Antibiotic resistant bacteria in food systems: Current status, resistance mechanisms, and mitigation strategies

The pervasive use of antibiotics in agriculture and animal husbandry has raised a significant concern—residual antibiotic contamination in food, which contributes to the natural evolution of antibiotic resistance in pathogenic microbial strains. The emergence of antibiotic resistance in microbial communities poses a global threat to food safety and security. Recently, the situation has been exacerbated by the discovery of novel strains of antibiotic resistant bacteria (ARB) in plant- and animal-derived foods. These microbes can enter the human body through direct contact with affected animals or through consumption of contaminated foods. In this review, we explore the prevalence of antibiotic contaminants in food at various locations around the world, delve into the molecular mechanisms behind acquisition of antimicrobial resistance, examine the current strategies employed to mitigate the evolution and spread of antibiotic resistant pathogens, and discuss emerging technologies aimed at halting the trend that projects 10 million annual deaths by 2050 as a result of ARB contamination in agriculture. Genetic processes, including mutations, efflux pump activity, and horizontal gene transfer, play crucial roles in the evolution and widespread distribution of ARB in the microbial community. Effectively addressing this global threat requires development of methodologies to rapidly detect ARB in the food supply chain. Therefore, we examine several established rapid diagnostic techniques such as the Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) methodology, aptasensors, and fluorescence-based Metal Organic Frameworks. Additionally, we explore innovative strategies to fight ARB such as nano-antibiotics, natural antibiotics, synthetic biology, bacteriophages, and predator bacteria. Here, we propose emerging technologies such as omics technologies and biochar use as potential tools for combating ARB. We anticipate that this review article will serve as a valuable resource for future research, particularly in the development of strategies designed not only to suppress the activities of antibiotic resistance genes but also to potentially reverse resistance mechanisms that are already widespread in microbial communities.