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Article: Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
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TitleGuidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
 
AuthorsWoo, PCY1
Teng, JLL1
Wu, JKL1
Leung, FPS1
Tse, H1
Fung, AMY1
Lau, SKP1
Yuen, KY1
 
Issue Date2009
 
PublisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org
 
CitationJournal Of Medical Microbiology, 2009, v. 58 n. 8, p. 1030-1036 [How to Cite?]
DOI: http://dx.doi.org/10.1099/jmm.0.008615-0
 
AbstractThis study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40% of medically important Gram-positive cocci (GPC), and 21 and 34% of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34% of medically important GPC and 14 and 25% of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0-2 and 2-13% of staphylococci, and 0 and 0-10% of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36-56 and 11-14% of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included. © 2009 SGM.
 
ISSN0022-2615
2012 Impact Factor: 2.297
2012 SCImago Journal Rankings: 0.886
 
DOIhttp://dx.doi.org/10.1099/jmm.0.008615-0
 
ISI Accession Number IDWOS:000268817900007
Funding AgencyGrant Number
Committee of Research and Conference Grants
University of Hong Kong
Funding Information:

This work is partly supported by the Committee of Research and Conference Grants and University Development Fund, University of Hong Kong.

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWoo, PCY
 
dc.contributor.authorTeng, JLL
 
dc.contributor.authorWu, JKL
 
dc.contributor.authorLeung, FPS
 
dc.contributor.authorTse, H
 
dc.contributor.authorFung, AMY
 
dc.contributor.authorLau, SKP
 
dc.contributor.authorYuen, KY
 
dc.date.accessioned2010-09-06T07:50:15Z
 
dc.date.available2010-09-06T07:50:15Z
 
dc.date.issued2009
 
dc.description.abstractThis study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40% of medically important Gram-positive cocci (GPC), and 21 and 34% of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34% of medically important GPC and 14 and 25% of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0-2 and 2-13% of staphylococci, and 0 and 0-10% of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36-56 and 11-14% of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included. © 2009 SGM.
 
dc.description.naturelink_to_OA_fulltext
 
dc.identifier.citationJournal Of Medical Microbiology, 2009, v. 58 n. 8, p. 1030-1036 [How to Cite?]
DOI: http://dx.doi.org/10.1099/jmm.0.008615-0
 
dc.identifier.doihttp://dx.doi.org/10.1099/jmm.0.008615-0
 
dc.identifier.epage1036
 
dc.identifier.hkuros160596
 
dc.identifier.isiWOS:000268817900007
Funding AgencyGrant Number
Committee of Research and Conference Grants
University of Hong Kong
Funding Information:

This work is partly supported by the Committee of Research and Conference Grants and University Development Fund, University of Hong Kong.

 
dc.identifier.issn0022-2615
2012 Impact Factor: 2.297
2012 SCImago Journal Rankings: 0.886
 
dc.identifier.issue8
 
dc.identifier.openurl
 
dc.identifier.pmid19528178
 
dc.identifier.scopuseid_2-s2.0-67650744613
 
dc.identifier.spage1030
 
dc.identifier.urihttp://hdl.handle.net/10722/79073
 
dc.identifier.volume58
 
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
 
dc.subject.meshBase Sequence
 
dc.subject.meshDatabases, Nucleic Acid
 
dc.subject.meshGram-Positive Bacteria - classification - genetics
 
dc.subject.meshRNA, Ribosomal, 16S - genetics
 
dc.titleGuidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong