BACKGROUND In South Africa, bovine TB (bTB) is a state-controlled disease but the monitoring of bTB in small ruminants is largely neglected, whereas bTB diagnosis and surveillance in cattle and buffalo are prioritised due to limited resources. In communities where bTB surveillance is not conducted regularly in herds, bTB surveillance data in cattle and other susceptible livestock are lacking. Goats co-existing with cattle, especially in areas where the prevalence of TB is high in both the cattle and the human populations, are not tested for TB. The prevalence of bTB in goats is unknown though they are known to be susceptible to Mycobacterium bovis. Thus, there was an opportunity to gather information from state veterinarians on their observations of bTB in goats. This information would assist to make a decision on whether to pursue further studies on bTB in goats in South Africa. METHODS A survey study design using a quantitative research approach was used. Data were collected through face-to-face interviews using a semi-structured questionnaire. Contacts of state veterinarians where obtained from the Department of Agriculture Forestry and Fisheries (DAFF) website. Participants were initially contacted via email. In the e-mail the participants were given a brief introduction of the researcher as well as his intention of carrying out the questionnaire. Participants that were willing to participate would either do so via email in which they would read and sign the consent form and then proceed to answer the questions on the questionnaire. They could either fill in with a pen or, type in their responses electronically. During the face-to-face interviews, participants were given the option to complete the questionnaire themselves or let the interviewer read out the questions and complete the questionnaire on their behalf. They were however requested to go through the consent form and fill it in before the interview could start. Other participants preferred to go through the questionnaire themselves while in the presence of the interviewer. RESULTS None of the 25 interviewed veterinarians had tested for or diagnosed bTB in goats. When asked the reason for not testing for bTB in goats, 55% said it was not mandatory and 25% cited limited resources as the reason. From the literature search, Spain and the United Kingdom had the most reported cases in Europe of TB in goats at 36% (n=355) and 27% (n=45) respectively. M. bovis was the most commonly encountered species and the mediastinum lymph nodes was the organ most often affected. In Africa, Ethiopia and Nigeria had the most reported cases of TB in goats with 54% (n=184) and 15.4% (n=9) respectively. M. bovis was most commonly encountered in these cases and unlike the European cases; the lungs were most frequently affected with a frequency of just under 80%. The only reported case of bTB in goats from South Africa was reported in 1928. CONCLUSION There is limited knowledge of bTB in goats in South Africa primarily driven by a bTB disease policy that is biased to focus on cattle and pay little attention to small stock such as goats. / Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

This project was conducted in order to ascertain the presence or absence of acaricide resistance in ticks in an area of KwaZulu-Natal (KZN) where tick-borne diseases pose a real and dire threat to communal and commercial livestock. The results of this study will assist farmers and state veterinarians in their tick control strategies and aid in the battle against stock losses due to ticks and tick-borne diseases. The aim of the project was to collect one-host Rhipicephalus spp. (blue ticks) from cattle presented at communal dip tanks and from cattle on commercial dairy and/or beef farms to test for the presence of acaricide resistance. The ticks were identified as either R. microplus or R. decoloratus, then the engorged female ticks were incubated and the hatched larvae subjected to the Shaw Larval Immersion test (SLIT). The Shaw Larval Immersion test was developed in 1966 by RD Shaw (Shaw, 1966) to determine the spectrum of acaricide resistance in tick populations. The three acaricides selected for the laboratory bio-assay are included in the classes of topical acaracides most frequently used in KZN, namely amidines, organophosphors and pyrethroids. Both tick species were present in the study area and two commercial farms showed a mixed population of both tick species. All fifteen populations of ticks tested in this study showed resistance to at least one class of acaricide, and four of the 15 (26%) showed resistance to two classes of acaricides. 80% of the tick samples tested was resistant to cypermethrin, a synthetic pyrethroid. It can be concluded from this study that: 1. acaricide resistance is present in one-host Rhipicephalus spp. in the KwaZulu-Natal Midlands and this poses a real and significant threat to tick control efforts in this region of KwaZulu-Natal, 2. resistance to pyrethroids is developing at a faster rate than other acaricides and, 3. both blue tick species were identified in the study area however only one or the other species was represented at almost all of the 15 sites sampled. The exceptions were two commercial farms, where both R. decoloratus and R. microplus were identified in a mixed population. / Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

