Article: In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria
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- Publisher Website: 10.1099/jmm.0.027805-0
- Scopus: eid_2-s2.0-80051768006
- PMID: 21498652
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| Title | In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Authors | Teng, JLL1 Yeung, MY1 Yue, G1 AuYeung, RKH1 Yeung, EYH1 Fung, AMY1 Tse, H1 Yuen, KY1 Lau, SKP1 Woo, PCY1 | ||||||||
| Issue Date | 2011 | ||||||||
| Publisher | Society 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?] DOI: http://dx.doi.org/10.1099/jmm.0.027805-0 | ||||||||
| 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. | ||||||||
| ISSN | 0022-2615 2011 Impact Factor: 2.502 2011 SCImago Journal Rankings: 0.222 | ||||||||
| DOI | http://dx.doi.org/10.1099/jmm.0.027805-0 | ||||||||
| ISI Accession Number ID | WOS:000295018700008
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 | References in Scopus |
| dc.contributor.author | Teng, JLL | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| dc.contributor.author | Yeung, MY | ||||||||
| dc.contributor.author | Yue, G | ||||||||
| dc.contributor.author | AuYeung, RKH | ||||||||
| dc.contributor.author | Yeung, EYH | ||||||||
| dc.contributor.author | Fung, AMY | ||||||||
| dc.contributor.author | Tse, H | ||||||||
| dc.contributor.author | Yuen, KY | ||||||||
| dc.contributor.author | Lau, SKP | ||||||||
| dc.contributor.author | Woo, PCY | ||||||||
| dc.date.accessioned | 2011-09-23T05:51:02Z | ||||||||
| dc.date.available | 2011-09-23T05:51:02Z | ||||||||
| dc.date.issued | 2011 | ||||||||
| dc.description.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. | ||||||||
| dc.description.nature | Link_to_subscribed_fulltext | ||||||||
| dc.identifier.citation | Journal 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.doi | http://dx.doi.org/10.1099/jmm.0.027805-0 | ||||||||
| dc.identifier.epage | 1286 | ||||||||
| dc.identifier.hkuros | 195238 | ||||||||
| dc.identifier.isi | WOS:000295018700008
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.issn | 0022-2615 2011 Impact Factor: 2.502 2011 SCImago Journal Rankings: 0.222 | ||||||||
| dc.identifier.issue | 9 | ||||||||
| dc.identifier.openurl | | ||||||||
| dc.identifier.pmid | 21498652 | ||||||||
| dc.identifier.scopus | eid_2-s2.0-80051768006 | ||||||||
| dc.identifier.spage | 1281 | ||||||||
| dc.identifier.uri | http://hdl.handle.net/10722/139519 | ||||||||
| dc.identifier.volume | 60 | ||||||||
| dc.language | eng | ||||||||
| dc.publisher | Society for General Microbiology. The Journal's web site is located at http://jmm.sgmjournals.org | ||||||||
| dc.publisher.place | United Kingdom | ||||||||
| dc.relation.ispartof | Journal of Medical Microbiology | ||||||||
| dc.relation.references | References in Scopus | ||||||||
| dc.rights | Journal of Medical Microbiology. Copyright © Society for General Microbiology. | ||||||||
| dc.subject.mesh | Bacteria, Aerobic - classification - genetics - isolation and purification | ||||||||
| dc.subject.mesh | Bacteriological Techniques - methods | ||||||||
| dc.subject.mesh | Computational Biology - methods | ||||||||
| dc.subject.mesh | Gram-Negative Bacteria - classification - genetics - isolation and purification | ||||||||
| dc.subject.mesh | Gram-Negative Bacterial Infections - diagnosis - microbiology | ||||||||
| dc.title | In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria | ||||||||
| dc.type | Article |
Author Affiliations
- The University of Hong Kong