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Missing pages 93, 264 & 313 from electronic and Vault (preservation) copy. / Leptospirosis has been reported in farmed deer in New Zealand since 1980 but knowledge was limited. Studies presented in this thesis investigated the epidemiology and distribution of infection associated with serovars Hardjobovis, Pomona, and Copenhageni in farmed deer, efficacy of a vaccine and the influence of maternally derived antibody, and aspects of exposure of humans to leptospirosis. Serology, bacteriology, and pathology were employed as determinants of infection and vaccine efficacy. A serological survey of 2016 deer from 110 herds confirmed leptospirosis throughout New Zealand with 61.3% of herds infected with Hardjobovis and 3.6% with Pomona alone, 16.4% with dual infections with those serovars, and none with Copenhageni, giving an overall herd prevalence of 81.3%. Epidemiological studies involved serological analysis of samples from a serum bank involving weaner, yearling and adult deer (n=10/group) from 15 farms sampled 3-monthly for 21 months, and intensive blood and urine sampling of young deer on three farms over 1-2 production cycles (n=15-65/group). Infection with Hardjobovis followed an age-related endemic cycle with some animals infected by 3-4 months of age and seroconversion peaking at up to 57% at 12-15 months and mild kidney lesions typical of a host-adapted organism. Infection with Pomona followed an epidemic pattern with seroprevalence of up to 100%, more severe kidney lesions, clinical signs and evidence of reduced growth and reproduction, typical of an accidental host relationship. Leptospira were observed in 30.4% of urine samples and 37.0% of kidneys. Vaccination with "Leptavoid 3" (Schering-Plough Animal Health Ltd) was studied on one non-infected, one Hardjobovis infected, and two dual Hardjobovis/Pomona infected herds. Vaccination produced sustained titres in uninfected young and adult deer, and no maternally derived antibody interference was observed in progeny vaccinated at approximately 3-4 months of age. In infected herds, vaccination enhanced seroprevalence and antibody titres, and reduced urine shedding by 44% and culture from urine and kidneys by 37% in the face of continued natural challenge. Analysis of previous data combined with pooled data from the above studies, indicated that 73.0% of lines and 29.0% of individual deer at slaughterhouses had kidney lesions indicative of leptospirosis with a relative risk (RR) of 1.08 and 1.6 for the relationship between seropositivity to Hardjobovis and Pomona, respectively. The overall RR between positive serology, lesion and culture was 2.1. The kidney culture rate ranged from 2.5-33% between herds demonstrating significant risk of exposure to humans, particularly slaughterhouse workers. This study has provided an understanding of the epidemiology in farmed deer and control options available to the industry.

Missing pages 93, 264 & 313 from electronic and Vault (preservation) copy. / Leptospirosis has been reported in farmed deer in New Zealand since 1980 but knowledge was limited. Studies presented in this thesis investigated the epidemiology and distribution of infection associated with serovars Hardjobovis, Pomona, and Copenhageni in farmed deer, efficacy of a vaccine and the influence of maternally derived antibody, and aspects of exposure of humans to leptospirosis. Serology, bacteriology, and pathology were employed as determinants of infection and vaccine efficacy. A serological survey of 2016 deer from 110 herds confirmed leptospirosis throughout New Zealand with 61.3% of herds infected with Hardjobovis and 3.6% with Pomona alone, 16.4% with dual infections with those serovars, and none with Copenhageni, giving an overall herd prevalence of 81.3%. Epidemiological studies involved serological analysis of samples from a serum bank involving weaner, yearling and adult deer (n=10/group) from 15 farms sampled 3-monthly for 21 months, and intensive blood and urine sampling of young deer on three farms over 1-2 production cycles (n=15-65/group). Infection with Hardjobovis followed an age-related endemic cycle with some animals infected by 3-4 months of age and seroconversion peaking at up to 57% at 12-15 months and mild kidney lesions typical of a host-adapted organism. Infection with Pomona followed an epidemic pattern with seroprevalence of up to 100%, more severe kidney lesions, clinical signs and evidence of reduced growth and reproduction, typical of an accidental host relationship. Leptospira were observed in 30.4% of urine samples and 37.0% of kidneys. Vaccination with "Leptavoid 3" (Schering-Plough Animal Health Ltd) was studied on one non-infected, one Hardjobovis infected, and two dual Hardjobovis/Pomona infected herds. Vaccination produced sustained titres in uninfected young and adult deer, and no maternally derived antibody interference was observed in progeny vaccinated at approximately 3-4 months of age. In infected herds, vaccination enhanced seroprevalence and antibody titres, and reduced urine shedding by 44% and culture from urine and kidneys by 37% in the face of continued natural challenge. Analysis of previous data combined with pooled data from the above studies, indicated that 73.0% of lines and 29.0% of individual deer at slaughterhouses had kidney lesions indicative of leptospirosis with a relative risk (RR) of 1.08 and 1.6 for the relationship between seropositivity to Hardjobovis and Pomona, respectively. The overall RR between positive serology, lesion and culture was 2.1. The kidney culture rate ranged from 2.5-33% between herds demonstrating significant risk of exposure to humans, particularly slaughterhouse workers. This study has provided an understanding of the epidemiology in farmed deer and control options available to the industry.

