This study was conducted to evaluate the effect of season on reproductive parameters in cattle in the temperate climate of the UK. In the first study, reproductive fertility data were collected from a local dairy herd. The results revealed that cows born in autumn were inseminated at an earlier age (P < 0.05) and calved earlier (P < 0.001) than spring and summer born animals. In addition, the conception rate within 90 days after calving was higher (P < 0.05) in autumn calving animals. Conception rate was higher (P < 0.05) when insemination was performed at a temperature range from 7 to 15°C compared with < 7 and >15°C and a temperature humidity index (THI) range from 40 to 59 compared with >60 units (10 days before and 21 days after insemination). In the second study, ovarian tissues were collected from a local abattoir to investigate the effect of season on follicular populations, corpus luteum (CL) development and incidence of multiple ovulations. There were no effects of season on antral follicle count. However, individual and total CL weight was heavier in the autumn. Additionally, season influenced multiple ovulations with a higher incidence (P < 0.05) in summer and autumn compared to winter and spring. The number of follicles >7mm in cows with multiple CLs was higher (P < 0.05) than cows with a single CL. The individual CL weight was heavier in single ovulation cows. However, the total luteal tissue weight and total progesterone (P4) content of luteal tissue was higher in cows with multiple ovulations. The third study investigated the effects of culturing granulosa cells (GCs) under low (5%; physiological oxygen (O2)) conditions rather than traditional culture (20%; atmospheric O2) systems. Granulosa cells from antral follicles were cultured in fibronectin coated plates in M199 for up to 144 hour (h) under physiological (5%) and atmospheric (20%) O2 tension. Melatonin was added at one of four concentrations (0, 20, 200, 2000 pg/ml). The number of viable GCs was greater (P < 0.05) under 5% O2 than 20% O2. Reactive oxygen species (ROS) generation was similar under both physiological and atmospheric O2, but was reduced (P < 0.05) by treatment with melatonin. Oestrogen concentration (P < 0.001) and aromatase activity (P < 0.014) were also influenced by O2 tension in a time dependent manner. Both oestradiol (E2) production and aromatase enzyme activity were maintained for up to 144 h of culture under 5% O2 conditions. Progesterone production was increased under 20% O2 compared with 5% O2 (P < 0.05). Additionally, the expression of hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 (HSD3B1) mRNA increased (P < 0.05) with time under 20% O2, but remained unchanged at 5% O2. Haemoglobin subunit alpha 1 (HBA) transcript was increased (P < 0.05) under 5% O2 levels. The final study quantified the effect of temperature and melatonin on GC function. Cells were cultured for up to 144 h under 5% O2 tension. Treatments commenced after 48 h of culture and consisted of two incubation temperatures (37.5 vs 40.0°C) and four melatonin treatments. Melatonin increased cell number at high temperature (40.0°C). However, BCL2-associated X protein (BAX) mRNA expression was greater (P < 0.05) in GCs cultured at 40.0°C than at 37.5°C by 144 h. Culture temperature did not affect ROS, but melatonin reduced (P < 0.001) generation of ROS. Oestradiol production increased with time (P < 0.001) and was not affected by temperature. In contrast, high temperature reduced P4 production (P < 0.001) at 144 h of culture. Similarly, the effect of melatonin treatment depended on temperature; melatonin increased P4 production at 37.5C, while reducing P4 at 40.0C. Temperature increased acetylserotonin O-methyltransferase (ASMT) mRNA expression (P < 0.05) though there was no significant effect of temperature and melatonin on tumour protein p53 (P53), HSD3B1, superoxide dismutase (SOD1 and SOD2), HBA and heat shock protein family A (Hsp70) member 1A (HSPA1A) gene expression. The results of this thesis contribute to our understanding of the effects of season on ovarian function and seasonal variation in cattle fertility particular in temperate climate regions where season influenced puberty, conception rate, incidence of multiple ovulations and CL development. In in vitro studies, low O2 (5%) enhance cell proliferation, reduced luteinisation and altered steroidogenesis as well as increasing the expression of HBA mRNA. Culture at higher temperature reduced P4 production and increased apoptotic mRNA while addition of melatonin reduced ROS generation and influenced P4 production. This new approach to culture could offer a valuable system for future investigation of the physiological function of cells in vitro.

