Theses and Dissertations (Production Animal Studies)

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Comparison of prevalence of avian pathogenic Escherichia coli in South African and US poultry
(University of Pretoria, 2023-07) Wandrag, D.B.R.; jlgoosen@gmail.com; Goosen, Jaco Louis
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
(University of Pretoria, 2023-10) Gummow, Bruce; Moerane, Rebone; vsimbizi@gmail.com; Simbizi, Vincent
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
(University of Pretoria, 2023) Petzer, Inge-Marie; Karzis, Joanne; kariegavet@gmail.com; Dreyer, Marette
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
(University of Pretoria, 2024) Michel, Anita Luise; antrobusmeg@gmail.com; Antrobus, Megan Elizabeth
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
(University of Pretoria, 2024-06) May, Catherine E.; Annandale, Annett; tendai.chiwome@up.ac.za; Chiwome, Tendai Joy
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
(University of Pretoria, 2024-04) Adesiyun, Abiodun Adewale; Gcebe, Nomakorinte; amanqele@gmail.com; Manqele, Ayanda
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
(University of Pretoria, 2020-02) Nothling, Johan O.; Forbes, Patricia B.C.; Myburgh, Jan G.; geoff.brown@up.ac.za; Brown, Geoffrey James
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
(University of Pretoria, 2020) Donkin, Edward Francis; Petzer, Inge-Marie; Naidoo, Vinny; joanne.karzis@up.ac.za; Karzis, Joanne
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
(University of Pretoria, 2019) Thompson, P.N. (Peter N.); Venter, Marietjie; nahanivet@yahoo.co.za; Bertram, Freude-Marié
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
(University of Pretoria, 2024-07-07) Somers, Michael J.; Shepstone, Craig; Van Essen, L.D.; johanndebeer5@gmail.com; De Beer, Johann Hermann
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
(University of Pretoria, 2020-10) Adesiyun, Abiodun Adewale; Van Heerden, Henriette; bbdogonyaro@gmail.com; Dogonyaro, Banenat Bajehson
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)
(University of Pretoria, 2021-03) Koeppel, Katja Natalie; Burroughs, R.E.J. (Richard); vfaber87@gmail.com; Faber, Vanessa
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
(University of Pretoria, 2023-10-31) Abolnik, Celia; christine.f3nn@gmail.com; Strydom, Christine
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.
Molecular characterisation of pigeon paramyxovirus and other viruses identified by deep sequencing in pigeons and doves in South Africa
(University of Pretoria, 2023-10-31) Abolnik, Celia; u18120122@tuks.co.za; Hayes, Michaela Catharine
Pigeons, whether feral or bred for meat or sport like pigeon racing, are susceptible to a variety of diseases, many of which are caused by viral infections. Newcastle disease (ND) caused by Orthoavulavirus javaense, an avian paramyxovirus 1 (APMV1) virus is an example of a viral infection. Pigeon paramyxovirus (PPMV), a pigeon-specific variant of NDV that causes pigeon epidemics, is one of the most serious infectious illnesses within this host. The focus of the first part of the study was dedicated to investigating the molecular epidemiology of PPMVs in South Africa from 2012 onwards. A total of thirty-six field samples and isolated viruses were initially examined using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) targeting a partial fragment of the M and F gene. Among these, it was observed that the kidneys from recent clinical cases exhibited the highest viral loads. Conventional RT-PCR, Sanger DNA sequencing, virus isolation in QH9/2-1 quail cells and Ion Torrent Next-Generation Sequencing (NGS) were applied, and the complete or partial genomes of twenty-one PPMVs were obtained for further analysis. Phylogenetic analysis grouped the recent South African viruses into subgenotypes VI.2.1.1.2.1 (VIj) and VI.2.1.1.2.2 (Vik). Based on a partial phylogenetic analysis of the fusion gene, these South African viruses displayed a close genetic relationship to PPMV strains sampled from pigeons in Switzerland and Belgium in 2005, 2007 and 2022. However, a phylogenetic analysis based on the complete fusion gene sequence revealed that the South Africa viruses were closely related to PPMV strains sampled from pigeons in Australia and Belgium in 2005, 2007 and 2011. South Africa PPMVs and other African PPMV strains included in a blast results analysis indicated no relatedness between each other, suggesting no intra-continental spread. The Ion Torrent reads obtained in the previous section were investigated further for the presence of other viruses by utilising a de novo assembly approach and BLAST analysis. Additional viruses detected included Autographacalifornica nucleopolyhedrovirus, Avian coronavirus (Pigeon coronavirus), Avian endogenous virus, Avian leukosis virus, Avian myeloblastosis virus, Avian orthoavula virus 1 (Pigeon v paramyxovirus), Avian sarcoma virus (Rous sarcoma virus), Bovine viral diarrhea virus, pigeon circovirus (PiCV), Human Gammaherpesvirus, Infectious bronchitis virus, porcine rotavirus, Semliki Forest virus, Tasmanian devil retrovirus, Torque teno virus (pigeon torque teno virus) and white spot syndrome virus. A phylogenetic analysis was performed with the three pigeon circovirus genomes discovered in a previous section through a metagenomic approach, plus eleven additional pigeon circovirus genome sequences previously detected during research at the University of Pretoria in recent years. The analysis of genotype classification yielded intriguing results, with 10 samples falling under the G genotype, two in the H genotype, and the final two in genotypes E and D, respectively. These samples displayed strong genetic association with PiCV strains obtained from pigeons in different countries, such as Belgium, Brazil, China, Germany, Italy, and Poland, from 2000 to 2021. This finding underscores the widespread distribution and genetic diversity of PiCV strains across international pigeon populations over the past two decades.
