ArticleInfection2025
Enhancing upper respiratory tract infection detection: exploring qPCR negative respiratory samples using targeted next-generation sequencing.
Article in Infection, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Multi-Route Administration Therapy for IntracranialInternational medical case reports journal · 2026Article
- Targeted next-generation sequencing for pediatric community-acquired pneumonia pathogen detection: a single-center study.Frontiers in cellular and infection microbiology · 2026Article
- Development and evaluation of a hybrid capture-based NGS panel for comprehensive detection of respiratory pathogens.Scientific reports · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
introductionRespiratory infections re-emerge unpredictably. Rapid pathogen identification is crucial for effective targeted therapy.
methodsFrom November 15, 2023, to December 15, 2023, 574 respiratory tract samples (nasopharyngeal and oropharyngeal swabs) were collected at Beijing Ditan Hospital and Beijing Haidian Hospital. Targeted next-generation sequencing (tNGS) was further used to examine the respiratory samples identified as unfavorable by quantitative real-time PCR (qPCR).
resultsUsing qPCR testing, 368 out of 574 samples (64.1%) were positive, while 206 samples (35.9%) showed no pathogen. TNGS further found that 167 out of these 206 cases (81.1%) had pathogens detected, with 58 different pathogens identified. The most frequent viruses, bacteria, and fungi were H3N2 (n = 73), Streptococcus pneumoniae (S. pneumoniae) (n = 18), Staphylococcus aureus (S. aureus) (n = 18), and Candida albicans (C. albicans) (n = 17). There were 102 cases of mixed infections, among which H3N2 appeared most frequently (51/102, 50%), and coinfections often involved Human betaherpesvirus 7 and S. aureus. In 20 cases where antibiotic resistance genes (ARGs) were detected, four were infected with H3N2. Among these, TEM and tetB were associated with Acinetobacter baumannii, APH was associated with Stenotrophomonas maltophilia, and the remaining resistance genes were linked to S. pneumoniae.
conclusionTNGS is more sensitive than qPCR for detecting pathogens, which is crucial for identifying prevalent and harmful ones like H3N2, S. pneumoniae, and S. aureus. Its integration into routine clinical testing is recommended, though more research is needed for clear guidelines.
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