Antimicrobial resistance in the swine production chain within a One Health perspective

Antimicrobial resistance (AMR) represents a critical and growing threat to global health. This doctoral thesis investigates AMR within the swine production chain from a One Health perspective, integrating pathogen-focused microbiology, metagenomic analyses, and environmental investigations to elucidate the mechanisms underlying its emergence, persistence, and dissemination. The first study identified the rare plasmid-mediated AmpC β-lactamase DHA-1 in Escherichia coli from the German food production chain. Although located on self-transferable plasmids and IS26-bounded structures, its spread appeared limited, possibly constrained by ecological competition with other ESBL/pAmpC plasmids or circulation in unmonitored Enterobacterales. These findings emphasize the importance of continuous surveillance and the combined use of molecular and phenotypic methods to assess emerging public health risks. The second study applied metagenomic sequencing to an Italian swine slaughterhouse, showing that microbiome profiles varied along processing zones and that Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus persisted across carcass and environmental samples. These taxa, strongly linked to macrolide, lincosamide, and β-lactam resistance genes, highlight the need for continuous monitoring and zone-specific hygiene strategies. Moreover, a higher abundance of mobile genetic element–associated resistance genes in dirty compared to clean areas indicated potential hotspots for AMR persistence and enrichment. The third study assessed wastewater and floor contamination in an Italian swine slaughterhouse, demonstrating that these environments function as reservoirs for antimicrobial-resistant bacteria and clinically relevant resistance genes, including ESBL- and carbapenemase-producing E. coli, livestock-associated MRSA and A. baumannii, even after sanitation. Collectively, the findings highlight slaughterhouses as active interfaces for AMR transmission between animal, food, and environmental compartments. The work underscores the need for integrated, evidence-based surveillance and control strategies to mitigate AMR dissemination and support sustainable management within the food production sector.