ArticleMicroorganisms2020
A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.
Article in Microorganisms, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
- Assessing the authenticity and purity of a commercialFrontiers in microbiology · 2025Article
- A metagenomics-based workflow for the detection and genomic characterization of GBS in raw freshwater fish.Microbiology spectrum · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.Frontiers in microbiology · 2024Article
- Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-ProducingMicroorganisms · 2023Article
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.Applied and environmental microbiology · 2023Article
- A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products.Food chemistry. Molecular sciences · 2021Article
- Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of aMicrobial genomics · 2021Article
- Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-ProducingFrontiers in cellular and infection microbiology · 2021Article
- Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient's isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing
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