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.

A reduction in voluntary feed intake is a major factor in the lost productivity of grazing lambs infected by gastrointestinal parasites yet the mechanisms involved are poorly understood. Potential pathways involved in parasite-induced feed intake depression were investigated in lambs with minimal previous exposure to parasites and artificially infected by the small intestinal parasite Trichostrongylus colubriformis. Six in vivo experiments were conducted on lambs housed in individual pens or metabolism crates with similar feeding and experimental procedures. In Experiment 1 (Chapter 4) the effect of T. colubriformis infection on short term feed intake in lambs and of some pharmacological agents on feed intake depression were investigated. Prior to and for the duration of infection, lambs were fed once per day and feed intake recorded at regular intervals over the day (8 h). Following the onset of feed intake depression in the infected group (9 weeks after commencing dosing), all animals were treated with an analgesic (codeine phosphate per os), an anti-inflammatory agent (indomethacin per os), a CCK antagonist (L364-718 by subcutaneous injection) or saline (control) in a replicated Latin square design (n = 8). Although the pattern of feed consumption was similar in infected and non-infected lambs, average daily intake was reduced 32 % and short term intake (recorded at 10 minute intervals for the first hour of feeding, 15 minute intervals for the second hour and hourly for the next 6 hours of feeding) reduced 40 % by infection. This identified the key component by which intake was depressed and enabled the use of a short term intake model and short duration of action compounds to identify the pathways involved in intake depression in this sequence of experiments. None of the pharmacological treatments increased intake in the infected group. These results suggest a reduction in the rate of consumption due to reduced hunger signals, rather than change of meal eating patterns, is the major cause of feed intake depression. Specific conclusions about the pathways investigated using the pharmacological agents could not be obtained. Experiment 2 (Chapter 5) was designed to investigate the roles of pain and osmolality on feed intake depression. Digesta samples collected prior to and during parasite infection and before and after feeding had similar osmolalities (240-260 mosmol/l) which indicated that feeding or infection had no effect on osmolality of digesta. Following the onset of feed intake depression in infected animals, all animals were treated in a Latin square design (n = 4) with no treatment, saline, local anaesthetic (xylocaine) or analgesic (codeine phosphate) solution 15 minutes before feeding, by slow injection into the duodenum. There was no effect of these treatments on food intake. In the second part of the experiment, hyperosmotic solutions (mannitol and NaCI) markedly depressed short term intake in non-infected animals, suggesting a role for osmoreceptors in intake regulation. However these effects were not blocked by local anaesthetic so the depressed intake may have resulted from generalised malaise rather than from specific osmoreceptor effects. In Experiment 3 (Chapter 6) the role of peripheral CCK on intake depression was examined by a dose-response study utilising the CCK antagonist, loxiglumide. Intravenous injection of 5, 10 or 20 mg/kg LW of loxiglumide to infected lambs 10-15 minutes before feeding (n = 6) had no effect on feed intake at any of the dose levels. In experiment 4 (Chapter 7) loxiglumide was infused intravenously for 10 minutes (30 mg/kg/h) before feeding and for the first 2 h (10 mg/kg/h) after feed was offered to minimise any effect of the rate of clearance of loxiglumide on the lack of feed intake response. As well, the rate of marker disappearance from the abomasum was recorded in both infected and non-infected animals. Continuous infusion of loxiglumide did not attenuate parasite induced intake depression nor did it have any effect on abomasal emptying. Abomasal volume was reduced by infection (66.3 vs 162 ml) as was the fractional outflow rate (2.2 vs 2.8 ml/min) but these differences were accounted for by the lower level of feed intake in the infected animals. In Experiment 5 (Chapter 8) brotizolam, a benzodiazepine appetite stimulant, thought to act on the hypothalamus, was administered in a dose-response study to infected and non-infected animals (n = 4) immediately prior to feeding or following termination of the first meal (45 minutes after feeding) and the feed intake response recorded. Brotizolam elevated both the short term (0-0.75 h), daily (22 h) intake and all time intervals in the first 5 h after feeding in infected and non-infected animals when administered after the first meal but when administered prior to feeding elevated intake only over the first 6 h of feeding. In both cases the magnitude of the response