Search

Controlling membrane morphology is crucial to improving the mechanical strength (MS) and hydrophilicity of porous membranes. Here we report on the fabrication of mixed matrix membranes (MMMs) free of macrovoids via non-solvent-induced phase separation (NIPS). Hydrophilic Halloysite nanotubes (HNTs) and poly (ethylene-co-vinyl alcohol) (EVOH) were mixed with Hydrophobic polysulfone (PSF) in the presence of polyethylene glycol (PEG) to fabricate MMMs. The results showed the formation of PSF/EVOH-MMMs with a spongy structure when the content of HNTs varied from 0.06- 0.12 wt.%, owing to the formation of strong hydrogen bonds between PSF, EVOH, PEG, and HNTs, confirmed by molecular dynamics (MD) simulations. The MS of MMMs with 0.12 wt.% HNTs was increased 2.2-fold (up to 6.22 MPa), while the contact angle (CA) was lowest at 47.42 ± 1.9°. In addition, the water permeability increased by a factor of 1.7 up to 419 L m−2 h−1 bar−1. The rejection rates of MMMs (M12) for oil and BSA were >90% and >95%, respectively. While the MMMs had > 90% flux recovery for both oil and BSA. We predict that this study will provide a method for controlling dope thermodynamics, formation dynamics, and morphology of MMMs while maintaining promising properties for improved separation performance.

In 2011, the South African HIV treatment eligibility criteria were expanded to allow all tuberculosis (TB) patients lifelong ART. The impact of this change on TB mortality in South Africa is not known. We evaluated mortality in all adults (≥ 15 years old) treated for drug-susceptible TB in South Africa between 2009 and 2016. Using a Cox regression model, we quantified risk factors for mortality during TB treatment and present standardised mortality ratios (SMR) stratified by year, age, sex, and HIV status. During the study period, 8.6% (219,618/2,551,058) of adults on TB treatment died. Older age, male sex, previous TB treatment and HIV infection (with or without the use of ART) were associated with increased hazard of mortality. There was a 19% reduction in hazard of mortality amongst all TB patients between 2009 and 2016 (adjusted hazard ratio: 0.81 95%CI 0.80–0.83). The highest SMR was in 15–24-year-old women, more than double that of men (42.3 in 2016). Between 2009 and 2016, the SMR for HIV-positive TB patients increased, from 9.0 to 19.6 in women, and 7.0 to 10.6 in men. In South Africa, case fatality during TB treatment is decreasing and further interventions to address specific risk factors for TB mortality are required. Young women (15–24-year-olds) with TB experience a disproportionate burden of mortality and interventions targeting this age-group are needed.

Human–wildlife cooperation occurs when humans and free‐living wild animals actively coordinate their behavior to achieve a mutually beneficial outcome. These interactions provide important benefits to both the human and wildlife communities involved, have wider impacts on the local ecosystem, and represent a unique intersection of human and animal cultures. The remaining active forms are human–honeyguide and human–dolphin cooperation, but these are at risk of joining several inactive forms (including human–wolf and human–orca cooperation). Human–wildlife cooperation faces a unique set of conservation challenges, as it requires multiple components—a motivated human and wildlife partner, a suitable environment, and compatible interspecies knowledge—which face threats from ecological and cultural changes. To safeguard human–wildlife cooperation, we recommend: (i) establishing ethically sound conservation strategies together with the participating human communities; (ii) conserving opportunities for human and wildlife participation; (iii) protecting suitable environments; (iv) facilitating cultural transmission of traditional knowledge; (v) accessibly archiving Indigenous and scientific knowledge; and (vi) conducting long‐term empirical studies to better understand these interactions and identify threats. Tailored safeguarding plans are therefore necessary to protect these diverse and irreplaceable interactions. Broadly, our review highlights that efforts to conserve biological and cultural diversity should carefully consider interactions between human and animal cultures. Please see AfricanHoneyguides.com/abstract‐translations for Kiswahili and Portuguese translations of the abstract.

