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Multiscale Modelling of Foodborne Diseases
No full textPh.D. (Mathematics)Department of Mathematical and Computational SciencesInfectious disease systems are essentially multiscale complex system wherein pathogens multiply
within hosts, spread across people, and infect entire populations of hosts. The description of most
biological processes involves multiple, interconnected phenomena occurring on different spatial
and temporal scales in the human body. Traditional approaches for modelling infectious disease
systems rely on the principles and concepts of the transmission mechanism theory that considers
transmission to be the primary cause of infectious disease spread at the macroscale. Modellers
of infectious diseases are increasingly using multiscale modelling approach in response to this
challenge. Multiscale models of infectious disease systems encompass intricate structures that
revolve around the interplay of three distinct sub-systems: the host, the pathogen, and the environmental
subsystems. The replication-transmission relativity theory is a novel theory designed
for the purpose of multiscale modeling of infectious disease systems, accounting for variations
in time and space by incorporating pathogen replication that leads to transmission. Replicationtransmission
relativity theory consists of seven distinct levels of organization within an infectious
disease system, each level including the within-host scale (microscale) and between-host scale
(macroscale). Five separate classifications of multiscale models can be formulated that integrate
the microscale and macroscale. A research gap has been created in an attempt to establish a multiscale
framework in order to understand the mechanisms on how foodborne pathogens cause
infections on human beings and animals, as very little has been done in modelling of foodborne
disease. The primary goal of this study is to create multiscale models for foodborne diseases to
examine whether a mutual influence exists between the microscale and macroscale, guided by the
principles of replication-relativity theory. The multiscale models are developed by considering
three environmental transmitted diseases at host level caused by pathogens: norovirus, E. coli
O157:H7 and taenia solium. We start by developing a single-scale model of foodborne diseases
caused by viruses in general, which is then extended to create a multiscale model for norovirus.
We formulate a non-standard finite difference scheme for the single-scale model, norovirus, and
E. coli O157:H7. For taenia solium, we use ODE solvers in Python, specifically, ODE int function
in the sci.integrate. The numerical findings from the study confirm the applicability of
the replication-transmission relativity theory in cases where the reciprocal impact between the
within-host scale and the between-host scale involves both infection/super-infection (for the effect
of the between-host scale on the within-host scale) and pathogen excretion/shedding (for the
effect of the within-host scale on the between-host scale). We expect that our study will help
modellers integrate microscale and macroscale dynamics across various levels of organization
within infectious disease systems.NR
Human immunodeficiency virus type 1 diversity in patients initiating treatment in Northern South Africa
No full textPhD (Microbiology)Department of Biochemistry and MicrobiologyBackground: Clinical trials carried out to determine when to start antiretroviral therapy (ART) have been showing that early ART initiation results in better health outcomes which are primarily indicated by suppressed viral loads and increase in CD4+ cell counts to healthy human ranges. This in turn is expected to reduce HIV transmission thereby, leading to a decreased spread of the virus and eventual elimination of the virus from the human population. Findings from these trials resulted in the near global adoption of universal test and treat program. The program stated that in the absence of contraindications, people living with HIV (PLWH) should start treatment as soon as they are diagnosed with HIV. However, these outcomes could differ in real world settings where some of the support provided in clinical trial settings are not available. Furthermore, there is historical data that showed variations in HIV prevalences and prevalences of HIV drug resistance within provinces and sub-regions of provinces in South Africa and to have an accurate perspective of the impact of universal test and treat (UTT) implementation, these geographical differences need to be investigated. This study hypothesized that UTT will result in improved health outcomes within a prospective, observational setting in Northern South Africa.
Objective: The main objective of the study was investigating treatment outcomes, pretreatment and acquired drug resistance and viral diversity in a cohort of HIV infected individuals entering universal test and treat program in Northern South Africa.
Study design and approaches: The study protocol was approved by the Human and Clinical Trials Research Ethics Committee of the University of Venda (Project Number: SMN/15/MBY/23/07/10). Permission to carry out the study from public health care centers was granted by the Limpopo Provincial Department of Health. This was an observational and prospective study which recruited participants from four public HIV treatment centers within Capricorn and Vhembe districts of Limpopo province, Northern
South Africa. All participants were over 18 years old and written informed consent was obtained prior to inclusion into the study. Phlebotomy was carried out by a registered nurse and identifiable participant information was concealed using unique codes generated during study initiation. Participants were recruited from April 2016 to March 2017 and followed up every 3 months from June 2016 to July 2018.
