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Article: Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

TitleGuidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
Authors
Issue Date2009
PublisherSociety for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org
Citation
Journal Of Medical Microbiology, 2009, v. 58 n. 8, p. 1030-1036 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/79073
ISSN
2014 Impact Factor: 2.248
2014 SCImago Journal Rankings: 0.907
ISI Accession Number ID
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.

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorTeng, JLLen_HK
dc.contributor.authorWu, JKLen_HK
dc.contributor.authorLeung, FPSen_HK
dc.contributor.authorTse, Hen_HK
dc.contributor.authorFung, AMYen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2010-09-06T07:50:15Z-
dc.date.available2010-09-06T07:50:15Z-
dc.date.issued2009en_HK
dc.identifier.citationJournal Of Medical Microbiology, 2009, v. 58 n. 8, p. 1030-1036en_HK
dc.identifier.issn0022-2615en_HK
dc.identifier.urihttp://hdl.handle.net/10722/79073-
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.en_HK
dc.languageengen_HK
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-
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 bacteriaen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0022-2615&volume=58&issue=8&spage=1030&epage=1036&date=2009&atitle=Guidelines+for+interpretation+of+16S+rRNA+gene+sequence-based+results+for+identification+of+medically+important+aerobic+Gram-positive+bacteriaen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailTeng, JLL:llteng@hku.hken_HK
dc.identifier.emailTse, H:herman@graduate.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.authorityTeng, JLL=rp00277en_HK
dc.identifier.authorityTse, H=rp00519en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1099/jmm.0.008615-0en_HK
dc.identifier.pmid19528178en_HK
dc.identifier.scopuseid_2-s2.0-67650744613en_HK
dc.identifier.hkuros160596en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-67650744613&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume58en_HK
dc.identifier.issue8en_HK
dc.identifier.spage1030en_HK
dc.identifier.epage1036en_HK
dc.identifier.isiWOS:000268817900007-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridTeng, JLL=7202560229en_HK
dc.identifier.scopusauthoridWu, JKL=35216629300en_HK
dc.identifier.scopusauthoridLeung, FPS=35215551500en_HK
dc.identifier.scopusauthoridTse, H=7006070596en_HK
dc.identifier.scopusauthoridFung, AMY=7101926801en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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