ArticleJournal of clinical microbiology2024
A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.
Article in Journal of clinical microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Emergence of a Novel, Phenotypically Difficult-to-Detect Vancomycin-Resistant Enterococcus faecium Clone (ST117/CT7799).MicrobiologyOpen · 2026Article
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026Article
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Article
- Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology.BMC medical genomics · 2026Article
- Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.Frontiers in microbiology · 2026Review
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
- From Methylomes to CRISPR Epigenetic Editing: New Paths in Antibiotic Resistance.Pathogens (Basel, Switzerland) · 2025Review
- A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis.Scientific data · 2025Article
- Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.Diagnostics (Basel, Switzerland) · 2025Review
- Pharmaceutical and biomedical challenges for crew autonomy in health preservation during future exploration missions.Communications medicine · 2025Review
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- Article
- Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data.Journal of clinical microbiology · 2025Article
- Rapid identification of a Serratia marcescens outbreak in a neonatal intensive care unit by third-generation long-read nanopore sequencing.Antimicrobial resistance and infection control · 2025Article
- Genomics for antimicrobial resistance-progress and future directions.Antimicrobial agents and chemotherapy · 2025Review
- Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications.BMC genomics · 2025Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across participants at read level. Depending on the frequency of incorrect target reads, this either leads to correct or incorrect typing, whereby only minimal frequency deviations can randomly determine the final result. PCR preamplification, recent basecalling model updates and an optimized polishing strategy notably diminished the non-reproducible typing. Our study highlights the potential for new errors to appear with each newly sequenced strain and lays the foundation for computational approaches to reduce such typing errors. In conclusion, our multicenter study shows the necessity for a new validation concept for nanopore sequencing-based, standardized bacterial typing, where single nucleotide accuracy is critical.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.