African swine fever (ASF) has been reported and confirmed in South Africa since the early 20th century, which lead to the inception of the Swine Fever control zone in 1935. In the South African context, the sylvatic cycle is the main maintenance and transmission cycle that leads to sporadic outbreaks in the domestic pig population, particularly reported in the designated ASF control area. ASF is endemic in sub-Saharan Africa and maintains itself through three different epidemiological cycles in different regions of the continent. The current outbreaks in the Caucasus and Russia have shown the ability of African swine fever virus (ASFV) to establish itself where low biosecurity conditions exist. In South Africa, the spread of ASF has been successfully controlled in the domestic pig populations with control based on the Animal Disease Act 35 of 1984. The act prohibits the movement of all suid species and their products from the ASF control area in the north, except where special permission has been granted by the Provincial Veterinary Services. One of the key uncertainties related to climate change is potential variations in the weather patterns and fluctuations in climatic conditions that could lead to alterations in production systems and land use patterns. These in turn raise the possibility of redistribution of both the arthropod vectors and wild suids to environmentally suitable areas. It is therefore critical for the zoning of ASF that patterns of distribution of the reservoir hosts are monitored in line with the possible variations in the weather patterns around and along the ASF control line. Nonetheless, there are no known records of the reassessment of the swine fever control line, which was instituted based on the distribution of previous outbreaks and the presence of warthogs and tampans, since its inception in 1935. The objective of this study was to evaluate the distribution of the ASF disease determinants; warthogs and warthog burrows, Ornithodoros moubata and ASFV; along the ASF control line with the view of determining whether there was a need to re-align the trajectory of the line or not. A total of 304 farms were randomly selected 20 km north and 20 km south of the ASF control line from the North West, Gauteng, Limpopo and Mpumalanga Provinces through proportional weighting. A total of 73 farms from the initial sample, distributed along the ASF control line, were sampled for the presence of warthogs, warthog burrows and soft ticks of the Ornithodoros spp. (tampans). One hundred and fifty seven warthog burrows were found, of which 92% were recently used by warthogs. Tampans were recovered from 22.2% of the 63 farms where warthog burrows were found and 12.74% of the total (157) warthog burrows. Of the infested warthog burrows, only 5% (one of the twenty burrows) constituting 7.14% (one out of 14 farms) found south but in close proximity to the ASF control line, was positive for ASFV DNA. There were no warthog burrows found with PCR positive tampans north of the ASF control line. The spread of tampans beyond the ASF control line poses a question on whether the control line needs to be moved further south in the affected parts of the country. The study confirmed that the reservoirs are found beyond the current ASF control line. Although the causes for this apparent re-distribution are unclear, changes in land use and the increase in wildlife farming may contribute to this finding. Examination of weather data along the control line between 1993 and 2012 found the maximum temperatures was increasing and humidity is decreasing. In the absence of previous data on warthog and tampan distribution along the control line, the present study cannot evaluate if these changes have had an impact on the distribution of warthogs and tampans in the vicinity of the control line. This study provides baseline data for future monitoring of the control line and concluded that there was currently no need to realign the trajectory of the ASF disease control line but to conduct scheduled monitoring of the O. moubata status in the future. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / Production Animal Studies / MSc / Unrestricted

