Flavour is a factor that has a large influence on meat quality. Pastoral flavour that results from the grazing of pasture is an undesirable characteristic of meat flavour for consumers more accustomed to meat produced by grain and concentrate feeding systems. In New Zealand there is a reliance on grazing systems for sheep meat production, however the resulting meat flavour is one factor that impedes the increase of sheep meat exports to discerning markets. Correlation of chemical analyses to sensory evaluations of sheep meat has identified that a high concentration of indole and skatole in the fat is associated with pastoral flavours. Indole and skatole are formed in the rumen from the microbial fermentation of tryptophan. New Zealand pasture is high in protein, which is both highly soluble and rapidly degraded in the rumen. As such, pasture diets provide a rich and ready source of tryptophan for the formation of indole and skatole in the rumen. Condensed tannins are known to slow the degradation of protein in the rumen. Therefore, one of the objectives of this study was to establish if dietary condensed tannin can reduce the ruminal biogenesis of indole and skatole and consequently, ameliorate pastoral flavour in sheep meat. White clover usually comprises up to 30% of the botanical composition of pastures in New Zealand, is highly degradable in the rumen and likely to result in a high availability of tryptophan in the rumen for conversion to indole and skatole. Therefore, another objective of this study was to determine if feeding white clover gave a significant increase in the formation of indole and skatole in the rumen compared to perennial ryegrass and if this has an effect on pastoral flavour in meat. These hypotheses were tested using a series of in vitro rumen fermentations that incorporated the use of fresh forages (Chapter 3 and 6). In vivo experiments were utilised to assess rumen formation of indole and skatole with different forages (Chapter 4) and to assess effects of dietary condensed tannin (CT; Chapter 5 and 7). Meat and fat samples from lambs used in Chapters 5 and 7 underwent sensory evaluation to determine if forage or CT treatments were having an effect on the fat odour or meat flavour. From the in vitro and in vivo experiments of (Chapter 3, 4, 6 and 7) it was calculated that the formation of indole and skatole with perennial ryegrass is generally only 6-41% of that formed with white clover. A higher concentration of indole and skatole was also observed in the blood plasma of lambs that were fed white clover compared to those that were fed perennial ryegrass (Chapter 7) and white clover gave an overall more intense flavour in the meat. Comparison of forages fermented in vitro (Chapter 3) showed that with forage legumes of a higher CT concentration, such as Lotus pedunculatus (98 gCT kg-1 DM) and Dorycnium rectum (122 gCT kg-1 DM), the indole and skatole formed was only 7-21% of that formed with white clover. With forages of an intermediate CT concentration such as sulla (Hedysarum coronarium) and Lotus corniculatus the indole and skatole concentration formed was 53-68% of that of white clover. From in vitro rumen fermentation of mixtures of white clover and Lotus pedunculatus it was concluded that the CT in Lotus pedunculatus was not reacting with the protein in white clover. Fermentation of fresh white clover in the presence of an increasing concentration of added CT extract showed that at a higher CT, indole and skatole formation were reduced to low levels. It was inferred that this was due to optimal protein binding and the availability of free condensed tannin to bind other sources of protein, including rumen microbes. However, in vivo dosing with a CT extract resulted in only a small reduction in rumen indole and skatole concentration. This indicated that when CT was dosed into the in vivo rumen of lambs fed fresh forages the CT probably passed from the rumen before adequate protein release from the forage had taken place. Thus, in the grazing situation it will be optimal to provide CT in planta to maximise protein binding and this, in combination with the high CT concentration needed (approximately 80 gCT kg-1 DM), makes Lotus pedunculatus or Dorycnium rectum the prime candidates for further grazing trials into pastoral flavour amelioration using CT forages. Grazing Lotus corniculatus (40 gCT kg-1 DM) in a field experiment resulted in a lower rumen and blood plasma and fat concentration of indole and skatole in comparison to the grazing of perennial ryegrass/white clover pasture. However, a change in the pastoral odour of the fat was not perceived by the sensory panel when comparing fat samples from lambs that had grazed Lotus corniculatus and perennial ryegrass/white clover pasture. The concentration of skatole in the body fat was less variable in the lambs that had grazed Lotus corniculatus and resulted in no lambs with a high outlying concentration (>100 ng g-1) of indole and skatole. This finding holds some potential for reducing pastoral flavour for consumers sensitive to high indole and skatole concentration in the fat. When condensed tannin was dosed to lambs that were fed white clover or perennial ryegrass in the form of a grape seed extract the intermittent supply of CT slightly reduced indole and skatole formation in the rumen and reduced the plasma concentration of indole and skatole. Flavour assessment of meat from the lambs fed white clover or perennial ryegrass with or without CT suggested that CT reduced the intensity of pastoral flavours. However, there were minimal effects on indole and skatole concentration in the body fat. It was possible that other pastoral flavour related compounds derived from the degradation of amino acids, in addition to indole and skatole that were measured, were having an effect on the meat flavour. It was concluded that dietary condensed tannin is able to reduce the formation of indole and skatole in the rumen and can alter the sensory attributes of sheep meat including reducing pastoral flavours. A higher CT concentration present within the forage plant (approximately 80 g kg-1 DM) will be best to minimise indole and skatole formation in the rumen and reduce pastoral flavours in the meat. Further research is required to confirm this in the grazing situation. Feeding white clover results in a greater rumen biogenesis of indole and skatole compared to perennial ryegrass and therefore, may be the primary contributor to pastoral flavours when ruminants graze conventional pastures. Further research is required to evaluate the flavour attributes that result from feeding white clover to meat producing ruminants in the New Zealand grazing situation.