Abstract Towards the end of 2019 the world experienced the Coronavirus disease (Covid 19) pandemic which affected operations of education systems. This reflective study examines how a lecturer and students built hope and self-efficacy under Covid 19 educational contexts. Self-efficacy–hopeful thinking model and Bernstein Framework were used in this study. The sample consisted of 515 students and 1 lecturer and it was sampled through purposeful stratified sampling. Data was collected through the lecturer’s self-reflection on his ability to build hope, self-efficacy to meet academic demands. The lecturer also observed students’ behaviours. The data was analysed through content analysis. Findings indicated that Covid 19 educational contexts mediated on students’ levels of hope, acadmic investment and created false impression that University academic year had been lost. Some students developed low level of self-efficacy belief which forced them to approach educational problems without conviction and hopeful thinking. The findings indicated that lecturer’s behaviour towards students contributed to the improvement of a high sense of self-efficacy belief and effort investment in their work. The lecturer maintained hopefullness and confidence among students. The study concluded that educational processes under the uncertainties of Covid 19 were paradigm shift for the lecturer and students’ academic life. It provided opportunities to transform and reconstruct pedagogical discourses in relation to Covid 19 educational contexts. It may be recommended that lecturers and others within institutions may be urged to reflect on Covid 19 educational challenges and embrace them rather than avoid them. Key words: Covid 19, Hope, Self-efficacy, Effort, Empathy

Background Up to a quarter of inpatients in high-income countries self-report beta-lactam allergy (BLA), which if incorrect, can increase use of alternative antibiotics that impact on bacterial resistance.. The epidemiology of BLA in low- and middle-income African countries is unknown. Methods Point-prevalence surveys were conducted at seven hospitals (adult, pediatric, government and private-funded, district- and tertiary-level) in Cape Town, South Africa between April 2019 and June 2021. Ward prescription records and interviews were conducted to identify BLA patients. De-labeling was attempted at the tertiary allergy clinic at Groote Schuur hospital. Findings A total of 1486 hospital inpatients were surveyed (1166 adults; 308 children). Only 48 (3.2%) patients self-reported a BLA with a higher rate amongst private- versus government-funded hospitals [6.3% vs 2.8%, p=0.014]. Using the PEN-FAST tool, only 10.4% (5/48) of self reported BLA patients were classified as high risk for true penicillin hypersensitivity. Antibiotics were prescribed to 70.8% (34/48) of self reported BLA patients, with 64.7% (22/34) receiving a beta-lactam. Despite three attempts to contact patients for de-labelling at the allergy clinic, only 3/36 underwent in vivo testing, with no positive results and one patient proceeded toa negative oral challenge. Interpretation Unlike high-income countries, self-reported BLA is low amongst inpatients in South Africa. The majority of self-reported BLA were low risk for type 1 hypersensitivity, but out-patient de-labeling efforts were largely unsuccessful. Funding None

The persistence and emergence of new multi-drug resistant Mycobacterium tuberculosis (M. tb) strains continues to advance the devastating tuberculosis (TB) epidemic. Robust systems are needed to accurately and rapidly perform drug-resistance profiling, and machine learning (ML) methods combined with genomic sequence data may provide novel insights into drug-resistance mechanisms. Using 372 M. tb isolates, the combined utility of ML and bioinformatics to perform drug-resistance profiling is demonstrated. SNPs, InDels, and dinucleotide frequencies are explored as input features for three ML models, namely Decision Trees, Random Forest, and the eXtreme Gradient Boosted model. Using SNPs and InDels, all three models performed equally well yielding a 99% accuracy, 97% recall, and 99% F1-score. Using dinucleotide frequencies, the XGBoost algorithm was superior with a 97% accuracy, 94% recall and 97% F1-score. This study validates the use of variants and presents dinucleotide features as another effective feature encoding method for ML-based phenotype classification.