To determine treatment outcomes for people in UTT, demographic, socioeconomic, and clinical data was collected using a structured questionnaire which was then captured in a spreadsheet. Missing and ambiguous data entries were clarified with participants. The data captured was age, sex, marital status, highest level of education, occupation, income level, probable place of infection, probable year of infection, current anti-retroviral (ARV) regimen, start date of treatment, place of residence, other diagnosis at start of treatment, clinical HIV stage as defined by World Health Organization (WHO), other medications taken with HIV treatment, cluster of differentiation 4 (CD4)+ cell count, percentage CD4, hemoglobulin, viral load in counts per millimeter of blood. During initial and follow up visits, three milliliters of whole blood was collected into each of two ethylenediaminetetraacetic acid (EDTA) coated tubes. One tube was shipped to a commercial laboratory for viral load measurements which was done on a COBAS Ampliprep/COBAS TaqMan analysis platform (Roche, USA). The platform uses reverse transcription polymerase chain reaction (RT-PCR) with DNA probe to quantify viral copies present within a sample. The second tube was shipped to the University of Venda laboratory for CD4+ cell count measurement using a Becton Dickinson FACSPresto system (BD Biosciences, San Jose CA). The system employs immunofluorescence and spectrophotometry techniques to quantify CD4+ cells and hemoglobulin within a test sample. The CD4+ cell count measurements and viral load measurements were also captured within the same spreadsheet that the demographic, socioeconomic, and clinical data was captured. The captured data was cleaned and imported into Rstudio for statistical analysis. The treatment outcomes investigated were viral suppression which was defined as reduction in baseline viral load to less than 50 viral copies per milliliter of blood after starting ART and immunological response which
was defined as an increase in baseline CD4+ cell count by 50 CD4+ cells after 6 months on ART. Participants were also categorized as early ART initiators which was defined as those with baseline CD4+ cell counts greater than 500 cells per microliter blood (cells/μL) and late ART initiators or those with baseline CD4+ cell counts less than 500 cells per micro-liter blood (cells/μL). The study inclusion criteria was people 18 year and older who had never been on ART. Demographic, socioeconomic, and clinical data collected while initiating study was summarized and presented as a table. Kaplan Meier curves were used to estimate viral suppression and immunological response. Hazard ratios for demographic, socioeconomic, and clinical data against the two outcome variables namely viral suppression and immunological response were determined using cox regression analysis.
To study pre-treatment drug resistance (PDR), total ribonucleic acid (RNA) was extracted from plasma using QIAamp Viral RNA mini kit (Qiagen, Netherlands). Complimentary deoxyribonucleic acid (DNA) was synthesized using cloned avian myeloblastosis virus (AMV) reverse transcriptase (RT) (Invitrogen, USA). The first 1600 nucleotides of the pol gene spanning the complete protease gene and about 1000 nucleotides of reverse transcriptase gene were amplified by nested polymerase chain reaction (PCR) using FastStart Taq DNA Polymerase kit (Sigma-Aldrich, USA). Expected PCR amplicons identified by gel electrophoresis; and samples with desired length were selected for next generation sequencing (NGS). PCR amplicons were purified using AMPure XP magnetic beads (Beckman Coulter, USA). Sequencing libraries were prepared from amplicons by normalizing the concentration of each sample’s amplicon to 0.2 nanogram per microliter. These normalized amplicons were the fragmented using transposase enzyme within the Nextera XT DNA library preparation kit (Illumina, San Diego, California, U.S.A.). Sequencing primers were then ligated to both 5-prime and 3-prime ends of the fragmented amplicons or DNA libraries through PCR. The concentration for each sample’s DNA library was determined using Qubit dsDNA High sensitivity florescent dye assay kit (Life technologies, U.S.A.). The libraries were normalized to four nanomolar prior to pooling the normalized libraries,
denaturing, and diluting the denatured or single stranded libraries to 1.8 picomolar. The denatured libraries were then spiked with 25% PhiX and loaded onto a sequencing cartridge (Illumina, San Diego, California, U.S.A.) and ran on a MiniSeq sequencing system. The sequencing reads generated after the run were demultiplexed and post-sequencing quality check report was generated. The reads were then exported from the machine and validated using FastQC program. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The reads were then imported into Geneious Prime 2020 (Biomatters, 2020) where the sequences were filtered and trimmed to remove reads shorter than 50 nucleotides and left-over sequencing adapters. The remaining high-quality reads were assembled to generate contigs which were mapped to a reference sequence and consensus sequences were extracted. Variants at each nucleotide position was called at >5% threshold to account for minority variants and >20% threshold. These variants were queried for surveillance drug resistance mutations (SDRM) using Calibrated Population Resistance (CPR) Tool from the Stanford drug resistance database. Univariate and multivariate logistic regression analysis was done to determine associations between SDRM and predictor variables namely, sex, age, CD4+ cell count and viral load.
To study acquired drug resistance (ADR), only samples collected within the first 12 months after initiating ART were considered. DNA was extracted from isolated peripheral blood mononuclear cells (PBMC) using QIAamp blood DNA midi kit (Qiagen, Netherlands). pol gene was amplified and sequenced. Sequencing for follow amplicons was prioritized based on if the baseline amplicons for each follow up sample had been successfully sequenced and analysis of the baseline sequences did not have drug resistance mutations within its >20% threshold. Variant calling was done at >1%, >5% and >20% viral thresholds and drug resistant mutations were queried from the Stanford drug resistance database at each of the thresholds. Wilcoxon method was used to determine correlations between viral load and drug resistance mutations in Rstudio and phylogenetic tree was constructed using Interactive Tree of Life (iTOL) https://itol.embl.de/.
To determine HIV diversity in the study population, baseline pol gene sequences were subtyped using Molecular Evolutionary Genetics Analysis Version 7.0 (MEGA7), Context-based Modeling for Expeditious Typing (COMET), Subtype Classification Using Evolutionary Algorithms (SQUEAL) and REGA HIV-1 Subtyping Tool Version 3.0. The sequences were screened for recombination using Recombinant Identification Program (RIP) and jumping profile Hidden Markov Model (jpHMM). Subtypes were assigned based on consensus achieved with all four of the subtyping tools. Recombination was inferred based on detection of mixed subtypes by recombinant identification program (RIP) or jumping profile hidden markov. Amplification of a 9084 base-pair HIV sequence was done in two overlapping fragments whereby the first 4516 nucleotides of the 9084 HIV sequence was amplified in a separate nested PCR reaction to the next 4680 nucleotides of the 9084 HIV sequence. Expanded long template enzyme (Roche, Germany) was used for amplification and then sequenced using Illumina MiniSeq sequencing system. Sequence reads were imported into Geneious Prime 2020 (Biomatters, 2020), filtered and trimmed and de novo assembled to obtain full length sequences. The full-length sequences and the extracted HIV genes were subtyped using phylogenetic means using MEGA 7 and COMET. Recombination was detected using RIP, jpHMM and Simplot. Consensus subtype was determined by detection of the subtype by two or more tools. The recombination pattern was illustrated using the recombinant HIV-1 Drawing tool (https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html).
