ArticleInfection and drug resistance2025
Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence.
Article in Infection and drug resistance, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The controversial interplay between hyperinflammation and immunosenescence in elderly critically ill co-infected patients.BMC geriatrics · 2026Article
- Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.Diagnostics (Basel, Switzerland) · 2026Review
- Clinical utility of the targeted next-generation sequencing for detection of Mycoplasma pneumoniae and antimicrobial resistance genes for adults.BMC infectious diseases · 2026Article
- A Pilot Study ofDiagnostics (Basel, Switzerland) · 2026Article
- Leveraging real-time genomic surveillance to combat infectious diseases and antimicrobial resistance in cancer patients.Frontiers in public health · 2026Article
- No culture? No problem: Clinical utility and pitfalls of non-culture diagnostics for pneumococcal parapneumonic effusions.Frontiers in medicine · 2026Review
- Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.Frontiers in cellular and infection microbiology · 2026Article
- Clinical evaluation of probe capture-based targeted next-generation sequencing in suspected infected pancreatic necrosis: a prospective pilot diagnostic study.BMC infectious diseases · 2025Article
- Targeted next-generation sequencing using bronchoalveolar lavage fluid samples for diagnosing pulmonary infections: a single-center retrospective study.Frontiers in microbiology · 2025Article
- Metagenomic sequencing for identification of nontuberculous mycobacteria and other pathogens in patients with mixed infection of the lung.Frontiers in cellular and infection microbiology · 2025Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Targeted next-generation sequencing (tNGS) is a high-throughput and cost-effective diagnostic alternative for pneumonia, with the ability to simultaneously detect pathogens, antimicrobial resistance genes, and virulence genes. We aimed to explore the applicability of tNGS in the co-detection of the responsible pathogens, antimicrobial resistance (AMR) genes, and virulence genes in patients with pneumonia. Methods: A prospective study was conducted among patients with suspected pneumonia at Ruijin Hospital from March 1 to May 31, 2023. Bronchoalveolar lavage fluid (BALF) or sputum samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and conventional microbiological tests (CMTs). Results: In total, 67 BALF and 11 sputum samples from 78 patients were included in the analyses. According to the composite reference standards, the accuracy of tNGS in the detection of responsible pathogens was 0.852 (95% confidence interval 0.786-0.918), which resembled that of mNGS and remarkably exceeded that of CMTs. In addition, 81 AMR genes associated with responsible pathogens were reported, and 75.8% (25/33) priority drug-resistant pathogens could be directly identified. A total of 144 virulence genes were detected for four common pathogens. And patients with virulence genes detected were of higher proportions of severe pneumonia (95.0% vs 42.9%, P = 0.009), acute respiratory distress syndrome (55.0% vs 0%, P = 0.022), and neutrophils (82.3% vs 62.2%, P = 0.026) than those not. Conclusion: In patients with pneumonia, tNGS could detect the responsible pathogens, AMR genes, and virulence genes simultaneously, serving as an efficient and cost-effective tool for the diagnosis, treatment, and severity indication of pneumonia.
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