ArticleScientific reports2019
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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Who cites it
31 citing papers in PubMed, 62 citations in OpenAlex.
- Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications.Veterinary sciences · 2026Review
- Retrospective analysis and decentralized distribution to improve the lifecycle of Ah receptor research assets.Biochemical pharmacology · 2025Article
- Preventing Multimer Formation in Commonly Used Synthetic Biology Plasmids.ACS synthetic biology · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery.Scientific reports · 2024Article
- Article
- Complete genome sequences of 17Microbiology resource announcements · 2024Article
- Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.BMC microbiology · 2024Article
- Genetic relatedness and virulence potential ofFrontiers in microbiology · 2024Article
- Comparison of next generation technologies and bioinformatics pipelines for capsular typing ofJournal of clinical microbiology · 2023Article
- Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.Veterinary sciences · 2023Review
- A preliminary study of the use of MinION sequencing to specifically detect Shiga toxin-producing Escherichia coli in culture swipes containing multiple serovars of this species.Scientific reports · 2023Article
- New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.Life science alliance · 2023Article
- Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device.BMC bioinformatics · 2023Article
- Rapid diagnosis ofFrontiers in cellular and infection microbiology · 2023Article
- Hybrid Genomic Analysis ofMicroorganisms · 2022Article
- Rapid Oxford Nanopore Technologies MinION Sequencing Workflow for Campylobacter jejuni Identification in Broilers on Site—A Proof-of-Concept StudyAnimals : an open access journal from MDPI · 2022Article
- Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection.NAR genomics and bioinformatics · 2022Article
- High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing.Microbial genomics · 2022Article
- Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli.PloS one · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
U.S. public health agencies have employed next-generation sequencing (NGS) as a tool to quickly identify foodborne pathogens during outbreaks. Although established short-read NGS technologies are known to provide highly accurate data, long-read sequencing is still needed to resolve highly-repetitive genomic regions and genomic arrangement, and to close the sequences of bacterial chromosomes and plasmids. Here, we report the use of long-read nanopore sequencing to simultaneously sequence the entire chromosome and plasmid of Salmonella enterica subsp. enterica serovar Bareilly and Escherichia coli O157:H7. We developed a rapid and random sequencing approach coupled with de novo genome assembly within a customized data analysis workflow that uses publicly-available tools. In sequencing runs as short as four hours, using the MinION instrument, we obtained full-length genomes with an average identity of 99.87% for Salmonella Bareilly and 99.89% for E. coli in comparison to the respective MiSeq references. These nanopore-only assemblies provided readily available information on serotype, virulence factors, and antimicrobial resistance genes. We also demonstrate the potential of nanopore sequencing assemblies for rapid preliminary phylogenetic inference. Nanopore sequencing provides additional advantages as very low capital investment and footprint, and shorter (10 hours library preparation and sequencing) turnaround time compared to other NGS technologies.
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