Microbiology Commons^™

Characterization Of Antimicrobial Properties Of Excrement And Functional Microbiome Of Black Vultures (Coragyps Atratus), Bridgette Gray

Theses

Black vultures, Coragyps atratus, are obligate scavenging birds that consume and dispose of decaying carcasses and carrion. They fulfill a key ecological niche in the environments in which they live. It has been observed that these vultures sometimes excrete bodily waste onto their legs. This adaptive behavior could help aid them in controlling bacteria and other microbes they encounter while stepping into a carcass to eat. This study directly examined the antimicrobial properties of the excrement of black vultures across various bacterial species utilizing a zone of inhibition test and a nematode species utilizing a survival assay. The black vulture …

Correlation Of Gut Alteration With The Progression Of Experimental Autoimmune Encephalomyelitis (Eae) In C57bl/6 Mice, Al Anood Ahmed Al Naqbi

Theses

Background: Experimental autoimmune encephalomyelitis (EAE) is the mouse disease model of multiple sclerosis (MS), a chronic autoimmune disease targeting the central nervous system (CNS) resulting in neuroinflammation, neuroaxonal degeneration, and demyelination. Autoreactive CD4⁺ T cells are known for their role in the pathogenesis of MS. CD8⁺ T cells and NK cells were also found to be associated with the disease.

Aim: There is a limited number of studies investigating the link between gut alterations and immune cells in the gut influencing the outcome of the disease since the vast majority of MS patients experience gastrointestinal (GI) problems. Here, …

Factors Affecting The Antibacterial Activity Of Cefiderocol On Klebsiella Pneumoniae With Diverse Characteristics, Lana Jamal Rashed Daoud

Theses

Antimicrobial resistance (AMR) is a growing serious threat that poses a burden on the healthcare system. Spread of AMR bacteria limits treatment options; thus, new antimicrobial agents are required. Cefiderocol (CFDC) is a novel siderophore cephalosporin, approved by the FDA in 2019 for use in treating infections caused by multi-drug resistant (MDR) pathogens; but it is not yet in clinical use in the UAE. CFDC is equipped with stabilizers against β-lactamases as well as a siderophore side chain that allows it to penetrate the outer membrane of bacteria through the iron uptake pathways. The aim of this study is to …

Mechanistic Insights On The Role Of Ambrisentan, An Endothelin Type-A Receptor Antagonist, In Breast Cancer, Ruba Saleem Lutfi Amer

Theses

The activation of the endothelin receptor type A (ETAR) by its ligand endothelin-1 (ET-1) is well known for its role in vasoconstriction. Interestingly, ET-1 and ETAR are over-expressed in various human tumours, including breast cancer. Several studies described the important role of ETAR in cancer progression and metastasis. The extensive network of interactions that exist between the ET-1 axis and other signalling pathways can trigger autocrine and paracrine signalling that modulates different tumorigenesis processes, such as cellular proliferation and survival, epithelial-to-mesenchymal transition (EMT) and chemoresistance. The main objective of this study was to investigate the antitumor effects of Ambrisentan, a …

Elucidation Of Novel And Established Campylobacter Species With Clinical And Agricultural Significance Through Phenotypic, Genotypic, And Taxonomic Investigation, Caoimhe Lynch

Theses

Campylobacter spp. are well-established human, veterinary and economic pathogens, with a broad host range spanning from terrestrial and marine mammalian, avian and reptilian hosts. The scope of the study includes novel and notorious species within the genus, with reference to zoonotic agents Campylobacter jejuni and Campylobacter coli - the leading cause of human bacterial gastroenteritis in the EU and Ireland, Campylobacter fetus that represents the most common campylobacter causing bacteraemia and two novel species isolated from pigs not described in the literature previously. C. jejuni and C. coli isolates (n = 350) recovered from broiler caecal and neck skin samples, …

Predicting, Monitoring And Controlling The Growth Of Listeria In Complex Food Matrices, Laura Mary Nyhan

Theses

Listeria monocytogenes is a foodborne pathogen which is a significant challenge in food production, particularly for ready-to-eat (RTE) products. Incidence of Listeria in RTE foods can be reduced by the application of intelligent combinations of preservative factors or hurdles, while data quantifying the efficacy of hurdle combinations can be exploited and used in the area of predictive microbiology. Traditional culture-based techniques, such as viable plate counts, are commonly used to monitor the growth/survival of microorganisms in foods, however these methods are tedious, time-consuming and due to their destructive nature, are associated with low reproducibility and high variability. Therefore, rapid, non-invasive …

