Making bacteria antibiotic-sensitive again: Towards understanding the genetic and physiological basis of persister cell awakening

A major cause of antibiotic therapy failure and the chronic nature of bacterial infections is a small fraction of transiently tolerant cells called persisters. These cells can survive antibiotic treatment and resume growth when the antibiotic pressure drops. Despite the threats posed by persisters, a thorough understanding of persistence in clinical and natural strains is still lacking and knowledge on how cells revert from the persistent state is scarce. We here propose to unravel genetic and physiological drivers of persister awakening in a large panel of clinical and natural Escherichia coli isolates. We will measure awakening lag times and look for genetic determinants of awakening using genome-wide association studies. In a parallel approach, we will implement an experimental evolution platform to select for strains with altered awakening times and scan the genomes of evolved lines for alterations. Genetic factors of interest will be subjected to thorough characterization to shed light on the physiology underlying persister awakening. Combined, data generated throughout this project will lead to novel fundamental insights into microbial persistence with broad implications for the field and will pave the way for developing novel approaches to treat infections.