Clinical performance of the fully automated quantitative LeaDEA Pneumocystis PCR Kit for the diagnosis of Pneumocystis jirovecii pneumonia.

Compared with microscopy, quantitative real-time PCR (qPCR) is more sensitive for the diagnosis of Pneumocystis jirovecii pneumonia (PcP) and may also help distinguish PcP from colonization based on fungal burden. In this retrospective cohort study, we evaluated the performance of the LeaDEA Pneumocystis PCR Kit, a single-packaged reagent system designed for use on a fully automated molecular testing platform, using respiratory specimens from immunocompromised patients. The analytical and clinical performance of the LeaDEA assay on the GeneLEAD VIII platform was compared with that of a previously described laboratory-developed reference qPCR assay targeting the major surface glycoprotein gene of P. jirovecii. The limit of detection was 500 copies/ml for both assays, with a quantification range of 10³-10⁸ copies/ml. Among 350 patients (158 bronchoalveolar lavage and 192 sputum [including induced sputum] samples), the reference assay-based European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium (EORTC/MSGERC) criteria classified 162 as having PcP (13 proven and 149 probable) and 188 as non-PcP. The overall concordance of qPCR results between the assays was 93% (kappa, 0.85). Compared with the reference assay-based diagnoses, the LeaDEA assay-based diagnoses showed 92.0% positive % agreement and 96.3% negative % agreement (kappa, 0.88). Among the PCR-positive non-HIV patients, the copy numbers measured by the LeaDEA assay distinguished PcP from colonization based on qPCR-independent diagnoses, with 63.8% sensitivity and 72.5% specificity, at an optimal cutoff of 20 427 copies/ml. The LeaDEA assay demonstrated analytical and clinical performance comparable to that of a reference qPCR assay, which may facilitate the diagnosis of PcP in routine clinical laboratories.