Veterinary Biosciences - Theses
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ItemEvaluation of Ki-67, goblet cell and MUC2 mucin RNA expression in dogs with lymphoplasmacytic and granulomatous colitis( 2023-08)Background: Intestinal mucus barrier disruption occurs with chronic inflammatory enteropathies. The lack of studies evaluating changes in mucus health in dogs with chronic colitis arises from inherent challenges with assessment of the intestinal mucus layer. It is therefore unknown if reduced expression of goblet cells and/or mucin 2 (MUC2), which are key players in mucus production and secretion, correlate with inflammation severity in dogs with granulomatous colitis (GC) or lymphocytic-plasmacytic colitis (LPC). It is also unknown if Ki-67 expression, which has been evaluated in dogs with small intestinal inflammation, similarly correlates to severity of colonic inflammation in dogs with GC and LPC. Objectives: Study objectives included assessing if Ki-67 expression is upregulated in dogs with GC compared to LPC and dogs without colitis; comparing GBC and MUC2 expression among GC, LPC and non-inflamed colon; and exploring the use of RNAscope in-situ hybridization (ISH) to evaluate MUC2 expression in canine colon. Methods: Formalin-fixed endoscopic colonic biopsies were obtained from 48 dogs between January 2015 and March 2022. A blinded pathologist reviewed all biopsies. Dogs were classified into the GC (n=19), LPC (n=19) or no colonic signs (NC) (n=10) group based on the final histopathological diagnosis. Ki-67 immunohistochemistry, Alcian-Blue/PAS staining to highlight GBCs, and RNAscope ISH using customized canine MUC2-targeted probes were performed. At least five microscopic fields per slide were selected to measure Ki-67 labelling index (KI67%), GBC staining percentage (GBC%) and MUC2 expression (MUC2%) using computer image analysis. Pearson correlation coefficients were used to determine associations between World Small Animal Veterinary Association histologic (WH) score and measured variables. Linear regression models were used to compare the relationships between WH scores with KI67%, GBC%, and MUC2%; and between GBC% and MUC2% across groups. Results: Median WH scores were highest in dogs with GC. Median KI67% was highest in the NC group (6.69%; range, 1.70-23.60%). Median GBC% did not correlate with colonic inflammation in all groups. Median MUC2% normalised to WH score (MUC2%*) was highest in the NC group (10.02%; range, 3.05-39.09%), which was two and three-fold higher compared to the GC and LPC groups respectively. Mucin 2 expression had a strongly positive correlation with GBC% in the NC group (5.71% increase in MUC2%; 95%-CI, 0.503–0.987, p =.12), while no significant trends were observed in the GC and LPC groups. With increased severity of colonic inflammation, MUC2 expression sharply declined in the LPC group (-8.90%; 95%-CI, -17.98-0.19, p =.05) but remained static in the GC group. Conclusion and relevance: Dogs with GC had the most severe histologic colonic inflammation. Dogs without colitis had the highest Ki-67 expression. Goblet cell expression did not correlate with histologic severity of colonic inflammation overall. Dogs with GC and LPC likely have differences in pathways regulating MUC2 biosynthesis and secretion. Changes in MUC2 expression appear influenced by pathways regulating GBC activity rather than quantity in GC and LPC. Development of therapeutic strategies aimed at modifying GBC function and MUC2 expression may help improve mucus barrier integrity and mucosal healing in dogs with chronic colitis.