Emerging small-scale pig farmers in Limpopo province perceive pig production and management as an important means of improving their livelihood and alternative investment option for the future. Their performance has not been optimal due to the lack of practical understanding of the basics of animal production, biosecurity and efficient production system. Thus, an attempt was made to evaluate the challenges and constrains of pig farm production systems identified and reported by emerging small scale pig farmers (ESSPF) in the province. In addition, the risk factors associated with pig movement by ESSPF by means of spatio-temporal analysis was evaluated. The study revealed that the average number of sows/farm was 7.4, while the number of boars/farm was 1.7. On average, the number of days that the sows take to return to oestrus from weaning was 42.9 days while the number of piglet s weaned/sow/year was 4.85 pigs. Also the study showed that 98.77% of ESSPF don t vaccinate their breeding stock against major pig diseases and only 2.47% ESSPF farmers had previously benefited from the infrastructure programme of the department referred to as Comprehensive Agricultural Support Programme (CASP). The majority of the respondents (82.61%) will prefer to sell their pigs at local points and within communities and only 9.32% and 14.09% will sell at the auctions or formal abattoir/supermarkets respectively. It is therefore recommended CASP be evaluated to reach and impact more pig farmers positively. Good animal husbandry and transfer of knowledge by the veterinary officials is central to the growth of farmers and their productivity. The provision of regional slaughter facilities will reduce the travelling costs to Bronkhorstspruit and Belfast, but also reduce the likelihood of the disease spread within or outside the province. The involvement of different stakeholders should be encouraged to ensure ESSPF are trained, mentored, coached, with the aim of improving their livelihood, food security and safety. / Limpopo provinsie is n belangrike vark produseerende gebied met n groot populasie van huishoudelike en wilde diere. Om die rede dien dit as n interfase tussen huishoudelike diere, mense en wilde diere.Alhoewel opkomende varkboere in die provinsie die produksie en bestuur as n belangrike verbetering in hul lewensbestaan asook alternatiewe finansiële beleggingsopsies vir die toekoms beskou, is hul prestasie nie optimaal nie as gevolg van die gebrek aan praktiese begrip van die basiese beginsels van diereproduksie, biosekuriteit en doeltreffende produksie stelsels. Dus, is 'n poging aangewend om die uitdagings en beperkings van varkplaas produksiestelsels te ïdentifiseer en die opkomende kleinskaalse varkboere (ESSPF) in die provinsie te evalueer. Bykomend is die risikofaktore wat verband hou met vark beweging deur ESSPF deur middel van tydruimtelike analise ontleed. Die studie het getoon dat die gemiddelde aantal sôe per plaas was 7,4 terwyl die aantal bere per plaas 1,7 was. Die sôe neem gemiddeld 42,9 dae om terug te keer na estrus vanaf speen, terwyl die aantal varkies gespeen / sog / jaar is 4,85 varkies. Die studie het ook getoon dat 98,77% van ESSPF nie hul teeldiere ent teen die hoof vark siektes en slegs 2,47% ESSPF boere het voorheen voordeel getrek uit die program infrastruktuur van die departement verwys na as omvattende landbou?ondersteuningsprogram (CASP). Die meerderheid van die respondente (82,61%) verkies om hul varke by plaaslike punte binne gemeenskappe te verkoop en slegs 9,32% en 14,09% onderskeidelik verkoop by veilings of formele slagpale/ supermarkte. Dit word dus aanbeveel dat CASP herevalueer om n positiewe impak te bereik by meer varkboere. Goeie veeteelt en die oordrag van kennis deur die veeartseny?amptenare is sentraal tot die groei van die boere en hul produktiwiteit. Die voorsiening van plaaslike slaggeriewe sal die reiskoste na Bronkhorstspruit en Belfast (beide buite die provinsie en tans gekiesde slagpale van die ESSPF) verminder, maar ook die waarskynlikheid van die verspreiding van siektes binne of buite die provinsie verminder. Die betrokkenheid van die verskillende belanghebbendes moet aangemoedig word om te verseker ESSPF opgelei word, gementor, afgerig, met die doel om van die verbetering van hul lewensbestaan, voedselsekuriteit en veiligheid. / Dissertation (MMedVet)--University of Pretoria, 2015. / tm2016 / Production Animal Studies / MMedVet

