Training in metagenomics-integrated risk assessment for food-borne pathogens in the Slovenian and Spanish meat chain (METAMEAT)

Next-generation sequencing (NGS) has become an essential tool for antimicrobial resistance (AMR) surveillance, enabling comprehensive detection of AMR determinants in both bacterial isolates and complex microbial communities. Metagenomic sequencing enables culture-independent profiling of antimicrobial resistance genes (ARGs) in different environments, while whole-genome sequencing (WGS) is widely used in AMR surveillance laboratories to predict phenotypic resistance in major food-borne pathogens. AMR risk assessment usually considers factors such as the pathogenicity of the ARG-carrying bacterial host, the abundance of ARGs and their mobility potential inferred from association with plasmids or other mobile genetic elements that facilitate horizontal gene transfer. Clinical relevance of antimicrobials and the severity of clinical outcomes can further be implemented in AMR risk assessment. Exposure assessment contextualises hazards within real-world scenarios by estimating consumer exposure to AMR bacteria or their ARGs through food or other routes. Despite challenges in fully quantitative assessments, the integration of NGS-based surveillance with risk modelling represents a critical step towards proactive AMR risk management. In this study, broiler samples from different stages of a Slovenian and a Spanish slaughterhouse were analysed using conventional microbiology, shotgun metagenomic sequencing and WGS of isolates of selected pathogenic species. A modular, semi-quantitative risk assessment model was developed that combines (meta)genomic data with key risk factors and, where available, exposure assessment. This approach prioritises AMR risks in broiler meat processing and supports evidence-based decision-making in the areas of food safety and public health.