ArticleEFSA journal. European Food Safety Authority2019
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.
Article in EFSA journal. European Food Safety Authority, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
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Who cites it
100 citing papers in PubMed, 1 synthesis or guideline pooled it, 163 citations in OpenAlex.
- A statistical modelling approach for source attribution meta-analysis of sporadic infection with foodborne pathogens.Zoonoses and public health · 2022Pooled it
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- Biocontrol of Mycotoxin-Producing Fungi by Lactic Acid Bacteria.Foods (Basel, Switzerland) · 2026Review
- Sources of Human Campylobacteriosis Cases in Estonia and the Genomic Associations with Broiler Chicken Meat Isolates.Pathogens (Basel, Switzerland) · 2026Article
- Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.Microbial genomics · 2026Article
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- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Phylogeographic clustering ofApplied and environmental microbiology · 2026Article
- Are fermented foods safe for human health? A systematic analysis of the literature.Frontiers in nutrition · 2026Review
- Whole-genome sequencing-based characterization of resistome and virulome inFrontiers in microbiology · 2026Article
- Phenotypic and molecular characterization of Salmonella enterica isolated from retail beef in Peshawar, Pakistan.PloS one · 2026Article
- Genomic and resistome characterization of a multidrug-resistantFrontiers in microbiology · 2026Article
- GWAS Study Applied to Phenotypically Slow Growth Strains ofMicroorganisms · 2025Article
- Can Metagenomic Analyses Be Used Effectively in Safe Food Production?Food science & nutrition · 2025Review
- Advancing microbial risk assessment: perspectives from the evolution of detection technologies.NPJ science of food · 2025Review
- Molecular epidemiology ofAntimicrobial agents and chemotherapy · 2025Article
- Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.Applied and environmental microbiology · 2025Article
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for
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