No description available.

No description available.

Antimicrobial resistance (AMR) poses a substantial threat to public health and clinical medicine. By 2050, it’s predicted that AMR will be responsible for a yearly mortality rate of 10 million people, surpassing the mortality of cancer. Despite this daunting future we face, there are many efforts currently employed to combat the growth of AMR. One significant effort involves surveillance and early identification of novel resistant bacteria circulating in high antibiotic exposure environments. The second chapter of this thesis focuses on sampling 25 patients from a hospital environment, rich with antibiotics, to build a collection of AMR bacteria that will be tested and added to surveillance efforts/future study. This chapter allowed for the identification of several worrying AMR bacteria that provide greater insights into circulating AMR in Canadian hospitals and their patients. From the AMR collection created in chapter 2, we are also able to advance our scientific understanding of how antibiotic resistance develops within us and causes issues with treatment. In chapter 3, we looked at the effects of antibiotic administration routes on the level of AMR observed in our patient sample. We saw that current approaches to limit selection for AMR in the gut still resulted in clinically significant and concerning increases in AMR. Furthermore, this chapter allowed greater understanding of contributors to increased AMR in patients. AMR increases are not fully explained by exposure/colonization in hospital settings, but also by evolution of AMR originating from non-resistant bacteria in the gut. Additionally, analysis of these bacteria will inform expected AMR evolutionary trajectories and help us plan against them. During analysis of patient data, we also came across evolution of a less understood resistance phenotype, hetero-resistance, to a very important antibiotic, colistin. We investigated a commonly prescribed antifungal, fluconazole, for its ability to promote this resistance phenotype; however, it appeared that fluconazole did not promote this phenotype. Ultimately, this thesis serves as a valuable reservoir of AMR bacteria for future study and contributes to a greater understanding of AMR development in patients, one day leading to more informed clinical decision making. / Thesis / Master of Science (MSc)

As a posttranslational modification, the sumoylation pathway plays a key role in a wide variety of cellular events such as cell proliferation, differentiation, stress response, DNA repair and apoptosis. Given the important role of protein sumoylation, it is not surprising that alternation of sumoylation will ultimately affect cell growth as well as cancer development. As an essential E2 conjugating enzyme for sumoylation, Ubc9 plays a central role in sumoylation-mediated cellular pathways. In this study, we investigate the role of Ubc9 in drug resistance as well as its regulation in cancer cells. An early gene product, Gam1, encoded by the avian adenovirus CELO, is an inhibitory protein for the sumoylation machinery by degrading E1 and E2 enzymes. Given the suppressive effect of Gam1 on Ubc9, in this study, we use this protein to study the role of Ubc9 in drug resistance as well as its underlying mechanism. Besides showing suppression of Ubc9 expression and sumoylation by Gam1, we found that Gam1 caused significant cell growth inhibition. Of interest, like the Ubc9 dominant negative mutant, Gam1 also sensitized cells to DNA damaging agents such as topotecan and doxorubicin as well as non-DNA-damaging agents such as paclitaxel and vincristine. Furthermore, we elucidated that Gam1-mediated cell growth inhibition was associated with induction of apoptosis. In particular, Gam1 induced caspase-3 activity as detected by immunostaining and Western blot. Taken together, our findings suggest that activation of the caspase pathways is at least in part responsible for the increased apoptosis in Gam1-expressing cells and, thus, contributes to the growth inhibition and enhanced chemosensitivity. Available evidence suggests that Ubc9 is a tumor promoting factor. However, little is known about the regulation of Ubc9. In this study, we first show that Ubc9 is overexpressed in several types of cancers, highlighting its clinical significance. We then investigate the underlying mechanism of Ubc9 upregulation. Of interest, we present evidence that Ubc9 is subjected to the post-transcriptional regulation by microRNAs and the miR-30 family, such as miR-30e, negatively regulate Ubc9 expression. In contrast to Ubc9, miR-30e is underexpressed in tumors. Moreover, ectopic expression of miR-30e suppresses cell growth which can be partially reversed by Ubc9. Finally, using luciferase-Ubc9-3'-UTR reporters, we show that Ubc9 is a direct target for miR-30e by interactions with the putative miR-30e binding sites. Therefore, our study suggests that Gam1 and miR-30e may serve as therapeutic agents for cancer treatment by targeting Ubc9.

No description available.

No description available.

