Theses and Dissertations (Production Animal Studies)

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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
UBAC mastitis vaccine performance in a South African pasture-based dairy herd
Dreyer, Marette (University of Pretoria, 2023)
Streptococcus uberis (Str. uberis) is a major gram-positive mastitis pathogen. It has various strains that differ in virulence. This organism is difficult to treat effectively. In 2021, 47.4% of major gram-positive bacteria isolated from milk in South African were Str. uberis. Vaccination is an essential tool for proactive udder health management. The UBAC Streptococcus mastitis vaccine (UBAC) is designed on the principle of inhibition of biofilm formation by this bacterium. A recent South African study observed that all Str uberis strains produce biofilms, the formation of which the UBAC vaccine is designed to inhibit. This field study evaluated the effect of the UBAC mastitis vaccine on several critical factors related to clinical mastitis caused by Str. uberis. These factors include lowering the prevalence and severity of clinical mastitis, improving clinical and bacterial cure rates, reducing new intramammary infections, lowering SCCs, and increasing milk yield or preventing milk loss associated with Str. uberis intramammary infection (IMI). Unexpectedly, there were no significant differences (P<0.05) established between the vaccinated and control groups for incidence and severity of clinical mastitis; clinical and bacterial cure of clinical mastitis; cows culled owing to mastitis; seven- day average milk yields; new IMI and prevalence of Str. uberis mastitis and level of somatic cell counts. Contrary to expectation, significantly (P<0.001) more Str. uberis IMIs were cured in the control group compared to the vaccinated group. The only statistically significant benefits observed in the vaccinated group were a significantly lower prevalence of chronic mastitis cases (P < 0.001) and a higher sensitivity to tetracyclines among Str. uberis isolates from clinical mastitis cases (P < 0.001).Fewer cows had an udder severity score of 2 in the vaccinated group (Group 1). The gluteal muscles were used as the injection site owing to the layout of facilities on the study farm, contrary to the recommended use of the neck muscles according to the directions. Incidentally, severe swellings were observed at the injection site in up to 42% of cows eight hours post-vaccination. These signs persisted for up to three days, causing discomfort to the animals and causing a milk loss of one to two litres per animal for the producer. In this herd, Str. uberis caused over 30% of infections of the clinical mastitis cases. It is recommended that the UBAC vaccine is tested as a management tool in herds with a higher prevalence of IMI Str. uberis and the discomfort of animals, when injected in the neck muscles as indicated in the directions for use, should be investigated. Based on these finding only, the vaccine cannot be recommended.
Mycobacterial safety of meat cuts from BCG-vaccinated African buffaloes (Syncerus caffer) experimentally infected with Mycobacterium bovis
Antrobus, Megan Elizabeth (University of Pretoria, 2024)
Tuberculosis is a global disease that affects humans and animals, both wild and domestic. Bacteria, of closely related sub-species, from the Mycobacterium tuberculosis complex are what cause tuberculosis (TB). There are two main forms of the disease: the human disease, mainly caused by Mycobacterium tuberculosis and the animal disease, caused predominantly by Mycobacterium bovis and Mycobacterium caprae. The animal form of the disease can be zoonotic, particularly M. bovis. The study was a qualitative study that set out to determine the safety of meat cuts (fillet, silverside, brisket, and rump) taken from vaccinated (inactivated M. bovis vaccine and BCG) and experimentally infected buffaloes with M. bovis in particular, for the presence of M. bovis and M. bovis BCG. The different cuts of meat were chosen due to their popularity in the consumer markets. The animals were held at the Skukuza bomas and were euthanised and full post mortem examinations were conducted in October 2021 at the Skukuza abattoir. Meat samples were collected at the abattoir and biobanked until the samples were needed for a study. The meat samples were then processed at Hans Hoheisen Wildlife Research Station, Orpen Gate, Kruger National Park, in February 2023. The methodology involved the culture of samples from different meat cuts (fillet, brisket, silverside and rump), on mycobacteria-selective media. In this study, a total of 378 media slopes were produced of which only ten showed colony-like growth. Speciation by PCR was conducted on these ten media slopes. The data were analysed by creating pivot tables. Pivot tables enable large amounts of data to be summarised in an easy and understandable format. The study concluded that the meat from vaccinated and experimentally infected buffaloes showed no positive results for M. bovis or M. bovis BCG. These results suggest that meat collected from vaccinated and experimentally infected buffaloes is likely to be safe for humans to consume, but larger sample sizes are needed to increase certainty.