Results: To determine treatment outcomes for people in UTT, a total of 548 participants were recruited. However, fourteen were excluded as they had started ART prior to recruitment. The study population was made up of 71% (378/534) female. The median age for the study population was 35 (IQR: 29 – 44). Seventy one percent (381/534) had baseline viral loads greater than one thousand copies per ml. The population had 75.3% (402/534) late ART initiators (LAI). There were eleven individuals within the cohort at 24 months. Dataset for the viral suppression analysis, excluded eighty-four of the participants who did not have baseline viral load measurements, 24 participants who
had suppressed baseline viral loads (less than 50 copies/ml) and 180 participants who were never followed up. Individuals were censored on the first follow up viral load that dropped to fifty copies/mL. The dataset for viral suppression analysis comprised of 246 individuals whose baseline and follow up viral loads were captured. Censoring occurred at the first viral load that dropped to or below 50 copies/mL after starting ART. Fifty percent (122/246) achieved viral suppression after approximately 6 months of ART and 73.6% (181/246) after approximately 12 months and 97% after approximately 24 months. Multivariable cox regression analysis showed that viral suppression in males was slower compared to females (AHR=0.642; CI: 0.41 – 0.92; p value=0.025) and this difference was statistically significant. There was also a statistically significant positive association between viral suppression and hemoglobulin counts above 12 grams per deciliter (AHR = 2.307; 95% CI: 1.6067 – 3.312; p<0.001). Dataset for immunological response analysis compromised of 104 individuals derived from the 246 individuals within the viral suppression analysis. All 104 individuals had baseline and follow up CD4+ cell counts. Censoring occurred when an increase of baseline CD4+ cell count by 50 cells/μL was observed at or after 6 months of ART initiation. There was 11.5% (12/104) individuals who achieved an immunological response after approximately 6 months of ART use and 39.4% (41/104) after approximately 12 months and 97.5% (101/104) after approximately 24 months. There was negative associations between immunological response and baseline viral loads greater than 50 to 1000 copies/mL (AHR = 0.108; 95% CI: 0.0303 – 0.388; p<0.001) as well as baseline viral loads greater than 1000 copies/mL (AHR = 0.125; 95% CI: 0.0541 – 0.291; p<0.001). Both associations were statistically significant. There was also negative associations between immunological response and individuals who were classified as WHO clinical stage 1 (AHR = 0.173; 95% CI: 0.0460 – 0.655; p=0.0097) as well as clinical stage 3 (AHR = 0.123; 95% CI: 0.0155 – 0.977; p=0.0475). Both of these associations with immunological response were statistically significant.
Whole blood was collected from 534 participants to determine diversity of drug resistance mutations for people starting ART. Low blood volume (less than 1 ml) was
collected from 135 individual of the 534 recruited at baseline and blood was recollected from them within 4 days of initial collection. Recollection was successful for fifty-four out of the 135 individuals whereas 81 participants could not be reached. From the fifty-four participants, only 21 had 2 ml to 3 ml of blood collected. RNA was isolated from 420 blood samples from which 338 were successfully amplified and sequenced. Twenty of the 338 failed to generate sequencing reads and seventy-seven had small numbers of high quality assembled contigs and could not generate a continuous sequence. Surveillance drug resistance mutation (SDRM) prevalence at >20% threshold was 9.5% (23/241) and 12.9% (31/241) at >5% threshold. SDRM associated with non-nucleoside reverse transcriptase inhibitor (NNRTI) had a 7.5% prevalence within the >20% threshold and 8.7% prevalence within >5% threshold. The NNRTI SDRMs that chiefly contributed to this prevalence at >20% threshold were K103N (6.2%; 15/241), V106M (1.7%; 4/241) and P225H (1.2%; 3/241) whereas at the >5% threshold were K103N (7.9%; 19/241), V106M (2.5%; 6/241) and P225H (1.7%; 4/241). Nucleoside reverse transcriptase inhibitors (NRTI) SDRMs prevalence at >20% threshold was 3% and 4.6% at >5% threshold. NRTI SDRM at the >20% threshold were M184V (0.8%; 2/241) and K65R (1.7%; 4/241) and at the 5% threshold were D67G/N (1.2% 3/241), K70R/E (1.7%; 4/241), M184V (1.2%; 3/241) and K65R (2.5%; 6/241). Protease inhibitor SDRMs prevalence was at 0.4% at >20% threshold and 2.1% at >5% threshold. The PI mutation D30N was the only SDRM detected at >20% threshold whereas the mutations F53L, G73S and M46I were detected with a prevalence of 0.4% each at >5% threshold. Associations between surveillance drug resistance mutations and predictor variables namely sex, age, viral load and CD4+ cell count showed that there were decreased odds risk for males having SDRM compared to females (aOR= 0.73; 95% CI: 0.29 – 1.83; p value = 0.499) and increased odds risk for people with baseline viral load over one million copies/mL having SDRMs (aOR = 1.25; 95% CI: 0.11 – 14.55; p value=0.86). None of these associations with SDRMs were statistically significant.
