Diagnostic value of metagenomic next-generation sequencing of lower respiratory tract specimen for the diagnosis of suspected Pneumocystis jirovecii pneumonia

Yang Liu; Xiaoning Wang; Jun Xu; Qiwen Yang; Huadong Zhu; Jing Yang

doi:10.1080/07853890.2023.2232358

Diagnostic value of metagenomic next-generation sequencing of lower respiratory tract specimen for the diagnosis of suspected Pneumocystis jirovecii pneumonia

Ann Med. 2023 Dec;55(1):2232358. doi: 10.1080/07853890.2023.2232358.

Authors

Yang Liu¹, Xiaoning Wang², Jun Xu¹, Qiwen Yang³, Huadong Zhu¹, Jing Yang¹

Affiliations

¹ Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
² Emergency Department, Zhengzhou Central Hospital, Zhengzhou, China.
³ Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.

Abstract

Aim: To evaluate diagnostic performance of metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PCP), in comparison with polymerase chain reaction (PCR), Gomori methenamine silver (GMS) staining and serum 1,3-β-d-Glucan (BG) assay.

Methods: 52 PCP patients and 103 patients with non-pneumocystic jirovecii pneumonia (non-PCP) were enrolled, and comparative analysis was conducted of different diagnostic tests. Clinical features and co-pathogen characteristics were reviewed.

Results: The diagnostic sensitivity (92.3%) and specificity (87.4%) of mNGS did not show significant differences compared with that of PCR while mNGS had the advantage over PCR in the detection of co-pathogens. Despite its excellent specificity, the sensitivity of GMS staining (9.3%) was inferior to that of mNGS (p < .001). The combination of mNGS with serum BG statistically outperformed mNGS or serum BG alone in the areas under the receiver operating characteristic curves (AUCs, p = .0013 and p = .0015, respectively). Notably, all the blood samples showing positive mNGS for Pneumocystis jirovecii came from PCP patients. The leading co-pathogens among patients with PCP were cytomegalovirus, Epstein-Barr virus and Torque teno virus.

Conclusions: mNGS shows superiority over several common clinical methods in the diagnosis of suspected PCP. Serum BG in conjunction with mNGS further improved the diagnostic efficacy of mNGS.

Keywords: Pneumocystis jirovecii pneumonia; diagnostic performance; lower respiratory tract specimen; metagenomic next-generation sequencing; pathogen detection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epstein-Barr Virus Infections*
Herpesvirus 4, Human
High-Throughput Nucleotide Sequencing
Humans
Pneumonia, Pneumocystis* / diagnosis
Respiratory System
Sensitivity and Specificity

Grants and funding

This study was supported by the National High Level Hospital Clinical Research Funding (Grant number: 2022-PUMCH-B-109), and the National Key Research and Development Program of China (Grant number: 2021YFC2501800).