ArticleInternational journal of molecular sciences2020
Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.Journal of translational medicine · 2025Article
- Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.Frontiers in microbiology · 2024Article
- Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.Applied and environmental microbiology · 2023Article
- Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producingFrontiers in microbiology · 2023Article
- Proof of Concept for the Detection with Custom Printed Electrodes of Enterobactin as a Marker ofInternational journal of molecular sciences · 2022Article
- Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool.Microorganisms · 2022Article
- Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics usingMicrobial genomics · 2021Article
- Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of aMicrobial genomics · 2021Article
- Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies.Frontiers in microbiology · 2021Article
- A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.Microorganisms · 2020Article
- The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country.Foods (Basel, Switzerland) · 2020Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same species, present in a microbial community, which has up until now not been demonstrated for this application. The current work shows the feasibility of strain-level metagenomics of enriched food matrix samples making use of data analysis tools that classify reads against a sequence database. It includes a brief comparison of two database-based read classification tools, Sigma and Sparse, using a mock community obtained by in vitro spiking minced meat with a Shiga toxin-producing
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Registered trials
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