Every year, about 550,000 patients receive medical attention for minor and major burns in the United States.1 In 2020, it was estimated that 11 million people worldwide suffered from burn injuries, with 150,000 of those burns being fatal.2 Burns are among the most painful and debilitating recalcitrant wounds that can often turn terminal when infection occurs. The different grades for burns that we aim to treat are first, second, and third degrees.2 Each burn type is susceptible to secondary infection that can be life threatening, and as a result, are extensively treated with antimicrobial agents.2 At present, only a handful of FDA-approved products are available in the market that can successfully treat second and third degree burn wounds and scars.3 Topical agents such as sodium hypochlorite, iodine, H2O2, silver etc. are used to combat burn wound infections.3 However, the relentless emergence of antibiotic resistant strains of pathogens, often with multiple antibiotic resistances together with the discovery of novel antibiotics, has necessitated investigating and developing better alternative treatments. In this effort, a cost-effective approach to engineer a microbe-resistant bandage system utilizing clay was undertaken as the research project. This unique microbe-resistant material has been developed using organo-modification and metal-ion exchanged clay scaffolds, and has been fully characterized using analytical techniques such as powder XRD, ATR-FTIR, XPS, ICP-OES etc. The hybrid clay samples have also been tested for their antimicrobial efficacy against Escherichia coli (gram-negative) and Staphylococcus aureus (gram-positive) bacteria in promoting the process of wound healing to serve as a representative of the ESKAPE group of bacteria, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. By leveraging the excellent hydrophilic and moisture retention properties of clay, we can postulate achieving optimal moisture transport from the dressing through the wound area to accelerate the healing cascade by hassle-free self-application at the point of injury.4 The proposed research deals with the antimicrobial effects associated with metal cations within a clay matrix that can be used for the treatment of burn injuries and scars. Currently, most burn treatments involve high doses of silver-based products that make them costly.3 Moreover, most of these treatments are ointment-based, which exposes the wounds to cross-contamination when in contact with dust, debris, moisture, water, liquids, particulates etc. The goal is to develop a free-standing film composed of controlled amounts of silver ions tethered to the clay scaffolds that can be used to treat severe burns and scars. Performing animal studies using in vivo models for first or second degree burn injuries and scars exceeded the budget for this project, hence, antimicrobial efficacy against ESKAPE pathogens, viz. gram-negative and gram-positive bacteria using the engineered hybrid films was the focal point for this project. This unique and cost-effective system is much cheaper compared to ointments and other bandage systems. Moreover, the meso- and micro-porosities present within the clay can be easily leveraged for easy moisture and oxygen transport from bandage to skin, which is essential for natural healing of the wounds and burn injuries.4 Additionally, the antimicrobial/antibacterial efficacy of this unique bandage system can be suitable for prolonged use, thereby minimizing the inconveniences of frequent changing and reapplication. This helps to reduce the risk of infection and contamination, drastically. Clay has the well-known property of retaining moisture and has been used as a promoter for hemostasis, thereby, helping the composite films to serve multiple purposes in the burn and scar healing process.8 The hydroxyl groups in the clay used will be functionalized with trimethyl glycine (Betaine), expanding the clay galleries through intercalation, while Group II metal ions and silver ions can be easily exchanged with the sodium cations present in clay within the interstitial space. The metal ions (Ag+) exchanged organo-clay gallery is the main driving force for eliminating the microbes or bacteria. Thus, one of the prime goals for this effort is to develop an organo-modified Betaine-composite film that can be conformable to various shapes and sizes and will garner anti-microbial/ bacterial/ fungal properties. Other future goals include developing films with optimal metal ion concentrations in the clay scaffolds to reduce the cost (by replacing Ag+ ions with group II metal ions in the silicate scaffolds) without compromising the efficacy of the product. This research exhibits a novel, cost-effective solution to engineer microbe-resistant “hybrid” clay membranes by chemical modification, metal incorporation, intercalation, and exfoliation of clay-silicate galleries to prevent infections from ESKAPE pathogens. Results from the physico-chemical analyses have shown mechanical durability of the films. Antimicrobial efficacy tests using Escherichia coli (gram-negative) and Staphylococcus aureus (gram-positive) showed a significant reduction in bacterial growth, which indicates the antimicrobial efficacy of the clay films. In typical bacterial kill study experiments, the zone of inhibition was at or above 1 cm for both the gram-positive and gram-negative bacteria, with four samples tested with three 0.6 cm diameter discs against a clay control. Evidently, these matrices are effective at preventing the growth of bacteria that can prove to be infectious. This unique “hybrid” bandage system promotes: (a) prevention and control of both gram-negative and gram-positive bacteria, (b) nontoxic and biodegradable features, (and c) easy application on wounds. Beyond the antimicrobial efficacy, physical tests have been used to analyze the resulting clay films. X-Ray photoelectron spectroscopy is used to determine the quantitative elemental analysis, and binding energies and oxidation states of the elements. Powder X-Ray diffraction, ATR-FTIR, X-Ray fluorescence spectroscopy and viscosity have been used to determine physical properties, structures, and mechanical durability of the films.