Irregular pagination: jumps from xix to 21 / New Zealand maintains the highest incidence rate of human campylobacteriosis of the industrialized countries (334.2 cases per 100,000 in 2002), it accounts for more than 56% of all disease notifications in the country. New Zealand is unique globally, with a 'notification-based surveillance system for notifiable diseases that is complemented by laboratory reporting. In other countries (Australia, US, UK), the notification system is entirely laboratory based. Thus, the high incidence of Campylobacteriosis in humans may be related to the methods of reporting rather than the reality of the disease situation. However, the reason for such high incidence has not yet been fully elucidated, and several studies conducted in New Zealand and overseas have implicated the consumption of poultry meat as the main cause of human infections. The reduction or elimination of Campylobacter jejuni in the food chain, particularly from poultry meat products, is a major strategy in efforts to control campylobacteriosis. One approach to this is to prevent C. jejuni colonization of broiler chickens, This approach has been used to control Salmonella contamination of poultry, but the measures put in place for control of Salmonella have not controlled C jejuni. It is generally unknown how frequently C. jejuni colonizes commercial broiler chickens in New Zealand, or what could be done to prevent these infections from occurring. The present study was undertaken in order to describe some of the basic epidemiology of C. jejuni in commercial broiler flocks in New Zealand. The thesis is intended to further describe the epidemiology of colonisation of commercial broiler chickens by C. jejuni in NZ, and present possible risk factors that could be controlled in future to decrease the number of positive flocks of birds that are processed. The thesis set out to elucidate first the extent of C. jejuni colonisation of birds, flocks and farms while the birds were on the farm, having had minimal risk of exposure to Campylobacter spp., by sampling 15 birds in 80 flocks belonging to two companies prior to the first partial depopulation, an event during which the flock are exposed to potentially contaminated fomites and biosecurity levels are dropped, doors opened and personnel movements are extensive. The resulting prevalence estimates are 25.6% of farms, and 12.5% of sheds, are likely to be used to rear broiler chickens colonised with C. jejuni. When a positive flock is discovered, 76.9% of the birds are likely to be colonised with C. jejuni. These figures are results across the whole study population of farms and sheds, as there were no significant differences between prevalence estimates between companies. Following this prevalence estimation, a longitudinal study was conducted involving 12 sheds, to determine whether the environment or the birds were colonised with C. jejuni first. Although 12 sheds were observed every other day from day 14 to the end of the rearing period, it was determined that the birds were positive either first, or at the same time as the environment. Having said that, the sensitivity of the testing method for the environment was dubious, as there were instances where a shed that had positive samples collected on one occasion appeared negative the next, before returning a positive result on the third consecutive sampling occasion. A cross-sectional study of 810 flocks was undertaken to determine the most relevant risk factors for colonisation of the broiler chickens with C. jejuni. Because of the vertically integrated structure of the poultry industry, these 810 flocks corresponded to data collected from 77 farmers about their farms and the 219 sheds on those farms. The caeca from ten birds from each flock processed were pooled and examined for the presence of C. jejuni. These results were used to create a case definition, such that the flocks could be analysed with the questionnaire data, and different risk factors were seen in each season. More flocks reared for Company One were colonised by C. jejuni than for Company Two. Protective factors included having hard (i.e. gravel, asphalt or concrete) pathways to the growout houses, being near to another broiler farm, using the reticulated town water supply for the birds drinking water, using tunnel or crossflow shaped growout houses, using a Chore-TimeTM feed delivery system within the growout house and chlorinating the water supply to the birds (only in winter). The odds of raising flocks colonised with C jejuni increased if rodents were seen on the farm, if the growout houses were constructed with a concrete nib wall, if gas heaters were used during brooding, if cattle were farmed on the property, or if workers were employed on the farm. Sanitising the annex at least as frequently as once per run decreased the odds during summer, and tended to have a similar effect in other seasons. Chlorinating the water supply appeared to have a protective effect in only one season, though the trend appeared towards protection in the other seasons. The risk factor was validated by sampling the drinking water that broilers chickens had access to for the FAC to sec whether the levels that were present in the drinking water could have an effect on C. jejuni 11 sheds that were known to chlorinate the water were sampled to determine whether they met the drinking water standards for humans in NZ, or met the requirements presented by one of the companies involved. Only three sheds met the human drinking water standards for FAC, and two of these (one from each company) met Company Two's requirements. This thesis is for both regulatory and industry stakeholders to assist with developing risk management approaches to diminishing the number of C. jejuni positive flocks. Where management practices are altered, it is hoped that the efficacy of such practices be measured by examining the changes in the rates of C jejuni colonization within the industry

