Expanding the human gut microbiome atlas of Africa.

Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.

Multimorbidity in African ancestry populations: a scoping review.

OBJECTIVES: Multimorbidity (MM) is a growing concern linked to poor outcomes and higher healthcare costs. While most MM research targets European ancestry populations, the prevalence and patterns in African ancestry groups remain underexplored. This study aimed to identify and summarise the available literature on MM in populations with African ancestry, on the continent, and in the diaspora. DESIGN: A scoping review was conducted in five databases (PubMed, Web of Science, Scopus, Science Direct and JSTOR) in July 2022. Studies were selected based on predefined criteria, with data extraction focusing on methodology and findings. Descriptive statistics summarised the data, and a narrative synthesis highlighted key themes. RESULTS: Of the 232 publications on MM in African-ancestry groups from 2010 to June 2022-113 examined continental African populations, 100 the diaspora and 19 both. Findings revealed diverse MM patterns within and beyond continental Africa. Cardiovascular and metabolic diseases are predominant in both groups (80% continental and 70% diaspora). Infectious diseases featured more in continental studies (58% continental and 16% diaspora). Although many papers did not specifically address these features, as in previous studies, older age, being women and having a lower socioeconomic status were associated with a higher prevalence of MM, with important exceptions. Research gaps identified included limited data on African-ancestry individuals, inadequate representation, under-represented disease groups, non-standardised methodologies, the need for innovative data strategies, and insufficient translational research. CONCLUSION: The growing global MM prevalence is mirrored in African-ancestry populations. Recognising the unique contexts of African-ancestry populations is essential when addressing the burden of MM. This review emphasises the need for additional research to guide and enhance healthcare approaches for African-ancestry populations, regardless of their geographic location.

Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study.

Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations.

Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study.

Most hypertension-related genome-wide association studies (GWAS) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure-related traits (systolic and diastolic blood pressure, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N=10,775), identified two genome-wide significant signals (p<5E-08): systolic blood pressure near P2RY1 (rs77846204; intergenic variant, p=4.25E-08) and pulse pressure near Linc01256 (rs80141533; intergenic variant, p=4.25E-08). No genome-wide signals were detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p<5E-06) were observed for all traits, with 29 displaying pleiotropic effects and several replicating known associations. Polygenic risk scores developed from studies on different ancestries had limited transferability, with multi-ancestry models providing better prediction. This study provides insights into the genetics and physiology of blood pressure variation in African populations.

Physical Activity and Its Association With Body Mass Index: A Cross-Sectional Analysis in Middle-Aged Adults From 4 Sub-Saharan African Countries.

BACKGROUND: This study aimed to explore association of self-reported physical activity domains of work, leisure, and transport-related physical activity and body mass index (BMI) in 9388 adult men and women from the Africa-Wits-INDEPTH partnership for Genomic (AWI-Gen) study in Africa. Africa-Wits-INDEPTH partnership for Genomic is a large, population-based cross-sectional cohort with participants from 6 sites from rural and urban areas in 4 sub-Saharan African countries. METHODS: A sex-stratified meta-analysis of cross-sectional data from men and women aged 29-82 years was used to assess the association of physical activity with BMI. RESULTS: Overall, meeting physical activity guidelines of at least 150 minutes per week was associated with 0.82 kg/m2 lower BMI in men (ß = -0.80 kg/m2; 95% confidence interval [CI], -1.14 to -0.47) and 0.68 kg/m2 lower BMI in women (ß = -0.68 kg/m2; 95% CI, -1.03 to -0.33). Sex and site-specific differences were observed in the associations between physical activity domains and BMI. Among those who met physical activity guidelines, there was an inverse association between transport-related physical activity and BMI in men from Nanoro (Burkina Faso) (ß = -0.79 kg/m2; 95% CI, -1.25 to -0.33) as well as work-related physical activity and BMI in Navrongo men (Ghana) (ß = -0.76 kg/m2; 95% CI, -1.25 to -0.27) and Nanoro women (ß = -0.90 kg/m2; 95% CI, -1.44 to -0.36). CONCLUSIONS: Physical activity may be an effective strategy to curb rising obesity in Africa. More studies are needed to assess the impact of sex and geographic location-specific physical activity interventions on obesity.

Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits.

Genetic associations for lipid traits have identified hundreds of variants with clear differences across European, Asian and African studies. Based on a sub-Saharan-African GWAS for lipid traits in the population cross-sectional AWI-Gen cohort (N = 10,603) we report a novel LDL-C association in the GATB region (P-value=1.56 × 10-8). Meta-analysis with four other African cohorts (N = 23,718) provides supporting evidence for the LDL-C association with the GATB/FHIP1A region and identifies a novel triglyceride association signal close to the FHIT gene (P-value =2.66 × 10-8). Our data enable fine-mapping of several well-known lipid-trait loci including LDLR, PMFBP1 and LPA. The transferability of signals detected in two large global studies (GLGC and PAGE) consistently improves with an increase in the size of the African replication cohort. Polygenic risk score analysis shows increased predictive accuracy for LDL-C levels with the narrowing of genetic distance between the discovery dataset and our cohort. Novel discovery is enhanced with the inclusion of African data.

Demand and supply-side barriers and opportunities to enhance access to healthcare for urban poor populations in Kenya: a qualitative study.

OBJECTIVE: To explore the barriers to and options for improving access to quality healthcare for the urban poor in Nairobi, Kenya. DESIGN AND PARTICIPANTS: This was a qualitative approach. In-depth interviews (n=12), focus group discussions with community members (n=12) and key informant interviews with health providers and policymakers (n=25) were conducted between August 2019 and September 2020. Four feedback and validation workshops were held in December 2019 and April-June 2021. SETTING: Korogocho and Viwandani urban slums in Nairobi, Kenya. RESULTS: The socioe-conomic status of individuals and their families, such as poverty and lack of health insurance, interact with community-level factors like poor infrastructure, limited availability of health facilities and insecurity; and health system factors such as limited facility opening hours, health providers' attitudes and skills and limited public health resources to limit healthcare access and perpetuate health inequities. Limited involvement in decision-making processes by service providers and other key stakeholders was identified as a major challenge with significant implications on how limited health system resources are managed. CONCLUSION: Despite many targeted interventions to improve the health and well-being of the urban poor, slum residents are still unable to obtain quality healthcare because of persistent and new barriers due to the COVID-19 pandemic. In a devolved health system, paying attention to health services managers' abilities to assess and respond to population health needs is vital. The limited use of existing accountability mechanisms requires attention to ensure that the mechanisms enhance, rather than limit, access to health services for the urban slum residents. The uniqueness of poor urban settings also requires in-depth and focused attention to social determinants of health within these contexts. To address individual, community and system-level barriers to quality healthcare in this and related settings and expand access to health services for all, multisectoral strategies tailored to each population group are needed.

Perspectives on returning individual and aggregate genomic research results to study participants and communities in Kenya: a qualitative study.

BACKGROUND: A fundamental ethical challenge in conducting genomics research is the question of what and how individual level genetic findings and aggregate genomic results should be conveyed to research participants and communities. This is within the context of minimal guidance, policies, and experiences, particularly in Africa. The aim of this study was to explore the perspectives of key stakeholders' on returning genomics research results to participants in Kenya. METHODS: This qualitative study involved focus group discussions (FGDs) and in-depth interviews (IDIs) with 69 stakeholders. The purposively selected participants, included research ethics committee (REC) members (8), community members (44), community resource persons (8), and researchers (9). A semi-structured interview guide was used to facilitate discussions. Six FGDs and twenty-five (IDIs) were conducted among the different stakeholders. The issues explored in the interviews included: (1) views on returning results, (2) kind of results to be returned, (3) value of returning results to participants, and (4) challenges anticipated in returning results to participants and communities. The interviews were audio-recorded, transcribed verbatim, and coded in Nvivo 12 pro. Thematic and content analysis was conducted. RESULTS: Participants agreed on the importance of returning genomic results either as individual or aggregate results. The most cited reasons for returning of genomic results included recognizing participants' contribution to research, encouraging participation in future research, and increasing the awareness of scientific progress. Other aspects on how genomic research results should be shared included sharing easy to understand results in the shortest time possible and maintaining confidentiality when sharing sensitive results. CONCLUSIONS: This study identified key stakeholders' perspectives on returning genomic results at the individual and community levels in two urban informal settlements of Nairobi. The majority of the participants expect to receive feedback about their genomic results, and it is an obligation for researchers to see how to best fulfil it.

