rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci.

Streptococcus pneumoniae, the leading etiological agent of pneumonia, shares a high degree of DNA sequence homology with the viridans group of streptococci. The clinical and pathological manifestations may present with different features, and discrimination between S. pneumoniae and its close viridans cocci relatives, such as Streptococcus mitis and Streptococcus oralis, is still quite difficult. The 445-bp sequences of the N-terminal region of rpoA from nine S. pneumoniae, seven S. mitis, ten S. oralis, and two related strains were determined and compared with their respective 16S rRNA gene sequences to establish their usefulness in phylogenetic analysis. Pairwise comparisons of rpoA sequences among the species showed higher rates of evolution with lower similarities (92.3-100%) than those of 16S rRNA genes (96.8-100%). The rpoA-based phylogeny generated deeper branches and presented improved discriminatory resolution than the 16S rRNA gene-based phylogeny. These results show that rpoA sequences represent a consistent, but more discriminating, genomic marker than 16S rRNA gene sequences for investigating the evolutionary relationships of Streptococcus at the species level. rpoA could be a useful marker for identifying and classifying S. pneumoniae, S. mitis, and S. oralis from closely related taxa.