ArticleScientific reports2023
Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- The African Polio Laboratory Network: Advancing Regional Poliovirus Detection, Genomic Surveillance, and Eradication.Vaccines · 2026Article
- Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.Animal microbiome · 2026Article
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- Article
- Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.Journal of epidemiology and global health · 2025Review
- Analytical techniques and molecular platforms for detection and surveillance of antimicrobial resistance: advancements of the past decade.3 Biotech · 2025Review
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing (mNGS) in Hospital-Acquired Pneumonia: A Stratified Retrospective Study of Responders and Non-Responders.Risk management and healthcare policy · 2025Article
- Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.Frontiers in microbiology · 2025Article
- Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.Frontiers in microbiology · 2024Article
- The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections.Frontiers in cellular and infection microbiology · 2024Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.
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Registered trials
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