Previous research has shown that even small numbers of lung and gastro-intestinal (GI) nematodes cause sub-clinical infections during autumn and can reduce voluntary feed intake (VFI) and liveweight gain (LWG) post-weaning in farmed deer. However, little is known about the effect of parasitism on growth of young farmed deer prior to weaning (summer and early autumn). At present, the control of deer parasites is largely by anthelmintic treatment. Alternatively, chicory sown as a pure sward has been shown to reduce parasitism and increase post-weaning growth of deer compared with perennial ryegrass-based pasture, although, neither forage plantain nor the inclusion of chicory in a pasture mix have yet been evaluated in this context. In addition, it has been suggested that to achieve a high pregnancy rate early in the mating season, deer calves should be weaned prior to mating to optimise nutrition and body condition of the hinds. At present there is no adequate evidence in the published literature to justify this. Two experiments were conducted in 2005 and 2006 respectively. The first experiment investigated the impact of early or late pre-rut weaning, with and without anthelmintic treatment, on parasitism and growth (LWG g/day) of deer calves during summer and early autumn. Weaning date effects on hind reproductive parameters were also investigated. The second experiment was a preliminary investigation to compare the effect of grazing permanent perennial ryegrass pasture (Lolium perenne) with chicory (Cichorium intybus) narrow-leaved plantain (Plantago lanceolata) and pasture mixes based on short-rotation tetraploid ryegrass (TSR-mix; nil endophyte) or long-rotation tetraploid ryegrass (TLR-mix; low endophyte), with both mixes sown with the same clover (white and red) and chicory, on post-weaning growth and endoparasitism of weaned farmed red deer calves in autumn. In 2005, seventy-six deer calves were randomly allocated in a 2x2 factorial design, involving sex, genotype, weaning date (February 17 or March 17), treatment with either topical moxidectin (0.5mg/kg) on January 14 and February 25 or no anthelmintic treatment. Liveweight gain, faecal gastrointestinal egg counts (FEC) and lungworm larval counts (FLC), haematological parameters and serum proteins concentrations (i.e., total protein, albumin and globulin) of calves were measured. Mixed-age adult hinds (64) were used to investigate the effect of weaning date on internal parasitism, conception date and pregnancy rate determined by ultrasound scanning. These hinds were not given anthelmintic treatment, but FLC and FEC were determined on January 12, February 17, March 17, March 31 and May 4. All deer rotationally grazed permanent perennial ryegrass-based pasture (Lolium perenne) together until weaning at which point calves were removed to separate but similar pasture. Calves weaned in March had a higher LWG to March 31 than those weaned in February (P<0.0001). Faecal larval count in treated calves was zero, but FEC remained similar to the untreated control calves, regardless of when they had been treated (average 136 epg, range 0-600 epg in mid February and average 92, range 0-350 epg at the end of March). Treated calves had higher serum albumin, and lower serum globulin concentrations than the untreated control group (albumin, 36.2 ± 0.3 vs 35.2 ± 0.3g/L; P<0.001; globulin, 23.9 ± 0.4 vs 25.5 ± 0.4g/L; P<0.005). In hinds, FLC averaged 5 lpg (range 0 – 122) and FEC averaged 26 (range 0- 200) with no significant relationship between weaning date and either FLC or FEC. No effect of weaning date on conception rate or date was observed. This study showed that pre-rut weaning date, (although confounded by weaning process management) and sub-clinical parasitism during summer and early autumn may influence LWG in young farmed deer. The failure of moxidectin to reduce FEC to zero raises the question of the efficacy of this macrocyclic lactone anthelmintic against GI nematodes in farmed deer and/or emergence of farmed deer GI nematode resistance. Potential diagnostic parameters such as serum albumin concentration, which was reduced in untreated control deer, warrant further investigation for clinical diagnostic use in farmed deer. The study also highlighted the need for further research to demonstrate the advantages or disadvantages of pre-rut weaning on growth of deer calves and hind reproduction. The 2006 grazing experiment investigated the effect of pasture species grazed on post-weaning growth and endoparasitism of farmed red deer from 3- 6 months of age. Ninety-five red deer calves were randomly allocated to five groups based on sex, LW, FEC and FLC. These calves rotationally grazed either a permanent pasture based on perennial ryegrass, chicory, narrow-leaved plantain, or one of two pasture mixes based on either a short-rotation tetraploid ryegrass (TSR-mix) or long-rotation tetraploid ryegrass (TLR-mix). Both mixes included the same white clover, red clover and chicory. All deer were initially treated with an anthelmintic (albendazole), with subsequent trigger treatment withheld until weight loss or clinical parasitism was observed. Anthelmintic trigger treatment (albendazole) was given on an individual animal basis. The anthelmintic trigger treatment and LWG data in this study suggest that plantain, TLR- and TSR-mixes and chicory may all have a role in aiding control of endoparasitism in young growing deer in autumn in deer production systems based on permanent perennial ryegrass-based pasture with low anthelmintic input. However, any potential effects of forage feeding value and anti-parasitic plant compounds of chicory, plantain and pasture-forage mixes on parasitism and growth could not be separated in this study. It is therefore acknowledged that these observations are preliminary and based on a design intended only to establish whether further replicated studies are warranted, particularly with plantain and pasture mixes. However, the study has shown that pasture species, either sown as a pure crop or in a pasture mix can influence LWG, resilience to internal parasitism and requirement for anthelmintic use in young farmed deer. Data from the first experiment (2005) has shown that pre-rut weaning date and sub-clinical parasitism during summer and early autumn can influence LWG in young farmed deer while the trigger treatment and LWG data from the second experiment (2006), suggest that plantain, TLR-and TSR-mixes and chicory may have a role in aiding control of internal parasitism in young deer in autumn. The outcome of the second experiment has application to deer production systems with low anthelmintic input. Serum protein and haematological parameters investigated in both studies demonstrated the need for further research to establish diagnostic markers for both sub-clinical and clinical internal parasitism in farmed young deer.

