Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Project description:IntroductionYouth engagement in HIV research is generally recognized as essential, but often neglected or minimally implemented in practice. Engagement is a process of working collaboratively with diverse groups of people to address common issues. We conducted a scoping review of youth HIV prevention interventions in sub-Saharan Africa to identify and categorize forms and levels of youth engagement across the lifespan of intervention research.MethodsWe followed Arksey and O'Malley's framework for organizing a scoping review. We searched seven databases for related articles on identified intervention studies through May 28th 2020. Included studies focused on youth (10 to 24 years old) HIV prevention interventions in sub-Saharan Africa. Two reviewers independently examined citations and full manuscripts for inclusion. Data were extracted on study characteristics, location, description of youth engagement and extent of engagement. Youth engagement approaches were categorized based on Hart's ladder as substantial engagement (strong youth decision-making power), moderate engagement (shared decision making with adults), minimal engagement (no youth decision-making power) or no engagement.ResultsWe identified 3149 citations and included 112 studies reporting on 74 unique HIV interventions. Twenty-two interventions were in low-income countries, 49 in middle-income countries, and three were in both. Overall, only nine interventions (12%) had substantial or moderate youth engagement, two-thirds (48, 65%) had minimal youth engagement and 17 interventions (23%) had no youth engagement. We also identified specific engagement strategies (e.g. youth-led research, crowdsourcing) that were feasible in multiple settings and resulted in substantial engagement.ConclusionsWe found limited youth engagement in youth HIV prevention intervention studies in sub-Saharan Africa. However, several activities resulted in substantial youth engagement and could be relevant in many low-and-middle-income-country (LMIC) settings.

Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects

Project description:Background:Non-communicable diseases (NCDs) cause a large and growing burden of morbidity and mortality in sub-Saharan Africa. Prospective cohort studies are key to study multiple risk factors and chronic diseases and are crucial to our understanding of the burden, aetiology and prognosis of NCDs in SSA. We aimed to identify the level of research output on NCDs and their risk factors collected by cohorts in SSA. Methods:We conducted a scoping review to map the extent of current NCDs research in SSA by identifying studies published after the year 2000 using prospectively collected cohort data on any of the six NCDs (cardiovascular diseases, diabetes, obesity, chronic kidney disease, chronic respiratory diseases, and cancers), ≥1 major risk factor (other than age and sex), set only within SSA, enrolled ≥500 participants, and ≥12 months of follow-up with ≥2 data collection points (or with plans to). We performed a systematic search of databases, a manual search of references lists from included articles and the INDEPTH network website, and study investigators from SSA were contacted for further articles. Results:We identified 30 cohort studies from the 101 included articles. Eighteen countries distributed in West, Central, East and Southern Africa, were represented. The majority (27%) set in South Africa. There were three studies including children, twenty with adults, and seven with both. 53% of cohorts were sampled in general populations, 47% in clinical populations, and 1 occupational cohort study. Hypertension (n = 23) was most commonly reported, followed by obesity (n = 16), diabetes (n = 15), CKD (n = 6), COPD (n = 2), cervical cancer (n = 3), and breast cancer (n = 1). The majority (n = 22) reported data on at least one demographic/environmental, lifestyle, or physiological risk factor but these data varied greatly. Conclusions:Most studies collected data on a combination of hypertension, diabetes, and obesity and few studies collected data on respiratory diseases and cancer. Although most collected data on different risk factors the methodologies varied greatly. Several methodological limitations were found including low recruitment rate, low retention rate, and lack of validated and standardized data collection. Our results could guide potential collaborations and maximize impact to improve our global understanding of NCDs (and their risk factors) in SSA and also to inform future research, as well as policies.

Project description:Background Cancer remains a major public health problem, especially in Sub-Saharan Africa (SSA) where the provision of health care is poor. This scoping review mapped evidence in the literature regarding the burden of cervical, breast and prostate cancers in SSA. Methods We conducted this scoping review using the Arksey and O'Malley framework, with five steps: identifying the research question; searching for relevant studies; selecting studies; charting the data; and collating, summarizing, and reporting the data. We performed all the steps independently and resolved disagreements through discussion. We used Endnote software to manage references and the Rayyan software to screen studies. Results We found 138 studies that met our inclusion criteria from 2,751 studies identified through the electronic databases. The majority were retrospective studies of mostly registries and patient files (n = 77, 55.8%), followed by cross-sectional studies (n = 51, 36.9%). We included studies published from 1990 to 2021, with a sharp increase from 2010 to 2021. The quality of studies was overall satisfactory. Most studies were done in South Africa (n = 20) and Nigeria (n = 17). The majority were on cervical cancer (n = 93, 67.4%), followed by breast cancer (67, 48.6%) and the least were on prostate cancer (48, 34.8%). Concerning the burden of cancer, most reported prevalence and incidence. We also found a few studies investigating mortality, disability-adjusted life years (DALYs), and years of life lost (YLL). Conclusions We found many retrospective record review cross-sectional studies, mainly in South Africa and Nigeria, reporting the prevalence and incidence of cervical, breast and prostate cancer in SSA. There were a few systematic and scoping reviews. There is a scarcity of cervical, breast and prostate cancer burden studies in several SSA countries. The findings in this study can inform policy on improving the public health systems and therefore reduce cancer incidence and mortality in SSA.

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The interplay of HIV and human papillomavirus-related cancers in sub-Saharan Africa: scoping review.

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