Theses and Dissertations (Production Animal Studies)

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Assessment of Good Agricultural Practices (GAPs) on sustainability outcomes in TMR, hybrid and pasture based dairy farms in South Africa
Blignaut, Tania (University of Pretoria, 2027-11-24)
The South African dairy industry faces growing pressure to balance production efficiency with environmental, social, and economic sustainability goals. Good Agricultural Practices (GAPs), implemented through the Dairy Standard Agency (DSA) Code of Practice for Producers, provide a structured framework to promote sustainable outcomes across various farming systems. This study examined how geographic, operational, and institutional factors—including region, feed regime, herd size, support level, and auditor—influence DSA_GAP compliance and sustainability performance on 152 dairy farms representing the four main production regions. It also compared DSA_GAP Sustainability results with RISE 3.0 sustainability outcomes. Data from 152 DSA_GAP sustainability audits and 24 RISE 3.0 assessments conducted on South African dairy farms with herd sizes from 50 to over 1000 lactating cows across seven provinces, grouped into the four main milk-producing regions - Eastern Cape, KwaZulu-Natal, Northern Regions, and Western Cape- were analysed. Quantitative data were processed using SAS (version 9.4, 2025). Descriptive statistics and Spearman’s correlations were estimated, and general linear models were applied to determine factors influencing sustainability performance. Analyses used a significance threshold of P<0.05 to identify meaningful differences. Findings showed that regional context and support frameworks had the most significant impact on Good Agricultural Practice and sustainability outcomes. The results revealed notable regional differences (P < 0.05): the Western Cape consistently achieved the highest average DSA_GAP Sustainability scores (>80% compliance), driven by strong environmental and compliance performance, whereas the Northern Region showed consistently weaker performance (<80% compliance), particularly under hybrid feeding systems. Pasture-based systems predominated nationally, but herds using Total Mixed Ration (TMR) systems exhibited greater risk resilience and economic sustainability (P<0.05). Herd size significantly affected the overall DSA_GAP sustainability score (P< 0.05), with smaller herds performing worse than medium and large-scale operations. Farms with structured support from processors or extension. Services consistently scored significantly higher (P < 0.05) on overall DSA_GAP sustainability criteria compliance and on the compliance subtheme. Positive monotonic associations between DSA_GAP and RISE 3.0 themes, particularly Environmental–Material (ρ = 0.405; P = 0.050), Social Responsibility–Quality of Life (ρ = 0.466; P = 0.022), and Social Responsibility–Working Conditions (ρ = 0.411; P = 0.046)—indicated measurable alignment between compliance-focused and outcome-based sustainability frameworks. Overall, the study demonstrates that structured GAP implementation is positively associated with improved sustainability performance in the dairy industry, particularly when supported by institutional frameworks and region-specific management systems.
The impact of primary animal health care training on cattle management and market confidence in Capricorn District, Limpopo, South Africa
Molefe, Cisky Kgabisa (University of Pretoria, 2025-05)
Abstract Background: Cattle and other livestock are significant in livelihoods and household economics, and food security of rural dwellers. Despite these significant roles, small scale and rural farmers continue to face persistent challenges that hinder optimal cattle health and productivity. Issues such as poor access to veterinary services, inadequate knowledge of animal health management, low adoption of improved husbandry practices, and limited agricultural extension services negatively impact production and productivity. Training and extension services are critical for improving livestock outcomes; however, it is unclear whether livestock extension service in Capricorn District and elsewhere in South Africa are impactful. Aim: This research aimed to evaluate the impact of the Afrivet Primary Animal Health Care (PAHC) training and extension model on selected management and production parameters, and marketing in cattle owned by small-scale and rural farmers in Capricorn District, Limpopo Province, South Africa. Methods: Using a quasi-experimental design, the immediate outcomes of the Afrivet Primary Animal Health Care (PAHC) training model were evaluated by comparing selected relevant indicators before and after the training implementation among the smallholder livestock farmers in Capricorn District, Limpopo Province. Farmers were selected by simple random assignment from prepopulated lists with the assistance of a random number generator. Four municipalities were selected and participants were allocated through proportional representation. Awareness creation, stakeholders’ engagement and demonstrations were conducted to familiarise farmers, and these were followed by targeted Afrivet PAHC trainings. Production, economic and health parameters were collected over 17 months and compared and contrasted for skills, knowledge, farm practices and other variables. Data were analysed using descriptive and inferential statistics. Findings: Four municipalities and nine villages were studied, and the majority of smallholder farmers were above 50 years with low literacy level. Livestock, especially cattle, serve multiple purposes and are rarely sold, except in emergencies or during critical needs. The out-of-hand transactional sale, followed by auction markets, were the popular forms of sale among smallholder farmers. Farmers hardly adopt farm adaptive programmes, technologies and practices that could improve their productivity and livelihoods, and 85% will do nothing even in livestock emergencies like ill health, and only 15% will call an animal health technician or a veterinarian. Following Afrivet PAHC training, mortality rates were significantly reduced, and participants gained significant knowledge and skills in defining PAHC and understanding the role of the veterinary professional. Significant increase was observed in the identification of disjointed cattle body parts, signs of health and listing specific causes of diseases. More importantly, farmers gained considerable confidence in the ability to sell livestock at auction, butchery, and at the feedlot market. No significant difference was observed in the ability to sell livestock at out-of-hand sale and at official abattoir. Response to livestock vaccination has been overwhelming in recent times, especially against anthrax and black quarter diseases. Syndrome-wise, farmers frequently reported ticks, nasal discharge, and diarrhea, occasionally reported skin problems, and moderately or less frequently reported other syndromes. Conclusion: Intensive Afrivet PAHC extension and training model was beneficial to smallholder livestock (cattle) farmers in Capricorn District, Limpopo Province, South Africa as it boosted farmers confidence in exploring new market channels for livestock offtake. The provincial and national veterinary authorities should create incentives that convert boosted confidence into concrete actions, and eliminate bottlenecks associated with infrastructural, logistics and institutional challenges. The low level of literacy and reluctance to act in the event of disease outbreaks, as well as the unwillingness to adopt new, easy-to-implement farm-level technologies and good farming practices, along with socio-demographic and economic barriers, will continue to hinder optimized productivity and production. These gaps must be bridged using a flexible, inclusive model that can incorporate feedback to continually improve the Afrivet PAHC training and extension model, mitigate identified constraints, and utilise enablers as low-hanging fruits to catalyse adoption and upscale smallholder farmers' livelihoods.
