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

The University of Hong Kong

¹ E-mail: hkumicro{at}hkucc.hku.hk

Received December 10, 2008
Accepted May 3, 2009

The study is the first that provides guidelines for facilitating interpretation of results based on full and 527-bp 16S rDNA sequencing and Microseq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527-bp 16S rDNA sequencing can identify 24% and 40% of medically important Gram-positive cocci and 21% and 34% of medically important Gram-positive rods confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15% and 34% of medically important Gram-positive cocci and 14% and 25% of medically important Gram-positive rods 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. On the other hand, 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. Fifteen medically important Gram-positive cocci and 18 medically important Gram-positive rods that should be confidently identified by full 16S rDNA sequencing are not included in the full-MicroSeq database. Nine medically important Gram-positive cocci and 21 medically important Gram-positive rods that should be confidently identified by 527-bp 16S rDNA sequencing are not included in the 500-MicroSeq database. 16S rDNA 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 rDNA sequencing but not included in the MicroSeq databases should be included.