In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria

• Published in: Journal of clinical pathology Vol. 60; no. 5; pp. 576 - 579
• Main Authors: Woo, Patrick C Y, Chung, Liliane M W, Teng, Jade L L, Tse, Herman, Pang, Sherby S Y, Lau, Veronica Y T, Wong, Vanessa W K, Kam, Kwok-ling, Lau, Susanna K P, Yuen, Kwok-Yung
• Format: Journal Article
• Language: English
• Published: London BMJ Publishing Group Ltd and Association of Clinical Pathologists 01-05-2007; BMJ; BMJ Publishing Group LTD; BMJ Group
• Subjects: Bacteria; Bacteria, Anaerobic - classification; Bacteria, Anaerobic - genetics; Bacterial Typing Techniques - methods; Biological and medical sciences; Databases, Nucleic Acid; Genes; Humans; Investigative techniques, diagnostic techniques (general aspects); Medical sciences; MicroSeq; MicroSeq 500 16S rDNA bacterial identification system; Pathology. Cytology. Biochemistry. Spectrometry. Miscellaneous investigative techniques; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; Sequence Analysis, RNA - methods; Short Reports; Anatomic pathology; Nucleotide sequence; Anaerobe; Ribosomal RNA; Ribosomal DNA; Bacteria; Identification; Method
• DOI: 10.1136/jcp.2006.038653
• EISSN: 1472-4146
• ISSN: 0021-9746

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.