Tabanidae (Diptera) is a diverse haematophagous fly family, known to transmit over 35 livestock pathogens both mechanically and biologically. Kruger National Park (KNP) (in Limpopo and Mpumalanga provinces), South Africa, has a high diversity of tabanids, representing 26 of the total indigenous species (n=213) present in South Africa. Little modern taxonomical work has been done on tabanids within South Africa despite their medical, veterinary and environmental importance. This study aimed to determine a cost-effective DNA extraction method as well as comparing the traditional alpha-taxonomic approach to species delimitation with molecular methods using two gene regions, mitochondrial cytochrome oxidase I (COI) and nuclear alanyl-tRNA-synthetase (AATS) of tabanids collected in KNP. Furthermore, the study aimed to elucidate the role of tabanids in the transmission of Besnoitia besnoiti as this pathogen has found to ciculate in impala (Aepyceros melampus) and blue wildebeest (Connochaetes taurinus). A comparative study on DNA extraction methods were conducted, of which the most effective method was selected for DNA extractions. Tabanids were captured in three locations within KNP. The flies were morphologically identified then homogenized. DNA was pooled for the B. besnoiti screening, followed by sequencing and phylogenetic analysis. In total, 856 flies were captured belonging to 16 species under five genera. The COI barcode indicated that some species are genetically uniform while others formed co-occurring haplotypes. This study found that COI alone was not adequate in distinguishing between all the species of the South African Tabanidae. It is apparent that the classification of Tabanidae should be placed under scrutiny. A larger sample size, especially with regards to the Tabanus genus, or the use of several markers will aid in clarifying their relationships. No B. besnoiti positives were detected in the screened tabanids. Furthermore, in-depth research should also be conducted in other regions of South Africa; not only on tabanid ecology and composition but their role as pathogen vectors. / Dissertation (MSc)--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc / Unrestricted

The tragelaphine antelopes comprise a group of nine species, namely Tragelaphus eurycerus (bongo), Tragelaphus scriptus (bushbuck), Tragelaphus oryx (common eland), Tragelaphus derbianus (giant eland), Tragelaphus strepsiceros (greater kudu), Tragelaphus imberbis (lesser kudu), Tragelaphus buxtoni (mountain nyala), Tragelaphus angasii (nyala) and Tragelaphus spekii (sitatunga) which are all confined to the African continent. Currently, a total of 72 species of helminth parasites from seven tragelaphine antelope species have been recorded, while no records exist for T. imberbis and T. buxtoni. Some helminth species are shared with domestic stock and only a few helminths have zoonotic implications. The clinical significance of most helminth species in tragelaphine antelopes is unknown. This information was compiled based on an extensive search for records in the literature ranging from the early nineteen-hundreds until August 2019. A synopsis of the results is presented in tabular form. / Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

Theileriosis is a lymphoproliferative tick-borne disease of cattle and other wild ruminants, caused by infection with a protozoan, Theileria parva. The disease is prevalent in cattle throughout Central, East and southern Africa, where it threatens 50% of the cattle population. There are various control and treatments methods used against theileriosis; however, they all have limitations. The available live immunisation method, the Muguga cocktail, does not confer protection against all field strains, particularly buffalo-derived T. parva. Attempts to develop a subunit vaccine have been promising but these have shown limited efficacy due to antigenic and genetic diversity of T. parva strains in the field. Thus, there is a need to search for additional vaccine candidates. A related study has identified potential vaccine candidates using a genome-wide in silico approach. Consequently, the aim of this study was to genotype one of the identified antigens. TP04_0028 was selected for genotyping among candidate genes with high expression levels in the schizont stage of both cattle- and buffalo-derived T. parva isolates. Specific primers were designed and optimised for PCR amplification and sequencing. The comprehensive analysis of sequences from 17 cattle- and 17 buffalo-derived T. parva, from East and southern Africa, showed conservation in 12 (60%) of the 20 TP04_0028 predicted epitopes, in both parasite types, irrespective of geographical origin. Eighteen of the 20 predicted epitopes are conserved amongst different BoLA alleles and an area of 7 overlapping epitopes could be the starting point for initial experimental evaluation of the immunogenic properties of TP04_0028. Once the immunogenicity of these epitopes have been tested and the extent to provide protection from cattle- and buffalo-derived infections have been verified, they may be considered for vaccine development. / Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

