A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe:Implications for Future Studies

Background: Gut microbiota play a key role in host health, with certain Bifidobacterium strains critical for immune development. The healthy gut of breastfed infants is dominated by these pioneer microbes, especially the strains that feed on human milk oligosaccharides.Objective: This is a scoping review of gut microbiome research from Zimbabwe. It focuses on distribution and dynamic changes of bifidobacteria, and milk components that promote growth of microbes in infants, together with the distribution of associated gut microbes in adults.Design: Online databases were searched for publications from 2000 to 2023.Results and Analysis: Fourteen publications on microbiota of infants and adults were included in this scoping review. Most were cross-sectional, while three were clinical trials/cohort protocols. Publications focused on pediatrics (78.5%), pregnant women (14.3%), and men (7.2%). Zimbabwe has a high burden of HIV; hence 35.7% of study populations were delineated by HIV status. The laboratory methods used included shotgun metagenomics (62%) or 16S rRNA gene amplicon sequencing. Almost 85% of the studies focused on total microbiome profiles and rarely reported the distribution of different Bifidobacterium species and variants. None of the papers studied human breast milk composition. There were reports of reduced abundance of beneficial genera in pregnant women, children, and adolescents living with HIV. Additionally, gut microbiota was reported to be poorly predictive of child growth and vaccine response, though this was not conclusive.Conclusion: There are few studies that characterize the gut microbiome by Zimbabwe-based researchers. However, studies on strain level diversity of Bifidobacterium and other key microbes, and their role in health during and beyond infancy, lag behind in Zimbabwe and other low- and middle-income countries. Such cohorts are needed to inform future mechanistic studies and downstream translational work such as next-generation probiotics and prebiotics

Pitfalls in Link Prediction with Graph Neural Networks: Understanding the Impact of Target-link Inclusion & Better Practices

While Graph Neural Networks (GNNs) are remarkably successful in a variety of high-impact applications, we demonstrate that, in link prediction, the common practices of including the edges being predicted in the graph at training and/or test have outsized impact on the performance of low-degree nodes. We theoretically and empirically investigate how these practices impact node-level performance across different degrees. Specifically, we explore three issues that arise: (I1) overfitting; (I2) distribution shift; and (I3) implicit test leakage. The former two issues lead to poor generalizability to the test data, while the latter leads to overestimation of the model's performance and directly impacts the deployment of GNNs. To address these issues in a systematic way, we introduce an effective and efficient GNN training framework, SpotTarget, which leverages our insight on low-degree nodes: (1) at training time, it excludes a (training) edge to be predicted if it is incident to at least one low-degree node; and (2) at test time, it excludes all test edges to be predicted (thus, mimicking real scenarios of using GNNs, where the test data is not included in the graph). SpotTarget helps researchers and practitioners adhere to best practices for learning from graph data, which are frequently overlooked even by the most widely-used frameworks. Our experiments on various real-world datasets show that SpotTarget makes GNNs up to 15x more accurate in sparse graphs, and significantly improves their performance for low-degree nodes in dense graphs.Comment: Extended Version of our WSDM'24 paper. 8 pages, 2 page appendi

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort

Introduction: Our understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa. Materials and method: From 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs). Results: The study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average. Conclusion: This study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights. Impact statement: This research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions

Effectiveness of a psychological intervention delivered by general nurses for alcohol use disorders in people living with HIV in Zimbabwe: a cluster randomized controlled trial.

INTRODUCTION: There have been very few randomized clinical trials of interventions for alcohol use disorders (AUD) in people living with HIV (PLWH) in African countries. This is despite the fact that alcohol use is one of the modifiable risk factors for poor virological control in PLWH on antiretroviral therapy. METHODS: Sixteen clinic clusters in Zimbabwe were selected through stratified randomization and randomized 1: 1 to Intervention and Control arms. Inclusion criteria for individual participants were being adult, living with HIV and a probable alcohol use disorder as defined by a score of 6 (women) or 7 (men) on the Alcohol Use Disorders Identification Test (AUDIT). In the Intervention clusters, participants received 8 to 10 sessions of Motivational Interviewing blended with brief Cognitive Behavioural Therapy (MI-CBT). In the control clusters, participants received four Enhanced Usual Care (EUC) sessions based on the alcohol treatment module from the World Health Organisation mhGAP intervention guide. General Nurses from the clinics were trained to deliver both treatments. The primary outcome was a change in AUDIT score at six-month post-randomization. Viral load, functioning and quality of life were secondary outcomes. A random-effects analysis-of-covariance model was used to account for the cluster design. RESULTS: Two hundred and thirty-four participants (n = 108 intervention and n = 126 control) were enrolled across 16 clinics. Participants were recruited from November 2016 to November 2017 and followed through to May 2018. Their mean age was 43.3 years (SD = 9.1) and 78.6% (n = 184) were male. At six months, the mean AUDIT score fell by -6.15 (95% CI -6.32; -6.00) in the MI-CBT arm, compared to a fall of - 3.09 95 % CI - 3.21; -2.93) in the EUC arm (mean difference -3.09 (95% CI -4.53 to -1.23) (p = 0.05). Viral load reduced and quality of life and functioning improved in both arms but the difference between arms was non-significant. CONCLUSIONS: Interventions for hazardous drinking and AUD comprising brief, multiple alcohol treatment sessions delivered by nurses in public HIV facilities in low-income African countries can reduce problematic drinking among PLWH. Such interventions should be integrated into the primary care management of AUD and HIV and delivered by non-specialist providers. Research is needed on cost-effectiveness and implementation of such interventions, and on validation of cut-points for alcohol use scales in low resource settings, in partnership with those with lived experience of HIV and AUD