Association between physical activity participation and perceived social isolation at older ages: Do social participation, age and sex differences matter?

BACKGROUND: Physical inactivity is a major risk factor for poor health. However, it is unclear how physical activity (PA) is associated with perceived social isolation (PSI) in older age. This study aims to explore 1) association between PA and PSI among older people in Ghana and 2) if social participation (SP), age and sex modify any associations. METHODS: The study focused on 1,201 men and women aged ≥50 years in the AgeHeaPsyWel-HeaSeeB Study. Multivariate ordinary least squares (OLS) models were specified to estimate the regression coefficients and standard errors for the associations of PA and SP with PSI adjusting for potential confounders. RESULTS: Multivariate OLS regressions showed that engagement in SP (b = -0.442; SE = 0.140; p < 0.001) and regular PA (b = -0.338; SE = 0.152; p < 0.005) were independently associated with decreasing PSI. Also, SP modified the PA-PSI association such that resourceful SP reinforced the link between PA and PSI (b = -0.709; SE = 0.276; p < .005). Finding revealed sex (men: b= -0.712; SE = 0.266; p < 0.005; women: p = 0.083) and age differences (65+: b = -0.437; SE = 0.206; p < 0.005; 50-64: b = -0.502; SE = 0.252; p < 0.05) in the effect of PA on PSI. CONCLUSIONS: Findings provide insight into the importance of specific and combined effects of SP and PA on PSI in older age. Public health, clinical practice, and social policy efforts should target social healing and group PA interventions to improve older adults' emotional health.

Persistent barriers to the use of maternal, newborn and child health services in Garissa sub-county, Kenya: a qualitative study.

BACKGROUND: North Eastern Kenya has persistently had poor maternal, new-born and child health (MNCH) indicators. Barriers to access and utilisation of MNCH services are structural, individual and community-level factors rooted in sociocultural norms. A package of interventions was designed and implemented in Garissa sub-County aimed at creating demand for services. Community Health Volunteers (CHVs) were trained to generate demand for and facilitate access to MNCH care in communities, while health care providers were trained on providing culturally acceptable and sensitive services. Minor structural improvements were made in the control areas of two facilities to absorb the demand created. Community leaders and other social actors were engaged as influencers for demand creation as well as to hold service providers accountable. This qualitative research was part of a larger mixed methods study and only the qualitative results are presented. In this paper, we explore the barriers to health care seeking that were deemed persistent by the end of the intervention period following a similar assessment at baseline. METHODS: An exploratory qualitative research design with participatory approach was undertaken as part of an impact evaluation of an innovation project in three sites (two interventions and one control). Semi-structured interviews were conducted with women who had given birth during the intervention period. Focus group discussions were conducted among the wider community members and key informant interviews among healthcare managers and other stakeholders. Participants were purposively selected. Data were analysed using content analysis by reading through transcripts. Interview data from different sources on a single event were triangulated to increase the internal validity and analysis of multiple cases strengthened external validity. RESULTS: Three themes were pre-established: 1) barriers and solutions to MNCH use at the community and health system level; 2) perceptions about women delivering in health facilities and 3) community/social norms on using health facilities. Generally, participants reported satisfaction with services offered in the intervention health facilities and many indicated that they would use the services again. There were notable differences between the intervention and control site in attitudes towards use of services (skilled birth attendance, postnatal care). Despite the apparent improvements, there still exist barriers to MNCH services use. Persistent barriers identified were gender of service provider, insecurity, poverty, lack of transport, distance from health facilities, lack of information, absence of staff especially at night-time and quality of maternity care. CONCLUSION: Attitudes towards MNCH services are generally positive, however some barriers still hinder utilization. The County health department and community leaders need to sustain the momentum gained by ensuring that service access and quality challenges are continually addressed.

