Bacteriophages and Antimicrobial Resistance in Agricultural Products

Antimicrobial resistance is a pressing global crisis, closely linked to the intensive use of antibiotics in agriculture. Agricultural ecosystems are critical interfaces where human, animal, and environmental microbiomes converge, creating ideal conditions for the emergence and dissemination of antibiotic resistance genes (ARGs). This chapter examines how bacteriophages, viruses that infect bacteria, contribute to the spread of ARGs within agroecosystems. Bacteria acquire resistance through mutations or via horizontal gene transfer mediated by mobile genetic elements such as plasmids, transposons, and, notably, bacteriophages. Phages facilitate horizontal gene transfer through transduction, a process in which fragments of bacterial DNA, including ARGs, are packaged into viral capsids and transported between cells. Mechanisms such as generalized, specialized, and lateral transduction enable phages to efficiently mobilize resistance traits, accelerating their dissemination in the environment. Phages carrying ARGs have been detected in diverse agricultural matrices, including manure, sewage sludge, irrigation water, soil, and even edible crops. The routine application of animal manure, treated wastewater, and biosolids to farmland introduces both residual antibiotics, which select for resistant bacteria and resistant microorganisms, and phage particles that mediate horizontal ARG transfer. The remarkable resilience of phages, including their resistance to disinfection and environmental stressors, supports their role in the long-term persistence of ARGs in agricultural settings. Phage-associated ARGs in soil can enter plant root systems, accumulate in edible tissues, and ultimately reach the human food chain, posing a direct risk to public health. This chapter highlights phages as key vectors of ARGs, linking agricultural practices to the global network of antibiotic resistance. A deeper understanding of phage-mediated gene transfer in soil–plant systems is essential for designing safer waste management, fertilization, and irrigation strategies that minimize the spread of ARGs from farm to fork.