Short-Term Influence of Fire on Herbaceous Composition, Diversity and Grass Biomass Production in Semi-Arid Savanna Woodland in Windhoek, Namibia

Abstract A co mparative study on short term in fluence of fire on herbaceous composition and grass biomass production was conducted in a semi-arid savanna woodland in Windhoek, to assess differences in herbaceous composition and grass biomass production after a late dry season fire. The study revealed that herbaceous composition and grass cover differ significantly between the burned and unburned areas. Grass cover differed significantly (p< 0.001) between the burned and unburned areas. Fire removes aging grass materials, growth inhib itors and moribund hence, enhancing the vitality grasses. There were no significant differences in species richness (t = -1.402, p > 0.05), species diversity (t = -1.391, df = 28, p > 0.05), grass biomass production (t = 1.724, p > 0.05) and forb densities (t = 0.361, p > 0.05) between the burned and unburned areas..The study findings suggested that short term fire does have a significant impact on grass cover and herbaceous dominance and insignificant impact on grass biomass production, forb densities, species richness and diversity in short term, but fire impact on these plant attributes also depend on the intensity of fire and time frame

A review of geographical distribution of marama bean [Tylosema esculentum (Burchell) Schreiber] and genetic diversity in the Namibian germplasm

Marama bean [Tylosema esculentum (Burchell) Schreiber] occurs naturally in the drier areas of Southern Africa, including Botswana and Namibia. The implementation of molecular breeding is important to advance the process of securing the world’s food supply. The development of molecular markers is vital for mapping important traits that can then be followed in subsequent breeding programs. This study assessed the distribution of marama bean in Namibia and isolated microsatellite regions for microsatellite primer design for the purpose of determining genetic diversity and construction of molecular genetic maps for marama. This will greatly enhance the process ofdomesticating marama bean, currently a wild plant that is still picked wild and unsustainably. The geographical distribution was geo-referenced using Geographic Positioning System (GPS) points andmicrosatellites were isolated from the germplasm using a modified FIASCO technique. The study revealed widespread, but patchy distribution of marama bean in Namibia. Five Marama beanmicrosatellite enriched libraries were created. The initial results provided vital information for the ongoing marama bean conservation function and improvement program

Clinical Evaluation of a Line-Probe Assay for Tuberculosis Detection and Drug-Resistance Prediction in Namibia.

Treatment of tuberculosis requires rapid information about Mycobacterium tuberculosis (Mtb) drug susceptibility to ensure effective therapy and optimal outcomes. At the tuberculosis referral hospital in Windhoek, Namibia, a country of high tuberculosis incidence, we evaluated the diagnostic accuracy of a line-probe-assay (LPA), GenID, for the molecular diagnosis of Mtb infection and drug resistance in patients with suspected tuberculosis (cohort 1) and confirmed rifampin (RIF)-resistant tuberculosis (cohort 2). GenID test results were compared to Xpert MTB/RIF and/or Mtb culture and antimicrobial suceptibilty testing. GenID LPA was applied to 79 and 55 samples from patients in cohort 1 and cohort 2, respectively. The overall sensitivity of GenID LPA for the detection of Mtb DNA in sputum from patients with detectable and undetectable acid-fast bacilli by sputum smear microscopy was 93.3% (56/60; 95% confidence interval = 83.8-98.2) and 22.7% (5/22; 7.8-45.4). The sensitivity/specificity for the detection of drug resistance was 84.2% (32/38; 68.7-94.0)/100% (19/19; 82.4-100.0) for RIF, 89.7% (26/29; 72.6-97.8)/91.7% (22/24; 73.0-99.0) for isoniazid, and 85.7% (6/7; 42.1-99.6)/94.7% (18/19; 74.0-99.9) for fluoroquinolones; 23.6% of tests for second-line injectable resistance were invalid despite repeat testing. The diagnosis of tuberculosis by detection of Mtb DNA in sputum by GenID LPA depends strongly on the detection of acid-fast bacilli in sputum specimen. Prediction of drug resistance by GenID did not reach the World Health Organization (WHO) target product profile. IMPORTANCE Mycobacterium tuberculosis (Mtb) drug-resistance detection is crucial for successful control of tuberculosis. Line-probe assays (LPA) are frequently used to detect resistance to rifampin, isoniazid, fluoroquinolones (FQs), and second-line injectables (SLIs). GenID RIF/isoniazid (INH), FQ, and SLI LPA have not been widely tested and used so far. This study tested the diagnostic performance of the GenID LPA in a high-incidence TB/HIV, real-world setting in Namibia. The LPA demonstrates only an acceptable diagnostic performance for Mtb and drug-resistance detection. The diagnostic sensitivity and specificity fall short of the WHO suggested target product profiles for LPA