Group B Streptococcus: Molecular Epidemiology, Pathogenic Profiling And Control Strategies, Katherine Mary Hayes

Theses

Group B Streptococcus (GBS) are frequent colonisers of the gastrointestinal tract of healthy adults with worldwide rates of 18% colonisation; however, they are also opportunistic pathogens capable of causing invasive disease, particularly in neonates and adults with underlying conditions. Indeed, GBS is the leading cause of invasive neonatal disease worldwide with a global incidence of 0.49 per 1000 live births and GBS disease in adults is increasing globally, with estimated rates of 10.9 cases per 100,000 people. While GBS remain largely susceptible to penicillin, there have been reports of reduced beta-lactam susceptibility in certain countries and resistance to other antibiotic …

Crystallographic Studies On Host-Interacting Proteins Of Phage K Virion, Antonio Pichel Beleiro

Theses

Phage K is a lytic bacteriophage that infects a broad range of staphylococci, including some methicillin-resistant Staphylococcus aureus strains. Phage K attaches to its host via a baseplate. The contracted conformation of the baseplate contains a fiber and two receptorbinding proteins responsible for the interaction with the host. The native conformation of the baseplate also includes a tail central spike that shears off after contraction. The aim of the thesis is the structural characterization of phage K receptor-binding proteins and tail central spike. Experimentally, the thesis relies on crystallographic methods, which encompass: production of suitable sample, crystallization, diffraction, and data …

The Occurrence Of Listeria Monocytogenes In The Mushroom Production Chain And The Use Of Bacteriophage For Its Control, Vincenzo Pennone

Theses

In Agaricus bisporus production, the occurrence of L. monocytogenes is still poorly understood. A number of studies have shown the presence of L. monocytogenes in the mushroom processing environment, suggesting its source from raw materials storage areas (Viswanath et al, 2013; Murugesan et al, 2015). In this study, 10 mushroom producers and three raw material (compost and casing) producers participated in two surveys on the occurrence of L. monocytogenes in the most high-risk areas of the production environment. In the first survey, floors, drains, platforms, crates, raw materials and mushrooms were tested for L. monocytogenes presence and the results were …

Crystallographic Structure Determination Of Bacteriophage-Encoded Enzymes That Specifically Target Pathogenic Bacteria, Marta Sanz Gaitero

Theses

Antibiotic resistance is becoming a serious public health concern. Infections that some decades ago could be treated with antibiotics now sometimes do not respond to traditional treatment, causing higher mortality and economic losses. An alternative to the use of antibiotics are bacteria's natural predators, bacteriophages (or phages), and specifically their lytic enzymes. These proteins are produced by phages to degrade bacterial peptidoglycan to inject their genetic material into the bacteria (virion-associated peptidoglycan hydrolases) or to release their progeny once the infection is finished (endolysins). They can be applied exogenously to lyse Gram-positive bacteria or be genetically engineered to lyse Gram-negative …

A Diagnostic And Control Programme For Johne’S Disease On Irish Dairy Farms, Aideen Kennedy

Theses

Johne’s disease (JD) is an enteritis of ruminants with potential zoonotic implications. JD diagnosis and control present difficulties given JDs prolonged subclinical nature. In order to improve JD control in Ireland, PhD aims included conducting a national survey documenting high-risk husbandry practices employed on Irish farms, thereby targeting areas for improved management. Furthermore as JD has been associated with on-farm economic losses internationally, this research programme aimed to analyse production losses associated with testing JD ELISA positive on Irish dairy farms. A longitudinal study was also conducted to assess if successful JD control can be achieved using gold-standard protocols. Due …

Microbiota, Diet And Medication In Human Gut Disorders, Adam Clooney

Theses

The microbiota, a community of micro-organisms in a particular environment, have been intensely researched in the past decade and interest appears to continue to increase. The human body is richly populated with bacterial cells (3.8x10'^) and alterations in these communities are associated with disease. The work presented in this thesis explores aspects of microbiota research methodologies with regard to optimisation and concerns over a lack of reproducibility. Additionally, we investigated the effects of medication, in particular Proton Pump Inhibitors, on the human gut microbiota, along with comparisons between the microbiota of patients with active and inactive Inflammatory Bowel Disease.