The North American Great Lakes are a vital source on a global scale, as they hold ~18 % of the potable water resources on our planet. Cyanobacteria of the genus Microcystis are commonly found in fresh water environments around the world, and since the mid-1990s also in Lake Erie. The reasons for the success for these potentially toxic cyanobacteria in Lake Erie are not completely understood. In this study we have applied modern molecular tools to analyze field samples to provide an insight into the genotypic composition and diversity of the Microcystis community in the past and present day Lake Erie. We have also analyzed a three-year data set to identify specific environmental factors that contribute to the abundance of Microcystis genotypes and microcystin production. In addition, in a laboratory-based study we examined the effect of nutrients on transcriptional activity of the microcystin synthetase gene mcyD. The results of this study suggest that, although toxic Microcystis form < 10 % of the total cyanobacterial population in Lake Erie, the toxin-producing Microcystis community in Lake Erie is diverse, and that these populations are stabile on a time scale of decades. Sediments acting as a reservoir of Microcystis are likely contributing to the persistence of the population. Although Microcystis is the dominant microcystin producer in the lake, other microcystin-producing cyanobacteria were also found in spatially isolated regions of the lake. While microcystin concentration in Lake Erie is correlated positively with total phosphorus (P<0.001) and surface reactive phosphorus (P<0.001), and negatively with the molar ratio total nitrogen to total phosphorus (P<0.001); toxic Microcystis abundance correlates negatively with NO3 concentration (P=0.04) and positively with surface water temperatures (ranging from 20.8 °C to 27.4 °C) (P=0.03). These observations, along with findings from culture based experiments, suggest decoupling of the factors governing proliferation of toxic cells and toxin production. Culture based experiments also suggested that the chemical form of phosphorus may be an important factor in regulating microcystin biosynthesis in Microcystis based on monitoring relative transcriptional activity of the mcyD gene. The transcriptional activity of mcyD was higher (P=0.118) in cells grown in BG11-medium containing 2.3 μM organic phosphorus (glycerol 2-phosphate disodium salt hydrate) than in cells grown in BG11-medium containing 2.3 μM inorganic phosphorus (K2HPO4).

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Traditionally, the analysis of soil health has overlooked the biological component of soil due to poor understanding of connections between the microbiome and empirically measured soil health indicators. The purpose of this study was to assess the effects of environmental and anthropogenic stressors on the soil microbiome, with the aim of identifying measurable soil biological indicators. Chosen soils were examined under distinct conditions to evaluate the effect of selected environmental and anthropogenic stressors on the microbiome. Soil biological responses were analyzed via enzymatic response, microbial functional genes, and microbial community. Environmental factors such as soil moisture and organic matter showed significant influence on the microbiome with each selected biological indicator showing importance. Anthropogenic factors provided various responses dependent largely on the nature of the soil amendment. This study demonstrates that in addition to traditional soil health indicators, soil biological indicators should be included in the process of determining healthy soils.

Since the work of John Snow, scientists and medical professionals have understood that individuals develop cholera by means of consuming contaminated water. Despite the knowledge of cholera's route of infection, many countries have experienced and still experience endemic cholera. Cholera is caused by the Vibrio cholerae (V. cholerae) bacterium and presents with acute diarrhea and vomiting. If untreated, infected individuals may die due to dehydration. Cholera is a disease that most commonly affects countries with poor infrastructure and water sanitation. Despite efforts to control cholera in such countries, the disease persists. One such example is Haiti which has been experiencing a cholera outbreak since 2010. While there has been much research in the field of microbiology to understand V. cholerae, there has been comparably less research in the field of mathematical biology to understand the dynamics of V. cholerae in the environment. A mathematical model of V. cholerae incorporating a phage population is coupled with a SIRS disease model to examine the impact of vibrio and phage interaction. It is shown that there might exist two endemic equilibria, besides the disease free equilibrium: one in which phage persist in the environment and one in which the phage fail to persist. Existence and stability of these equilibria are established. Disease control strategies based on vibrio and phage interactions are discussed.

