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

Background and objective Diagnosis 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. Methods Patients 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. Results One 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 (7.55×102 vs. 3.67×102; P =0.05). Conclusion P. 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 Glance Using 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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded by a Study, Education, and Research Trust Fund grant from Pathology Queensland. RC was supported by the UK Government through a Commonwealth Scholarship and the Royal Australasian College of Physicians through the Bushell Travelling Fellowship in Medicine or the Allied Sciences. The funders had no role in study design, data collection, data analysis, data interpretation, or writing of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Royal Brisbane and Womens Hospital Ethics Committee gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.