Herpesviruses are ubiquitous and are found worldwide, most animal species can be infected with multiple herpesviruses. Some cause clinical disease and others remain symptomatic throughout life. Herpesviruses are found in both captive and wild animals including Asian elephants (Elephas maximus). Elephant Endothelioltropic Herpesvirus (EEHV) has been reported in both captive and wild Asian elephants, with a number of cases being reported in North America, Europe and Asia. It has been suggested that EEHV is associated with haemorrhagic disease, which has been attributed to a number of Asian elephant deaths, affecting mostly juveniles and calves. Clinical signs can vary from weight loss, lethargy, depression, cyanosis of the tongue and sudden death. Molecular testing using qPCR has enabled the detection of individual variants of EEHV, this thesis investigates the EEHV1 variant. EEHV1 has been highlighted as the variant that is more frequently associated with deaths. This thesis includes five studies investigating different aspects of EEHV. Including, the relationship between pregnancy and EEHV viral shedding, the use of an amended human protocol for culturing endothelial cells, EEHV tissue tropism, a potential genetic or familial link between EEHV associated deaths and the detection of potential co-pathogens. The main findings from this thesis include: 1) the use of a longitudinal study investigating a potential link between the physiological stress of pregnancy and EEHV viral shedding. This study suggested there was no link between pregnancy and EEHV viral shedding however other stressors may be involved. 2) Using an amended human umbilical vein endothelial cell protocol, the culture of Asian elephant endothelial cells was successful. The cells from this study may be used in subsequent drug testing and vaccine development. 3) Quantitative PCR was used to determine EEHV1 tropism in tissues from two deaths associated with the virus. Tropism appeared to be for the heart and liver. 4) This thesis provides results from a preliminary study into a potential link between EEHV associated deaths. The data from an Asian elephant genogram shows there is the possibility of a genetic or familial link, which requires further investigation. 5) A number of tissues from deaths associated with EEHV and or death from other causes were investigated for the presence of potential co-pathogens, including the presence of encephalomyocarditis virus (EMCV), using microarray technology. The results indicated there were no co-pathogens present in the tissues. This thesis adds to the current published data, and includes the first known preliminary study investigating a potential genetic link between elephant deaths due to EEHV.

Veterinary communication is a core clinical skill and is believed to have a positive impact on client satisfaction, trust and adherence to patient management recommendations. Veterinary communication skills training has therefore been incorporated into veterinary undergraduate and postgraduate education. This thesis focuses on the topic of veterinary communication and comprises two studies. The aim of the first study was to gain a current understanding of the state, adequacy, and relevance of veterinary communication skills and training in the United Kingdom (UK) and United States of America (USA). This was done by conducting a survey of a sample of veterinary surgeons in each country about communication skills and training in the context of a veterinary consultation. A quantitative and qualitative analysis of the data from the survey was undertaken. Key findings were that 98 percent of respondents (1,708/1,748) believed communication skills to be equal in importance to, or more important than, clinical knowledge, whereas only 40 percent (705/1,759) were interested in further communication skills training. Barriers to participation in communication CPD appear to include lack of time and/or employer support, and a belief among some practitioners that communication training could no longer benefit them or was inadequately matched to real-world communication challenges. The aim of the second study was to assess several factors that may impact on communication dynamics during a consultation. Fifty-five video-recorded veterinary consultations in the UK and USA were analysed as follows: 1. The complexity of the consultations was assessed using a tool previously validated for recording information via direct observation of consultations. Elements recorded included details on the patient(s) and reasons for the visit, problems investigated, body systems involved, tests performed, diagnoses, and outcomes. Categorical data statistics were recorded as whole numbers and percentages and Chi-Square calculations were done to measure differences between UK and USA data. Continuous data statistics were recorded as median, range, and interquartile ratio (IQR) and Mann-Whitney U tests were performed to measure UK versus USA differences. (Continuous data for the remaining elements in the study were analysed in the same manner.) Key findings were that consultations were complex, involving multiple problems, body systems, tests, diagnoses, and outcomes. 