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ItemThe health of the captive Leadbeater's possum, (Gymnobelideus leadbeateri): implications for the conservation of the wild population.( 2023-05)The Leadbeater’s possum, Gymnobelideus leadbeateri, is a critically endangered marsupial with a range-restricted habitat and high risk of extinction. Two genetically distinct populations of the possums are described, the highland population found in the Victorian Central Highlands, Australia, and the lowland population, found in a single remnant of swamp forest. The highland Leadbeater’s possums entered captivity within Zoos Victoria in 1970. In Australia, highland animals were kept in captivity from 1970-2012 with smaller numbers kept internationally. Institutional memory within Zoos Victoria suggested that the highland population bred without difficulty and often in excess of enclosure space available and that the species had very few health issues with simple husbandry requirements. This captive population inbred with limited founders and senesced in the late 1980s and early 1990s. The last highland animal of this population died in 2012. In 2012, the wild remnant lowlands population was noted to have rapidly decreased from ~100 animals to approximately 60 animals over four years (2012-2016). From 2012-2021, 21 animals were brought into captivity to form a captive breeding program and insurance population. Despite ongoing pairing of these animals, and breeding continuing in the slowly disappearing wild population, no lowland animal has produced young in captivity. This study aimed to investigate Leadbeater’s possum health and disease, focusing on captive populations, with the aim of informing species recovery efforts and conservation measures. Fecundity and longevity in captive Leadbeater’s possums were studied using detailed analysis of historical records. Fecundity can be used as a broad indicator of health or adaptation to captivity. Institutional memory of keeping this species in captivity suggested that the breeding population of highland possums was ‘healthier’ than lowland animals, which may have corresponded with increased longevity. Analysis via Kaplan Meier survival graphs indicated that there was no significant difference in longevity regardless of sex, institution, captive conditions, or population groups, with some longer-lived outliers in the highland population. If longevity is a metric for health or adaption to captivity, the study findings suggest no appreciable differences. Fecund animals lived significantly longer – perhaps suggesting a correlation between adaptation to captivity and being able to breed in these conditions. Fecundity of the highland’s population was examined and revealed that the population had limited wild-born founder animals and fewer still that bred. Animals that did breed successfully were either wild born or of the first filial generation, and a small subset of these animals were highly fecund with six males and six females each producing greater than ten offspring. This resulted in a closely related population that petered out due to heavy inbreeding and lack of interest in a species thought to be abundant. A review of all mortality data was undertaken with a particular focus on diseases of significance to the population and to reproduction. Females had a range of pathology. Pyometra or cystic ovaries or uteri were commonly observed – all potentially associated with nulliparous. Many lowland possum males had histopathology consistent with infertility with no obvious aetiology, as a diagnosis of exclusion, mineral deficiency is likely. Chronic nephropathy was the most frequently clinically significant post-mortem finding, with unknown aetiology and an increase in diagnosis with age, suggesting a species predilection. Cardiovascular disease was the second most common pathology, and appeared to be associated with advanced age, and with diagnoses including atherosclerosis and arteriosclerosis. It is likely these findings are associated with obesity and increased caloric intake. It was important to consider these diseases in a holistic framework however as organ systems do not differentiate their borders. Leadbeater’s possums appeared very sensitive to disseminated infection, with the reproductive system being a common seed point. Possum health and diet are inextricably linked. The gut microbiome of three captive lowland female possums was characterised over a temporal diet change using next generation sequencing to analyse diversity. The possums had a narrow ‘core’ biome of bacteria that remained consistent across time and diet changes. When the diet altered over the opportunistic study period, the microbiome shifted in diversity and abundance with a similar trend across all three animals. There appeared to be some consistencies with the way each possum’s biome changed when diet changed and there were fluctuations within the most abundant species that appeared to be related to the fluctuation of macro-nutrients, particularly energy density. Opportunistic comparison with the gut microbiome of wild caught animals as they adjusted to a captive diet provided context for understanding the microbiome of this species, but further work is needed to elucidate the links between diet, microbiome, health, and disease. Examination of ectoparasite assemblages of wild highland and lowland populations revealed that flea assemblage varied by habitat type and /or elevation and thus population of possums. Two host-specific flea species, Stephanocircus domrowi and Wurunjerria warnekei were detected only on possums in highland habitats while generalist marsupial fleas Acanthopsylla r. rothschildii and Choristopsylla tristis were found in lowland habitat. Wurunjerria warnekei was suspected to be extinct prior to this study. A novel haemoparasite nematode was described, Breinlia sp. from an aged lowland Leadbeater’s possum found deceased in a nest box. Histology indicated that this haemoparasite was likely largely benign, with mild skin pathology found from migration of the nematode to the dermis. Translocation has already occurred within the two populations of Leadbeater’s possum, with little known about the microbiome, health and resilience to stressors, viruses, and parasites and the impact of change on the host’s health; this research has filled knowledge gaps and informed conservation actions.
