ArticleNature microbiology2025
The food-associated resistome is shaped by processing and production environments.
Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Age- and diet-driven assembly of the gut antibiotic resistome in humans and food-producing animals.Gut microbes · 2026Review
- Evaluating packaged ice safety using culture-based and metagenomic methods.Microbiology (Reading, England) · 2026Article
- Occurrence and Antimicrobial Resistance ofFoods (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
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Retrieving of diguanylate cyclases responsible for biofilm formation and antibiotic resistance in Acinetobacter baumannii.BMC microbiology · 2026Article
- DiverseMicrobiology spectrum · 2026Article
- Antimicrobial Resistance Along the Food Chain: Spread and Integrated Strategies for Mitigation and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Microbial succession accompanies increased antibiotic resistance risk during grass carp (Ctenopharyngodon idella) spoilage under ambient household conditions.BMC microbiology · 2026Article
- Ecological context structures duplication and mobilization of antibiotic and metal resistance genes in bacteria.bioRxiv : the preprint server for biology · 2026Article
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- Combined Effect of Plasma-Activated Water, Edible Coating, and Active Packaging on Cherry Tomato Shelf-Life: Kinetics and Microbiome Approach.Foods (Basel, Switzerland) · 2026Article
- From farm to factory to fork.Nature microbiology · 2025Article
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Food production systems may act as transmission routes for antimicrobial-resistant (AMR) bacteria and AMR genes (AMRGs) to humans. However, the food resistome remains poorly characterized. Here 1,780 raw-material (milk, brine, fresh meat and so on), end-product (cheese, fish, meat products and vegetables) and surface (processing, cooling, smoking, ripening and packing rooms) samples from 113 food processing facilities were subjected to whole-metagenome sequencing. Assembly-free analyses demonstrated that >70% of all known AMRGs, including many predicted to confer resistance to critically important antibiotics, circulate throughout food production chains, with those conferring resistance to tetracyclines, β-lactams, aminoglycosides and macrolides being the most abundant overall. An assembly-based analysis highlighted that bacteria from the ESKAPEE group, together with Staphylococcus equorum and Acinetobacter johnsonii, were the main AMRG carriers. Further evaluation demonstrated that ~40% of the AMRGs were associated with mobile genetic elements, mainly plasmids. These findings will help guide the appropriate use of biocides and other antimicrobials in food production settings when designing efficient antimicrobial stewardship policies.
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