Effects of supplementation with Mimosa tannin (Acacia mearnsii) extracts on ovine sperm cryopreservation, and viability
Liman, Mohammed Sulaiman (University of Pretoria, 2025-11-01)
The increase in human population has placed pressure on livestock industries to increase production. Livestock farming contributes up to 49% of agricultural output in South Africa, with lamb and mutton production increasing in the past decade (Meissner et al., 2013). To ensure cost-effective production practices, farmers use genetic selection and assisted reproductive technologies (ART) to enhance reproductive efficiency and to counter the local deficit and demand (Meissner et al., 2013). Genetic breeding programmes in small ruminants focus on the selection of traits that contribute to improving the production and reproductive efficiency of livestock species (Granleese et al., 2015). The important selected traits especially improve feed conversion, disease resistance, optimal reproductive ability, and the utilisation of ART (Granleese et al., 2015). Selection of animals according to certain traits to specifically improve or optimise production and reproduction efficiency is geared towards improving the genetic composition of the particular animal species, which is vital in food security (Haile et al., 2019). Reproductive performance of male livestock is of economic importance as well as in improving sperm quality and fertility for artificial insemination (AI) programmes which will help minimise losses from genotype (Haile et al., 2019). The addition of antioxidants with very good preservation techniques improves sperm function during storage with good capacitation/fertilization in the female reproductive tract (Ros-Santaella and Pintus, 2021). Plants containing combinations of complex polymeric phenols (tannins) are amongst the most studied phytochemicals because of their biological functions and health-promoting effects (Ros-Santaella and Pintus, 2021; Wurlina et al., 2020). A commercially available tannin-rich extract of black wattle bark, Acacia mearnsii (ATE), comprises a complex mixture of chemicals yet to be identified (Pizzi, 2021). A previous study of supplementation of non-encapsulated tannin extract (TE), and capsulated tannin extract (ETE) improved the reproductive performance of South African mutton merino rams and motivated this study. In the first study, the ATE dried powder underwent ethanol extraction (to recover polyphenolic compounds while excluding water-soluble sugars and salts), yielding MTE_0 (484.28 g, 89.7%), which was fractionated, and antioxidant activity and cytotoxicity of these samples was investigated. For fractionation, part of the MTE_0 extract (1.4 g) was solubilised in methanol and fractionated using column chromatography with Amberlite XAD-16 resin. Following chromatography, the total eluate of 1.24 g (83.8% of MTE_0) was divided into four fractions: MTE_1 (200 mL; 0.52g), MTE_2 (100 mL; 0.02g), MTE_3 (100 mL; 0.63g), and MTE_4 (200 mL; 0.08g) and stored at -20°C. Ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) analysis was employed to tentatively identify the constituent compounds. In all, six samples (2 extracts: ATE, and MTE_0, with 4 fractions: MTE_1, MTE_2, MTE_3, and MTE_4) were tested. Antioxidant activity was determined by the 2, 2’ -azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays which resulted in inhibition concentration (IC50) values of ATE (2.9 × 10⁻³ and 2.4 × 10⁻²), while the extract MTE_0 (1.0 × 10⁻³ and 1.8 × 10⁻²), and fraction MTE_3 (1.4 × 10⁻³ and 2.0 × 10⁻²) had the most active antioxidant capacity amongst the samples when compared to that of ascorbic acid (1.3 × 10⁻³ and 1.2 × 10⁻³). The cytotoxic effects of the extracts and fractions was evaluated on the rat Leydig (LC-540) cells using the AlamarBlue®, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays and transmission electron microscopy (TEM) to validate their potential as non-cytotoxic natural antioxidants on the reproductive cells. UPLC-HRMS resulted in the tentative identification of sucrose (341.1084 (-1.8ppm) m/z, [M-H].- in all the extracts, and seven flavonoid compounds were detected in the various fractions, namely gallocatechin (305.0661 (-3.6) m/z, [MH₋], glucosyringic acid (359.0978 (0.8 ppm) m/z, [M-H]-, gallocatechin-(4α→8)-catechin (593.1295 (-3.0 pm) m/z, [M-H]₋₋, fisetinidol-(4α→8)-catechin (577.1346 (1.6ppm) m/z, [M-H].- , arecatannin A1 (865.1980 (0.8ppm) m/z, [M-H]- , fisetinidol-(4α→6')-fisetinidol-(4α→6)-gallocatechin (849.2031 (1.4ppm) m/z, [M-H].- and fisetinidol-(4α→8)-catechin-(6→4α)-fisetinidol (833.2082 (4.0ppm) m/z, [M-H]-. The common flavonoid compounds that were present in both the MTE_0 extract, as well as in the fraction MTE_3 with the most active antioxidant capacity, were gallocatechin-(4α→8)-catechin, arecatannin A1, fisetinidol-(4α→6')-fisetinidol-(4α→6)-gallocatechin and fisetinidol-(4α→8)-catechin-(6→4α)-fisetinidol. In addition, cytotoxicity evaluation on rat Leydig cells (LC-540) demonstrated favourable safety profiles, with IC₅₀ values ranging from 8.21-58.04 µg/mL for extracts and fractions (MTT and AlamarBlue® assays), substantially higher than the positive control doxorubicin (0.60 µg/mL). Transmission electron microscopy revealed no ultrastructural damage at functional antioxidant concentrations, with fraction MTE_1 (IC₅₀ 58.04 µg/mL) exhibiting the lowest cytotoxicity. In the second experiment, ejaculates (n=6) of matured merino ram live body weight (LBW) of 120 kg were added to the extract and gallocatechin with OptidylTM, a commercial extender for chilled semen storage at different concentrations (0, 12.5, 25, 50, and 100 µM) of MTE_0, and gallocatechin and stored for 10 days at 4 to 10°C. The aliquots of MTE_0 and gallocatechin-treated spermatozoa were assessed for viability, acrosomal integrity, mitochondrial membrane potential, and capacitation status at the end of incubation. The kinematics parameters were evaluated by computer-assisted sperm analysis (CASA) with the trial performed in triplicate. Data were analysed by a one-way ANOVA procedure of IBM SPSS 21.0 for Windows. In chilled semen stored at 4-10°C for 10 days, gallocatechin at 25 µM significantly (p<0.001) improved the live spermatozoa proportions (32.38±0.55%; 19.54±0.26%), while affecting ROS levels (35.38±0.55%; 25.60±0.55%) and capacitation status (31.48±0.81%; 20.46±0.81%) compared to control. In the third experiment, 6 adult (3 ± 5 years) Merino rams with average LBW (116kg) (n=6) were used. The rams were kept in individual pens at a commercial semen station (RAMSEM) in Bloemfontein. The ejaculates were collected by trained attendants with artificial vaginas (AV) twice weekly for 3 weeks. Immediately, ejaculates were transferred to a water bath at 37°C. Ejaculates with at least 1 mL per ejaculate, creamy fresh semen of an average of 2.3 x 109 sperm mL-1, with 60% live sperm, and mass motility of 3-4 out of 5 scales were used for the experiment. This was extended to a final concentration of 13 X 106 sperm mL-1 with the tris-based extender Optidyl TM (Biovet, France). This was pooled and divided into five aliquots (0, 12.5, 25, 50, and 100 µM). Immediately after the collection, we determined the volume, the mass motility, and the percentage of live sperm of the fresh semen. For each aliquot, a concentration of gallocatechin (0, 12.5, 25, 50, and 100 µM) was added before freezing, and stored inside liquid nitrogen tanks. The spermatozoa were assessed for viability, acrosomal integrity, mitochondrial membrane potential, and capacitation status at the end of incubation. The motility parameters were evaluated by CASA with the trial performed in triplicate and the data were analysed by ANOVA. In conclusion, the review was the first to recommend the addition of tannin-rich extract or compounds into semen destined for cryopreservation, exploiting their diverse effects on biological antioxidation (Liman et al., 2022). Furthermore, it was recommended that future studies be conducted on the biological activities of tannins by determining their chemical structure, biological activities, and structural activity relationships so that potential applications can be explored (Liman et al., 2022). The initial laboratory-based experiment was the first to fractionate ATE and explore its antioxidant activity, and constituents were tentatively identified using UPLC-HRMS. It was concluded that gallocatechin is a promising candidate antioxidant for use in semen during preservation. Gallocatechin has a higher number of hydroxyl groups and greater polymerization that afforded the greatest antioxidation activities. In this study, gallocatechin addition to chilled semen recorded a significant (p ≤ 0.001) positive effect compared to the MTE_0 extract). The addition of gallocatechin at 25 µM resulted in significantly (p ≤ 0.001) improved proportions of live spermatozoa (32.38 ± 0.55: CTL 19.54 ± 0.26 %), modified ROS (35.38 ± 0.55: CTL 25.60 ± 0.55 %), and capacitation status (31.48 ± 0.81: CTL 20.46 ± 0.81 %) compared to control (CTL). On the contrary, in a further experiment, gallocatechin at 100 µM significantly affected (p ≤ 0.001) kinematic parameters such as average path velocity (VAP) (97.29 ± 2.04: CTL 89.31 ± 1.54 %), progressive velocity (VSL) (80.95 ± 2.18: CTL 72.36 ± 2.03) and beat cross frequency (BCF) (36.27 ± 0.39; CTL 34.06 ± 0.57%) of cryopreserved semen compared with control. Gallocatechin addition to semen resulted in a significant (p≤0.001) positive effect compared with the MTE_0 extract. Thus, gallocatechin addition to ovine semen significantly reduces semen deterioration following cryopreservation. The findings in the second experiment are an important fertility indicator, while the findings in the third experiment demonstrated improved post-thawed ovine semen quality and longevity. This study is the first to introduce gallocatechin as an efficient antioxidant additive to ovine semen to improve its quality during storage, assisting with improving post-thaw ovine semen quality and longevity. Future studies to elucidate the mechanism of anti-oxidative stress action of gallocatechin and its derivatives on semen motility and longevity are recommended.