Final-year veterinary student performance on an ovariohysterectomy model predicts surgical performance
Chiwome, Tendai Joy (University of Pretoria, 2024-06)
Background: A veterinary student's first soft tissue surgery on a live animal is a major milestone during their clinical training. It can however, be a somewhat overwhelming experience if they are inadequately prepared. Canine ovariohysterectomy (OVH) is a commonly performed procedure in general veterinary practice and requires competence in a broad range of surgical skills such as haemostasis, ligation and tissue handling, all of which have been identified as critical Day One skills for a new graduate to possess. At the Faculty of Veterinary Science, University of Pretoria, students receive lectures and notes on performing an OVH and during their clinical year, they have access to a step-by-step video showing the procedure, a live demonstration and a practical session in the Clinical Skills Laboratory where they perform a canine OVH on a model prior to doing the procedure on a live animal. Objective: To determine whether student performance on the OVH model had a predictive value in relation to their surgical performance on a live-animal. Study design: Prospective descriptive cohort cross-sectional study Materials & Methods: One hundred and eight students participated in the study and their performance on the model and live animals was assessed using a predetermined rubric. Results: The results showed that the OVH model assessment mark is a strong predictor of the subsequent live surgery assessment mark. Conclusions and clinical relevance: These results will enable us to provide timely targeted intervention to students that require additional skills training.
Molecular characterization of Listeria spp. isolated from cattle farms, abattoirs, and beef products in Mpumalanga and North-West Provinces, South Africa
Manqele, Ayanda (University of Pretoria, 2024-04)
Listeria monocytogenes is a foodborne pathogen that has serious public health implications. Since the advent of the largest outbreak of listeriosis in South Africa, it has become important to understand the genomic characteristics of L. monocytogenes from food products. This study aimed to use molecular techniques to characterize Listeria isolates (n=214) recovered from cattle farms, beef and beef-based products from retails. PCR was used to classify the isolates into Listeria species. The identified L. monocytogenes were further classified into serogroups and Multilocus Variable-Number Tandem Repeat Analysis (MLVA) types using conventional PCR protocols. Likewise, L. innocua (165) isolates were also typed using MLVA. As the only pathogenic species identified in this study, L. monocytogenes was further characterized using whole genome sequencing (WGS) and bioinformatics tools to determine the population structure, antimicrobial resistance genes, virulence profile, mobile genetic elements (plasmids, prophages), genomic islands, insertion sequences, the type VII secretion system, and sortases. Listeria isolates were classified into L. innocua (77.10%, n=165), L. monocytogenes (11.21%, n=24), L. welshimeri (5.61%, n=12), L. grayi (1.40%, n=3), L. seeligeri (0.93%, n=2), and L. species (3.73%, n=8). L. monocytogenes serogroups determined by PCR were: IVb (4b-4d-4e) (37.50%), IIa (1/2a-3a) (29.16%), IIb (1/2b-3b) (12.50%), IIc (1/2c-3c) (8.33%), and IVb-1 (4.16%). MLVA was able to cluster L. monocytogenes isolates into 10 MLVA types and L. innocua into 34 MLVA types based on their relatedness. The isolates clustered irrespective of sample category, geographical origin and serogroup for L. monocytogenes. Multilocus Sequence Type (MLST) analysis revealed that ST204 of CC204 (Lineage II, serogroup IIa (1/2a, 3a) was the most common sequence type (ST). Other sequence types detected included ST1 of CC1 (Lineage I, serogroups IVb (4b,4d,4e), ST5 of CC5 (Lineage I, serogroup IIb (1/2b,3b,7), ST9 of CC9 (Lineage II, serogroup IIc (2c, 3c), ST88 of CC88 (Lineage I, serogroup IIb (1/2b,3b,7), ST876 of CC1, (Lineage II, serogroup IVb (4b,4d,4e), ST2 of CC2 (Lineage I, serogroup IVb (4b, 4d, 4e), ST321 of CC321 (Lineage II, serogroup IIa (1/2a, 3a) and ST1430 of CC2 (Lineage I, serogroup IVb (4b,4d,4e). All the L. monocytogenes STs carried four intrinsic resistance genes, fosX, lin, norB, and mprF, conferring resistance to antimicrobials, fosfomycin, lincosamide, quinolones, and cationic peptides, respectively. Genes encoding for virulence factors LIPI-1 (pfrA-hly-plcA-plcB-mpl-ActA) and internalin genes inlABCJKF, were present in most STs. Prophages profile, vB_LmoS_188, was overrepresented amongst the isolates, followed by LP_101, LmoS_293_028989, LP_030_2_021539, A006 and LP_HM00113468. Plasmid pLGUG1 (40%) was the most represented and only found in ST204 types. Similarly, plasmid J1776 (40%) was also significantly represented amongst the STs, followed by pLI100 (13%), and pLM5578 (7%). Mobile genetic elements did not harbour any virulence or resistance genes. Listeria genomic island 2 (LGI-2) was found present in all the isolates, whilst Listeria genomic island 3 (LGI-3) was present in a subset of isolates (25%). The type VII secretion system was found in 42% of the isolates, and sortase A was found in all L. monocytogenes genomes. This study revealed that non-pathogenic and pathogenic Listeria spp. could be contaminants of meat products and the farm environment. The strains of L. innocua and L. monocytogenes displayed diversity even though they all originated from bovine samples. MLVA proved to be an affordable, simple, and discriminatory method that can be used routinely to type L. monocytogenes and L. innocua isolates. The isolates did not carry genes conferring resistance to first-line drugs used against listeriosis and, therefore, did not pose a threat to antimicrobial therapy. Characterization of L. monocytogenes in the current study highlighted the virulence capability of L. monocytogenes and the risk posed to the public by this pathogen, as it is often found in food and food processing environments.