To determine diversity of drug resistance mutations for PLWH on ART, 203 baseline participants who were followed up at the four timepoints within the first year of ART with
155 followed up at 3 months timepoint, 111 at 6 months, 96 at 9 months and 94 at 12 months. Amplification was successful for 108, 67, 50 and 28 samples at 3, 6, 9 and 12 months, respectively. Follow ups amplicons were selected for NGS sequencing based on the absence of DRM at >20% threshold for their baseline sequences. This meant that 34, 46, 37 and 20 follow up amplicons for 3, 6, 9 and 12 months respectively were selected for Illumina sequencing. High-quality (Q score >=30) sequences were obtained from 29, 37, 33 and 15 samples at 3, 6, 9 and 12 months, respectively. Forty-six percent (52/114) of the 114 total follow up sequences had at least one DRM at >20% threshold with 55% (63/114) with at least one DRM at >5% threshold. The NNRTI DRM prevalence at >20% threshold was 6.9% (2/29), 8.1% (3/37), 9.1% (3/33) and 6.7% (1/15) at 3 months, 6 months, 9 months, and 12 months timepoints, respectively. The NNRTI DRM prevalence at >5% threshold was 6.9% (2/29), 8.1% (3/37), 12.1% (4/33) and 6.7% (1/15) at 3 months, 6 months, 9 months, and 12 months timepoints, respectively. The frequent NNRTI DRM at >20% threshold was K103N, P225H and E138A. The NNRTI mutation K101E was observed at >5% threshold. The NRTI DRM prevalence at >20% threshold was 3.4% (1/29) at 3 months, 2.7% (1/37) at 6 months, 6.1% (2/33) at 9 months, and 0% at 12 months. The NRTI DRM prevalence at >5% threshold was 3.4% (1/29) at 3 months, 2.7% (1/37) at 6 months, 9.1% (3/33) at 9 months, and 0% at 12 months. The commonly occurring NRTI DRM at 20% threshold was M184V, K70ER and at >5% threshold was T215I. Primary PI DRM prevalence was 0% at >20% threshold however, at >5% threshold the prevalence was 3.4% (1/29) and 3% (1/33) at 3 months and 9 months respectively and 0% at 6 months and 12 months. The PI mutations that contributed at >5% threshold was M46I and V82A. Correlation of viral loads among majority variants (at greater 20% threshold) and minority variants (less than 20% threshold) showed a slight difference in median viral loads at 3 months (median log10 copies per ml for majority variant = 2.08; IQR: 1.59 – 2.28; median log10 copies per ml for minority variant = 1.81; IQR: 1.30 – 2.31; p value = 0.55) with no difference in viral loads at 6, 9 and 12 months. The differences in viral loads between the groups were not statistically significant at any of the timepoints. Subtypes inferred through phylogenetic means showed that all sequences were HIV subtype C.
To determine HIV diversity for people starting ART, 241 baseline sequences were screened for non-C subtypes using four subtyping tools. The four tools showed that 99% (238/241) of the sequences were HIV-1 subtype C. However, subtyping of three samples (AHDR-R244, AHDR-R118 and AHDR-S100) revealed non-C subtypes within their sequences. Phylogenetic analysis revealed that AHDR-R244 was a subtype G whereas COMET showed the sample to be a subtype G and C whereas SQUEAL inferred it to be a subtype C and REGA inferred it to be a subtype G and C. AHDR-R188 was inferred to be a subtype C when analyzed by phylogenetic means, COMET and REGA but was inferred as subtype A by SQUEAL analysis. AHDR-S100 was inferred to be a subtype C when analyzed by phylogenetic means, SQUEAL and REGA whereas it was inferred to be a recombinant of subtype F2 and C with COMET. The recombinant detection tool jpHMM detected AHDR-R244 was a recombinant of subtypes G and C whereas AHDR-R118 was a recombinant of subtypes A2 and C and AHDR-S100 was subtype C. The recombinant detection tool RIP detected AHDR-R244 as recombinant of G and C, AHDR-R118 as subtype C and AHDR-S100 as recombinant of subtype C and F2. Near full genome amplification and sequencing was successful for all three samples including AHDR-R114 which was used as a quality control sample. Screening of AHDR-R114 using all four subtyping tools inferred it was a subtype C sequence. Subtyping the HIV genes with 2 subtyping tools and recombination tools revealed that AHDR-R244 had a mix of subtypes C and G for gag and pol genes, subtypes G and H for env gene, subtypes B and C for vif, subtype C for vpu, subtypes G and C for rev, subtypes J and D for vpr, subtype C and recombinant CRF01_AE for tat, subtypes J and C for nef. Analysis with the three recombinant tools revealed that same subtypes were present within the HIV genes analyzed. The consensus of the complete genome was a recombinant with subtypes A1, C, G and recombinant CRF01_AE. Subtyping of HIV genes using phylogenetic means for AHDR-R118 and AHDR-S100 revealed that all the HIV genes for these two samples were subtype C however, there was a recombinant CRF88 detected within tat gene for AHDR-R118 and AHDR-S100. COMET analysis revealed that AHDR-R118 was a subtype C for all HIV genes whereas AHDR-S100 was subtype F2 for pol gene with the remaining genes being subtype C. RIP revealed that AHDR-R118 pol gene was a
