Veterinary Medicine Theses

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This collection is made up of doctoral and master theses by research, which have been received in accordance with university regulations.

For more information, please visit the UCD Library Theses Information guide.


Recent Submissions

Now showing 1 - 5 of 18
  • Publication
    The application of whole genome sequencing approaches to elucidate the genetic structure, phylogeny and infection dynamics of Mycobacterium avium subspecies paratuberculosis in Ireland
    (University College Dublin. School of Veterinary Medicine, 2022) ;
    Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) in ruminants, a chronic enteric disease that is a burden on the cattle industry. Having a clear picture of the genetic diversity of a pathogen provides an understanding of its biology and epidemiology, both of which are crucial for improving and refining control of the disease. The main aim of this thesis was therefore to apply whole genome sequencing (WGS) methodology as a means of studying MAP genetic diversity and infection dynamics across the island of Ireland. To initiate the WGS analyses, several techniques for method optimisation were first pursued, including DNA extraction, library preparation and computational analysis of sequence data. I then used these optimised methods to explore whether there was an obvious genetic basis for the suspected attenuation of a clinical Irish MAP isolate, CIT003, that had been used in an experimental infection study of cattle that failed to progress to infection. These analyses found mutations in several genes that may have led to attenuation of the CIT003 strain used, including prpB, which encodes methylcitrate lyase (MCL), a key enzyme in the methylcitrate metabolic cycle responsible for metabolising fatty acids. These in silico leads these were then followed up by in vitro culture experiments, revealing the potential impact of these mutations on growth in vivo. The next stage was to apply WGS to a collection of 197 MAP isolates from the years 2013- 2019, spanning 27 Irish counties. When compared with previously used MIRU-VNTR methods, WGS demonstrated considerably better resolution, revealing that Irish isolates fell into eight distinct clades separated by as much as ~200 SNPs. Isolate data also revealed cases of mixed infection within herds, as well as identical isolates being present in different areas of the country, suggesting MAP infection is spread across the island via cattle trade networks. An attempt to expand upon the temporal depth in the Irish MAP dataset by sequencing isolates from 2004 and 2005 was attempted, but this effort was met with contamination issues present in the samples. By integrating published datasets from across Europe, Australia, Canada, and the US it was found that most European isolates clustered together with Irish isolates, while most Canadian, US and Australian isolates formed their own clades. A simple preliminary coalescent model in BEAST indicated that most Irish and European isolates share a common ancestry somewhere within the last 50-100 years. The BEAST model also estimated a substitution rate of 0.25-0.27 SNPs/genome/year for MAP, which is consistent with previously published rates. The final approach was to use WGS at a finer scale on specific problem herds identified during the work, seeking to establish the levels of genetic diversity within these herds, and resolve potential transmission chains. Isolates within the problem herd ‘Cork 10’ were found to be highly similar, with the combination of WGS and computational approaches able to resolve a transmission chain linking the similar isolates together. However, herd ‘Tyrone CaA’ showed high intra-herd variation, confounding the resolution transmission chains. The opportunistic nature of sampling carried out in these herds limited the temporal depth captured, and in both cases affected the ability to resolve transmission chains. Overall, the data presented in this thesis highlights the utility and resolution offered by WGS and sheds new light on the MAP global genetic diversity, as well as infection transmission and persistent infection in herds in Ireland.
  • Publication
    Validating and optimizing feedback of Precision Livestock Farming technologies and Meat Inspection to improve welfare and respiratory health in finisher pigs
    (University College Dublin. School of Veterinary Medicine, 2022) ;
    Currently, the pig industry faces the need for a dramatic reduction in antimicrobial use (AMU) to fight antimicrobial resistance; increasing concerns about emissions of environmental pollutants; and growing societal concerns about pig welfare, with associated increases in legislation. Respiratory diseases and poor welfare are major barriers for the pig industry in meeting these challenges. This thesis focused on the optimization and validation of Precision Livestock Farming technologies and meat inspection data to improve welfare and respiratory health in finisher pigs. The reasoning for this PhD research was the need to connect farmers with the abattoir by creating a feedback loop of information on pig health and welfare. Chapter 2 showed that the prevalence of lung lesions recorded at slaughter was associated with coughs recorded on farm by the cough monitor and by manual quantitative assessments at the end of the finisher stage. In contrast, though coughing was recorded in the earlier weeks of the finisher stage, it was not reflected in a higher prevalence of lung lesions at slaughter. This indicates that respiratory health of pigs in the earlier production stages is not reflected in lung lesions recorded at slaughter. This highlights the benefit of including measures of coughing frequency to complement post mortem findings, to improve the management of respiratory disease on farm. Chapter 3 elucidated information on levels of coughing in healthy pigs which is crucial to calibrate alarm systems for respiratory health - such as the cough monitor used in this study. Furthermore, the work demonstrated the underappreciated influence of ammonia and other environmental risk factors on coughing in pigs. Finally, it emphasised the importance of continuously measuring ammonia concentrations, and the urgent need to integrate sensor technology with ventilation systems to improve pig health. In Chapter 4 we outline the modest predictive power of farm assessments of animal-based welfare outcomes and information on AMU in relation to different meat inspection outcomes (pluck lesions, partial and total condemnations, and low cold carcass weight). The insights gained from chapter 5 are applicable to the current efforts to develop an automated recording tool for routine post mortem meat inspection in the Republic of Ireland, but are also important given the EU focus on measuring animal-based welfare outcomes at slaughter. The optimal simplified pneumonia lesion scoring system involves counting the number of lung lobes affected while excluding the intermediate lobe. This provides the best trade-off between value of information and feasibility. Pleurisy is best evaluated by considering the presence or absence of cranial pleurisy while scoring only moderate and severe lesions in the dorsocaudal region. This thesis represents an important contribution to enhance the sustainability of the pig industry.