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ItemD-Dimer in dogs, cats and horses: Investigations into immunoreactivity and structure( 2023)Background: D-dimer is a degradation product of cross-linked fibrin generated during thrombolysis. D-dimer is measured in human medicine for the early detection and exclusion of thrombotic syndromes. Commercially available D-dimer assays use monoclonal antibodies against human D-dimer, and there is limited sensitivity and specificity data for these antibodies in companion animals, thus the accuracy of human assays in veterinary species remains uncertain. Little is known about the sequence and structure of D-dimer in companion animals. Objectives: To evaluate the immunoreactivity of D-dimer in dogs, horses and cats with commercially available antibodies, and investigate potential differences in sequence and structure between species. Methods: A cross-linked fibrin lysate was prepared from canine, feline and equine plasma samples, and immunoblotting performed with a variety of commercially available D-dimer antibodies. Amino acid sequences of fibrinogen fragments involved in D-dimer were compared between species (cat, horse, dog and human), using available sequences for fibrinogen chains, and these were used for multiple sequence alignment, estimation of physiochemical properties, analysis of conserved structural domains, and prediction of three-dimensional structure by homology modelling. Results: The antibodies evaluated demonstrated variable reactivity with D-dimer in each species. The monoclonal antibody DD44 bound canine D-dimer with good specificity and sensitivity, but this antibody did not react with feline or equine D-dimer. The polyclonal antibody D2D bound putative D-dimer in dogs, cats and horses with good specificity, and increased sensitivity compared to human D-dimer. Analysis of sequence and structure revealed high inter-species homology, and three-dimensional models were prepared using a human template. Conclusions: Commercially available antibodies to human D-dimer have variable immunoreactivity with D-dimer in companion animals, suggesting that the use of human assays is inappropriate until analytical and/or clinical validation of the antibody used in that assay has been performed for each species. There are no overt structural variations to explain the variation in immunoreactivity between species, and this could reflect minor variations in structure at the site of binding for each antibody, which is largely unknown.
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ItemCharacterising the prevalence of Coxiella burnetii in Victorian wildlife( 2018)Coxiella burnetii (C. burnetii) is an intracellular gram-negative bacterium, which is the causative agent of the widespread zoonotic disease Q fever. Q fever infection in humans can cause flu-like symptoms and sometimes develop into chronic Q fever, possibly leading to endocarditis. Animals infected by C. burnetii often show no clinical signs, although some may develop reproductive problems such as stillbirth and abortion in cattle, sheep, and goats. Worldwide, investigations into the prevalence of C. burnetii in wildlife have been conducted, and results indicate that free-ranging animals could be potential reservoirs of this bacterium, although the role of wildlife in C. burnetii transmission is unclear. Australian marsupials, such as kangaroos, wallabies and bandicoots have also been found to be carriers of C. burnetii. Nevertheless, there has not been a study investigating the prevalence of C. burnetii in Victorian wildlife. Immunodetection and molecular detection are commonly used to diagnose infection with C. burnetii. However, with the discovery and study of Coxiella-like bacteria (CLB), many PCR genes targeted in routine molecular detection assays were found to also be present in CLB. Thus, it is not possible to distinguish between C. burnetii and CLB based on assays targeting these genes. Immunogenicity tests are commonly used for detection of antibodies against C. burnetii in wildlife species. ELISA is a preferred test due to its performance, objective interpretation, and capacity in high-throughput screening. There is, however, no validated ELISA test for detection of C. burnetii antibodies across Australian wildlife species. This project therefore aimed to: a) differentiate C. burnetii from CLB; b) study the prevalence of C. burnetii in Victorian wildlife using PCR/qPCR methods; and c) investigate the possibility of developing an ELISA to detect serum antibodies in a wide range of wildlife species. An overall prevalence of 3.4% (95% CI 1.7 - 5.2%) of C. burnetii was detected in 406 Victorian wildlife samples by qPCR, indicating that Victorian wildlife may act as potential reservoirs of C. burnetii. The highest prevalence of C. burnetii was found in eastern grey kangaroos (Macropus giganteus) at 7.9% (95% CI 3.2 - 12.6%). Other wildlife samples were found to be positive for Coxiella, but the species remained undetermined. These samples may represent samples that are positive for CLB. Three out of the four C. burnetii proteins selected (CBU0109, CBU0612, CBU0891, and CBU1910) as antigen candidates for ELISA development were expressed and purified. Immunogenicity tests were applied to three antigen candidates using C. burnetii positive and negative goat serum samples by Western blotting and indirect ELISA. The results revealed that none of the antigen candidates were suitable for ELISA development as all reacted with C. burnetii negative goat sera. Findings from this project address the importance of appropriate molecular methods used for the detection of C. burnetii. Future investigations into C. burnetii in wildlife should aim to perform the tests on a larger population of animals and wider range of species. The cross-reactivity between antigen candidates and C. burnetii negative goat sera indicates the necessity of validation for immunological methods when they are applied to a new species.