2. Consultations were analysed for alignment with two consultation models, the Calgary-Cambridge Model for Veterinary Consultations (GCCVM) and the Patient-centred Clinical Method, by coding elements of each consultation model in the consultation transcripts. The frequency and proportion of model elements demonstrated in each consultation were assessed, as was the alignment of the consultations to each model, defined by the percent of possible model elements demonstrated in each consultation. There was 86.67% alignment with the GCCVM and 62.50% alignment with the Patient-centred Clinical Method. Veterinary surgeons in the study spent more time gathering information and explaining than empathising or soliciting client input. 3. Consultations were also analysed for dominance of medical versus lifeworld dialogue using the Mishler Discourse Analysis, and medical dialogue dominated over lifeworld dialogue (65.62% to 34.48%). 4. Client/relationship centredness was evaluated using a novel application of a tool in veterinary communication research, the Verona Patient-centred Communication Evaluation Scale (VR-COPE). Results suggested a relatively high degree of client/relationship centredness (a median score of 76/100), though with somewhat lower scores for elements related to client emotions and the veterinary surgeon responding to them. 5. Client satisfaction was evaluated using the previously validated Client Satisfaction Quotient (CSQ). There was a high degree of satisfaction expressed by clients (median score of 94/114), though average scores were slightly lower for topics related to cost and expression of interest in the client’s opinion. Limitations of the research included the low response rate of US veterinary surgeons to the survey, the small, convenience-based sample used in the consultation study, the reliance on the researcher for maintaining quality and validity, and the scoring of client/relationship-centredness with a tool that heretofore had not been used in veterinary medicine and was not subjected to extensive inter-rater variability testing. The findings in this thesis support the contention that communication skills are important for veterinary practitioners. The work also highlights the need for making communication training a priority in undergraduate veterinary education and an accessible and relevant component of postgraduate CPD. The findings also suggest a need to equip veterinary students and practitioners for communication during consultations that are relatively complex with highly iterative flow between topics, as well as for addressing emotions and inviting input of clients. Elements of the GCCVM and other models may help provide a framework for training in these competencies.

In carnivorous fish farming industry, there are progressive increase demands for the finite resource of fish meal. A potential alternative to fish meal is to use legume meals which are free of enzyme inhibitors. In selected underutilised legumes the most effective processing method for eliminating trypsin (TIA), chymotrypsin (CIA) and alpha-amylase (AIA) inhibitors, without affecting the crude protein content, was investigated. These methods included soaking (S), wet heating (W), autoclaving (A) and dry freezing (D). No single method was effective at removing all the inhibitors. In all legumes tested, the combined processing methods which involved A were most effective in reducing CIA and AIA (p < 0.05), but not TIA. However, in adzuki bean both TIA and CIA were reduced by the D+A combined method (p < 0.05), whereas AIA of soybean and adzuki bean was decreased by combined methods of S+A (84.7 % and 99.3 % reduction respectively, p < 0.05) or A+D (99.1 % and 72.6 % reduction respectively, p < 0.05). All the processing methods retained 86.5 – 90.5 % of crude protein. Replacement of 10 % (w/w) of fish meal with D+A treated legume meal (either bambara groundnut or adzuki bean) for 28 days showed no significant difference in growth performance or inflammatory effects in Danio rerio or Lates calcarifer. Compared to Lates calcarifer given feed containing unprocessed adzuki bean meal, those on feed containing processed adzuki bean meal had increased hepatic gene expression of alanine aminotransferase (p < 0.01), indicating an enhanced ability to utilise amino acids. The project identified specific food processing methods which are effective at removing enzyme inhibitors in legumes, thereby facilitating the application of legumes as aquafeed ingredients. Future studies are required to examine what inclusion level of treated legume meal can promote growth performance in specific commercial fish species.