  • Publication
    Investigation of novel strategies to control Campylobacter in commercial broiler flocks
    (University College Dublin. School of Veterinary Medicine, 2022)
    Campylobacter is the most common cause of bacterial food poisoning in the world. Campylobacteriosis is generally mild and self-limiting, typically characterised by 1-3 days of fever, followed by 3-7 days of abdominal cramping and bloody or watery diarrhoea, however, in a minor number of cases Campylobacter can be a precursor to a number of more serious illnesses such as Guillian-Barré syndrome (GBS) or Miller Fisher syndrome (MFS). Broilers are a natural host for Campylobacter with poultry accounting for an estimated 50 – 80% of campylobacteriosis cases. In 2018, it was found that 26% of broilers and 72% of turkeys within the European Union (EU) were colonised with Campylobacter. Therefore, it has been suggested that reducing Campylobacter carriage in broilers by 2-3 log10 could result in a 76 – 100% reduction in campylobacteriosis cases, and so, extensive research has been carried out to eliminate Campylobacter at farm level. The aims of this project were to investigate novel strategies that could be implemented for use in the control of Campylobacter in commercial Irish broiler flocks such as enhanced biosecurity and the use of natural feed/water additives, and to investigate the effects of feed and antibiotic use on the broiler microbiome throughout the broiler rearing period. It was found that enhanced biosecurity through the use of a biosecurity framework consisting of biosecurity pens presents a potential solution to prevent broiler colonisation by campylobacters while also increasing productivity up to 20% by limiting contact between broilers and farm staff and sub-dividing broilers into smaller flocks while maintaining the same stocking density. OA, EO, and MCFA based treatments were found to show great potential as anti-Campylobacter additives when tested in vitro, however when tested in vivo, these compounds had a negative impact on broiler performance, significantly impacting the caecal microbiota, casting doubt on their effectiveness within the broiler industry. In vitro broiler feed digestates were found to be incapable of supporting Campylobacter growth and so it was concluded that the nutrients available in the feed digestates capable of supporting C. jejuni growth and additional factors may be at play in the avian gastrointestinal tract potentially explaining Campylobacter’s affinity towards the broiler GIT. The microbiota in the broiler GIT was found to be influenced by the age of the birds, the location within the GIT, and antibiotic treatment. With major changes observed in the broiler microbiota as the birds aged and antibiotic treatment in early life significantly altering the microbiota throughout the remainder of the rearing period. It was therefore concluded that: • Enhanced biosecurity shows great potential for the reduction and possible elimination of Campylobacter from commercial broiler flocks, and the implementation of a biosecurity framework could both reduce colonisation of broilers while increasing productivity. • Natural OA, EO, and MCFA based water additives were promising anti-Campylobacter water additives in vitro, however, these results do not transfer well in vivo and highlight the need for further research into their development. • Broiler aging and antibiotic therapy both cause significant changes in the broiler microbiota providing a potential explanation for the delayed Campylobacter colonisation seen in broilers, while the microbiota shifts associated with antibiotic therapy could impact broiler performance.
