Pneumocystis jirovecii pneumonia PCR test on upper respiratory tract swab.

Abstract

Pneumocystis jirovecii pneumonia (PCP) is an opportunistic fungal infection with high morbidity and mortality among people living with HIV. Upper respiratory tract (URT) swabs are routinely taken for testing viral and bacterial pathogens when patients present with respiratory symptoms in our hospital. We conducted a pilot service improvement project to explore the utility of URT swabs for PCP diagnosis using in-house real-time polymerase chain reaction (PCR). Ten URT swab samples obtained from HIV-positive patients with PCP and a positive PCP PCR (AusDiagnostics) from lower respiratory tract (LRT) samples were retrospectively identified. Nine HIV-positive patients with a negative PCR for PCP from LRT samples were identified. Stored aliquots of DNA extracted from these samples were retrieved and tested by an in-house real-time PCR for the presence of PCP DNA. Among PCP-positive cases, URT swabs collected after PCP treatment initiation were excluded from the study. In all, 10 URT samples from PCP-positive patients and nine URT samples from PCP-negative patients were tested for PCP by real-time PCR. Eighteen out of 19 URT sample had a concordant result with the LRT samples. The sensitivity and specificity for URT sample PCR were 90% [confidence interval (CI): 55.50-99.75%] and 100% (CI: 66.37-100%). The positive predictive value was 100% and the negative predictive value was 90.9% (CI: 60.90-98.47%). Upper respiratory tract swab can reliably detect PCP DNA on real-time PCR among people living with HIV with PCP.