https://phaidra.vetmeduni.ac.at/o:4882 The food-associated resistome is shaped by processing and production environments Quijada, Narciso M. Narciso M. Quijada 0000-0002-1956-7205 University of Veterinary Medicine Vienna Barcenilla, Coral Coral Barcenilla De Filippis, Francesca Francesca De Filippis 0000-0002-3474-2884 Cabrera-Rubio, Raul Raul Cabrera-Rubio Carlino, Niccolò Niccolò Carlino 0009-0004-7409-449X Pinto, Federica Federica Pinto Dzieciol, Monika Monika Dzieciol 0000-0002-0972-6241 University of Veterinary Medicine Vienna Calvete-Torre, Inés Inés Calvete-Torre 0000-0001-5509-7696 Sabater, Carlos Carlos Sabater 0000-0002-6098-895X Rubino, Francesco Francesco Rubino 0000-0001-9090-6794 Knobloch, Stephen Stephen Knobloch Skirnisdottir, Sigurlaug Sigurlaug Skirnisdottir 0000-0003-4478-6001 Ruiz, Lorena Lorena Ruiz 0000-0001-8199-5502 López, Mercedes Mercedes López Prieto, Miguel Miguel Prieto 0000-0001-9202-3856 Marteinsson, Viggó Thór Viggó Thór Marteinsson Margolles, Abelardo Abelardo Margolles Segata, Nicola Nicola Segata 0000-0002-1583-5794 Cotter, Paul D. Paul D. Cotter 0000-0002-5465-9068 Wagner, Martin Martin Wagner 0000-0001-8032-9858 University of Veterinary Medicine Vienna Ercolini, Danilo Danilo Ercolini Alvarez-Ordóñez, Avelino Avelino Alvarez-Ordóñez 0000-0002-9951-4786 Cobo-Díaz, José F. José F. Cobo-Díaz 0000-0002-0898-2358 Valentino, Vincenzo Vincenzo Valentino 0000-0002-6055-4721 Springer journal article open access 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. Antimicrobial Resistance Microbiome http://creativecommons.org/licenses/by-nc-nd/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:4882/download 10.1038/s41564-025-02059-8 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Nature Microbiology issn:2058-5276 VoR Nature Microbiology 10 8 1854 1867 10.70 MB 2025