title: In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria.
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 Gram-negative bacteria than aerobic Gram-positive and Gram-negative bacteria.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Jade L L
authors.initials: JLL
authors.lastname: Teng
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Ming-Yiu
authors.initials: MY
authors.lastname: Yeung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Yue
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Rex K H
authors.initials: RKH
authors.lastname: Au-Yeung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Eugene Y H
authors.initials: EYH
authors.lastname: Yeung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Ami M Y
authors.initials: AMY
authors.lastname: Fung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.
authors.forename: Herman
authors.initials: H
authors.lastname: Tse
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR.|Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Susanna K P
authors.initials: SKP
authors.lastname: Lau
authors.affiliation: Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.|Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Patrick C Y
authors.initials: PCY
authors.lastname: Woo
mesh_terms: D001420:Bacteria, Aerobic / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001431:Bacteriological Techniques / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D006090:Gram-Negative Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016905:Gram-Negative Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology; D006801:Humans; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S