ArticleBMC infectious diseases2025
Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection.
Article in BMC infectious diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.Diagnostics (Basel, Switzerland) · 2026Review
- Respiratory Infection-Related Pathogens in the Pediatric Intensive Care Unit During 2019-2024 in Hubei, China.Pathogens (Basel, Switzerland) · 2026Article
- Etiological characteristics and risk factors for severe disease in bocavirus-associated community-acquired pneumonia in children: a multicenter retrospective study.BMC infectious diseases · 2026Article
- Spatio-temporal differences and associations between upper and lower respiratory microbiota in ventilator-associated pneumonia.Frontiers in cellular and infection microbiology · 2026Article
- Associations of targeted next-generation sequencing with antimicrobial stewardship and clinical outcomes in pediatric lower respiratory tract infections.Respiratory research · 2025Article
- 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
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10 authors.
Funding
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Abstract
backgroundAcute respiratory infections (ARIs) pose a significant global health burden, particularly affecting infants and young children with high morbidity and mortality rates. Targeted next-generation sequencing (tNGS) has emerged as a rapid and cost-effective diagnostic tool capable of identifying a broad range of respiratory tract infections.
methodsOropharyngeal swabs and sputum samples were collected from patients and subjected to tNGS and sputum culture, respectively, for diagnosing ARIs. A retrospective analysis was conducted on clinical data to explore the clinical diagnosis and therapeutic application of tNGS.
resultsThis study included 336 pediatric patients with confirmed ARIs. tNGS detected 38 potential pathogens, comprising 25 species (15 bacteria and 10 viruses) and 13 viral subtypes. The overall microbial detection rate using tNGS was 100%. The leading bacterial pathogens identified were Streptococcus pneumoniae (36.0%), Stenotrophomonas maltophilia (30.4%), Streptococcus intermedius (29.5%), Moraxella catarrhalis (27.1%), and Hemophilus influenzae (20.2%). The predominant viral pathogens included human adenovirus (31.3%), human rhinovirus (26.5%), human parainfluenza virus (25.0%), cytomegalovirus (19.0%), and human bocavirus (11.0%). Among the 94 patients who underwent simultaneous sputum culture and Gram staining, tNGS exhibited a superior detection rate compared to sputum culture (100% vs. 53.2%). Among the 50 patients with concordant positive results for both tNGS and sputum culture, 80% (40/50) demonstrated full or partial agreement. Additionally, tNGS revealed age-specific heterogeneity in pathogen distribution across different age groups.
conclusionTraditional diagnostic methods often fall short of meeting the diagnostic demands of ARIs. This study underscores the potential of tNGS in oropharyngeal swabs for enhancing pathogen detection, thereby improving the diagnosis, treatment, and prevention of ARIs. IMPORTANCE: This study represents the first investigation utilizing oropharyngeal swabs for tNGS in diagnosing and treating ARIs. By analyzing surveillance data from a local hospital's patients with ARIs, we have identified the spectrum of bacterial and viral pathogens and explored demographic differences among patients. These findings underscore the potential of tNGS in ARI surveillance, diagnosis, pathogen detection, and prevention.
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