Theileriosis is a lymphoproliferative tick-borne disease of cattle and other wild ruminants, caused by infection with a protozoan, Theileria parva. The disease is prevalent in cattle throughout Central, East and southern Africa, where it threatens 50% of the cattle population. There are various control and treatments methods used against theileriosis; however, they all have limitations. The available live immunisation method, the Muguga cocktail, does not confer protection against all field strains, particularly buffalo-derived T. parva. Attempts to develop a subunit vaccine have been promising but these have shown limited efficacy due to antigenic and genetic diversity of T. parva strains in the field. Thus, there is a need to search for additional vaccine candidates. A related study has identified potential vaccine candidates using a genome-wide in silico approach. Consequently, the aim of this study was to genotype one of the identified antigens. TP04_0028 was selected for genotyping among candidate genes with high expression levels in the schizont stage of both cattle- and buffalo-derived T. parva isolates. Specific primers were designed and optimised for PCR amplification and sequencing. The comprehensive analysis of sequences from 17 cattle- and 17 buffalo-derived T. parva, from East and southern Africa, showed conservation in 12 (60%) of the 20 TP04_0028 predicted epitopes, in both parasite types, irrespective of geographical origin. Eighteen of the 20 predicted epitopes are conserved amongst different BoLA alleles and an area of 7 overlapping epitopes could be the starting point for initial experimental evaluation of the immunogenic properties of TP04_0028. Once the immunogenicity of these epitopes have been tested and the extent to provide protection from cattle- and buffalo-derived infections have been verified, they may be considered for vaccine development. / Dissertation (MSc (Veterinary Science))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Veterinary Science) / Unrestricted

Heartwater, caused by Ehrlichia ruminantium, causes significant economic losses to commercial small stock farmers, including commercial boer goat farmers in the Limpopo Province of South Africa. Heartwater is endemic in this region where Amblyomma hebraeum, the South African bont tick and the vector for this disease occurs. Due to their long mouthparts and specific attachment sites on goats, A. hebraeum is also associated with wounds, secondary abscess formation and lameness. Small stock farmers in the Limpopo Province employ various methods to control A. hebraeum and the negative effects associated with this tick, including heartwater. Two approaches where followed to focus on the control of A. hebraeum on the one hand and the detection and cryo-preservation of E. ruminantium from A. hebraeum on the other hand. The aim of this study was therefore twofold. By firstly determining the efficacy of a 1.0% fipronil pour-on solution against A. hebraeum by performing a therapeutic- and persistent efficacy trial and secondly to detect and cryo-preserve E. ruminantium from A. hebraeum ticks from a heartwater endemic region in the Limpopo province of South Africa. It was demonstrated that a 1.0% fipronil pour-on solution is 100% effective and has a persistent efficacy of seven days against A. hebraeum, but only if a targeted treatment approach is followed whereby the pour-on solution is applied to the predilection sites of A. hebraeum. A 1.0% fipronil pour-on solution can therefore be used by boer goat farmers to control A. hebraeum and the negative effects associated with this tick. In order to detect and cryo-preserve E. ruminantium from A. hebraeum ticks, ground-up-tick-supernatant samples were prepared in the laboratory from A. hebraeum ticks collected from goats and cattle at specified time intervals. To determine whether E. ruminantium was present in A. hebraeum ticks, DNA extraction, nested PCR of the pCS20 region of the E. ruminantium genome and demonstration of the amplified DNA by agarose gel electrophoresis was performed. The results demonstrated that E. ruminantium was indeed present in eight out of eight ground-up-tick-supernatant samples that were cryo-preserved. In future research, these samples may become very useful for isolating current strains of heartwater, which will ultimately lead to a better understanding of the disease and to facilitate the implementation of novel control methods. / Dissertation (MSc)--University of Pretoria, 2018. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

