Potential use of serum based quantitative real-time PCR for the detection of pneumonia pathogens in a densely colonised population.

Molecular methods offer improvement in the detection of causative pneumonia pathogens, but there are concerns of false positive results. Here we validate quantitative real-time PCR (qPCR) assays for the detection of and in: (a) spiked serum samples and (b) in matched serum and nasopharyngeal swabs from a population of Indigenous Australian children without pneumonia, but with a high nasopharyngeal carriage prevalence of and . Matched sera and nasopharyngeal swabs were selected from Indigenous children less than 5 years of age without a diagnosis of pneumonia. Specimens were assayed by qPCR targeting the and genes from and , respectively. Using qPCR, neither nor DNA was detected in serum samples, even after concentration of serum DNA. In matched nasopharyngeal swabs, bacterial load was high with up to 106 cells/ml detected by qPCR. In this cohort of children with a high nasopharyngeal carriage, prevalence and bacterial load of pneumonia pathogens, qPCR on sera would not have produced a false pneumonia diagnosis. Thus, qPCR analysis of sera appears to be an appropriate method to aid aetiological diagnosis of pneumonia in this population.