Clinical Utility of a Droplet Digital PCR-Based Assay for Quantitative Detection of Pneumocystis jirovecii in Suspected Fungal Pneumonia

Purpose: Pneumocystis jirovecii typically causes life-threatening Pneumocystis pneumonia (PCP), calling for accurate detection of P. jirovecii in clinical samples to facilitate PCP management. Patients and Methods: An observational cohort of 193 patients with suspected fungal pneumonia was enrolled. The cell-free DNA (cfDNA) in bronchoalveolar lavage fluid (BALF) and serum samples was prepared and quantitated via a ddPCR assay targeting the mitochondrial large subunit rRNA gene of P. jirovecii . The correlations between ddPCR results and medical data were analyzed. Results: The cases with complete data were classified into a PCP group (N=30) and a non-PCP group (N=139). This ddPCR assay demonstrated a sensitivity of 91.3% and a specificity of 96.8% for BALF, in contrast to a sensitivity of 57.1% and a specificity of 100% for serum. The area under the curve of 0.896 for diagnosis was obtained via ddPCR assay, compared with 0.627 via G-test ( P < 0.0001). The cfDNA copies were positively correlated with antifungal agents usage, certain clinical characteristics, lactate dehydrogenase levels, and G-test results (all P< 0.05). Moreover, higher cfDNA copies were associated with increased in-hospital mortality (aHR> 1, P< 0.05). Conclusion: The ddPCR assay exhibited robust diagnostic performance for PCP in BALF samples and cfDNA copies may serve as an indicator for improving the management of patients. Keywords: cell-free DNA, droplet digital PCR, Pneumocystis jirovecii , pneumonia, diagnosis, quantitative detection