recombinant of subtypes A2 and C and the rest of the HIV genes were subtype C. RIP revealed that AHDR-S100 pol gene was a recombinant of subtypes B, C and F2 and env gene was a recombinant of subtypes C and F2 and recombinant CDF01_AE with the remaining HIV genes being a subtype C. The recombinant tool jpHMM revealed that AHDR-R118 had subtypes A2 and C within pol gene and subtypes C and J within tat gene with the rest of the HIV genes being a subtype C. The jpHMM tool revealed that AHDR-S100 had subtypes A2 and C within gag gene and subtypes C and J within tat gene with the rest of the HIV genes being a subtype C. Simplot revealed AHDR-R118 had subtypes C and D within env gene
Knowledge, Attitudes, and Practices of learners towards COVID-19 Guidelines in Bushbuckridge Local Municipality, Mpumalanga Province
No full textMPHDepartment of Public HealthGlobally, as of 28 March 2022, Covid-19 cases were reported to have reached more than four hundred and eighty margin, with the death tall reported by World Health Organisation to be over 6,1 million across the globe. In Africa alone more than 8,5 million positive cases of Covid-19 were confirmed. The good level of knowledge, positive attitudes, and good practices of learners towards Covid-19 guidelines play a pivotal role in minimizing the spread of Covid-19, and ensure safe, healthy learning environments. The purpose of the present study was to assess knowledge, attitudes, and practices of learners towards Covid-19 guidelines at Bushbuckridge Local Municipality, Mpumalanga Province. This study employed a quantitative cross-sectional descriptive design. Two-stage cluster sampling was used and systematic sampling was used to select respondents in each sampled school cluster and data was gathered using a questionnaire that was administered to sampled respondents. The questionnaire was partitioned into four segments: demographic questions, knowledge, attitudes, and practices of learners towards Covid-19 guidelines. Descriptive statistics was used to analyse data. The results were presented statistically through tables, charts and diagrams following the sequence of the research objectives. During analysis of data, it was discovered that majority of secondary school learners have good level of knowledge towards Covid-19 guidelines. The study found that majority of Secondary school learners, 77,60% have positive attitudes towards Covid-19 guidelines. The study also discovered that majority of secondary school learners, 72,26% have proactive practices towards Covid-19 guidelines, Therefore, the following recommendations are made: The Department of Basic Education should emphasize the integration of health education in schools to enhance the knowledge base of learners on Covid-19 guidelines and Covid-19 in general, Learners need to be continuously educated about the hygiene practices and Covid-19 guidelines, this may increase their knowledge and develop further positive attitudes, as a result, future Covid-19 infections may be reduced in schools, the health guidelines that were implemented during the pandemic should be gazetted and enforced at schools to proactively prevent further outbreaks of Covid-19 and other pandemics, lastly, more research must be conducted to assess knowledge, attitudes and practices towards Covid-19 guidelines in Mpumalanga Province and South Africa as a whole to extend the knowledge base on the subject matter.NR
A support framework of enhancing business performance of ruaral SMME's in the Limpopo Province, South Africa
No full textPh.D. (Business Management)Department of Business ManagementSouth Africa's aspiration for inclusive growth and development acknowledges the pivotal role of small, medium, and micro enterprises (SMMEs) given the country's pervasive unemployment and poverty rates, particularly in rural regions. Since the inception of democracy in 1994 with the Reconstruction and Development Programme (RDP) to the present National Development Plan: Vision 2030, the focal point of South Africa's developmental endeavours has been the alleviation of poverty and inequality. This study aimed to devise a support framework to enhance the performance of SMMEs in the rural expanse of Limpopo Province, South Africa, while also fostering entrepreneurship expansion. Its primary objectives encompassed identifying the determinants affecting rural SMME performance, crafting a conceptual framework to bolster it, utilizing empirical research outcomes to formulate recommendations, and drawing conclusions to augment SMMEs' performance in Limpopo. Additionally, the study proffered actionable insights for stakeholders, including policymakers and entrepreneurs, to ensure the sustained viability of SMMEs in rural South Africa. Employing a quantitative research design aligned with the educational positivist paradigm, the study collected data from 377 entrepreneurs through questionnaires. A Convenience Sampling method was employed. Validity and reliability were ensured through exploratory factor analysis and Cronbach alpha coefficients determination. Pearson's correlation coefficient tests were employed to discern relationships among independent variables. The resultant path model addressed prevalent challenges confronting rural small businesses, proposing a roadmap for enhancing their operational performance.NR
Undergraduate Students’ Experiences with Blended Learning during the COVID-19 Pandemic at a Rural Based University in South Africa.
