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The aim of this study was to investigate the economics of damage to crops and infrastructure, injuries and loss of life at the human-elephant interface within Tsavo Conservation Area between 2010 and 2013. Data was generated from the Kenya Wildlife Service occurrence data base. A total of 488 cases with complete data were extracted. Both descriptive and inferential statistics was used in data analysis. The study established that zones with a higher incidence of conflict were proximate to the park and near main water points. Crop damage was the most (83%) prominent reason for human-elephant conflict. Others were property destruction (8%), human injuries (5%) and human deaths (4%). Crop damage occurred more often during wet seasons than dry seasons. Correlation analyses showed that the size of land was significantly associated with the value of the crop destroyed, with mean land size being 0.7 (+/- 0.99) acres. This was equivalent to 984,254 kg of crop yields over four years with an average of 246 063.71 (+/- 21 288) kg/annum. The main crop destroyed was maize, planted as a single crop. The majority (76%) of those affected were small holders with less than 0.7acres and they practiced subsistence farming. Men were the only gender killed by elephants (n=21), although both sexes were injured (n=24). In total, 40 incidents recorded damage to buildings and infrastructure. The value of crop damage, human injuries and deaths was Kenyan shillings 32,618,500 over the four year study period. It is recommended that the government should reduce human/elephant interaction in Tsavo Conservation Area by erecting an electric fence around the park, involving the community and compensating them for the entire cost of the loss incurred due to elephants from the Park. / Dissertation (MSc)--University of Pretoria, 2015. / tm2016 / Veterinary Tropical Diseases / MSc / Unrestricted

Mastitis is one of the most economically important diseases in dairy cattle worldwide. Not only does it have a negative effect on milk production, it also is one of the main reasons for culling dairy cattle. Pathogens causing mastitis in dairy cattle can be grouped into either contagious (or host adapted) or environmental pathogens. In different parts of the world it was shown that the prevalence of these differently grouped pathogens is dependent on various risk factors. Furthermore, it was shown that control measures implemented against contagious intramammary infections caused a relative shift over time towards a higher prevalence of environmental intramammary infections. In this study udder health data from the Onderstepoort Milk Laboratory (OML) was compared over two different years, 2008 and 2013, with regards to the prevalence of specified mastitogenic pathogens in total mixed ration (TMR) dairies and pasture-based dairies. Furthermore, the within-herd prevalence of Streptococcus uberis (Str. uberis) in Str. uberis positive herds was compared between the two years and the two management systems. Statistically significant differences were found in the prevalence of most of the major contagious and environmental mastitogenic pathogens between 2008 and 2013 and between the TMR and pasture-based dairies. Coagulase-negative staphylococci (CNS) has the highest prevalence in both TMR and pasture-based for both 2008 and 2013. Streptococcus uberis overall showed an increase in prevalence from 2008 to 2013, with the highest prevalence in pasture-based dairies in 2013. Staphylococcus aureus (S. aureus) showed a statistically significant decrease in TMR and pasture-based dairies from 2008 to 2013. The within-herd prevalence of Str. uberis increased from 2008 to 2013 with the highest within-herd prevalence in pasture-based dairies in 2013. / Dissertation (MMedVet)--University of Pretoria, 2015. / tm2016 / Production Animal Studies / MMedVet

South African farmers have struggled for many years with the loss of livestock on their farms due to predators such as black backed jackals (Canis mesomelas) and caracal (Caracal caracal). These farmers have been known to use both lethal and non-lethal methods to control these predators on their properties. This study investigates the use of livestock guarding animals (LGAs) as a non-lethal method of controlling predators on farms. The study investigated the use of dogs, alpacas and donkeys on farms through the use of an online survey. Despite multiple appeals being sent out to different media outlets the response was modest. A structured, quantifiable and analysable questionnaire was sent to 34 farmers of whom 31 farmers completed the entire survey. The survey was used to gather information regarding the success of using these LGAs as well as the factors leading to