An Evaluation of the OLM Pneum ID Real-Time Polymerase Chain Reaction to Aid in the Diagnosis of Pneumocystis Pneumonia

Abstract

Background: The use of the PCR to aid in the diagnosis of Pneumocystis pneumonia (PcP) has demonstrated excellent clinical performance, as evidenced through various systematic reviews and meta-analyses, yet there are concerns over the interpretation of positive results due to the potential presence of Pneumocystis colonization of the airways. While this can be overcome by applying designated positivity thresholds to PCR testing, the shear number of assays described limits the development of a universal threshold. Commercial assays provide the opportunity to overcome this problem, provided satisfactory performance is determined through large-scale, multi-centre evaluations.

Methods: Retrospective case/control and consecutive cohort performance evaluations of the OLM PneumID real-time PCR assay were performed on DNA eluates from a range of samples sent from patients where "in-house" PCR had been performed as part of routine diagnostic testing. The clinical performance of the PneumID assay was determined before including it in a diagnostic algorithm to provide the probability of PcP (dependent on diagnostic evidence).

Results: After being used to test 317 patients (32 with PcP), the overall performance of the PneumID assay was found to be excellent (Sensitivity/Specificity: 96.9%/95.1%). False positivity could be removed by applying a threshold specific to sample type (<33.1 cycles for BAL fluid; <37.0 cycles for throat swabs), whereas considering any positive respiratory samples as significant generated 100% sensitivity, making absolute negativity sufficient to exclude PcP. Incorporating the PneumID assay into diagnostic algorithms alongside (1-3)-β-D-Glucan testing provided high probabilities of PcP (up to 85.2%) when both were positive and very low probabilities (<1%) when both were negative.

Conclusions: The OLM PneumID qPCR provides a commercial option for the accurate diagnosis of PcP, generating excellent sensitivity and specificity, particularly when testing respiratory specimens. The combination of PcP PCR with serum (1-3)-β-D-Glucan provides excellent clinical utility for diagnosing PcP.

Keywords: OLM PneumID; PcP PCR; Pneumocystis jirovecii; Pneumocystosis.

Figure 1

A diagnostic algorithm incorporating the OLM PneumID and the Associates of Cape Cod Fungitell (1-3)-β-D-Glucan (BDG) assay highlighting the probability of Pneumocystis pneumonia (PcP) in the HIV-negative patient. PcP PCR performance is based on the combined PneumID performance, as described in Table 3, with PCR positivity defined irrespective of the number of quantification cycles. BDG performance is based on the meta-analysis of Del Corpo et al., where the performance of BDG dependent on HIV status was evaluated, and any result with a BDG concentration >80 pg/mL was considered positive [15]. The incidence of PcP in the renal transplant population was derived from the study of Lee et al. [16].

Figure 2

A diagnostic algorithm incorporating the OLM PneumID and the Associates of Cape Cod Fungitell (1-3)-β-D-Glucan (BDG) assay highlighting the probability of Pneumocystis pneumonia (PcP) in the HIV-positive patient. PcP PCR performance is based on the combined PneumID performance, as described in Table 3, with PCR positivity defined irrespective of the number of quantification cycles. BDG performance is based on the meta-analysis of Del Corpo et al., where the performance of BDG dependent on HIV status was evaluated, and any result with a BDG concentration >80 pg/mL was considered positive [15]. The incidence of PcP in the HIV cohort was derived from the study of Elango et al. [17].