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ItemDiscovery of new chemicals with anthelmintic activity against the barber’s pole worm and other parasitic nematodes( 2018)Parasitic nematodes cause a substantial disease burden on humans and animals worldwide. A review of the literature (Chapter 1) showed that, on one hand, neglected tropical diseases caused by parasitic nematodes have a devastating, long-term impact on human health; on the other hand, gastrointestinal nematodes are a major constraint to the livestock industries, causing subclinical infections and diseases in animals and leading to a substantial reduction in meat, milk and fibre production. Currently, anthelmintic treatment remains the mainstay of controlling parasitic nematode infections. However, the massive and widespread resistance to the limited number of commercial anthelmintics, particularly in the veterinary and agricultural contexts, demonstrates an urgency to discover new and effective anthelmintics to sustain the economic and health benefits from the application of anthelmintics. Thus, the key focus of this thesis was to discover new chemical entities and/or known drugs with anthelmintic activities against Haemonchus contortus and/or other socioeconomically important parasitic nematodes for subsequent development. Whole worm-based phenotypic screening assays were employed, compound collections were obtained via product-development-partnerships and/or collaborators, and active compounds were assessed for their potential as anthelmintic candidates. In this thesis, one new chemical entity (designated SN00797439), two human kinase inhibitors (SNS-032 and AG-1295), 14 AG-1295 (tetrahydroquinoxaline) analogues, one insecticide (tolfenpyrad) and two tolfenpyrad (pyrazole-5-carboxamide) derivatives (a-15 and a-17) with anthelmintic activity in vitro were discovered following the screening of a total of 15,333 chemicals from five distinct compound collections against H. contortus. In Chapter 2, a new chemical entity, SN00797439, was identified with activity against a range of parasitic nematodes, including H. contortus, Ancylostoma ceylanicum, Brugia malayi, Dirofilaria immitis and/or Trichuris muris in vitro, offering a novel, lead-like scaffold for the development of a relatively broad-spectrum anthelmintic. In Chapter 3, two human kinase inhibitors under pharmaceutical development, SNS-032 (piperidinecarboxamide) and AG-1295 (quinoxaline), were identified to have inhibitory activity on the motility and development of parasitic larvae of H. contortus in vitro. AG-1295 had limited cytotoxicity against a normal mammalian epithelial cell line (designated MCF10A). In Chapters 4 and 5, three pyrazole-5-carboxamides (tolfenpyrad, a-15 and a-17) were shown to possess significant inhibitory effects on H. contortus without detectable toxicity on a human neonatal foreskin fibroblast (NFF) cell line in vitro. All three of these chemicals were shown to inhibit the oxygen consumption in H. contortus larvae, a finding that was consistent with the known, specific inhibition of complex I of the respiratory electron transport chain by selected pyrazole-5-carboxamides in arthropods. The evaluation of these hit compounds using various technologies employed in parasitology, drug discovery, chemistry, histology, toxicology, molecular biology and bioinformatics should offer data to support their potential as leads for future drug development and to facilitate the exploration of their mode(s) of action in this and related nematodes. Encouraged by the findings in Chapter 3 and the detection of a non-wildtype phenotype in treated worms in vitro, Chapter 6 investigated the activities of 14 additional tetrahydroquinoxaline (AG-1295) analogues on H. contortus. Qualitative and quantitative assessments of larval motility, development and morphological alterations showed that these 14 chemicals all affected the viability of parasitic larvae and, interestingly, induced an eviscerated larval phenotype and led to cuticular damage and/or stunted growth in in vitro H. contortus. Taken together, Chapters 2 to 6 identified a series of 20 hit compounds, some of which have selectivity against H. contortus compared with selected human cell lines tested. In Chapter 7, the research achievements are summarised, and the next steps to be pursued in future research are outlined, including (i) the chemical optimisation of representative chemicals via structure-activity relationship (SAR) evaluations; (ii) assessment of the breadth of spectrum of anthelmintic activity on other parasitic nematodes, such as other strongyloids, ascaridoids, enoplids and filarioids; (iii) detailed investigations of the absorption, distribution, metabolism, excretion and toxicity (ADMET) of optimised chemicals with broad nematocidal or nematostatic activity; (iv) establishment of the modes of action of lead candidates. The findings from the thesis are then put into a broad context and discussed. In conclusion, the present thesis contributes to the fields of parasitology and anthelmintic discovery by identifying compounds with in vitro anthelmintic activity that represent sound starting points for ‘lead’ discovery.