  • Publication
    Molecular characterization of Mycobacterium bovis virulence factors
    (University College Dublin. School of Veterinary Medicine, 2022)
    Tuberculosis (TB) is a major disease of humans and animals. TB in mammals is caused by different species of mycobacteria that are clustered in the same genetically compact group named the Mycobacterium tuberculosis complex (MTBC). The members of the MTBC can be separated in two independent clades with distinct host preferences: the human-adapted strains, and the animal-adapted strains. Mycobacterium tuberculosis is responsible for the vast majority of human TB cases and shows host specificity for humans. On the other hand, Mycobacterium bovis can infect and sustain across a wide range of mammalian hosts, being primarily a pathogen of cattle but being also able to cause TB in humans trough zoonotic infections. M. tuberculosis and M. bovis have traditionally been the most studied species of the MTBC as they are the main human and animal TB pathogens, respectively. One key protein system of the MTBC is the PhoPR system, which is a two component signal transduction system that regulates many mycobacterial processes including lipid metabolism, secretion of virulence proteins and intracellular adaptation. Previous studies have shown that the phoPR locus shows variation across the members of the MTBC, with the identification of three single nucleotide polymorphisms (SNPs) in the phoPR locus of M. bovis compared to M. tuberculosis. Experiments suggested that these SNPs render the PhoPR system of M. bovis non-functional. However, later studies by other groups have provided evidence for the functionality of the M. bovis PhoPR system. The aim of this thesis was to elucidate the functional role of the PhoPR system of M. bovis. To achieve this, M. bovis mutants were constructed, transcriptomics of mutants and wild type used to define the PhoPR regulon, and in vitro experiments performed for functional characterization. The results of this thesis provide evidence that the M. bovis PhoPR system is indeed functional and that it shows differential control of genes as compared to the PhoPR system of M. tuberculosis, including many virulence genes. As such, this thesis opens new avenues for research into the molecular basis of host tropism of M. bovis, and the potential role of the PhoPR system in this process.
  • Publication
    The role of Calcareous Marine Algae in Reducing the Negative Health and Production Consequences of Disrupted Rumen Fermentation in Dairy Cows
    (University College Dublin. School of Veterinary Medicine, 2022)
    The objective of the thesis was to investigate the effects of calcareous marine algae (CMA) on rumen pH and fermentation, digestion, feed intake, milk production, and inflammation in dairy cows during a dietary challenge. Different types of dietary challenges were used to achieve our objective. The dietary challenges included: the transition period; a high starch total mixed ration (TMR), a grain (GR) induced sub-acute ruminal acidosis (SARA); and a ryegrass (RY) induced SARA. Calcareous marine algae was compared to a control (CON) diet, containing no dietary additive, in chapter 3, 5, and 6. In chapter 4, CMA was compared to a combination of CMA and marine magnesium oxide (MM), sodium bicarbonate (SB) and a CON treatment. Chapter 3 investigated the effects of CMA on feed intake, milk production, energy balance, serum mineral metabolites and inflammatory markers in 32 cows during the transition period compared to a CON treatment. The CMA treatment had higher prepartum dry matter intake (DMI), postpartum DMI, milk fat concentration, fat corrected milk yield, and reduced plasma serum amyloid A (SAA) compared to the CON treatment. Chapter 4 investigated the effects of CMA, with or without MM, and SB on rumen pH parameters, volatile fatty acid (VFA) production, apparent total tract digestion, and the kinetics of digestion using 4 cannulated cows in a 4 × 4 Latin square design. The CMA and CMA+MM increased mean, median and minimum rumen pH, and reduced time spent below rumen pH 5.6 and 5.4 compared to the CON treatment. There was less variation in rumen pH with the CMA treatment compared to the SB treatment. Acetate: propionate ratio was reduced, and the molar proportion of propionate increased with CMA+MM compared to CON, CMA, and SB. The CMA+MM treatment increased neutral detergent fibre (NDF) digestibility compared to CON. There were no differences in rumen fluid and particulate outflow rates, rumen retention time, or rumen in-sacco degradability between treatments. Chapter 5 determined the effects of CMA on rumen pH, rumen fermentation, and plasma inflammatory markers during a GR and RY induced SARA challenge using eight ruminally cannulated cows in a 2 × 2 split-plot crossover design. The experiment consisted of three phases: acclimatisation; challenge; and recovery. Both GR and RY diets successfully induced SARA temporarily. The CMA treatment reduced the minutes below rumen pH 5.4, 5.6, and 5.8 during the ACC phase, and minutes below rumen pH 5.6 and 5.8 during the REC phase. The RY diet had a lower concentration of rumen lipopolysaccharide compared to the GR diet during the challenge. There was a greater reduction in SAA with the CMA treatment compared to the CON during the recovery phase. Chapter 6 investigated the effects of CMA on feeding behaviour, rumen fermentation products, milk fatty acid profiles, and total tract digestibility of dry matter (DM) and organic matter (OM) in 32 early lactation dairy cows compared to a CON treatment. The CMA treatment reduced the proportion of trans-9 18:1 fatty acid and the omega-6 to omega-3 fatty acid ratio in milk compared to the CON treatment. Daily TMR intake and feeding rate were increased in cows fed the CMA treatment compared to cows fed the CON treatment. These findings demonstrate the benefits of CMA on reducing rumen pH depressions and increasing digestion of DM and OM. Calcareous marine algae can be an effective tool for preventing rumen fermentation disruptions during a dietary change and for increasing DMI and energy balance during the transition period.