Diagnostic value of metagenomic next-generation sequencing in detecting Pneumocystis jirovecii pneumonia in HIV-infected patients

TL;DR

This study shows that metagenomic next-generation sequencing (mNGS) is more accurate than traditional methods for diagnosing Pneumocystis jirovecii pneumonia in HIV patients and better detects co-infections.

Contribution

The study demonstrates mNGS's superior diagnostic performance and co-infection detection in PJP compared to PCR, GMS, and BG assays.

Findings

mNGS and PCR both achieved 100% sensitivity for PJP detection.

mNGS showed higher specificity (91.3%) and AUC (0.898) than PCR (88% and 0.940).

mNGS detected co-infections in 67.6% of PJP cases, including cytomegalovirus and Epstein–Barr virus.

Abstract

Accurate diagnosis of Pneumocystis jirovecii pneumonia (PJP) in HIV patients remains challenging. This study compares metagenomic next-generation sequencing (mNGS) with PCR, GMS staining, and serum β-D-glucan (BG) assays for PJP detection and co-infection identification.

BALF samples from 34 HIV-positive PJP patients and 50 non-PJP controls were analyzed. Diagnostic performance metrics (sensitivity, specificity, NPV, AUC) and co-pathogen profiles were evaluated for mNGS versus conventional methods.

mNGS and PCR both achieved 100% sensitivity. mNGS showed higher specificity (91.3% vs. 88%) and AUC (0.898 vs. 0.940 for PCR). Co-infections were detected in 67.6% of PJP cases by mNGS, including cytomegalovirus (41.2%), Epstein–Barr virus (29.4%), and non-tuberculous mycobacteria (14.7%). GMS and BG assays exhibited lower sensitivity (64.7% and 76.5%, respectively).

mNGS offers superior specificity, accuracy, and co-infection detection compared to traditional methods. Its high NPV (100%) supports clinical utility in ruling out PJP. While resource-intensive, mNGS is a promising first-line diagnostic tool for HIV-associated PJP, particularly in polymicrobial infection settings.

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