Pharmaceutical residues in agricultural systems pose a significant risk to environmental health and contribute to the emergence of antimicrobial resistance (AMR). This study aimed to investigate the presence and impacts of pharmaceutical residues on AMR development in agricultural soils, water, and plant tissues. Samples were collected from various agricultural sites and analyzed for antibiotic concentrations, microbial resistance profiles, and the presence of resistance genes using advanced chromatographic and molecular techniques. Horizontal gene transfer (HGT) experiments were conducted to evaluate the potential for resistance gene dissemination. Statistical tools, including ANOVA and Pearson’s correlation analysis, were applied to explore associations between pharmaceutical residue concentrations and resistance parameters.

The results revealed significant contamination of agricultural matrices, with tetracyclines being the most prevalent, followed by macrolides and beta-lactams. Soil samples exhibited the highest concentrations of residues, correlating strongly with the prevalence of resistance genes (bla, tet, mecA) and resistant bacterial strains such as E. coli and Salmonella spp. HGT experiments demonstrated elevated transfer rates of resistance genes in soil samples compared to water and plant tissues, highlighting soil as a critical hotspot for resistance propagation. Multivariate analysis further confirmed distinct clustering patterns of microbial communities based on pharmaceutical residue exposure.