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    Genetic diversity of microbes and its impacts on host switching : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2025-08-25) Dos Anjos Almeida, Valter
    Land use around forests, leading to habitat overlap, increases the risk of anthroponotic and zoonotic pathogen/microorganism transmission between humans, livestock, and wildlife. This scenario is exemplified by Buhoma, a village where most residents are primarily subsistence farmers who raise livestock and cultivate crops near the Bwindi Impenetrable National Park (BINP) in Southwestern Uganda, creating an ideal interface for understanding these dynamics. Given the significance of this geographic location and the underrepresentation of African populations in global microbiome research, this project aims to characterise the gut microbiome diversity and potential novel bacterial species, as well as microorganism sharing within a multi-host system in a rural area with documented interactions between humans, livestock, and wildlife. For microbial detection, DNA extracted from 553 faecal samples collected from humans, gorillas, and livestock was processed and sequenced to analyse microbial species communities in different hosts using shotgun high-throughput sequencing and bioinformatics tools. The analysis of 2,411 bacterial metagenome-assembled genomes (MAGs) confirmed the presence of numerous putative novel bacterial species in the gut microbiomes of the Ugandan hosts studied in this project. While many species were host-specific, others were detected across multiple host gut microbiomes from Buhoma and BINP, and in different host samples from other geographic locations (by comparing the MAGs generated in this thesis with other publicly available genomes). Among the bacterial MAGs assembled in this project, genera such as Prevotella and Treponema—considered markers of the gut microbiome in individuals with traditional agricultural lifestyles—and Campylobacter—which comprises species that are leading causes of bacterial gastroenteritis globally—were further investigated. These genera were found to contain numerous putative novel species, contributing to our knowledge of the human and animal gut microbiomes and enhancing our understanding of the species associated with them. The results of this study reveal a high diversity of previously unknown microbes recovered from human, gorilla, and livestock gut microbiomes collected simultaneously at the same wild rural interface. The Treponema genus includes species that inhabit a wide range of hosts and types of microbiotas. In the Ugandan host samples, 75 Treponema MAGs were reconstructed, enabling the identification of sixteen intestinal species, including thirteen putative novel species. Three of the detected species were found in human samples from this study, as well as in publicly available Treponema genomes recovered from animals such as pigs, cattle, wild boars, roe deer, and goats. This detection underscores the potential for interspecies transmission and the establishment of these bacteria in different hosts. Overall, these findings highlight the complex interplay between humans, animals, and their gut microbiomes, emphasising the need for further research to elucidate the implications for public health. Prevotella species are prevalent and abundant components of microbial communities associated with mammals. This bacterial genus influences individual clinical and metabolic responses to dietary changes and overall health conditions. In humans, Prevotella species have been identified in various body sites such as the skin, oral cavity, vagina, and gastrointestinal tract. In the gut microbiome, they are commonly linked with diets abundant in plant-based foods and are particularly prevalent among agriculturalist populations, where they tend to dominate the microbiota. In the investigation of this genus, 37 MAGs were assembled, all belonging to yet-to-be-described species. Phylogenetic analysis revealed that they represented fifteen putative novel intestinal Prevotella species. The nimJ gene, which confers resistance to metronidazole (a nitroimidazole-class drug), was detected in one of the human intestinal Prevotella species. Given the widespread use of antibiotics like metronidazole for treating both humans and animals in regions of Uganda, including Buhoma, the presence of this gene provides evidence that Prevotella species can acquire resistance to commonly used nitroimidazole-class drugs in areas where their use is prevalent. Of the seven putative novel species identified in human gut microbiomes, two were also present in publicly available genomes in the gut microbiomes from pigs and rhesus macaques living in different geographic locations, providing evidence that the same Prevotella intestinal species can inhabit multiple hosts. Overall, these findings expand knowledge of intestinal Prevotella by introducing numerous previously unknown species, offering a species-level perspective for future studies on Prevotella’s impact on health. Campylobacter species are leading causes of bacterial gastroenteritis worldwide, yet their diversity and transmission dynamics at wildlife–livestock–human interfaces remain poorly characterised. I investigated Campylobacter diversity among sympatric mountain gorillas, livestock, and humans in Uganda, assembling 44 Campylobacter MAGs representing seven species—including five putative novel taxa. Three novel species were found in mountain gorillas, livestock harboured C. vicugnae (goats) and C. sp017646085 (cattle), while human gut microbiomes revealed Candidatus Campylobacter infans (not associated with disease) and C. sp900539255, which was significantly enriched in clinical samples (p=0.001) and displayed unique sulfur and nitrogen metabolic pathways. Antimicrobial resistance genes, including blaOXA-471_1, were detected in Ca. C. infans MAGs. Overall, our findings demonstrate high Campylobacter diversity at the human–animal interface in Buhoma and highlight the importance of expanding reference databases for accurate surveillance and effective public health interventions. In summary, this thesis introduces a substantial amount of new information on gut microbiome bacterial species in gorillas, livestock, and humans living at a wild-livestock-human interface. It also provides detailed insights into three bacterial genera present in the gut microbiomes of human populations, as well as other mammals such as gorillas, cattle, and goats.