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ItemThe epidemiology of pork-borne parasitic zoonoses in rural communities in the central highlands of Vietnam( 2018)Background Food-borne parasitic zoonoses impact negatively on humans in terms of health and loss of productivity as well as economically, through loss of market access and trade. Taenia and Trichinella are two of the most important meat-borne zoonoses globally. In the Central Highlands of Vietnam, living standards are poor; open defaecation via use of outdoor latrines is commonly practiced and livestock access to these latrine areas is, for the most part, unrestricted. Moreover, the consumption of undercooked or raw pork dishes is common traditional practice. These factors combined are highly conducive for the transmission of several pork-borne parasitic zoonoses, including taeniasis, Taenia solium cysticercosis and trichinellosis. In this context, developing and validating diagnostic assays to study the epidemiology of these pork-borne parasites within these communities allows risk factors for exposure and infection to be ascertained and this, in turn, allows community-based control programs to be better targeted. Methodology/Principle findings This project was conducted as a cross-sectional study in Buon Don, Krong Nang and M’Drak district in Dak Lak province in the Central Highlands of Vietnam. A combination of parasitological, serological and molecular diagnostic methods were utilised to determine the levels of infection of Taenia spp. in humans and Trichinella spp. in pigs, and seroexposure to T. solium in humans and pigs. The data were analysed in relation to host, management and environmental risk factors using frequentist and Bayesian multivariable analyses. In Chapter 2, a systematic review on previous research on taeniasis, T. solium cysticercosis and trichinellosis was performed and showed that little to no data are available on the prevalence of these food-borne zoonoses in the central and southern areas of the country. Moreover, utilisation of tests with either low sensitivity or poor specificity for the diagnosis of taeniasis in humans and T. solium cysticercosis in humans and pigs produced either an over- or underestimation of their TP. To address this, a Bayesian model was used to estimate the TP of taeniasis and Taenia solium cysticercosis and demonstrated a true prevalences of up to 25% and 24%, respectively for specific rural ‘hotspots’. In Chapter 3, a multiplex Taq-Man probe-based real-time PCR for the species-specific detection of three Taenia species in human stool was developed and its diagnostic parameters compared with the Kato-Katz thick smear and coproantigen ELISA assay using field samples collected as part of a cross-sectional survey in Dak Lak province. The overall AP of human taeniasis by the multiplex qPCR was 6.7% (95% CI 4.4 to 10). The sympatric existence of Taenia solium, Taenia asiatica and Taenia saginata in Dak Lak province was confirmed for the first time, as was the extension of the known distribution of T. asiatica to southern Vietnam. Risk factors associated with Taenia spp. infection included the routine consumption of undercooked beef and pork, routine consumption of pork tongue, and personal observation of Taenia proglottids in stool. Chapter 4 describes a cross-sectional study on the seroprevalence of human T. solium cysticercosis in Dak Lak determined by two diagnostic assays, the apDia-ELISA, a commercial antigen detection assay and the LLGP-EITB antibody detection assay. The seroprevalence of exposure to T. solium in humans was 5% (95% CI 3 to 8), while the apDia-ELISA, detected circulating T. solium antigens in 7.3% (95% CI 4.9 to 10.8) of the sampled population. Consuming raw vegetables, drinking water sourced from lakes, streams or ponds, and outdoor defaecation were associated with increased T. solium exposure risk in humans. In Chapter 5, the seroexposure of pigs to T. solium cysticercosis in Dak Lak was determined using rT24H and native LLGP antigens in series, in an EITB format. The seroprevalence of exposure to T. solium was low at 0.94 (95% CI 0.51 to 1.68). Coprophagy of human faeces and scavenging for food were factors significantly associated with T. solium exposure in pigs. In Chapter 6, the contribution of all modifiable risk factors for taeniasis, T. solium exposure in humans and pigs is explored and this was estimated to range from 24% to 77%. Spatial analyses demonstrated that human- or pig-T. solium exposure-positive households were more likely to be surrounded by other exposure-positive households in some study locations. This spatial aggregation of human exposure-positive households was hypothesised to be due to a combination of demographic, anthropological and micro environmental factors, whilst scavenging for food and coprophagy of human faeces are likely to drive the aggregation of pig exposure-positive households. Finally, no Trichinella larvae were detected in the confined and free-roaming pig populations using the artificial digestion technique on tongue, diaphragm and masseter muscle. The estimated TP of Trichinella was low, ranging from 0.09 to 0.80% in domestic pigs. Further diagnostic screening using serology was beyond the scope of this current project but advocated for future research. Conclusions This thesis has contributed significantly to a better understanding of the epidemiological characteristics of Taenia spp. infection, and seroexposure to T. solium and Trichinella spp. infection among humans and pigs in the Central Highlands of Vietnam. This information will assist local government and residents to develop appropriate methods and strategies to reduce or mitigate the burden of these diseases in Dak Lak.