This thesis describes a series of three experiments designed to estimate the nutritional cost of the immune response to the gastrointestinal nematodes Trichostrongylus colubriformis and Teladorsagia circumcincta in sheep. For each experiment, animals were allocated hierarchically by liveweight into one of four groups that were either infected (group IF), similarly infected and concurrently immuno-suppressed with weekly intramuscular injections of 1.3mg kg liveweight (LW)⁻¹ of methylprednisolone acetate (group ISIF), immunosuppressed only (group IS) or remained as controls (group C). Body composition of all animals was estimated using x-ray computer tomography prior to infection and at the conclusion of each study with bodyweight and faecal nematode egg counts (FEC; eggs gram⁻¹ of fresh faeces (epg)) measured along with blood samples taken for the determination of levels of serum proteins, phosphate and antibodies. In the first trial (Chapter 3), the nutritional cost of both the acquisition and maintenance of immunity to gastro-intestinal nematodes was investigated using immunologically naive 5-month-old lambs and immunologically competent 17-month-old ewes during infection with 2,000 and 4,000 L3 infective T. colubriformis larvae d⁻¹, respectively (80 L3 T. colubriformis larvae kgLW⁻¹ d⁻¹). Profiles of FEC and comparative worm burdens at slaughter indicated an effective immune response was maintained in IF ewes and developed in IF lambs while successfully suppressed in both ISIF lambs and ISIF ewes and was confirmed by serum antibody titres. The typical reduction in voluntary feed intake as a consequence of infection was observed in IF lambs (0.30, p<0.001) but not in IF ewes, ISIF lambs or ISIF ewes, and appeared to be associated with L3 IgA. Gross efficiency of use of metabolizable energy (ME) for net energy (NE) deposition was reduced by 0.20 in lambs during acquisition of immunity and by 0.16 in ewes maintaining an established immunity. Infection in immuno-suppressed animals reduced efficiency by 0.05 and 0.15 for lambs and ewes. These findings allowed the hypothesis that the reduction in feed intake and nutrient utilization in young parasitized sheep is caused by physiological signalling associated with the acquisition phase of the host immune response to infection, rather than simply the damage caused by the parasite per se. The second trial (Chapter 4) investigated the influence of metabolizable protein (MP) supply on the metabolic disturbances associated with the acquisition phase of the immune response during infection with 2,000 L3 T. colubriformis d⁻¹. Groups of lambs were offered either a low protein (L; 62g MP kgDM⁻¹) or high protein diet (H; 95g MP kgDM⁻¹). Patterns of total daily egg excretion indicated that an effective immune response was developed in HIF, but not LIF, HISIF nor LISF and was confirmed by comparative worm burdens. The proportionate reduction in feed intake in immunologically normal animals was reduced through the provision of additional protein, being 0.12 in HIF and 0.23 in LIF. Regardless of diet, infection did not cause a reduction in feed intake in immuno-suppressed animals (p>0.05). Infection proportionately reduced the gross efficiency of ME utilization in immunologically normal animals by 0.23 in HIF (p=0.09) and by 0.51 in LIF (p=0.01), but not in immuno-suppressed animals. Immuno-suppression did not suppress serum L3 IgA levels in seven of the eight HISIF and four of the eight LISIF animals. Furthermore, only four out of the eight immunologically normal animals from both the HIF and LIF groups displayed an L3 IgA response. Consequently, regardless of immunosuppression treatment, animals were termed as IgA responders (HR or LR) or non-responders (HN or LN). Feed intake was proportionately reduced from day 22 by 0.15 in HR (p=0.03) and by 0.32 in LR (p=0.01), but was not significantly reduced in HN or LN. Gross efficiency of ME utilization was significantly reduced for LN animals only, being proportionately 0.59 (p<0.01). These findings allowed the conclusion that additional MP reduced the consequence of immunological signalling that was displayed in reduced feed intake and in nutrient utilization, both of which appeared to be associated with an IgA response. It is hypothesized that the lessening of nutritional disturbance observed in high protein and immuno-suppressed animals could be a consequence of altered physiological signalling during the immunological cascade. The third trial (Chapter 5) utilized lambs infected with the abomasal parasite T. circumcincta to explore the possibility that the reduction in feed intake and nutrient utilization is a universal phenomenon of the acquisition phase of the immune response to nematode parasites inhabiting different organs along the gastrointestinal tract. In addition, immunological changes at the site of parasite infestation in the abomasal mucosa were measured from serial biopsy tissue samples taken from a further twelve animals that were surgically fitted with an abomasal cannula and either infected (CIF) or concurrently infected and immuno-suppressed as described previously (CISIF). The development of immunity in IF animals was accompanied by a 0.17 proportional decrease in feed intake between days 15 to 28 of infection (p<0.05) and a 0.20 proportional reduction in nutrient utilization (p=0.07), none of which were observed in ISIF animals. While FEC and worm burdens indicated successful immunosuppression in ISIF animals, both serum IgA and total antibody production were not reduced. The development of immunity in CIF was reflected in an increase in both mast cells and globule leukocytes in serial abomasal tissue biopsies, both of which were reduced in CISIF (p<0.01 for both). In serial biopsy tissue, immuno-suppression did prevent a rise in tissue IgA that was apparent in CIF animals (p<0.01) although these changes were not reflected in serum IgA levels. It appears that the alleviation of the reduction in feed intake and nutrient utilization in young lambs through the use of corticosteroid induced immuno-suppression may be a universal phenomenon for both intestinal and abomasal parasites, but the association with and/or role of IgA during infection with T. circumcincta is unclear. In summary, the reduction in feed intake and nutrient utilization in sheep during infection with both the abomasal nematode T. circumcincta and the small intestine nematode T. colubriformis appears to be associated with a component(s) of the acquisition phase of the host immune response, rather than, as conventionally assumed, the direct mechanical damage of the parasite per se. It is hypothesised that the nutritional disturbance as a consequence of infection in young lambs may be the result of pro-inflammatory cytokines involved in immunological signalling that may also be associated with the production of IgA, the effects of which can be reduced through the provision of adequate MP. These studies provide evidence that the immune response to gastrointestinal parasites is nutritionally costly to the animal and have implications for application of manipulations that are intended to promote the development of a strong immune reaction in high producing animals.