Effect of different dietary fibre raw material sources on production and gut development in fast-growing broilers
(University of Pretoria, 2023-08) Wandrag, D.B.R.; driesfour@gmail.com; Fourie, Andries Benjamin
Many recent studies have been published about the beneficial effect of different fibre sources in a broiler diet. To assess these effects with raw material sources available in Southern Africa, a trial was done with four treatments; control diet, 2% sunflower hulls, 2% malt culms and 0.8% of a commercial lignocellulose product. Using a completely randomised block design, each treatment had 24 repetitions (96 pens in total), with 48 birds per pen. The effects were measured weekly by assessing production parameters, gut development and the humoral immune response. Production parameters were measured per pen, gut measurements were done on 12 birds per treatment each week, and humoral immune response on 24 birds per treatment at 32 days. The promising responses seen in previous studies on fibre sources such as sugar beet pulp and oat hulls, were not fully repeated here with the local fibre sources. There were no significant differences from the control group based on production parameters. Concerning gut development, sunflower hulls produced a significant improvement compared to the control group with regards to caecal and overall intestinal lengths at 7 days. There was a numerical improvement in gizzard weights at 7 days for the malt culms group. No significant differences were detected on the serology. The results show that there could be merit in including sunflower hulls in the pre-starter period (days 0-7), although it did not translate to production advantages here. Different inclusion levels should be trialed.
Systematic review of Halioticida noduliformans infection in South African abalone (Haliotis midae)
(University of Pretoria, 2022-10) Thompson, P.N. (Peter N.); Grewar, John Duncan; shutabei@gmail.com; Tabei, Shuichi
The South African abalone (Haliotis midae) industry is a growing and significant market in terms of export potential as well as job creation. The present abalone industry in South Africa is made up of a single species, Haliotis midae. Halioticida noduliformans infection has been associated with elevated mortalities in South African abalone, marked by necrosis of the epithelium and superficial muscle tissues. The disease condition itself has been termed abalone tubercle mycosis (ATM). There is a perception that the disease can have a substantial impact on producers, but there appears to be little published information on this. There is also a lack of cohesive information regarding its control. Through the use of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, this systematic review aimed: 1) to provide a clear and comprehensive overview of available information on Halioticida noduliformans infection in South Africa, from sources including scientific and grey literature, technical reports and legislation; 2) if possible, to produce summary estimates of relevant epidemiological parameters; and 3) to identify deficiencies in research which will guide future investigations by formulating relevant research questions. Relevant legislation and surveillance policy and practices were also summarised. The amount of primary literature was found to be very limited with the same sources being cited repeatedly. Where quantitative data was found, it was traced to a single source. Although the available information regarding this organism covers pathology and diagnostic test ability, there are no reports of prevalence, risk factors, assessment of treatments or intervention, and numerous areas for further research were identified.
