Understanding the Genetics and Evolution of Antimicrobial Resistance in Escherichia Coli

Antimicrobial resistance (AMR) has emerged as a global public health challenge. The central goals of my PhD research are to better understand AMR evolution, with the long-term goal of developing novel strategies to mitigate the problem of AMR. This involves gaining comprehensive insights into the evolutionary trajectories of resistance evolution, investigation of the availability of resistance mutations and their pleiotropic consequences, and identification of genetic targets for the prevention/slowing of resistance evolution.In a systematic study, I have investigated the effects of different chromosomal quinolone resistance mutations, and the pleiotropic effects of such mutations in Escherichia coli. I identified 50 spontaneous resistance mutants on nalidixic acid, ciprofloxacin, and levofloxacin, with mutations in regions ofgyrA,gyrB, andmarR, which are known contributors of resistance in quinolones. Resistant isolates had increased resistance levels, widespread cross-resistance to other quinolones, and overall significant costs of resistance in the absence of antibiotic. To investigate novel strategies to combat AMR, I carried out a small RNA screen on a quinolone resistantgyrAbackground, to identify alternative drug targets. This screen led to the identification of 30 genes whose knockdown reduced the level of gyrase-mediated quinolone resistance inE. coli. Finally, to gain understanding of the network of genes contributing to intrinsic and phenotypic resistance, I have studiedE. coli's two-component signal transduction systems (TCS). TCSs are involved in bacterial responses to many stresses, including antibiotics. I examined interactions between antibiotic stress and other environmental stressors in a set of eight TCS mutants. Mutants showed different types of responses to antibiotics and stressor+antibiotic combinations.In this research, I have used novel approaches to understand bacterial resistance evolution and to combat AMR. On an applied level, these studies have implications for public health strategies. This research can help lead to better selection of appropriate antibiotics, alternative drug targets involved in resistance, and has prospects for development of new therapeutic approaches for combating AMR.