This thesis describes a series of three experiments designed to estimate the nutritional cost of the immune response to the gastrointestinal nematodes Trichostrongylus colubriformis and Teladorsagia circumcincta in sheep. For each experiment, animals were allocated hierarchically by liveweight into one of four groups that were either infected (group IF), similarly infected and concurrently immuno-suppressed with weekly intramuscular injections of 1.3mg kg liveweight (LW)⁻¹ of methylprednisolone acetate (group ISIF), immunosuppressed only (group IS) or remained as controls (group C). Body composition of all animals was estimated using x-ray computer tomography prior to infection and at the conclusion of each study with bodyweight and faecal nematode egg counts (FEC; eggs gram⁻¹ of fresh faeces (epg)) measured along with blood samples taken for the determination of levels of serum proteins, phosphate and antibodies. In the first trial (Chapter 3), the nutritional cost of both the acquisition and maintenance of immunity to gastro-intestinal nematodes was investigated using immunologically naive 5-month-old lambs and immunologically competent 17-month-old ewes during infection with 2,000 and 4,000 L3 infective T. colubriformis larvae d⁻¹, respectively (80 L3 T. colubriformis larvae kgLW⁻¹ d⁻¹). Profiles of FEC and comparative worm burdens at slaughter indicated an effective immune response was maintained in IF ewes and developed in IF lambs while successfully suppressed in both ISIF lambs and ISIF ewes and was confirmed by serum antibody titres. The typical reduction in voluntary feed intake as a consequence of infection was observed in IF lambs (0.30, p<0.001) but not in IF ewes, ISIF lambs or ISIF ewes, and appeared to be associated with L3 IgA. Gross efficiency of use of metabolizable energy (ME) for net energy (NE) deposition was reduced by 0.20 in lambs during acquisition of immunity and by 0.16 in ewes maintaining an established immunity. Infection in immuno-suppressed animals reduced efficiency by 0.05 and 0.15 for lambs and ewes. These findings allowed the hypothesis that the reduction in feed intake and nutrient utilization in young parasitized sheep is caused by physiological signalling associated with the acquisition phase of the host immune response to infection, rather than simply the damage caused by the parasite per se. The second trial (Chapter 4) investigated the influence of metabolizable protein (MP) supply on the metabolic disturbances associated with the acquisition phase of the immune response during infection with 2,000 L3 T. colubriformis d⁻¹. Groups of lambs were offered either a low protein (L; 62g MP kgDM⁻¹) or high protein diet (H; 95g MP kgDM⁻¹). Patterns of total daily egg excretion indicated that an effective immune response was developed in HIF, but not LIF, HISIF nor LISF and was confirmed by comparative worm burdens. The proportionate reduction in feed intake in immunologically normal animals was reduced through the provision of additional protein, being 0.12 in HIF and 0.23 in LIF. Regardless of diet, infection did not cause a reduction in feed intake in immuno-suppressed animals (p>0.05). Infection proportionately reduced the gross efficiency of ME utilization in immunologically normal animals by 0.23 in HIF (p=0.09) and by 0.51 in LIF (p=0.01), but not in immuno-suppressed animals. Immuno-suppression did not suppress serum L3 IgA levels in seven of the eight HISIF and four of the eight LISIF animals. Furthermore, only four out of the eight immunologically normal animals from both the HIF and LIF groups displayed an L3 IgA response. Consequently, regardless of immunosuppression treatment, animals were termed as IgA responders (HR or LR) or non-responders (HN or LN). Feed intake was proportionately reduced from day 22 by 0.15 in HR (p=0.03) and by 0.32 in LR (p=0.01), but was not significantly reduced in HN or LN. Gross efficiency of ME utilization was significantly reduced for LN animals only, being proportionately 0.59 (p<0.01). These findings allowed the conclusion that additional MP reduced the consequence of immunological signalling that was displayed in reduced feed intake and in nutrient utilization, both of which appeared to be associated with an IgA response. It is hypothesized that the lessening of nutritional disturbance observed in high protein and immuno-suppressed animals could be a consequence of altered physiological signalling during the immunological cascade. The third trial (Chapter 5) utilized lambs infected with the abomasal parasite T. circumcincta to explore the possibility that the reduction in feed intake and nutrient utilization is a universal phenomenon of the acquisition phase of the immune response to nematode parasites inhabiting different organs along the gastrointestinal tract. In addition, immunological changes at the site of parasite infestation in the abomasal mucosa were measured from serial biopsy tissue samples taken from a further twelve animals that were surgically fitted with an abomasal cannula and either infected (CIF) or concurrently infected and immuno-suppressed as described previously (CISIF). The development of immunity in IF animals was accompanied by a 0.17 proportional decrease in feed intake between days 15 to 28 of infection (p<0.05) and a 0.20 proportional reduction in nutrient utilization (p=0.07), none of which were observed in ISIF animals. While FEC and worm burdens indicated successful immunosuppression in ISIF animals, both serum IgA and total antibody production were not reduced. The development of immunity in CIF was reflected in an increase in both mast cells and globule leukocytes in serial abomasal tissue biopsies, both of which were reduced in CISIF (p<0.01 for both). In serial biopsy tissue, immuno-suppression did prevent a rise in tissue IgA that was apparent in CIF animals (p<0.01) although these changes were not reflected in serum IgA levels. It appears that the alleviation of the reduction in feed intake and nutrient utilization in young lambs through the use of corticosteroid induced immuno-suppression may be a universal phenomenon for both intestinal and abomasal parasites, but the association with and/or role of IgA during infection with T. circumcincta is unclear. In summary, the reduction in feed intake and nutrient utilization in sheep during infection with both the abomasal nematode T. circumcincta and the small intestine nematode T. colubriformis appears to be associated with a component(s) of the acquisition phase of the host immune response, rather than, as conventionally assumed, the direct mechanical damage of the parasite per se. It is hypothesised that the nutritional disturbance as a consequence of infection in young lambs may be the result of pro-inflammatory cytokines involved in immunological signalling that may also be associated with the production of IgA, the effects of which can be reduced through the provision of adequate MP. These studies provide evidence that the immune response to gastrointestinal parasites is nutritionally costly to the animal and have implications for application of manipulations that are intended to promote the development of a strong immune reaction in high producing animals.