The world is grappling with the COVID-19 pandemic caused by the 2019 novel SARS-CoV-2. To better understand this novel virus and its relationship with other pathogens, new methods for analyzing the genome are required. In this study, intrinsic dinucleotide genomic signatures were analyzed for whole genome sequence data of eight pathogenic species, including SARS-CoV-2. The genome sequences were transformed into dinucleotide relative frequencies and classified using the extreme gradient boosting (XGBoost) model. The classification models were trained to a) distinguish between the sequences of all eight species and b) distinguish between sequences of SARS-CoV-2 that originate from different geographic regions. Our method attained 100% in all performance metrics and for all tasks in the eight-species classification problem. Moreover, the models achieved 67% balanced accuracy for the task of classifying the SARS-CoV-2 sequences into the six continental regions and achieved 86% balanced accuracy for the task of classifying SARS-CoV-2 samples as either originating from Asia or not. Analysis of the dinucleotide genomic profiles of the eight species revealed a similarity between the SARS-CoV-2 and MERS-CoV viral sequences. Further analysis of SARS-CoV-2 viral sequences from the six continents revealed that samples from Oceania had the highest frequency of TT dinucleotides as well as the lowest CG frequency compared to the other continents. The dinucleotide signatures of AC, AG,CA, CT, GA, GT, TC, and TG were well conserved across most genomes, while the frequencies of other dinucleotide signatures varied considerably. Altogether, the results from this study demonstrate the utility of dinucleotide relative frequencies for discriminating and identifying similar species.

Tuberculous meningitis (TBM) is the most lethal form of tuberculosis. The incidence and mortality of TBM is unknown due to diagnostic challenges and limited disaggregated reporting of treated TBM by existing surveillance systems. We aimed to estimate the incidence and mortality of TBM in adults (15+ years) globally. Using national surveillance data from Brazil, South Africa, the United Kingdom, the United States of America, and Vietnam, we estimated the fraction of reported tuberculosis that is TBM, and the case fatality ratios for treated TBM in each of these countries. We adjusted these estimates according to findings from a systematic review and meta-analysis and applied them to World Health Organization tuberculosis notifications and estimates to model the global TBM incidence and mortality. Assuming the case detection ratio (CDR) for TBM was the same as all TB, we estimated that in 2019, 164,000 (95% UI; 129,000–199,000) adults developed TBM globally; 23% were among people living with HIV. Almost 60% of incident TBM occurred in males and 20% were in adults 25–34 years old. 70% of global TBM incidence occurred in Southeast Asia and Africa. We estimated that 78,200 (95% UI; 52,300–104,000) adults died of TBM in 2019, representing 48% of incident TBM. TBM case fatality in those treated was on average 27%. Sensitivity analysis assuming improved detection of TBM compared to other forms of TB (CDR odds ratio of 2) reduced estimated global mortality to 54,900 (95% UI; 32,200–77,700); assuming instead worse detection for TBM (CDR odds ratio of 0.5) increased estimated mortality to 125,000 (95% UI; 88,800–161,000). Our results highlight the need for improved routine TBM monitoring, especially in high burden countries. Reducing TBM incidence and mortality will be necessary to achieve the End TB Strategy targets.

Background. Estimates of prevalence of anti-SARS-CoV-2 antibody positivity (seroprevalence) for tracking the COVID-19 epidemic are lacking for most African countries. Objectives. To determine the prevalence of antibodies against SARS-CoV-2 in a sentinel cohort of patient samples received for routine testing at tertiary laboratories in Johannesburg, South Africa. Methods. This sentinel study was conducted using remnant serum samples received at three National Health Laboratory Service laboratories in the City of Johannesburg (CoJ) district. Collection was from 1 August to 31 October 2020. We extracted accompanying laboratory results for glycated haemoglobin (HbA1c), creatinine, HIV, viral load and CD4 T-cell count. An anti-SARS-CoV-2 targeting the nucleocapsid (N) protein of the coronavirus with higher affinity for IgM and IgG antibodies was used. We reported crude as well as population-weighted and test-adjusted seroprevalence. Multivariate logistic regression analysis was used to determine whether age, sex, HIV and diabetic status were associated with increased risk for seropositivity. Results. A total of 6 477 samples were analysed, the majority ( n =5 290) from the CoJ region. After excluding samples with no age or sex stated, the model population-weighted and test-adjusted seroprevalence for the CoJ ( n =4 393) was 27.0% (95% confidence interval (CI) 25.4 - 28.6). Seroprevalence was highest in those aged 45 - 49 years (29.8%; 95% CI 25.5 - 35.0) and in those from the most densely populated areas of the CoJ. Risk for seropositivity was highest in those aged 18 - 49 years (adjusted odds ratio (aOR) 1.52; 95% CI 1.13 - 2.13; p =0.0005) and in samples from diabetics (aOR 1.36; 95% CI 1.13 - 1.63; p =0.001). Conclusions. Our study conducted between the first and second waves of the pandemic shows high levels of current infection among patients attending public health facilities in Gauteng Province.