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    Ecology of infectious diseases in wild bats : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Sciences at Massey University, New Zealand
    (Massey University, 2019) Hranac, Carter Reed
    Emerging infectious diseases present significant threats to the health of humans and wildlife. The ecology of emerging infectious diseases is a data hungry field in a world of rare events. Bats are both the source of human pathogens globally and the victims of a novel fungal pathogen causing continent-wide population declines in North America. By using the principals of iterative model design and model guided field work I leverage the mechanistic relationships between seasonally limiting biotic and abiotic factors of wild bats to understand spatio-temporal disease emergence dynamics from and within bat populations. I first use a novel ecological niche modeling technique to relate the seasonal availability of resources to predict African bat birthing events. I then use these model results to test hypotheses that Ebola virus disease (EVD) transmission to humans and non-reservoir animal hosts are related to the birthing events of bats through the use of a spatiotemporal Poisson point process model. The results suggest EVD emergence in Africa may be driven in part by the pattern of births among bats, especially fruit bats. Further, the identified temporal lag terms between bat birthing terms and EVD emergence are consistent with hypothesized viral dynamics in bat populations. Out of sample testing on the two most recent EVD outbreaks in the Democratic Republic of the Congo reveal a high predictive model performance and suggest the existence of both strong regional seasonality and locations persistently at risk of EVD outbreaks in humans and susceptible wildlife. Finally, I model North American winter duration and incorporate spatial variation in host traits related to body mass and composition to update survival estimates for hibernating Myotis lucifugus infected with Pseudogymnoascus destructans, the causative agent of the emerging disease white- nose syndrome (WNS) killing bats in Eastern North American populations. Results indicate that hibernating M. lucifugus in the West are likely to suffer populations declines similar to those observed in the East. All my findings will require further ground-truthing to validate the results, yet demonstrate the predictive power of identified mechanistic relationships on complex infectious disease systems.
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    Modelling infectious diseases in multiple species : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Applied Mathematics at Massey University, Albany, New Zealand
    (Massey University, 2019) Babylon, Andrea
    Leptospirosis is an infectious disease caused by bacteria in the genus Leptospira and is considered as the disease of interest in this thesis. It is the highest occurring occupational disease in New Zealand and the country has one of the highest (per capita) incidences of human leptospirosis in the world. Transmission commonly occurs by contact with infectious animals, or materials contaminated by them. The disease is the cause of great financial losses to the country due to both the medical cost of treating infectious individuals, as well as due to production losses in the farming industry. As such, studying the dynamics of infection and possible control measures for the disease in animals, which also minimises exposure to humans, is an important area of research. This thesis aims to develop New Zealand specific models demonstrating the dynamics of leptospirosis infection within and between multiple host species, specifically rats and sheep, thus contributing towards an understanding of not only how ecological exchanges between different host populations influence the spreading of the disease, but also how the incidence of leptospirosis may be diminished. This is achieved with the use of compartmental SI type models of increasing complexity, with simpler models used as building blocks in constructing the more advanced systems. The models presented involving only rats consider an age structure within the population, with different behaviours and infection risks associated with each age class. Models involving only sheep focus on the periodic forcing implemented on the host population by the farmer, and also include an age structure, albeit a somewhat simpler one than the one in the rat models. The seasonal forcing on the livestock population results in a cyclical system which is displayed using limit cycle diagrams. This behaviour is mirrored in the model considering both host species in concert. Each model presents a variety of results, including bifurcation diagrams and quasi-basic reproduction numbers which display the behaviour of the system. The effect of varying various parameter values on the system is explored, and how these may change in relation to climate change is discussed. Parameter values used in numerical results demonstrating analytical ones are New Zealand specific and the model is used to predict conditions under which the infection will persist in the population.
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    Development of a method for optimal detection of emerging disease incursions : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
    (Massey University, 2016) Wang, Shiyong
    Emerging and re-emerging infectious diseases (ERID) are capable of generating sizable economic loss, and causing loss of life and social instability. To prevent and mitigate the negative impacts of ERID, it is imperative to have a sensitive surveillance system for early disease detection. Furthermore, from the economic perspective, resources are always scarce and have opportunity cost, so investment in surveillance programs has to demonstrate that it can maximize the utility of available resources. The thesis was focused on development and application of a software toolbox, Human and Animal Disease Response Program (HandiResponse), designed for (i) visualizing the disease risk landscape and representing spatial variation in the expected occurrence of a zoonotic disease both quantitatively and visually; (ii) evaluating economic benefit and costs of a single surveillance activity or a multi-component portfolio; (iii) identifying optimal use of resources for surveillance. It comprises four modules: (i) risk map development – HandiMap; (ii) surveillance portfolio development – HandiSurv; (iii) economic impact assessment – HandiEcon and (iv) surveillance optimization – OptiSurv. The modules developed were tested on a number of data sets from various countries. The experience demonstrated that using satellite-derived data in combination with national statistical data to produce a disease risk map improved spatial prediction of avian influenza H5N1 outbreaks in southern Vietnam. Development of a risk map from satellite data for Crimean Congo Haemorrhagic Fever for Mongolia guided a field surveillance program which provided the first evidence that this disease is present in both animals and people in Mongolia. Finally an invented disease affecting pigs and people was used to investigate the likely consequences of an incursion of such a novel disease into Australia, involving both domestic and feral pigs and transferring to people. Risk-based and classical disease surveillance options were then tested for disease detection, and modelling work confirmed that a portfolio consisting of different options was the most technically and economically appropriate. HandiResponse is a practical tool that could promote the implementation of risk-based surveillance approaches, and improve both technical and economic efficiency of surveillance programs for infectious diseases, particularly those affecting both people and animals.