their success and failure. There were 23 respondents who made use of dogs, eight who made use of alpacas and three using donkeys. Many studies have been done in the past on the use of dogs to protect livestock, these studies were done in Europe, the United states of America, Australia and Southern Africa. The use of both donkeys and alpacas have not been studied to the same degree. The hypothesis was that the use of LGAs (dogs, alpacas and donkeys), was successful in reducing predation by 50% or more on 75% or more of the farms surveyed. It was found that 21 of the 31 farmers who completed the survey said that predation decreased by 50% or more after acquiring a LGA. The factors leading to the success or failure in using these animals was determined for dogs, alpacas and donkeys individually. The questionnaire was designed to gather information about the farms such their size, terrain, the proximity to other farms, towns and nature reserves, and the wildlife found on the farm. We then looked at what livestock were being farmed and what LGA is being used by the farmer and how many of them are being used with the livestock. The questionnaire then went on to collect information on conception rates, lambing percentages, weaning percentages and percentages of livestock lost due to disease, predation and other factors. Looking specifically at predation we wanted to find out how much predation the farmers would attribute to which predator, how they determined which predator was responsible and how the predation changed over the time they had been using the LGA. It was also important to determine what methods of lethal control had been used previously on the farm and what was still being used by the farmers. Finally, the questionnaire covered the factors that contribute to the success and failure of the LGA as well as the cost of keeping the LGA. It was found that 33 of the 34 farmers had both sheep and cattle on their farms and only 11 farmed with goats. Nineteen of the farmers were farming on flat open plains. The farms were mostly in close proximity to other small livestock farms while others were on communal land. The number of LGAs used by the farmers were mostly determined by the size of the farm and the number of livestock. Supervision with livestock was not used by many farmers; 56% said it was unnecessary while 26% always had supervision with their animals. The rest of the farmers only occasionally had supervision with their animals. It was also found that the number of farmers making use of lethal control methods on their farms decreased from 80.65% before acquiring a LGA to 64.52% after acquiring a LGA. Predation was attributed to jackals on all farms, to caracal on 28 of the 31 farms of respondents that chose to answer this question, three farmers had problems with dogs and one farmer had predation due to leopards on his property. It was found that LGA had the greatest potential to decrease predation by jackals. The factors that were important for the use of dogs were their management, training and feeding. It was also found that dogs had the greatest financial impact on farmers as they cost more to acquire and maintain. The mean annual running cost as given by farmers was R11970.05. It was also seen that they had the greatest impact in reducing predation. The mean change in predation was 64% when making use of dogs. It was also seen that the weaning percentage on these farms increased by 25.23%. There was a change seen in the conception rate as well as the lambing percentage but neither was as large as with the weaning percentage. This is consistent with the fact that more lambs would survive if a LGA is keeping predators away. The factors that were listed as the most important factors in the use of alpacas were their temperament, the number of livestock you place with the alpaca and the age of the alpaca. The information collected on alpacas was small but showed that only four of the eight respondents saw an improvement on their properties after acquiring their alpaca. The cost of using an alpaca was not as significant as for dogs as they do not require extra housing or feed. The average running cost per annum for the use of alpacas was given as R525. There was no significant change in the conception rate, lambing percentage or weaning percentage of farmers making use of alpacas. There were only three responses for farmers making use of donkeys therefore there is no clear trend in the data but it has been reported on. The factors that were given as important were the gender of the donkey, specifically jennies (females) being more suitable, the donkey’s temperament, management and the number of livestock placed with the donkey. This was all in line with what was found in previous studies done on donkeys. Two of the three farmers using donkeys said that there was a 50% or more improvement in predation reduction on their farms. The average running cost of using a donkey was R2560 per annum. From the study it can be seen that these LGAs are successful in reducing predation but that more can still be done to encourage the use of alpacas and donkeys and to determine how successful they are. / Dissertation (MSc)--University of Pretoria, 2018. / Production Animal Studies / MSc / Unrestricted