This thesis addresses issues related to surveillance for disease in commercial and non-commercial poultry populations. The motivation for this work has largely arisen from the unprecedented outbreaks of highly pathogenic avian influenza (HPAI) H5N1 that have occurred in 52 countries in Asia, Africa and Europe since 2003. A series of studies are presented using data derived from two countries, Vietnam and New Zealand. The two Vietnamese studies provide in-depth epidemiological analyses of the outbreak of HPAI H5N1 from December 2003 to March 2004. The three New Zealand studies deal with issues related to the development of effective surveillance strategies for HPAI — informed both directly and indirectly by the findings from the Vietnamese studies. This approach provides an example of how ‘lessons’ learnt from countries that have experienced large scale infectious disease epidemics can be used to assist in the design of surveillance activities in (as yet) unaffected countries. The descriptive analyses of the 2003 – 2004 outbreak of HPAI H5N1 in Vietnam indicate that the epidemic was seeded simultaneously in the north and south of the country in the later part of 2003 with 87% of provinces affected by February 2004. HPAI risk was concentrated around the Mekong and Red River Deltas. The broad scale spatial distribution of disease is likely to have been associated with regional differences in the poultry farming, trade in poultry, and environmental conditions such as the presence of bodies of water which would support reservoir species for the virus. A Bayesian zero-inflated Poisson regression model was used to quantify the influence of environmental and demographic factors on the spatial distribution of HPAI positive communes. In areas where disease was reported, our results show that HPAI risk was positively associated with the presence of irrigation and negatively associated with elevation. After controlling for these fixed effects, a single large area of elevated risk in the Red River Delta area was identified, presumably arising from similarities in the likelihood of reporting disease or the presence of factors increasing disease transmission and spread. Further investigations to elucidate likely transmission mechanisms, targeting this area of the country, would be a profitable area of future research. The second part of this thesis presents three studies that address issues related to the development of effective surveillance strategies for HPAI in New Zealand. The first was a cross-sectional study to enumerate the prevalence of backyard poultry ownership in two areas (one urban and the other rural) close to a large provincial city in the North Island of New Zealand. The prevalence of poultry ownership was 2% (95% CI 1% – 4%) in the urban area and 19% (95% CI 12% – 30%) in the rural area. The relatively low numbers of land parcels where poultry are present indicates that these areas, in the event of an infectious disease incursion, would be unlikely to pose a risk for spread of infectious agent. A cross-sectional survey of all members of the Poultry Industry Association of New Zealand was conducted in the later half of 2007. Respondents were asked to document contacts made with other enterprises related to feed, live birds and hatching eggs, table eggs and poultry product, and waste litter and manure. Patterns of contact were analysed using social network analyses. Each of the four networks had scale-free properties, meaning that for each movement type there were small numbers of enterprises that had contacts with large numbers of enterprises (potential ‘super-spreaders’ of disease). The presence of an undetected infectious disease in enterprises with super-spreader characteristics increases the likelihood that an epidemic will propagate rapidly through the population, assuming there is a directly proportional relationship between the number of contacts an enterprise makes and the probability that disease will be transferred from one location to another. While the finding that feed suppliers had large numbers of poultry farm contacts in the feed network came as no surprise, what was of greater interest was that there were small numbers of poultry farms that reported off-farm movements of feed. This should serve as an important reminder for disease control authorities: movement (and other) restrictions applied during the course of an animal health emergency should be applied across a range of industry sectors, recognising that some industry participants may practice activities that are not entirely typical for their enterprise type (e.g. poultry farms on-selling feed to other farms). In the absence of perfect and up-to-date network data, knowledge of the characteristics of individual enterprises that render them more likely to be atypical (e.g. size, type, and geographic location) would be of value, since this information could be used to inform a risk based approach to disease surveillance and control. A scenario tree model was developed as an approach for evaluating the effectiveness of New Zealand’s passive surveillance system for HPAI. The model was developed in two stages. In the first, factors thought to influence the geographic distribution of NAI risk of introduction and spread (and therefore surveillance strategy) were combined to create a spatial risk surface. In the second stage, a scenario tree model of the passive surveillance system for NAI was developed using the spatial risk surface and the HPAI surveillance strategy prescribed by Biosecurity New Zealand. The model was most sensitive to farmers reporting the presence of suspected cases of disease. This implies that the sensitivity of the system as a whole stands to increase if the importance of reporting suspicious clinical signs is reiterated to poultry producers. The studies presented in this thesis have presented a range of techniques and methodological approaches that are sufficiently generic to be used in any country to inform the design of surveillance strategies for a variety of animal diseases, not just those of poultry. Although epidemiology, as a discipline, is endoured with a vast range of analytical techniques that can be used to enhance the understanding of factors influencing the spread of disease among animal populations, the quality of data used to support these techniques is often lacking. The challenge in the years ahead, for both developed and developing countries, is to set in place the appropriate infrastructures to collect details of animal populations consistent in quality over time and space.

