Insights into antimicrobial resistance and pathogenesis in the slaughterhouse environment and the impact of disinfection strategies

Slaughterhouses are critical points in the food chain where animal microbiota, antimicrobial use, and disinfection practices can significantly impact the dissemination of multidrug resistant (MDR) bacteria and their antimicrobial resistance genes (ARGs) and virulence determinants (VRs). This study investigates the resistome and virulome in three slaughterhouses by means of metagenomic analysis, revealing a high diversity and richness of ARGs, including those conferring resistance to aminoglycosides, lincosamides, tetracyclines, and beta-lactams. We found frequent ARG spread within these environments, confirming slaughterhouses as potential reservoirs of antimicrobial resistance. Furthermore, we explored the potential roles of biocides in driving antibiotic resistance through co-selection and cross-resistance mechanisms, alongside the significant presence of metal and heavy metal resistance genes and virulence determinants (virulence factors and toxins), which may also contribute to the selection and persistence of ARGs. Evaluating disinfection strategies showed that routine "Company" disinfectants and UV exposure often increased the prevalence of these genes by selecting for resistant microbes. This highlights the urgent need for new strategies to mitigate antimicrobial resistance spread, aligning with the One Health approach. The application of HLE disinfectant proved as a more effective and sustainable solution for slaughterhouse surfaces, demonstrating superior decontamination efficiency by leaving no residual DNA. • Slaughterhouses as hotspots of antimicrobial resistance and virulence genes. • Specific differences in antimicrobial resistance/pathogenesis in slaughterhouses. • Frequent spread of ARGs, BRGs and VRGs in slaughterhouses and their areas. • Conventional disinfection methods can boost ARG/BRG/VR prevalence. • HLE disinfectant as an effective and sustainable decontamination strategy.