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Within-Host Diversity of Multidrug-Resistant Escherichia Coli in the Gut and Bladder Sofiya G. Shevchenko a Dissertation Submitt

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Within-Host Diversity of Multidrug-Resistant Escherichia Coli in the Gut and Bladder Sofiya G. Shevchenko a Dissertation Submitt Within-host Diversity of Multidrug-Resistant Escherichia coli in the Gut and Bladder Sofiya G. Shevchenko A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2019 Reading committee: Evgeni Sokurenko, Chair John Mittler Kevin Hybiske Program Authorized to Offer Degree: Microbiology ©Copyright 2019 Sofiya G. Shevchenko University of Washington Abstract Within-host Diversity of Escherichia coli in the Gut and Bladder Sofiya G. Shevchenko Chair of the Supervisory Committee: Evgeni V. Sokurenko Department of Microbiology Uropathogenic E. coli are paradoxically able to both cause disease in the urinary tract, and reside there asymptomatically. The pandemic, multi-drug resistant E. coli subclone ST131-H30 (H30) is of special interest, as it has been found to persist in the gut and bladder of healthy people. In order to understand this persistence, we investigated whether H30 is competitive in these niches and thus able to persist by excluding other E. coli, as well as whether H30 may persist via within-host adaptation. In order to assess the E. coli clonal landscape, we developed a novel method based on deep sequencing of two loci, along with an algorithm for analysis of resulting data. Using this method, we assessed fecal and urinary samples from healthy women carrying H30, and found that even in the absence of antibiotic use, H30 could completely dominate the gut and, especially, urine of healthy carriers. In order to ascertain whether H30 adapts within- host, we employed population-level whole genome sequencing, and determined that H30 undergoes changes in genes affecting respiration in the gut, similar to commensal gut E. coli. Furthermore, we find that in the bladder, H30 undergoes changes potentially adaptive for growth in urine, including nonsynonymous mutations in iron and amino acid metabolism genes. Contents CHAPTER 1: INTRODUCTION .................................................................................................. 6 The human gut microbiome .................................................................................................... 6 Benefits of the gut microbiome ............................................................................................ 6 Role of Escherichia coli in the gut microbiome ........................................................................ 7 E. coli gut colonization ........................................................................................................ 8 Adaptation of E. coli to the gut ............................................................................................ 9 Antibiotic-resistance and E. coli .......................................................................................... 9 Uropathogenic E. coli: pathogenicity and adaptation .............................................................10 UPEC pathogenicity and metabolism .................................................................................10 Preliminary evidence for UPEC adaptation to the host .......................................................11 ST131-H30: a pandemic UPEC clone ................................................................................12 CHAPTER 2: DEVELOPMENT OF A NOVEL METHOD FOR ASSESSMENT OF E. coli STRAIN CONTENT IN HUMAN SAMPLES ..............................................................................14 Introduction ...........................................................................................................................14 Results ..................................................................................................................................15 Deep amplicon sequencing of defined samples .................................................................15 Deep sequencing of study samples and allele prediction ...................................................18 Prediction of allele prevalence in multi-allele samples ........................................................23 Matching fumC and fimH alleles to predict sample strain content .......................................26 Predicted strain diversity of fecal and urine samples ..........................................................29 Novel clones ......................................................................................................................32 Clones below error threshold .............................................................................................32 Predicted strain diversity in H30-containing urine and fecal samples .................................33 Strain turnover in fecal samples .........................................................................................36 Discussion .............................................................................................................................37 CHAPTER 3: ASSESSMENT OF WITHIN-HOST H30 MICROEVOLUTION .............................41 Introduction ...........................................................................................................................41 Results ..................................................................................................................................43 Within-host relatedness of gut and bladder H30 isolates ....................................................43 Genomic changes in fecal and bladder H30 isolates ..........................................................43 Validation of H30 fecal and urinary changes ......................................................................48 Population frequency of within-host H30 changes ..............................................................49 Genomic heterogeneity in H30 fecal and urinary populations .............................................53 4 Validation of H30 population genomic heterogeneity ..........................................................56 Location of changes in H30 fecal and urinary populations ..................................................63 Discussion .............................................................................................................................69 CHAPTER 4: Experimental evolution of fecal H30 isolates in human urine ...............................72 Introduction ...........................................................................................................................72 Results ..................................................................................................................................74 Discussion .............................................................................................................................78 CHAPTER 5: MATERIALS AND METHODS .............................................................................80 Study design and sample processing ....................................................................................80 Deep amplicon sequencing for characterization of E. coli diversity ........................................81 Preparation of predefined control samples .........................................................................81 Deep sequencing and allele analysis of fecal and urine samples .......................................82 Determining within-sample clonal group breakdown ..........................................................84 Determining prevalence of clonal groups by culturing ........................................................85 Statistical and phylogenetic analysis ..................................................................................85 Analysis of diversity within fecal and urinary H30 populations ...............................................86 Sequencing of single-colony isolates and H30 population genomes ..................................86 Phylogeny construction and analysis of sequencing data ...................................................86 Experimental evolution of fecal H30 isolates ......................................................................87 Chapter 6: FUTURE DIRECTIONS ...........................................................................................88 Dominance of H30 in the gut and bladder ..............................................................................88 Perspectives in H30 within-host adaptation ...........................................................................89 ACKNOWLEDGEMENTS .........................................................................................................91 SUPPLEMENTAL DATA ...........................................................................................................92 Supplemental Table 1 ............................................................................................................92 Supplemental Table 2 ............................................................................................................98 Supplemental Table 3 .......................................................................................................... 102 References ............................................................................................................................. 134 5 CHAPTER 1: INTRODUCTION The human gut microbiome Far from sterile, the human body is colonized with millions of microbes that are part of the basic functioning of the body. This includes bacteria, fungi, and other microorganisms that participate in digestion, resistance to disease, and even some emotional states(1–5). While various parts of the body are colonized,
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