A systematic study for evolution of bacterial drug resistance: phenotype to genotype

Official URL: http://risc01.sabanciuniv.edu/record=b1589822 (Table of Contents)

Bacterial drug resistance is a worldwide problem threatening millions of lives. Several studies showed that bacteria develop direct resistance against an antibiotic compound used throughout treatment. However, recent studies demonstrated that resistance to one antibiotic can pleiotropically lead to resistance to other antibiotics, a concept known as cross-resistance, imposing serious limitations for combating against infectious diseases. Therefore, slowing down evolution of cross-resistance is critical and important task for developing effective antibiotic therapies. Despite its importance, mechanisms behind crossresistance are not well understood due to lack of systematic studies. Here in this systematic study, we aim to provide a better understanding of evolution of antibiotic resistance using state of the art genetic tools. In this study, we evolved 88 initially isogenic Escherichia coli populations against 22 different antibiotics for 21 days. For each drug, two populations were evolved under strong selection and two populations were evolved under mild selection. Representative clones from each evolved population were phenotyped against all 22 drugs we used in our experiments and their resistance levels were carefully quantified. Furthermore, these clones were genotyped by Illumina whole genome sequencing and resistance-conferring mutations were identified. Bacterial populations evolved under strong selection acquired stronger resistance against higher number of antibiotics compared to populations evolved under mild selection. Strongly selected populations also acquired higher number of mutations compared mildly selected populations and there mutations were found to be more pathway specific among strongly selected populations. Finally, populations evolved against aminoglycosides were found to develop hypersensitivity against several other antibiotic classes due to mutations in trkH gene, coding for a membrane protein. Our study provides a thorough understanding for phenotype to genotype in the context of antibiotic resistance and demonstrates that selection strength is an important parameter contributing to the complexity of evolution of antibiotic resistance.