A Novel Genetic Screening Method Systematically Identifies Nutrients That Alter Sulfamethoxazole Potency
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Abstract
The spread of antibiotic resistance is a global threat that is fueled by a decades-long gap in antibiotic discovery. There exists an urgent need to implement strategies to improve the usefulness of existing antibiotics. Bacterial metabolism is a rich source of potential targets for antibiotic adjuvant therapies, but we lack methods to systematically identify metabolic processes that can sensitize bacteria to antibiotics. This work demonstrates the strong impact of the nutrient environment on antibiotic potency and provides a novel method to comprehensively map metabolic pathways that can alter antibiotic efficacy. I conducted antibiotic sensitivity screens in Escherichia coli across 21 different media conditions and 11 antibiotics to systematically evaluate media-dependent changes in antibiotic potency. The potency of most antibiotics fluctuated substantially across media conditions, but these potency changes did not follow universal patterns across antibiotic classes. Folate synthesis targeting antibiotics sulfamethoxazole and trimethoprim displayed highly dissimilar resistance profiles, with sulfamethoxazole demonstrating far greater media-dependence. I developed a novel genetic screening-based approach to predict metabolic pathways that drive environmental changes in antibiotic potency. This method successfully identified metabolites known to confer resistance to sulfamethoxazole by improving tetrahydrofolate recycling and made the novel prediction that ethanolamine potentiates sulfamethoxazole efficacy. I experimentally validated that these metabolites alter sulfonamide potency, and not the potency of other antibiotics, including trimethoprim. This work therefore presents a genetic screening method capable of identifying metabolic pathways that can be targeted to alter the efficacy of existing antibiotics.