ArticleInfection and drug resistance2023
Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach.
Article in Infection and drug resistance, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Pooled it
- Optimisation and validation of capture mNGS for predicting antimicrobial resistance.EBioMedicine · 2026Article
- Clinical utility of the targeted next-generation sequencing for detection of Mycoplasma pneumoniae and antimicrobial resistance genes for adults.BMC infectious diseases · 2026Article
- Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.Frontiers in microbiology · 2026Article
- Article
- Metagenomics and its impact on environmental and therapeutic microbiology.Archives of microbiology · 2025Review
- Epidemiology and prediction of non-targeted bacteria by the filmarray pneumonia plus panel in culture-positive ventilator-associated pneumonia: a retrospective multicentre analysis.Annals of intensive care · 2025Article
- Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future.Diagnostics (Basel, Switzerland) · 2025Review
- Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluids Improves Pathogen Detection and Antimicrobial Stewardship in Lower Respiratory Tract Infections: A Retrospective Study.Infection and drug resistance · 2025Article
- Comparative Evaluation of mNGS and Traditional Culture Methods in Pathogen Detection for Pulmonary Infections.Infection and drug resistance · 2025Article
- Solving the diagnostic dilemma in bone infections: metagenomic next generation sequencing enhances pathogen identification accuracy.Frontiers in medicine · 2025Article
- The diagnostic value of RNA-mNGS and DNA-mNGS in differentiating bacterial infection from colonization in the lower respiratory tract.Frontiers in cellular and infection microbiology · 2025Article
- Effect of metagenomic next-generation sequencing on clinical outcomes in adults with severe pneumonia post-cardiac surgery: a single-center retrospective study.Scientific reports · 2024Article
- High utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing approach for etiological diagnosis of pneumonia.BMC infectious diseases · 2024Article
- Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario.Frontiers in cellular and infection microbiology · 2024Article
- Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia.Infection and drug resistance · 2024Article
- Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.Frontiers in microbiology · 2024Article
- Uncovering the Resistance Mechanisms in Extended-Drug-ResistantMicroorganisms · 2023Article
- Antimicrobial Resistance in Ventilator-Associated Pneumonia: Predictive Microbiology and Evidence-Based Therapy.Infectious diseases and therapy · 2023Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs). Patients and Methods: Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS. Results: ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP ( Conclusion: In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.
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