A risk assessment was conducted for Salmonella enteritidis (SE) in the broiler production chain of the Western Cape of South Africa, using a literature review, historical data analysis, microbiological sampling from abattoirs and questionnaire responses. A questionnaire to characterise the risk pathway in the broiler chain was developed based on a review of the literature. Spatio-temporal analysis was conducted using historical data of reported SE outbreaks. The data showed spatio-temporal clustering, however, the analysis was not correct for groups of farms that form part of the same organisation. Neck skin samples were collected from five abattoirs and tested for salmonella. In total, 499 samples were collected, representing 46 broiler farms of which nine (20%) were positive. Salmonella positive cultures (2.81%) were serotyped. No SE was identified during the study. The questionnaire was completed for all stages of the broiler production chain. Significant risk factors were found using univariate analysis (Odds Ratio,OR). The significant risk factors identified by OR were further analysed using principal component analysis (PCA). The factors moving with or opposing, farm positivity were analysed using logistic regression and one layer farm was found to be a significant factor. The farms receiving eggs or chicks from that layer farm had a number of factors that were found to be significant using OR and therefore the presence of this layer farm could be a representation of these factors at the broiler farm level. SE was not identified in the samples collected from abattoirs, a number of other non-typhoidal Salmonella subspecies enterica were isolated. Given the high rates of immunosuppressive diseases within the South African population, it is important for broiler producers to be aware of the zoonotic potential of non-typhoidal Salmonella and continually improve their control measures. / Dissertation (MSc)--University of Pretoria, 2018. / Veterinary Tropical Diseases / MSc / Unrestricted

Rift Valley fever virus (RVFV) is a mosquito-borne virus and a member of the family Phenuiviridae and genus Phlebovirus. The single stranded RNA genome consists of three segments, Large (L), Medium (M) and Small (S). Rift Valley fever (RVF) is a mosquito-borne zoonotic disease that may cause large epidemics in ruminants and humans. Infection in humans causes influenza-like symptoms but the disease can also be more severe and fatal. Outbreaks in livestock are classified by abortion storms and young and newborn animals are severely affected with a high mortality rate. Rift Valley fever causes severe health and economic consequences in the areas where it occurs. Since the first recorded incidence of RVF in Kenya in 1930, South Africa has had three major countrywide outbreaks: in 1950-1951, 1973-1975 and 2008-2011. The disease is characterized in southern Africa by large epidemics at long, irregular intervals. The epidemics are usually associated with conditions favourable for proliferation of mosquito populations, such as high rainfall and flooding. Rift Valley fever has previously been isolated from 12 different mosquito species in South Africa including 5 Aedes spp., 3 Culex spp., 3 Anopheles spp. and 1 Eretmapodites sp. The presence of the virus and patterns of occurrence of the disease in the eastern parts of South Africa are poorly understood. Multiple studies were conducted; the aim of the first study was to detect the presence of RVFV in far northern KwaZulu-Natal Province, South Africa and to estimate the incidence rate of seroconversion. Cross-sectional studies were performed in communally farmed cattle (n=423) and goats (n=104), followed by longitudinal follow-up of seronegative livestock (n=253) 14 times over 24 months, representing 160.3 animal-years at risk. Exposure to RVFV was assessed using an IgG sandwich ELISA and a serum neutralization test (SNT) and seroconversion was assessed using SNT. Initial overall seroprevalence was 34.0% (95%CI: 29.5-38.8%) in cattle and 31.7% (95%CI: 22.9-41.6%) in goats, varying by locality from 18-54%. Overall seroconversion rate in cattle was 0.59 per animal-year (95% CI: 0.46-0.75) and in goats 0.41 per animal-year (95% CI: 0.25-0.64), varying significantly over short distances. The high