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ItemThe effect of tonB deletion on the expression of the genes encoding Shiga toxin, TonB-dependent receptors and fimbriae in the 16001 oedema disease strain of E. coli( 2018)Oedema disease is caused by Shiga toxin producing Escherichia coli (STEC) and generally affects piglets at one to two weeks after weaning. The stress related to dietary change and loss of lactogenic immunity after weaning are believed to contribute to the onset of the disease. Affected piglets typically have oedematous lesions in multiple organs, including the stomach, colon and eyelids, and also neurological signs, such as ataxia and paralysis. Occasionally, the disease can result in sudden death without any apparent clinical signs. The Shiga toxin and fimbriae are the two key virulence factors and they play an essential role in the pathogenesis of the disease. Multiple attempts have been made to develop active, passive and maternal approaches to immunization. These studies have mainly focussed on attenuating the organism by manipulating these virulence factors at the molecular level. Although the disease is endemic and has a considerable economic impact, there is no commercial vaccine available in Australia. Control measures mainly focus on antibiotic treatment but this has been challenged by the emergence of drug resistance in the strain. Iron is one of the most important micronutrients for the growth of bacteria and its availability to pathogens is restricted both inside and outside the host. Pathogenic bacteria respond by elaboration of siderophores in order to transport iron across the outer membrane, and the TonB protein supplies the necessary energy for this transport. The aims of this research project were to develop tonB mutants of an Australian STEC strain (16001) isolated from pigs with oedema disease by deleting the tonB gene using the lambda Red recombination system and to investigate whether the transcription of the virulence factors Shiga toxin 2e (stx2e) and the F18 fimbriae and TonB-dependent transporter genes was influenced by the tonB deletion. The lambda Red recombination system was used to replace the target gene with an antibiotic resistance cassette, and successful mutagenesis was confirmed by molecular and phenotypic characterisation of the mutant. Sequencing studies showed that the tonB gene was replaced with a kanamycin resistance gene. The mutant had a slower growth rate and produced greater concentrations of siderophores on chrome azurol S (CAS) agar. In general, phenotypic characterization of the tonB mutant indicated that it had reduced intracellular iron levels as a result of the tonB deletion. The aim of deleting tonB was to reduce intracellular iron levels, which was anticipated to attenuate the organism and also upregulate the iron regulon to increase the production of protective antigens. During iron shortage, siderophore synthesis and expression of siderophore transporters is increased, thus eliciting an enhanced immune response against these antigens. Upregulation of the genes for some outer membrane receptors, as well as those for the key virulence factors Stx2e and F18 fimbriae, was demonstrated in this study. In conclusion, the deletion mutant generated in this study may be able to be used as the basis for development of a vaccine candidate for control of this important disease of pigs.
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ItemViruses of the other mammals: genomics and epidemiology of marsupial herpesviruses( 2018)Improving wildlife population health requires an understanding of the infectious agents within those populations. Historical accounts of herpesviruses in marsupials indicate that they can have a significant impact on animal health. This evidence is strongest for the macropodid alphaherpesviruses, but with improvements in molecular diagnostics the discovery of novel viruses has outpaced our understanding of their impact and significance. This thesis aimed to expand our knowledge of marsupial herpesviruses by examining relationships between marsupial herpesviruses and other herpesviruses, and by describing the clinical significance of infection. This thesis also aimed to improve diagnostic tools for detecting herpesvirus infection in marsupials. The core genomes of three marsupial herpesviruses were determined; macropodid alphaherpesvirus 1 (MaHV1, infecting wallabies), phascolarctid gammaherpesvirus 1 (PhaHV1, infecting koalas) and vombatid gammaherpesvirus 1 (VoHV1, infecting wombats). MaHV1 had a similar genome arrangement to other simplexviruses, but contained gene clusters that may be unique to the macropodid simplexviruses. PhaHV1 and VoHV1 had a shared gene arrangement and were likely to have speciated from a common ancestor. Over 30 new ORFs were identified within the genomes. Functional enzymatic characterisation was performed on two viral NTPDase homologs encoded within the two gammaherpesviruses. NTPDase activity was confirmed for the PhaHV1 homolog but not the VoHV1 homolog. Koalas are host to two divergent gammaherpesvirus species, PhaHV1 and -2. To understand the clinical significance of each individual virus a large molecular epidemiological study of 810 koalas from 7 separate geographic regions was conducted. Samples were tested using a rapid and differential PCR-HRM assay. Available signalment and clinical observation data was analysed in comparison to infection status through univariable and multivariable logistic regression analysis. Additional factors considered were location, year, body condition, fecundity