Despite the occurrence of S. Typhimurium infections, little is known on the genetic diversity, virulence characteristics and antimicrobial resistance profiles of poultry S. Typhimurium in South Africa. Therefore, S. Typhimurium (n=141) isolated from organs (n=115) and environments (n=26) of diseased poultry between 1995 and 2002 were screened by PCR for bacteriophages, plasmids and Salmonella pathogenicity islands (SPIs) - encoded virulence genes (virulotyping) which are essential for invasion (invA, sopB, gtgB, sspH1, sopE, spvC, and pefA), survival (sifA, gipA, sodC1, gtgE, mig5, and sspH2) and serum killing (rck, and srgA) of the pathogen in the host. Isolates were also characterized by: pulsed field gel electrophoresis (PFGE) for genetic relatedness, and plasmid profiling (n=43). Furthermore, isolates (n=141) were tested for susceptibility to 16 antimicrobials by disk diffusion and further screened by PCR for the carriage of 27 resistance genes, and integrons. Multi-resistant S. Typhimurium definitive phage type (DT) 104 were determined by disk diffusion and confirmed by PCR. All isolates carried SPIs-encoded genes: invA, sopB, and sifA. Bacteriophages-encoded genes (sspH2, sspH1, sodC1, gtgB, and gtgE) occurred in more than 74.5% of the isolates expect for gipA (57.6%), and sopE (19%). The occurrence of plasmid-encoded genes (pefA, mig5, rck, spvC, and srgA) ranged from 48.2% to 74.5%. Two sample t - test showed that virulence genes: gtgB, spvC, gipA, gtgE, mig5, rck and srgA were more frequent (p ? 0.05) in S. Typhimurium isolates from environments. Virulotyping clustered 141 isolates into 59 virulotypes with 97 isolates clustering in 5 predominant virulotypes while 44 were single isolate virulotypes. PFGE grouped 140 isolates into 55 pulsotypes with 66 isolates clustering in 5 major pulsotypes, 51 isolates clustering in small pulsotypes (containing less than 5 isolates) while 33 were single isolate pulsotypes. Ten plasmid profiles ranging from 2kb to 90kb were observed. The most common plasmid profile contained the 90kb plasmid and was observed in 12/43 isolates. Major virulotypes and plasmid profiles corresponded approximately to pulsotypes and clustered isolates recovered from the same farms or during the same period. Virulotyping and PFGE showed identical discriminatory index (D=0.93). Multidrug resistance (resistance to ? 2 antimicrobials) was observed in 97.2% of isolates. High levels of resistance phenotypes and their respective resistance genes were observed for: streptomycin (94.3%) conferred by ant3'Ia (60.3%) and str (50.4%), sulphonamides (87.2%) conferred by sul1 (66%) and sul3 (31.9%), ciprofloxacin (79.4%) conferred by qnrA (79.4%), tetracycline (61%) conferred by tetB (35.5%) and tetG (28.4%), and cefotaxime (55.3%) conferred by blaSHV (57.4%). Two sample t - test revealed that isolates from poultry organs were more resistant (p?0.05) to ampicillin, amoxicillin clavulanic acid, chloramphenicol, tetracycline and sulfamethoxazole - trimethoprim while isolates collected from poultry environments were more resistant to cephalothin, cefotaxime, ceftazidime, colistin sulphate and nalidixic acid. Using the Kappa statistics, there were agreements ranging from good to perfect between phenotype and genotype. In addition, for every phenotypic resistance recorded, at least one corresponding resistance gene was detected. DT104 strains and class1 integrons were observed in 34.7% and 83% of the isolates respectively. Multi-resistant S. Typhimurium (97.2%) also carried SPIs - encoded virulence genes involved in invasion and survival in the host. In addition, more than 50% of resistant isolates to each of the antimicrobials also carried at least 12 virulence genes: invA, sopB, sifA, sspH2, sspH1, sodC1, gtgB, gtgE, pefA, mig5, spvC, and srgA. A significant number (44.9%) of the DT104 strains that were clustered in the same pulsotype X25 also belonged to virulotype V3a which contained 13 virulence genes: invA, sopB, sifA, sspH2, sspH1, sodC1, gtgB, gtgE, pefA, rck, mig5, spvC, and srgA. Most of isolates that belonged to the same antimicrobial resistance profile (phenotype and genotype) carried at least 8 common virulence genes. In conclusion, these data indicate that S. Typhimurium isolated from diseased poultry carry virulence genes that are usually incriminated in Salmonella human outbreaks. Virulotyping and PFGE showed the same discriminatory index (D=0.93) indicating that virulotyping can be an alternative subtyping method in laboratories where PFGE is not available. Salmonella Typhimurium are also genetically diverse since they were recovered from multiple farms and during a period spanning 8 years. Furthermore, isolates were resistant to multiple antimicrobials used in poultry operations (streptomycin, sulphonamides, and tetracycline) and