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Updated: Feb 8, 2026
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Metagenomic next-generation sequencing to detect Pneumocystis jirovecii pneumonia in critically ill, HIV-negative
Liming He1, Yibing Cheng2, Li Huang3
1Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China.
Background:
Metagenomic next-generation sequencing (mNGS) plays a critical role in the rapid detection of infectious pathogens. We aimed to analyze the clinical characteristics of Pneumocystis jirovecii infection in children without HIV infection and to evaluate the performance of mNGS in distinguishing P. jirovecii colonization from true infection.
Methods:
A multicenter, retrospective analysis was conducted on critically ill, non-HIV-infected pediatric patients who tested positive for P. jirovecii via mNGS analysis of bronchoalveolar lavage fluid (BALF). Group differences were assessed using Mann-Whitney U-tests (for continuous data) and chi-square tests (for categorical data). Discriminatory performance was evaluated by calculating the area under the receiver operating characteristic curve.
Results:
A total of 59 HIV-negative children (age range: 2 months to 14 years) from four children's hospitals were included and classified into two groups based on P. jirovecii status: P. jirovecii pneumonia (PCP; n = 51) and P. jirovecii colonization (PCC; n = 8). Compared with the PCC group, the PCP group had significantly higher serum C-reactive protein levels and median P. jirovecii read counts in mNGS (both P < 0.05). The optimal threshold value for discriminating P. jirovecii infection from colonization appeared to be 556 reads (sensitivity, 77.6%; specificity, 100.0%). Eighteen patients (35.3%) in the PCP group died. Compared with survivors, these patients were significantly younger, had lower T-cell subset counts (CD3+, CD4+, and CD8+), and a higher prevalence of primary immunodeficiency (all P < 0.05).
Conclusions:
BALF mNGS analysis may have utility for differentiating between colonization and infection by P. jirovecii, warranting further investigation.
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