Whole-Genome Sequencing for Resistance Prediction and Transmission Analysis of Mycobacterium tuberculosis Complex Strains from Namibia.

Namibia is among 30 countries with a high burden of tuberculosis (TB), with an estimated incidence of 460 per 100,000 population and around 800 new multidrug-resistant (MDR) TB cases per year. Still, data on the transmission and evolution of drug-resistant Mycobacterium tuberculosis complex (Mtbc) strains are not available. Whole-genome sequencing data of 136 rifampicin-resistant (RIFr) Mtbc strains obtained from 2016 to 2018 were used for phylogenetic classification, resistance prediction, and cluster analysis and linked with phenotypic drug susceptibility testing (pDST) data. Roughly 50% of the strains investigated were resistant to all first-line drugs. Furthermore, 13% of the MDR Mtbc strains were already pre-extensively drug resistant (pre-XDR). The cluster rates were high, at 74.6% among MDR and 85% among pre-XDR strains. A significant proportion of strains had borderline resistance-conferring mutations, e.g., inhA promoter mutations or rpoB L430P. Accordingly, 25% of the RIFr strains tested susceptible by pDST. Finally, we determined a potentially new bedaquiline resistance mutation (Rv0678 D88G) occurring in two independent clusters. High rates of resistance to first-line drugs in line with emerging pre-XDR and likely bedaquiline resistance linked with the ongoing recent transmission of MDR Mtbc clones underline the urgent need for the implementation of interventions that allow rapid diagnostics to break MDR TB transmission chains in the country. A borderline RIFr mutation in the dominant outbreak strain causing discrepancies between phenotypic and genotypic resistance testing results may require breakpoint adjustments but also may allow individualized regimens with high-dose treatment. IMPORTANCE The transmission of drug-resistant tuberculosis (TB) is a major problem for global TB control. Using genome sequencing, we showed that 13% of the multidrug-resistant (MDR) M. tuberculosis complex strains from Namibia are already pre-extensively drug resistant (pre-XDR), which is substantial in an African setting. Our data also indicate that the ongoing transmission of MDR and pre-XDR strains contributes significantly to the problem. In contrast to other settings with higher rates of drug resistance, we found a high proportion of strains having so-called borderline low-level resistance mutations, e.g., inhA promoter mutations or rpoB L430P. This led to the misclassification of 25% of the rifampicin-resistant strains as susceptible by phenotypic drug susceptibility testing. This observation potentially allows individualized regimens with high-dose treatment as a potential option for patients with few treatment options. We also found a potentially new bedaquiline resistance mutation in rv0678

Development and use of microsatellites markers for genetic variantion analysis, in the Namibian germplasm, both within and between populations of marama bean (Tylosema esculentum)

Tylosema esculentum (marama) has long been identified as a candidate crop for arid and semi-arid environments due to its success in these environments and the high nutritional value of the seed. Molecular markers are essential for the assessment of the levels of genetic variation present within and between populations of marama as well for future marker-assisted breeding efforts. Microsatellites were isolated using a modified FIASCO enrichment technique. Eighty pairs of primers were designed to amplify across a selected set of perfect microsatellite repeats with greater than 5 repeat units. Of the 80 primer pairs screened, 76% were able to detect polymorphism and 21% gave monomorphic bands while the other 3% gave inconsistent results. Four of the polymorphic SSR’s were used for genetic variation analysis and have proved to be useful and informative markers for assessing intra-specific and interspecific variability of marama bean. Heterozygosity (H) within and between populations of marama bean in the Namibian germplasm ranged from 0.30 to 0.74. Some of the populations had low genetic variation while others had high genetic variation