Periparturient milk fever is a widespread metabolic disease within the dairy industry, with a number of potential impacts on the affected animals’ health and productivity in the subsequent lactation that can have a considerable economic impact on farmers. This thesis aimed to investigate current attitudes of both UK dairy farmers and veterinarians towards milk fever and subclinical hypocalcaemia, as well as investigating the feeding of rumen-protected rice bran during the dry period as a milk fever preventative, due to its reported potential as a calcium binder, within a commercial UK dairy herd. A retrospective study was also carried out in order to investigate associations between recorded milk fever events and other outcomes from farm records obtained from 78 UK dairy herds. The levels of agreement between three different blood sample types (serum, lithium heparin plasma, and lithium heparin whole blood) were also considered with regard to testing for concentrations of calcium, magnesium and phosphorous. Questionnaires were distributed to UK dairy farmers and veterinarians in order to assess current attitudes towards milk fever and its prevention. When choosing a prevention strategy, farmers were most concerned with its efficacy, with its ease of use being their second priority. Veterinarians placed a greater importance on metabolic disease than farmers, and it appears that vets may have an important role in education on the subject of hypocalcaemia. A retrospective study of over 59,000 lactations from 78 UK dairy herds found associations between recorded events of milk fever and an increased risk of dystocia, and an increased risk of a cow exiting the herd during the first 30 days of the lactation. Twin pregnancies were associated with a 30% reduction in the risk of milk fever. Rumen-protected rice bran was trialled against a control feed on a UK dairy herd during the dry period as a potential milk fever preventative. Serum calcium concentrations in the control group were significantly higher pre-calving than in the group that received rumen-protected rice bran. Cows fed rumen-protected rice bran were more likely to experience an elevated NEFA concentration post-calving than the control group. No feed-related differences were found in the subsequent 100 day yields. Limits of agreement were examined to investigate whether bovine serum, plasma and whole blood samples can be interchangeably used for the analysis of calcium, phosphorous and magnesium concentrations. Serum and plasma results appeared to show high levels of agreement for all three of the analytes. Whole blood results were more variable. In conclusion, the findings of this thesis provide an insight into the current attitudes within the UK dairy industry towards hypocalcaemia and its prevention. This thesis has also provided information on the effects and practicalities of feeding rumen-protected rice bran during the dry period in a commercial dairy herd and highlights the need for further research on the subject.

Weaning is a stressful period in the early life of a pig. This stress manifests as immediate weight loss coinciding with increases in intestinal transepithelial resistance. This study aims to identify the transcriptional differences in the colon between suckling and weaned animals over this period using RNA-seq. This approach identified the maximal transcriptional differences at one-day post-weaning with 353 transcripts differentially expressed compared to 78 and three transcripts at four and fourteen days post weaning respectively (q < 0.1, FC > 2). This work identified increased transcription of pro-inflammatory cytokine genes including IL1A (FC=2.63) and IL1B2 (FC = 2.98) in the colon of weaned animals at one-day post weaning, suggesting activation of the immune system. The same time points at one, four and 14 days post weaning was used to assess the transcriptional effect of supplementation with probiotic Saccharomyces cerevisiae boulardii (4.43 Log10 CFU per day from seven days of age) on the colon. A distinct effect of probiotic yeast supplementation on transcription in the colon was identified in both weaned and suckling pigs. One, 77 and one transcripts were affected by the probiotic in weaned animals at the three time points respectively compared to 197, six and two in suckling animals. However, evidence of an anti-inflammatory effect (including increased expression of IL10, FC = 2.88) was identified in weaned animals at four days post-weaning. The clear distinction between differential expression in weaned and suckling animals suggests that the transcriptional effect of Saccharomyces cerevisiae boulardii supplementation may depend on the physiological state of the host. These differences may be due to the interaction of the probiotic with the host immune system as a result of weaning related bowel disruption.