in females, as well as the presence of other infectious agents (Chlamydia pecorum and koala retrovirus). PhaHV1 and -2 were present in 17% and 22% of koalas tested (state-wide), although some variation from the state average was observed in particular populations. Neither virus was associated with a particular sex. PhaHV1 detection was uniquely associated with the presence of koala retrovirus as well as increasing age. PhaHV2 detection did not change with age, which may indicate differences in how these two viruses are acquired over the life of the animal. Both viruses were positively associated with genital tract abnormalities, lowered fertility in females, emaciated body condition, urinary tract infection (wet bottom) and detection of C. pecorum, although the strength of these associations varied by sex and herpesvirus species. To further the development of herpesviruses serological tools, this thesis examined the ability of four commercially-available immunoglobulin-binding reagents to bind serum antibodies from 17 species within the Marsupialia and Monotremata. Serum samples were assessed for binding using immunoblots and ELISAs to three microbially-derived proteins; staphylococcal protein A, streptococcal protein G and peptostreptococcal protein L, and to an anti-kangaroo antibody. The inter- and intra-familial binding patterns of the reagents to serum immunoglobulins varied and evolutionary distance between animal species was not an accurate predictor of the ability of reagents to bind immunoglobulins.
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ItemInvestigations into bacterial causes of disease in swine with emphasis on airborne pathogens( 2018)Pig farming is a major agricultural production system globally. Over the years, many aspects of pig farming have been investigated. However, controlling infectious diseases remains an area of ongoing research, with new technologies allowing the development of improved management strategies and vaccines. The family Pasteurellaceae is mainly composed of commensal species, but includes notable pathogens of livestock. The species of major concern in pigs include Actinobacillus pleuropneumoniae and Glaesserella parasuis. Although publication of the genomes of both species has advanced understanding of their virulence existing vaccines for these pathogens have limited efficacy. Therefore, control of A. pleuropneumoniae and G. parasuis currently relies heavily on farm management. The studies in this thesis sought to develop novel non-invasive methods for detecting A. pleuropneumoniae on farms. The Coriolis µ air sampler, with a qPCR designed for the detection of the apxIV gene, which is specific for A. pleuropneumoniae, were used for this purpose. Application of the assay on two commercial farms revealed that one farm had circulating levels of A. pleuropneumoniae in houses containing pigs aged between 8 and 21. This method could be used for the detection of A. pleuropneumoniae in clinically healthy populations. A novel member of the Pasteurellaceae family isolated from pigs with severe respiratory infections was characterised at the pathological, biochemical, genomic and phylogenetic levels. This bacterium was identified as a member of the genus Glaesserella, and found to be most closely related to Glaesserella parasuis. Analysis of the predicted proteins encoded by its genome showed that it had a mosaic structure, with 60% of the coding sequences sharing closest identity with G. parasuis, while 20% had closest identity with other members of Pasteurellaceae and 20% were related to proteins encoded by other bacterial genomes. A gene homologous to A. pleuropneumoniae apxIII was identified in the genome of this new species and is proposed to have been acquired by horizontal gene transfer. The isolation and identification of this novel Glaesserella species highlights the need for large scale epidemiological studies to understand the impact of this pathogen on pig health. Genome analysis of this organism identified other putative virulence factors, leading to studying its pathogenicity. As many pathogenic species in the Pasteurellaceae family have been explored using mouse models, one was sought for this novel pathogen. The organism was compared to A. pleuropneumoniae in BALB/c mice inoculated either intraperitoneally or intranasally. While no bacteria were recovered from the infected mice, intranasal inoculation resulted in formation of significant lung lesions, and intranasal and intraperitoneal inoculation resulted in significantly increased levels of cytokines in the lungs. These experiments demonstrated that the pathological response to infection with the novel Glaesserella sp. significantly differed from that seen with A. pleuropneumoniae and suggest that the mouse model is a promising method for studying this organism. Finally, assays were developed to detect changes in the dependence of A. pleuropneumoniae on environmental iron concentrations. Growth in presence or absence of streptonigrin and 2,2′dipyridyl was measured by monitoring the optical density of the cultures over time. There was a clear and consistent difference in growth rate between groups, allowing the differentiation of a clone’s ability to grow under iron restricted conditions. These assays were designed to help assist with the identification of a live attenuated vaccine candidate with an impaired iron uptake capacity. The studies in this thesis further understanding of respiratory disease caused by members of the family Pasteurellaceae and highlight areas needing further research.