Component mass as well as calcium and phosphorus content of unbanded and fertile Nile crocodile (Crocodylus niloticus) eggs
Brown, Geoffrey James (University of Pretoria, 2020-02)
The Nile crocodile (Crocodylus niloticus) is a predator, scavenger and an economically valuable aquaculture species in sub-Saharan Africa. Nile crocodiles are farmed principally for their skins, which are used to manufacture high-value leather goods. By-products of this process, such as meat and fat, also have economic value. Despite its economic importance, little is known of the Nile crocodile’s reproductive physiology beyond behavioural and anatomical descriptions, and some cursory seasonal endocrine profiles. In this manner, C. niloticus is not unique: such a paucity of knowledge of the reproductive processes exists for all crocodilian species worldwide, though some species are better researched than others. Furthermore, very little is known about factors that affect egg fertility, foetal survival and resulting hatchling survival. If environmental influences during incubation can be controlled for, the effect of maternally- and paternally-associated factors on embryo, foetal or hatchling survival or performance can be investigated. The egg phase is a critical, self-contained period of the crocodile life cycle, and, compared to the juvenile or adult phases, is an accessible, relatively inexpensive specimen type that can be used to investigate these factors. During the first half of embryonic development, the formation of the chorioallantois and its fusion with the overlying shell membrane results in a macroscopically visible, circumferential opaque band immediately beneath the shell around the lesser diameter of the egg. This band grows as incubation progresses. Crocodilian eggs that were not fertilised, or which contain embryos that died early in development, have no such visible band, and are referred to as ‘unbanded’. In research described in this thesis, the grouping effect of clutch on the mass of the various components (shell, shell membrane, yolk and albumen) of unbanded eggs was evaluated. The effect of potential confounding variables on egg mass and the mass of individual egg components was assessed. Clutch was found to have a strong grouping effect on egg mass, as well as on the masses of individual unbanded egg components. The mass of each component of unbanded eggs was strongly positively correlated with the mass of the egg. Fertile eggs had substantially lighter yolks and shells than unbanded eggs of similar mass. Controlling for egg mass and incubation period, foetal mass was inversely associated with the mass of the intra-abdominal yolk. The period within the laying season during which an egg was laid, had no significant effect on its mass, nor on the mass of any of its components. The occurrence of runt hatchlings is a pervasive issue in captive crocodile hatcheries. Such hatchlings are either severely underweight at hatching, or fail to thrive after hatching to the point that they inevitably succumb. Disorders of calcium (Ca) and phosphorus (P) metabolism have been well described in reptiles, and may arise either from insufficient provision, or aberrant metabolism of these elements. Prior researchers found an association between runt Crocodylus porosus hatchlings and low plasma Ca (although based on their findings, this relationship was not manifestly causal). Given the potential role of these elements in foetal and hatchling pathologies, the present research sought to measure and describe Ca and P concentration and content (and variabilities thereof) in the various components of unbanded and fertile C. niloticus eggs. The grouping effect of clutch on the concentration and content of these elements was determined, and the effect of potential confounders was assessed. The Ca and P content of the unbanded egg’s shell and yolk were influenced principally by the mass of the respective component, and to a lesser extent by the concentration of the element in that component. Contrastingly, shell membrane and albumen Ca and P content were influenced primarily by the concentration of the element. Shell Ca concentration was similar to that of pure calcium carbonate. Fertile egg yolk Ca content was significantly lower than that of size-matched unbanded eggs, suggesting a net depletion of Ca, however yolk Ca concentration of fertile eggs was found to exceed that of unbanded eggs in some cases, which could suggest temporary storage of shell-derived Ca. Yolk P concentration and content of fertile eggs was found to be consistently lower than that of unbanded eggs. It was concluded that the yolk is the primary source of P for the developing foetus, while Ca is derived principally from shell and yolk. Research reflected in this thesis will hopefully be of value in preparation for future research, and in the planning of clinical diagnostic and therapeutic interventions on crocodile farms.