No full textM.A. (Sociology)Department of Arts and Social SciencesThis qualitative study aimed to investigate the undergraduate students’ experiences of Blended Learning at one rural based university in Thulamela municipality in the Vhembe district, Limpopo province. The study draws from the transitional distance and social learning theory to investigate how the undergraduate students in the university adjusted from face-to-face learning to online learning. Non-probability sampling was used to select thirty participants. Telephonically semi-structured interviews were used to collect data and the data was thematically analysed following the six stages of thematic data analysis. The data indicate that students were unable to actively take part in online learning, mostly because of low signal strength, poor infrastructural facilities, financial constraints, which characterises students’ life in rural-based universities in South Africa. Hence, they devised coping strategies such as consultations with returning students, learning independently, going to places where there is a stable internet connectivity, attending classes in groups, searching for information where they felt that the information provided by the lecturers were unsatisfactory, consulting with fellow classmates and asking lecturers to use other online platforms to deliver lessons. The data also showed that the University also tried to help the students by devising significant orthodox support systems. These includes faculty student online support services and provision of internet data and, financial support to the students. Together, these innovative inputs made it possible for the students to navigate particularly from face-to-face learning to online learning during the pandemic. Insights regarding students’ experiences from this study, potentially provides policy direction for both universities in South Africa, as well as the Department of Higher Education and Training on the use of Blended Learning in rural based universities in South Africa.NR
The occurrence of toxic and non-toxic cyanobacteria species in water supplies destined for maize meal preparation process: A case study of Vhembe District
No full textPhD (Hydrology and Water Resources)Department of Earth SciencesCyanobacteria are common organisms in the phytoplankton of eutrophic rivers, lakes, and freshwater reservoirs, and have become part of human diet for thousands of years. Cyanobacteria can multiply quickly in surface waters and form blooms when favourable conditions prevail, such as high temperature, intense light, high pH, and increased availability of nutrients, especially phosphate and nitrate artificially released by anthropogenic activities. Cyanobacteria produce secondary metabolites called cyanotoxins, which are harmful to human health. Human exposure to cyanotoxins can occur in various ways, however, the oral route is the most important. This is mainly through drinking water or eating contaminated food.
Studies on cyanotoxin contamination of food have been conducted on aquatic products (fish, prawns, and crayfish), grains (rice, soybean, and wheat), fresh produce (Lettuce), and dietary supplements. However, no study has been conducted on cyanotoxin contamination of maize meal during maize meal processing. The present study was motivated by the presence of blue-green algae that formed biofilms in 25 L white plastic containers. The process water stored in these containers was used to soften the maize seed and then ground the seed maize into maize meal. The main objective of the present study was to investigate the occurrence of toxic and non-toxic cyanobacteria species in water supplies destined for maize meal processing. To achieve this aim, the present work was subdivided into two specific objectives.
In the first objective, the diversity and identities of cyanobacteria in the samples (process water, uncooked maize meal, and cooked maize meal (porridge)) were assessed using Polymerase Chain Reaction (PCR) and Advanced digital flow cytometry (FlowCAM). The molecular techniques, 16S Primers (forward and reverse) tailed with Universal Sequences were used for amplification and sequencing of full-length 16S rRNA genes from cyanobacteria found in all samples. Cyanobacterial species from order Nostocales, Pseudanabaenales, Oscillatoriales, Chroococcales, Synechococcales, and unclassified cyanobacterial order, some of which have the potential to produce cyanotoxins were amplified and identified in process water, raw maize meal and pap porridge samples using PCR. The cyanobacteria species, of the genus Microcystis, Phormidium,
and Leptolyngbya were found in process water samples and maize meal samples and none of the cyanobacteria species were found pap porridge using FlowCAM.
Maize meal samples were exposed to different thermal temperatures inside the grinding machines during the grinding processes. Temperatures were ranging from 59.8 – 66.0 oC, 21.1 – 25.4 oC, and 28.9 – 29.8 oC in grinding machine 1, grinding machine 2, and grinding machine 3, respectively. Loss of diversity could be expected for the cyanobacteria community when exposed to air with hot temperatures. Another sample that was exposed to extremely high temperatures during its preparation is the porridge sample. An electric stove was used to cook during the preparation of this sample and the temperatures during cooking ranged between 89.5 – 92.7 oC. After cooking and analysis, this sample was found with lowest proportion of cyanobacteria species compared to other samples. Toxic cyanobacteria species die when exposed to these temperatures and they release cyanotoxins. Therefore, for the first time, the present study reveals that cyanotoxins can be transferred from cyanotoxins-contaminated water to food during processing, which could then present another significant route of human exposure to cyanotoxins; and then an analytical method for accurate quantification and identification of these cyanotoxins using LC-MS/MS was developed in the present study.
In the second objective, the occurrence of cyanotoxins in water supplies (process water), raw maize meal, and cooked maize (porridge) was investigated; and this was achieved by applying a simple, sensitive, and reliable analytical method developed for the determination of these toxins at ppb (parts per billion) levels. These compounds were extracted using Solid Phase Extraction (SPE) with optimized parameters; thereafter, Liquid Chromatography-Mass Spectrometry (LC-MS/MS) was used for the rapid determination of the analytes selected for the present study. The method developed was applied to samples collected from the meal grinding station and was able to detect and quantify all the target cyanotoxins. MC-LR, MC-YR, and MC-RR were detected at concentrations ranging from 9.2 – 13.3 μg/L, 5.5 – 10.2 μg/L, and 2.3 – 11.2 μg/L, in all the samples, respectively.
Toxic cyanobacterial blooms producing cyanotoxins exist where water is collected and may proliferate inside the water containers due to favourable conditions such as light and nutrient
availability. However, when environmental conditions are not favourable, cyanobacteria die and release cyanotoxins in process water. Moreover, the effects of grinding machines and their temperatures on the viability of cyanobacteria species was observed in the present study. Proportion of cyanobacteria species detected in maize samples were lower than proportion of cyanobacteria species detected in water samples, implying that different temperatures or extremely warm air within the grinding machines could have killed some cyanobacterial species during the grinding processes. Also, the proportion of cyanobacteria species in maize (used for pap porridge sample) was low compared to pap porridge sample as this sample was subjected to high temperatures during sample preparation (cooking). It was further reported that cyanobacteria species die at high temperatures. Consequently, cyanotoxins were released into maize and porridge during processing as cyanobacteria cells burst and die, which then increased toxin levels.
