Enabling Novel Strategies for the Clinical Care of Urinary Tract Infection via Microbial Engineering

Each year, urinary tract infections (UTI) affect over 400 million people worldwide, such that nearly half of all women will have a UTI within their lifetime. However, the exponential rise in antibiotic resistance of uropathogenic bacteria profoundly threatens our ability to treat UTI. Thus, it is imperative that measures are quickly taken to reduce the rise of resistance and develop alternative strategies to treating UTI. The goal of this proposal is two- fold: develop a point-of-care diagnostic which can rapidly detect UTI and develop a novel treatment for UTI via in situ commensal microbiome engineering. 1) Conventional diagnostic strategies for UTI (e.g., urine culture) are insensitive, non-specific, and/or time consuming. As a result, antibiotics are primarily prescribed before diagnostic results are received, which can result in unnecessary antibiotic use and in turn, contribute to the rise of resistance. To address this, I will combine padlock probes and in vitro transcription and translation systems to detect pathogenic bacteria and antibiotic resistance genes in urine in less than an hour at the point-of-care. This should reduce unnecessary antibiotic use by providing rapid and accurate UTI diagnoses. 2) Commensal urobiota have been shown to decrease the pathogenicity of UTIs. However, attempts to modulate the microbiome via probiotics have seen inconsistent efficacy in the treatment of UTI, which may be due to poor colonization. To address this, I will engineer the urinary microbiome in situ to downregulate UTI pathogenicity. Briefly, phages will be engineered to deliver therapeutic genes to diverse strains common to the urinary microbiome. These phages will be validated to work in in vitro and in vivo models of UTI. In total, this proposal will enable a novel diagnostic and therapeutic approach for the clinical care of UTI which could be leveraged for a variety of microbiome-based urological and kidney diseases.