Microbiota …

Metabolic Characteristics Of Macrophage Activation With Phenotype Microarrays, Tanya Kathryn D'Souza

Theses

Inflammation is a natural protective response and is characterised by the activation of numerous immune cells, including macrophages which can release a variety of inflammatory mediators. Macrophages play a flexible role in the initiation and effector phases of the immune response and change their behaviour to respond to environmental stimuli. The main objectives in this study were to create and characterise different macrophage behaviours and employ a novel metabolic characterisation platform the Phenotype Microarray^TM to attribute additional characteristics to the currently well recognised phenotypes. Five activated macrophage states were demonstrated and characterised. Unactivated macrophages (MO) demonstrated undetectable levels of …

Mycobacterium Species Identification In An Acute Hospital: Towards Rapid Identification, And Improved Epidemiology, Using Novel Mass Spectrometry Analysis, James Anthony O'Connor

Theses

Mycobacteria are a heterogeneous group of bacteria that cause a wide spectrum of disease, including Tuberculosis (TB), the single biggest killer worldwide. The genus also incorporates over 170 nontuberculosis (NTM) species, many of which are opportunistic pathogens. The aim of this project was to ascertain the burden of mycobacterial disease in the region and to determine the efficacy of Matrix-Assisted Laser Desorption/Ionisation time-of-flight (MALDI-tof) mass spectrometry (MS) for novel uses as a rapid identification method for clinical mycobacteria and as a typing tool for Mycobacterium tuberculosis complex isolates. A five-year retrospective epidemiological study of the region was conducted, the first …

The Development Of New Molecular Tools To Detect Mycobacterium Avium Subspecies Paratuberculosis From A Bovine Faecal Environment By Real-Time Pcr, Marcel De Kruijf

Theses

The slow-growing intracellular pathogen Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s disease in domesticated and wild ruminants. Johne’s disease inflicts severe annual economic losses to the dairy industry worldwide. This thesis is divided into five chapters that consist of a literature review' chapter and four experimental chapters focusing on MAP strain genotyping and the development of novel molecular MAP detection tools using real-time PCR. Chapter 1 describes published information regarding MAP characteristics, Johne’s disease, MAP genomes, available MAP detection methods, MAP epidemiology and genotyping.

To efficiently control and monitor MAP infection, molecular t>ping of MAP strains provides extensive knowledge …

An Investigation Of The Use Of Natural Agents To Control Mycobacteria, Olga Lesniak

Theses

Economic losses that are caused by Mycobacterium avium paratuberculosis (MAP) infections represent a major obstacle for farmers and also for the dairy industry. In order to control the population of MAP, alternative control agents must be investigated. One of the studies described in this thesis focused on using a bacteriophage therapy based approach to assess its efficacy on simulated industrial environments and food models. Another study described in this thesis investigated the antimicrobial effects of parsley and garlic on a range of mycobacteria species. Both studies used conventional microbiological methods such as plaque assays, AlamarBlue assay (MABA) and growth curves, …

Clinical Coagulase-Negative Staphylococci; Identification, Characterisation And Treatment, Emma Gabriel

Theses

The work presented in this thesis focuses on clinically significant staphylococci (with an emphasis on coagulase-negative staphylococci) in terms of their isolation, identification, characterisation, and biocontrol.

CoNS are increasingly being recognised as true nosocomial pathogens yet remain under-characterised, particularly from an Irish clinical perspective. We examined a large cohort of clinically-derived CoNS, isolated from blood (n=l35), identifying them to species level. Extensive antibiotic resistance against nine clinically-relevant antibiotics was recorded. Additionally, widespread biofilm forming capabilities associated with increased virulence was detected both phenotypically and genotypically. We identified multiple species of CoNS in circulation in an Irish healthcare setting, and determined …

Molecular Targets Of Manuka Honey In Human Breast Cancer, Sarah Saif Al Qubaisi

Theses

The medicinal properties of Manuka honey have been extensively studied, particularly in terms of its wound healing and antimicrobial activities. We have previously demonstrated that Manuka honey also has anti-cancer properties against a variety of cancer cell types in vitro as well as in preclinical cancer models. The cellular targets of the anti-cancer activity of Manuka honey, however, remain unknown. For the present study, we selected the triple negative human breast cancer cell line, MDA-MB-231, to investigate susceptibility to Manuka honey and to identify the potential signaling pathways affected. MDA-MB-231 cancer cells are known to constitutively express activated STAT3 transcription …

