ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Antimicrobials, Resistance and Chemotherapy
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1615965
This article is part of the Research TopicNext-Generation Technologies for Antibiotic Susceptibility TestingView all 6 articles
Evaluation of targeted next-generation sequencing for microbiological diagnosis of acute lower respiratory infection
Provisionally accepted- Yantai Yuhuangding Hospital, Yantai, China
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Purpose: To evaluate the performance of targeted next-generation sequencing (tNGS) in pathogen detection in acute lower respiratory infection.: The retrospective study was conducted between July 2023 and May 2024 at the Yantai Yuhuangding Hospital. Patients with acute lower respiratory infections were included. Qualified sputum or bronchoalveolar lavage fluid samples were collected for tNGS and conventional microbiological tests(CMTs), including culture, staining, polymerase chain reaction (PCR), and reverse transcription-PCR (RT-PCR). The time required and cost were counted.Results: A total of 968 patients were enrolled. Study analysis discovered 1,019 strains of bacteria, 259 strains of fungi, 302 strains of viruses, 76 strains of Mycoplasma pneumoniae, and two strains of Chlamydia psittaci using tNGS. In addition, tNGS also identified 39 mecA, four KPC, 19 NDM, and two OXA-48 genes. The positive rates for bacteria, fungi, viruses, mycoplasma, and chlamydia obtained using tNGS were significantly higher than those determined using traditional methods.Among them, tNGS showed high consistence with mycobacterium DNA test, influenza A (H1N1) virus nucleic acid test and COVID-19 nucleic acid test. Poor consistency between drug resistance genes and bacterial 3 resistance phenotypes was found. In addition, tNGS also had advantages over traditional methods in terms of detection time and cost. Conclusion: Compared to traditional methods, tNGS had higher sensitivity in detecting bacteria, fungi, viruses, and other pathogens in acute lower respiratory infection, and also had the advantages of timeliness and cost-effectiveness, making it a promising method for guiding clinical diagnosis.
Keywords: Next-generation sequencing, Acute lower respiratory infection, Microorganism, resistance gene, Microbiological diagnosis
Received: 22 Apr 2025; Accepted: 01 Aug 2025.
Copyright: © 2025 Yang, Jiang, Cao, Yi and Zhao. 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: Qi Zhao, Yantai Yuhuangding Hospital, Yantai, China
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