Antibiotic resistance of coagulase positive staphylococci isolated from milk of South African dairy herds
Karzis, Joanne (University of Pretoria, 2020)
The discovery and the subsequent global use of antibiotics has led to the survival of resistant microorganisms and suppression of susceptible species. This has caused a worldwide interest in antibiotic resistance and its threat to human and animal health. World-wide and particularly in South Africa there is a lack of antibiotic resistance surveillance data specifically for dairy cattle. The routine sampling of the Milk Laboratory Faculty of Veterinary Science at the University of Pretoria, as part of the pro-active udder health programme, has generated such data which needed to be analysed, interpreted and applied in practice. Staphylococcus aureus (S. aureus), one of the biggest problems in the dairy industry, was chosen as the organism to be used as the starting point for this ongoing project. The retrospective antibiotic resistance data (Kirby Bauer) were analysed for S. aureus (n= 2532) to eight commonly used antibiotics available as intramammary remedies for specific mastitis treatments in Southern Africa from 2000 to 2010. While overall antibiotic resistance was generally increasing over time as shown worldwide, antibiotic resistance was in fact decreasing over time for twenty well-managed herds (nineteen in South Africa and one in Zambia). This was attributed mostly to the effects of good management in the herds that were regularly tested as part of the pro-active udder health programme. There were also significant effects of seasons and regions on antibiotic resistance in tested isolates. All of the antibiotics tested, barring cephalosporins, showed a predicted prevalence of resistance of above 50% in most provinces. This is a concern. The lowest prevalence of resistance to the majority of the categories of antibiotics tested was in KwaZulu-Natal Province during spring. The reasons for the differences in antimicrobial rsistance between seasons and provinces are obscure. These differences may be a secondary effect related to the amount of antibiotic usage. The cephalosporins had the lowest levels of prevalence of bacterial resistance in Gauteng Province during winter. Although, mostly unexplained, such effects on antibiotic resistance could possibly be attributed to the different weather conditions in different regions of the country during different seasons. The conventional procedures for the identification of S. aureus led to the identification of coagulase positive and maltose negative staphylococci with doubtful identification of species. This research aimed at confirming the identification of this organism (conventional microbiology), which seemed to be an emerging pathogen, using molecular methods (MALDI-TOF MS, and 16s rRNA sequencing). The isolates of the maltose negative Staphylococcus sp. tested, were confirmed as being S. aureus by both molecular methods (100% correlation). However, it is also important to differentiate between maltose negative and maltose positive S. aureus isolates during routine diagnostics because these organisms react differently and thus need to be treated differently in practice. Also, maltose negative S. aureus tested positive for both malA and malR genes. A stop codon was discovered at position 844 of the malA gene caused by a cytosine to thymine transition which resulted in early termination of the α-glucosidase protein which would most likely be inactivated. This truncated protein may be the cause of the maltose negative phenotype. The discovery of this stop codon proves that maltose negative S. aureus ST 2992 is indeed different to conventionally identified maltose positive S. aureus. Antibiotic resistance of maltose negative S. aureus was analysed using retrospective data of this pathogen (n = 271), from milk samples of 117 farms between 2010 and 2017 (Kirby Bauer). The analysis was done using both the previous system (intermediate grouped with resistant) and more recent system (intermediate grouped with susceptible) CLSI breakpoints. The results between the previous and more recent analysis differed for tylosin, cefalonium, oxy-tetracycline and cloxacillin. Neither the previous system nor more recent system of analysis showed any difference between provinces for the maltose negative S. aureus. Strains of S. aureus which differed on phenotypic identification with the maltose test, also differed in antibiotic resistance patterns over time, per province, per season and SCC category. Further antibiotic susceptibility testing (MIC) was carried out, using the automated broth microdilution method for both maltose positive (n= 57) and maltose negative (n = 57) S. aureus from 34 farms. The MIC results for maltose negative S. aureus confirmed the results of the Kirby Bauer for the products tested. MIC 50 and MIC 90 were susceptible for both maltose negative and maltose positive S. aureus, except for MIC 90 of maltose negative S. aureus. This MIC analysis indicated more resistance in general seen in the maltose negative S. aureus, than in the maltose positive strains. Uncommon resistance patterns such as the resistance to vancomycin, oxacillin and carpapenems were shown for maltose negative S. aureus isolates, implying a possible anthroponosis (previously known as reverse zoonosis or zooanthroponosis). It is still unclear why this is found and how this might be linked to the difference in the phenotypic identification of this organism. The surveillance and monitoring of antibiotic resistance is important in order to assist decision makers, influence legislation, control antibiotic resistance, preserve human and animal health and to promote food security.
