Department of Microbiology    The University of Hong Kong

16SpathDB 2.0: identification of medically important bacteria by 16S rRNA gene sequencing


Since the discovery of polymerase chain reaction (PCR) and DNA sequencing, comparison of the gene sequences of bacterial species showed that the 16S ribosomal DNA (rRNA) gene is highly conserved within a species and among species of the same genus. Therefore, 16S rRNA gene sequencing has been used as the new gold standard for identification of clinical isolates with ambiguous biochemical profiles.

BLAST query of 16S rRNA sequence against GenBank database is one of the traditional approach for identification of clinical isolates. However, GenBank database may contain 16S rRNA sequences of environmental bacterial isolates that are of limited interest. Besides, misclassification of 16S rRNA sequences in GenBank is not infrequent that may proprogate and result in misidentification of clinical isolates.

In view of this, we designed a database of 16S rRNA sequences of medically important bacteria according to the 10th edition of "Manual of Clinical Microbiology".16S rRNA sequence of each bacterial species in the GenBank database was inspected by bioinformatics analyses such as mulitple sequence alignment so as to select the most representative sequence and to avoid the inclusion of misclassified sequences. Users can submit a query sequence to the database to compare against each 16S rRNA sequence in the database such that the most likely identity of the query will be reported.