Ovine footrot is an infectious cause of lameness in sheep that has significant economic impact for the UK sheep farming industry. It is also a major concern for animal health and welfare. The causal agent is Dichelobacter nodosus, and Fusobacterium necrophorum is an opportunistic secondary pathogen that increases disease severity. The primary reservoirs for F. necrophorum in sheep were believed to be sheep faeces and the environment, however, no studies had demonstrated the presence of F. necrophorum at either of these sites. Two longitudinal studies (Study A and Study B) were conducted to determine reservoir sites of F. necrophorum in ovine footrot. Study A included 10 sheep sampled on four occasions at two week intervals. Study B included 40 sheep sampled weekly for 20 weeks. Samples collected from sheep and their environment were foot swabs, mouth swabs, faeces, soil and grass. Quantitative PCR was used to detect and quantify F. necrophorum. A multiple locus variable number tandem repeat analysis (MLVA) community typing scheme for F. necrophorum was developed and validated, and used to analyse samples from Study A and Study B. Contrary to prior assumption, the environment was not a significant reservoir of F. necrophorum. F. necrophorum persisted in sheep, primarily on feet with footrot. MLVA indicated that the strains of F. necrophorum found on the feet of sheep were closely related, and they may therefore share characteristics that make them well adapted to feet and footrot. Mouths and faeces were an intermittent reservoir for the strains of F. necrophorum involved in footrot. Mouths and faeces may therefore facilitate persistence of F. necrophorum in the absence of footrot, or facilitate transmission of F. necrophorum between flocks. Mouths were a persistent reservoir for strains of F. necrophorum not involved in footrot.

Ovine footrot (FR) is an economically important disease that causes lameness and affects sheep flocks worldwide. It is characterized by interdigital skin inflammation (interdigital dermatitis [ID]) with, or without, separation of the hoof horn from the underlying tissue (severe footrot [SFR]). The primary causative agent is the gram-negative anaerobic bacterium Dichelobacter nodosus, which is present in diseased feet and thought to be transmitted via contaminated surfaces. Periods of apparent zero prevalence of FR in a flock can be followed by disease occurrence when the climate becomes favourable for pathogen transmission. This suggests that there are sites where D. nodosus persists in the absence of disease. These sites might include healthy feet, the gingival cavity and faeces of sheep and also the environment. The aim of this thesis was to investigate persistence of D. nodosus, by investigating possible sites of survival of D. nodosus over time. Prospective longitudinal studies were used to investigate persistence. Samples were collected from sheep and from the pasture in three studies (Studies 1 and 2: England, study 3: Spain). Quantitative PCR was used to detect and quantify D. nodosus and to investigate associations between D. nodosus presence in feet, in the gingival cavity and on pasture and a range of predictor variables including climate. A multiple locus variable number tandem repeat analysis (MLVA) suitable for use on mixed DNA and environmental samples was optimized and validated to investigate D. nodosus strains within and between sites. A novel approach to characterize individual strains in a sample was designed. D. nodosus was detected in all sample types in all studies but not on all occasions. The feet of sheep were the only site where D. nodosus was detected in loads exceeding 103 cells per swab. In study 1, D. nodosus was detected in amounts exceeding103 cells in samples collected from the pasture in week 1 only, when detection frequency of D. nodosus on feet was high and the weather was wet. A minimum of 14 strains of D. nodosus were detected on the feet of sheep by MLVA. A decline in detection of D. nodosus in the environment coincided with periods of dry weather, however, dry weather did not coincide with a decline in D. nodosus loads on feet or incidence of disease. D. nodosus was more likely to be detected in the gingival cavity when a sheep had FR. It was detected in 25 % of gingival cavity samples and strain types identified in the gingival cavity were the same as the dominant strain types on the feet of sheep. In study 2, disease prevalence and D. nodosus detection frequencies were lower than in study 1. When sheep from the study group were separated from the main flock in week 1 and moved onto pasture that had been unoccupied for 10 days, D. nodosus was transferred to the study group on healthy feet. One dominant strain of D. nodosus persisted throughout an episode of disease and this strain was present on the healthy feet of sheep until up to 5 weeks before the development of lesions in high bacterial loads. There was a reduction in lesion severity and reduced detection of D. nodosus in soil in a period of dry weather. Only 1 sample from the gingival cavity was positive for D. nodosus. Two faecal sample were positive for D. nodosus, indicating for the first time that faecal shedding is possible. In study 3, there were high loads of D. nodosus on healthy feet of a sheep that was classed as susceptible when there had been no cases of FR for at least 2 month. D. nodosus was still present in the flock during the long non-transmission period in the summer. We conclude that D. nodosus is more likely to persist on the feet of sheep, whereas long-term environmental reservoirs of D. nodosus are unlikely. Future research should focus on the feet of sheep and possibly faeces as possible sites of persistence of D. nodosus in the absence of disease.

