Amee Manges

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease with limited durable treatment options, particularly for patients with refractory CRS (rCRS). Increasing evidence implicates microbial imbalance, loss of commensal diversity, and biofilm persistence in CRS pathophysiology; however, few therapies directly target the sinonasal microbiome. This thesis investigates SinoNasal Microbiota Transfer (SNMT), the first endoscopically delivered transplant of intact donor sinonasal microbiota, as a potential therapeutic strategy for rCRS.A three-phase research approach was undertaken. First, a systematic review of randomized controlled trials assessing microbiome-modifying therapies for CRS was conducted. Across antibiotic, probiotic, antimicrobial, and biologically based interventions, few studies incorporated microbial analyses, and none demonstrated consistent improvements linked to microbiota modification, highlighting a significant evidence gap. Second, a first-in-human pilot case series evaluated the feasibility, safety, and preliminary efficacy of SNMT, with or without antimicrobial photodynamic therapy (aPDT) pretreatment. SNMT was safely administered and technically feasible. Two of three SNMT-only recipients experienced clinically meaningful improvement, while aPDT was poorly tolerated. Microbiome analyses showed transient increases in diversity but no durable donor engraftment. Third, an ongoing randomized, double-blind, placebo-controlled trial compared SNMT with saline sham. Interim analyses from the first 50 participants showed no significant differences between treatment arms in the primary endpoint (≥1-point mLK reduction at day 45) or in secondary outcomes including SNOT-22 or olfactory scores. Donor material exhibited higher alpha diversity and enrichment of commensal taxa, but patient microbiota remained individualized and stable over time without treatment-associated shifts. Donor-recipient species sharing was low, and full engraftment was rare. Exploratory modeling did identify microbial features to be early improvement predictors.Together, these findings demonstrate that while SNMT is safe and feasible, it does not confer clinical benefit over sham and does not durably modify the sinonasal microbiome. The stability of the CRS microbiome and limited donor engraftment suggest that more targeted, mechanistically informed microbial therapies may be required to restore sinonasal microbial homeostasis.

View record

Breast cancer is the most common cancer among females, with hormone-receptor– positive tumors comprising most cases. Growing evidence links the gut microbiome to carcinogenesis, and the estrobolome—a subset of gut microbes involved in estrogen metabolism—has been proposed as a contributor to breast cancer risk. However, specific estrobolome targets and underlying mechanisms remain poorly defined, and few studies integrate microbial, metabolomic, and dietary data to explore these pathways.This thesis synthesized findings from three components: 1) a scoping review identified relevant estrobolome features from mechanistic and experimental evidence in the literature; 2) a case–control study of newly diagnosed postmenopausal breast cancer in Canada used whole- metagenome shotgun sequencing and plasma and stool metabolomics at baseline and 6-months to both compare baseline case–control differences and to evaluate within-person changes over time; and 3) a case–cohort study of incident breast cancer in France to examine diet and metabolite associations with breast cancer incidence.The scoping review showed that estrobolome targets remain incompletely annotated and evidence showing their association to breast cancer is inconsistent. In the case–control study, baseline comparisons revealed no clear differences in estrogens or directly related microbial functions between cases and controls. Instead, case–control differences appeared in the broader hormone environment—including estrogen precursors, downstream metabolites, and phytoestrogens—and beyond hormones, including Alistipes spp., conjugated bile acids, and microbial pathways related to vitamin K2 biosynthesis, TCA-linked energy metabolism, amino acid metabolism, and NAD salvage. Follow-up analyses indicated that many of these same features changed from baseline to six months. The French case–cohort study supported the relevance of glycine-conjugated bile acids and vitamin K pathways and suggested potential diet– metabolite interactions that may contribute to breast cancer risk.Overall, this work expands the understanding of breast cancer–associated microbiome and metabolic pathways. Several microbial pathways warrant further mechanistic study and validation, including phytoestrogen metabolism, glycine-conjugated bile acid metabolism, vitamin K2 biosynthesis, TCA-related energy metabolism, amino acid metabolism, and NAD salvage pathways. These findings lay the groundwork for future multi-omics research to clarify microbiome-mediated pathways and evaluate their potential as targets for breast cancer prevention or treatment.