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ItemUse of multiplex-tandem polymerase chain reaction in an operational environment to assess cyanotoxins and taste and odour metabolites of cyanobacterial blooms in Victorian waters( 2018)Cyanobacterial blooms represent a major water quality and public health issue due to their potential to produce taste and odour (T/O) compounds, and a variety of toxic metabolites. Monitoring and management of cyanobacterial blooms in various water resources is in turn dependent on the availability of accurate and sensitive diagnostic tools, and contemporary or prior knowledge of the regional distribution of toxin and T/O types. For example, in Victoria, Australia, there is limited knowledge of the distribution/ecology of geosmin producers, such that prioritising taxa for routine monitoring is difficult. Additionally, knowledge about the prevalence of many yet to be identified or emerging toxic cyanobacteria (eg., anatoxin producers) in Australia, remains poorly understood. Due to the many limitations of commonly used detection methods (i.e., microscopy and direct detection techniques), to identify toxic and T/O producing cyanobacteria, there is a need to develop sensitive and accurate diagnostic tools. PCR-based tools have shown potential to accurately identify toxic or T/O producing cyanobacteria; however, they have important limitations for routine monitoring. Although multiplex-tandem PCR (MT-PCR) tool has shown significant potential to accurately detect four major cyanotoxins (i.e., MC, NOD, STX and CYN) in Australia, it requires additional field testing and further, this tool is not presently suitable to detect anatoxin and geosmin-producing cyanobacteria. The work presented in this study used PCR-based genetic screening tools (i.e., conventional PCR, nested-PCR or MT-PCR) for accurate diagnosis of cyanotoxins and geosmin-producing cyanobacteria on environmental cyanobacterial bloom samples collected from various parts of Victoria, Australia, over a period of eight years (i.e., from 2010 to 2018). The study also employed metagenomic approaches (eg., Illumina MiSeq and PacBio) using biomarker genes [eg., 16S ribosomal RNA (16S rRNA) and phycocyanin intergenic spacer sequence (PC-IGS or cpcBA-IGS)] to elucidate the community structure of a recent (i.e., 2016) cyanobacterial bloom in the Murray River, Victoria, Australia. Based on conventional PCR-based genetic screening (using three different primer pairs) of more than 250 cyanobacteria bloom samples collected over a period of six years (i.e., 2010-2016), we detected Dolichospermum ucrainicum as the major geosmin producer in 87% of sequenced samples. Using these data, we developed a novel, small amplicon PCR primer pair capable to broadly identify all geosmin-producing cyanobacteria identified in the current study using a single standardised protocol. Additionally, genetic screening using nested-PCR on samples (n=226) collected from 2010-2017 revealed the presence and distribution of several anatoxin-producing cyanobacteria, including Cuspidothrix issatschenkoi, Aphanizomenon sp., Dolichospermum sp., at an overall sample prevalence of 30.1%. An overwhelming majority (86.8%) of anatoxin positive nested-PCR detections were from samples collected from 2016 to 2017, as compared to only 6% of samples collected prior to 2016. Using this data obtained, novel, short amplicon, PCR primers were designed for better PCR-based detection of geosmin primers. This study is the first confirming the presence of anatoxin producers in Australia. Further, field evaluation of the efficiency of MT-PCR to assess toxic cyanobacterial blooms and analysis of total community composition on samples (n=194) collected from the Murray River bloom (March 2016 – May 2016) have shown to greatly supplement microscopic examination, and highlights the potential utility of combining targeted qPCR with metagenomic amplicon sequencing methods. Based on these findings, the MT-PCR assay was expanded to detect anatoxin and major geosmin-producing cyanobacteria. The expanded MT-PCR demonstrated superior performance in comparison to conventional or nested PCRs for all but one (anatoxin) gene target in all samples (i.e., n=91 from March 2016 – February 2018) tested. Here, we report a diagnostic specificity of 100% and diagnostic sensitivity of ≥ 81% for all gene targets, and the MT-PCR platform may provide a much-needed tool for routine monitoring of toxic and geosmin-producing cyanobacterial blooms of global relevance.