The role of indigenous knowledge in agricultural production: the case of the Svosve community

A dissertation presented to The Department of Sociology School of Social Sciences Faculty of Humanities University of the Witwatersrand In fulfilment of the requirements for the degree Master of Industrial Sociology 12 October 2015World Hunger (2013) declared that to solve the food crisis in the global south, the solution lay in incorporating indigenous knowledge in mainstream development programmes. On the other hand, the Brussels conference of (2005) resolved that the indigenous knowledge systems are on the verge of extinction due to marginalisation from mainstream development programs. The capitalist State was identified as the major force undermining indigenous knowledge. However, there is no consensus to the meaning of indigenous knowledge. This thesis sought an in depth understanding of indigenous knowledge and its role in agricultural production in the Svosve community. Furthermore, it sought to find out how the farmers in the Svosve community react to the development initiatives by the State. Semi-structured interview schedules were used to allow farmers, government administrators and extension workers to narrate their experiences with farming. The research was able to pick on the features of indigenous knowledge which are beliefs practices and skills. The key findings of this research are that the farmers in the Svosve community have long relied on indigenous beliefs and practices to farm. This knowledge extends to other land-based means of livelihood that support the Svosve community. However, the State’s economic policy which promotes market farming, ahead of the community’s indigenous initiatives tends to undermine the use of indigenous knowledge. Therefore, in the Svosve community, there is a tension between the indigenous beliefs and practices and the Western beliefs and practices

Mutations in rpoB and katG genes of multidrug resistant mycobacterium tuberculosis undetectable using genotyping diagnostic methods

Introduction: Tuberculosis remains the leading causes of death worldwide with frequencies of mutations in rifampicin and isoniazid resistant Mycobacterium tuberculosis isolates varying according to geographical location. There is limited information in Zimbabwe on specific antibiotic resistance gene mutation patterns in MTB and hence, increased rate of discordant results and mortality due to inappropriate antibiotic prescriptions. The rpoB and katG genes molecular markers are used for detecting rifampicin and isoniazid resistance respectively. Some mutations within these gene sequences are associated with drug resistance as they directly alter gene function. The objectives of this research was to determine the drug resistance profiles in M. tuberculosis isolates that are phenotypically resistant but not detected by the GeneXpert and MTBDRplus kit and also to detect mutations in the rpoB and katG genes which are not detected by the Hain Genotype MTBDRplus kit and GeneXpert diagnosis.Methods: PCR was used for the amplification of the rpoB and katG genes from MTB isolates collected from human clinical samples between 2008 and 2015. The genes were sequenced and compared to the wild type MTB H37Rv rpoB (accession number L27989) and kat G genes (KP46920), respectively. Sequence analysis results were compared to genotyping results obtained from molecular assays and culture results of all isolates.Results: The most frequent mutation responsible for rifampicin resistance was (25/92) S531L that was detected by using all molecular assays. Some inconsistencies were observed between phenotypic and genotypic assay results for both katG and rpoB genes in 30 strains. For these, eight codons; G507S, T508A, L511V, del513-526, P520P, L524L, R528H, R529Q and S531F were novel mutations. In addition, the I572P/F, E562Q, P564S, and Q490Y mutations were identified as novel mutations outside the rifampicin resistance determining region. In katG gene, amino acid changes to threonine, asparagine and isoleucine exhibited high degrees of polymorphism such as V473N, D311N, and L427I. The R463L (20/92) amino acid substitution was most common but was not associated with isoniazid resistance.Conclusion: These finding indicate that molecular assay kit diagnosis that is based on the rpoB and katG genes should be improved to cater for the genetic variations associated with the geographic specificity of the target genes and be able to detect most prevalent mutations in different areas.Keywords: Mutation, rpoB, katG, GeneXpert, hains genotype MTBDRplus, mycobacterium tuberculosis, sequencing, DNA and PC

Faecal carriage of ESBL producing and colistin resistant Escherichia coli in avian species over a 2-year period (2017-2019) in Zimbabwe