"If there are no female nurses to attend to me, I will just go and deliver at home": a qualitative study in Garissa, Kenya.

BACKGROUND: The North Eastern region in Kenya experiences challenges in the utilization of maternal and newborn health services. In this region, culture and religion play a major role in influencing healthcare seeking behaviour of the community. This study was conducted to (i) understand key inherent barriers to health facility delivery in the Somali community of North Eastern Kenya and (ii) inform interventions on specific needs of this community. METHODS: The study was conducted among community members of Garissa sub-County as part of a baseline assessment before the implementation of an intervention package aimed at creating demand and increasing utilization of maternal and newborn services. Focus group discussions and key informant interviews were conducted with clan leaders, Imams, health managers, member of the county assembly, and service users (women and men) in three locations of Garissa sub-County. Data were analysed through content analysis, by coding recurrent themes and pre-established themes. RESULTS: Using health facility for delivery was widely acceptable and most respondents acknowledged the advantages and benefits of skilled birth delivery. However, a commonly cited barrier in using health facility delivery was the issue of male nurses and doctors attending to women in labour. According to participants, it is against their culture and thus a key disincentive to using maternity services. Living far from the health facility and lack of a proper and reliable means of transportation was also highlighted as a reason for home delivery. At the health facility level, respondents complained about the poor attitude of health care providers, especially female nurses being disrespectful; and the limited availability of healthcare workers, equipment and supplies. Lack of awareness and information on the importance of skilled birth attendance was also noted. CONCLUSION: To increase health facility delivery, interventions need to offer services that take into consideration the sociocultural aspect of the recipients. Culturally acceptable and sensitive services, and awareness on the benefits of skilled birth attendance among the community members are likely to attract more women to use maternity services and thus reduce adverse maternal and newborn health outcomes.

Assessment of iron status among preschool children (6 to 59 months) with and without malaria in Western Province, Kenya.

INTRODUCTION: Iron deficiency is a major public health concern. Globally, iron deficiency ranks number 9 and is responsible for about 60% of all anemia cases among preschool children. In Africa iron deficiency is 43-52% while in Kenya, children under 5 years constitute the largest burden with 69% of them being deficient. There is limited iron deficiency data in Kenya. This study determined haemoglobin levels, serum ferritin levels, nutritional status and P.falciparum malaria infection in preschool children. METHODS: A household cross sectional study was undertaken among 125 preschoolers in Western province, drawn from 37 clusters. Systematic random sampling was used for sample selection. Data was collected using pretested structured questionnaires, entered in Microsoft package. Data analysis was done in Statistical package for social science (SPSS) version 20 using bivariate and multivariate logistic regression and differences were considered significant at P < 0.05. RESULTS: The prevalence of iron deficiency (Serum ferritin <12mg/l), anaemia (Hb < 110g/l) and plasmodium falciparum malaria were 20.8%, 25% and 6.8% respectively. There was a significant association between iron deficiency and anaemia (OR = 3.43, 95% CI: 1.33-8.84, p = 0.008). A preschool child with anaemia was 3.43 times likely to be iron deficient compared to a preschool child who was not anaemic. CONCLUSION: Iron deficiency, anaemia and plasmodium falciparum malaria was prevalent among preschool children. The findings revealed a significant association between iron deficiency and anaemia. Therefore effective interventions to improve iron status will have large health benefits by greatly reducing anaemia in preschool children.