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Article: In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria

TitleIn silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria
Authors
Issue Date2011
PublisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org
Citation
Journal Of Medical Microbiology, 2011, v. 60 n. 9, p. 1281-1286 How to Cite?
Abstract
This study provides guidelines on the usefulness of full and 527 bp 16S rRNA gene sequencing and Microseq databases for identifying medically important aerobic Gram-negative bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 26.1% and 32.6%, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15.2% and 26.1%, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level. Among the major groups of aerobic Gram-negative bacteria, the methods and databases are least useful for identification of Aeromonas, Bordetella and Bartonella species. None of the Aeromonas species can be confidently or doubtfully identified, whereas only 0% and 0-33.3% of Bordetella species and 0-10% and 0-10% of Bartonella species can be confidently and doubtfully identified, respectively. On the other hand, these methods and databases are most useful for identification of members of the families Pasteurellaceae and Legionellaceae and Campylobacter species: 29.6-59.3% and 7.4-18.5% of members of Pasteurellaceae, 36-52% and 12-24% of members of Legionellaceae, and 26.7-60% and 0-13.3% of Campylobacter species can be confidently and doubtfully identified, respectively. Thirty-nine medically important aerobic Gram-negative bacteria that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. Twenty-three medically important aerobic Gram-negative bacteria that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. Compared with results of our previous studies on anaerobic and Gram-positive bacteria, full and 527 bp 16S rRNA gene sequencing are able to confidently identify significantly more anaerobic Gram-positive and Gramnegative bacteria than aerobic Gram-positive and Gram-negative bacteria. © 2011 SGM.
Persistent Identifierhttp://hdl.handle.net/10722/139519
ISSN
2013 Impact Factor: 2.266
2013 SCImago Journal Rankings: 1.025
ISI Accession Number ID
Funding AgencyGrant Number
HKSAR Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau
University of Hong Kong
Committee of Research and Conference Grants
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, Committee of Research and Conference Grants and University Development Fund, The University of Hong Kong.

References

 

Author Affiliations
  1. The University of Hong Kong
DC FieldValueLanguage
dc.contributor.authorTeng, JLLen_HK
dc.contributor.authorYeung, MYen_HK
dc.contributor.authorYue, Gen_HK
dc.contributor.authorAuYeung, RKHen_HK
dc.contributor.authorYeung, EYHen_HK
dc.contributor.authorFung, AMYen_HK
dc.contributor.authorTse, Hen_HK
dc.contributor.authorYuen, KYen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorWoo, PCYen_HK
dc.date.accessioned2011-09-23T05:51:02Z-
dc.date.available2011-09-23T05:51:02Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of Medical Microbiology, 2011, v. 60 n. 9, p. 1281-1286en_HK
dc.identifier.issn0022-2615en_HK
dc.identifier.urihttp://hdl.handle.net/10722/139519-
dc.description.abstractThis study provides guidelines on the usefulness of full and 527 bp 16S rRNA gene sequencing and Microseq databases for identifying medically important aerobic Gram-negative bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 26.1% and 32.6%, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15.2% and 26.1%, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level. Among the major groups of aerobic Gram-negative bacteria, the methods and databases are least useful for identification of Aeromonas, Bordetella and Bartonella species. None of the Aeromonas species can be confidently or doubtfully identified, whereas only 0% and 0-33.3% of Bordetella species and 0-10% and 0-10% of Bartonella species can be confidently and doubtfully identified, respectively. On the other hand, these methods and databases are most useful for identification of members of the families Pasteurellaceae and Legionellaceae and Campylobacter species: 29.6-59.3% and 7.4-18.5% of members of Pasteurellaceae, 36-52% and 12-24% of members of Legionellaceae, and 26.7-60% and 0-13.3% of Campylobacter species can be confidently and doubtfully identified, respectively. Thirty-nine medically important aerobic Gram-negative bacteria that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. Twenty-three medically important aerobic Gram-negative bacteria that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. Compared with results of our previous studies on anaerobic and Gram-positive bacteria, full and 527 bp 16S rRNA gene sequencing are able to confidently identify significantly more anaerobic Gram-positive and Gramnegative bacteria than aerobic Gram-positive and Gram-negative bacteria. © 2011 SGM.en_HK
dc.languageengen_US
dc.publisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.orgen_HK
dc.relation.ispartofJournal of Medical Microbiologyen_HK
dc.rightsJournal of Medical Microbiology. Copyright © Society for General Microbiology.-
dc.subject.meshBacteria, Aerobic - classification - genetics - isolation and purification-
dc.subject.meshBacteriological Techniques - methods-
dc.subject.meshComputational Biology - methods-
dc.subject.meshGram-Negative Bacteria - classification - genetics - isolation and purification-
dc.subject.meshGram-Negative Bacterial Infections - diagnosis - microbiology-
dc.titleIn silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteriaen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0022-2615&volume=60&issue=9&spage=1281&epage=1286&date=2011&atitle=In+silico+analysis+of+16S+rRNA+gene+sequencing+based+methods+for+identification+of+medically+important+aerobic+Gram-negative+bacteria-
dc.identifier.emailTeng, JLL:llteng@hku.hken_HK
dc.identifier.emailTse, H:herman@graduate.hku.hken_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.authorityTeng, JLL=rp00277en_HK
dc.identifier.authorityTse, H=rp00519en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1099/jmm.0.027805-0en_HK
dc.identifier.pmid21498652en_HK
dc.identifier.scopuseid_2-s2.0-80051768006en_HK
dc.identifier.hkuros195238en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-80051768006&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume60en_HK
dc.identifier.issue9en_HK
dc.identifier.spage1281en_HK
dc.identifier.epage1286en_HK
dc.identifier.isiWOS:000295018700008-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridTeng, JLL=7202560229en_HK
dc.identifier.scopusauthoridYeung, MY=16029841800en_HK
dc.identifier.scopusauthoridYue, G=53868384600en_HK
dc.identifier.scopusauthoridAuYeung, RKH=22833521900en_HK
dc.identifier.scopusauthoridYeung, EYH=53868613200en_HK
dc.identifier.scopusauthoridFung, AMY=7101926801en_HK
dc.identifier.scopusauthoridTse, H=7006070596en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK

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