Exploiting Evolutionary Tradeoffs to Fight Evolution of Antibiotic Resistance

Evolution of antibiotic resistance is a growing public health problem around the world, and the identification of novel antimicrobials is no longer a viable approach to tackling this problem. To design smart technologies that take the evolutionary dimension into account, it is essential to understand the evolutionary process underlying the development of resistance. In nature, a single organism cannot be the most fit under all possible conditions, implying that bacterial populations that evolve resistance to antimicrobials should be less fit under other conditions. In this thesis, we report two examples of two tradeoffs in antibiotic-resistant bacterial populations. First, by studying biophysical and biochemical properties of the dihydrofolate reductase (DHFR) enzyme in Escherichia coli, we found that some mutations that conferred resistance to trimethoprim, a DHFR inhibitor, decreased drug affinity while substantially increasing substrate affinity. In addition, many of the epistatic interactions between such mutations were due to changes in the catalytic activities of DHFR mutants, rather than changes in trimethoprim affinity. We found that the high-order epistasis in catalytic power of DHFR (kcat and Km) created a rugged fitness landscape under trimethoprim selection. Taken together, these data provide a concrete illustration of how epistatic coupling at the level of biochemical parameters can give rise to complex fitness landscapes, suggesting new strategies for developing mutant specific inhibitors. In the second part of the thesis, we report that E. coli cells that evolved resistance against aminoglycosides pleiotropically evolved hypersensitivity against non-aminoglycoside antibiotics. A point mutation in a the potassium channel called TrkH decreases antibiotic efflux by altering the bacterial membrane potential. To mimic this phenotype, we designed and successfully used peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) to silence efflux genes. Specifically, by silencing the acrA gene, we transiently induced antibiotic hypersensitivity in E. coli. This sequence-specific perturbation decreased the minimum lethal dose of several antibiotics. Moreover, this approach enables combination therapies using several pairs of antagonistic drugs with non-overlapping resistance mechanisms.