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Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

Patrick C. Y. Woo^1,2,3,, Jade L. L. Teng^3,, Jeff K. L. Wu³, Fion P. S. Leung³, Herman Tse^1,2,3, Ami M. Y. Fung³, Susanna K. P. Lau^1,2,3 and Kwok-yung Yuen^1,2,3

¹ State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong SAR

² Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong SAR

³ Department of Microbiology, University of Hong Kong, Hong Kong SAR

Correspondence
Kwok-yung Yuen
hkumicro{at}hkucc.hku.hk

Received December 10, 2008
Accepted May 3, 2009

This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40 % of medically important Gram-positive cocci (GPC), and 21 and 34 % of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34 % of medically important GPC and 14 and 25 % of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0–2 and 2–13 % of staphylococci, and 0 and 0–10 % of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36–56 and 11–14 % of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included.

These authors contributed equally to this work.

Tables of sequence comparison and identification data are available as supplementary material with the online version of this paper.