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Effectiveness of a real-time PCR for diagnosis of Pneumocystis pneumonia in immunocompromised patients – Experience from a tertiary care center, India - 18/05/22

Doi : 10.1016/j.mycmed.2021.101241 
Dhanalakshmi S a, , Thambu David S b, Richa Gupta c, Santosh Varughese d, George M Varghese e, Biju George f, Joy S Michael a
a Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India 
b Department of Medicine, Christian Medical College and Hospital, Vellore, India 
c Department of Pulmonary Medicine, Christian Medical College and Hospital, Vellore, India 
d Department of Nephrology, Christian Medical College and Hospital, Vellore, India 
e Department of Infectious Diseases, Christian Medical College and Hospital, Vellore, India 
f Department of Hematology, Christian Medical College and Hospital, Vellore, India 

Corresponding author at: Department of Clinical Microbiology, Christian Medical College & Hospital, Vellore, Tamil Nadu, India, 632004.Department of Clinical MicrobiologyChristian Medical College & HospitalVelloreTamil Nadu632004India

Abstract

Pneumocystis jirovecii pneumonia (PCP) is a life-threatening fungal infection in immunocompromised patients. Traditionally, the laboratory diagnosis of PCP relied on the visualization of organisms by microscopy as Pneumocystis cannot be readily cultured in the laboratory. The polymerase chain reaction (PCR) method is preferred over the conventional microscopic methods as PCR is rapid and found to have higher sensitivity. This retrospective study aimed to analyze the diagnostic value of a real-time PCR (qPCR) for routine diagnosis of PCP in immunocompromised patients with various underlying conditions. The qPCR targets a 121 bp fragment of P.jirovecii mitochondrial large subunit rRNA gene. The study was conducted in a 2600-bed tertiary care hospital between January and December 2019. All patients whose respiratory samples were tested for PCP by qPCR were included. The clinical diagnosis was made for each patient and categorized into PCP and non-PCP based on multi-component clinical criteria by a multi-disciplinary team. The performance characteristics of qPCR were analyzed using clinical diagnosis as the reference. A total of 339 respiratory samples from 289 patients were tested for PCP by qPCR during the study period. The overall sensitivity and specificity of qPCR were 84.75% (95% CI, 73.01% to 92.78%) and 96.1% (95% CI, 92.7 to 98.2), respectively. The sensitivity was slightly higher among HIV-infected patients (91%) than the non- HIV group (81%). The PCR exhibited higher sensitivity in bronchoalveolar lavage (BAL) (94%) than in sputum samples (81%). The colonization can be ruled out with the cycle threshold (CT) value of below 34 with a sensitivity and specificity of 100% and 78%, respectively.

The real-time PCR showed good sensitivity and specificity for routine diagnosis of PCP in patients with various underlying conditions. In addition, a cut-off CT value (≤ 34) was determined to exclude colonization from active pneumonia.

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Keywords : PCP, qPCR, Pneumocystis, CT value, Colonization


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Vol 32 - N° 2

Article 101241- mai 2022 Retour au numéro
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