those used to treat human salmonellosis: ciprofloxacin, and cefotaxime. Multidrug resistant isolates carried most of virulence genes. This relationship between virulence and antimicrobial resistance suggests that the adaptation of isolates against antimicrobial effects may induce expression of virulence factors. The increasing incidence of DT104 threatens the public health since DT104 strains are associated with hospitalizations and deaths in humans. Salmonella Typhimurium carried mobile genetic elements (bacteriophages, integrons and plasmids) which pose a public hazard as they propagate virulence and resistance genes with emerging new pathogenic bacteria as a result. Therefore, monitoring and surveillance of salmonellosis and prudent antimicrobials use need more efforts to ensure animal health and food safety for consumers in South Africa. / Dissertation (MSc)--University of Pretoria, 2016. / Paraclinical Sciences / MSc / Unrestricted

Cyanobacteria or blue green algae are known for their extensive and highly visible blooms in rivers or dams. One of the most important cyanobacteria is Microcystis aeruginosa which can synthesize various microcystins that can affect the health of terrestrial and aquatic animals. Commercial Nile crocodile (Crocodylus niloticus) farming in South Africa is based on keeping breeders (adult males and females) in big dams on farms (captive-bred approach). Unfortunately, cyanobacterial blooms in the breeder dams are a concern to farm owners, managers and veterinarians. This research project focussed on the monitoring of microcystins in the Hartbeespoort Dam and a crocodile breeding dam over a period of nine months. A commercial, but expensive, Abraxis ELISA kit was compared to a much cheaper and robust Norwegian-developed ELISA to detect microcystins in fresh water. Another objective was to determine if microcystins were present in the contents of crocodile eggs and dead hatchlings. Water samples were collected monthly from August 2014 to April 2015 at two sites, the Hartbeespoort Dam (control site) and the breeding dam of a commercial Nile crocodile (Crocodylus niloticus) farm. In addition, various water quality parameters including nitrate, phosphorous, chlorophyll a, oxygen saturation, pH and total dissolved solids (TDS) were determined to assess eutrophication. During the crocodile hatching season microcystin concentrations in unfertilized eggs, egg-shell membranes and in the yolk and liver of dead hatchlings were determined using liquid chromatography-mass spectrometry (LC-MS). Water quality parameters showed that there was no significant difference between the two dams' (the Hartbeespoort and the breeding dam) eutrophic state i.e. phosphates, TKN and nitrates; they both seemed to be becoming more eutrophic as the nutrient supply to the dam was increasing. Furthermore, microcystin concentrations during peak summer months were generally higher at the Hartbeespoort Dam compared to the crocodile breeding dam. The two ELISAs as performed on water samples "as is" and following an adsorbent disk/methanol extraction method were positively correlated; however, the correlation between the two assays was much stronger when using the adsorbent disk/methanol extraction as compared to using water "as is". Besides dissolved oxygen all the other water quality parameters were not significantly different (p > 0.05) between the two sites. Microcystin concentrations (MC-LR, MC-RR, MC-YR) in the crocodile egg and hatchling samples collected from batches with a good hatching rate (? 90%) ranged between 0 - 1.76 ng/g, with the highest concentration in the eggshell membranes. Microcystin concentrations in samples collected from batches with a bad hatching rate (? 10%) ranged from 0 - 1.63 ng/g with the highest concentration detected in the hatchling yolk. Although the "tissue" concentration levels were probably underestimated with the extraction method employed for LC-MS as the percentage recovery from spiked samples were very low. Bayesian analysis suggests that the liver, yolk and unfertilized egg all have similar microcystin concentrations, while the membranes have (with moderate to high certainty) higher microcystin concentrations. In conclusion, when using the Norwegian ELISA it seems as though the use of a resin-containing adsorbent disk followed by methanol extraction is more reliable than analysing water "as is". Following methanol extraction the results of the two ELISAs were strongly