Quantitative PCR to Discriminate Between Pneumocystis Pneumonia and Colonization in HIV and Non-HIV Immunocompromised
Patsharaporn T Sarasombath1, Jerapas Thongpiya1, Monrat Chulanetra1
1Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
Abstract:
Pneumocystis pneumonia (PCP) is an opportunistic infection that commonly occurs in immunocompromised individuals. A definite diagnosis of PCP can be made only when the organism is identified in a respiratory specimen. It remains unclear whether qPCR can differentiate patients with PCP from those with Pneumocystis jirovecii colonization. In this study, we retrospectively collected data from HIV and non-HIV patients during 2013-2019. A diagnosis of definite, probable PCP, or PCP excluded was made based on clinical criteria, radiological reports, and three standard laboratory staining methods with blinding to qPCR data. Data from qPCR that was performed to determine the fungal burden (DNA copies/μl) in the BAL specimens of 69 HIV and 286 non-HIV patients were then obtained and reviewed. Receiver Operating Characteristic (ROC) curve analysis was performed to determine the upper and lower cut-off values for PCP diagnosis in HIV and non-HIV groups. In the non-HIV group, the lower cut-off value of 1,480 DNA copies/μl yielded a sensitivity of 100% (95% confidence interval [CI], 91.0-100), specificity of 72.9% (95% CI, 64.0-80.7), a positive predictive value (PPV) of 54.9% (95% CI, 47.6-62.1), and a negative predictive value (NPV) of 100% with Youden index of 0.73 for PCP diagnosis. In this group, the upper cut-off value of 9,655 DNA copies/μl showed the sensitivity of 100% (95% CI, 91.0-100) and specificity of 95.8% (95% CI, 90.4-98.6) with PPV of 88.6% (95% CI, 76.8-94.8) and a NPV of 100% with Youden index of 0.96 for PCP diagnosis. Regarding the HIV group, the lower cut-off value of 1,480 DNA copies/μl showed the sensitivity of 100% (95% CI, 92.5-100%) and specificity of 91.7% (95% CI, 61.5-99.8) with PPV of 97.9% (95% CI, 87.8-99.7) and a NPV of 100% with Youden index of 0.92 for PCP diagnosis. The sensitivity and specificity of the upper cut-off value of 12,718 DNA copies/μl in this group were 97.9% (95%CI, 88.7-100) and 100% (95%CI, 73.5-100), respectively. The values above the upper cut-off point had a PPV of 100% (95% CI, N/A) and a NPV of 92.3% (95% CI, 63.3-98.8) with Youden index of 0.98 for PCP diagnosis in the HIV group.
Insights
Quantitative PCR (qPCR) can differentiate Pneumocystis pneumonia (PCP) from colonization in immunocompromised patients. This study established specific DNA copy/μl cut-off values for accurate PCP diagnosis in HIV and non-HIV individuals.
Area of Science:
- Medical Microbiology
- Infectious Diseases
- Diagnostic Imaging
Background:
- Pneumocystis pneumonia (PCP) is a significant opportunistic infection in immunocompromised individuals.
- Definitive PCP diagnosis requires organism identification in respiratory specimens, but differentiating infection from colonization using qPCR remains challenging.
Purpose of the Study:
- To evaluate the utility of quantitative PCR (qPCR) in differentiating Pneumocystis pneumonia (PCP) from Pneumocystis jirovecii colonization.
- To establish diagnostic cut-off values for fungal burden in bronchoalveolar lavage (BAL) specimens.
Main Methods:
- Retrospective analysis of data from HIV and non-HIV patients diagnosed between 2013-2019.
- Diagnosis of PCP was based on clinical criteria, radiology, and standard staining methods, blinded to qPCR results.
- Receiver Operating Characteristic (ROC) curve analysis was used to determine optimal qPCR cut-off values for PCP diagnosis.
Main Results:
- In non-HIV patients, lower (1,480 DNA copies/μl) and upper (9,655 DNA copies/μl) cut-offs showed high sensitivity (100%) and specificity (72.9% and 95.8%, respectively).
- In HIV patients, lower (1,480 DNA copies/μl) and upper (12,718 DNA copies/μl) cut-offs demonstrated high sensitivity (100% and 97.9%) and specificity (91.7% and 100%, respectively).
- Specific cut-off values provided high positive and negative predictive values for PCP diagnosis in both patient groups.
Conclusions:
- qPCR, with established cut-off values, can effectively differentiate Pneumocystis pneumonia from colonization in both HIV-positive and HIV-negative immunocompromised patients.
- The established qPCR thresholds offer valuable tools for improving the accuracy and speed of PCP diagnosis.
