In-depth Characterization of Microbiome and Resistome of Carcasses and Processing Environments in a Swine Slaughterhouse

A metagenomic study of a pig slaughterhouse shows that all stages of the production environment carry bacteria with antimicrobial resistance genes, with the “dirty zone” and carcasses containing more diverse and concerning profiles than the “clean zone.” Dominant bacterial groups included Actinomycetota and Pseudomonadota, while food-safety-relevant resistant species such as Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus were particularly prominent. Resistance genes for tetracyclines, β-lactams, aminoglycosides, macrolides, and lincosamides were widespread, and plasmid-associated and lateral-gene-transfer events were more common in dirty areas and on carcasses, indicating higher potential for AMR spread. The study underscores how zone-specific microbiomes reflect processing conditions and highlights the need for strict hygiene and control measures to prevent foodborne pathogens and antimicrobial resistance from disseminating along the pork production chain.