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Woodward, Sarah E.

University of British Columbia

The gastrointestinal environment plays a critical role in shaping enteric infections. Host environmental factors create ‘bottlenecks’ which are restrictive events that can control the size and genetic diversity of invading bacterial populations. Despite this, little is known about the extent to which bacterial pathogens encounter bottlenecks, where bottlenecks occur, or how these events impact the pathogen founding population size (Nb′). I explored the population dynamics of murine gastrointestinal pathogen Citrobacter rodentium, a well-established model for human pathogenic Escherichia coli infection. To investigate bottlenecks, I created a library of 2,000+ isogenic but uniquely-tagged C. rodentium through the insertion of genomic barcodes. Following infection of mice, sequencing of recovered barcodes allowed for the quantification of population size. An average Nb′ of only 12-43 individual lineages was found across all timepoints and intestinal sites. We further identified passage through the stomach and intestinal escape to the systemic organs as major bottleneck events. These data demonstrate the effectiveness of bottlenecks in host protection, such that even highly adapted pathogens are subject to significant population loss. To fully appreciate their impact during infection, I manipulated key host protective bottlenecks caused by gastric acid and microbiota colonization. In both cases pathogen Nb′ increased (up to 6.8-fold and 35-fold following antacid treatment and treatment with the antibiotic vancomycin, respectively), as did host morbidity and mortality. Following host vancomycin treatment the differential abundance of growth-altering metabolites and commensal microbes which benefit pathogen colonization likely allows for lowered inter- and intra-species competition within the gut and promotes colonization by diverse pathogen lineages. Such environmental changes highlight the need for enteric pathogens to sense and respond to numerous environmental signals for successful intestinal navigation, demonstrating fluid regulation of bacterial processes even under typical infection conditions. Having established extreme pH as a barrier to infection, I further demonstrated that regional intestinal pH fluctuations are a signal of intestinal geography for invading pathogens, influencing C. rodentium growth, epithelial attachment and virulence. Altogether, the data presented in this thesis furthers our understanding of bottleneck events during enteric infection, demonstrating their potential to impact pathogen fitness and thereby the overall population-level diversity of epidemics.

Text

2025-01-31

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/83582

Microbiology and Immunology

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/