View record

Chronic rhinosinusitis (CRS) is a debilitating disease that affects the sinonasal cavity and significantly reduces patients’ quality of life. Sinonasal endoscopy is the main strategy for evaluating and monitoring CRS patients. There are several endoscopic grading systems available, but they all have important shortcomings and limitations. There is an urgent need for a reliable score that can accurately reflect patient’s disease burden that is easy to use and applicable to all CRS subtypes.In chapter 1 of this thesis, I review the main endoscopic scoring systems and describe their main advantages and disadvantages. Based on these findings, Chapter 2 describes the design and validation of the SiNonasal Endoscopic Score (SiNES), a new scoring system that incorporates the strengths of previous scores while addressing their limitations. This chapter further investigates the relationship between the newly developed SiNES and patient reported outcome measures (PROMs).Chapter 3 explores the minimal clinical important difference (MCID) for the SiNES. This chapter incorporates the perspectives of both surgeons and patients and produces an MCID value that can be used for clinical trial development and patient monitoring.Chapter 4 further validates the SiNES using data from the first 45 participants in the SinoNasal Microbiota Transfer (SNMT) trial, a landmark study that will determine whether SNMT can improve the health of recalcitrant CRS patients. The chapter includes data on how the SiNES correlates with objective olfactory outcomes, quality of life measures, and a diverse set of type 2 and non-type 2 cytokines.Finally, Chapter 5 consolidates the findings of the entire thesis and gives some perspectives on future research directions.

View record

Background: Direct-acting antivirals (DAAs) have demonstrated efficacy in reducing morbidity and mortality related to extrahepatic outcomes of chronic hepatitis C (HCV) infection. However, population-based evidence assessing the impact of DAA treatment on extrahepatic manifestations (EHMs) and their burden across ethnic groups remains limited.Objective: We evaluated the impact of DAA treatment on incident EHMs and EHM-related mortality risks, while also assessing ethnic disparities in EHMs among people diagnosed with HCV in British Columbia (BC).Methods: We used data from the BC Hepatitis Testers Cohort, including ~1.3 million people tested for or diagnosed with HCV between 1990 and 2015. To assess the impact of DAA treatment on EHMs, we created a 1:1 matched study population of individuals who were treated with DAAs and those who were never treated. We applied inverse probability of treatment weights and competing risk modelling to assess DAA treatment effects on incident EHMs and EHM-related mortality. Ethnic disparities in incident EHMs were examined across East Asians, South Asians, and Other ethnicities, further stratified by HCV treatment status (never treated, before treatment, after treatment, and spontaneously cleared).Results: Successful DAA treatment was associated with reduced risks of renal, cerebrovascular, cardiovascular and neurocognitive conditions (36-48%), but not type 2 diabetes. It also decreased EHM-related mortality risks by 78-84% for all EHMs. In BC, South and East Asians had higher EHM incidence rates compared to other ethnicities, especially among untreated individuals. Following treatment completion, these rates decreased in both Asian groups. Adjusted analyses showed that South Asians had the highest risk of renal diseases and type 2 diabetes, while East Asians had lower risks of cardiovascular diseases and neurocognitive disorders. HCV treatment mitigated ethnic disparities in EHMs, except for diabetes. Conclusions: DAA treatment can significantly reduce the risks of EHMs and EHM-related mortality, while mitigating most ethnic disparities in EHM incidence among Asian populations. These findings emphasize the importance of expanding strategies to diagnose and treat individuals living with HCV as early as possible to improve health outcomes and address ethnic disparities related to EHMs.