The transition from unicellular to multicellular life is captivating because free-living individuals become complex, coordinated assemblages that display unique properties and behaviors. It is a transformative step in biology that optimizes survival and resource utilization, especially in fluctuating environments. In microbiology, this multicellular organization assumes an intriguing form known as biofilms. Bacterial biofilms, assemblages of cells encased in a self-produced matrix, are sophisticated structures that provide protection from environmental challenges. The emerging understanding of biofilms reveals that bacteria within them do not exist as passive, isolated entities. Instead, they display spatial organization, physiological differentiation, and even metabolic interactions such as cross-feeding. The pathogenic bacterium Pseudomonas aeruginosa, which is a common cause of biofilm-based infections and a popular model organism, has been shown to form metabolic subpopulations and differentially regulate gene expression across depth in biofilms. However, one open question is the nature of this cellular arrangement in P. aeruginosa biofilms, the mechanisms governing it, and its physiological ramifications. My thesis addresses the overarching question: Does cellular arrangement in P. aeruginosa biofilms influence nutrient distribution, metabolic activity, antibiotic tolerance, and metabolic cross feeding? Through the use of paraffin embedding, thin-sectioning, and confocal microscopy, I delve deep into the biofilm, particularly in the z-direction, byproducing high-resolution images that provide insights into the three-dimensional structure and dynamics of these bacterial communities. The first chapter, serving as the foundation of this exploration, provides an introduction of the principles of multicellularity. It draws attention to the hallmarks of multicellularity, encompassing metabolic cross-feeding, protective advantages, and labor specialization while also shedding light on its challenges. In the context of multicellularity, biofilms are introduced, emphasizing the formation of bacterial biofilms, their environmental and medical implications, and specifically highlighting the importance of P. aeruginosa biofilms for understanding microanatomy and physiology. Chapter 2 presents the crux of our exploration, underlining how cellular arrangement directly impacts metabolic activity and antibiotic tolerance in P. aeruginosa biofilms. A striking observation was the presence of vertical, clonal striations, suggesting the presence of an organized architecture within mature biofilms. Mutants with disordered cell arrangements, particularly in O-antigen attachment, showed altered patterns of nutrient distribution and metabolic activity in addition to distinct patterns of antibiotic- induced cell death. Such findings build on prior knowledge by illuminating the intricate relationships between biofilm anatomy, metabolic differentiation, and drug tolerance. Chapter 3 introduces the use of light-sheet microscopy for live imaging of pellicle biofilms, which offers a real-time window into biofilm development and cellular dynamics. In Chapter 4, the narrative takes a broader perspective, focusing on the influence of various carbon sources on cellular arrangement. It introduces the presence of metabolic cross-feeding among different biofilm subpopulations and hints at the potential relationship between cell arrangement and heterogeneous metabolic activity patterns. The work in this thesis reveals that the arrangement of cells within P. aeruginosa biofilms determines metabolic outcomes, antibiotic responses, and potential cross- feeding interactions. In a world where biofilm-related infections account for an alarming 80% of persistent bacterial infections, understanding biofilm microanatomy has implications for therapeutic strategies and possibly reshaping our battle against antibiotic tolerance. A more detailed picture of the relationship between cell arrangement, physiological differentiation, and metabolic cooperation within biofilms has the potential to provide inroads toward new approaches to combating these recalcitrant structures.