Animal health surveillance is an important part of animal health care, particularly in countries dependent on livestock for food production and international trade. There are two major issues related to the provision of e®ective surveillance activities. Firstly, for good information to become available, the design and conduct of data collection activ- ities should be carried out following sound statistical principles. In reality, constraints such as imperfect tests and unavoidably-biased sampling strategies hinder straightfor- ward analysis and interpretation of survey results. Risk-based surveillance is used to target high-risk sub-populations to increase e±ciency of disease detection; however, biased datasets are generated. This thesis develops methodologies to design risk-based surveillance systems and al- low statistically valid analysis of the inherently biased data they generate. The ¯rst example describes the development of a method to analyse surveillance data gathered for bovine spongiform encephalopathy (BSE). The data are collected from four dif- ferent surveillance streams of animals tested for BSE, with each stream containing unavoidable biases and limitations. In the BSurvE model, these data are combined with demographic information for each birth cohort to estimate the proportion of each birth cohort infected with BSE. The prevalence of BSE in a national herd can then be estimated using the method of moments, whereby the observed number of infected animals is equated with the expected number. The upper 95% con¯dence limit for the prevalence is estimated both for infected countries and for those where no BSE has previously been detected. A similar approach to that used in BSurvE is then applied to surveillance data for trichinellosis, for which risk-based post-mortem testing is also performed. Negative results from multiple species using di®erent, imperfect tests are combined to give an estimate of the upper 95% con¯dence limit of the national prevalence of trichinellosis in a reference population. This method is used to provide support for freedom from trichinellosis in Great Britain. A di®erent approach to risk-based surveillance is explored as the surveillance strategy for detection of exotic causes of abortion in sheep and goats in New Zealand is examined. Using a geographic information system (GIS) maps of disease risk factors were overlain to produce a risk landscape for the lower North Island. This was used to demonstrate how areas of high- and low-risk of disease occurrence can be identi¯ed and used to guide the design of a risk-based surveillance programme. Secondly, within one surveillance objective there may be many ways in which the available funds or human resources could be distributed. This thesis develops a method to assess BSE surveillance programmes, and provides tools to facilitate BSE detection on the basis of infection risk and to increase the e±ciency of surveillance strategies. A novel approach to allocation of resources is developed, where portfolio theory con- cepts from ¯nance are applied to animal health surveillance. The example of surveil- lance for exotic causes of sheep and goat abortion is expanded upon. Risk of disease occurrence is assessed for a population over di®erent time periods and geographical areas within a country, and portfolio theory used to allocate the number of tests to be carried out within each of these boundaries. This method is shown to be more likely to detect disease in a population when compared to proportional allocation of the available resources. The studies presented here show new approaches that allow better utilisation of imperfect data and more e±cient use of available resources. They allow development of surveillance programmes containing an appropriate balance of scanning and targeted surveillance activities. Application of these methods will enhance the implementation and value of surveillance in animal health.

