Harnessing CRISPRi screening for unravelling genetic mechanisms underlying persistence in Escherichia coli

Urinary tract infections (UTIs) are a worldwide health concern and are mainly caused by uropathogenic Escherichia coli (UPEC). Antibiotic therapy failure and the chronic nature of UTIs can be ttributed to a small fraction of transiently non-growing, antibiotictolerant cells called persisters. An innovative method to cure chronic UTIs would be to induce growth resumption in UPEC persisters, thereby re-sensitizing them to conventional antibiotics. However, our current understanding of persister awakening is far from complete, hampering the development of anti-persister drugs. The aim of this project is to gain mechanistic insight in persister awakening in UPEC using proteomics-based approaches. First, we will unravel the mode of action of a persister regulator that was recently discovered in our group. Second, we will perform proteome analyses on awakening persister cells to find determinants that underlie awakening. These proteins will be subjected to extensive functional and biochemical examination, which will contribute immensely to our understanding of persister awakening. Finally, we will develop and implement a noninvasive mouse model for persistence to validate our findings in vivo. This project will lead to novel insights in persister awakening and will pave the way for the development of diagnostic tests for persistence as well as anti-persister drugs to effectively clear UTIs.