Unveiling Antibiotic and Biocide Resistance Genes in Slaughterhouse Environments: A One Health qPCR Study

Slaughterhouse surfaces can act as a reservoir of antibiotic (ARGs) and biocide resistance genes (BRGs), yet the impact of disinfection strategies on their abundance remains unclear. Using qPCR, we analysed bacterial DNA obtained from various slaughterhouse facilities and surface types exposed to different disinfection treatments. These notably included UV, HLE (hydrogen peroxide, lactic acid, and EDTA), standard industrial disinfectants and their combinations. Analysis of ARG and BRG in particular focused on genes related to efflux pumps, stress-response regulators and detoxification pathways. gly.bleo and ugd were identified as the most abundant and stable genes, forming part of the “core resistome” across all locations. In contrast, the differences in golS abundance were statistically significant between different origins. Furthermore, analysis of different disinfection treatments showed that the abundance of arlR was statistically variable depending on the disinfection protocol, highlighting the efficacy of HLE treatment by significantly reducing the abundance of the arlR gene, as no detectable DNA was obtained. These results suggest that arlR could be used as a molecular biomarker for evaluating disinfection efficacy in food processing environments. Overall, our study shows that genetic insights enable sustainable disinfection protocols that mitigate contamination without promoting antimicrobial or biocide resistance in the food chain. • gly.bleo and ugd genes constitute the slaughterhouses surface core resistome. • The arlR gene serves as a key biomarker for monitoring disinfection efficacy. • HLE disinfectant effectively reduces ARG abundance in slaughterhouse environments. • Conventional cleaning protocols may unintentionally select for specific BRGs. • DNA biomarkers enable optimized hygiene strategies against microbial resistance.