was greater in infected animals than in non-infected animals. Brotizolam appeared to increase the rate of eating without having a major impact on meal eating patterns when administered before feeding. Where administration was after the first meal, the effect was due to an "extra" meal being consumed. These findings showed that infected animals can respond to central stimulators of intake although the mechanism of the response is not known. Opioids were implicated in intake depression as the rate of intake rather than meal patterns appeared to be the major parameter depressed under parasitism. This was examined in experiment 6 (Chapter 9) where animals (n = 6) were fasted for 26 h or not fasted, then treated with saline (control), brotizolam (intake stimulant) or naloxone (opioid antagonist) immediately prior to feeding. Fasting stimulated feed intake in the short term (100 % increase in 75 min) and over the day (12 % increase) in both infected and non-infected animals. Following fasting, infected animals ate a similar amount of feed to the non-infected, fasted animals and more than the non-infected, non-fasted animals. The signals resulting from a one day fast were sufficient in the short term to override parasite induced mechanisms causing feed intake depression. Naloxone suppressed the intake stimulatory effects of a 26 h fast in both infected and non-infected animals, which supports a role for endogenous opioids as hunger signals. Where animals were not fasted, naloxone reduced intake only in the non-infected animals which suggested endogenous opioid levels may be lower in infected animals than in non-infected animals. In the final experiment (Experiment 7, Chapter 10) the role of central hunger and satiety mechanism were investigated. Infected and non-infected animals (n = 6) were treated with naloxone or saline by intravenous injection, or saline and met-enkephalinamide (an opioid analogue) by intracerebral infusion, or naloxone and the opioid analogue simultaneously to investigate the role of central opioids in feed intake depression. To determine the role of CCK induced satiety signals on feed intake at a central level, loxiglumide and CCK were infused separately and in combination for 30 minutes prior to feeding and for the first 60 minutes of feed on offer, into a lateral cerebral ventricle of the brain of infected and control animals (n = 6). The opioid analogue tended to increase intake in infected animals but the effect was not significant probably because the dose used was too low to elicit a response in sheep. Naloxone depressed intake only in the infected animals, which conflicted with the results of Experiment 4. As a consequence these results were inconclusive because of the single low dose of opioid analogue used and the conflicting naloxone responses. CCK alone depressed intake by 39-52 % only in infected animals and this effect of the 90 minute infusion was evident over the 8 h short term recording period. Loxiglumide attenuated the feed intake depressive effects of CCK in the infected animals to the extent that intake was elevated above control levels. Loxiglumide alone was an intake stimulant in both infected and non-infected animals. Intake was increased over the entire 8 h but mostly in the second hour when intake was increased by 188 % in infected animals and by 16 % in the non-infected animals and resulted in almost continuous eating. These results showed loxiglumide will temporarily block the effect of parasite infection on feed intake in sheep when administered centrally and the fact that it blocked the effects of exogenous CCK on intake indicated that the effect is mediated via CCK receptors. In conclusion GIT parasite infection reduced both short term and daily feed intake apparently by a change in rate of intake rather than any alteration in meal patterns. It was further suggested that anyone of a number of potential peripheral pathways, including changes to osmolality, gut emptying, pain and inflammation of the gut, alone is not involved in anorexia in sofar as the compounds used could block these factors and the results support the idea that intake depression is mediated via a central mechanism. Intake in infected animals responded to a much greater extent when fasting, i.c.v. loxiglumide or brotizolam were employed. Feed intake thus appears to be regulated through the same mechanisms in infected and non-infected animals. The results from compounds affecting the central mechanism suggest central CCK receptors are important in parasite induced anorexia, possibly by changing the onset of satiety or by interacting with endogenous opioids to reduce the rate of feed intake. Secondly reduced endogenous opioids may be causing the reduction in the rate of feed consumption alone or as a result of other interactions. It was concluded that intake in parasitised animals could be increased to that of control animals by employing procedures and compounds thought to act on the hypothalamus.

