ArticleGenome medicine2024
Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology.
Article in Genome medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.Clinical microbiology reviews · 2026Review
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.Microbiology spectrum · 2026Article
- Review
- Proof-of-principle: nanopore adaptive sampling enables full blood group genome analysis and resolution of hybrid alleles.Blood advances · 2026Article
- Antibiotic resistance inFrontiers in microbiology · 2026Review
- Recent Advances and Future Perspectives in the Detection of Carbapenem-ResistantInfection and drug resistance · 2026Review
- Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review.Frontiers in public health · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Advances in the detection of Drug-Resistant bacteria: current trends and innovations.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Review
- Case Report: Rare Community-Acquired Pneumonia with Concurrent Methicillin-ResistantInfection and drug resistance · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Research advances in the application of microfluidic chip technology for rapid detection of antibiotic-resistant bacteria.Frontiers in cellular and infection microbiology · 2026Review
- GGut microbes · 2025Review
- Deep learning-driven morphological fingerprinting: rapid, accurate and low-cost pathogen identification via the analysis of dried patterns of droplets.Journal of nanobiotechnology · 2025Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.Diagnostics (Basel, Switzerland) · 2025Review
- The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research.npj antimicrobials and resistance · 2025Review
- Methodological Comparison of Short-Read and Long-Read Sequencing Methods on Colorectal Cancer Samples.International journal of molecular sciences · 2025Article
- Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance.Frontiers in cellular and infection microbiology · 2025Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBlood cultures are essential for diagnosing bloodstream infections, but current phenotypic tests for antimicrobial resistance (AMR) provide limited information. Oxford Nanopore Technologies introduces nanopore sequencing with adaptive sampling, capable of real-time host genome depletion, yet its application directly from blood cultures remains unexplored. This study aimed to identify pathogens and predict AMR using nanopore sequencing.
methodsIn this cross-sectional genomic study, 458 positive blood cultures from bloodstream infection patients in central Taiwan were analyzed. Parallel experiments involved routine microbiologic tests and nanopore sequencing with a 15-h run. A bioinformatic pipeline was proposed to analyze the real-time sequencing reads. Subsequently, a comparative analysis was performed to evaluate the performance of species identification and AMR prediction.
resultsThe pipeline identified 76 species, with 88 Escherichia coli, 74 Klebsiella pneumoniae, 43 Staphylococcus aureus, and 9 Candida samples. Novel species were also discovered. Notably, precise species identification was achieved not only for monomicrobial infections but also for polymicrobial infections, which was detected in 23 samples and further confirmed by full-length 16S rRNA amplicon sequencing. Using a modified ResFinder database, AMR predictions showed a categorical agreement rate exceeding 90% (3799/4195) for monomicrobial infections, with minimal very major errors observed for K. pneumoniae (2/186, 1.1%) and S. aureus (1/90, 1.1%).
conclusionsNanopore sequencing with adaptive sampling can directly analyze positive blood cultures, facilitating pathogen detection, AMR prediction, and outbreak investigation. Integrating nanopore sequencing into clinical practices signifies a revolutionary advancement in managing bloodstream infections, offering an effective antimicrobial stewardship strategy, and improving patient outcomes.
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