The emergence and spread of drug resistance in Plasmodium falciparum has consistently been a major barrier to the control and eradication of malaria. Resistance to the affordable and fast-acting former first-line drug chloroquine (CQ) was first observed in the 1950s near the Thai-Cambodian border and in South America. Resistance later spread from Asia to highly endemic regions in Africa, with reports of up to 6-fold increases in regional malaria mortality rates. The replacement drug, sulfadoxine-pyrimethamine (SP), encountered resistance within one year of clinical use. Artemisinin-(ART) based combination therapies (ACTs), which consist of a fast-acting ART derivative and a slower-acting partner drug, became the global first-line standard in 2000 and, along with mosquito vector control measures, helped decrease mortality rates by 60%. Unfortunately, parasites resistant to ART derivatives arose in Southeast Asia. This compromised the effectiveness of the ACT partner drug piperaquine (PPQ) and resistance to this drug was first reported in 2015, around a decade after the introduction of dihydroartemisinin-PPQ. By 2019, PPQ resistance, driven primarily by a series of mutations in the P. falciparum chloroquine resistance transporter (PfCRT), was widespread in Southeast Asia, resulting in >50% failure upon treatment with dihydroartemisinin-PPQ. Malaria mortality rates have surged recently, causing an estimated 619,000 deaths in 2021. Sub-Saharan Africa is most heavily affected by this disease where 78.9% of deaths are of young children. To this date, PPQ remains effective in Africa. It is a major concern that PPQ resistance will arise on this continent, however, given the importance of PPQ in current efforts to expand the range of antimalarial interventions and reverse the current rise of malaria cases in Africa. Understanding PPQ resistance mechanisms and their effect on parasite biology is critical to creating effective treatments and minimizing the impact of drug-resistant P. falciparum malaria. This thesis aims to investigate the earliest reports of PPQ resistance, to define the PPQ susceptibility and parasite fitness of contemporary SE Asian parasite strains, and to predict future dominant strains in the field to further our understanding of parasite resistance mechanisms and combat the spread of drug-resistant malaria. In Chapter 3, we show that earlier reports of PPQ resistance in Yunnan Province, China could be explained by the unique China C PfCRT variant. Using gene editing, we reveal that this variant confers a loss of fitness and parasite re-sensitization to the chemically related former first-line antimalarial CQ, while acquiring PPQ resistance via drug efflux. We employ biochemical assays to measure mutant PfCRT-mediated drug transport and molecular dynamics simulations with the recently solved PfCRT structure to assess changes in the central drug-binding cavity. This study provides impetus for adding CQ into an antimalarial treatment regimen where PPQ has lost efficacy. In response to widespread treatment failures, PPQ was removed as a first-line partner drug. Recently, additional mutations have been observed on the highly-resistant Dd2+F145I PfCRT isoform. These mutations developed in parasites in long-term in vitro culture or in Southeast Asian field isolates. In Chapter 4, I characterized the impact of these mutations on parasite fitness and antimalarial susceptibility by editing asexual blood stage parasites to express these mutant PfCRT haplotypes. Competitive growth assays with a GFP-expressing reporter line revealed that these additional mutations reduce the fitness defect imposed by F145I, likely the primary driver of their emergence. I found that these mutations differentially impact parasite susceptibility to PPQ and CQ in in vitro dose-response assays. I used proteoliposome-based drug uptake studies, molecular dynamic simulations, and peptidomics to detail the molecular features of drug resistance and parasite physiology of these lines. These experiments provide insight into parasite responses to the changing drug selective pressures in SE Asia to inform treatment strategies in this region moving forward. In Chapter 5, I sought to determine whether Asian PPQ-resistant PfCRT mutations could also mediate PPQ resistance on African PfCRT haplotypes. Using zinc-finger nuclease-based gene editing, I introduce the most common African mutant pfcrt alleles with a SE Asian PfCRT mutation into Dd2 parasites. In PPQ survival assays, these mutations only confer high-grade PPQ resistance (defined as ≥10% survival at 200 nM) on the FCB PfCRT background. I assessed the susceptibility of these gene-edited isogenic lines to other clinical antimalarials and the relative fitness of these engineered lines with in vitro assays. These experiments clearly show that there is a genetic path to PPQ resistance in African parasites; however, they also suggest that fitness costs associated with these mutations may hinder the spread of resistance. Our data provide important insights into PPQ resistance. In chapter 6, these findings are summarized along with future studies to strengthen and expand on the findings presented herein.

No description available.

Antibiotic resistance occurs when bacteria change in response to selective pressures induced by antibiotics, which has become a major concern worldwide and one of the biggest threats to global health. Antibiotic resistance can occur naturally, but the misuse and overuse of antibiotics is accelerating the process. One way to combat this process is to understand the different relationships between microbes, also known as polymicrobial interactions. Bacteria can interact with one another synergistically or antagonistically and understanding the mechanisms behind these interactions can lead to the discovery of new therapeutics or targets to fight and kill pathogenic microbes. The rarely pathogenic Gram-negative bacterium, Alcaligenes faecalis, has previously been shown in our lab as playing an important role in potentially fighting antibiotic and antifungal resistance due to its competitiveness during polymicrobial interaction. Our research has found that A. faecalis kills Bacillus cereus, Staphylococcus aureus, and Candida albicans. This is a unique characteristic as these targets encompass both prokaryotic (bacteria) and eukaryotic (fungi) microbes. These three species are known to cause numerous infections in humans and have increased cases of antibiotic and antifungal resistance. In the present study, we investigated the genetic elements A. faecalis utilizes to inhibit growth when interacting with B. cereus, S. aureus, and C. albicans. Transposon mutagenesis was performed to create a genetic library of A. faecalis loss-of-function mutants. These strains were then screened against all three microorganisms to determine which mutants no longer inhibited growth. The mutants that lacked zones-of-inhibition were sequenced to determine the gene that had been interrupted. BLAST analysis of these sequences identified a MFS transporter, a 2FE-2S iron sulfur binding protein, a mechanosensitive ion channel, and a glucose-6-phosphate isomerase as instrumental in this inhibitory mechanism. Results from this research study can be used to further study polymicrobial interactions and potentially discover new therapeutics to combat antimicrobial resistance.