<p>Bovine respiratory disease (BRD) is an ongoing health and economic issue in the dairy and beef cattle industry. Also, there are multiple risk factors that make an animal susceptible to BRD and it's diagnosis and treatment is a challenge for producers. Four bacterial species, <em>Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, </em>and<em> Mycoplasma bovis</em> have been associated with BRD mortalities. Hence, this study aims to characterize the cattle nasal microbiome as a potential additional diagnostic method to identify animals suspected to have a lung infection. Quantitative PCR and 16S rRNA gene sequencing were used to determine the bacterial load of these four bacterial pathogens in the nasal microbiome of apparently healthy (N=75) and (N=58) affected by BRD Holstein steers. We then sought to identify a value or equation that could be used to discriminate between BRD and healthy animals using a Linear Discriminant Model (LDA). Additionally, co-occurrence between commensal bacterial and BRD-pathogens were also identified. Cattle diagnosed with BRD presented lower richness, evenness and phylogenetic diversity than healthy pen-mates. Bacterial species and genera <em>Truperella pyrogenes </em>and <em>Bibersteina</em> were increased in the BRD group, and the species <em>Mycoplasma bovirhinis</em> and <em>Clostridium sensu stricto</em> increased in the healthy group. Prevalence of <em>H. somni </em>(98%)<em> </em>and <em>P. multocida </em>(97%) were the highest regardless of disease diagnosis in all the samples. Prevalence of <em>M. haemolytica </em>(81 vs. 61%) and<em> M. bovis </em>(74 vs. 50.7%) were higher in the BRD group. The bacterial density of <em>M. haemolytica</em> and<em> M. bovis </em>was also higher in the BRD group, whereas <em>Histophilus somni</em> was lower in the BRD group. Five different models were tested using LDA, and one model produced a sensitivity and specificity of 60% and 81% agreement with diagnosis based on animal symptoms. Co-occurrence analysis demonstrated that the nasal microbiome members are more likely to interact with each other than associations between BRD-pathogens and nasal microbiome members. This study offers insight into the BRD-pathogens prevalence and difference in nasal microbiome between healthy and BRD animals and provides a potential platform for future studies and potential pen-side diagnostic testing.</p>

Understanding the complex nature of social-ecological cascades, or chain reactions of events that lead to widespread change in a system, is crucial for navigating the challenges they present. Emerging pests and pathogens, such as the fall armyworm, provide an opportunity to study these cascades in greater detail. I use topic modeling of digital news articles to investigate the potential social-ecological cascades associated with the ongoing fall armyworm invasion of multiple geographic regions. My findings reveal regional thematic shifts in the popular news media discourse surrounding the fall armyworm invasion. Notably, in the discourse surrounding Oceania, I observed a pronounced focus on invasion preparation, a theme significantly more emphasized compared to regions like Africa and Asia. These regional variations shed light on some of the localized priorities in addressing this invasive species. By highlighting the significance of employing comprehensive case studies of emerging pests and pathogens, this research underscores the need for more in- depth analyses of social-ecological cascades to better manage and mitigate their impacts.

