SHORT REPORT

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

Patrick C Y Woo^1,2, Liliane M W Chung¹, Jade L L Teng¹, Herman Tse^1,2, Sherby S Y Pang¹, Veronica Y T Lau¹, Vanessa W K Wong¹, Kwok-ling Kam¹, Susanna K P Lau^1,2 and Kwok-Yung Yuen^1,2

¹ Department of Microbiology, The University of Hong Kong, Hong Kong
² Research 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:
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; hkumicro{at}hkucc.hku.hk

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.

Abbreviations: MicroSeq, MicroSeq 500 16S rDNA bacterial identification system

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