Retrospective analysis of the epidemiology and clinical presentation of West Nile virus infection in horses in South Africa, 2016 - 2017
Bertram, Freude-Marié (University of Pretoria, 2019)
West Nile virus (WNV) has gained international attention in recent years as a globally emerging disease, particularly after large epidemics occurred in North America in the past 20 years. Although endemic to South Africa, it has only been recognised as a significant cause of neurological disease in either humans or horses since 2008. This retrospective study provides an epidemiological and clinical description of WNV disease in horses in South Africa during 2016–2017, when 54 cases, most of which occurred during 2017, were diagnosed by passive surveillance at the Centre for Viral Zoonoses (CVZ), University of Pretoria. Cases were followed up and then statistically compared to a randomly selected set of 120 WNV-negative controls from the CVZ database of the same time period, which complied with similar case descriptions. Clinical presentation of WNV cases was found to be remarkably similar to international trends, with 89% neuroinvasive disease and 39% case fatality rate, mostly displaying typical, significant neurological signs: ataxia (74%), hindleg paralysis (35%), paresis (30%), total paralysis (28%), tremors / muscle fasciculations (19%), foreleg paralysis (17%) and laminitic stance (9%). Approximately half of the cases exhibited pyrexia. Cases that had only neurological signs were more likely to die while cases with pyrexia, with or without neurological signs, were more likely to recover. Most of the cases were in Thoroughbred, Warmblood or Arabian horses, while local or mixed breed horses were the least represented. Cases occurred mostly in WNVunvaccinated horses less than 5 years old, specifically in the late summer and autumn months after heavy rain in the temperate to warm Eastern parts of South Africa. Cases were located mainly in Gauteng, KwaZulu-Natal Midlands and the Northern Cape with fewer cases in the Free State and Western Cape provinces. In the multivariable logistic regression analysis, the odds of WNV infection was associated with season (higher during March-April vs. all other times), altitude (higher at 1293–1466 m vs. other categories), breed (lowest in mixed and local breeds), younger age and failure to vaccinate against WNV. Based on these findings, risk-based recommendations may be made to horse owners; in particular, vaccination against WNV, which is currently the most effective prophylactic measure available to reduce disease, severity of clinical signs and mortality.
Comparison of continuous and rotational grazing systems on veld condition, calving percentages and body condition of selected wildlife species
De Beer, Johann Hermann (University of Pretoria, 2024-07-07)
This study aimed to determine the effect of different grazing systems on veld conditions, body conditions, and calving percentages (production parameters) of African buffalo (Syncerus caffer caffer), sable antelope (Hippotragus niger niger), and roan antelope (Hippotragus equinus equinus). The study was conducted on Dronfield Nature Reserve, which is located in the Kimberly thornveld savanna vegetation type. Veld condition was assessed by estimating the ecological grazing capacities (ha/GU) of the camps in the two different grazing systems, namely, continuous and rotational grazing systems. Animal production was determined by recording births, mortalities, conception rates, and body condition scores. Incorrect veld management may lead to veld degradation, which negatively affects veld condition, grazing capacity, and consequently animal production. Rotational grazing systems, such as those used in livestock ranching can be used to increase the number of animals kept on a ranch while ensuring that the condition of the veld remains favourable. No significant difference in veld condition was seen when comparing the camps in the rotational grazing system to those in the continuous grazing system. In addition, the mean calving percentage of the different herds was close to 85 % in both systems, and the body condition of all three species remained at a constant greater than three body condition score throughout the year. These findings indicate that a rotational grazing system can be safely implemented to replace a continuous grazing system on a game ranch without negatively affecting veld condition or animal production. Implementing a rotational grazing system will, therefore, enable ranchers to keep more animals on the same-sized property, thereby increasing profitability. The optimal body condition score and high calving percentages of the animals in the breeding camps on Dronfield Nature Reserve can be ascribed to the correct supplementation given at the correct times throughout the year, negating any nutrient shortfalls / deficiencies the animals my experience as the quality of the natural veld changes throughout the year. Without supplementary feeding the animal’s body condition score, calving percentages, and general health will decline.
