Comparison of Positive Results With End-Point and Real-Time Polymerase Chain Reaction Assays for the Diagnosis of Pneumocystis Pneumonia

Abstract

Background The definitive diagnosis of Pneumocystis pneumonia requires direct visualization of the organism; in recent years, polymerase chain reaction (PCR) assays, although not standardized, have become widely used diagnostic tools. A concern is that newer, more sensitive PCR assays will not differentiate colonization from infection. We evaluated the clinical implications of 2 different PCR assays for the diagnosis of Pneumocystis pneumonia. Methods Adult patients with a bronchoalveolar lavage or sputum sample positive for Pneumocystis by PCR from February 2014 to February 2018 were studied. Samples were tested with end-point (EP) PCR before February 2017 and with real-time (RT) PCR after February 2017. A strict case definition based on host factors, clinical presentation, radiological and pathological findings, and response to therapy was used to categorize cases as proven, probable, possible, and no Pneumocystis pneumonia. Positive EP-PCR and RT-PCR results were deemed to be true positives or false positives based on this categorization of patients. Results Of 1693 patients tested, 153 (9%) had a positive PCR test result, and 118 met the case definitions for proven (n = 2), probable (n = 70), and possible (n = 46) Pneumocystis pneumonia., Among 35 patients with a positive PCR test result who did not the meet criteria for Pneumocystis infection and who had a verified alternative diagnosis, 8 (23%) were false positive by EP-PCR and 27 (77%) by RT-PCR (P < 0.0001). Among the 27 patients who did not have host factors that would classically place them at risk of Pneumocystis infection, RT-PCR gave significantly more false-positive results (n = 12; 44%) than did EP-PCR (n = 2; 7%; P < 0.001). Conclusions Reverse transcription PCR gave significantly more positive results than did EP-PCR in patients who likely were colonized only and did not have Pneumocystis infection. Host risk factors, clinical presentation, and radiological findings should be considered before ordering PCR testing for Pneumocystis.