There are various routes through which humans may be exposed to cyanotoxins, but the most important one is the oral, which occurs through the consumption of cyanotoxins-contaminated water or food. Therefore, the present study conducted the assessment of human health risks from exposure to microcystins available in water supplies (tap and groundwater), maize meal, and porridge. For this assessment, the hazard quotient index (HQi) was used to assess the non-carcinogenic risks of MCs to humans. The HQi levels found in the present study ranged between 2.26 – 2.75 for adults, whereas for children the HQi levels ranged between 0.84 – 1.02, representing greater potential risks to human health.
These findings show the presence of cyanobacteria species in processed water and maize meal and the absence in cooked maize meal. However, the microcystins (MC-LR, MC-YR, and MC-RR) were found in the process water, maize meal, and in the pap porridge in excess of the WHO guideline of 1 μg/L. Furthermore, it was revealed that cyanotoxins can be transferred from water to food during food processing using cyanotoxins-contaminated water. The presence of cyanobacteria in process water is likely another route of human exposure to cyanotoxins. Moreover, the methods developed in the present study can be used by environmental and health agencies to strengthen the monitoring of cyanotoxins in water and food. Furthermore, the findings of the present study contribute to the understating of cyanotoxin contamination of maize meal
during the grinding processes. The basis for the development of a cyanotoxins management framework and assessment of human health risk is provided by the findings of the present studyNR
Microbial, metabolic and molecular determinants of neonatal mortality in the rural areas of Limpopo Province, South Africa: umblical cord blood metabolomic profile and bacterial anaysis and their association with perinatal complications
No full textM.Sc. (Microbiology)Department of Biochemistry and MicrobiologyBACKGROUND: Neonatal mortality continues to pose a substantial public health challenge globally,
particularly in developing countries. Some primary contributors are microbial infections, adverse
pregnancy and birth outcomes (APBOs), and labor or obstetric complications. Despite this recognition,
the underlying molecular mechanisms of these infections and perinatal complications are poorly
understood. Interestingly, microbial and metabolomic approaches have emerged as effective techniques
for the early detection and identification of biomarkers for microbial infections and perinatal
complications, shedding more light on understanding the underlying molecular mechanisms of these
adverse outcomes. Hence, this study employed microbial analysis (through 16S rRNA PCR assay and
antibiotic susceptibility test profiling) and metabolomic profiling of umbilical cord blood to identify
potential biomarkers for perinatal complications.
METHODS: A cross-sectional study utilizing purposive sampling was conducted at selected district
hospitals in the Vhembe district from May 2023 to September 2023. Following participants' consent,
questionnaires were used for data collection and umbilical cord blood samples were collected from 129
participants. Blood culture was done, and antibiotic susceptibility testing was conducted on the isolates.
Additionally, genomic DNA was isolated from the blood samples for the detection of pathogenic bacterial
strains, using a conventional PCR assay. Untargeted metabolomic profiling approach using Liquid
Chromatography-Quadrupole-Time-of-flight Mass Spectrometry (LC-q-tof-MS) was conducted. The data
were entered into REDCap and exported to IBM Statistical Package for the Social Sciences (SPSS)
software, version 26, for analysis. Descriptive analysis and multivariate logistic regression analysis were
conducted, with statistical significance set at a p-value less than 0.05 at a 95% confidence level. For
metabolomic analysis, multivariate analysis approaches were employed to identify signals that differed
between perinatal complications and uncomplicated pregnancies. Metabolic pathway analysis of perturbed
metabolites was conducted using MetaboAnalyst 6.0.
RESULTS: Among 129 participants, the overall occurrence of perinatal complications stood at 35/129
(27.13%). The majority of participants, accounting for 55/129 (42.64%), fell within the age range of 20 to
29 years, while a significant portion (83.7%), were unemployed. Factors such as maternal age, birth
weight, maternal blood pressure, anesthesia use, and delivery mode showed associations with perinatal
complication risk, with corresponding P-values of 0.032, 0.027, 0.041, <0.001, and <0.001, respectively.
Additionally, bloodstream infection (bacteremia) prevalence, as detected by culture-dependent and 16S
rRNA PCR assays, was recorded at 30.23% and 26.36%, respectively. The majority of culture-confirmed
bacterial isolates (58.06%) were gram-positive, with S. epidermidis (36.73%) and S. aureus (20.43%)
being the predominant strains. Notably, E. coli infections showed a significant association with perinatal
complications (P = 0.001). Bloodstream infection (Bacteremia) correlated significantly with maternal
educational level, maternal blood pressure at birth, gestational booking stage, and pre-pregnancy BMI.
Most culture-confirmed isolates exhibited high levels of antibiotic resistance to ampicillin, ceftazidime,
and cefoxitin, while gentamicin, imipenem, amikacin, and ciprofloxacin proved effective against both
gram-positive and gram-negative isolates. Furthermore, 93.38% of the tested isolates displayed multidrug
resistance (MDR). Through untargeted metabolomic profiling analysis and multivariate analysis using the
orthogonal partial least squares discriminant analysis (OPLS-DA) model, 107 metabolites were identified,
showcasing differences between perinatal complications and uncomplicated pregnancies. Among the 107
perturbed metabolites, univariate analysis highlighted 50 upregulated and 57 downregulated metabolites
in perinatal complications at P<0.05. Furthermore, the affected metabolic pathways, including ethyl lipid
metabolism, sphingolipid metabolism, and glycerophospholipid metabolism, were identified as
statistically significant.
