Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Besides being generally considered to be extracellular infections and easily treated with antibiotics, they are often incompletely resolved. About 25% of patients experience a recurrent UTI and the resulting repetitive administration of antibiotics contributed to higher antibiotic resistance rates in uropathogens. Up to 90% of UTIs are caused by uropathogenic E. coli (UPEC), which can proliferate in the bladder lumen but are also capable of invading uroepithelial cells where they form intracellular bacterial communities, protecting the pathogen from host defenses and antibiotics.
By using an integrative approach of mass spectrometry, (cryo-correlative) light microscopy, cryo-focused ion beam (FIB) milling and cryo-electron tomography (cryo-ET), we aim to dissect the different infection stages of UPEC in vitro and directly in patient samples. In a first step, we resolved the architecture of the most abundant protein in our urine, uromodulin, and could show how it serves as a multivalent antagonist against UPEC adhesion. However, many bacteria can overcome the uromodulin barrier and infect bladder epithelial cells to form intracellular communities. We optimized an infection protocol and transferred it to cells seeded on electron microscopy (EM) grids. Using cryo-fluorescent light microscopy, we correlate our subsequent cryo-FIB milling step to different maturation stages of intracellular bacterial communities to reveal their native in situ architecture and composition. To transfer our insights to actual patients, we are working on analyzing infected cells found in patient urine and in bladder biopsies with high-resolution imaging methods.