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Footrot is a contagious hoof disease of ruminants. It is endemic in New Zealand and throughout sheep and goat farming regions of the world. The disease results from a mixed bacterial infection, but the essential agent is Dichelobacter nodosus, a Gram-negative, anaerobic bacterium that possesses type-IV fimbriae on its surface. Genetic variation in the fimbriae of D. nodosus was investigated in this study. Using the polymerase chain reaction (PCR), the variable region of the gene encoding the fimbrial subunit (fimA) was amplified from bacterial DNA extracted from footrot lesions. Different fimA amplimers were differentiated by single-strand conformation polymorphism (SSCP) analysis. In conjunction with DNA sequencing, 15 unique sequences of D. nodosus fimA were obtained from 14 footrot samples taken from 6 farming regions throughout New Zealand. When these sequences were compared to fimA of known serogroups, it revealed that there were at least 15 D. nodosus strains, representing 8 serogroups, present on New Zealand farms. The predominant serogroup was B which contained 6 strains, followed by serogroups F, H and G. No strains from serogroups D and I were detected in this investigation. Twelve out of the 15 New Zealand D. nodosus strains had fimbriae different to those previously reported and the presence of multiple strains on a single hoof was common (86% of samples). The fimA sequences from the 12 D. nodosus strains incorporated into the footrot vaccine currently available in New Zealand were determined. A primer set targeting the relatively conserved fimA regions and based on the published sequence of serogroup M Nepalese isolates (designated M-Nep), failed to amplify fimA from the vaccine serotype M strain (designated as M-SPAHL). When the downstream primer was substituted with a primer that was specific for other serogroups of D. nodosus, the fimA gene was successfully amplified. Cloning followed by DNA sequencing, revealed that M-SPAHL fimA was different to M-Nep fimA. The predicted amino acid sequence of M-SPAHL fimA did not show homology to any known serogroups or serotypes. The most similar sequence was from serotype F1, and not M-Nep. The sequence difference between M-SPAHL and M-Nep was larger than that expected within a serogroup. The consequences of serological relatedness and sequence dissimilarity are discussed. Only eight of the 15 New Zealand field strains had fimbriae identical to those of the vaccine strains, while the remaining seven strains possessed different fimbriae. In addition, the vaccine contained two more D. nodosus strains, representing two sera groups, that were not found on the New Zealand farms investigated in this study. This may, to some extent, explain why the current footrot vaccine is at times less efficient in New Zealand. Another 17 footrot samples were screened for new or additional D. nodosus strains. Two PCR amplimers (designated X and Y) derived from footrot samples generated SSCP patterns different to those of previously identified strains. DNA sequencing revealed that these two fragments possessed novel sequences. The upstream of X (nt 1-183) was identical to serotype M1 while its downstream (nt 223-414) was identical to serotype F1; the upstream of Y (nt 1-116) was identical to serotype E1 whereas its downstream (nt 148-423) was identical to serotype F1. A 14-mer sequence consisting of two partially overlapping Chi-like sequences, 5'-GCTGGTGCTGGTGA-3', was also found in these fragments. Two primer sets with the downstream primer specific for serotype Fl and the upstream primer specific for serotype M1 or E1, produced PCR products of the expected sizes from the footrot samples from which fragments X and Y were isolated, respectively. These primer sets did not appear to amplify artificially mixed genomic DNA from serotypes M1 and F1 or E1 and F1. However, when the reactions were re-amplified, PCR recombination artefacts were observed, suggesting that PCR recombination does occur, but at a low frequency. It therefore seems more likely that fragments X and Y reflect genuine fimA sequences of D. nodosus which have resulted from in vivo DNA recombination, than from a PCR recombination artifact. The genetic capability for recombination at the fimbrial subunit locus may therefore endow D. nodosus with the ability to alter its antigenic appearance. D. nodosus strains present in footrot lesions can be genotyped using a PCR-SSCP/sequencing technique. However, this typing technique requires cloning and screening of D. nodosus fimA sequences, which is both laborious and costly. A rapid molecular typing system for D. nodosus was therefore developed in this study. A close examination of available D. nodosus fimA sequences revealed regions that appear to be specific for serogroups and serotypes. These regions were used to design a panel of sequence-specific oligonucleotide probes (SSOPs), and a rapid and accurate D. nodosus typing system using PCR and reverse dot-blot hybridisation (PCR/oligotyping) was subsequently developed. The variable region of D. nodosus fimA, amplified and labelled with digoxigenin (DIG) in a single multiplex PCR amplification, was hybridised to a panel of group- and type-specific, poly-dT tailed oligonucleotides that were immobilised on a nylon membrane strip. A mixture of positive control poly-dT tailed oligonucleotides was also included on the membrane. After hybridisation the membrane was washed to a defined specificity, and DIG-labelled fragments that had hybridised were detected. The specificity of the oligonucleotides was verified by the lack of cross-reactivity with D. nodosus fimA sequences that had a single base difference. DNA from 14 footrot samples previously genotyped by PCR-SSCP/sequencing, was assayed using the PCR/oligotyping technique. All types of D. nodosus which had been detected previously with a PCR-SSCP/sequencing method were detected by this procedure. However, for three of the 14 footrot samples, PCR/oligotyping detected additional types of D. nodosus. Further PCR amplification using type-specific primers, confirmed that these types were present in the original footrot samples. These results indicate that PCR/oligotyping is a specific, accurate, and useful tool for typing footrot samples. In combination with a rapid DNA extraction protocol, D. nodosus present in a footrot sample can be accurately genotyped in less than two days. Individual animals from the same farm, or the same paddock, were often infected by different strains of D. nodosus. This suggests a host role in mediating footrot infection, or that the interaction between the pathogen and the host is important. In order to better understand the interaction between the bacterium and the host, two polymorphic ovine class II MHC genes DQA1 and DQA2, which have been previously shown to be important in footrot infection, were also investigated in this study. PCR-SSCP/sequencing analysis of the DQA1 locus revealed ten unique ovine DQA1 sequences, with five of them being newly identified. This increases the number of known ovine DQA1 alleles from 8 to 13 (including a null allele), implying a high level of polymorphism at the ovine DQA1 locus. D. nodosus present on 20 footrot infected sheep from the same flock were genotyped, together with the ovine DQA1 and DQA2 genotypes of their hosts. Preliminary results showed that sheep with the same DQA1 and DQA2 genotypes tended to be infected by similar types of D. nodosus. Different types of D. nodosus were generally found on sheep with different genotypes at either the DQA1 or the DQA2 locus. This suggests the diversity in D. nodosus infection may be associated with the heterogeneity in the host MHC. However, as only a small number of animals from the same sire were analysed, further investigation is needed to gain a better understanding of the interaction between D. nodosus and the host MHC.

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>