<p>Thyroid hormone is essential for regulating adult metabolism and proper fetal development. Under normal conditions, maternal and fetal thyroid hormones are subject to metabolism at the placenta and within fetal tissues through deiodination and sulfation to regulate fetal exposure to the bioactive hormone. Disruptions of the thyroid hormone system can result in non-thyroidal illness syndrome (NTIS), which is classified as the dysregulation of thyroid hormone homeostasis. The exact cause of the alterations in circulating thyroid hormone levels during NTIS is not well- known. In comparison, hypothyroidism results from the absence of thyroid hormone production and presents as low thyroid hormone levels.</p> <p>Porcine reproductive and respiratory syndrome virus (PRRSV) crosses the late gestation placenta and causes suppression of circulating maternal and fetal thyroid hormone. Chapter 2 investigates the potential role of thyroid hormone metabolism in this disruption. Pregnant gilts were challenged with PRRSV2 (n=22) or sham inoculated (n=5) at gestation day 85. Samples were collected on day 106, and viral load was assessed in fetal serum and thymus. From the entire fetal population, three distinct subsets of fetuses representing biological extremes were identified, including uninfected with no detectable viral load (UNIF), high viral load viable (HV-VIA), or high viral load with severe meconium staining (HV-MEC). In addition, control fetuses from sham inoculated gilts (CON) were used as a reference group. Samples of fetal liver, kidney, and the corresponding fetal placenta and maternal endometrium for n=10 fetuses per group were then used to evaluate gene expression. A total of 11 genes associated with thyroid hormone metabolism including deiodinases (DIO1,2,3), sulfotransferases (SULT1A3,1B1,1C2,1E1,2A1), sulfatase (STS), and solute carriers (SLC16A2,16A10) were quantified using absolute quantification qPCR. Evidence of fetal decompensation was observed within the high viral fetuses in the form of decreased DIO1 expression within the fetal liver and increased DIO3 expression in both components of the placenta. Circulating levels of T4 and inactive thyroid hormone metabolites, reverse-triiodothyronine (rT3) and two diiodothyronines (3,5-T2 and 3,3’-T2), were measured in fetal serum. While T4 was depressed, no change was observed in circulating rT3 levels, and neither T2 metabolite reached the lower detection limit. This may suggest that alterations in thyroid hormone metabolism generate a localized effect on hormone metabolites in the respective tissues.</p> <p>Alternatively, the low levels of available T3 and T4 limit the production of downstream metabolites to be found in serum.</p> <p>The cause-and-effect relationship between PRRSV infection, fetal thyroid disruption, and the effects on fetal thyroid hormone metabolism are unclear. Therefore, Chapter 3 developed a non-pathogenic model using methimazole (MMI) to induce hypothyroidism in the late gestation fetus and evaluate the impact on fetal development and thyroid hormone metabolism. Pregnant gilts were either treated with oral methimazole or equivalent sham from gestation day 85-106 (n=4/group), followed by classification of all fetuses as live, live but meconium stained, or dead. Fetuses exposed to MMI in-utero were notably hypothyroid with significantly suppressed serum T3 and T4 and histological evidence of goiter. Surprisingly, fetuses from MMI-treated dams were substantially larger but appeared to exhibit non-allometric growth with an increase in girth but not length. The liver, kidney, and the corresponding fetal placenta and maternal endometrium were collected from a subset of 16 fetuses per group to evaluate the relative expression of five genes associated with thyroid hormone metabolism, including three deiodinases and two solute carriers known to transport thyroid hormone. Compensatory transcription of DIO3 was observed in all tissues evaluated, suggesting increased vertical transfer of maternal thyroid hormone at the placenta and decreased breakdown of thyroid hormone within fetal organs.</p> <p>The evaluation of thyroid hormone metabolism within the fetus and within the placenta has allowed us to differentiate suppressed thyroid hormone levels of the pig fetus under pathogenic and non-pathogenic conditions. In the context of PRRSV infection, the observed decompensation of thyroid hormone metabolism would further exacerbate the hypothyroid state and is therefore consistent with NTIS. In contrast, fetuses with induced thyroid hormone suppression following maternal exposure to MMI showed compensatory thyroid hormone metabolism in the same tissues. This indicates true hypothyroidism and clearly demonstrates a fetal capacity to respond to such endocrine disruption.</p>

