Skip to main content

ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 14 - 2024 | doi: 10.3389/fcimb.2024.1439472
This article is part of the Research Topic Targeted metagenomics in pathogen detection View all 9 articles

Application of metagenomic next-generation sequencing and targeted metagenomic nextgeneration sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients

Provisionally accepted
Yong Liu Yong Liu 1*Wencai Wu Wencai Wu 2Yunping Xiao Yunping Xiao 1Hongyan Zou Hongyan Zou 1Sijia Hao Sijia Hao 1Yanfang Jiang Yanfang Jiang 1*
  • 1 First Affiliated Hospital of Jilin University, Changchun, China
  • 2 Xi'an Jiaotong University, Xi an, China

The final, formatted version of the article will be published soon.

    Background Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.

    Keywords: pulmonary infection, Bronchoalveolar Lavage Fluid, TNGS, MNGs, Immunocompetent and immunocompromised

    Received: 28 May 2024; Accepted: 09 Jul 2024.

    Copyright: © 2024 Liu, Wu, Xiao, Zou, Hao and Jiang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Yong Liu, First Affiliated Hospital of Jilin University, Changchun, China
    Yanfang Jiang, First Affiliated Hospital of Jilin University, Changchun, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.