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

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

¹Department of Microbiology, The University of Hong Kong, Hong Kong
²Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong

Correspondence to: Dr K-Y Yuen Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital Compound, Pokfulam Road, Hong Kong; [email protected]

Accepted 18 September 2006

This work was partly supported by the Committee of Research and Conference Grants and University Development Fund, The University of Hong Kong, Hong Kong.

Published Online First 17 October 2006

Competing interests: None.

Journal of Clinical Pathology 60(5):p 576-579, May 2007.

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.