Induction Of Anti-Microbial Immune Responses In Severely Immunodeficient Hosts By Ifn-Expressing Salmonella Enterica Serovar Typhimurium Correlates With Efficient Activation Of Macrophage Effectors, Mohammed Achraf Al-Sbiei This

Theses

Susceptibility to infection by the intracellular bacterial pathogen, Salmonella enterica serovar Typhimurium (S. typhimurium), is controlled by many genes of innate and adaptive immunity. One of the most critical genes is IFN- and mice deficient in IFN- synthesis are highly susceptible to Salmonella. Previously, we demonstrated that mice deficient in MyD88, an adaptor that regulates TLR signaling, are susceptible to Salmonella infection. In the current study, we compared immune responses in mice deficient in IFN- or MyD88 with wild-type controls following infection with an attenuated strain of S. typhimurium (designated BRD509E) or a recombinant derivative engineered to express murine IFN- …

Identification Of The Molecular Mechanisms Governing The Osmotolerance Of The Emerging Gastrointestinal Pathogen Cronobacter Sakazakii, Audrey Feeney

Theses

Cronobacter sakazakii is an organism which has been associated with severe life- threatening diseases in infants and neonates. Mortality rates of up to 80% have been recorded in infants infected with Cronobacter sakazakii. Infants often suffer from septicaemia, necrotising enterocolitis and meningitis as a result of infection. A characteristic feature of the opportunistic foodborne pathogen Cronobacter sakazakii is its ability to survive in extremely arid environments such as powdered infant formula, making it a dangerous opportunistic pathogen of neonates. Herein, we provide a brief overview of the pathogen; clinical manifestations, environmental reservoirs and our current understanding of stress response mechanisms …

Characterisation And Applications Of Natural Lactic Acid Bacteria With Emphasis On Weissella Cibaria And Associated Exopolysaccharide, Kieran M. Lynch

Theses

The work presented in this thesis characterises natural cereal-derived lactic acid bacteria and examines their potential application in the dairy fermentation area, with special emphasis on the sourdough isolate, Weissella cibaria MGl and its associated glucan homoexopolysaccharide. This strain is notable for its high-level production of dextran, being termed a “hyper-producef’. Genome sequencing and analysis of a number of IV. cibaria strains was performed in the context of available genomic data for other Weissella species, with special focus on the metabolic traits of W. cibaria MGl, and the results represent the first study to explore members of the Weissella genus …

Exploiting Bacteriophages And Associated Peptidoglycan Hydrolases With Potential For Biocontrol In Food Related Applications, Lorraine Endersen

Theses

The work presented in this thesis describes the isolation and characterisation of novel bacteriophages, and the subsequent exploitation of their bactericidal properties against two opportunistic food related pathogens, Mycobacterium avium subsp. paratuberculosis (MAP) and Cronobacter sakazakii.

MAP is a proven animal pathogen known to cause Johne’s disease in cattle but has been implicated as a causative agent of Crohn’s disease in humans. Despite the fact that this association has yet to be proven, significant focus has been directed towards evaluating the consequences of consuming milk contaminated with MAP. Accordingly, six mycobacteriophages were isolated and characterised in terms of temperature and …

Gastroenteritis Viruses In Ireland: Epidemiology And Evolution, Lynda Gunn

Theses

Viral gastroenteritis is a common disease of both humans and animals. This thesis focuses on the use of classical virology, coupled with phylogenetics to study gastroenteritis viruses [Bocavirus (BoV), Coronavirus (CoV), and Rotavirus A (RVA)], isolated from selected samples from humans and animals. RVA was associated with outbreaks in elderly care facilities in Northern Ireland, isolates were genotyped and we reported the first detection of G2 lineage lie RVA in Ireland, with other common human RVA genotypes G1P[8], G2P[4] and G9P[8]. Evolutionary dynamics of human RVA VP7 genotypes was examined using codon models of evolution, results show heterogeneous selective pressure …

Detection, Identification And Characterization Of The Novel Campylobacter Species: Campylobacter Ureolyticus And Campylobacter Corcagiensis From Their Reservoirs., Monika Koziel

Theses

Campylobacter ureolyticus has been identified in a large proportion of diarrhoeal samples from patients in Ireland. However, the source of human infections has not been established and little is currently known about the potential reservoirs of C. ureolyticus in nature.