Epidemiology, control, and economic impact of foot-and-mouth disease in Malawi
Chimera, Elizabeth Thandiwe (University of Pretoria, 2026-02-09)
Foot-and-mouth disease (FMD) is a transboundary animal disease that has negative economic impact on the livestock sector, regional and international trade in endemic settings. The foot-and-mouth disease virus (FMDV), a single-stranded RNA virus, is responsible for infection in cloven-hoofed livestock and wildlife. Implementation of efficient and economically feasible control measures decreases the number of animals at risk and economically benefits smallholder farmers and endemic countries. An increasing number of FMD outbreaks in Malawi raises concerns and calls for more intensive control measures, yet very little information exists about the epidemiology and economic impact of FMD in Malawi. This research provides insight into the epidemiology of FMD in Malawi to guide decision making by establishing the spatio-temporal distribution and determining the risk factors associated with FMD. This work also evaluates four potential FMD control strategies and assesses the economic impact of FMD in Malawi.The distribution of FMD and its associated risk factors in Malawi from 1957 to 2016 were assessed using a retrospective space-time analysis alongside a matched case-control analysis. Additionally, four potential strategies for controlling FMD were examined through a multi-criteria decision analysis (MCDA) approach. The economic costs related to FMD in Malawi from 2018 to 2023 were estimated, and a benefit-cost analysis was conducted to evaluate the profitability of implementing more intensive control measures. This analysis included Control Option 1 (reactive emergency ring vaccination, movement control, and surveillance) and Control Option 2 (emergency ring vaccination, surveillance, movement control, and biannual vaccination), which were compared against the absence of an official control program. The retrospective analysis revealed two significant spatio-temporal clusters of FMD: in the southern and northern region. Factors associated with an increased risk of FMD included higher beef and higher pig densities, greater distances from roads, and proximity to international borders. Among the assessed control strategies, the one that combined enhanced surveillance, movement control, emergency ring vaccination, and biannual vaccination of cattle in high-risk areas was the most favoured according to the MCDA. While both control strategies mitigated the impact of FMD compared to the no control option, neither demonstrated economic profitability. These findings establish a fundamental understanding of the epidemiological and economic dynamics of FMD in Malawi and underscores the necessity for further evaluation of the efficacy and cost-effectiveness of FMD control strategies in the country.
Epidemiology of high pathogenicity avian influenza in key ostrich producing areas of South Africa
Marimwe, Miriam Chengeto (University of Pretoria, 2025-10)
High pathogenicity avian influenza (HPAI) has become a major focus for countries on all continents due to its zoonotic potential and economic effects resulting from trade restrictions and high mortality rates in poultry. HPAI outbreaks have occurred in key ostrich producing provinces of South Africa disrupting exports and raising questions on the disease introduction, transmission and control in ostriches. This thesis analyzed spatiotemporal occurrence patterns and risk factors during two HPAI outbreaks as well as the early detection surveillance system of the current active surveillance system in ostriches in the Western Cape Province of South Africa, with the aim to inform surveillance and control measures in South African ostrich population. The first study investigated the spatiotemporal patterns associated with the 2011 (H5N2) and 2017 (H5N8) HPAI outbreaks in the key ostrich producing areas of South Africa, The second study similarly investigated risk factors associated with the 2011 H5N2 and 2017 H5N8 HPAI outbreaks on ostrich farms within the Western Cape Province of South Africa, using a questionnaire on ostrich farming practices as well as historical weather records and spatial agro-ecological information. The third study created a stochastic model to analyze the early detection surveillance sensitivity of the different surveillance components of the avian influenza (AI) sero-surveillance system in ostriches of the Western Cape Province. The spatial, temporal and directional distributions of both outbreaks were different, suggesting potential dissimilarities in the important risk factors for introduction and possible transmission pathways. The risk factors associated with each outbreak also differed, further corroborating the dissimilarities in introduction and transmission. The early detection surveillance sensitivity of the current overall active surveillance system is low within the first month and it could be improved by incorporating temporal risk in the surveillance planning. Continual research is essential in this field to further understand the epidemiology of the avian influenza virus in ostriches and inform surveillance as well as control of AI in the ostrich population of South Africa.
Thoracic imaging and bronchoalveolar lavage findings in captive Black-footed cats (Felis nigripes) in South Africa
Humphreys, Jessica (University of Pretoria, 2025-10-28)
Black-footed cats (BFCs) are endemic to southern Africa, and due to their vulnerable status (IUCN), research efforts are focused on identifying risks in wild populations, and captive population management. Evidence shows that this species suffers high stress and reduced survivorship in captivity, the latter primarily due to renal amyloidosis. Unpublished post-mortem examinations in South Africa have noted excess mucus in respiratory tracts as a cause of death, with the presence of goblet cell hyperplasia in a number of animals from captive populations. This pilot study aimed to investigate bronchoalveolar lavage (BAL) cytology, explore lung pathology and develop standardised imaging protocols for BFCs in captivity. Sixteen cats from two captive breeding facilities were sampled opportunistically during annual health examinations. Eight (50%) of the animals sampled showed radiographic signs of lung pathology, particularly a bronchial pattern. An ultrasound examination technique adapted from the Thoracic Focused Assessment with Sonography in Trauma (TFAST) method, found that all animals sampled exhibited a degree of lung consolidation. In addition, mean vertebral heart scores were 8.84 ± 0.42, which were greater than standard normal ranges for domestic cats, suggesting that the species' standard range is not comparable to that of domestic cats. Moderate to high amounts of clear mucus were found in 13/15 (87%) of BAL samples. Cytological evaluation confirmed the presence of mucus, mucus-associated goblet cells and high numbers of neutrophils. Bacterial culture of BAL samples (n=14) exhibited no significant growth. Further investigation is needed to identify risk factors associated with this severe chronic bronchitis.
Population dynamics, host biting networks and dispersal distances of potential vectors of Rift Valley fever virus in north-eastern KwaZulu-Natal and western Free State provinces, South Africa
Makhanthisa, Takalani Irene (University of Pretoria, 2025-10-31)
Rift Valley fever virus (RVFV) is a single stranded RNA zoonotic mosquito-borne virus that causes periodic outbreaks with significant animal health, public health and economic consequences. The virus is endemic in the sub-Saharan Africa but has also spread to the Arabian Peninsula and other African regions. Three major Rift Valley fever (RVF) outbreaks have been reported in South Africa, from 1950-1951, 1973-1976 and 2010-2011. Recent circulation of RVFV has been reported in north-eastern KwaZulu-Natal (neKZN), South Africa, where the virus is suspected to be endemic, although outbreaks have not been reported in the area. The vectors of RVFV in this area are poorly understood, although several mosquito species such as Aedes (Aedimorphus) durbanensis, Aedes (Neomelaniconion) circumluteolus, Culex (Culex) tritaeniorhynchus and Culex (Lasioconops) poicilipes are the suspected vectors since they have previously been associated with transmission of RVFV. The first aim of the study was to describe the species diversity, abundance and seasonal population dynamics of potential RVFV vectors in neKZN, to identify potential RVFV vectors. A total of 141,594 mosquitoes consisting of 46 species from 8 genera including Aedes (n = 2,610), Culex (89,143), Mansonia (44,029), Anopheles (4,709) and others (n = 1,103) were sampled over a three-year period from pans located in three sites (Namaneni, Mpala and Bumbe). Culex tritaeniorhynchus (n = 55,491, 39.19%), Mansonia (Mansonioides) uniformis (n = 35,453, 25.04%) and Cx. poicilipes (n = 14,192, 10.02%) were the most frequently collected species. The most common Aedes species were Ae. durbanensis (n = 1,473), Ae. mcintoshi (n = 526) and Ae. circumluteolus (n = 265). The mosquito abundance changed significantly over the study period (p < 0.001). Overall mosquito abundance peaked significantly between January and April, while a substantial increase in Aedes spp. was observed in May. Namaneni (n = 107,204) had the highest species abundance and diversity (H = 1.79 and 1-D = 0.77) while Mpala (n = 32,213) had the highest species richness (S = 39). The second aim was to determine the vertebrate blood meal sources of potential RVFV mosquito vectors in neKZN and to characterize the host-biting network. A total of 561 blood-fed mosquitoes were collected from rural areas (n = 445) and Ndumo Game Reserve (n = 116). Nyala (Tragelaphus angasii) was the most frequent host from the reserve (n = 61) while cattle (Bos taurus) was the most common vertebrate blood meal sources from the rural area (n = 195). The rural network comprised 42 species (24 mosquitoes and 18 hosts) with 314 interactions and the reserve network consisted of 13 species (4 mosquitoes and 9 hosts) with 95 interactions. Most of the blood meals for floodwater Ae. circumluteolus and Ae. mcintoshi in the rural areas originated from cattle while nyala was the most common vertebrate blood meal source in the reserve and a source of blood for majority of Ae. circumluteolus meals. The third aim was to detect RVFV in mosquitoes using real time reverse transcriptase polymerase reaction (RT-PCR). A total of 55,113 mosquitoes (Aedes = 2,606, Culex = 36,624, Mansonia = 15 149 and others = 734) from neKZN, including blood-fed mosquitoes, were screened for RVFV and all tested negative. Low RVFV detection rates in mosquitoes have also been reported in other studies. The fourth aim was to estimate the dispersal distances of various potential RVFV mosquito vector species from a seasonally flooded wetland in the western Free State, where large RVF outbreaks occur. A capture mark release recapture (CMRR) study was conducted in a seasonal pan after a period of heavy rainfall. A total of 5,622 mosquitoes were marked with fluorescent dye and released. A total of 281,254 mosquitoes, of which 163 (0.06%) were marked, were collected using 30 CDC traps at distances between 250 and 1000 m over the following 6 days. Neomelaniconion spp. accounted for 19% of the recaptures, while Cx. theileri (43%) and other Culex mosquitoes (32%) were the most frequently recaptured mosquitoes. The mean distance travelled by Neomelaniconion spp. and Ae. (Ochlerotatus) caballus/juppi was 250 m while for Cx. theileri it was 489 m. This study has demonstrated that several mosquitoes such as Cx. tritaeniorhynchus, Cx. poicilipes, Cx. antennatus and Mansonia spp., that have been implicated in RVFV transmission are abundant in neKZN and could play an important role in transmission. Other RVFV suspected vectors including Ae. circumluteolus, Ae. mcintoshi and Ae. durbanensis were also collected. Vertebrate host species such as cattle, goats and nyala likely also play a central role in RVFV transmission and maintenance. Results from the dispersal study contribute to the knowledge of dispersal of potential RVFV mosquito vectors, which is important for predicting the local spread of mosquito-borne diseases.