Prevalence and characterization of Leptospira spp. in slaughter animals at abattoirs in Gauteng, South Africa and the zoonotic risk posed to abattoir workers
Dogonyaro, Banenat Bajehson (University of Pretoria, 2020-10)
Leptospirosis is an important global re-emerging, occupational, environmental and zoonotic disease. It is an under-estimated disease of public health and veterinary importance caused by the pathogenic spirochetes belonging to the genus Leptospira. Currently in South Africa, there is limited information on leptospirosis and veterinarians’ beliefs that leptospirosis is not an important disease in the country. The primary aim of the investigation was to determine the prevalence of Leptospira spp. in slaughtered livestock and workers at abattoirs in Gauteng province, South Africa. To achieve this aim, retrospective analysis of laboratory data and cross-sectional serological, bacteriological and molecular studies were conducted on livestock and abattoir workers during the study period. The objective of the retrospective analysis of 11-year (2007 – 2017) data was to determine the seropositivity and infecting serovars of Leptospira in the sera of livestock (suspected or clinical cases of leptospirosis), submitted to the Agricultural Research Council (ARC)-Ondersterpoort Veterinary Research (OVR), Bacteriology serology laboratory. The overall seropositivity for leptospirosis in livestock was, 20.5% (1,425/6,945), using an eight-serovar microscopic agglutination test (MAT) panel. The frequency of seropositivity was 22.0% (1,133/5,168), 16.2% (286/1,763) and 0.0% (0/14) for cattle, pigs and sheep respectively (p<0.00 01). Australis (sv. Bratislava) was the predominant serovar having been detected in 29.4% (333/1,133) and 32.0% (91/286) of seropositive cattle and pigs respectively. The year 2016 of the 11 years retrospective data, had seroprevalence overall of 22.0% (102/466), with 100% (2/2) and 21.6% (101/466) for pigs and cattle respectively. It is important to note that, this was the same period (2016) we conducted the current cross-sectional study. A cross-sectional study was conducted on pigs and cattle slaughtered at Gauteng abattoirs in South Africa: Eighty-five (n=85) sera from slaughtered pigs at 5 consented abattoirs were analysed by MAT. The overall seropositive was, 24.7% (21/85) using 26 antigens panel for pigs in South Africa for the first time; Predominant serogroup was serogroup Australis-Bratislava reported as the predominant in seropositive pigs, 90.5% (19/21), 22.4% (19/85). For the cattle, 199 serum samples were analysed from slaughtered cattle from 11 abattoirs that consent was granted. Seropositive from cattle sera, 27.6% (55/199) with serogroup Sejroe (Hardjo), 10.5% (21/199) as the predominant circulating in the Country. The study demonstrated, for the first time in South Africa, the occurrence of four serovars, namely, Hardjo bovis strain lely 607; Topaz, 3.5% (7/199); Hebdomadis, 2.5% (5/199) and Medanensis, 1.5% (3/199) in slaughtered cattle. The vaccine used to prevent cattle leptospirosis in South Africa does not contain three of the newly detected serovars (Topaz, Hebdomadis and Medensis), an indication that the seropositive cattle acquired infection through natural exposure. There were statistically significant differences (P<0.05) in the detection of the serogroups of Leptospira. Of the five variables analysed, only one variable (abattoir) had statistically significantly (P<0.001) differences in the seroprevalence of leptospirosis in cattle. With the bacteriological culture of 305 kidneys using Ellinghausen McCaullough Johnson Harris (EMJH) media, the isolation rate for Leptospira spp. was 3.9% (12/305), with species-rate being 4.8% (9/186), 4.1% (3/74) and 0.0% (0/45) for cattle, pigs and sheep respectively (P>0.05). The use of quantitative polymerase chain reaction (qPCR) assays detected Leptospira DNA in 27.5% (84/305) of the livestock kidneys tested. Of the animals tested, 26.9% (50/186), 20.3% (15/74) and 42.2% (19/45) of cattle, pigs and sheep kidneys respectively (P=0.03) were positive for Leptospira DNA. It was significant that, although all sheep samples tested for leptospirosis by isolation and serology were negative for Leptospira spp., a high frequency (42.2%) was positive for Leptospira DNA. Sequencing of DNA from isolates of Leptospira spp. and kidney tissues from cattle identified 13 as L. interrogans and 2 as L. borgpetersenii), from pigs 4 were L. interrogans and from sheep kidney tissues, 2 were L. interrogans and 1 was L. borgpetersenii. The phylogenetic tree analyses revealed that all the isolates and the kidney tissue samples grouped together with the pathogenic L. interrogans serovar Icterohaemorrhagiae and L. borgpetersenii serovar Hardjo bovis strain lely 607 from the GenBank retrieved sequences. This study is also the first reported genetic analyses of the pathogenic L. interrogans and L. borgpetersenii, in slaughtered livestock in South Africa. To determine the exposure experience of Leptospira spp. in abattoir workers sampled from six abattoirs, two serological tests (MAT and IgM ELISA) and one molecular method (qPCR) were used. The seroprevalence of Leptospira in 103 workers was 10.7% and 7.8% by IgM ELISA and MAT respectively, and the prevalence of Leptospira DNA in whole blood by qPCR was 16.5% (P>0.05). The overall prevalence (serology and PCR) of Leptospira spp. was 30.1% (31/103). The predominant serovar detected in seropositive workers was Djasiman (50.0%) and the abattoir-related risk factors identified were working in high throughput (HT) abattoirs and exposure to blood and/or water splashes during and after slaughter. Antibodies to Serogroups sejroe (Sv. Wolffi) and Pomona (Sv. Djasiman) were both found in animals and abattoir workers. Although, the main serovars in abattoir workers were different from those in animals. It was concluded that the detection of new serovars Leptospira spp. in South Africa which are not currently in the leptospirosis vaccine used in livestock coupled with the fact that these serovars are not in the diagnostic eight-antigen MAT panel indicate a need to re-assess the status of livestock leptospirosis, as well as to revisit the existing policy and practices on leptospirosis in the country. The use of a diagnostic strategy which included both serological and molecular methods will increase the sensitivity of such an approach. The zoonotic risk of leptospirosis to abattoir workers identified in the study is for the first time in South Africa and it indicates the need to introduce measures to mitigate abattoir-associated risk exposure to leptospirosis in abattoir workers in the country.
