Date of Award
Master of Science (MS)
Bioinformatics & Computational Biology
In the US, around 60% of females will be diagnosed with a Urinary Tract Infection (UTI) in their lifetime, and Escherichia coli is the most implicated etiological agent in UTIs. Despite its frequent association with lower urinary tract symptoms, recent studies have found that the urinary microbiome (UMB), the viral, bacterial, and fungal resident members of the urinary tract, of healthy females can also consist of E. coli. While most research has focused on the bacterial constituents of the UMB, bacteriophages, viruses that infect bacteria, are far more abundant. Bacteriophages (phages) of other human microbiomes have been shown to play a significant role in shaping the bacterial community dynamics. While a handful of E. coli infecting phages (coliphages) have been characterized, little is known about the diversity of coliphages of the human UMB or their role within this microbial community. Of the known types of phages in nature, temperate phages have complex, broad impacts on bacterial populations and therefore, community dynamics, through both lytic and lysogenic means. One such widely studied impact is lysogenic conversion, the alteration of host phenotype by the infection and integration of a temperate phage. Lysogenic conversion has the potential to offer a host bacterium human-relevant phenotypes including antibiotic resistance or virulence factor production. Since it has been shown that UMB phages can exhibit host ranges broader than just their native host, phages could be facilitating the horizontal gene transfer of potentially harmful genes within the human UMB. Despite the threat posed by UMB temperate phages, little work has been done characterizing their integrated form, prophages, in UMB E. coli. Additionally, the ability of these phages to be induced form their native host, then infect and integrate into a non-native host has not been shown previously by phages of the human UMB. Here I present a two-part study into (i) the diversity of E. coli prophages within the human UMB and (ii) the ability of UMB temperate coliphages to be induced from a native host, engineered to be obligately lytic to then infect and lyse a non-native UMB host. First, 3,177 predicted intact prophages were identified from 961 urinary E. coli genome assemblies by the prophage predicting tool PHASTER. Prophages were pervasive; 95% of the strains contained at least one intact prophage (average >3 prophages per genome assembly). Furthermore, ~50% of these predicted prophages did not share significant sequence similarity to characterized phages, thus likely representing novel phages. Some predicted prophage sequences contained antibiotic resistance and virulence genes, but these genes were not common among the prophage sequences. Investigation of the predicted prophages’ integrase gene suggests that the UMB coliphages share common attachment sites for integration in the E. coli chromosome. Collectively, this study provides the first catalog of urinary E. coli temperate phages. Next, predicted intact prophages were induced from urinary E. coli strains using biologically relevant pH conditions. The induced phages were identified using PCR with primers designed based on the PHASTER sequence predictions. One of these induced prophages was then engineered from temperate to obligately lytic through the removal of its integrase gene sequence, and the host range of this engineered phage (d700) and its ancestral strain (i700) was assessed. d700 was able to lyse one strain of UMB E. coli that i700 was not suggesting that i700 infected and lysogenized the bacterium. This study shows that there is substantial diversity in UMB E. coli prophages and shows that some temperate coliphages can be induced, engineered to be obligately lytic, and lyse non-native hosts.
Crum, Elias, "Cataloging and Engineering Temperate Coliphages of the Human Urinary Microbiome" (2022). Master's Theses. 4434.
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