Foot-and-Mouth Disease (FMD) is a disease of cloven-hoofed animals well-known not only for significant production losses but also restricted market access for livestock and livestock products from affected areas. It severely limits market opportunities for poor farmers and nations wishing to access more lucrative markets, both regionally and internationally. In the Northern Communal Area (NCA) of Namibia, FMD has not been detected in Kunene, Omusati, Oshana, Oshikoto and Ohangwena regions for the past 45 years or more, while outbreaks occurred in Eastern Kavango towards the end of 2008 as well as beginning of 2009 and there have been frequent outbreaks in the Zambezi region. Although, FMD has not been detected in five of the six regions of the Namibian NCA, no studies have been carried out to substantiate the FMD status in this highly potential livestock production area as required by the World Organisation for Animal Health (OIE). It is based on this fact that a study was carried out in the above mentioned regions to determine whether there is Foot-and-Mouth Disease Virus (FMDV) circulating in the cattle population of the NCA Namibia. A set of 4214 serum samples were taken from non-vaccinated animals against FMD in Area A, which included Kunene north, Omusati south, Oshikoto(NCA) and Oshana. Meanwhile, 5228 serum samples were taken from Area B, which consisted of Omusati north, Ohangwena and Kavango region where cattle had been vaccinated against FMD for the past 15 years or more. Samples were primarily screened for FMDV using the Ceditest® NSP ELISA and positive samples were subsequently tested with the Viral Neutralization Test (VNT). Herds containing animals that were positive on both tests were followed up and retested with the Ceditest® NSP ELISA and examined clinically for FMD signs. The initial results of the Ceditest® NSP ELISA in Area A and B revealed an apparent prevalence of 0.24% and 0.27% with corresponding 95% confidence intervals between 0.13, 0.44 and 0.16, 0.45 respectively. The follow up results found no clinical evidence of FMD and all subsequent Ceditest® NSP ELISA results were negative. The results indicate that the initial Ceditest® NSP ELISA positive cattle were false positive. Thus the overall outcome indicates that there is little chance of FMD virus circulation in the NCA Namibia. The survey also highlighted the need for taking into account sociological and cultural practices when designing a survey of communal cattle in order to get a representative sample of the cattle population. The study also recommended that Directorates of Veterinary Services (DVS) Namibia should maintain and continuously review FMD surveillance activities in the NCA, especially along the Angola – Namibia border and continuously harmonise these activities with Angolan counterparts. A more comprehensive study should be carried out to address the insufficient knowledge on sociological factors, which may influence sampling strategies in communal farming areas. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / ab2016 / Production Animal Studies / MSc / Unrestricted

Protein is a fundamental part of nutrition in all animals but ruminants have the ability to metabolise and utilise non-protein nitrogen for this use. This allows for an economical alternative source of protein that does not compete with human resources. Previous evidence suggests that feeding high levels of protein to support increased demands for growth and production may have a negative impact on reproduction, since protein is rapidly converted to ammonia and further metabolised to urea which are both toxic to the reproductive system. Investigations within the South African climate indicated that the Nguni cow maintained higher blood urea nitrogen (BUN) levels during periods of drought than other cattle breeds. The Nguni breed is well adapted to extreme situations but as its popularity grows and the breed is promoted for emerging farmers it becomes essential to know if it possesses adaptations which could predispose it to reproductive failure if supplemented in the same manner as other commercial breeds. In this prospective experimental study, 22 multiparous cows of two breeds, the Hereford and the Nguni, were block randomised into a cross over design whereby all animals were fed a total mixed ration (TMR). The test group was provided with an increasing rumen degradable protein content in the form of feed grade urea. The control group was maintained on a urea free TMR. In the test group, the urea inclusion rate was increased weekly by 50 g to allow for rumen microflora adaptation and prevent acute urea toxicity. They reached a maximum inclusion rate of 200 g urea per cow per day. All animals had serum collected and oocytes aspirated by transvaginal ultrasound guided oocyte pick up (OPU) were counted and graded twice weekly. Following this, all usable oocytes were pooled per breed and treatment, and were subject to in vitro maturation, fertilisation and culture in order to assess the effect of elevated protein on oocyte competence and viability. Oocyte quality was defined as the number of oocytes with cumulus cells (Grade 1 3 oocytes) harvested per OPU, and oocyte viability was defined as the number of oocytes that cleaved by day 2 or that reached at least the morula stage by day 7 in the in vitro embryo system. Multivariable analyses were performed on BUN, antral follicle count (AFC) and number of grade 1 3 oocytes harvested per OPU session, and on the oocyte viability outcomes in the vitro embryo system. Nguni cows receiving 150 g dietary urea per day had lower mean BUN levels than Herefords (17.5 and 19.3 mg/dL respectively, P = 0.02). However dietary urea inclusion level, serum albumin level and sampling day were the only independent predictors of serum BUN. Nguni cows had lower mean antral follicle count (AFC) and number of oocytes harvested than Herefords (9.1 and 3.1, and 11.7 and 4.3 respectively, P < 0.01). The vet performing the aspiration, within day sampling order and BUN level >20 mg/dL were independently associated with the number of grade 1-3 oocytes after adjusting for AFC and the random effect of the individual animal. Increasing weighted mean serum albumin and decreasing weighted mean beta-hydroxybutyric acid (BHBA) were independently associated with the number of oocytes that cleaved (day 2) or that reached the morula stage (day 7) (P = 0.01 and P = 0.08 respectively). It was concluded that increasing dietary urea, low BCS and increasing serum albumin, but not breed, were associated with increasing BUN levels in cows. It was further concluded that BUN >20 mg/dL adversely affected the occurrence of cumulus cells around oocytes and that serum albumin and BHBA were, but neither dietary urea level nor breed was independently associated with viability of bovine oocytes in this study. Although the data were inconclusive about breed differences in protein metabolism, this study suggests that serum albumin has the potential to be used as predictor of the interaction between protein and energy metabolism and its effect on oocyte development. / Dissertation (MMedVet)--University of Pretoria, 2015. / tm2016 / Production Animal Studies / MMedVet

