ArticleMicrobial genomics2023
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen,
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 41 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Observational
- Prospective genomic and epidemiologic surveillance of Klebsiella pneumoniae in a tertiary NICU.Antimicrobial resistance and infection control · 2026Article
- De-novo assembly of 82 bacterial genomes using Nanopore sequencing and prediction of biosynthetic capacity.Scientific data · 2026Article
- Decentralized nanopore genomics reveals diverseMicrobial genomics · 2026Article
- Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes.PLoS biology · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Hybrid genome assembly and comprehensive genomic analysis of Lactiplantibacillus pentosus LP309 reveal its probiotic and technological potential.BMC genomics · 2026Article
- Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting.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
- Nanopore sequencing in suitcase lab enables improved detection ofFrontiers in microbiology · 2026Article
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
- A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis.Scientific data · 2025Article
- Nanopore Sequencing-Driven Mapping of Antimicrobial Resistance Genes in SelectedAntibiotics (Basel, Switzerland) · 2025Article
- Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.Genome research · 2025Article
- Reassessing the promise of NGS in sepsis diagnosis: overcoming scalability barriers.Future microbiology · 2025Article
- Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers.Antibiotics (Basel, Switzerland) · 2025Article
- Fast and accurateMicrobial genomics · 2025Article
- Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka.BMC veterinary research · 2025Article
- Analytical techniques and molecular platforms for detection and surveillance of antimicrobial resistance: advancements of the past decade.3 Biotech · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs. We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique
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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.