The series of experiments described in this thesis were designed to investigate the role of suckling or late weaning in the response of young lambs to nematode infection. All experiments were conducted outdoors with grazing animals and no supplementation but for suckled groups of lambs whose counterparts were weaned to ryegrass – white clover swards. The parasite of interest was mainly Teladorsagia circumcincta solely but with mixed infection of Trichostrongylus colubriformis in one instance. In Chapter 3 (first experiment), the hypothesis that milk per se may have a direct effect on nematode development, rather than an indirect effect through enhancement of host immunity by superior nutrient supply was tested. Sixty, twinborn lambs were used, allocated to one of eight groups formed by either dosing lambs from 42 days of age or not with the equivalent of 1000 or 250 L₃ T. circumcincta larvae d⁻¹ until five days before necropsy, while a twin was either weaned at 39 days of age, suckled as single or twin until necropsy on day 84. The possibility that weaning one of a twin set onto pasture in close proximity to the ewe would cause abnormal ewe and lamb behaviour was tested by replicating the work in twins maintained as twins but in which one twin received equivalent of 250 and the other 1000 L₃ T. circumcincta larvae d⁻¹. This showed no abnormal ewe nursing or lamb suckling behaviour as a result of weaning a twin in a set. Relatively low faecal egg counts (FEC) and a two to three fold lower worm burdens suggest suckling could reduce larval establishment. Inability to detect peripheral titres of immunoglobulins supports this conclusion. An intra worm-population regulation of T. circumcincta, indicated by a pattern of greater egg-laying by a numerically smaller but physiologically better developed nematode population in suckled lambs measured in eggs 'in utero' and worm length made interpretation of FEC difficult. Suckling significantly improved weight gain and carcass weights, but early weaning did not reduce resilience to infection. In Chapter 4 (second experiment), 40 pairs of twin lambs, average age of 39 days, were either infected with the equivalent of 1000 L₃ T. circumcincta larvae d⁻¹ or not, while one twin was weaned and the other allowed to continue suckling. Necropsy was carried out on groups of five and six lambs from each of the uninfected and infected treatments, respectively, at mean age of 84, 112, and on six lambs from each group at 140 days of age. This serial slaughter allowed further confirmation of the hypothesis in Chapter 3 but also investigated the long-term effect of suckling on resistance or resilience of lambs at the trial when immune responses were anticipated to be developing. An in vitro direct larval challenge (IVDC) study, to monitor larval establishment, was carried out on tissue explants from necropsied lambs. Suckled lambs consistently showed lower FEC (P < 0.05) and worm burdens (P < 0.05) at every phase of the trial. Within the infected groups, % in vitro larval rejection suggested earlier immune responses in the weaned lambs by day 84, which was not consistent with lower worm burdens in suckled lambs but appeared similar in the subsequent necropsies. Lambs continued to show better growth due to suckling while weaning did not reduce the resilience of lambs confirming observations in Chapter 3. The immunoglobulin profile suggested the commencement of immune responses in lambs from the period after the 84th day necropsy, with significantly greater (P < 0.01) IgA titre in the infected groups, and the suckled lambs towards the end of the trial on day 140. A vaccinating effect of early exposure to parasites was coincidentally revealed as a result of unintentional pasture larval contamination, seen in suckled non-infected lambs shedding fewer eggs and harbouring fewer worms during the later necropsies compared with their weaned non-infected counterparts. In Chapter 5 (third trial), 93 pairs of twin lambs, 47 pairs of which received a vaccinating mixed infection of T. circumcincta and T. colubriformis larvae (60 L₃ / kg W / d) at ratio 40:60, respectively during the period 36 – 103 days of age, were either weaned early on day 51 or later on day 108. All lambs were drenched on day 108 and groups received challenge infections from day 116, at same rate with the vaccinating infection, or not, which ceased five days before respective necropsies. Necropsies were carried out on selected lambs on days 108, 184 and 218. The direct effect of milk on larval establishment appeared to feature only in the T. circumcincta populations on slaughter day 108. The long-term benefit of late weaning for development of resistance was conditional on lambs receiving the vaccinating infection, and appeared to be more pronounced in the small intestine, reflected by a greater reduction of T. colubriformis populations in that organ than of T. circumcincta populations in the abomasum. A negative consequence of enhanced immune response was the suggestion of an increased metabolic cost in reduced performance of lambs. In conclusion, the work provides support to the hypotheses that: (a.) suckling may reduce the establishment of nematode larvae through the direct effect of milk, (b.) may enhance rapid development of host immunity to infection, and (c.) it further suggests that lack of larval experience during suckling may have long term negative implications for host resistance. Finally, it suggests that milk may play little role in the enhancement of host resilience to infection and, on the contrary, that additional metabolic cost may be associated with a more rapid development of immunity resulting from larval challenge while suckling.