Zoonotic risk, communal farming and livestock trade : the example of Rift Valley fever in north-eastern KwaZulu-Natal
Ngoshe, Yusuf Bitrus (University of Pretoria, 2025)
The emergence and spread of Rift Valley fever (RVF) present a significant challenge to both animal and human health across Africa and the Middle East. This zoonotic disease, caused by the RVF virus (RVFV), primarily affects livestock but can also infect humans, leading to substantial economic losses through livestock deaths and trade restrictions. In South Africa, major outbreaks occurred in 1950-51, 1974-76, and 2010-2011, resulting in significant livestock losses and human infections. Recent studies have found that RVFV is endemic among livestock and wildlife in the northern coastal areas of the KwaZulu-Natal (KZN) province. To investigate factors potentially impacting the risk of RVFV spread in and out of northern KZN, three interconnected studies were conducted focusing on the uMkhanyakude District. The first examined communal livestock farmers' knowledge, attitudes, and practices regarding livestock and zoonotic diseases. Surveying 504 farmers across 45 dip tanks, the research revealed moderate overall knowledge (53.2%) of animal disease transmission. Despite this, over 40% of farmers were unaware of the zoonotic risks from wildlife and livestock. This finding highlighted the critical need for targeted educational interventions. Building on these insights, the second study analysed livestock movement patterns within the wildlife-livestock interface area. The analysis of movement permits from 2015 to 2018 revealed 3,598 movements involving 33,561 animals. Sixty-three percent of these movements were directed outside the study area, including into areas which have previously experienced RVF outbreaks, with distinct patterns for cattle and goats. The study demonstrated the potential for disease spread across provincial boundaries and identified certain dip tanks acting as key movement nodes, emphasizing the need for enhanced surveillance measures. The final study evaluated the risk of RVFV spread from north-eastern KZN using a stochastic risk assessment model to evaluate the monthly probability of at least one viraemic animal arriving at a destination outside the study area via a legal animal movement. Temporal modelling showed peak risks in January-March for goats (0.77) and February for cattle (0.44), aligning with high movement and favourable vector conditions. Within the study area, coastal and riverine areas presented moderate, variable risk, while mountain areas remained consistently low. Sensitivity analysis identified RVFV infection incidence rate, monthly animal movement volume, duration of viraemia, and duration of transport as the most influential parameters in terms of variability. These findings collectively underscore the importance of adopting a One Health approach to RVF control, integrating disease surveillance, environmental monitoring, movement control, and community education. The research highlights the critical need for enhanced surveillance systems, particularly in identified high-risk areas, and emphasizes the importance of collaborative efforts between veterinary and public health authorities. Furthermore, the studies suggest that effective disease control strategies must consider both the ecological factors driving disease transmission and the social contexts in which livestock farming occurs.
A reassessment of the epidemiology, pathogenesis and prevention strategies of bovine keratoconjunctivitis in Western Cape dairy cattle
Maartens, Louis Henning (University of Pretoria, 2025)
Bovine keratoconjunctivitis (BK) is an inflammatory eye condition of cattle that poses significant challenges to animal welfare, dairy and beef productivity, and antimicrobial stewardship in food-producing systems. The principal bacterial agents associated with BK, Moraxella bovis and M. bovoculi, are part of the core ocular surface microbiota in cattle. Rather than behaving as classical infectious agents, these symbionts demonstrate pathogenic potential under permissive conditions, while a range of animal- and herd-level factors modulate disease expression. This research aimed to address the scarcity of epidemiological data on BK in dairy systems and to facilitate evidence-based recommendations for its prevention and control in the Mediterranean climatic zone of South Africa’s Western Cape. A multifaceted investigative framework was employed, integrating a narrative literature review with causal mapping via directed acyclic graphs, analytical validations, and observational studies conducted on commercial dairy herds. Both cross-sectional and prospective cohort designs were used, supported by statistical modelling to define disease patterns and identify associated risk factors. A substantial BK prevalence of 19.4% (95% CI: 15.0–24.8%) was found among dairy cattle exposed to the region’s hot, dry summer conditions. Among heifers, the incidence density rate was 25.1 cases per 100 eye-years (95% CI: 20.7–30.4) over a twelve-month period, peaking at 55.9 cases per 100 eye-years during summer. Neither M. bovis nor M. bovoculi was consistently associated with clinical BK occurrence. Animal-level risk factors included breed, younger age, poor nutritional status, and concurrent facial or palpebral skin conditions such as ringworm. At herd level, intense solar radiation and elevated fly densities were associated with increased BK incidence. Management practices, including open herd strategies, inadequate shade provisioning, increased pyrethroid use in fly control programmes, and infrequent manure removal, were also associated with higher disease levels. No protective effect could be shown for the available vaccine under natural exposure conditions. These findings support a reframing of BK prevention strategies, shifting away from pathogen exclusion and minimalistic, vaccine-centric approaches towards ecologically informed, management-driven interventions. Priority should be given to nutritional resilience, welfare-oriented heifer management, integrated pest control, and judicious pesticide use. Biosecurity policies must acknowledge the microbial connectivity facilitated by tear-feeding insects and the limited efficacy of conventional exclusion measures in controlling commensal organisms with pathogenic potential. Collectively, this work advances a more holistic and context-sensitive framework for safeguarding bovine ocular health within dairy production systems.