The South African crocodile industry has the potential to produce Nile crocodile skins, which are in high demand by the global fashion industry. The crocodile industry is an important economic resource to South Africa and Southern Africa. The main purpose of rearing Nile crocodiles at intensive production units is to produce viable hatchlings which will be grown to produce quality skins. The production of sufficient hatchlings depends on high hatching percentage of clutches. It has been observed that the hatching percentage varies among clutches. We do not know that whether the poor hatching percentages are associated with the microbial load from the incubation boxes or not. The aims of the study were to determine whether eggs in boxes that had more aerobic bacterial colonies and more fungal colonies before they received vermiculite and eggs are more prone to become lost from the pool potentially capable of yielding conceptuses developing to term than eggs in boxes that had fewer colonies before they received vermiculite and eggs, and whether there are species of aerobic bacteria, anaerobic bacteria and fungi that are present in unhatched eggs from clutches with low hatching percentage but not in clutches with high hatching percentage without the converse being true. At the time of hatching the farm personnel classify hatchlings or unhatched eggs into different categories e.g. hatchling survived, culled, foetus died in the shell, hatchling died, unfertilised egg, banded (the foetus died long before hatching), or rotten egg (putrefaction rendering the fertilisation status unknown). We assumed that banded or rotten eggs are more likely to have lost conceptuses due to the microbial load that was present in the incubation boxes before they were loaded with vermiculite and eggs than the other classes of eggs. A response variable Perhapsloststatus was therefore created. For each egg that was either classified as Banded or Rotten Perhapsloststatus was assigned the value of one. For each egg belonging to other categories Perhapsloststatus was assigned the value of zero. Eggs classified as unfertilised were excluded from Perhapsloststatus. The microbial load of aerobic bacteria and fungi from the incubation boxes before they were loaded with vermiculite and eggs was measured as colony forming units (CFU). The independent variable of interest was Count category (a categorical variable of aerobic bacteria and fungi colony counts), which was compiled as follows: 0 = Counts zero to below the 25th percentile, 1 = Counts from the 25th percentile to below the 50th percentile, 2 = Counts ranging the 50th percentile to below the 75th percentile, 3 = Counts from the 75th percentile to the maximum that was countable and 4 = Too numerous to count. Sterile swabs were used to collect samples from unhatched eggs for isolation and identification of aerobic bacteria, anaerobic bacteria and fungi from the 10 boxes with the lowest and highest hatching percentages, respectively. We used a population-averaged mixed-effect logistic regression model to determine the effect of Count category on Perhapsloststatus. The odds for eggs being banded or rotten (Perhapsloststatus = 1) in boxes with too numerous to count aerobic bacterial colonies (Count category 4) tended to be higher than for eggs in boxes with colony counts between zero and the 25% percentile (Count category 0) (P = 0.06). The odds of eggs being banded or rotten (Perhapsloststatus = 1) in boxes with fungal colony counts falling in any count categories 1 to 4 were the same as the odds of eggs being banded or rotten in boxes with fungal colony counts falling in Count category 0. The variety and frequency of species of aerobic bacteria, anaerobic bacteria and fungi from unhatched eggs of lowest hatching boxes and highest hatching boxes was almost the same. The species isolated from unhatched eggs are more likely pertaining to contamination from the cloaca of female crocodile or from the environment i.e. nesting material, personnel handling, vermiculite, incubation box or the incubator environment, as most of the isolated species present are normally present in soil, water, dust and also opportunistic pathogens in animals. This observational study shows that there is a trend of association between the aerobic bacterial load from the incubation boxes and the eggs in them to become either banded or rotten. / Dissertation (MSc)--University of Pretoria, 2015. / tm2016 / Production Animal Studies / MSc