Date of Award

Fall 9-8-2025

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Bioinformatics & Computational Biology

First Advisor

Catherine Putonti

Abstract

In 2019, there was a 140.19% increase in deaths due to urinary tract infections (UTIs) compared to 1990, worldwide. One of the common uropathogens known to associate with UTIs in females is Escherichia coli. The prevailing belief is that E. coli in the bladder originates in the rectum, passing its way from the perineal, to the vagina, and finally into the bladder. Known as the Fecal-Perineal-Urethral (FPU) hypothesis, this “origin story” has been supported by several studies that have relied on genotyping or serotyping isolates collected from the bladder and rectum. Most notably, culturing isolates from samples has been central to these studies. Metagenomics avoids cultural biases, and to our knowledge, it has yet to be employed to test the FPU Hypothesis. Here I present a metagenomic study of the microbial diversity present at four anatomical sites, the bladder, periurethral, vagina, and rectum, collected from 19 female participants with E. coli-associated UTIs. Each of the site samples was amplified using three different types of media, which created 12 treatments for each participant. Each treatment was sequenced, and metagenome-assembled genomes (MAGs) of E. coli in the bladder samples were created. Using these MAGs, we were able to generate MAGs for the other anatomical sites to ascertain if they represented the same strain as present in the bladder, signifying that the bladder E. coli strain is a recent acquisition from the rectum. Ten of the 19 participants clearly supported the FPU hypothesis; the same strain of E. coli was found at each site (ANI ≥ 99.99%). Three participants (1, 3, and 38) were missing data for one of the sites; however, the other 3 sites contained the same strain. For the remaining six participants, one or more of the sites had evidence of more than one E. coli strain present, and as a result, determining if the same strain was present was unclear, as separating these two strains posed significant bioinformatic challenges. Overall, we hypothesize that 10 of these participants show strong evidence, 6 may support, and 3 need new bioinformatic approaches to determine if the E. coli found in the bladder is a recent acquisition from the rectum.

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