This thesis is concerned with the application of recently developed epidemiological and statistical tools to inform the optimisation of a national surveillance strategy of considerable importance to human health. The results of a series of epidemiological investigations of surveillance strategies for zoonotic Salmonella are presented. Salmonella are one of the most common and serious zoonotic foodborne pathogenic bacteria globally. These studies were motivated by the increasing focus on the cost-effectiveness of surveillance while maintaining consumer confidence in food supply. Although data from the Danish Salmonella surveillance and control programme has been used in these investigations, the techniques may be readily applied to other surveillance data of similar quality. The first study describes the spatial epidemiological features of Danish Salmonella surveillance and control programme data from 1995 to 2004, using a novel method of spatially adaptive smoothing. The conditional probability of a farm being a case was consistently high in the the south-west of Sonderjylland on the Jutland peninsula, identifying this area for further investigation and targeted surveillance. The identification of clustering of case farms led into the next study, which closely examines one year of data, 2003, for patterns of spatial dependency. K-function analyses provided evidence for aggregation of Salmonella case farms over that of all farms at distances of up to six kilometres. Visual semivariogram analyses of random farm-level effects from a Bayesian logistic regression model (adjusted for herd size) of Salmonella seropositivity, revealed spatial dependency between pairs of farms up to a distance of four kilometres apart. The strength of the spatial dependency was positively associated with slaughter pig farm density. We describe how this might inform the surveillance programme by potentially targeting herds within a four kilometre radius of those with high levels of Salmonella infection. In the third study, farm location details, routinely recorded surveillance information, and industry survey data from 1995 were combined to build a logistic seroprevalence model. This identified wet-feeding and specific pathogen free herd health status as protective factors for Salmonella seropositivity, while purchasing feed was a risk factor. Once adjusting for these covariates, we identified pockets of unexplained risk for Salmonella seropositivity and found spatial dependency at distances of up to six km (95% CI: 2–35 km) between farms. A generalised linear spatial model was fitted to the Jutland data allowing formal estimation of the range of spatial correlation and a measure of the uncertainty about it. There was a large within-farm component to the variance, suggesting that gathering more farm level information would be advantageous if this approach was to be used to target surveillance strategy. The fourth study again considers data from the whole study period, 1995 to 2004. A detailed temporal analysis of the data revealed there was no consistent seasonal pattern and correspondingly no benefit in targeting sampling to particular times of the year. Spatiotemporal analyses suggested a local epidemic of increased seroprevalence occured in west Jutland in late 2000. Lorelogram analyses showed a defined period of statistically significant temporal dependency, suggesting that there is little value in sampling more frequently than every 10 weeks on the average farm. The final study uses findings from the preceding chapters to develop a zero-inflated binomial model which predicts which farms are most at risk of Salmonella, and then preferentially samples these high-risk farms. This type of modelling allows assessment of similarities and differences between factors that affect herd infection status (introduction) and those that affect the seroprevalence in infected herds (persistence and spread). The model suggested that many of the herds where Salmonella was not detected were infected but at a low prevalence. Using cost and sensitivity, we compared the results with those under the standard sampling scheme based on herd size, and the recently introduced risk-based approach. Model based results were less sensitive, but showed significant cost savings. Further model refinements, sampling schemes, and the methods to evaluate their performance are important areas for future work, and should continue to occur in direct consultation with Danish authorities.

The objectives of this thesis were to investigate patterns of lamb pneumonia prevalence of a large sample of New Zealand flocks including an investigation of spatial patterns, to evaluate farm-level risk factors for lamb pneumonia, to determine the efficacy of a commercially available vaccine for the disease and to estimate the likely cost of lamb pneumonia and pleurisy for New Zealand sheep farmers. Data were collected by ASURE NZ Ltd. meat inspectors at processing plants in Canterbury, Manawatu and Gisborne between December 2000 and September 2001. All lambs processed at these plants were scored for pneumonia (scores: 0, <10% or ≥10% lung surface area affected) involving 1,899,556 lambs from 1,719 farms. Pneumonia prevalence was evaluated for spatial patterns at farm level and for hierarchical patterns at lamb, mob and farm levels (Chapter 3). The average pneumonia prevalence in Canterbury, Feilding and Gisborne was 34.2%, 19.1% and 21.4% respectively. Odds ratios of lambs slaughtered between March and May were vastly higher than those slaughtered in other months indicating longer growth periods due to pneumonia. Since pneumonia scores were more variable between mobs within a flock than between flocks, it was concluded that pneumonia scores were poor indicators for the flock pneumonia level due to their lack of repeatability. There was no statistically significant spatial autocorrelation in pneumonia prevalence for any region, hence lamb pneumonia appeared to be largely independent of topographical and geo-climatic factors. A questionnaire-based case-control study was conducted investigating farm-level factors from a sample of farms with either high (case) or zero (control) pneumonia prevalence at slaughter (Chapter 4). Significant risk factors for case farms were: (1) shearing lambs on the day of weaning, (2) breeding ewe replacements on-farm (3) number of lambs sold (an indicator of flock size) and (4) increased percentage of lambs sold late in the season (March to May). Significant protective factors included: (1) set stocking lambs after weaning, (2) injecting lambs with Vitamin B12 at the time of tailing, (3) injecting lambs with Vitamin B12 at weaning. In Canterbury, flocks with Romney ewes and other ewes had a higher risk of pneumonia than those with fine wool type ewes (Merinos, Corriedales or Halfbreds). In a clinical trial, 8,364 lambs from seven commercial sheep farms with a history of lamb pneumonia were vaccinated with Ovipast Plus® or placebo by systematic random allocation within mob and farm. An assessment of the extent of pneumonic lesions was conducted at slaughter and lamb growth rate was monitored through the growth period (Chapter 5). The vaccination trial showed no statistically significant effect of Ovipast® vaccination on the extent of lung lesions at slaughter or ADG of lambs from the first treatment until slaughter. No significant differences were found between isolation rates of Pasteurella spp and patho-histological classifications from pneumonic lung samples of placebo and vaccinated lambs. A spreadsheet-based stochastic model was constructed to estimate the cost of lamb pneumonia and pleurisy to New Zealand farmers. The estimate was based on data of the effect of pneumonia on lamb growth rate, distributions of pneumonia severity, prevalence of moderate to severe pneumonia (≥10% lung surface area) and pleurisy prevalence (Chapter 6). The simulated annual average cost of pneumonia was NZ $28.1 million and that of pleurisy NZ $25.1 million. The combined cost of pneumonia and pleurisy to New Zealand farmers had an average of NZ $53.2 million (95% stochastic interval = $32.4-$78.9 million), or US $31.9 million per annum. This would equate to NZ $2.32 per lamb. In comparison, animal health, shearing expenses and feed expenses cost NZ $2.37, $2.62 and $1.85 per lamb, respectively. This research has demonstrated sub-clinical pneumonia to be a widespread disease in the New Zealand sheep farming population while previous research has focussed on case studies of affected farms. The estimated costs of pneumonia and pleurisy to New Zealand farmers ($53.2 million) highlight the financial effects of these diseases and the need for further research. We also found that the commercially available vaccine could neither prevent sub-clinical effects (lamb growth rate) nor clinical manifestations (pneumonic lung lesions) of lamb pneumonia. The case-control study has revealed farm-level factors which, in the absence of effective vaccines, indicated management practices that farmers might perceive as opportunities to control lamb pneumonia. However, it is advisable to evaluate the efficiency of such management changes. Pneumonia is aetiologically complex disease involving the interplay of many environmental, host and pathogen factors. It is also a difficult disease to study in the absence of diagnostic tests in live animals. However, further research should focus on the development of management changes until effective vaccines are available. A starting point for this research would be to evaluate the impact of such management changes in reducing the incidence of lamb pneumonia. More specifically, the roles of stress during crowding of lambs for extended periods warrants further investigation. The development of efficient vaccines requires an analysis of pathogens, especially Pasteurella (Mannheimia) haemolytica and Mycoplasma species, the sources of infection, their strain diversity and transmission dynamics.