Low-dose thiafentanil in combination with azaperone alone or azaperone and medetomidine for the immobilization of African buffalo (Syncerus caffer)
Faber, Vanessa (University of Pretoria, 2021-03)
Objective To determine the efficacy, safety and cost of a novel drug regime comprising of a low thiafentanil dose in combination with medetomidine and azaperone; to the more established thiafentanil and azaperone combination for the immobilization of African buffalo (Syncerus caffer) Study design Prospective, randomised, cross-over study. Animals Twelve adult African buffalo (Syncerus caffer) bulls. Material and methods This randomized cross-over study on twelve African buffalo (Syncerus caffer) was performed on a buffalo farm located in the Sekhukhune District Municipality, Limpopo, South Africa. The study consisted of two data collection periods. The two combinations used were the more conventional thiafentanil-azaperone (TA) drug combination comprising of thiafentanil oxalate at 6-7 mg/animal and azaperone at 40 mg/animal as described by Burroughs et al. (2012b), and the novel thiafentanil-medetomidine-azaperone (TMA) combination comprising of a relatively low dose of thiafentanil oxalate at 1 mg/animal, medetomidine hydrochloride at 3-4 mg/animal and azaperone at 40 mg/animal. During the first data collection period, each buffalo was immobilized once with either the TA or the TMA combination. Six buffalo received the TA combination and six buffalo received the TMA combination. After twenty-one days, each buffalo was immobilized with the alternate combination. One animal was immobilized at a time. Before each data collection period, the animals were brought from the breeding camps into the boma where food and water was withheld for 24 hours and 12 hours respectively to minimize the risk of regurgitation during immobilization. For the immobilization and data collection, the respective buffalo was separated from the herd and moved into a separate pen. The buffalo were dosed according to its estimated weight and body condition score (BCS) as visualised by the immobilisation team. After dart placement, a stopwatch was started and the time to immobilization as well as quality of induction was recorded. Once recumbent, the animal was instrumented with a digital rectal thermometer (HI98509 Checktemp 1, HANNA Instruments (Pty) Ltd., USA), a pulse oximeter (Veterinary Pulse Oximeter, Model 9847V, Nonin Medical, USA) to measure the peripheral oxygen haemoglobin saturation (SpO2) and a multi-parameter monitor (M3T Mini vet, TooToo Meditech, China) which was used to measure the end-tidal carbon dioxide (ETCO₂). The caudal auricular artery was aseptically cannulated for continuous arterial blood pressure measurement using an intra-arterial blood pressure monitor (IntraTorr, IntraVitals, United Kingdom) and blood sampling. Blood was drawn at 10-, 20- and 35-min post immobilization and was analysed on site with a portable blood gas analyser (epoc® SIEMENS Blood Analysis System, Siemens Healthcare GmbH, Erlangen, Germany) using single-use epoc® BGEM Test Cards. Physiological values and anaesthetic plane were recorded at 5-min intervals until 40 minutes. Variables measured were the heart and respiratory rate, body temperature, SpO₂ and ETCO₂. After 40 minutes, the buffalo was de-instrumented, antagonized and the recovery times were recorded. The TA combination was antagonized using naltrexone hydrochloride intravenously at 10 mg/mg thiafentanil. The animals immobilized with the TMA combination received a standardized mixture of atipamezole and yohimbine intravenously at 0.5 ml/mg medetomidine hydrochloride followed by naltrexone hydrochloride at 10 mg/mg thiafentanil. The immobilization costs were compared descriptively. Results The mean dosages (range) of the thiafentanil-azaperone combination were 0.0136 (0.011 to 0.0163) mg kg-1 thiafentanil and 0.0792 (0.063 to 0.093) mg/kg azaperone; and of the thiafentanil-medetomidine-azaperone combination were 0.00216 (0.0016 to 0.0023) mg kg-1 thiafentanil, 0.00688 (0.0047 to 0.0084) mg/kg medetomidine, and 0.0688 (0.047 to 0.084) mg/kg azaperone. The TA combination induced recumbency in a significantly shorter