Epidemiological studies to inform control strategies for paratuberculosis in farmed deer : 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

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Paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), occurs in a range of ruminant species, and has been diagnosed in wild and domesticated deer worldwide. The disease process in other ruminants is chronic and fatal, with the highest clinical disease incidence generally seen in older animals. However, in farmed deer, disease incidence is highest in young animals, occurring as an acute syndrome in deer as young as eight months of age. The deer industry in New Zealand is concerned about the on-farm impact of paratuberculosis, and the consequences for the venison market should MAP be classified as a zoonosis. Research is thus directed at investigating tools for paratuberculosis control, to reduce the threat to the industry. The aim of the research presented in this thesis was to provide epidemiological evidence that can be used to inform strategy, at industry and farm-level, for control of paratuberculosis in deer. A survey of the deer slaughter population established a baseline prevalence of MAP infection, against which the effects of control initiatives can be measured. Infection was widespread in individuals (45%) and herds (59%), suggesting control rather than eradication as the goal of any industry programme. On-farm disease control was investigated in a randomised controlled trial of vaccine efficacy in young naturally-infected deer. Vaccination reduced the incidence of clinical disease and subclinical pathology; no significant effect on mean production parameters was seen. There was no effect of vaccination on faecal MAP excretion, indicating vaccination may not reduce infection prevalence. Vaccinated deer had an increased risk of testing positively to diagnostic screening tests for bovine tuberculosis. Non-specificity was resolved by ancillary testing, but such tests come at an increased financial and test sensitivity cost. Paratuberculosis control at the industry level may involve schemes to classify herd infection status. For this purpose, the sensitivity and specificity of individual faecal culture and an IgG1 ELISA (Paralisa) to detect young deer infected with MAP was estimated using Bayesian latent class analysis. Paralisa and faecal culture had sensitivity of 19%and 77%, and specificity of 94% and 99%, respectively. Improved diagnostics are therefore needed if herd infection status is to be classified in a sensitive, specific, cost-effective and timely system. The studies contribute to knowledge on different aspects of paratuberculosis control in the New Zealand farmed deer population, providing an evidence base for informed decisionmaking at farm and industry level.
Deer diseases, Paratuberculosis, Farmed deer, Mycobacterium avium subsp. paratuberculosis, Vaccination, Epidemiology, New Zealand