Yellow-eyed penguins have suffered major population declines and periodic mass mortality without an established cause. On Stewart Island a high incidence of regional chick mortality was associated with infection by a novel Leucocytozoon sp. The prevalence, structure and molecular characteristics of this leucocytozoon sp. were examined in the 2006-07 breeding season. In 2006-07, 100% of chicks (n=32) on the Anglem coast of Stewart Island died prior to fledging. Neonates showed poor growth and died acutely at approximately 10 days old. Clinical signs in older chicks up to 108 days included anaemia, loss of body condition, subcutaneous ecchymotic haemorrhages and sudden death. Infected adults on Stewart Island showed no clinical signs and were in good body condition, suggesting adequate food availability and a potential reservoir source of ongoing infections. A polymerase chain reaction (PCR) survey of blood samples from the South Island, Stewart and Codfish Island found Leucocytozoon infection exclusively on Stewart Island. The prevalence of Leucocytozoon infection in yellow-eyed penguin populations from each island ranged from 0-2.8% (South Island), to 0-21.25% (Codfish Island) and 51.6-97.9% (Stewart Island). The high prevalence on Stewart Island represented the infection of 100% of chicks and 83% of adult yellow-eyed penguins when tested by PCR. Sequencing of Leucocytozoon sp. DNA found similarities between infections in yellow-eyed penguin adults and chicks, but differences to Leucocytozoon sp. DNA obtained from Fiordland crested penguins. These findings support the suggestion of cross infection between adults and chicks, and indicate that endemic infection in yellow-eyed penguins is unrelated to that in Fiordland crested penguins. Examination by histology and electron microscopy showed tissue megaloschizonts and circulating round gametocytes. Megaloschizonts up to 440µm diameter showed an affinity for hepatic and splenic tissue and were observed releasing occasional intact cytomeres. Round gametocytes were observed within leucocytes in visceral sections, but not peripheral blood smears. The morphology of Leucocytozoon sp. in yellow-eyed penguins showed similarities to the pathogenic species L. simondi and L. sakharoffi but not L. tawaki. A successful treatment protocol for leucocytozoonosis has not been established, although treatment in a Fiordland crested penguin was able to suppress parasitaemia. The role of Leucocytozoon in yellow-eyed penguins as a cause of morbidity and mortality remains unclear. Further investigation into direct pathogenicity, and the interaction of concurrent disease and environmental influences is required. The findings of this thesis provide potential management recommendations and highlight areas requiring further investigation.

