Mapping the resistome of five meat-processing facilities through long-read metagenomics

Antimicrobial resistance (AMR) is a major global public health threat, and the food chain may play a key role in its dissemination. From livestock production to processing and consumption, antimicrobial resistance genes (ARGs) can spread across animals, food products, processing environments, and humans, compromising food safety and the effectiveness of antimicrobials. This study examines the resistome, and its association with mobile genetic elements, in various meat-processing facilities using long-read sequencing, providing a comprehensive overview of the main ARGs circulating across beef, pork, and poultry environments. The results showed a progressive decline in ARG abundance along processing lines, from slaughterhouses to cutting plants, in the different sample types analysed, which included non-food contact surfaces, drains, and carcasses/meat cuts. Acinetobacter, Aeromonas, and Psychrobacter were identified as the main ARG-carrying genera, and clustering analyses highlighted distinct ARG profiles and the role of drains as reservoirs of critical ARGs. The most abundant ARGs found were associated with resistance against tetracyclines, lincosamides, aminoglycosides and beta-lactams. Additionally, more than 100 plasmidic contigs and long reads carrying multiple ARGs were recovered and thoroughly characterised. Furthermore, metagenome-assembled genomes were reconstructed, revealing distinct taxonomic profiles across facilities while showing similar ARG patterns across related surfaces. These findings underscore the persistence and transfer potential of ARGs in meat-processing environments and demonstrate the value of long-read sequencing for detecting plasmid-mediated resistance. Such approaches can support targeted surveillance and mitigation strategies to limit the spread of AMR within food production systems.