Determining Uropathogenic Escherichia coli Fitness Factors in Different Gut Niches

About This Grant

PROJECT SUMMARY Urinary tract infections (UTIs) affect approximately 150 million people per year worldwide. An estimated 50% of women report having had a UTI at some point in their lifetime. Antibiotic use, while the mainstay of UTI treatment, has contributed to the rise in antimicrobial resistance. Uropathogenic E. coli (UPEC) is implicated in about 75% of uncomplicated UTI cases, which has led to interest in understanding the mechanisms utilized by UPEC cause UTI. Previous work has shown that UPEC colonizes both the bladder and gastrointestinal (GI) tract, where UPEC is thought to establish a long-term reservoir and seeds the urinary tract. Thus, targeting UPEC in the GI tract could contribute considerably to UTI prevention by reducing UPEC shedding in the feces and subsequent colonization of the urinary tract. Previous work from our lab has shown that the susceptibility of UPEC to the host mucosal immune response in the GI tract depends on the localization of UPEC within the gut, which in turn is determined by the degree of microbial competition from other members of the gut microbiota. This competition can drive UPEC strains to occupy two distinct gut compartments depending on when they were introduced. When UPEC is introduced first in the gut, it inhabits the luminal and mucosal compartment, while a second strain, introduced after the first strain, prefers the mucosal compartment. Interested in the fitness factors and metabolic requirements that enable this differential localization, we created a barcoded transposon library in UPEC strain UTI89. Transposon libraries are an established tool for conducting genome-wide screens in bacteria. Furthermore, barcoding the library simplifies sequencing preparation, allowing users to test more experimental conditions. We tested our UTI89 pooled barcoded transposon library by growing it in different growth medias, which would allow us to both validate the library and reveal nutritional dependencies of UPEC in different environments. Aim 1 focuses on identifying UPEC fitness factors in vitro under conditions that mimic the gut environment. First, we will conduct an in vitro UTI89 pooled library screen in five different conditions. After validating the pooled library and identifying genes of interest in the mucin media condition, we will conduct another in vitro pooled library screen using the control, mucin-containing and glucose-containing media under anaerobic conditions, which we use to model the physiological gut environment. We have also assembled an arrayed version of this library which we will use to test gene candidates identified in both screens. Aim 2 will use gnotobiotic mice to perform an in vivo pooled library screen to identify fitness factors important in UPEC gut colonization when UPEC is introduced as a primary colonizer to a naïve gut and as a secondary invader in the presence of an existing gut microbiome. We will also test whether a low-fiber diet changes the landscape of UPEC gut colonization and repeat the above in vivo screen with mice on a low-fiber diet as an additional arm. Identifying UPEC fitness determinants will elucidate UPEC biogeographical niche occupancy and inform design of antibiotic-sparing interventions for UTI.