Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus

Abstract

Background: Streptococcus is an economically important genus as a number of species belonging to this genus are human and animal pathogens. The genus has been divided into different groups based on 16S rRNA gene sequence similarity. The variability observed among the members of these groups is low and it is difficult to distinguish them. The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus.

Methods: 16S rRNA gene sequences belonging to the isolates of S. dysgalactiae, S. equi, S. pyogenes, S. agalactiae, S. bovis, S. gallolyticus, S. mutans, S. sobrinus, S. mitis, S. pneumoniae, S. thermophilus and S. anginosus were analyzed with the purpose to define genetic variability within each species to generate a phylogenetic framework, to identify species-specific signatures and in-silico restriction enzyme analysis.

Results: The framework based analysis was used to segregate Streptococcus spp. previously identified upto genus level. This segregation was validated using species-specific signatures and in-silico restriction enzyme analysis. 43 uncharacterized Streptococcus spp. could be identified using this approach.

Conclusions: The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus.

Figure 1

Phylogenetic tree based on 63 representative 16S rRNA gene sequences from 12 Streptococcus species. The tree was constructed by neighbour-joining method with Jukes and Cantor correction. The numbers at node represent bootstrap values (based on 1000 resampling). The accession numbers are shown in parenthesis.

Figure 2

Phylogenetic tree of 63 framework sequences (bold values) and uncharacterized Streptococcus spp. The tree was constructed by neighbour-joining method with Jukes and Cantor correction. The numbers at node represent bootstrap values (based on 1000 resampling). The accession numbers are shown in parenthesis.