CONCLUSION: Our study revealed a high occurrence rate of perinatal complications (25.58%), with
maternal high blood pressure, maternal age (10-19 years), low birth weight, delivery mode, and anesthesia
for C-sections identified as significant contributors. Proactive healthcare interventions during antenatal
care visits are crucial to minimize complications. Additionally, when looking at microbial analysis, there
was no significant association between bacteremia and perinatal complications but highlighted a higher
prevalence of bloodstream infections, linked to factors like maternal education level and BMI.
Furthermore, upon conducting metabolic profiling, it was evident that specific umbilical cord blood
processes were closely associated with perinatal complications, indicating their potential as biomarkers
for assessment, prediction, and early intervention strategies.NR
Application of ethics in the provision of municipal services in Makhado Local Municipality
No full textMAdminDepartment of Public and Development AdministrationAccess to basic municipal services is a major challenge in South Africa. Section 152 of the Constitution of the Republic of South Africa, 1996, makes provision for municipalities to deliver basic services to their local communities. Local government plays an important role in ensuring that communities are provided with basic services. Research has shown that South Africa is experiencing challenges in providing basic services. This study focused on the application of ethics in the provision of municipal services in Makhado Local Municipality. The study was conducted at Makhado Local Municipality in Limpopo Province, South Africa. This study aims to evaluate the application of ethics in the provision of municipal services at Makhado Local Municipality and suggest recommendations on how to eradicate challenges regarding basic municipal services.
The researcher utilised a mixed research method in which both qualitative and quantitative methods were adopted. A sample of 284 participants consisting of traditional leaders, selected community members, municipal staff members, and ward councillors was selected using probability sampling and non-probability sampling techniques. The instruments used to collect data were questionnaires and interview schedules. The quantitative and quantitative data were analysed using descriptive statistics and thematic analysis respectively. The main findings of this study indicate that the application of ethics has not significantly contributed to the improvement of municipal service delivery at Makhado Local Municipality. The main recommendations based on the findings are that decision-making on basic municipal services should be centred on ethics and that the municipality should aim to solve community issues in a sustainable manner rather than just following protocol.NR
Secondary school teachers and learners attitudes towards information and communications technology instructional use in Sibasa Circuit, Vhembe District, Limpopo
No full textM.Ed. (Curriculum Studies)Department of Professional and Curriculum StudiesThe main goal of this quantitative, descriptive, explorative survey was to explore and describe secondary school teachers’ and learners’ attitudes towards ICT (information and communication technology) instructional use in Sibasa circuit, Vhembe district, Limpopo province, South Africa, using the Technology Acceptance Model 2 (TAM 2) framework. ICT use in education continued to be a contentious topic globally following the COVID-19 pandemic. The reason for bringing this issue on board was the recognition that the use of ICTs for teaching and learning can improve the overall standard of teaching and learning. In this study, four hundred (400) participants from the four Proof of Concept (PoC) secondary schools with ICT connectivity for teaching and learning in the Sibasa Circuit of Vhembe-East District were purposively sampled to complete a self-administered questionnaire. The study revealed that both teachers and learners understand what ICT is and both teachers and learners had a favourable attitude towards utilising ICTs to assist teaching and learning as they are using them on a daily basis for lesson preparations, accessing digital libraries as well as online learning resources. However, the quality and the quantity of ICT equipment in schools are hindering the obstructing factors in the adoption of ICTs for instructional purposes. The Department of Basic Education should increase the provision of ICT tools such as data projectors, whiteboards, and laptops and strong internet connection to schools to support effective teaching and learning .It is also recommended that the provincial Department of Basic Education should increase the extent of training for teachers and learners on how to use ICTs to support teaching and learning.NR
The role of performance management in promoting good governance with specific reference to the Vhembe District Municipality
No full textMPMDepartment of Public and Development AdministrationThe purpose of the study is to evaluate how performance management advances good governance, with a particular emphasis on the Vhembe District Municipality. For towns to manage public resources effectively, efficiency and effectiveness in service delivery must be strategically pursued. This strategy is now required to guarantee high-quality services in the dynamic and ever-evolving public sector. An institution's future direction, core competencies, and values are shaped and communicated in large part by performance management, an integrated and continuous process. Thorough computerised desktop research was done to compile relevant data, and pertinent performance management-related rules and papers from the Vhembe District Municipality were evaluated and closely examined. The desktop and descriptive research designs were employed by the researcher. The collected data was subjected to thematic analysis and statistical analysis. The statistical descriptive analysis of the desktop data was conducted using International Business Machinery (IBM): Statistical Product and Service Solution (SPSS) version 28.0 computer software. The data was given in both tabular and narrative form. The main finding emanating from the study is that municipalities must develop performance management to promote good governance. It was also revealed that Vhembe District Municipality has successfully handled the demands of the community using performance management. The findings also revealed that one of the challenges affecting the effectiveness of performance management lies in the absence of well-defined performance metrics. The study recommends that implementing a robust and streamlined performance management system is crucial for optimizing organisational efficiency. The study concludes that effective performance management is crucial for the municipality to establish and monitor goals, ensuring efficient addressability of the community's needs.NR