ArticleEBioMedicine2024
Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing.
Article in EBioMedicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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Who cites it
103 citing papers in PubMed.
- [Value of targeted next-generation sequencing in pathogen detection for neonates with respiratory distress syndrome: a prospective randomized controlled trial].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2025Trial
- Myxovirus resistance protein A to differentiate between viral and non-viral respiratory infections in adults: a prospective study.Emerging microbes & infections · 2026Article
- Landscape of the upper and lower airway microbiota in children with community-acquired pneumonia.Virulence · 2026Article
- Development of a recombinase-aided amplification assay for rapid and sensitive detection ofExperimental and therapeutic medicine · 2026Article
- Rapid diagnosis ofExperimental and therapeutic medicine · 2026Article
- Positive Syphilis Serology With Concurrent Disseminated Talaromycosis marneffei in a Patient With HIV: A Case Report.The American journal of case reports · 2026Article
- Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.Clinical microbiology reviews · 2026Review
- Development and Initial Analytical Evaluation of a Multiplex PCR-Based Targeted NGS Assay for Expanded Viral Detection in Clinical Respiratory Specimens.Diagnostics (Basel, Switzerland) · 2026Article
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- Occupational exposure to freshwater crustaceans as a route of paragonimiasis presenting with eosinophilic pleural effusion misdiagnosed as tuberculous pleurisy: A case report and literature review.Experimental and therapeutic medicine · 2026Article
- Article
- Application of targeted next-generation sequencing in children with community-acquired pneumonia.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Epidemiological and pathogen characteristics of symptomatic male reproductive tract infections in Hunan province: retrospective study.Scientific reports · 2026Article
- Associations of Mycoplasma pneumoniae load, co-infections, and macrolide resistance with clinical-laboratory profiles in hospitalized pediatric pneumonia: a targeted next-generation sequencing study of bronchoalveolar lavage fluid.Annals of clinical microbiology and antimicrobials · 2026Article
- Early targeted next-generation sequencing accelerates clinical recovery in children with community-acquired pneumonia: A retrospective study.Pakistan journal of medical sciences · 2026Article
- Next-generation sequencing: Driving a paradigm shift from pathogen detection to systems-level analysis.Infectious medicine · 2026Article
- Quantitative interpretation models for targeted next-generation sequencing in lower respiratory tract infections: a multicenter prospective study.Respiratory research · 2026Article
- Association between normalizedTranslational pediatrics · 2026Article
- Targeted next-generation sequencing for comprehensive diagnosis and drug resistance detection in pulmonary and extrapulmonary tuberculosis: a single-center retrospective study.Microbiology spectrum · 2026Article
- Diagnostic and Clinical Value of Targeted Next-Generation Sequencing for Pediatric Respiratory Infections in Northern China.The clinical respiratory journal · 2026Article
43 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
backgroundShotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice.
methodsWe used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed.
findingsmp-tNGS and hc-tNGS took 10.3 and 16 h, respectively, with low sequencing data sizes of 0.1 M and 1 M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450 CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P < 0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS.
interpretationtNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections.
fundingNational Natural Science Foundation of China (81625014 and 82202535).
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