seroprevalence in all age groups and evidence of year-round viral circulation provide evidence for a hyperendemic situation in the study area. The second study investigated the seroprevalence and associated risk factors of RVFV in antelope in the Tembe Elephant Park (TEP) and the Ndumo Game Reserve (NGR), using 326 sera from nyala (Tragelaphus angasii) and impala (Aepyceros melampus) routinely culled over a two-year period. The overall seroprevalence of RVFV was 35.0% (114/326; 95% CI 29.8-40.4%); the presence of antibodies in juveniles (6/21; 28.6%; 95% CI 11.3-52.2%) and sub-adults (13/65; 20.0%; 95% CI 11.1-37.8%) confirmed that infections had occurred subsequent to the 2008-2011 RVF outbreaks in South Africa. Seroprevalence was highest in adults and inversely associated with distance from a swamp or floodplain. The third study aimed to investigate the diversity, abundance, and seasonal dynamics of mosquitoes in the study area, and to screen mosquitoes for RVFV. Monthly collections of adult mosquitoes were carried out from January 2017 to June 2018 at three sites using CO2-baited tent traps. Mosquitoes were identified, pooled and screened for RVFV by quantitative reverse transcriptase (RT)-polymerase chain reaction (PCR) directed toward amplification of a 217-bp fragment of the L segment. A total of 34,848 mosquitoes of 7 genera and 48 species, were captured; Culex (Cux.) tritaeniorhynchus (31%), Cx. (Cux.) antennatus (29%), Aedes (Adm.) durbanensis (12%) and Cx. (Cux.) neavei (10%) were the most abundant species collected. Genera differences were noted between the collection sites. Cumulative rainfall and average minimum temperatures 30 days prior to collection were positively associated with the number of mosquitoes collected while maximum temperatures were only associated with the number of Culex mosquitoes caught. A single pool of Ae. durbanensis was found to be positive for RVFV genomic RNA. The same pool was also positive for Chikungunya virus (Family Togaviridae, genus Alphavirus) (CHIKV) and Sindbis virus (Family Togaviridae, genus Alphavirus) (SINV). The RVFV isolate was closely related to one obtained from Ae. (Neo.) circumluteolus at Simbu pan in 1955, ±20 km from the collection sites for this study. Further investigation should be done on the human health implications of the presence of these three zoonotic arboviruses. It is possible that these viruses are causing disease among the communities in the area and that the diseases are under-reported. The results of this study show that RVFV is circulating in the area in domestic ruminants and wildlife, in the absence of apparent clinical disease, at a rate that varies by location, season and year. It appears that, under similar ecological conditions, domestic and wild ruminants may play a similar role in maintenance of viral circulation, and either or both may serve as the mammalian host in a vector-host maintenance system. The study also demonstrates the presence of a wide variety of mosquito species, several of which are known to be competent RVFV vectors. / Thesis (PhD)--University of Pretoria, 2019. / Veterinary Tropical Diseases / PhD / Unrestricted

In Mnisi, a rural community in South Africa, Rhipicephalus sanguineus is one of the most prevalent ticks found on dogs. The community lies at the wildlife/livestock/human interface where humans are at risk of tick-borne diseases. The aim of this study was to investigate the diversity of the bacterial microbiome in R. sanguineus that may impact human health. Over a 12-month period, R. sanguineus (n=1,788), Rhipicephalus simus (n=61), Rhipicephalus turanicus (n=73), Amblyomma hebraeum (n=68), Haemaphysalis leachi (n=219) and Hyalomma truncatum (n=1) ticks were collected from 64 dogs. Genomic DNA was extracted from salivary gland and midgut tissues of 62 R. sanguineus tick pools (1 pool = 10 ticks); identifications were confirmed using Cytochrome c oxidase I barcoding. The 16S rRNA gene was amplified using barcoded primers and sent for Pacific Bioscience’s circular consensus sequencing. Characterisation of the bacterial microbiome of midgut and salivary gland pools revealed a total of 260,312 sequences with Proteobacteria (85.44%) being the most prevalent phylum found; with Anaplasma (21.69%), Coxiella (12.12%) and Ehrlichia (19.94%) species dominating the microbiome. Further classification of Ehrlichia revealed 95.46% Ehrlichia canis and 4.54% Ehrlichia species Anaplasma consisted of 15.36% Anaplasma centrale, 75.82% Anaplasma platys and 8.82% Anaplasma species Phylogenetic analysis indicated that the A. centrale and A. platys clustered with various other published A. centrale and A. platys sequences, respectively. It also confirmed that all Ehrlichia species sequences detected in this study are