time compared to the TMA combination. Mean (range) induction times for the TA and TMA combinations were 5.7 (4 - 9.5) and 10.95 (6 - 20) minutes, respectively. Both combinations provided sufficient immobilization throughout the procedure of 40 minutes for routine veterinary and management procedures. Heart rates were significantly different (p < 0.001) between the two combinations with a mean heart rate of 139 bpm (± 25) and 70 bpm (± 27) in the TA and TMA combination, respectively. There was a significant difference in the PaO₂ (p < 0.05) between the two combinations. All buffalo were hypoxaemic during immobilization with a mean (SD, range) PaO₂ value of 44 mmHg (± 14, 24 – 77 mmHg) and 51 (± 13, 33 – 80 mmHg) in the TMA and TA combination, respectively. The A-a gradient was significantly different (p < 0.01) between the two combinations and was significantly wider in the TMA than in the TA combination: TMA (mean, ±SD): 40 (± 9) mmHg; TA (mean, ± SD): 27 (± 13) mmHg. The costs to chemically immobilize and antagonise an adult buffalo bull using the TA combination were ± R 593/buffalo. This is four times more expensive than the TMA combination which was calculated at ± R 146/buffalo. Conclusions and clinical relevance Both combinations were effective in providing a sufficient immobilization for routine veterinary and management procedures in African buffalo with quick recoveries and no mortalities. The TMA combination induced immobilization with only 1/7th of the higher dose of opioid and at only a quarter of the cost. Hypoxaemia was a concern in both combinations and resulted mainly from decreased pulmonary oxygen diffusion rather than hypoventilation. Importantly, despite respiratory rates and partial pressure of carbon dioxide (PaCO2) values being within the normal expected physiological range, hypoxaemia was more severe in the TMA combination. Supplementary oxygen is considered mandatory during immobilisation with both combinations. The enormous reduction in costs with the TMA combination could be beneficial for the wildlife industry. However, the longer induction times, and risks from marked hypoxaemia need to be considered and addressed when this combination is used.
Molecular epidemiology of infectious bronchitis coronavirus in southern African poultry from 2011 to 2020
Strydom, Christine (University of Pretoria, 2023-10-31)
Infectious bronchitis virus (IBV) (family Gammacoronavirus) is an ever-evolving avian pathogen that causes major economic losses within the poultry industry worldwide. Antigenic variations allow the virus to evade vaccine induced immunity and produce new variants at an alarming rate. Epidemiological studies of IBV are imperative to selection of vaccines. Field isolates (n=385) grown in SPF embryonated chicken eggs at Deltamune (Pty) Laboratory, that originated in commercial flocks were collected from Botswana, Eswatini, Namibia and South Africa’s Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West, and Western Cape provinces from 2011-2020, were analysed in this study. A 745 bp region of the spike protein gene was amplified and sequenced, and phylogenetic analysis was performed. Twenty-four (6,2 %) samples contained mixed sequences from viral coinfections and were not evaluated further. In the remaining 364 isolates, 7 genetic lineages were identified. 184 (50,5%) viruses were identified as GI-19 (QX) strains and 78 (21,4%) as the GI-1 (Mass/H120) strain. 39 (10,7%) samples were identified as the GI-13 (4/91) lineage detected between 2011 and 2019, 29 (8,0%) as the GVI-1 (TC07-2) lineage detected from 2010-2020, 19 (5,2%) as the GI-23 (Var II) lineage from 2019-2020 with single isolates in 2010 and 2015, and 13 (3,6%) as the GI-11 (UFMG/G - Brazil) lineage detected from 2011-2020. Two (0.5%) viruses were closely related to GIV-1 (DE/072/92) lineages but were only isolated in 2011 and 2013. Three viruses from GI-1 and GI-13 may have been recombinants, but further analysis is required to confirm this. Overall, this study reveals the co-circulation of diverse IBV field and vaccine-derived genotypes in southern African poultry flocks for the first time.

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