The aim of this project was to investigate a range of environmental and animal samples for the presence of this emerging pathogen using a molecular approach, to support the hypothesis of its zoonotic origin.

During the study, C. ureolyticus was detected in 30 out of 1,254 (2.4%) human diarrheic samples and isolated from 11 patients, describing, to the best of …

Characterisation Of The Enzybiotic Potential Of Selected Staphylococcus Aureus Bacteriophages, Ruth Keary

Theses

The work presented in this thesis focuses on harnessing the bactericidal potential of bacteriophage (phage) encoded peptidoglycan hydrolase enzymes to combat the significant pathogen Staphylococcus aureus. In order to identify novel peptidoglycan hydrolases lytic against S. aureus, the complete genomes of two staphylococcal temperate Siphoviridae bacteriophages, DW2 and CSl, were sequenced and annotated. Screening of these genomes identified genes for several putative peptidoglycan hydrolases including two endolysins and three virion-associated peptidoglycan hydrolases. The identification of putative genes relating to virulence and host fitness lends to the understanding of the role played by such temperate phages in the evolution of this …

Development Of A Recombinant Lactobacillus Salivarius For Prophylactic Applications Against Mycobacterium Avium Subspecies Paratuberculosis And Johne’S Disease, Christopher Johnston

Theses

Current whole-cell vaccines against Mycobacterium avium subsp. paratuberculosis, the etiological agent of Johne’s disease, are unable to provide complete protection against infection. Moreover, such whole-cell formulations interfere with diagnostic tests for bovine tuberculosis (Mycobacterium bovis). The development of subunit vaccines, those which are preferentially based on one, or a select few, immunodominant protective antigens is considered as the realistic next step in overcoming these issues. The (MAP) K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs. In order to identify MAP specific proteins for subsequent incorporation within a mucosal based vaccine development, a …

Identification And Characterisation Of Campylobacter Ureolyticus: A New And Emerging Gastrointestinal Pathogen, Susan Bullman

Theses

Campylobacter jejuni is universally recognized as the leading bacterial cause of human gastroenteritis. However, within recent years a growing number of non- jejuni/coli Campylobacter species have been acknowledged as emerging human and animal pathogens. Advances in molecular diagnostics and development of pioneering culture methodologies have led to the detection of a range of under-appreciated and nutritionally fastidious Campylobacter species, including C. ureolyticus. Herein, we provide the first report of C ureolyticus in the faeces of patients presenting with gastroenteritis and suggest a role for this organism as an emerging enteric pathogen.

Employing a two-tiered molecular study, we report C. ureolyticus …

The Isolation And Characterisation Of Acientobacter Baumannii Bacteriophage, Mohamed Farag M. Elbreki

Theses

Acinetobacter baumannii is a pathogen, which has an increasing prevalence of multidrug resistance. It exists widely in natural environments, and frequently in health-care settings where it has proven difficult to eradicate using antibiotic therapy. A possible alternative to conventional antibiotics is the use of bacteriophages (phages) as antibacterials. In this project, extensive screening of environmental samples such as soils, sewage and waters was undertaken to identify suitable phages. Three phages were successfully isolated from municipal waste in the Cork area. These were subsequently characterized in detail and examined by electron microscopy, which showed that they were all of the Myoviridae …

Exploitation Of The Bacteriophage-Derived Peptidase Chapk, Pierre-Mehdi Hadbi

Theses

This project investigated an anti-staphylococcal bacteriophage-derived peptidoglycan hydrolase enzyme, namely a cysteine-histidine amydohydrolase/peptidase (CHAP_k). The study focused firstly on optimizing the production of recombinant CHAP_k, which was previously cloned in an E. coli expression system, and sets out the resulting optimal Standard Operating Procedures (SOPs) for production, purification and determination of concentration and activity of the resulting protein stock. A typical yield resulting from the investigation was 300pg of CHAP_k from one litre of E.coli culture. The activity of the purified enzyme was typically in the region of 190U nmol ’. Secondly, the project investigated …

Study Of Cellular Responses Under Chemically Induced Hypoxia, George Coricor

Theses

No abstract provided.