Beyond Outbreak Detection: Mandatory Genomic Surveillance in the EU as an Opportunity to Quantify Metal-Mediated Co-Selection of Antimicrobial Resistance from a One Health Perspective

Copper supplementation in European pig production selects for the pandemic multidrug-resistant (MDR) monophasic Salmonella Typhimurium ST34 clone through Salmonella Genomic Island 4, which co-carries copper/silver resistance and antimicrobial resistance determinants on the same mobile genetic element — a paradigmatic example of non-antibiotic co-selective pressure connecting animal health, food safety, and public health under the One Health paradigm. EU Regulation 2025/179, which mandates whole-genome sequencing for foodborne outbreak investigation from August 2026, will generate an unprecedented genomic data infrastructure across Europe; this infrastructure contains, as an inherent by-product of sequencing, the metal resistance markers that would enable quantification of such co-selective pressures — a capability that extends beyond the outbreak detection purpose for which it was conceived. Multi-dimensional genomic risk assessment frameworks integrating virulence, environmental persistence, and antimicrobial resistance into quantitative actionable indices represent a pathway to realise this opportunity, connecting copper reduction in animal feed (Regulation 2018/1039) with genomic surveillance (Regulation 2025/179) along a One Health continuum from farm to patient.