ArticleJournal of clinical microbiology2023
Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.
Article in Journal of clinical microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 56 citations in OpenAlex.
- Emergence of a Novel, Phenotypically Difficult-to-Detect Vancomycin-Resistant Enterococcus faecium Clone (ST117/CT7799).MicrobiologyOpen · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- Prospective genomic and epidemiologic surveillance of Klebsiella pneumoniae in a tertiary NICU.Antimicrobial resistance and infection control · 2026Article
- Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial 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
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- Article
- An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.Journal of clinical microbiology · 2025Article
- Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.Genome research · 2025Article
- Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.Diagnostics (Basel, Switzerland) · 2025Review
- Review
- Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens likeJournal of clinical microbiology · 2025Article
- Comparison of Illumina and Oxford Nanopore sequencing data quality for Clostridioides difficile genome analysis and their application for epidemiological surveillance.BMC genomics · 2025Article
- PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.GigaScience · 2025Article
- A One Health approach for the genomic characterization of antibiotic-resistantFrontiers in microbiology · 2025Article
- Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2025Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.
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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.