Development of a fully automated PCR assay for the detection of Pneumocystis jirovecii using the GENECUBE system.

We developed a fully automated polymerase chain reaction (PCR) assay for the detection of Pneumocystis jirovecii using the GENECUBE system. This assay was evaluated against an in-house real-time PCR assay using 82 bronchoalveolar lavage and 139 sputum samples from 221 immunocompromised patients who were suspected of having Pneumocystis pneumonia (PCP). After loading the maximum of eight samples into the GENECUBE system, the results were obtained within approximately 60 minutes. The overall positivity rate of both assays was 35%, and the concordance rate was 89% (kappa, 0.76). Based on the clinical diagnosis of 39 PCP and 105 non-PCP patients, the GENECUBE and real-time assays had sensitivities of 92.3% and 94.9% and specificities of 85.7% and 85.7%, respectively. This automated and rapid assay is a promising tool for the detection of P. jirovecii in routine clinical laboratory practice.