We employ the normalized revealed comparative advantage index to examine the competitiveness of the African, Caribbean, and Pacific (ACP) countries in the global sugar market. Results indic...

Climate projection at local scale is one of the crucial challenges that affects the development of water management-related mitigation plans. Moreover, the currently available climate models do not directly simulate some of the hydro-climatic parameters (e.g., effective rainfall, reference evapotranspiration, irrigation requirements), which are of interest in irrigation sector. Modeling crop-water demands under changing climate involves several step-by-step approaches that are tedious and time-consuming for many water users. This study developed a water management tool, hereafter called Climate-Smart Decision-Support System (CSDSS), for modeling water demand of rice irrigation schemes under climate change impacts. The CSDSS is a user-friendly interactive program consisting of three main modules integrated in MATLAB and a graphical user interface development environment (GUIDE). The model runs with ten Global Climate Models (GCMs) and three emission scenarios (RCP 4.5, 6.0 and 8.5). It can generate several hydro-climatic parameters based on a daily water balance model, with input data from GCMs projections, crop, soil and field conditions. The model allows water managers to make fast decision for paddy water management. The generated outputs can be obtained through individual GCMs as well as through multi-models (ensemble) projection and can be converted into excel format for further analysis. The model was applied to evaluate the impacts of climate change on irrigation water demand and other key hydro-climatic parameters in Tanjung Karang Rice Irrigation Scheme in Malaysia for the period 2010–2099 with reference to the baseline period of 1976–2005. The results show that irrigation water demand will increase during the off-season (January–June) but decrease during the main season (July–December) due to significant contribution from effective rainfall in the latter season. The CSDSS tool can be used for managing water resources under changing climate and would, therefore, be helpful in promoting appropriate adaptation and mitigation strategies that can lead to more sustainable water use at farm level. Some future improvements of the tool, due to methodological limitations of the study, will however improve its performance.

Amaranth is a traditional leafy vegetable of the genus Amaranthus spp., which has been consumed throughout history. Amaranth has great potential as a sustainable crop that could improve household food security, nutrition security and farm incomes. The growth environment of amaranth, can have a major impact not only on the productivity of the crop but its nutritional value as well. Production of amaranth in developing countries like Swaziland is very low, if any at all. This could be attributed to, among some reasons, lack of agronomic information on production of amaranth. The objective of this study was to determine the effects of different types of fertilisers on the growth and yield of Amaranthus hybridus. The trial was done at Malkerns Research Station, in Swaziland. The treatments were 20 t ha(-1) kraal manure, 40 t ha(-1) kraal manure, 100 kg ha(-1) 2.3.4 (39) + 5% Zn (compound NPK), 150 kg ha(-1) 2.3.4 (39) + 5% Zn and the control (no fertiliser). The experimental design was a randomised complete block design. Data were collected at 4, 5 and 6 weeks after planting. The data were subjected to analysis of variance through SPSS 20. Mean separation test was performed by the Duncan's new multiple range test at P=0.05 significant level. Addition of any type of fertiliser had significant (P 0.05) different from each other in all the growth and yield parameters at the different harvest stages. It was concluded that addition of fertiliser, either organic or inorganic, promotes the growth rate and yield of Amaranthus hybridus.

Follow the DOI link at the top of the record to access the full-text of the article on the publisher's web site

This review looks into the efforts made towards commercializing nano-enable flat sheet membranes as well as the challenges that need to be overcome. There is a question mark on the argument that the nano-pores of the fillers play a significant role in the performance of the membrane. Non porous nanomaterials have been reported to cause in increase in water flux, yet there are still articles that credit the nano-pores of the nanomaterials for improved membrane performance. There are two points that are important to highlight: (1) the nanoparticles, e.g. zeolites, are smaller in diameter compared to the thickness, (2) the loading rate of the filler phase is significantly small in relation to continuous phase. Therefore, it cannot be correct to assume that the nanomaterials provide continuous flow channels in the selective layer. There is no dispute here that the addition of NP enhances the performance of a membrane, but it is the perception that the nano-pores are the reason that we disagree with.

