anatipestifer), and two (5.4%) were misidentified at the species level (Actinomyces odontolyticus was misidentified as Actinomyces meyeri and Arcobacter cryaerophilus was misidentified as Arcobacter butzleri). When the same 527-bp DNA sequences of these seven isolates were compared to the known 16S rRNA gene sequences in the GenBank, five yielded the correct identity, with good discrimination between the best and second best match sequences, meaning that the reason for misidentification in these five isolates was due to a lack of the 16S rRNA gene sequences of these bacteria in the database of the MicroSeq 500 16S rDNA-based bacterial identification system. In conclusion, the MicroSeq 500 16S rDNA-based bacterial identification system is useful for identification of most clinically important bacterial strains with ambiguous biochemical profiles, but the database of the MicroSeq 500 16S rDNA-based bacterial identification system has to be expanded in order to encompass the rarely encountered bacterial species and achieve better accuracy in bacterial identification.en_HK
dc.format.extent386 bytes-
dc.format.mimetypetext/html-
dc.languageengen_HK
dc.publisherAmerican Society for Microbiology.en_HK
dc.relation.ispartofJournal of Clinical Microbiologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsJournal of Clinical Microbiology. Copyright © American Society for Microbiology.en_HK
dc.rightsCopyright © American Society for Microbiology, Journal of Clinical Microbiology, 2003, v. 41 n. 5, p. 1996-2001en_HK
dc.subject.meshBacteria - classification - genetics - isolation & purification - metabolismen_HK
dc.subject.meshDNA, Bacterial - geneticsen_HK
dc.subject.meshDNA, Ribosomal - geneticsen_HK
dc.subject.meshBacterial Typing Techniquesen_HK
dc.subject.meshBase Sequenceen_HK
dc.titleUsefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profilesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0095-1137&volume=41&issue=5&spage=1996&epage=2001&date=2003&atitle=Usefulness+of+the+MicroSeq+500+16S+ribosomal+DNA-based+bacterial+identification+system+for+identification+of+clinically+significant+bacterial+isolates+with+ambiguous+biochemical+profilesen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.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.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1128/JCM.41.5.1996-2001.2003en_HK
dc.identifier.pmid12734240-
dc.identifier.pmcidPMC154750en_HK
dc.identifier.scopuseid_2-s2.0-0037952695en_HK
dc.identifier.hkuros80119-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0037952695&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume41en_HK
dc.identifier.issue5en_HK
dc.identifier.spage1996en_HK
dc.identifier.epage2001en_HK
dc.identifier.isiWOS:000182934500031-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridNg, KHL=27467782600en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYip, KT=7101909925en_HK
dc.identifier.scopusauthoridFung, AMY=7101926801en_HK
dc.identifier.scopusauthoridLeung, KW=7401860831en_HK
dc.identifier.scopusauthoridTam, DMW=7006053712en_HK
dc.identifier.scopusauthoridQue, TL=7003786628en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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