ArticlePloS one2019
Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 92 citations in OpenAlex.
- Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction.Scientific reports · 2026Article
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- An Outbreak of Multidrug-ResistantTropical medicine and infectious disease · 2025Review
- Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy.Briefings in functional genomics · 2025Review
- Pathogenomes of Shiga Toxin Positive and NegativeMicroorganisms · 2024Article
- Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing.Scientific reports · 2024Article
- Article
- Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria.Diagnostics (Basel, Switzerland) · 2023Review
- The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing.BMC biotechnology · 2023Article
- 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
- Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device.BMC bioinformatics · 2023Article
- Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.PLoS computational biology · 2023Article
- Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing.Antimicrobial agents and chemotherapy · 2023Article
- Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producingFrontiers in microbiology · 2023Article
- Phylogenetic relationship and virulence composition ofFrontiers in microbiology · 2023Article
- Article
- Hybrid Genomic Analysis ofMicroorganisms · 2022Article
- A step forward for Shiga toxin-producingMicrobial genomics · 2022Article
- Subtyping Evaluation ofApplied and environmental microbiology · 2022Article
- Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche.BMC genomics · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete Shiga toxin-producing Escherichia coli (STEC) O26:H11/H- genomes from two different sequence types (ST21 and 29), each acquired using the Nextera XT MiSeq, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read whole genome sequencing (WGS) using Nextera XT MiSeq failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobial genes, and composition/location of Stx phages. Taken together, positive correlations between the two long-read methods for determining plasmids, virulome, antimicrobial resistance genes, and phage composition support MinION sequencing as one accurate and economical option for closing STEC genomes and identifying specific virulence markers.
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