Gene-Drug Interactions and the Evolution of Antibiotic Resistance

Abstract

The evolution of antibiotic resistance is shaped by interactions between genes, the chemical environment, and an antibiotic's mechanism of action. This thesis explores these interactions with experiments, theory, and analysis, seeking a mechanistic understanding of how different interactions between genes and drugs can enhance or constrain the evolution of antibiotic resistance. Chapter 1 investigates the effects of the chemical decay of an antibiotic. Tetracycline resistant and sensitive bacteria were grown competitively in the presence of tetracycline and its decay products. Antibiotic decay did not only remove selection for resistance, but long-lived decay products favored tetracycline sensitivity by inducing costly drug efflux pumps in the resistant strain. Selection against resistance by antibiotic-related compounds may contribute to the coexistence of drug-sensitive and resistant bacteria in nature. Chapter 2 investigates how genetic interactions can favor particular combinations of resistance-conferring mutations. All possible combinations of a set of trimethoprim resistance-conferring mutations in the drug's target gene were constructed and phenotyped. Incompatibilities between mutations arose in a high-order, not pairwise, manner. One mutation was found to induce this ruggedness and create a multi-peaked adaptive landscape. Chapters 1 and 2 observed that non-optimal expression of a drug resistance gene or a drug's target could compromise antibiotic resistance. Chapter 3 broadly characterizes non-optimal gene expression under antibiotic treatment, using a functional genetic screen to identify over one hundred pathways to antibiotic resistance through positive and negative changes in gene expression. Genes with the potential to confer antibiotic resistance were found to often go unused during antibiotic stress. The optimization of gene expression for drug-free growth was found to cause non-optimal expression under drug treatment, creating a situation where regulatory mutations can confer resistance by correcting errors in gene expression. Chapter 4 investigates whether it is beneficial to up-regulate the genes encoding antibiotic targets when they are inhibited. Drug target genes were quantitatively over-expressed, and drug resistance was found to not always increase, but alternatively to remain unchanged or even decrease. These diverse effects were explained by simple models that consider toxicity arising from gene over-expression, and mechanisms of drug action in which drugs induce harmful enzymatic reactions.