Production of plant-expressed virus-like particle vaccines against infectious bronchitis coronavirus and vaccine efficacy in chickens
(University of Pretoria, 2022) Abolnik, Celia; O’Kennedy, Martha M.; sepotokelekamogelo@yahoo.com; Sepotokele, Kamogelo Mmapitso
Infectious Bronchitis Virus (or IBV) is the root cause of extremely infectious respiratory disease that occurs in chickens. It has a high mutation rate that causes the emergence of multiple variants that are difficult to control, leading to major worldwide economic losses to the poultry industry. In this study, virus-like particles (VLPs) were produced using Agrobacteriummediated transient protein expression in Nicotiana benthamiana plants as potential vaccines against IBV. Modifying the full-length IBV Spike (S) protein resulted in high levels of VLPs resembling native IBV particles visualised under transmission electron microscopy. The highest VLP expression levels were obtained when the native IBV S protein transmembrane (TM) domain and cytosolic tail (CT) sequences were substituted with the equivalent sequences of the Fusion (F) protein of Newcastle Disease Virus (NDV), and co-infiltrated with the NDV matrix protein. The second highest VLP expression levels were obtained when the TM and CT were substituted with the equivalent sequences of the Influenza A Virus (IAV) Haemagglutinin (HA) protein, and co-infiltrated with the IAV M2 protein. The lowest VLP expression levels were obtained when the chimeric modified S protein with its native TM and CT was coinfiltrated with the IBV Membrane, Envelope, and Nucleocapsid proteins. There was seroconversion in SPF chickens that received a single intramuscular immunisation of 5 μg or 20 μg (S protein content) adjuvanted IBV VLPs, with geometric mean S protein specific haemagglutination inhibition (HI) titres of 9.1 log2 and 10.5 log2 respectively after two weeks. In a challenge study with the live virus, the VLP vaccinated chickens elicited S protein specific antibodies at a level comparable to those elicited by those vaccinated with a live-attenuated vaccine mix (IBV Ma-5 and 4-91 vaccines) with geometric mean HI titres of 6.8 and 7.2 log2 respectively. The VLP vaccine was able to reduce both oropharyngeal and cloacal viral shedding between 3 and 7 days post challenge, which was similar to the reduction seen in the birds vaccinated with the live-attenuated vaccine mix. The birds vaccinated with the plantproduced VLP vaccine showed higher tracheal ciliary motility than those vaccinated with the live vaccines, with no adverse vaccine effects observed. These plant-produced IB VLPs have great potential for the global poultry industry as they are highly immunogenic, safe, and they can easily be updated to antigenically match any circulating IBV variant both speedily and cost-effectively.
A risk assessment for the export of fresh beef products after an outbreak of foot and mouth disease in the free zone of South Africa
(University of Pretoria, 2019) Oguttu, James Wabwire; cher.qekwana@gmail.com; Qekwana, Cher Phoebe
Foot-and-mouth disease has been recognised as one of the most important diseases constraining international trade in animals and animal products. Economic losses due to reduced exports as well as additional costs of implementation of control measures associated with FMD outbreaks in South Africa have been reported. In order to participate in the international market, countries with FMD endemic areas including South Africa must demonstrate that the likelihood of FMD in fresh beef products is negligible. However, the quantitative risk of FMD virus survival in beef and beef products destined for export from the FMD free zone in South Africa has not been done. This study aims to assess the probability of FMD virus surviving in fresh beef products after implementation of the risk reduction measures at different steps along a beef value chain using quantitative risk assessment stochastic modelling. A quantitative risk assessment was conducted throughout the beef value chain using data from previously published studies in Science Direct, Google Scholar, Web of Science, and PubMed. In addition, an expert opinion questionnaire survey was used to collect additional data on the likelihood of FMD in South Africa. A scenario tree was developed and equations for input variables were created. A probability distribution using A Monte Carlo simulation with 100 000 iterations to model the probability of occurrence of the FMD virus at each node. The overall likelihood of FMD virus contamination of fresh beef products was calculated by adding the probabilities at farm, feedlot and abattoir. A sensitivity analysis was used to determine inputs in the value chain that are correlated with the overall FMD likelihood in fresh beef products using correlation coefficients. A correlation coefficient is the quantification of a statistical relationship between two variables. In addition, the impact of changes in the initial prevalence of FMD in the country and the likelihood of an animal been asymptomatic on the overall FMD likelihood in fresh beef products were also assessed. The overall probability of FMD virus contaminating fresh beef products was negligible (2.1×〖10〗^(-9)). The probability of FMD virus circulation in the country (correlation coefficient (r) =0.72) and the inability to diagnose asymptomatic cattle (r=0.59) were strongly correlated with the probability of FMD virus in fresh beef products. Weak correlations were observed between FMD transmission rate (r=0.17), antemortem, inspection (r=0.9), post-mortem inspection (r=0.09) and the probability of FMD virus in fresh beef products. When the initial probability was increased to 3.4× , the likelihood increased to 1.6 ×〖10〗^(-4) .Similarly, increasing the probability of not detecting asymptomatic animal to 0.6 increased the probability of FMD virus in fresh beef products to 5.2×〖10〗^(-9). The likelihood of FMD virus in fresh beef products destined for export from the FMDV free zone was negligible. The initial prevalence of FMD in the country and the asymptomatic status of FMD infected cattle were strongly associated with the probability of the presence of FMD virus in fresh beef products intended for export from the FMD free zone. Therefore, it is important for regulators and farmers to ENSURE that FMD free status is always maintained and that control measures at farms and abattoirs such as biosecurity, vaccination, passive surveillance, and processing must continue in order to maintain the disease-free status of the FMDV free zone. The addition of active surveillance in the FMD free zone could potentially further decrease the likelihood of FMD survival in fresh beef products.