E. canis sequences (94.46%). Furthermore, we determined that the Coxiella sequences detected in the study belong to the R. sanguineus Coxiella-like endosymbionts group. Assessment of risk factors for R. sanguineus infestation indicates that higher average monthly temperatures have a significant association with an increased risk of R. sanguineus tick infestations on dogs. Additionally, rearing chickens at the household was significantly associated with a decreased risk of R. sanguineus tick infestations on dogs. Our study indicated that R. sanguineus could be a potential reservoir for important bacterial pathogens of zoonotic importance. / Dissertation (MSc (Veterinary Science))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Veterinary Science) / Unrestricted

Ticks and tick-borne diseases (TBDs) cause significant losses, through their effects on health, production of animals and humans worldwide. Notably, the countries located within the tropics and subtropics such as Uganda are the most affected due to abundance and distribution of the tick vector. Unfortunately, there is little data in Karamoja Region regarding tick species and the pathogens they transmit. Therefore, a cross-sectional study was undertaken to determine the various tick species, and to detect the tick-borne pathogens within the ticks collected from cattle in Karamoja Region, northeastern Uganda. Between June 2017 and early September 2017 (wet season), a total of 4,897 ixodid ticks were collected from 100 cattle in 20 purposively-selected herds. Three genera of ticks, namely Amblyomma (96.8%), Hyalomma (0.6%) and Rhipicephalus (2.6%) were identified. From the ticks collected, the most dominant species was A. lepidum (93.85%), followed by A. variegatum (2.0%), R. evertsi evertsi (1.0%) and A. gemma (0.98%). Tick species that have not been reported in recent studies in Uganda were found amongst cattle in Karamoja, and these were R. pravus, R. praetextatus and R. turanicus. A representative number of ticks, from each tick species identified in the present study were placed in pools of 1 to 10. Subsequently, a reverse line blot (RLB) hybridization assay was performed to screen for the presence of tick-borne pathogens. Out of the 40 tick pools, 30 (75%) were positive for tick-borne pathogens of the genera Ehrlichia, Anaplasma, Babesia and Theileria. The RLB assay results showed that 57% (n=17) of the tick pools were positive for single infections, while 43% (n=13) had mixed infections. The most frequently detected tick-borne pathogens were T. parva (10 pools), T. velifera (10 pools), T. mutans (9 pools) and Theileria sp. (sable) (5 pools). Other pathogens detected were E. ruminantium, B. microti, B. rossi, T. separata and B. bigemina. The tick-borne species B. microti, B. rossi, Theileria sp. (sable) and T. separata are not common in cattle, or not known to infect cattle, but were detected from the ticks collected. The detection of B. microti in this study may point to incidental infections with implications for human health. There could have also been a possibility of cross reactions during the RLB analysis leading to the detection of B. microti in this study. These findings provide knowledge of the distribution of ticks and epidemiology of tick-borne pathogens in cattle and may provide support for control of TBDs and improve cattle productivity. / Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc (Tropical Animal Health) / Unrestricted

Rift Valley fever (RVF), is a mosquito-borne viral disease affecting humans and some species of ruminants including sheep, cattle, goats, buffalos and to a lesser extent wild animals. It is a re-emerging disease responsible for major losses in livestock production, with negative impacts on livelihoods of both commercial and resource- poor farmers in sub-Saharan African and some countries in the Middle East. It remains a threat to both endemic and non-endemic countries where competent mosquito vectors exist. The RVF virus (RVFV) causes the disease and though only a single serotype exists, differences in virulence and pathogenicity of the virus have been observed in a wide range of affected mammalian host species. This necessitates the need for a detailed genetic characterization of various isolates of the virus and whether the causal factors for host tissue tropism can be explained. Therefore, the aims of this study were to obtain comprehensive information on the genetic composition of the RVFVs circulating in South Africa between 2008 and 2010 and to differentiate these isolates based on cell infectivity and genomic parameters. In the first chapter the status of some published literature on the disease as well as the virus are reviewed. Viral characteristics, replication, assembly and release of the