As a potential remedy for addressing water shortage challenges, membrane distillation (MD) presents the possibility of alleviating the water demand in water scarce countries. It offers a promising approach to explore untraditional water resources. In the field of urine treatment, MD enables water recovery for potable use and the recovery of nutrients that can be used in boosting agricultural production. It is in this light that polyvinylidene fluoride/polytetrafluoroethylene (PVDF/PTFE) membranes modified with methyl functionalized silica nanoparticles (MfSNPs) were fabricated to produce microporous hydrophobic composite membranes for water recovery from urine. Contact angles of the membranes indicated an increase in the hydrophobicity brought about by the increase in PTFE loading. The increase in PTFE loading improved the membrane structure (as shown by SEM images) resulting in smaller evenly distributed pores and a porous spongy structure. The composite membrane attained the maximum water recovery of 80% from hydrolysed human urine samples at pH 10.5, against a water vapour gradient of 30 °C. The feed side temperature was kept at 50 °C and the permeate side at 20 °C. The highest permeate flux for the PVDF/PTFE nanocomposite membranes was 8 J/Jo,which is comparable to fluxes reported in the literature obtained in direct contact membrane distillation (DCMD) setups operated at the same temperature gradient. The permeate water quality was assessed and the results showed high rejection of ammonia (>95%), TOC (>98%), Na+ (>98%) and K+ (>89%) by the membranes. This suggests that the (combination/hybrid) convergence of membrane technology and nanotechnology in MD application is a viable alternative for urine treatment to provide sustainable and reliable clean water supply.

Follow the DOI link at the top of the record to access the full-text of this article on the publisher's web-site

The decline in pressure driven membrane performance as a result of fouling is still a major challenge in membrane technology application to wastewater treatment. Efforts have been directed at mitigating fouling of pressure driven membranes by modifying the polymer through addition of hydrophilic materials. However, these materials are not yet a viable solution because are they are not cost-effective. Polysulfone (PSf) membranes incorporated with hydrophilic Lantana camara powder were prepared using the phase inversion method via the immersion precipitation technique to obtain PSf/LC (L. camara) mixed matric membranes. L. camara is one of the invasive and ready available plant species in Southern Africa. The PSf/ LC membranes were used for the removal of dyes from water. Contact angle measurements of modified membranes revealed higher hydrophilicity (contact angle of 44°). Addition of L. camara in PSf membranes improved the water permeability up to 91% compared to the pure PSf membrane. The highest salt rejection recorded amongst the modified membranes was 20% for NaCl and 27% for MgSO4. Congo red dye rejection was 99% at pH 4. Therefore L. camara can be used as an additive in membrane technology to improve the hydrophilicity and permeability of PSf membranes.

Determining sustainability harvesting levels for most non-timber forest products (NTFPs) is an evolving science. A monitoring programme that will continually assess the health and vitality of the natural resources base should be implemented. Though there is some information on individual species, ecosystem dynamics are still not well understood, commercialization of natural products makes it imperative to manage proactively through monitoring, harvesting and replanting and tree succession plans. Important steps in sustainable natural products management include the following: Identification and demarcation of the resource base by ecosystem type (forest, pasture, farmland, rock outcrop, and so on) and map of the locations of various ecosystems types; identification of resource supply areas of the preferred products; and estimating the volume based on current harvesting and trade or use. Further, identify potential threats to standing stock of natural resource base. In addition to conducting group meetings to investigate where and how products have been harvested, extracted or collected over the last 3 to 5 years; undertaking resource inventory of standing stock and also conducting user surveys and engaging resource collectors. Ultimately, for business development, the following logical issues are examined and critically analyzed; enterprise opportunity and location-specific overview of the community forestry subsector, sustainability of supply of forest products, regulatory environment and forest resource users/groups, technology, management and finance, and lastly marketing and sales.