Validation and optimization of host immunological bio-signatures for a point-of-care test for TB disease

The development of a non-sputum-based, point-of-care diagnostic test for tuberculosis (TB) is a priority in the global effort to combat this disease, particularly in resource-constrained settings. Previous studies have identified host biomarker signatures which showed potential, but there is a need to validate and refine these for development as a test. We recruited 1,403 adults presenting with symptoms suggestive of pulmonary TB at primary healthcare clinics in six countries from West, East and Southern Africa. Of the study cohort, 326 were diagnosed with TB and 787 with other respiratory diseases, from whom we randomly selected 1005 participants. Using Luminex(R) technology, we measured the levels of 20 host biomarkers in serum samples which we used to evaluate the diagnostic accuracy of previously identified and novel bio-signatures. Our previously identified seven-marker bio-signature did not perform well (sensitivity: 89%, specificity: 60%). We also identified an optimal, two-marker bio-signature with a sensitivity of 94% and specificity of 69% in patients with no history of previous TB. This signature performed slightly better than C-reactive protein (CRP) alone. The cut-off value for a positive diagnosis differed for human immuno-deficiency virus (HIV)-positive and -negative individuals. Notably, we also found that no signature was able to diagnose TB adequately in patients with a prior history of the disease. We have identified a two-marker, pan-African bio-signature which is more robust than CRP alone and meets the World Health Organization (WHO) target product profile requirements for a triage test in both HIV-negative and HIV-positive individuals. This signature could be incorporated into a point-of-care device, greatly reducing the necessity for expensive confirmatory diagnostics and potentially reducing the number of cases currently lost to follow-up. It might also potentially be useful with individuals unable to provide sputum or with paucibacillary disease. We suggest that the performance of TB diagnostic signatures can be improved by incorporating the HIV-status of the patient. We further suggest that only patients who have never had TB be subjected to a triage test and that those with a history of previous TB be evaluated using more direct diagnostic techniques.Cancer Signaling networks and Molecular Therapeutic

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

Development of marama bean, an orphan legume, as a crop

Advances have been recently made in the breeding and characterization of three major legume crops of the semiarid tropics, chickpea, pigeon pea, and groundnut. However, other wild-growing legumes, called “orphan legumes,” with potential as crops, but are not yet cultivated would benefit from further attention. This review considers the domestication of one such plant, marama bean (Tylosema esculentum). Marama has long been recognized as a potential crop particularly for southern Africa, but coordinated, long-term research and development has been lacking. Marama is a perennial, outcrossing hexaploid, growing under extreme conditions in a restricted geographic range; only natural stands exist that are likely to be overexploited. Marama has two potential units of economic yield, seed and tuber. The seed is protein- and oil-rich, with potential in the pharmaceutical and cosmetic industries while the tuber is high in carbohydrates. In this review, the different aspects of bringing a wild plant into cultivation are considered, together with the additional socioeconomic benefits of developing a breeding program. An international collaboration is analyzing aspects of the plant structure and physiology, molecular biology, and its interactions with environment with a view to developing marama as a crop, with a role in food security, that could be harvested by local communities. Molecular topics considered include next-generation sequencing for developing molecular maps, genotyping by sequencing, identification of quantitative trait loci for important agronomic traits, protein quality, and incompatibility mechanisms. To achieve domestication requires seed gardens and fields, and the phenotyping of marama material from different locations. Community engagement will also ensure agronomic sustainability and farmer participation. This review describes an approach for a successful outcome of a breeding program to introduce improved marama and highlights the challenges in achieving this, which is a paradigm for the difficulties in the cultivation of “orphan species.”NRF Incentive Funding; the Oglebay Fund; and the Kirkhouse Trust.http://wileyonlinelibrary.com/journal/fes3am2020Forestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