DATA AVAILABILITY STATEMENT : The data presented in this study are deposited in the NCBI BioProject Number PRJNA 799483 with accession numbers listed in the Supplementary Datasheet 1.INTRODUCTION : Extended spectrum beta-lactamase (ESBL) producing Escherichia coli have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact. METHODS : This study investigated the faecal carriage of ESBL producing and colistin resistant E. coli in poultry over a 2-year period (2017-2019) from Zimbabwe. A total of 21 ESBL positive isolates from poultry cloacal specimens were selected for whole genome sequencing from animal E. coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Program to provide representation of different geographical regions and year of isolation. Cloacal swabs were collected from 3000 broiler live birds from farm 1 and fromfarm2, 40 backyard chickens and 10 duckswere sampled. Antimicrobial susceptibility and ESBL testing were performed as per Clinical Laboratory Standards Institute guidelines. Whole genome sequencing of ESBL producing isolates was used to determine sequence types (STs), ARGs, and phylogroups. RESULTS : Twenty-one of the included E. coli isolates were confirmed as ESBL producers. Three defined sequence type clonal complexes (CCs) were identified (ST10CC, ST155CC and ST23CC), with ST10CC associated with the most antibiotic resistant profile. The ESBL phenotype was linked to the presence of either cefotaximase-Munich-14 (CTX-M-14) or CTX-M-79. Plasmid mediated quinolone resistant determinants identified were qnrB19 and qnrS1 and one ST10CC isolate from farm 1 broiler chickens harbored a mobile colistin resistance gene (mcr-1). Phylogenetic groups most identified were B1, A and unknown. DISCUSSIONS : The avian ESBL producing E. coli belonged to a diverse group of strains. The detection of several ARGs highlights the importance of implementing enhanced control measures to limit the spread in animals, environment, and humans. This is the first report of mcr-1 in Zimbabwe, which further underscores the importance of the One Health approach to control the spread and development of AMR.The National Health Laboratory Service (NHLS) and the University of Pretoria, South Africa, a strategic partnership between National Microbiology Reference Laboratory and Quadram BioSciences Institute.https://www.frontiersin.org/journals/cellular-and-infection-microbiologyam2023Medical Microbiolog

Molecular epidemiology of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli strains over a 2-year period (2017-2019) from Zimbabwe

This study was designed to characterize extended-spectrum beta-lactamase (ESBL)–producing extra-intestinal pathogenic Escherichia coli (E.coli) (ExPEC) associated with urinary tract infections in nine different geographic regions of Zimbabwe over a 2-year period (2017–2019). A total of 48 ESBL-positive isolates from urine specimen were selected for whole-genome sequencing from 1246 Escherichia coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Programme to provide representation of different geographical regions and year of isolation. The majority of ESBL E. coli isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-27, and CTX-M-14. In this study, sequence types (ST) 131 and ST410 were the most predominant antimicrobial-resistant clones and responsible for the increase in ESBL–producing E. coli strains since 2017. Novel ST131 complex strains were recorded during the period 2017 to 2018, thus showing the establishment and evolution of this antimicrobial-resistant ESBL clone in Zimbabwe posing an important public health threat. Incompatibility group F plasmids were predominant among ST131 and ST410 isolates with the following replicons recorded most frequently: F1:A2:B20 (9/19, 47%), F2:A1: B (5/19, 26%), and F1:A1:B49 (8/13, 62%). The results indicate the need for continuous tracking of different ESBL ExPEC clones on a global scale, while targeting specific STs (e.g. ST131 and ST410) through control programs will substantially decrease the spread of ESBLs among ExPEC

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limite

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Molecular epidemiology of extra-intestinal pathogenic Escherichia coli circulating in humans, animals, food, and the environment in Zimbabwe