<p>Microbes are ubiquitous in the biosphere and play important roles in natural ecosystems. They are typically present as diverse, complex communities, and in humans these communities are present on all exposed surfaces and mucosal tissues. The human upper respiratory tract harbors a complex microbiome and the composition includes what are traditionally considered commensal organisms, including a significant proportion of anaerobic bacteria. It is generally assumed that most of the bacteria from any particular environment cannot be readily cultivated, including the human microbiome. Some<em> in vitro </em>microfluidic and <em>in vivo </em>models are available to study the airway microbial communities, however these methods are expensive, limited and are not practical for experiments manipulating the community. A robust culture-based approach that can propagate these polymicrobial communities has been developed in this study to investigate spatial-temporal changes in bacterial populations <em>in vitro</em>. Matrix embedded synthetic bacterial communities, comprised of aerobes and anaerobes, were cultivated in continuous flow cell systems. The structure of communities propagated in these systems was compared to those in static and shaken batch cultures. The data shows that reproducible stable bacterial communities can be propagated with these culture methods, however the community composition varies considerably with the approach used. Only matrix embedded communities, cultured under continuous flow conditions, could successfully retain obligate anaerobes when flow cell systems were operated in an aerobic environment. This optimized method was used for culturing complex and diverse natural communities from clinical samples (sputum). The majority of bacteria present in the original sample were recovered in flow cell cultures and the methodology was consistent. This study provides an experimental system that can be used for examining microbial community dynamics and community structure-function relationship.</p> / Master of Science (MSc)

The provision of high quality, clean water is of paramount importance to both human public health and the welfare of all biodiversity. Maintaining this quality also helps to promote sustainability of water globally through programs involving public health, watershed (ecosystem) protection, water-resource management and water governance and regulation. These initiatives allow for more effective risk assessment and management of the world’s usable water supply. Pathogenic microorganisms such as bacteria, viruses and protozoa which are present in faecal-contaminated water have always been a major threat to human health. Monitoring every single pathogen present in water is impractical, therefore the use of microbial water-quality indicators has been recommended. Escherichia coli (E. coli) and Enterococcus sp. are the main microbial indicators used for assessing fresh and marine water (recreational water), respectively. E. coli testing is conducted all over the world and there are good tests readily available, but tests for Enterococcus are limited, even though these bacteria are often better indicators of faecal contamination. We are developing an Enterococcus test by adapting technology that was developed at Queen’s University for detecting E. coli and Total coliforms. Different growth media types were used and Todd-Hewitt broth (THB) was found to be the most effective media for the Enterococcus test and can be used at full strength or half strength. The test was optimized for temperature; 41oC elicited the best results. In order to promote selective Enterococcus growth, different antibiotics were administered. It was found that 6 mg / L of amikacin in half strength THB was optimal to make the THB media selective to Enterococcus in the presence of potentially interfering E. coli bacteria. This novel test will complement the tools already available for global water-quality monitoring, thereby promoting sustainable water-use, and thus enhancing the protection of the public’s health. / Thesis (Master, Environmental Studies) -- Queen's University, 2013-05-01 20:31:16.331

Knowledge about whether/how natural water chemistry influences the fate, dissolution, and toxicity of silver nanoparticles (AgNPs) should contribute to ecological risk assessment and informed decision making. The effects of three critical water chemistry parameters – dissolved organic carbon (DOC), pH, and hardness – were investigated on the colloidal stability, dissolution dynamics, and antimicrobial activity of citrate-functionalized AgNPs (citrate–AgNPs) against Escherichia coli. Toxicities of citrate–AgNPs and AgNO3 were also determined in the river water samples collected across three seasons (for seven months). Detectable changes in hydrodynamic diameter, surface charge, and plasmonic resonance revealed the modulating effects of the water chemistry parameters on the colloidal stability of citrate–AgNPs. Although, overall Ag release from citrate–AgNPs was low (0.33–3.62%), it increased with increasing DOC concentrations (0–20 mg L−1) but decreased with increasing pH (5–7.5) or hardness (150–280 mg L−1). Citrate–AgNP toxicity was 3–44 fold lower than of AgNO3 (Ag mass basis). Notably, higher DOC or pH conferred protection to E. coli against citrate–AgNPs or AgNO3; increasing solution hardness tended to enhance toxicity, however. Citrate–AgNPs or AgNO3 toxicity in the river water matrix revealed no seasonality. Generalized linear models developed, by parameterizing particle properties, could fairly predict empirically-derived nanotoxicity. Our results show that particle size, surface properties, ion release kinetics, and toxicity of citrate–AgNPs can be modified upon release into aquatic environments, suggesting potential implications to ecosystem health and functions.