Metagenomic Next-Generation Sequencing Is Highly Efficient in Diagnosing Pneumocystis Jirovecii Pneumonia in the Immunocompromised Patients

Dongsheng Wang; Shihua Fang; Xiaowen Hu; Qixia Xu; Xinmin Chu; Xiaodong Mei; Wang Xie

doi:10.3389/fmicb.2022.913405

Metagenomic Next-Generation Sequencing Is Highly Efficient in Diagnosing Pneumocystis Jirovecii Pneumonia in the Immunocompromised Patients

Front Microbiol. 2022 Jun 17:13:913405. doi: 10.3389/fmicb.2022.913405. eCollection 2022.

Authors

Dongsheng Wang^{1

2}, Shihua Fang^{2

3}, Xiaowen Hu², Qixia Xu², Xinmin Chu⁴, Xiaodong Mei², Wang Xie²

Affiliations

¹ Department of Pulmonary and Critical Care Medicine, Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
² Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
³ Wannan Medical College, Wuhu, China.
⁴ Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Abstract

Purposes: To explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pneumocystis jiroveciipneumonia (PJP) in the immunocompromised patients.

Methods: Data of 122 patients with PJP in an immunosuppressed state and 67 non-PJP patients were collected. The diagnostic efficacy of mNGS was compared with the conventional methods, including Gomori methenamine silver (GMS) staining and serum (1,3)-β-D-glucan (BDG). Changes of anti-microbial therapy for patients with PJP based on mNGS results were also reviewed.

Results: The diagnostic sensitivity of mNGS to PJP was higher than that of GMS and BDG (100% vs. 15 and 74.5%, p < 0.001). The diagnostic specificity (91.%) was lower than that of GMS (100%), and similar with BDG (89.6%). In addition to P. jirovecii, mNGS revealed co-pathogens like human β-herpesvirus 5, human γ-pesvirus 4, and some other opportunistic pathogens. The reads of mNGS were remarkably higher in BALF than in blood samples. Initial antimicrobial treatment was modified in 89.3% patients based on the mNGS results, and 74 cases (60.7%) were treated with anti-P. jirovecii therapy.

Conclusion: mNGS is highly efficient in diagnosing PJP and good at identifying pathogens in mixed infections.

Keywords: diagnosis; immunocompromised host; metagenomics next-generation sequencing (mNGS); pathogens; pneumocystis jiroveci pneumonia.