Background To achieve universal health coverage by 2030, sub-Saharan African countries are planning to develop large scale tele-consultation public health services. However, there is a lack of knowledge regarding the level of peoples’ willingness to use this kind of tele-health services. To address this gap and inform policymakers, the present study aims at accessing the Mozambican people’s willingness to use tele-consultation public health services and the determinants associate to their willingness. Methods A total of 403 adults participated in the study. The material consisted of 32 vignettes (scenarios) describing realistic health problem situations in which an individual was proposed to use a tele-consultation public health service, varying as a function of five factors: consultation category, health problem category, health problem severity, physician category, and the consultation price. For each health problem situation presented in the vignettes, the participants were asked to rate their willingness to use the proposed tele-consultation service on an 11-point scale. A cluster analysis using the K-means procedure was applied to the quantitative raw data to capture the participants’ different perspectives. ANOVA, x2 and t-test analyses were also conducted to examine the effects of the different health problem situations and the sociodemographic characteristics on the participant ratings. Results Five different perspectives (clusters) were found: never-willing (15% of the sample), severity (26%), consultation-category (22%), undecided (16%), and price-severity (21%). These perspectives were associated with participants’ sociodemographic characteristics. Conclusion According to the main results, it seems that the majority of the participants (69%) were highly willing to use tele-consultation public health services in the case of mild illness, cheaper prices and follow-up consultation. In addition, the participants’ willingness was significantly affected by some of the participants’ sociodemographic characteristics.

BACKGROUND: In South Africa, tuberculosis (TB) is a leading cause of death among those METHODS: Retrospective analysis of all patients RESULTS: Between 2004 and 2016, 729 463 children and adolescents were recorded on TB treatment; 84.0% had treatment outcomes and 2.5% (18 539) died during TB treatment. The case fatality ratio decreased from 3.3% in 2007 to 1.9% in 2016. In the multivariable Cox regression model, ages 0 to 4, 10 to 14, and 15 to 19 years (compared with ages 5 to 9 years) were associated with increased risk of mortality, as was HIV infection, previous TB treatment, and extrapulmonary involvement. The SMR of 15 to 19-year-old female patients was more than double that of male patients the same age (55.3 vs 26.2). Among 10 to 14-year-olds and those who were HIV-positive, SMRs increased over time. CONCLUSIONS: Mortality in South African children and adolescents treated for TB is declining but remains considerable, with 2% dying during 2016. Adolescents (10 to 19 years) and those people living with HIV have the highest risk of mortality and the greatest SMRs. Interventions to reduce mortality during TB treatment, specifically targeting those at highest risk, are urgently needed.

Background: Cancer remains a public health challenge in low-and-middle income countries (LMICs). Over 30% of those in need of palliative care (PC) worldwide suffer from cancer and 80% of patients with cancer in LMICs are diagnosed at advanced stages, by which time they can only benefit from PC services. The aim of this study was to determine factors influencing PC utilisation among patients with cancer in KwaZulu-Natal (KZN). Methods: A study was conducted among patients who had been diagnosed with different cancers and attending Inkosi Albert Luthuli Central Hospital, Addington Hospital, Pietermaritzburg Grey’s hospital, Msunduzi Hospice and Chatsworth Hospice, using cross-sectional mixed methods. A systematic random sampling technique was used to select the participants. Semi-structured questionnaires were administered to a total of 394 patients with cancer. The questionnaire included two open-ended questions and 59 closed-ended questions. Data from open-ended questions were manually coded and converted into themes, while the closed ended-questions were entered into the REDCap (v.8.11.7) and exported to Stata for analysis. Results: The mean (+SD) age of the 394 participants was 51.89 (+14.67) years and about 22.9% were within the 41–50 years age-group. The majority of participants were females (77.7%) and were unmarried (60.6%). Most of the participants’ racial classification was black (81.5%) and 64.5% had primary education. More than four-fifths (82.7%) were unemployed, 55.8% lived in urban areas and 24.6% had cervical cancer. The analysis of the two open-ended questions incorporated into the questionnaire revealed five major barriers preventing cancer patients from seeking PC services. These themes included lack of cancer knowledge, pursuit of alternative treatment options and long waiting periods at healthcare institutions. In addition, stigma and discrimination, lack of screening and diagnostic equipment and socio-economic barriers, contributed to the underutilisation of PC services by patients with cancer. Participants recommended that cancer awareness campaigns, healthcare services and continuous professional development (CPD) be improved.Conclusion: Cancer patients in low-to middle-income countries, such as South Africa, are still facing barriers to pursuing PC. Better education of the public could contribute to increased knowledge and awareness on cancer and PC services. Utilisation of PC could be maximised, thereby providing a better quality of life for the sufferers and their families until the end of life’s journey. The study also provides information that can be used to strengthen and/or to develop PC guidelines for addressing PC issues.