Prevalence and characterisation of Mycobacterium species in cattle and sheep at Gauteng abattoirs
Mareledwane, Vuyokazi Epipodia (University of Pretoria, 2022-04)
Bovine tuberculosis (bTB) is a zoonotic disease with a great economic impact estimated at billions of dollars annually worldwide. It is a highly infectious disease infecting mainly wildlife, domestic animals, and humans. The causative agent for the disease is a group of bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). The current study aimed at investigating the prevalence and characterize Mycobacterium species in slaughter animals at Gauteng province abattoirs and to assess the risk of zoonotic tuberculosis posed to abattoir workers. In an attempt to fulfil the objective samples were collected from Gauteng province abattoirs. There is limited data available on abattoir-based studies on bovine tuberculosis (bTB) in South Africa. Abattoirs were chosen for this study as they provide important information of data and they play a key role in passive surveillance on the status of the prevalence of bTB in livestock. The study first reviewed the retrospective data for Mycobacterium spp. in the laboratory data in the Tuberculosis Laboratory at the Agricultural Research Council-Onderstepoort Veterinary Research (ARC-OVR) between 2007 and 2016. Samples that were submitted at the ARC-OVR from nine provinces of South Africa, were analysed for the prevalence of Mycobacterium spp. over these 10 years. The findings revealed that the total prevalence of Mycobacterium spp. was 18.47% [834/4516; 95% Confidence Interval: 17.37 – 19.63] with individual species prevalence at 11.47%, 5.20%, 1.53%, 0.24%, and 0.02%, for Mycobacterium bovis, Mycobacterium Other Than Tuberculosis (MOTT), Mycobacterium tuberculosis, Mycobacterium avium, and Mycobacterium orygis respectively. The findings revealed that M.bovis seems to be the most prevalent Mycobacterium species in both domestic animals at 62.26% and wildlife at 63.68%. The study found that factors for bTB such as the presence of wildlife reservoirs and contact with these reservoirs are a great influence on the transmission of the disease that could result in animals testing positive for Mycobacterium spp. Samples from Limpopo, Mpumalanga, and Gauteng provinces were most likely positive for Mycobacterium spp. The majority of samples from Gauteng province originated from captive wildlife. M. tuberculosis, which is mostly a human pathogen rather than M. bovis, was isolated. The study also highlights that wild carnivores and marine animals are more likely to test positive as these animals are likely to feed off infected prey. Study results showed that most of the organs were prone to infection by Mycobacterium spp. Improved data collection is required so that scientific research can target several aspects highlighted by the information obtained from the records. The laboratory data obtained in this study gave insight into the occurrence of Mycobacterium spp. in wildlife, livestock and their environment in South Africa and the factors that influence the transmission of mycobacteriosis such as bTB. Furthermore, we reviewed serological laboratory data in the Tuberculosis Laboratory at the Agricultural Research Council-Onderstepoort Veterinary Research (ARC-OVR) for the period 2011 - 2016. This was done to further highlight the importance that the combination of both bacteriological data and serology provide better insight into the epidermiology. Out of 10,369 fresh blood samples that were submitted from all of the provinces around South Africa and tested using the Bovigam® kit, the results showed that 1.54% (95% Confidence Interval: 1.30 – 1.78) were positive for bTB, 3.75% (95% Confidence Interval: 3.38 - 4.11) were avian reactors, and 2.29% (95% Confidence Interval: 3.38 - 4.11) were a combination of multiple reactors, equal reactors as well as animals that had a positive screening test. (A multiple reactor means an animal reacted positively to all tuberculin suggesting a possible infection with either Mycobacterium bovis or Mycobacterium forfuitum or both and in some instances even Mycobacterium avium. An equal reactor means an animal reacted positively to both avian or bovine tuberculin due to possible infection with either Mycobacterium bovis or Mycobacterium avium or both). Also, the results showed that the most number of samples tested were buffalo samples with 88.96% (95% Confidence Interval: 88.35-89.56), followed by domestic bovine (cattle) at 9.94% (95% Confidence Interval: 9.37 – 10.52). Our results showed that there is generally a low prevalence of bTB in South Africa. Furthermore, we collected fresh blood samples with corresponding tissue samples at the point of slaughter at abattoirs and samples were subjected to serological assays and bacterial cultureto detect the active interferon-gamma (IFN-γ) and isolate mycobacterial species respectively. The study was conducted at selected abattoirs in the Gauteng Province in South Africa where animals were also subjected to routine meat inspection. A total of 410 fresh blood samples were collected during the slaughter of animals (369 cattle and 41 sheep) from 15 abattoirs and analysed using a Bovigam® 1G-test kit (Prionics AG, Lelystad, The Netherlands) Bovigam test kit with bovine, avian, and fortuitum purified protein derivatives (PPD) as blood stimulating antigens. The estimated prevalence of bTB in cattle was 4.4% (95% Confidence Interval: 2.4%-7.3%) and the prevalence of avian reactors was 6.0% (95% Confidence Interval: 3.6%-9.2%). None of the sheep with valid test results (i.e. test samples that have passed quality control checks) were positive for bTB and none were avian reactors (95% Confidence Interval: 0% - 15%). Additionally, we collected a total of 2000 tissue samples comprising of lungs, liver, spleen, and lymph nodes were collected from 19 abattoirs. Additionally, 19 environmental samples were collected from feedlots, where animals usually drink as they await slaughter. These samples were cultured on Lowenstein-Jensen (LJ) media containing both pyruvate and glycerol. The cultures were monitored for growth over 10 weeks. Colonies that displayed morphology resembling that of Mycobacteria were first subjected to Ziehl-Neelsen (ZN) staining, then acid fast bacteria were subjected to a polymerase chain reaction (PCR) assay targeting Mycobacterium tuberculosis complex bacteria. No MTBC species were detected by PCR. The same isolates were subjected to the 16S rRNA PCR and gene sequence analysis to investigate and identify non-tuberculous mycobacteria (NTM) species. Isolations were made from eight animals originating from four abattoirs and were identified as Mycobacterium species by amplification of a product corresponding to 577 bp in size following gel electrophoresis. Sequence data analysis of the 8 isolates revealed only two of the isolates to be Mycobacterium colombiense (99.81% identity) and Mycobacterium simiae (99.42% identity). The remaining six isolates were identified as members of the Actinomadura species. From the environmental samples, isolation was made from three samples, and two were identified to genus level (Mycobacterium species). The remaining isolate was identified as Mycobacterium senuense (99.22% identity). For the slaughtered livestock, the results suggest that there was no risk of transmission of bTB to abattoir workers and the meat was probably safe to consume. Although NTM have been implicated to be potentially involved in causing tuberculosis-like diseases, their rate of occurrence in the current study was extremely low, hence insignificant. The study has,however, highlighted that the additional use of serological assays such as the interferon-gamma (IFN-γ) assay can help detect early signs of infection, thus establishing the status of infection. Additionally, interviews were conducted in the form of questionnaires to establish the knowledge, attitude, and practices (KAP) of abattoir workers regarding Tuberculosis (TB). The objective of the study was to obtain data from abattoir workers in Gauteng Province, South Africa and to assess the risk of zoonotic tuberculosis transmission among workers. This study revealed an overall knowledge score of the respondents to be 42% (95% Confidence Interval: 37.48 - 46.42) (P<0.001), with 88.35% of the respondents knowing of the disease. The overall knowledge of TB score was determined by calculating the overall average knowledge of the respondents. More than 45% of the participants were aware of zoonotic TB and how the disease is transmitted. Overall, the results of the study suggested that there are certain practices that abattoir workers are engaged in, such as the consumption of unpasteurized milk and undercooked or raw meat, slaughtering of animals at home as well as taking care of animals at home/work that may promote transmission of zoonotic tuberculosis among themselves and their communities at large. In conclusion, we report on the prevalence of Mycobacterium spp in slaughter animals in abattoirs in Gauteng Province, South Africa, the potential zoonotic risks posed to abattoir workers and on the 10-year retrospective data on samples submitted to the Tuberculosis laboratory (ARC-OVR) analysed for the prevalence of Mycobacterium spp. over this 10-year
Development and implementation of the Rhinoceros DNA Index System (RhODIS®) for the forensic analysis and biological management of African rhinoceros
Harper, Cindy Kim (University of Pretoria, 2018-10)
Rhinoceros horn is now worth more, per unit weight, than gold, diamonds, or cocaine. Rhinoceros horn has been used in traditional Asian medicine as a presumed cure for a wide range of ailments. Rhinoceros poaching in South Africa has, on average, more than doubled each year over the past 5 years with the rapid economic growth in east and southeast Asia being assumed to be the primary factor driving the increased demand for horn. Here we report on the characterization of methods for genomic DNA extraction from rhinoceros horn and on DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. The DNA profiling system described includes 22 short tandem repeat (STR), or microsatellite, markers and a gender marker (ZF1), which have been used previously in various studies on rhinoceros. Using a u value of 0.1, a conservative estimate of random match probability in 5 white rhinoceros ranged from 1:7.3 x 106 to 1:3.0 x 108. Given that the total population of white rhinoceros is approximately 20,000 such random match probabilities indicate that the genotyping system described provides data which can be used for evidentiary purposes. Furthermore, the methods are appropriate for use in investigations involving trace amounts of rhinoceros horn and the matching of profiles obtained from seized rhinoceros horn with material collected from live animals or poached carcasses.