correlated, which suggests that the two ELISAs provide comparable results. There appears to be no difference in microcystin concentrations among good and bad clutches across all tissue types or within a specific tissue type. Vertical transmission of microcystins to the Nile crocodile egg does occur, but due to the small sample size, final conclusion cannot be made if microcystin affects Nile crocodile hatchling mortality and/or hatching of eggs. Future studies will include a longitudinal study to be done since a single season of breeding is insufficient to conclude that microcystins do not contribute to the low hatching rate in Nile crocodiles. / Dissertation (MSc)--University of Pretoria, 2016. / Paraclinical Sciences / MSc / Unrestricted

Shiga toxin-producing E. coli (STEC) is a food pathogen causing infections characterised by mild watery to severe bloody diarrhea and complications such as the hemolytic uremic syndrome (HUS). Humans acquire STEC through consumption of contaminated foods of animal origin, vegetables and water. Cattle are the main reservoir of STEC. The severity of STEC infections in humans depends on a number of virulence factors encoded in the bacterium’s genome. The seven major STEC serogroups most frequently incriminated in severe human disease outbreaks and HUS worldwide include O157, O45, O103, O111, O121, O145 and, O26, commonly referred to as the "top/big seven". Although STEC has been incriminated in human disease in South Africa, data on the role of played by cattle in human disease and virulence characteristics of cattle STEC are lacking. Therefore, the objectives of this study were to (i) investigate the presence of the seven major STEC serotypes in healthy beef cattle (cow-calf operations) and (ii) characterise isolates by serotype, virulence genes and markers, and antimicrobial resistance profiles. Polymerase chain reaction (PCR) was carried out to identify STEC serotypes (O and H antigens) and characterize the isolates by virulence factors and markers. The disk diffusion technique (Kirby Bauer test) was used to determine the antimicrobial resistance profiles of STEC isolates against a panel of 15 antimicrobials. Five hundred and seventy-eight STEC isolates (N=578), which had been previously recovered from 559 cattle from five beef farms were screened for STEC O26, O45, O103, O111, O121, O145 and O157. Confirmed STEC belonging to serogroups O26, O45, O103, O111, O121, O145 and O157 to isolates were characterised for major virulence genes including stx1, stx2, eaeA and ehxA. Furthermore, 140 isolates were characterised for xiii Shiga toxins (stx) subtypes, plasmid and pathogenicity island-encoded genes, and antimicrobials resistance profiles. / Dissertation (MSc)--University of Pretoria, 2017. / Paraclinical Sciences / MSc / Unrestricted

Introduction: Campylobacter spp. is the most frequent cause of bacterial gastroenteritis in humans globally. Campylobacter spp. infections are characterized by acute watery or bloody diarrhoea, fever, weight loss and abdominal cramps. Campylobacteriosis complications include extra-intestinal diseases such as Guillain-Barre Syndrome (GBS) or its variant the Miller Fisher Syndrome (MFS). Consumption of contaminated foods of animal origin including undercooked meat, contaminated dairy products has been associated with foodborne campylobacteriosis in humans. Cattle are considered an important reservoir of Campylobacter spp. and a source of foodborne Campylobacteriosis. Antimicrobial treatment failure in most bacterial infections including campylobacteriosis has emerged and led to the increase of animal and human health care costs. The use of antimicrobials in cattle for therapy in both cattle and humans and for growth promotion in exerts selective pressure on bacterial pathogens, which may result in the emergence of antimicrobial resistant Campylobacter spp. strains which can be transferred from animals to humans along the food chain or through contact between animals and humans. In South Africa, studies on the occurrence and antimicrobial resistance profiles of Campylobacter spp. of public health importance are lacking. The main objectives of this study were to: 1) investigate the occurrence of Campylobacter spp. in beef cattle on cow-calf operations in Gauteng and North West Provinces and 2) determine the antimicrobial resistance profiles of Campylobacter spp. isolates. The overall aim of the study was to contribute to monitoring and surveillance of