Feasibility of a quantitative polymerase chain reaction assay for diagnosing Streptococcus pneumoniae associated Community Acquired Pneumonia (CAP)

Background: Current diagnostic microbial techniques detect S. pneumoniae in less than 30% of patients with CAP. A polymerase chain reaction (PCR) targeting autolysin (LytA) might be able to increase this rate. Colonization with S. pneumoniae may influence the interpretation of a PCR. Therefore a quantitative assay is needed. Our aim was to set up and validate a quantitative PCR (qPCR) and to evaluate the feasibility of the qPCR in a pilot study. Methods: Quantification of a S. pneumoniae standard (ATCC49619) by picogreen fluorescence method and 16Sr DNA PCRs. Intra- and inter-run variability, analytical specificity and sensitivity of an in-house qPCR using the LytA gene as target were tested by serial dilution series of S. pneumoniae ATCC 49619 and a panel of Streptococci species. We then took samples from 11 patients with pneumococcal pneumonia and 13 with CAP caused by other or unknown pathogens and looked at performance of this qPCR on oropharyngeal swabs. Results: Analysis of the clinical specimens yielded a sensitivity of 63.6% and specificity of 92.3% (AUC 0.78) with a cutoff value of 10 copies/μL. However our study population is too low to get a reliable cutoff value for pneumococcal infection. Conclusions: qPCR seems a promising technique to increase the diagnostic rate of pneumococcal infections. However, the clinical value of this test needs further investigation.