Morphological and molecular characterisation of coccidia (Eimeria spp.) in kiwi (Apteryx spp.) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand

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Massey University
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The coccidia of kiwi were first reported in the 1970s; however, in-depth, morphological descriptions of oocysts and endogenous stages were not described until 2013. The development and success of Operation Nest Egg (ONE) between 1994 to the present provided the ideal environment for the proliferation of coccidia, i.e., increased density of immunologically naïve hosts. These conditions led to an increase in morbidity and mortality of kiwi chicks due to high coccidial burdens. Current methods of detection and treatment rely heavily on husbandry practices and, potentially, over medication with coccidiocides. Treatment-resistant species of coccidia may exacerbate these problems causing increased cost of frequent hospitalisation and additional supportive care required by kiwi with high coccidial burdens. This thesis advances the ability to quantify oocyst loads in kiwi droppings by determining that a modified Mini-FLOTAC protocol is more accurate than the current method used in New Zealand diagnostic labs. This alternative protocol has the added benefit of not requiring large centrifuges, potentially enabling practitioners to determine coccidial burdens on site. The morphological descriptions of oocysts are continued in brown kiwi and established in Haast tokoeka. The four morphotypes previously described were represented in the brown kiwi dataset; however, E. paraurii was not described in Haast tokoeka. A new morphotype similar to E. kiwii was described in both brown kiwi and Haast tokoeka. This thesis provides the first genetic data at the mitochondrial cytochrome c oxidase I gene, which was initially amplified from the morphologically described species using Sanger sequencing. A larger dataset that included brown kiwi, Haast tokoeka, rowi, and a great spotted kiwi was targeted and sequenced using Illumina amplicon technology. This in-depth analysis allowed for the detection of the full variation of sequences within the samples, informing the development of diagnostic testing, pathogenicity studies, and treatment efficacy monitoring in the future. Further, extensive optimisation of extraction protocols provides key guidelines for breaking open unsporulated oocyst walls to ensure all the oocysts in a sample are represented in the results.
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Eimeria, Kiwis, Parasites, Diseases