ArticleJournal of clinical microbiology2024
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation 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 52 papers, 2 of them syntheses that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 2 syntheses or guidelines pooled it, 71 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
- Diagnostic accuracy of nanopore sequencing for detecting Mycobacterium tuberculosis and drug-resistant strains: a systematic review and meta-analysis.Scientific reports · 2025Pooled it
- Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.Microbiology spectrum · 2026Article
- Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- Fluoroquinolone resistance in Escherichia coli in the broiler production chain: the role of parent stock and hatchery.Poultry science · 2026Article
- Enhancing low-level genome-edited crop detection and identification in food mixtures using nanopore adaptive sampling: Rice-Soybean mixture as proof-of-concept.NPJ science of food · 2026Article
- From Diagnostic Accuracy to Decision-Grade Respiratory Nanopore Metagenomics: Minimum Standards, Stewardship Endpoints, and Equitable Implementation.Current microbiology · 2026Article
- Technical feasibility of a long read, fourth generation sequencing platform in diagnostic profiling of clinical routine samples: a proof-of-concept study.Pathologica · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- 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
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Genomic characterization of non-CC398 methicillin-resistantFrontiers in public health · 2026Article
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.mSystems · 2025Article
- A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis.Scientific data · 2025Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing
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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.