The food-associated resistome is shaped by processing and production environments

Title (eng)
The food-associated resistome is shaped by processing and production environments
Author
Narciso M. Quijada
Author
Coral Barcenilla
Author
Francesca De Filippis
Author
Raul Cabrera-Rubio
Author
Niccolò Carlino
Author
Federica Pinto
Author
Monika Dzieciol
Author
Inés Calvete-Torre
Author
Carlos Sabater
Author
Francesco Rubino
Author
Stephen Knobloch
Author
Sigurlaug Skirnisdottir
Author
Lorena Ruiz
Author
Mercedes López
Author
Miguel Prieto
Author
Viggó Thór Marteinsson
Author
Abelardo Margolles
Author
Nicola Segata
Author
Paul D. Cotter
Author
Martin Wagner
Author
Danilo Ercolini
Author
Avelino Alvarez-Ordóñez
Author
José F. Cobo-Díaz
Author
Vincenzo Valentino
Description (eng)
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.
Keywords (eng)
Antimicrobial ResistanceMicrobiome
Type (eng)
journal article
Language
[eng]
Persistent identifier
https://phaidra.vetmeduni.ac.at/o:4882
DOI
10.1038/s41564-025-02059-8
Is in series
Title (eng)
Nature Microbiology
Volume
10
Issue
8
ISSN
2058-5276
Issued
2025
Number of pages
25
From page
1854
To page
1867
Publication
Springer
Version type (eng)
version of record (published version)
Date issued
2025
Access rights (eng)
open access
License
CC BY-NC-ND 4.0 International
Rights statement (eng)
© 2025, The Author(s)