Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene

Abstract We sequenced the evolutionarily conserved genes 16S rRNA, atpD, tuf , and recA from Streptococcus pseudopneumoniae, Streptococcus pneumoniae, Streptococcus mitis , and Streptococcus oralis . Phylogenetic analysis revealed that recA provided good resolution between these species, including discrimination of the novel species S. pseudopneumoniae . By contrast, the more conserved 16S rRNA, tuf and atpD are not sufficiently discriminatory. Therefore, recA sequences were used to develop a real-time PCR assay with a locked nucleic acid-mediated TaqMan probe for the specific detection and identification of S. pseudopneumoniae . The PCR assay showed excellent specificity and a detection limit of S. pseudopneumoniae strains, which makes it a promising tool for molecular identification and epidemiological studies. In conclusion, this article describes for the first time a PCR assay for the specific identification of S. pseudopneumoniae .