Animal health surveillance is an important part of animal health care, particularly in countries dependent on livestock for food production and international trade. There are two major issues related to the provision of e®ective surveillance activities. Firstly, for good information to become available, the design and conduct of data collection activ- ities should be carried out following sound statistical principles. In reality, constraints such as imperfect tests and unavoidably-biased sampling strategies hinder straightfor- ward analysis and interpretation of survey results. Risk-based surveillance is used to target high-risk sub-populations to increase e±ciency of disease detection; however, biased datasets are generated. This thesis develops methodologies to design risk-based surveillance systems and al- low statistically valid analysis of the inherently biased data they generate. The ¯rst example describes the development of a method to analyse surveillance data gathered for bovine spongiform encephalopathy (BSE). The data are collected from four dif- ferent surveillance streams of animals tested for BSE, with each stream containing unavoidable biases and limitations. In the BSurvE model, these data are combined with demographic information for each birth cohort to estimate the proportion of each birth cohort infected with BSE. The prevalence of BSE in a national herd can then be estimated using the method of moments, whereby the observed number of infected animals is equated with the expected number. The upper 95% con¯dence limit for the prevalence is estimated both for infected countries and for those where no BSE has previously been detected. A similar approach to that used in BSurvE is then applied to surveillance data for trichinellosis, for which risk-based post-mortem testing is also performed. Negative results from multiple species using di®erent, imperfect tests are combined to give an estimate of the upper 95% con¯dence limit of the national prevalence of trichinellosis in a reference population. This method is used to provide support for freedom from trichinellosis in Great Britain. A di®erent approach to risk-based surveillance is explored as the surveillance strategy for detection of exotic causes of abortion in sheep and goats in New Zealand is examined. Using a geographic information system (GIS) maps of disease risk factors were overlain to produce a risk landscape for the lower North Island. This was used to demonstrate how areas of high- and low-risk of disease occurrence can be identi¯ed and used to guide the design of a risk-based surveillance programme. Secondly, within one surveillance objective there may be many ways in which the available funds or human resources could be distributed. This thesis develops a method to assess BSE surveillance programmes, and provides tools to facilitate BSE detection on the basis of infection risk and to increase the e±ciency of surveillance strategies. A novel approach to allocation of resources is developed, where portfolio theory con- cepts from ¯nance are applied to animal health surveillance. The example of surveil- lance for exotic causes of sheep and goat abortion is expanded upon. Risk of disease occurrence is assessed for a population over di®erent time periods and geographical areas within a country, and portfolio theory used to allocate the number of tests to be carried out within each of these boundaries. This method is shown to be more likely to detect disease in a population when compared to proportional allocation of the available resources. The studies presented here show new approaches that allow better utilisation of imperfect data and more e±cient use of available resources. They allow development of surveillance programmes containing an appropriate balance of scanning and targeted surveillance activities. Application of these methods will enhance the implementation and value of surveillance in animal health.

Animal health surveillance is an important part of animal health care, particularly in countries dependent on livestock for food production and international trade. There are two major issues related to the provision of e®ective surveillance activities. Firstly, for good information to become available, the design and conduct of data collection activ- ities should be carried out following sound statistical principles. In reality, constraints such as imperfect tests and unavoidably-biased sampling strategies hinder straightfor- ward analysis and interpretation of survey results. Risk-based surveillance is used to target high-risk sub-populations to increase e±ciency of disease detection; however, biased datasets are generated. This thesis develops methodologies to design risk-based surveillance systems and al- low statistically valid analysis of the inherently biased data they generate. The ¯rst example describes the development of a method to analyse surveillance data gathered for bovine spongiform encephalopathy (BSE). The data are collected from four dif- ferent surveillance streams of animals tested for BSE, with each stream containing unavoidable biases and limitations. In the BSurvE model, these data are combined with demographic information for each birth cohort to estimate the proportion of each birth cohort infected with BSE. The prevalence of BSE in a national herd can then be estimated using the method of moments, whereby the observed number of infected animals is equated with the expected number. The upper 95% con¯dence limit for the prevalence is estimated both for infected countries and for those where no BSE has previously been detected. A similar approach to that used in BSurvE is then applied to surveillance data for trichinellosis, for which risk-based post-mortem testing is also performed. Negative results from multiple species using di®erent, imperfect tests are combined to give an estimate of the upper 95% con¯dence limit of the national prevalence of trichinellosis in a reference population. This method is used to provide support for freedom from trichinellosis in Great Britain. A di®erent approach to risk-based surveillance is explored as the surveillance strategy for detection of exotic causes of abortion in sheep and goats in New Zealand is examined. Using a geographic information system (GIS) maps of disease risk factors were overlain to produce a risk landscape for the lower North Island. This was used to demonstrate how areas of high- and low-risk of disease occurrence can be identi¯ed and used to guide the design of a risk-based surveillance programme. Secondly, within one surveillance objective there may be many ways in which the available funds or human resources could be distributed. This thesis develops a method to assess BSE surveillance programmes, and provides tools to facilitate BSE detection on the basis of infection risk and to increase the e±ciency of surveillance strategies. A novel approach to allocation of resources is developed, where portfolio theory con- cepts from ¯nance are applied to animal health surveillance. The example of surveil- lance for exotic causes of sheep and goat abortion is expanded upon. Risk of disease occurrence is assessed for a population over di®erent time periods and geographical areas within a country, and portfolio theory used to allocate the number of tests to be carried out within each of these boundaries. This method is shown to be more likely to detect disease in a population when compared to proportional allocation of the available resources. The studies presented here show new approaches that allow better utilisation of imperfect data and more e±cient use of available resources. They allow development of surveillance programmes containing an appropriate balance of scanning and targeted surveillance activities. Application of these methods will enhance the implementation and value of surveillance in animal health.