Eight studies of the epidemiological dynamics of avian influenza viruses were conducted on poultry in Hong Kong, with special focus on the movement of birds through the live poultry marketing system, and the implications for avian influenza transmission. The first involved analysis of virus isolation data from faecal samples obtained from cooperating stalls in live poultry markets in Hong Kong in a routine sampling program undertaken between 1999 and 2001. This showed that two subtypes of avian influenza viruses, H9N2 and H6N1, have become well established in the Hong Kong live poultry markets, especially in chickens (mainly H9N2) and quail (mainly H6N1). In addition, a wave of H5N1 virus infection occurred in 2001 after it had been absent through the earlier period of the study. The second study was an evaluation of long term changes in the marketing systems for live poultry in Hong Kong, their likely effects on avian influenza epidemiology, and documented evidence of the prevalence of various H subtypes of avian influenza in sampling undertaken during three periods from 1975 to 2001. The third project involved two cross-sectional studies and one longitudinal study on local quail farms in Hong Kong. Results showed that quail could act as a reservoir host for H9N2 and H6N1 subtype viruses, but each subtype differed in its epidemiology. H9 virus usually infected quail at around 10 days of age, whereas H6 infected quail at 15-20 days of age. At 35 days of age (usual market age in Hong Kong), a proportion of market quail were likely to be susceptible to H6 (50%) and H9 viruses (20%), and were able to transmit the virus in the markets. Due to these findings, the Hong Kong Government closed the quail farming operations and restricted the sale of quail in live poultry markets. A longitudinal study was conducted on three live poultry market stalls to assess the time from stall entry to sale, and evaluate the influence of this delay on avian influenza virus transmission to other poultry in the same stall. Participating stalls varied from high volume/rapid turnover to low volume/slow turnover. Turnover for tagged poultry was rapid, although some chickens became infected with H9 virus before sale. Birds which stayed longer, such as quail, became infected and maintained infection in the stall. As well as spread by direct contact and on typical fomites, keeping of pet roosters and re-use of washing water were identified as factors increasing the ability of avian influenza strains to persist in market stalls. An experimental replica of a market stall was created to study the transmission of low pathogenic avian influenza virus (H9N2) in a controlled environment, with different rates of population turnover and different immune status with respect to both H5 and H9 subtypes. Transmission was influenced by distance between birds, the proportion of birds carrying antibody to H9 and the rate of introduction of susceptible birds, but not by the use of H5N2 vaccine. In order to assess the effectiveness of temporary depopulation of stalls, a study was conducted to compare the prevalence of avian influenza virus and Newcastle disease virus before and shortly after the monthly rest day in live poultry markets in Hong Kong, by virus isolation. Prevalence of H9N2 avian influenza virus was reduced by the rest day, but Newcastle disease virus prevalence was unaffected. During the 2002 avian influenza H5N1 outbreak in local chicken farms, a case-control study was undertaken to identify risk factors that may have contributed to this outbreak. A questionnaire was administered by interview to collect the data for this study. Multivariate logistic regression models showed that movement of people and fomites from live poultry markets to farms were important influences on transmission, and that the live bird markets were the likely source of virus for farms. A spatial stochastic computer model was constructed to predict the spread of avian influenza virus in local chicken farms and live poultry markets in Hong Kong, and the effectiveness of control measures. The data used in model parameter setting was derived from the case-control study. The reference model produced an epidemic curve which was similar to the true epidemic curve in the 2002 outbreak. Control strategies such as rest day and vaccination were evaluated within the model, and found to produce results comparable with field experience. Results from these studies clarify various aspects of the epidemiological features and transmission dynamics of avian influenza viruses, and provide guidance on appropriate control and prevention strategies for highly pathogenic avian influenza viruses within poultry marketing systems in Asia.

The aim of this research was to describe training and racing patterns, and causes of wastage in New Zealand Thoroughbred racehorses. Two separate studies were performed. The first involved analysis of data from before and after construction of a new training track at the Matamata Racing Club. Comparisons of measures of performance failed to detect any adverse impact that could be attributed to the new track. The second involved a longitudinal study over a 34-month period, and that involved 1,571 horses. Duration of training preparations and spell periods were associated with horse age, and with the reason for ending a training preparation. Most horses began a training preparation doing slow work and then progressively advanced to a first start. Incidence rates were estimated for starts per 100 training-days, and other summary measures were estimated including training-days to first start, and between successive starts. A total of 834 musculoskeletal injuries (MSI) were observed, resulting in either a spell period, retirement, or death of the horse. There were 165 respiratory disease events, and 58 conditions involving other body systems. Multivariate statistical models were used to explore risk factors for different types of MSI. Older horses were at higher risk of lower limb MSI, and injury to either the superficial digital flexor tendon (SDFT) or suspensory apparatus (SA), while they were at lower risk of shin soreness and other conditions. Male horses had higher risk of tendon and ligament injury than females. Lower risk of injury was observed in Autumn and Winter months compared with December, and in the 1999-2000 year relative to 1997-1998. Measures of cumulative exercise intensity showed a complex relationship with risk of injury that varied with type of injury. The risk of SDFT and SA injury was higher for those preparations without starts, while that for shin soreness was increased after the first start. For lameness conditions other than shin soreness or injury to the SDFT, the hazard was increased after the first start in a preparation, but the magnitude of effect was dependent on the number of days from the beginning of a preparation to the first start.