A review of geographical distribution of marama bean [Tylosema esculentum (Bruchell) Schreiber] and genetic diversity in the Namibian germplasm

Marama bean [Tylosema esculentum (Burchell) Schreiber] occurs naturally in the drier areas of Southern Africa, including Botswana and Namibia. The implementation of molecular breeding is important to advance the process of securing the world’s food supply. The development of molecular markers is vital for mapping important traits that can then be followed in subsequent breeding programs. This study assessed the distribution of marama bean in Namibia and isolated microsatellite regions for microsatellite primer design for the purpose of determining genetic diversity and construction of molecular genetic maps for marama. This will greatly enhance the process of domesticating marama bean, currently a wild plant that is still picked wild and unsustainably. The geographical distribution was geo-referenced using Geographic Positioning System (GPS) points and microsatellites were isolated from the germplasm using a modified FIASCO technique. The study revealed widespread, but patchy distribution of marama bean in Namibia. Five Marama bean microsatellite enriched libraries were created. The initial results provided vital information for the ongoing marama bean conservation function and improvement program

Drug-resistant tuberculosis case-finding strategies: a scoping review protocol

Background: Transmission of drug-resistant tuberculosis (DR-TB) is ongoing. Finding individuals with DR-TB and initiating treatment as early as possible is important to improve patient clinical outcomes and to break the chain of transmission to control the pandemic. To our knowledge systematic reviews assessing effectiveness, cost-effectiveness, acceptability, and feasibility of different case-finding strategies for DR-TB to inform research, policy, and practice have not been conducted, and it is unknown whether enough research exists to conduct such reviews. It is unknown whether case-finding strategies are similar for DR-TB and drug-susceptible TB and whether we can draw on findings from drug-susceptible reviews to inform decisions on case-finding strategies for DR-TB. Objective: This protocol aims to describe the available literature on case-finding for DR-TB and to describe case-finding strategies. Methods: We will screen systematic reviews, trials, qualitative studies, diagnostic test accuracy studies, and other primary research that specifically sought to improve DR-TB case detection. We will exclude studies that invited individuals seeking care for TB symptoms, those including individuals already diagnosed with TB, or laboratory-based studies. We will search the academic databases including MEDLINE, Embase, The Cochrane Library, Africa-Wide Information, CINAHL, Epistemonikos, and PROSPERO with no language or date restrictions. We will screen titles, abstracts, and full-text articles in duplicate. Data extraction and analyses will be performed using Excel (Microsoft Corp). Results: We will provide a narrative report with supporting figures or tables to summarize the data. A systems-based logic model, developed from a synthesis of case-finding strategies for drug-susceptible TB, will be used as a framework to describe different strategies, resulting pathways, and enhancements of pathways. The search will be conducted at the end of 2021. Title and abstract screening, full text screening, and data extraction will be undertaken from January to June 2022. Thereafter, analysis will be conducted, and results compiled. Conclusions: This scoping review will chart existing literature on case-finding for DR-TB—this will help determine whether primary studies on effectiveness, cost-effectiveness, acceptability, and feasibility of different case-finding strategies for DR-TB exist and will help formulate potential questions for a systematic review. We will also describe case-finding strategies for DR-TB and how they fit into a model of case-finding pathways for drug-susceptible TB. This review has some limitations. One limitation is the diverse, inconsistent use of intervention terminology within the literature, which may result in missing relevant studies. Poor reporting of intervention strategies may also cause misunderstanding and misclassification of interventions. Lastly, case-finding strategies for DR-TB may not fit into a model developed from strategies for drug-susceptible TB. Nevertheless, such a situation will provide an opportunity to refine the model for future research. The review will guide further research to inform decisions on case-finding policies and practices for DR-TB. International Registered Report Identifier (IRRID): DERR1-10.2196/4000