Advancements made in high-throughput sequencing technologies have continued to generate large amounts of sequencing data enabling the holistic investigation of complex biological phenomena. Genomic sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid expansion in available sequence data poses a tremendous computational challenge, calling for the development of novel data processing and analytic methods, as well as computing resources to match the volume of these datasets. In this work, a machine- and statistical learning approach for classification based on k-mer representations of DNA sequence data is proposed. While targeted sequencing focuses on a specific region of interest, whole genome sequencing enables a view of a species’ entire genome. Thus, the approach is tested using whole genome sequences of Mycobacterium tuberculosis isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, and (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate. Furthermore, the computing challenges associated with whole genome sequence data analyses in producing interpretable and explainable insights are described. Classification models were trained using 104 Mycobacterium tuberculosis isolates. Cluster analyses showed that k-mers can be used to discriminate phenotypes and the discrimination becomes more concise as the k-mer size increases. The best performing classification model had a k-mer size of 10 (longest k-mer considered in this study) an accuracy, recall, precision, specificity, and Matthews Correlation coefficient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4, respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biologically explainable results, highlighting the interplay that exists between accuracy, computing resources such as processing and memory, and explainability of classification results. Furthermore, the analysis provides a new way to extract genetic information from genomic data and identify phenotype relationships which are integral for explaining complex biological mechanisms.

No Abstract

Background Few studies have evaluated tuberculosis control in children and adolescents. We used routine tuberculosis surveillance data to quantify age- and human immunodeficiency virus (HIV)-stratified trends over time and investigate the relationship between tuberculosis, HIV, age, and sex. Methods All children and adolescents (0–19 years) routinely treated for drug-susceptible tuberculosis in South Africa and recorded in a de-duplicated national electronic tuberculosis treatment register (2004–2016) were included. Age- and HIV-stratified tuberculosis case notification rates (CNRs) were calculated in four age bands: 0–4, 5–9, 10–14, and 15–19 years. The association between HIV infection, age, and sex in children and adolescents with tuberculosis was evaluated using multivariable logistic regression. Results Of 719 400 children and adolescents included, 339 112 (47%) were 0–4 year olds. The overall tuberculosis CNR for 0–19 year olds declined by 54% between 2009 and 2016 (incidence rate ratio [IRR] = 0.46; 95% confidence interval [CI], .45–.47). Trends varied by age and HIV, with the smallest reductions (2013–2016) in HIV-positive 0–4 year olds (IRR = 0.90; 95% CI, .85–.95) and both HIV-positive (IRR = .84; 95% CI, .80–.88) and HIV-negative (IRR = 0.89; 95% CI, .86–.92) 15–19 year olds. Compared with 0- to 4-year-old males, odds of HIV coinfection among 15–19 year olds were nearly twice as high in females (adjusted odds ratio [aOR] = 2.49; 95% CI, 2.38–2.60) than in males (aOR = 1.35; 95% CI, 1.29–1.42). Conclusions South Africa’s national response to the HIV epidemic has made a substantial contribution to the observed declining trends in tuberculosis CNRs in children and adolescents. The slow decline of tuberculosis CNRs in adolescents and young HIV-positive children is concerning. Understanding how tuberculosis affects children and adolescents beyond conventional age bands and by sex can inform targeted tuberculosis control strategies.

The SARS-CoV-2 pandemic has presented clinicians with an enormous challenge in managing a respiratory virus that is not only capable of causing severe pneumonia and acute respiratory distress syndrome, but also multisystem disease. The extraordinary pace of clinical research, and particularly the surge in adaptive trials of new and repurposed treatments, have provided rapid answers to questions of whether such treatments work, and has resulted in corticosteroids taking centre stage in the management of hospitalised patients requiring oxygen support. Some treatment modalities, such as the role of anticoagulation to prevent and treat potential thromboembolic complications, remain controversial, as does the use of high-level oxygen support, outside of an intensive care unit setting. In this paper, we describe the clinical management of COVID-19 patients admitted to Groote Schuur Hospital, a major tertiary level hospital at the epicentre of South Africa's SARS-CoV-2 epidemic during its first 4 months.