Effects of automatic cluster remover switch-point settings on milking performance and overmilking in dairy cows
(University of Pretoria, 2021) Petzer, Inge-Marie; Karzis, Joanne; pvermaak@ymail.com; Vermaak, Pieter
The ideal milking machine harvests milk from dairy cows in a fast, effective manner without causing teat or udder damage, cow discomfort or loss in milk quality. Due to economic pressure many swing-over systems with high milk-lines were installed in South Africa, extending take-off delay with standard milking machine settings and increasing the risk of new intra-mammary infections. The aim of the study was to investigate the effect of three automatic cluster removal (ACR) switch-point settings on machine-on time, over-milking duration, total average, peak flow- and over-milking vacuums. In a randomised trial using 65 (n = 65) performed on one dairy farm. Cows were selected based on their teat size, stage of lactation and udder palpation results. The trial cows were exposed for 15 milkings to each of three ACR switch-point settings (0.504 kg/min, 0.630 kg/min and 0.840 kg/min). The parlour was a 10-point, low-line, herringbone Waikato machine with the Afimilk system. Pre-milking preparations were observed while a VaDia-Biocontrol (Norway) apparatus was used to determine machine-on time and vacuums at the claw, mouthpiece and pulsator chambers during the whole milking process. Results indicated that total machine-on time varied significantly (p < 0.05) between the 0.840 and 0.504 kg/min settings (290.0 to 289.2 sec) and between 0.630 and 0.504 kg/min (p < 0.01) (289.2 to 303.3 sec) settings respectively. Over-milking time differed significantly (p<0.0001) from 76.5 to 108.2 seconds between the highest and lowest volume setting. The three vacuum level measurements also differed significantly (p<0.0001) at each switch-point setting. Over-milking duration, as a percentage of total machine-on time, decreased from 35.7 % (at 0.504 kg/min) to 35.9 % (at 0.630 kg/min) and 26.4 % (at 0.840 kg/min) respectively. The knowledge gained from different switch-point settings can be applied on individual dairy farms with different parlours and milking machines, to optimise settings in order to obtain a balance between milking efficiency and udder health.
Towards producing infectious bronchitis virus-like particles in plants as potential vaccine candidates
(University of Pretoria, 2019) Abolnik, Celia; O’Kennedy, Martha. M.; sepotokelekamogelo@yahoo.com; Sepotokele, Kamogelo Mmapitso
Infectious Bronchitis Virus (IBV) causes a highly contagious respiratory disease that affects chickens and other poultry. This OIE-listed disease has global economic implications with losses per flock estimated at 10% to 20% of the market value. The South African poultry industry makes up the largest subsector within the country’s agricultural sector, producing an annual turnover of over R40 billion. Therefore, it would be beneficial to the poultry industry to prevent economic losses due to diseases such as IBV. Current autogenous IBV vaccines are effective but require the passage of live viruses in embryonated chicken eggs. Therefore, safe, efficacious, new-generation vaccines are imperative. Biopharming is the production of recombinant pharmaceutical proteins by making use of plants as bioreactors. Plants are capable of producing large quantities of target proteins cost-effectively, offering attractive alternatives for the production of vaccines, antigens for diagnostics, and other pharmaceuticals. The aim of this project was to produce infectious bronchitis virus-like particles (VLPs) displaying the major surface antigen, the Spike protein, in Nicotiana benthamiana plants by transiently co-expressing and assembling the structural proteins of IBV. VLPs are multiprotein structures that mimic the authentic virus, while lacking the genome, resulting in safe, efficacious, DIVA (distinguish between infected and vaccinated animals) compliant vaccine candidates that induce both cellular and humoral immune responses. In addition, the speed of gene synthesis and production of VLPs in plants will facilitate a rapid update of the IBV spike protein that is tailored and antigenically matched, in vaccine formulations. The native as well as recombinant versions of the spike glycoprotein of QX-like IBV were individually cloned into a plant expression vector, as were the membrane, envelope and nucleocapsid proteins. Various Agrobacterium strains were tested to identify the most appropriate strain to mediate the production of IB VLPs in plants. IBV structural proteins were successfully expressed in N. benthamiana ΔXT/FT plant leaf material, as confirmed by immunological detection, but low yields were obtained. No VLPs were detected using transmission electron microscopy, indicating that VLPs may not have assembled. In future, alternative designs of the spike protein and the addition of molecular chaperone genes will potentially elevate the numbers of VLPs produced, resulting in a commercially viable vaccine product.

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