View record

The application of next-generation sequencing technologies to answer more routinediagnostic and applied microbiological questions is becoming increasingly feasible. Currentreference-standard molecular diagnostic strategies are limited in that they require a prioriknowledge of a pathogen’s genome. Metagenomic next generation sequencing (mNGS) is apathogen-agnostic diagnostic approach that can be used for detection of viral pathogens andcharacterization of viral infections. Chapter 1 of this thesis describes technological advancementsin mNGS technology for viral pathogen detection and diagnosis. This narrative review highlightstechnical, logistical, and translational barriers to the widespread use of this technology in clinicalsettings. In chapter 2, I describe the use of full-length 16S rRNA nanopore sequencing forcharacterization of the upper respiratory tract microbiome in hospitalized and community-dwellingindividuals with and without active SARS-CoV-2 infection. We found significantdifferences in beta-diversity, but not alpha-diversity in our study groups and identified severaldifferentially abundant taxa associated with SARS-CoV-2 infection status and disease severity.Chapter 3 outlines the feasibility and performance of long-read mNGS as a diagnostic tool fordetection and characterization of SARS-CoV-2. We reported that mNGS is a highly specificmethod for SARS-CoV-2 detection and is sensitive for specimens with higher viral loads. Weshowed that this technology can also be used to characterize viral genomes. Finally, chapters 4and 5 outline the development, optimization, and validation of a novel mNGS assay for detectionof viral pathogens. This assay was developed to address translational barriers to mNGS adoption.We developed and clinically validated an assay that is sensitive, specific, rapid, cost-effective,and inclusive. In addition to successfully detecting four known viral pathogens, the assaydetected a total of nine respiratory pathogens that were missed by conventional moleculardiagnostic testing when originally tested. In summary, the work presented in this thesishighlights the feasibility of using next-generation sequencing workflows in routine clinicalservice for diagnosis of viral pathogens and characterization of viral infections. This thesisrepresents novel, applied work that contributes to the field of microbiology and can haveimmediate impact on clinical microbiology and diagnostic services for human and animal healthand public health surveillance.

View record

Antibiotic resistance is the third largest contributor to mortality worldwide, and 30% of these deaths occur in newborns. The burden of resistant infections in children is disproportionately higher in low- and middle-income countries (LMICs) due to the overuse of antibiotics in food, food animals and health care settings. The prevalence of childhood co-morbidities like severe acute malnutrition (SAM) and human immunodeficiency virus (HIV) in LMICs increases the need for treatment and prophylactic antibiotic use. These conditions also increase the likelihood of secondary disease, thereby further increasing the need for antibiotics. Antibiotic resistance genes (ARGs) are the primary source of resistance in pathogens and are amplified with antibiotic exposure. There is an urgent need to understand the role of ARGs in diseases amongst infants and children, especially in LMICs, where their impact on mortality and morbidity is large. In this dissertation, chapter one reviews previous knowledge about the presence or carriage of ARGs and the impact ARGs have on morbidity and mortality in LMICs, especially morbidity and mortality due to SAM and HIV. Chapter 2 examines the natural acquisition of ARGs in healthy children living in rural areas of a LMIC using longitudinal data from the Sanitation Hygiene and Infant Nutrition Efficacy (SHINE) trial. Chapter 3 examines the changes in ARG carriage during hospitalization with SAM and HIV, and during SAM recovery using longitudinal data from the Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM) observational study. Chapter 4 investigates the impact of stopping or continuing prophylactic antibiotic use in HIV-positive children using data from the Antiretroviral Research for Watoto (ARROW) trial. I find that healthy children acquire a diverse array of ARGs upon birth, ARG carriage decreases significantly with age in healthy children, and most ARGs are closely associated with the abundance of Enterobacteriaceae that colonize the infant gut. Hospitalization for SAM leads to a less mature microbiota, associated with increases in Enterobacteriaceae-related ARG abundance. This effect was transient and decayed over time following hospital discharge. Continued prophylactic antibiotic treatment in HIV-positive children does not significantly alter ARG carriage but does selectively increase resistance specific to antibiotics used.

View record