Abstract
The use of antibiotics in livestock production enhances animal growth and health but risks regarding the development of antibiotic resistant bacteria have led to consumer and regulatory pressures to reduce antibiotic use in animal agriculture. The increase and spread of antibiotic resistance genes (ARGs) in the agroecosystem could complicate the treatment of human and animal infections in the future. Across multiple swine and poultry studies, we have found that antibiotic use significantly increased the abundance of ARGs, and the abundance of genes that could facilitate in the horizontal transmission of ARGs. In an individual controlled swine study, we found that ARGs were enriched up to 28,000-fold compared to antibiotic-free control animals. In commercial swine farms, ARG levels were, on average, 200 times higher than background ARGs levels in soils, and individual ARGs were (co-)selected 10- to 100-fold. ARGs frequently clustered in multidrug resistance (MDR) regions, where the abundance of genes conferring resistance to multiple antibiotic classes were tightly correlated. Importantly, therapeutic zinc supplementation also increased the abundance of ARGs, highlighting the role of metals in the co-selection of ARGs. Beyond ARG enrichment, antibiotics also increased the abundance of mobile genetic elements (MGEs), genes that are involved in transferring a gene within or between bacterial cells, abundance, 10 times more than ARGs. ARG and MGE abundances were highly correlated (r² = 0.96), supporting their role in horizontal gene transfer (HGT). Carbadox, a widely used swine antibiotic, promoted lytic bacteriophage activity, increasing the potential for phage-mediated ARG transduction. Bacitracin methylene disalicylate (BMD) in turkeys significantly enriched conjugation-related genes and transduction-associated elements, further demonstrating that antibiotic alternatives may inadvertently promote HGT. The presence of resistance clusters occurred independently of microbiome shifts, suggesting that ARG dissemination is not limited by microbial composition. In addition to increasing ARG and MGE abundance, antibiotic use was also associated with changes in bacterial community composition, including an increase in Proteobacteria, particularly Escherichia coli. Functional metagenomic analyses revealed that antibiotic-fed animals exhibited elevated expression of genes related to energy metabolism, bacterial growth, and stress response, suggesting that antibiotic selection pressures reshape microbial function beyond resistance traits. These findings highlight the need for a comprehensive reassessment of antimicrobial use in livestock production with a One-Health perspective. The widespread selection and mobility of ARGs and MGEs in agricultural systems pose a risk for AMR dissemination into animal, human and environmental reservoirs. Future research should focus on microbiome-based interventions, antibiotic-free growth promoters, and improved surveillance and diagnostic testing strategies to mitigate the spread of resistance while maintaining animal health and productivity.