Development of improved foot-and-mouth disease (FMD) assays with a focus on small ruminants in southern Africa
Seoke, La-Toya (University of Pretoria, 2024-07)
As an economically important livestock disease, foot-and-mouth disease (FMD) requires adequate strategies for its control. In southern Africa, FMD is endemic and threatens the livelihood of smallholder farmers who rear goats, sheep and cattle for subsistence. However, goats and sheep (small ruminants) are largely ignored in routine surveillance and vaccination campaigns in endemic areas. Furthermore, due to the occurrence of subclinical infection, they pose the risk of facilitating the silent spread of the disease to other livestock animals. To improve the effectiveness of FMD control, established diagnostic assays should be validated/verified for use in small ruminant species in addition to the development of rapid and accurate next-generation assays. The aim of this study was to improve FMD diagnostic tests used on small ruminants and to investigate the molecular evolution of Foot-and-Mouth-Disease Virus (FMDV) in sub-Saharan Africa as a first step to future development of advanced diagnostic tools tailored to the region. The first study optimized and verified a single-spot solid-phase competitive ELISA (ss-SPCE) for the detection of antibodies against FMDV Southern African Territories (SAT) serotypes in goats and sheep sera collected from South Africa. The second study developed and preliminarily validated a field-deployable reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of FMDV serotype SAT1 topotype II viruses. The third study explored the molecular evolution of FMDV SAT serotypes from sub-Saharan African isolates sampled between 1934 and 2022. The optimized ss-SPCE assay successfully measured the prevalence of disease in small ruminants during an active SAT2 outbreak in South Africa. The developed RT-LAMP test was highly specific and proved to be a propitious next-generation assay for the diagnosis of SAT serotypes in southern Africa. The molecular evolution findings indicated that the SAT serotypes continue to evolve as seen with the continuous discovery of new topotypes across the continent over the years. With continued disease surveillance and outbreak investigations, the data will be beneficial to the development of tailored diagnostic tools for the region.
Evidence-based guidelines for triage and prognostication for domestic ruminants burned in wildfires
Cardoso, Claudia L. (University of Pretoria, 2024-11)
Worldwide, wildfires affect livestock farmers emotionally and financially, and due to global warming, the risk of wildfires is expected to increase in the next thirty years. The losses experienced by farmers include feed, facilities, livestock, and the future reproductive performance of any surviving animals exposed to smoke. Many factors, such as animal welfare, the clinical prognosis of cases, and treatment costs, are all important considerations in decision-making. There is a paucity of data regarding decision-making processes with burn injuries in livestock, and this study aims to derive evidence-based guidelines for decision-making regarding domestic ruminants affected by wildfires in the context of field animal production practice. Most evidence found corresponds to case reports (expert opinion) and observational trials derived from real events. However, scientific controlled trials were widely performed during the eighties and nineties using sheep as a test model for skin burns and smoke inhalation and have significantly contributed to the current understanding of burn injuries in humans and animals. Databases from Web of Science, Medline, and Google Scholar were searched with chosen keywords connected with burn injuries in livestock in publications in both English and Spanish. A research matrix was populated with relevant information according to inclusion criteria and strength of evidence, and as a result, triage guidelines were synthesised and integrated for both sheep and cattle in a visual, instructional format. Key clinical factors such as burn depth and extent, anatomic localisation of burns, and smoke inhalation were considered when categorising animals according to clinical severity. Additionally, core indications for decision-making were summarised, including non-clinical factors, implying that the lack of resources affecting their provision will severely compromise animal welfare, leading to the consideration of euthanasia as a strong recommendation.
Epidemiology and management of high pathogenicity avian influenza in South African coastal seabirds, 2018-2022
Roberts, Laura Christl (University of Pretoria, 2025-02)
High pathogenicity avian influenza (HPAI) is a viral disease of birds that has caused increasing harm to global poultry production and food security and, more recently, to the conservation of wild bird and marine mammal populations. Avian influenza viruses are also closely monitored because of their inherent human pandemic potential. Since 2016, Clade 2.3.4.4b viruses of the Goose-Guangdong HPAI lineage have spread from Asia to all continents, except Oceania, in an unprecedented manner. Two different clade 2.3.4.4b viruses reached South Africa in 2018 and 2021 respectively and at least thirty thousand South African coastal seabirds died, mostly Endangered Cape Cormorants and African Penguins. This was followed by severe seabird outbreaks elsewhere around the globe and increasing discussion around suitable response measures, which have remained limited. This dissertation aimed to document lessons learnt during the South African seabird HPAI outbreaks, address epidemiological knowledge gaps and examine options for future outbreak response. It begins with a description of the 2018 and 2021/2022 outbreaks of HPAI in coastal birds and the lessons learnt from the outbreak responses. To improve understanding of the epidemiology of HPAI in African Penguins, and inform future outbreak response, a cross-sectional survey was conducted across their breeding range in 2021 and 2022. This involved sampling of 530 adult penguins in breeding colonies and 382 penguins of varying ages, admitted to a rehabilitation centre. Possible risk factors, such as colony density, were linked with the detection of virus in penguins admitted for rehabilitation. Vaccination is a potential option for managing HPAI in seabirds, though fully effective vaccines are not yet available and suitable formulations and vaccination protocols have not been explored. A randomised trial was conducted in captive African Penguins. It compared the magnitude and duration of antibody response to a conventional inactivated clade 2.3.4.4b H5N8 HPAI whole virus vaccine, with the response to a tobacco leaf-produced H5 hemagglutinin based virus-like particle (VLP) vaccine. The VLP vaccine induced significantly higher antibody titres by day 14 and one dose induced similar titres to two doses of the inactivated vaccine. VLP vaccines therefore provide an example of a vaccine technology that may help vaccination to become more feasible for wild birds. The results of this research were used to compile preparedness plans for disease outbreaks generally, and HPAI specifically in South African coastal birds. Stakeholders were consulted and international workshops attended to identify information required by those involved in responding to an outbreak. It was challenging to obtain input during writing of the plans, but they contain the necessary background information, responsibilities of different stakeholder groups and activities to prepare for outbreaks and they discuss the options for response. There is currently very little that can be done to stop or slow an HPAI outbreak in wild birds, so preparation for outbreaks, efficient use of resources and consolidation of accumulated knowledge is vital. This dissertation documents lessons learnt from responding to and planning for unprecedented seabird outbreaks in South Africa, which can be built on and refined for other scenarios. The mortality rate, attributed to HPAI, varied across African Penguin colonies, most likely due to high environmental viral load and proximity of breeding birds in some colonies. This information can be used to estimate risk, compile surveillance plans and prioritise potential mitigation measures. Adult African penguins appear more susceptible to the virus than juveniles, which has a relatively more serious population implications, and vaccination is one of the few potential tools to protect these valuable birds. This dissertation illustrates that avian influenza vaccines should be safe and effective in African Penguins and that technology is available that could make vaccination programs feasible, especially if less invasive application methods can be developed.