There is mounting evidence that parasitic infections change nutrient utilisation within the tissues, and that this is responsible for the reduction in animal performance that has been observed. Feeding forages that contain condensed tannins (CT) are thought to alleviate the impact of parasite infection on amino acid (AA) and protein metabolism by improving protein supply post-ruminally. However, there has been no quantification of how nutrients are partitioned in the lamb fed fresh forages during a parasitic infection. Therefore, the objective of this study was to quantify the partitioning of AA between the gastrointestinal tract (GIT), liver and the hind limb tissues (muscle, skin, fat) in lambs during an established parasite infection. It was hypothesised that the feeding of CT would alter the partitioning of AA between the GIT, liver and hind limbs in lambs with an established parasite burden due to the increased availability of dietary AA to the small intestine. This hypothesis was tested in two separate experiments, which had a similar experimental design. In the first experiment (Experiment One; 1999) lambs were fed fresh Lucerne (Medicago sativa; contains no CT). In Experiment Two, which was conducted in 2000, the lambs were fed fresh Sulla (Hedysarum coronarium; 2.2% CT; Experiment Two). One week prior to infection, permanent indwelling catheters were placed in the mesenteric artery, and the mesenteric, portal and hepatic veins and vena cava for blood sampling. Additional permanent catheters were placed in the mesenteric vein (upstream from the sampling catheter) and abdominal aorta for infusion of para-aminohippuric acid (PAH) and indocyanin green (ICG) respectively, to measure plasma flow across the splanchnic tissues (PAH) and the hind limbs (ICG). A permanent Teflon cannula was fitted in the abomasum for the infusion of [1-13C]-valine and [35S]-cysteine (Chapters Five, Six and Seven only) on day 48 post infection to measure valine and cysteine kinetics across the mesenteric-drained viscera (MDV), portal-drained viscera (PDV), liver, total splanchnic tissues (TSP; PDV + liver) and hind limbs. A temporary catheter was inserted into the jugular vein two days before the start of blood sampling for the infusion of deuterium oxide (D2O), and [13C]-sodium bicarbonate and [35S]-sulfate (Chapters Five, Six and Seven only) on day 45 post infection, and [3,4-3H]-valine on day 48 post infection. Lambs were dosed with 6 000 L3 T. colubriformis larvae for 6 d (n=5) or kept as parasite free controls (n=6). Faecal egg production was monitored every second day from day 22 to day 48 post infection and total intestinal worm burdens were determined at slaughter. Blood was continuously collected from the mesenteric, portal and hepatic veins, the mesenteric artery and the vena cava in 2-hour aliquots. Plasma was harvested and AA and metabolite concentrations measured and the specific radioactivity (SRA) and isotopic enrichment (IE) of valine and cysteine were determined. After the completion of blood sampling, but while the [3, 4-3H]-valine infusate was still being administered, the sheep were euthanased by an intravenous overdose of sodium pentobarbitone. Tissue samples were rapidly collected from the sheep in the following order: skin, muscle (biceps femoris), liver, duodenum, ileum, spleen, mesenteric lymph nodes and thymus. Digesta was also sampled from the abomasum and ileum after slaughter in order for the apparent absorption of AA to be determined. The results from Experiment One (Lucerne-fed lambs) suggest that there is no re-partitioning of AA from the posterior hind limbs to the GIT and liver during an established infection- The changes that occurred within the PDV suggests that an established parasitic infection may trigger a localised alteration in AA metabolism and/or protein turnover without significantly changing the metabolism of AA and proteins in tissues peripheral to the TSP tissues and impacting negatively on the growth of the parasitised lambs. In Experiment Two (Sulla-fed lambs) a reduction in feed intake was likely to be the reason for the alterations in the first pass metabolism of AA in the TSP tissues due to the decreased apparent AA absorption by the MDV observed in the parasitised lambs. However, the results from this experiment are in agreement with those from Experiment One confirming that there is no increase in partitioning of AA from the hind limbs to the GIT or liver during an established parasite infection. Although a statistical comparison cannot be made between the data in Experiment One (Lucerne-fed) and Experiment Two (Sulla-fed), it appears that the beneficial effects of feeding CT during a parasitic infection is due to the reduction in larval establishment in the GIT of the lamb, rather than increased AA availability. In conclusion, an established infection imposes no measurable metabolic cost on the lamb, when feed intake is not reduced. When feed intake is reduced, there is no detectable mobilisation of protein from the hind limb. Therefore, localised or other sources of AA and/or energy substrates may be utilised.