viral particle from the cell as well as virus-host receptors documented are also mentioned in this chapter. Chapter two focused on the genetic composition of RVFVs that caused outbreaks during 2008- 2010 in South Africa. Complete genome sequence analysis of isolates from different hosts and tissues collected at discrete foci of outbreaks were analysed and compared with virus sequences from earlier outbreaks in South Africa and from other countries. Phylogenetic analysis indicated that viruses that caused outbreaks during 2008-2010 were most probably reassortants, resulting from exchange of portions of the genome of different isolates, particularly of Segment M. In addition, the analysis indicated that the viruses were not introduced from outside the country but mutated in time and caused the outbreaks when the environmental conditions became favourable. Although no clear association between the virus genotype and phenotype has been established, various amino acid substitutions have been implicated for changes in the phenotype. The third chapter describes the characterization of isolates derived from different hosts (bovine and ovine), but from the same tissue (liver). The isolates from bovine liver presented a different growth phenotype in a cell culture-based system as well as some amino acid substitutions when compared with isolates from ovine livers. Although the codon usage patterns of the six isolates were the same, they differed with those of their hosts. Further investigation of the coding regions of the genome, molecular modelling of glycoproteins and codon usage bias failed to explain the phenotypic changes. The fourth chapter focused on an attempt to identify RVFV glycoprotein receptors using the yeast two-hybrid (Y2H) system. Baby hamster kidney cells were chosen as host cells in the laboratory because hamsters are known to be highly susceptible to RVFV. The complexity of the cDNA library constructed from BHK cells were assessed by random sequencing of 100 clones and revealed that 51 clones were genes from mRNA from the Syrian/Golden hamster using BLAST. The constructed library can also be used to study other animal pathogens such as bluetongue virus and African horse sickness virus. The constructed bait plasmids did not show any autoactivation or toxicity in yeast, thus making them suitable to be used in the Y2H system. Twelve unique clones (4 clones using transformants of the glycoprotein Gn and 8 clones using transformants of glycoprotein Gc) were screened from the cDNA library. Identification and further characterization of the clones is necessary. Sampling of the isolates that caused the 2008-2010 outbreaks in South Africa and full genome sequencing indicated that the isolates were genetically distinct, grouping in different clades, namely C and H. Reassortment have been identified in some of these isolates, particularly in their M segments. The majority of isolates that emerged in the outbreaks accumulated mutations over time while circulating in South Africa. The impact of these mutations on the pathogenicity of RVFV should be further investigated. Sequencing should be done on clinical samples directly to have a better idea of the phenotype and the effect of amino acid substitutions. Different phenotypes observed between cattle and sheep in tissue culture systems should be further investigated including investigation of different phenotypes in vivo using small experimental animals. The study has laid a foundation in understanding the pathogenicity of RVFV and necessitates the importance of understanding molecular mechanisms of the virus. / Thesis (PhD)--University of Pretoria, 2019. / Veterinary Tropical Diseases / PhD / Unrestricted

Foetal loss can be devastating to a cattle farmer. In the Free State province many commercial cattle farms contend with foetal loss due to abortion. The causes of most of these abortions are never diagnosed because of inappropriate samples submitted; diagnostics being too expensive or non-submission of samples due to ignorance. The aim of this study was to investigate the apparent seroprevalence of Brucella species and Coxiella burnetii in commercial cattle of five epidemiological units. The overall apparent seroprevalence in this study was 22% and 11% respectively for Brucella species and Coxiella burnetii antibodies. Although the presence of antibodies does not lead to a definitive diagnosis, it is now known that there are bacterial challenges in these commercial cattle, and this could form the basis of future studies. Improved education of the public as well as communication with the human health sector is necessary to effectively control brucellosis and Q-fever. / Dissertation (MSc)--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc / Unrestricted