Precision feeding of feedlot cattle based on phenotypic production profiles that predict performance
Hentzen, Andreas Herman Reinhold (University of Pretoria, 2024-08)
Feeding feeder calves to the average production with an average diet is the current norm in the South African feedlot industry and needs improvement. The feedlot industry is a low-margin high volume industry. Because of the low financial margins, financial risk and the mitigation thereof, are of utmost importance. Currently, most feedlots feed their calves to the average. The pen is made up of average feeder calves and they are fed with an average diet that has evolved to be the best match. To further advance in the mitigation of financial risk management, feeding diets to classified production groups that unlock their production potential is investigated. This is the problem statement that this research is investigating and presented in this thesis. First, a literature review was done to find that as far back as 1954, attempts have been made to evaluate feeder calves to predict the production in the feedlot. The research focused on different phenotypic traits, like hip height, which is an indication of maturity, length of body, and so forth. The principle was good, but the tools to measure, yardstick, and rulers, were relevant at that time but led to possible less accurate measurements and resulted in different conclusions. The beef cattle phenotype has changed over the years and measurements done years ago might not be relevant today. The exact point from where the measurement was done, was poorly and inconsistently defined. The measurements focused on specific areas of the body, like the forearm, height, length of the body, and head dimensions, to name a few. No data could be found that incorporated a holistic approach in evaluating the phenotype of feeder calves before the feeding period in the feedlot. New data were generated in our first research, where a novel production profile classification system was developed to categorise feeder calves into production groups to precision feed them to their potential. The phenotype of arriving feeder calves, that underwent a 60-day precondition period, were visually categorised into four production profiles (PP). The visual classification enabled a holistic approach and was done before the feeding period, with the prediction of production in mind. The average feeder calf was used as the reference and was called production profile 2. Feeder calves considered to have a better production potential as PP 2 were classified as PP 1, and the feeder calves considered to have the poorest production potential were classified as PP 3. The classification of the feeder calf before the feeding period was based on muscle and skeletal development. Animals considered to have superior, compared to average PP 2, skeletal development and thus the necessary framework for the attachment of the developing muscle in the feedlot environment were considered PP 1. The PP 3 feeder calf represented calves with poorer skeletal and muscle development. Feeder calves were classified into PP before the feedlot period and then fed commingled on different rations and under different management. The mean PP 1 feeder calf gained 29.66 kg more carcass, compared to the mean PP 3 feeder calf, thereby producing heavier carcasses and higher dressing percentages (Table 3.3). The data were analysed and concluded that feeder calves can be successfully categorised into the defined production profiles to predict production in the feedlot. The second and third experiments were designed for precision feeding. The value of the novel production profile classification system was evaluated through a precision feeding experiment, consisting of 2 approaches. In experiment 1 feeder calves that were first classified into PP, were subsequently randomly allocated into 3 different diets, High Producing Diet (HPD), Medium Producing Diet (MPD), and the Low Producing Diet (LPD). The MPD was considered as the control and represented the diet fed in the commercial feedlot where experiment 1 was conducted. Each diet was fed to a pen to which calves were block randomised based on PP classification and entry-weight. In this experiment, interactions between PP and diet were analysed. It was concluded that interactions between PP and the diet exist. The subdued reaction of PP 1 to the HPD called for reformulation and increasing the metabolizable energy (ME) and protein as not being the first limiting. This led to experiment 2, where a similar methodology was followed. This experiment was conducted in an experimental unit, in a different location. In experiment 2 the feeder calves were grouped by PP and fed in pens containing 1 – 4 animals, which allowed for intake and its monetary value to be determined, leading to additional information on the carcass feed conversion ratio (CFCR) and the calculation of carcass feed cost of gain (CFCOG). After analysing the data, it was found that the reformulation done in experiment 2, additional energy and protein not being the first limiting diet formulation, enabled the inherent production potential of PP 1 calves, which was not achieved in experiment 1. The design of experiment 2 had the additional benefit of providing the data to determine feed-to-gain ratio on a carcass basis, as well as the cost to gain a kg of beef. It was found that the PP 2 on the MPD (feedlot equivalent, or “control” diet) had the lowest CFCOG, confirming the concept that South African feeder calves are fed to the average: average calves fed the average diet established over time, provided the best economic outcome. Devolving from the average (PP 2 fed the MPD) resulted in a better carcass growth rate (CADG), carcass gain (kg), and CFCR tended (P=0.06) to be better when PP 1 was fed the HPD. However, the cost of the HPD was still too high, resulting in the PP 1 CFCOG being higher than the control (PP 2 fed the MPD). The results establish the possibility for nutritionists to formulate diets on a cost-effective way to feed feeder calves to their production potential. Artificial Intelligence (AI) with Convolutional Neural Networks (CNN) can replace the current subjective visual classification method. Feeder calves will be digitalised by a 3-D image, after which they will be classified into the different PP classifications, based on the methodology of the subjective method. The digitalisation of the feeder calf is the switch from subjective eye to objective computerised image. It is on the digitalised feeder calf where CNN will be applied as machine learning tool to establish an automated, objective, AI driven classification system for the production profile of incoming feeder calves. Once established, this technology will open the doors to the fine-tuning of precision feeding of feeder calves. The production profiling of feeder calves before the feedlot period, and the subsequent precision feeding by supplying nutrients to the production potential, in a cost-effective way, was successfully established. Further research is called for to find the most cost-effective diet for calves with different production profiles in each feedlot and country. This improved efficiency has the potential to benefit the entire beef value chain, and also the environment, by lowering the cost, as well as the environmental impact of beef production worldwide.
Molecular characterization of Streptococcus uberis strains, isolated in a longitudinal study from milk of a commercial South African dairy herd.
Van Lelyveld, Grant Kevin (University of Pretoria, 2025)
Streptococcus uberis is a significant emerging mastitis pathogen with environmental and hostadaptive properties. Mastitis caused by Strep. uberis is increasing in South Africa, particularly in pasture-based herds irrigating with slurry. This field study aimed to identify strain types using MALDI-TOF and MLST and evaluate the Strep's behavioural patterns (host-adaptive versus environmental). uberis isolates over an extended period from a South African dairy herd with a high prevalence of Strep. uberis intramammary infection. The study involved 70 (63 retrospective and seven recent) samples, isolated from 53 cows, which were used for MLST sequencing of the seven housekeeping genes (gki, recP, ddl, tdk, arc, tpi, and yqiL). The study disclosed a herd prevalence of 7.44% Strep. uberis intramammary infection (IMI), responsible for 21.26% of clinical mastitis cases in this herd. Of the Strep. uberis positive clinical cases, 25% had repeat occurrences during the same lactation period. The consecutive repeat Strep. uberis cases were 34 (2x), 13 (3x), and 7 (4x). The study identified 41 novel Strep. uberis strain types from 64/70 isolates, attributable to novel alleles (29) or novel sequences of existing alleles of previously identified alleles. The study revealed that one existing Strep. uberis strain type (ST) 1613 (6/70) was to be identified and belonged to the clonal complex (CC) ST-86. All the other strain types of the isolates investigated in this study were novel. They were within the common CC (ST-5, ST-86, and ST-143) or not allocated (owing to the lack of data generated from whole genome sequencing). The longitudinal study 2021 (three-monthly milk samples) n=64/70 and 2024 (specific milk samples) n=7/70 from cows identified as high-interest cows, possibly showing as chronic cases on repeat collections (culture, MALDI-TOF, and Kirby Bauer). The finding was not entirely down to suspected hostadaptive strains of Strep. uberis but relatively novel strains creating new infections. The heterogeneity of the Strep. uberis isolates in this study agreed with other research identifying the environment as the primary source of strains. This study can aid farmers and veterinarians in managing Strep. uberis mastitis is more effective in the field by better classifying what is meant by repeat, non-cure, and new infections amid farming practices favouring higher pathogen loads (environment) and challenges for the cows. Contrary to what was expected, the study identified new infections with diverse Strep caused most suspected chronic intramammary infection (IMI). Uberis strains are dominated by novel environmental strains (high heterogeneity of ST and CC from all 70 isolates).
Comparison of thiafentanil-azaperone and etorphine-azaperone for the immobilisation of free-ranging black rhinoceros (Diceros bicornis)
Gazendam, Bart Adriaan Theodorus (University of Pretoria, 2024-10)
This study aimed to determine the efficacy, safety and cardiorespiratory effects of etorphine, azaperone and hyaluronidase (EA treatment) vs thiafentanil, azaperone and hyaluronidase (TA treatment), for immobilization of free-ranging black rhinoceros (Diceros bicornis). Comparing and determining whether one of these drug combinations resulted in a more effective and safer immobilisation of black rhinoceros, will allow improvements in the welfare and conservation of these animals, and thus also ensuring the safety of personnel involved in such capture events. In this randomised, prospective field study, twelve male and twelve female, adult, black rhinoceros were included. Animals were randomly immobilised with EA (n = 12) or TA (n = 12). The dose administered was based on age group and sex of the animal. Treatments were administered intramuscularly via remote dart injection. Induction, immobilisation and recovery times and scores were recorded and compared between treatments. Respiratory rate, heart rate, rectal temperature, oxygen haemoglobin saturation and arterial blood pressure were measured at 5-min intervals for 30 minutes. Arterial blood gases were obtained and measured every 10 minutes. Significant faster induction times were recorded in the TA group (2.88 ± 0.75 minutes) compared to the EA group (3,95 ± 0.77 minutes). Immobilisation was successful in all animals. The heartrate (HR) and blood pressure decreased significantly in both groups over time. Both the use of TA and EA resulted in a reduced PaO2 and increased PaCO2, but no differences were observed between or within treatments. An increased alveolar to arterial oxygen gradient was noted in both treatments. Acidaemia, decreased base excess and bicarbonate levels, hypercapnia and hyperlactatemia indicated that respiratory and metabolic lactic acidosis occurred in both treatments. Both combinations provide an acceptable induction, immobilisation and recovery for black rhinoceros, however, hypoxaemia, hypercapnia and acidosis occurred. Safety was evaluated based on cardiorespiratory parameters and the absence of adverse effects during immobilisation and recovery. Either etorphine or thiafentanil with azaperone and hyaluronidase, can therefore safely be used for the immobilisation of black rhinoceros. The use of the thiafentanil combination can provide a faster induction, minimising run time, potentially reducing stress and overexertion, and their associated metabolic derangements.
