title: In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria.
abstract: This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5'-end 527-bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin-Elmer Applied Biosystems Division, Foster City, California, USA) databases for the identification of all existing medically important anaerobic bacteria. Full and 527-bp 16S rRNA sequencing are able to identify 52-63% of 130 Gram-positive anaerobic rods, 72-73% of 86 Gram-negative anaerobic rods and 78% of 23 anaerobic cocci. The existing MicroSeq databases are able to identify only 19-25% of 130 Gram-positive anaerobic rods, 38% of 86 Gram-negative anaerobic rods and 39% of 23 anaerobic cocci. These represent only 45-46% of those that should be confidently identified by full and 527-bp 16S rRNA sequencing. To improve the usefulness of MicroSeq, bacterial species that should be confidently identified by full and/or 527-bp 16S rRNA sequencing but not included in the existing MicroSeq databases should be included.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
authors.forename: Liliane M W
authors.initials: LM
authors.lastname: Chung
authors.forename: Jade L L
authors.initials: JL
authors.lastname: Teng
authors.forename: Herman
authors.initials: H
authors.lastname: Tse
authors.forename: Sherby S Y
authors.initials: SS
authors.lastname: Pang
authors.forename: Veronica Y T
authors.initials: VY
authors.lastname: Lau
authors.forename: Vanessa W K
authors.initials: VW
authors.lastname: Wong
authors.forename: Kwok-ling
authors.initials: KL
authors.lastname: Kam
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D001421:Bacteria, Anaerobic / Q000145:classification* / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000379:methods*; D030561:Databases, Nucleic Acid; D006801:Humans; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S