Horses are extensively exposed to various kinds of medication. However, limited information is available about how these medications are metabolised in this species. Hence, the development of strategies and methods that provide a better understanding of different metabolic pathways for different drugs is of major importance. Although, the horse is considered as a monogastric animal, it is also a hind gut fermenting animal, i.e. most of the feed is degraded in the cecum and colon. Thus, it is hypothesised that this could result in an evolutionary difference in xenobiotic metabolising enzymes between human and horses which may lead to different pharmacokinetics. Therefore, the main aim of this study is to develop an in vitro model as a preclinical testing system of newly developed substances for horses using freshly isolated, cryopreserved equine hepatocytes and liver microsomes. Fresh hepatocytes were isolated and liver microsomes were prepared using livers which were obtained from horses, post slaughter. Part of the freshly isolated hepatocytes were cryopreserved. A comparison metabolic study was carried out to compare the three in vitro systems. The intrinsic clearance (Clint) of three drugs used in equine medicine omeprazole, flunixin and phenylbutazone, was determined via the substrate depletion method. The determined Clint values were extrapolated to in vivo hepatic clearance (ClH) using two in vitro liver models, namely, well stirred and parallel tube models. To perform the extrapolation step, the values of microsomal protein per gram of liver (MPPGL) and the number of hepatocytes per gram of liver in the horse (HPGL), also known as the hepatocellularity, key scaling factors in both the well-stirred and parallel tube models, were obtained for horse. These scaling factors were determined by comparing the CYP P450 content in microsomes and cryopreserved hepatocytes against the CYP P450 content of the liver. Additionally, HPGL was also calculated from the ratio of liver protein concentration to matched hepatocyte suspension protein concentration. Effects of ageing on CYP P450 content, MPPGL and HPGL values were also investigated. Furthermore, chloramphenicol’s potential effect on the in vivo AUC for omeprazole was predicted using microsomes. In the present study, freshly isolated equine hepatocytes were successfully cryopreserved and the viability of recovered cells, after a 30% Percoll gradient, was 77 ± 11% and estimated recovery rate was approximately 27%. MPPGL and HPGL values ranged 41-73 mg/gram of liver (mean= 57 mg/gram of liver, n=39) and 146 - 320 × 106 cells/g of liver (Average = 227× 106 cells/g of liver, n=18) using CYP P450 method; and 156 - 352 × 106 cells/g of liver (Average = 232× 106 cells/g of liver) using protein method. It was found that increase in age had no effect on CYP P450/mg microsomal protein content. This study successfully predicted the in vivo clearance for omeprazole, flunixin and phenylbutazone using, both, freshly isolated and cryopreserved equine hepatocytes. Meanwhile, microsomes significantly underpredicted the in vivo hepatic clearance ClH. However, microsomes were used in present study to perform drug-drug interaction (DDI) in vitro study between omeprazole and chloramphenicol. The average of IC50 and the inhibitor constant Ki of the three horses were 17.7±5.8 μM and 15.4±5 μM, respectively. The work presented in this thesis paves the way to develop in vitro models using equine hepatocytes and liver microsomes, which are reproducible, scalable and compatible with screening platforms. These models can be applied to the improvement of predicted detection times (DT) in horse racing which may aid veterinarians to estimate accurate withdrawal times; hence, the horse welfare will be improved. Moreover, further phase II metabolism, drug induction and comparative studies can be performed.