Elevations Of Serum Total Cholesterol Differ By Trimester In Pregnant Women At Chitungwiza Central Hospital Ante-Natal Clinic In Zimbabwe

Abstract: A physiological increase in serum total cholesterol levels occurs during pregnancy. This hypercholesterolaemia may lead to metabolic disorders in the foetus and the mother. Little information is available on pregnancy-induced lipid metabolism disturbances in the Zimbabwe setting. A cross-sectional study of total serum cholesterol levels in pregnant women who attended Chitungwiza Central Hospital Antenatal Clinic between 24 January 2013 and 14 February 2013 was carried out. All recruited women were either in the second or third trimester of pregnancy. Samples were analysed using a BS120 ® Chemistry Analyser. The paired t test proportion was used to test the hypothesis at 5 % significance level.There were a significant proportion of women with moderately elevated total serum cholesterol compared to pregnant women reference ranges but it could not be determined whether the elevations were pathological or physiological hence further studies are required to determine whether this could develop into overt hypercholesterolaemia post- partum.Of significance, in this study the third trimester women had significantly higher mean total cholesterol levels compared to the second trimester women, p value = 0.0033 (p< 0.05)

Incidence of non-communicable diseases (NCDs) in HIV patients on ART in a developing country: Case of Zimbabwe's Chitungwiza Central Hospital-A retrospective cohort study (2010-2019).

IntroductionThe incidence of non-communicable diseases (NCDs) has been reported to be rising over the years leading up to 2010. In Zimbabwe, there are few studies done to examine the incidence of NCDs in people living with HIV (PLHIV) on anti-retroviral treatment (ART).ObjectiveTo determine the incidence of NCDs in HIV patients on ART at the Chitungwiza Central Hospital over ten years and the associated risk factors.MethodsThis was a retrospective cohort study using data from 203 patients enrolled on ART at the Chitungwiza Central Hospital between 2010 and 2019. All 500 records were considered and the selection was based on participants' consenting to the study and their strict adherence to ART without absconding. The incidence of NCDs was determined and generalized estimating equations (GEE) were used to estimate the association between NCDs and the selected risk factors.FindingsData collected at the study's baseline (2010) showed that the most prevalent NCD was hypertension, found in (18/203) 8.9% of the study participants, followed by diabetes (6.9%), then followed by cardiovascular diseases (CVD) (3.9%), and the least common NCD was cancer (1.9%). Incidences of all of these NCDs showed an increasing trend as the time of follow-up progressed. The factors found to be significantly associated with the development of NCDs were gender (p = 0.002) and follow-up time (pConclusionsNCDs and HIV comorbidity is common with women more likely than males to develop NCDs as they advance in age. There is need to devise targeted intervention approach to the respective NCDs and risk factors since they affect differently in relation to the demographic details of the participants.RecommendationsThis paper recommends a multi-stakeholder approach to the management of NCDs, with researchers, clinicians and the government and its various arms taking a leading role

Benefits of annual chemotherapeutic control of schistosomiasis on the development of protective immunity

Abstract Background Schistosomiasis is a devastating parasitic disease. The mainstay of schistosomiasis control is by praziquantel treatment. The study aimed to determine benefits of annual chemotherapy of schistosomiasis on development of protective immunity in school children in a selected endemic rural area in Zimbabwe. Methods Urine specimens from 212 school children (7–13 years) were collected and examined to determine prevalence, intensity and reinfection of S.haematobium at baseline, 6 weeks and 2 years following annual rounds of praziquantel treatment. Blood samples from the participants were assayed for total and S. haematobium (Sh13)-specific antibodies before and 2 years after annual rounds of treatment. Results Annual treatment reduced the prevalence of S. haematobium infection (p < 0.05) from 23.1% at baseline to 0.47% after 2 years. Overall cure rate was 97.8%. Intensity of infection declined (p < 0.05) from 15.9 eggs/10 ml urine at baseline to 2 eggs/10 ml urine. After two years, overall rate of reinfection was 0.96%. At baseline, total IgG4 was higher in S. haematobium-infected children (p = 0.042) ,while all other immunoglobulins were within normal ranges. There was an increase in total IgG2 (p = 0.044) levels and a decrease in total IgG4 (p = 0.031) levels 2 years post-treatment; and no significant changes in other total immunoglobulins. Schistosoma-infected children at baseline showed an increase in anti-Sh13 IgG1 (p = 0.005) and a decrease in Sh13 IgG4 levels (p = 0.012) following treatment. Conclusion Annual praziquantel treatment delivered to school children over 2 years significantly reduce prevalence, intensity of infection and reinfection of S. haematobium infection. Treatment was also observed to cause a reduction in schistosome-specific blocking IgG4 and an increase in Schistosoma-specific protecting IgG1