Campylobacter spp. of public health importance in South Africa. Methodology: A total of 537 fresh faecal samples from beef cattle consisting of 453 from adult cows and 102 from calves were collected on 5 cow-calf operations in Gauteng and North West provinces. The samples were screened for Campylobacter spp., including C. jejuni subsp. jejuni, C. coli and C. upsaliensis by culture and the polymerase chain reaction (PCR). Furthermore, 86 Campylobacter spp. isolates consisting of 46 C. jejuni subs. jejuni, 24 C. coli and 16 C. upsaliensis were tested for antimicrobial resistance against a panel of nine antimicrobial agents including azithromycin, ciprofloxacin, erythromycin, gentamicin, tetracycline, florfenicol, nalidixic acid, telithromycin and clindamycin by the broth microdilution method. Results: Out the 537 cattle faecal samples tested in this study, PCR revealed that 29.4% (158/537) [16.23%-42.57%] 95%CI of cattle carried Campylobacter spp. Among the 158 Campylobacter spp. positive cattle, 62.6% (99/158) carried C. jejuni subsp. jejuni, 25.3% (40/158) C. coli, 10.1% (16/158) C. upsaliensis and 3.1% (5/158) cows that had mixed infections. Three cows harbored both C. jejuni and C. coli, one cow carried C. jejuni and C. upsaliensis and one cow carried both C. coli and C. upsaliensis. Further antimicrobial resistance profiling of 86 Campylobacter spp. isolates (46 C. jejuni isolates, 24 C. coli and 16 C. upsaliensis) by the broth microdilution method revealed that the highest resistance rates for clindamycin (36%), nalidixic acid (19.7%), tetracycline (18.6%) and erythromycin (17.4%). However, lower resistance rates against florfenicol (3.4%), gentamicin (4.6%), telithromycin and ciprofloxacin (5.8%) were observed. The isolates were multidrug resistant against tetracycline/clindamycin, erythromycin/tetracycline/clindamycin, and nalidixic acid/clindamycin. Conclusion: Little is known about the occurrence rates of Campylobacter spp. in beef cattle in South Africa. The prevalence of Campylobacter recorded in this study was consistent with various studies that have reported Campylobacter spp. prevalence rates within the same range in cattle in a number of countries with C. jejuni subsp. jejuni as the most predominant species. Campylobacter spp. isolates were mainly resistant to clindamycin, nalidixic acid and tetracycline. Findings from this study highlight the importance of beef cattle as a reservoir and a potential source of clinically relevant and antimicrobial resistant Campylobacter spp. isolates in South Africa. / Dissertation (MSc)--University of Pretoria, 2018. / Paraclinical Sciences / MSc / Unrestricted

This study evaluated eighteen commercial farms within Gauteng, Northwest and Limpopo provinces, where a representative sample of grow-out fish from each farm, was humanely euthanased, weighed, measured, and each fish’s overall health assessed through microscopic examination of skin and gills. A full necropsy and histo-pathological evaluation of all key organs followed. Farm production parameters were assessed by means of a questionnaire with a detailed history and a comprehensive water analysis that included water temperature, dissolved oxygen, CO2, ammonia, nitrite, nitrate, pH, hardness and alkalinity. These production parameters, together with stocking density and underlying nutrition, were compared with the macro- and microscopic findings for positive and negative correlations / relationships. Significantly high burdens of ecto-parasites and very poor water quality, with compromisingly low dissolved oxygen and temperatures, and high carbon dioxide and nitrite, were found in association with severe gill pathology. This was compounded by inadequate filtration for the density of fish stocked, with resultant toxic nitrogenous waste accumulation. Other key abnormalities observed were chronic-active hepatic lipid oxidation, low hepatocellular lipid, evidence of secondary opportunistic infectious disease, and extremely poor growth. Poor farm management practises were prevalent, with evidence of uneconomical fish sex ratios, and poor implementation of biosecurity and disease management. The study serves to highlight the factors that currently dominate as critical issues affecting overall health and growth of aqua-cultured tilapia in the South African context. / Dissertation (MSc)--University of Pretoria, 2019. / TM2019 / Paraclinical Sciences / MSc / Unrestricted

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