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Article: In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria
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TitleIn silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria
 
AuthorsTeng, JLL1
Yeung, MY1
Yue, G1
AuYeung, RKH1
Yeung, EYH1
Fung, AMY1
Tse, H1
Yuen, KY1
Lau, SKP1
Woo, PCY1
 
Issue Date2011
 
PublisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org
 
CitationJournal Of Medical Microbiology, 2011, v. 60 n. 9, p. 1281-1286 [How to Cite?]
DOI: http://dx.doi.org/10.1099/jmm.0.027805-0
 
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.
 
ISSN0022-2615
2012 Impact Factor: 2.297
2012 SCImago Journal Rankings: 0.886
 
DOIhttp://dx.doi.org/10.1099/jmm.0.027805-0
 
ISI Accession Number IDWOS:000295018700008
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.

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorTeng, JLL
 
dc.contributor.authorYeung, MY
 
dc.contributor.authorYue, G
 
dc.contributor.authorAuYeung, RKH
 
dc.contributor.authorYeung, EYH
 
dc.contributor.authorFung, AMY
 
dc.contributor.authorTse, H
 
dc.contributor.authorYuen, KY
 
dc.contributor.authorLau, SKP
 
dc.contributor.authorWoo, PCY
 
dc.date.accessioned2011-09-23T05:51:02Z
 
dc.date.available2011-09-23T05:51:02Z
 
dc.date.issued2011
 
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.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationJournal Of Medical Microbiology, 2011, v. 60 n. 9, p. 1281-1286 [How to Cite?]
DOI: http://dx.doi.org/10.1099/jmm.0.027805-0
 
dc.identifier.doihttp://dx.doi.org/10.1099/jmm.0.027805-0
 
dc.identifier.epage1286
 
dc.identifier.hkuros195238
 
dc.identifier.isiWOS:000295018700008
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.

 
dc.identifier.issn0022-2615
2012 Impact Factor: 2.297
2012 SCImago Journal Rankings: 0.886
 
dc.identifier.issue9
 
dc.identifier.openurl
 
dc.identifier.pmid21498652
 
dc.identifier.scopuseid_2-s2.0-80051768006
 
dc.identifier.spage1281
 
dc.identifier.urihttp://hdl.handle.net/10722/139519
 
dc.identifier.volume60
 
dc.languageeng
 
dc.publisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofJournal of Medical Microbiology
 
dc.relation.referencesReferences in Scopus
 
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 bacteria
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong