ArticleJournal of translational medicine2025
Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections.
Article in Journal of translational medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.The Journal of infectious diseases · 2026Article
- Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.Respiratory research · 2026Article
- Analytic and Diagnostic Validation of a Targeted Next-Generation Sequencing Panel for Common and Emerging Swine Respiratory Pathogens.Microorganisms · 2026Article
- Cell-free DNA methylation-based detection of organ damage following proton versus photon radiotherapy: a case series.Translational pediatrics · 2026Article
- Clinical features and prognostic factors ofFrontiers in medicine · 2026Article
- Clinical characteristics, co-detection patterns and prognostic risk factors of human metapneumovirus infection in children: a retrospective study.Frontiers in cellular and infection microbiology · 2026Article
- Diagnostic Insights Into Pathogen Spectrum and Mixed Microbial Detection in Critically Ill Patients With Pulmonary Infection Using Targeted Next-Generation Sequencing.Canadian respiratory journal · 2026Article
- Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia.Infection and drug resistance · 2026Article
- The diagnostic value of targeted next-generation sequencing for smear-negative and sputum-scarce pulmonary tuberculosis.American journal of translational research · 2026Article
- Targeted next-generation sequencing-based pathogens detection in children with severe pneumonia in the pediatric intensive care unit.Frontiers in pediatrics · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Post-endoscopic neurosurgicalFrontiers in medicine · 2026Article
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Research progress on the current status of respiratory pathogen infections and their detection methods.Frontiers in microbiology · 2026Review
- The value of metagenomic next-generation sequencing in lower respiratory tract infections among critically ill patients in the ICU.Frontiers in cellular and infection microbiology · 2026Article
- Ultra-broad hybrid capture-based targeted next-generation sequencing for sensitive plasma pathogen cfDNA detection in bloodstream infections.Journal of translational medicine · 2025Article
- From Panels to Pathogen Networks: The Expanding Role of Targeted Sequencing in Veterinary Medicine.Biology · 2025Review
- Performance of broad-spectrum targeted next-generation sequencing in lower respiratory tract infections in ICU patients: a prospective observational study.Critical care (London, England) · 2025Observational
- tNGS-based detection of respiratory pathogens in a single center: associations with age, gender, season, and co-infections.Frontiers in cellular and infection microbiology · 2025Article
- Targeted next-generation sequencing using bronchoalveolar lavage fluid samples for diagnosing pulmonary infections: a single-center retrospective study.Frontiers in microbiology · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundThe clinical value of shotgun metagenomic next-generation sequencing (mNGS) in improving the detection rates of respiratory pathogens is well-established. However, mNGS is complex and expensive. This study designed and evaluated the performance of targeted NGS (tNGS) in diagnosing respiratory infections.
methodsWe retrospectively included samples from 281 patients with lower respiratory tract infections to establish thresholds of pathogens. Subsequently, target pathogens were selected and a probe hybridization system was established. The performance and clinical manifestations of tNGS for 306 pathogens were evaluated using clinical and simulated samples.
resultsThe tNGS method took 16 h with sequencing data sizes of 5 M reads. The limit-of-detection of tNGS was 100-200 CFU/mL, respectively. Bioinformatics simulation confirmed the method's high specificity and robustness. In 281 patients of clinical validation cohort, tNGS exhibited a sensitivity of 97.73% and specificity of 75.41% compared to the composite reference standard, which notably surpasses those of culture-based and conventional microbiological methods (CMT). In detecting bacterial and viral infection, tNGS demonstrated superior sensitivity relative to CMT. Notably, 61.40% of target viruses were subtype-resolved with the initial establishment of reliable typing cutoffs, with the subtyping results being completely consistent with the PCR results. tNGS allowed for concurrent identification of antimicrobial resistance (AMR) markers and viral subtyping. 80.56% of AMR markers identified by tNGS were consistent with antimicrobial susceptibility testing.
conclusionThis research established the robust performance of our tailored tNGS assay in the simultaneous detection of DNA and RNA pathogens, underscoring its prospective suitability for widespread use in clinical diagnostics.
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