Comparison of nasopharyngeal swab vs. lower respiratory tract specimen PCR for the diagnosis of Pneumocystis jirovecii pneumonia

Background and objectiveDiagnosis of P. jirovecii pneumonia (PJP) is by PCR on lower respiratory tract specimens, the collection of which is not always well-tolerated and requires trained staff and costly equipment not usually available in low-resource settings. We aimed to evaluate P. jirovecii PCR performed on nasopharyngeal swabs (NPS) as a diagnostic test for PJP, as well as the impact of specimen quality on test performance. MethodsPatients with clinically-suspected PJP in public hospitals in Queensland, Australia, who had quantitative P. jirovecii PCR performed on lower respiratory tract specimens from 1 January 2015 to 31 December 2016, and also had NPS collected by healthcare staff within seven days of lower respiratory tract specimen collection were included in this retrospective cohort study. Quantitative P. jirovecii PCR was performed, and sensitivity, specificity, and positive and negative predictive values were calculated. Specimen quality was assessed by quantifying endogenous retrovirus 3 (ERV3) loads, with higher values indicating better specimen quality. ResultsOne hundred and eleven patients were included. The sensitivity of NPS P. jirovecii PCR was 0.66 and specificity was 1.0. The positive predictive value was 1.0 and the negative predictive value was 0.63. Median ERV3 loads in lower respiratory tract specimens and NPS were not significantly different in true positive vs. true negative patients, but was significantly higher in true positives vs. false negatives (7.55x102 vs. 3.67x102; P=0.05). ConclusionP. jirovecii PCR on NPS was highly specific but poorly sensitive. Proper specimen collection is essential to ensure adequate quality and prevent misclassification. Summary at a GlanceUsing nasopharyngeal swabs instead of lower respiratory tract specimens for PCR to diagnose P. jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this two-year retrospective cohort study of patients with clinically-suspected PJP from Queensland, Australia, P. jirovecii PCR on NPS had high specificity but low sensitivity.