Antimicrobial resistance (AMR) in Enterobacterales is an emerging threat for human health globally, including in low-to-middle income countries (LMICs). The misuse of antibiotics has resulted in the establishment of various enzyme mediated AMR mechanisms, e.g. extended spectrum beta-lactamases (ESBLs), carbapenemases and colistin resistance, which are difficult to control. Developing countries like Zimbabwe are vulnerable to AMR due to poor pathogen surveillance, unhygienic and unregulated conditions of the agricultural and food production process, and poor sanitation. Limited information is available on the real burden of the extra-intestinal pathogenic Escherichia coli (ExPEC) and the population structure of such isolates in Zimbabwe. Active pathogen surveillance systems (One Health approach) in Zimbabwe’s healthcare setting is important for the continuous identification, tracking and control of the spread of circulating ExPEC clones. The aim of this study was to determine the molecular epidemiology of ExPEC isolates circulating in humans, animals, food, and the environment in Zimbabwe through phenotypic and genomic analysis. A total of 200 human urine isolates, 200 animal avian isolates and 50 environmental isolates were selected from the National Microbiology Reference Laboratory E. coli Biobank, which were collected over a 2-year period (2017-2019). All available demographic data was collected. No food product isolates were included in this study. This study utilised both phenotypic and molecular typing methods. The molecular typing methods included polymerase chain reaction (PCR) for identification of virulence genes (clinical urine isolates), Sequence type (ST)131, etc., real-time PCR for identifying clinical urine ExPEC clones, and whole genome sequencing (WGS) on ESBL positive isolates from human, animal, and environmental origin. Representative isolates from different geographical locations and time points were selected for WGS analysis based on ESBL prevalence. Among the 200 human isolates included for screening with the 7-SNP real time PCR method, 61% were confirmed ESBL positive. The isolates included for WGS analysis were recovered from the 200 human urine isolates (n= 48 ESBL positives), avian (n=21 ESBL positives), environment borehole (n =4 ESBL positives) and were multidrug resistant (MDR). Sequence type 131 (17/48, 35%) and ST410 (13/48, 27%) (in human isolates), and ST10 (7/21, 33%) (in animal isolates) were the most dominant clones detected in this study. No carbapenem resistant isolate was detected. One isolate (avian) harboured the mobilised colistin resistance (mcr)-1 gene. The majority of urine isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-14; and oxacillinase (OXA)-1. Avian isolates produced CTX-M-14, and Temoneira (TEM)-1, while the environmental isolates had sulfhydryl-variable (SHV), and TEM-1. The majority of isolates carried the incompatibility group (Inc) F plasmids depending on strain type. The use of a cost effective, rapid and reliable 7-Single Nucleotide Polymorphism real time PCR (7-SNP-PCR) typing method described the population structure of the clinical collection (urine) of ExPEC obtained in Zimbabwe. This technique was validated for human urine isolate only and hence was used for all the human isolates from this study. The presence of E. coli ST131 and ST410 shows that it has spread across various communities included in this study and poses complex challenges to infection control and prevention programs as well as to the planning of correct treatment regimens. This study provides baseline molecular data on the detection of specific lineages of ExPEC circulating in the Zimbabwean communities using both 7-SNP-PCR and WGS. The rapid identification of high-risk clones is critical to curb the dissemination and emergence of pandemic clones. Keywords: Escherichia coli, ExPEC, ESBL, ST131, ST410, ST10, ZimbabweThesis (PhD (Medical Microbiology))--University of Pretoria, 2021.National Health Laboratory Service (NHLS), the University of Pretoria, South Africa, National Microbiology Reference Laboratory, Zimbabwe, Quadrum BioSciences Institute, UKMedical MicrobiologyPhD (Medical Microbiology)Unrestricte

Molecular epidemiology of extended-spectrum beta-lactamase–producing extra-intestinal pathogenic Escherichia coli strains over a 2-year period (2017–2019) from Zimbabwe

This study was designed to characterize extended-spectrum beta-lactamase (ESBL)–producing extra-intestinal pathogenic Escherichia coli (E.coli) (ExPEC) associated with urinary tract infections in nine different geographic regions of Zimbabwe over a 2-year period (2017–2019). A total of 48 ESBL-positive isolates from urine specimen were selected for whole-genome sequencing from 1246 Escherichia coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Programme to provide representation of different geographical regions and year of isolation. The majority of ESBL E. coli isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-27, and CTX-M-14. In this study, sequence types (ST) 131 and ST410 were the most predominant antimicrobial-resistant clones and responsible for the increase in ESBL–producing E. coli strains since 2017. Novel ST131 complex strains were recorded during the period 2017 to 2018, thus showing the establishment and evolution of this antimicrobial-resistant ESBL clone in Zimbabwe posing an important public health threat. Incompatibility group F plasmids were predominant among ST131 and ST410 isolates with the following replicons recorded most frequently: F1:A2:B20 (9/19, 47%), F2:A1: B (5/19, 26%), and F1:A1:B49 (8/13, 62%). The results indicate the need for continuous tracking of different ESBL ExPEC clones on a global scale, while targeting specific STs (e.g. ST131 and ST410) through control programs will substantially decrease the spread of ESBLs among ExPEC.The National Health Laboratory Service (NHLS), the University of Pretoria, South Africa, and a strategic partnership between National Microbiology Reference Laboratory and Quadrum Institute Biosciences.http://link.springer.com/journal/100962022-11-15hj2022Medical Microbiolog