Narciso M. Quijada Narciso M. Quijada Coral Barcenilla Coral Barcenilla Francesca De Filippis Francesca De Filippis Raul Cabrera-Rubio Raul Cabrera-Rubio Niccolò Carlino Niccolò Carlino Federica Pinto Federica Pinto Monika Dzieciol Monika Dzieciol Inés Calvete-Torre Inés Calvete-Torre Carlos Sabater Carlos Sabater Francesco Rubino Francesco Rubino Stephen Knobloch Stephen Knobloch Sigurlaug Skirnisdottir Sigurlaug Skirnisdottir Lorena Ruiz Lorena Ruiz Mercedes López Mercedes López Miguel Prieto Miguel Prieto Viggó Thór Marteinsson Viggó Thór Marteinsson Abelardo Margolles Abelardo Margolles Nicola Segata Nicola Segata Paul D. Cotter Paul D. Cotter Martin Wagner Martin Wagner Danilo Ercolini Danilo Ercolini Avelino Alvarez-Ordóñez Avelino Alvarez-Ordóñez José F. Cobo-Díaz José F. Cobo-Díaz Vincenzo Valentino Vincenzo Valentino Springer 2025 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. PDFDocument eng 2026-02-05T09:32:18.417971Z 2025 Antimicrobial Resistance Microbiome 11224703 b application/pdf http://creativecommons.org/licenses/by-nc-nd/4.0/