ArticlePloS one2021
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 57 citations in OpenAlex.
- Genomic Characterization of an O-Antigen-Deficient, Hydrogen Sulfide-NegativeMicroorganisms · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications.Veterinary sciences · 2026Review
- Article
- Origin and development of twoMicrobial genomics · 2025Article
- Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.Applied and environmental microbiology · 2025Review
- Centriflaken: An automated data analysis pipeline for assembly and in silico analyses of foodborne pathogens from metagenomic samples.PloS one · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of AllMicroorganisms · 2024Article
- Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.International journal of molecular sciences · 2024Article
- Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef.Foods (Basel, Switzerland) · 2024Article
- Evaluation of Long-Read Sequencing Simulators to Assess Real-World Applications for Food Safety.Foods (Basel, Switzerland) · 2023Article
- Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction.BMC genomics · 2023Article
- Resistance and Virulence Surveillance inMicroorganisms · 2023Article
- Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-ProducingMicroorganisms · 2023Article
- Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum.Scientific reports · 2023Article
- Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.Foods (Basel, Switzerland) · 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
- Tunable Magneto-Plasmonic Nanosensor for Sensitive Detection of Foodborne Pathogens.Biosensors · 2023Article
- Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producingFrontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial genomes from whole genome sequencing play an important role in source tracking. We aimed to determine the limits of detection and classification of STECs by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL933). We determined the limit of STEC detection by qPCR to be 30 CFU/reaction, which is equivalent to 105 CFU/ml in the enrichment. By using Oxford Nanopore's EPI2ME WIMP workflow and de novo assembly with Flye followed by taxon classification with a k-mer analysis software (Kraken2), E. coli O157:H7 could be detected at 103 CFU/ml (68 reads) and a complete fragmented E. coli O157:H7 metagenome-assembled genome (MAG) was obtained at 105-108 CFU/ml. Using a custom script to extract the E. coli reads, a completely closed MAG was obtained at 107-108 CFU/ml and a complete, fragmented MAG was obtained at 105-106 CFU/ml. In silico virulence detection for E. coli MAGs for 105-108 CFU/ml showed that the virulotype was indistinguishable from the spiked E. coli O157:H7 strain. We further identified the bacterial species in the un-spiked enrichment, including antimicrobial resistance genes, which could have important implications to food safety. We propose this workflow provides proof of concept for faster detection and complete genomic characterization of STECs from a complex microbial sample compared to current reporting protocols and could be applied to determine the limit of detection and assembly of other foodborne bacterial pathogens.
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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.