Enteritis is a very frequent cause of morbidity and mortality in young calves and pigs. They may be infected with 54 known pathogens, particularly in the first months of their life. Simultaneous infection with multiple pathogens occurs frequently and produces a synergistic effect in terms of the severity of clinical disease. In this study two microarray platforms (Agilent and Alere) were used to detect enteric pathogens. A total of 15993 probes were designed from viral, bacterial and parasitic sequences using four different software (UPS, Picky, eArray and GoArray). The probes for the Alere platform were assessed thermodynamically individually for secondary structure formation and hybridised to their complementary sequences in silico. Specificity and sensitivity testing was done with reference strains and porcine and bovine clinical samples and were performed with both platforms. The Alere ArrayTube platform holding 201 probes was used to identify viruses in reference and clinical samples. Among eight reference virus strains, five (PEDV, TGEV, PCV-2, BVDV and PPV) were identified correctly and of these PEDV, TGEV, PCV-2 were confirmed by PCR using designed primers Two viruses, P. rotavirus A and P. bocavirus were negative by array but were confirmed by PCR, rotavirus by designed primers and bocavirus by published primers. In two hybridisations using multiplex PCR products from two separate sets each of 5 mixed pathogens, the ArrayTube detected all viruses for one set and only one virus out of two in the other set. The specificity test using three non-enteric viruses showed high background noise for Bunyamwera virus and Schmallenberg virus, however only one probe cross-hybridised with Equine influenza virus. The sensitivity of this platform showed that it can detect an amount of 2.065 x 109 copy number (2 ng) of PCV-2 and 2.420 x 105 copy number (39 pg) of TGEV present in the sample. The results of hybridised reference viral strains and clinical samples showed that random amplification was more favourable for reference strain detection compared to specific amplification. However, specific amplification performed better for clinical samples. The Agilent microarray platform, comprising 44000 probes of enteric bacteria, viruses and parasites, was subjected to hybridisation of 12 reference strains for specificity testing (four viruses, seven bacteria and one parasite). All hybridised strains were correctly detected except P. rotavirus A which showed only 7 positive probes, however with high signal intensities. A high level of cross-hybridisation was observed with this platform due to the 16S rRNA and 18S rRNA probes as these two genes were amplified in their entirety prior to hybridisation and a high degree of similarity exists between of 16S rRNA and 18S rRNA among different strains of bacteria and parasites respectively. Hybridisation of PCR products to the Agilent platform from two sets of five multiplexed pathogens showed that all ten pathogens were correctly identified. The sensitivity results of this platform showed that it can detect 2.065 x 109 copy number of PCV-2, equivalent to a viral load of 2 ng. On the other hand the detection limit of E. coli F5 was comparable to the real-time PCR technique with a minimum of 2.089 x 108 copy number of E. coli fimbrial gene present in the sample. In bovine clinical samples, the Agilent microarray was able to identify the presence of E. coli F5 in two samples out of four tested. However, in porcine clinical samples, the array successfully detected all pathogens whose presence was confirmed by PCR. Mixed infections in porcine samples were also detected by microarray, where Clostridium difficile with its toxins (toxin A tcdA and binary toxin cdt), P. rotavirus and P. kobuvirus were detected simultaneously in one sample. It also detected the presence of the C. difficile clindamycin resistance gene (ermF) in another sample. In this study microarray technology has been shown to have the potential to detect mixtures of enteric pathogens in bovine and porcine faecal samples. It also has genotyping abilities for exploration of genetic variation. However, the sensitivity and specificity could be improved with more in silico assessments of designed probes. Eventually testing with a higher number of reference strains and clinical samples is necessary.