Factors affecting warthog (Phacochoerus africanus) occupancy with presence of aardvark (Orycteropus afer) as a keystone species
Jenkins, Dean (University of Pretoria, 2024-08)
This study investigated the dynamics of warthog (Phacochoerus africanus) occupancy across two diverse properties. Warthog are a common mammal species prevalent across diverse landscapes in Africa. The distribution of warthog has undergone notable shifts due to climate change and species reintroduction, with consequential impacts on farmlands through activities such as damage to fences, pipelines, and crops. Moreover, warthog are carriers of African swine fever, posing a threat to swine biosecurity. The primary objective of this research is to determine the variables influencing warthog occupancy, focusing on the presence of aardvark (Orycteropus afer) as a possible keystone due to its facilitative capabilities supporting burrowing species. The findings provide a foundation for future studies aiming to map potential warthog distribution based on influential covariates. My hypothesis considered a range of factors such as the presence of aardvark, the presence of predators, vegetation type, soil composition, distance to perennial water sources, proximity to roads, distance to the nearest 10 trees (tree cover at site level), and camera efficiency, was tested using occupancy modelling with camera trap data from Atherstone Private Game Reserve and Mountain Zebra National Park. My hypothesis is that multiple drivers/factors influence warthog occupancy. The results revealed that warthog occupancy is positively influenced by the presence of aardvark and camera efficiency, while it is negatively influenced by the presence of predators (lion, Panthera leo and leopard, Panthera pardus), increased distance to perennial water sources, and shorter average distance to the nearest ten trees (potentially linked to vegetation structure/type). These covariates also impacted the detection probability of warthog at both study sites, highlighting the complexity of the factors influencing their occupancy. The understanding gained from this study emphasises the significance of considering multiple variables to predict and manage warthog occupancy, particularly as climate change likely can shape their distribution. Therefore, my hypothesis is supported based on the covariates that significantly influence warthog occupancy. The findings underscore the importance of ongoing research, incorporating additional covariates, to refine our understanding of the multifaceted influences on species (warthog) occupancy to improve effective management and conservation.
Comparison of prevalence of avian pathogenic Escherichia coli in South African and US poultry
Goosen, Jaco Louis (University of Pretoria, 2023-07)
Avian pathogenic Escherichia coli (APEC) as the etiological agent for Colibacillosis has extensively been described, with numerous research papers dissecting and elaborating on the prevalence and population dynamics of APEC throughout the world. The South African landscape however has not been elucidated to the same extent. In this study, 3025 South African E. coli samples were analysed for the period 2017 – 2022. Data were also analysed to compare the prevalence of APEC in the United States of America (USA) versus South Africa (SA). The USA isolates were all from broiler operations, with SA isolates from different operations. The study investigated the prevalence of APEC in SA, whether population differences occur for specific virulence - associated genes (VAGs) between operations, as well as the possible differences of virulence - associated gene (VAG) prevalence over time (2017 – 2022) within SA. The data available were also analysed to establish the potential difference of VAG prevalence between SA and USA. The extracted DNA was screened by a multiplex PCR for five APEC VAGs (cvaC, iss, iucC, tsh and irp2). The pathogenicity of each isolate was determined by comparing the number of genes detected in each isolate to a positive control. Isolates with two or more virulence genes were considered APEC positive. This research provides supporting evidence for the theory that geographical and environmental factors influence the genetic diversity and subsequent virulence of APEC. It would therefore suggest that prophylactic measures would need to be tailored to regional needs as required by each operation for a specific period in time.
A unique cost-effective disease surveillance model for southern African village pigs and chickens
Simbizi, Vincent (University of Pretoria, 2023-10)
Pig and chicken farming provide an important protein and revenue source for communities in developing countries. Despite these benefits, these two sectors in the Eastern Cape Province (ECP) of South Africa are still underdeveloped and poorly surveyed for pig and chicken diseases. The mechanisms for early detection of diseases remain a challenge, consequently, mortalities due to important infectious diseases are frequent. While the province faces a critical shortage of veterinary resources including limited budget, this tudy aims to examine ways by which animal disease surveillance in the ECP could be better targeted to enable more efficient use of existing veterinary resources. Consequently, the overall objective of this study was to propose a system to promote early detection of pig and chicken diseases, based on social network and value chain analyses, which could be combined using ensemble modelling. Ensemble modelling is the process of running two or more related but different analytical models and then synthesizing the results into a single outcome. The work presented in this thesis was broken down into a hazard analysis component, farming and disease management component, risk analysis component and a proposal on a placement of surveillance units in the trade hubs identified by social network analysis. Each component had its own separate outcome. These components were thereafter combined to create an ensemble model for cost-effective surveillance of the smallholder pig and chicken farming sector in the ECP. Within this context, a hazard analysis was a review of pig and chicken diseases in the province from 2000–2020. This review included relevant published papers identified by a computerized literature search from Web of Science; provincial animal health reports; the national database from the Department of Agriculture, Land Reform and Rural Development (DALRRD); animal health reports submitted by DALRRD to the World Organization for Animal Health (WOAH) via the World Animal Health Information Database (WAHID) interface and laboratory records. The review identified 174 publications of which 26 were relevant based on the selection criteria. Classical swine fever and Newcastle disease were the most reported diseases in pigs and chickens respectively, and they were consistently recorded in both the National database and WOAH database. These diseases were therefore used as the primary hazards in the ensemble model. The retrieved literature on pig and chicken diseases was scarce and no longer up to date, providing decision makers with no current information on which disease to prioritize. The review identified zoonotic diseases that require further studies yet failed to find information on important neglected diseases like leptospirosis. To establish how farmers dealt with chicken diseases, a sociological survey of chicken farmers and the remedies most used to prevent diseases in their flocks was conducted throughout the ECP between February 2019 and June 2019, alongside a serological survey to estimate the apparent seroprevalence of selected chicken diseases in the province (from August 2019 to March 2020). Most chicken farmers in the survey were females and pensioners (69 % and 66.1 % respectively) and had a primary school education (47.1 %). Traditional remedies were commonly used by farmers (47.15 %) and among the remedies, 136 Aloe plant (Aloe ferox Mill.) or “ikhala” in local language (isiXhosa) was the most used product (28.23 %) to prevent and reduce mortalities among village chickens. The second 138 group of remedies used by farmers was antibiotics with tetracyclines being the most used remedy under this category (17.42 %) followed by Sulpha products (12.01 %). The conclusions drawn from this component were: i) the sector was dominated by pensioners with a low level of education; ii) village chickens could be a potential source of emerging diseases including virulent Newcastle disease virus (NDV) because of the lack of vaccination and biosecurity by farmers; iii) the use of antibiotics by untrained chicken farmers was a major public health concern as it could serve as a source of antimicrobial resistance (AMR); iv) the overall seroprevalence of Newcastle disease 146 (ND), avian influenza (AI), avian infectious bronchitis (IB) and Mycoplasma 147 gallisepticum (MG) in the province were 69.2 % (95 % CI 51.9 - 86.5%); 1.8 % (95 % 148 CI 0.2 - 3.4%); 78.5 % (95 % CI 74.9 - 82%) and 55.8 % (95 % CI 41.3 - 70.3%) 149 respectively with clustering found at the district level; v) chickens were exposed to the 150 ND vaccine strains caused by spent hens from commercial operations that were being sold to rural farmers by traders and released into rural settings; vi) AI ELISA-positive samples were tested using HIs against the H5, H6 and H7-subtypes, but only H6-specific antibodies were detected (H6N2). Since these viruses can mutate and reassort among

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