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:BackgroundThe aim of this systematic review was to evaluate the evidence and clinical outcomes of screening interventions and implementation trials in sub-Saharan Africa (SSA) and also appraise some ethical issues related to screening in the region through quantitative and qualitative narrative synthesis of the literature.MethodsWe searched Pubmed, OvidMEDLINE, Embase, and Web of Science to identify studies published on breast cancer screening interventions and outcomes in SSA. Descriptive statistics were used to summarize the frequency and proportions of extracted variables, and narrative syntheses was used to evaluate the clinical outcomes of the different screening modalities. The mixed methods appraisal tool was used to assess the quality of studies included in the review.ResultsFifteen studies were included, which consisted of 72,572 women in ten countries in SSA. 63% (8/15) of the included publications evaluated Clinical Breast Examination (CBE), 47% (7/15) evaluated mammography and 7% (1/15) evaluated ultrasound screening. The cancer detection rate was < 1/1000 to 3.3/1000 and 3.3/100 to 56/1000 for CBE and mammography screening respectively. There was a lot of heterogeneity in CBE methods, target age for screening and no clear documentation of screening interval. Cost-effective analyses showed that CBE screening linked to comprehensive cancer care is most cost effective. There was limited discussion of the ethics of screening, including the possible harms of screening in the absence of linkage to care. The gap between conducting good screening program and the appropriate follow-up with diagnosis and treatment remains one of the major challenges of screening in SSA.DiscussionThere is insufficient real-world data to support the systematic implementation of national breast cancer screening in SSA. Further research is needed to answer important questions about screening, and national and international partnerships are needed to ensure that appropriate diagnostic and treatment modalities are available to patients who screen positive.

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:IntroductionThe dynamics of intimate partner violence (IPV)-one of the world's leading public health problems-in urban Africa remain poorly understood. Yet, urban areas are key to the future of women's health in Africa.Study objectivesWe explored survivor-, partner-, and household-level correlates of prevalence rates for types of IPV in urban SSA women.MethodThe study uses DHS data from 42,143 urban women aged 15-49 in 27 SSA countries. Associations at the bivariate level were examined using the Pearson Chi-square test. The modified Poisson regression test estimated the relative prevalence of IPV subtypes in the study population at the multivariate level.ResultsApproximately 36% of women in urban SSA experienced at least one form of IPV; 12.8% experienced two types; and 4.6% experienced all three types. SSA urban women who had only primary-level education, had 3 or more living children, were informally employed, were in polygynous unions, or who approved of wife-beating similarly displayed higher adjusted prevalence rates for all three forms of IPV compared respectively to their counterparts without formal education, without a living child, were unemployed, in monogamous unions, or who do not approve of wife-beating. On the other hand, the region's urban women who began cohabiting between ages 25 and 35 years or who lived in higher wealth households showed consistently lower adjusted prevalence rates for all three forms of IPV relative to their counterparts who began cohabiting before 18 years or who lived in lower wealth households. Compared to their counterparts without formal education, without a living child, or whose partners did not have formal education, women with secondary and higher education, with 1-2 living children, or whose partners had only primary level schooling displayed higher adjusted prevalence rates for both IPEV and IPPV, but not for IPSV. However, relative to their counterparts whose partners were aged 25 years or below, living with a partner aged 40 years and above was associated with statistically significant reduced prevalence rates for IPPV and IPSV, but not for IPEV. Only for IPPV did women with partners educated at secondary and above levels display statistically significant higher adjusted prevalence rates relative to their counterparts with uneducated partners. Also, solely for IPPV did women who began cohabiting between ages 18 and 24 years or whose partners were employed (whether formally or informally) show decreased adjusted prevalence rates relative to their counterparts who started cohabiting before 18 years or whose partners were unemployed. In addition, only for IPSV did women aged 40 years and above or living in middle wealth households show statistically significant reduced adjusted prevalence rates relative to their counterparts aged less than 25 years or living in lower wealth households.Discussion and conclusionBy 2030, the majority of SSA women will be urban dwellers. Complexities surround IPV in urban SSA, highlighting the unique dynamics of the problem in this setting. While affirming the link between IPV and marital power inequities and dynamics, findings suggest that the specific correlates of prevalence rates for different IPV sub-types in urban SSA women can, at once, be both similar and unique. The contextual drivers of the differences and similarities in the correlates of the prevalence rates of IPV sub-types among the region's urban women need further interrogation.

Project description:BackgroundSub-Saharan African (SSA) countries are experiencing rapid transitions with increased life expectancy. As a result the burden of age-related conditions such as neurodegenerative diseases might be increasing. We conducted a systematic review of published studies on common neurodegenerative diseases, and HIV-related neurocognitive impairment in SSA, in order to identify research gaps and inform prevention and control solutions.MethodsWe searched MEDLINE via PubMed, 'Banque de Données de Santé Publique' and the database of the 'Institut d'Epidemiologie Neurologique et de Neurologie Tropicale' from inception to February 2013 for published original studies from SSA on neurodegenerative diseases and HIV-related neurocognitive impairment. Screening and data extraction were conducted by two investigators. Bibliographies and citations of eligible studies were investigated.ResultsIn all 144 publications reporting on dementia (n = 49 publications, mainly Alzheimer disease), Parkinsonism (PD, n = 20), HIV-related neurocognitive impairment (n = 47), Huntington disease (HD, n = 19), amyotrophic lateral sclerosis (ALS, n = 15), cerebellar degeneration (n = 4) and Lewy body dementia (n = 1). Of these studies, largely based on prevalent cases from retrospective data on urban populations, half originated from Nigeria and South Africa. The prevalence of dementia (Alzheimer disease) varied between <1% and 10.1% (0.7% and 5.6%) in population-based studies and from <1% to 47.8% in hospital-based studies. Incidence of dementia (Alzheimer disease) ranged from 8.7 to 21.8/1000/year (9.5 to 11.1), and major risk factors were advanced age and female sex. HIV-related neurocognitive impairment's prevalence (all from hospital-based studies) ranged from <1% to 80%. Population-based prevalence of PD and ALS varied from 10 to 235/100,000, and from 5 to 15/100,000 respectively while that for Huntington disease was 3.5/100,000. Equivalent figures for hospital based studies were the following: PD (0.41 to 7.2%), ALS (0.2 to 8.0/1000), and HD (0.2/100,000 to 46.0/100,000).ConclusionsThe body of literature on neurodegenerative disorders in SSA is large with regard to dementia and HIV-related neurocognitive disorders but limited for other neurodegenerative disorders. Shortcomings include few population-based studies, heterogeneous diagnostic criteria and uneven representation of countries on the continent. There are important knowledge gaps that need urgent action, in order to prepare the sub-continent for the anticipated local surge in neurodegenerative diseases.

Dataset Information

Risk Factors for Infectious Diseases in Urban Environments of Sub-Saharan Africa: A Systematic Review and Critical Appraisal of Evidence.

Publications

Risk Factors for Infectious Diseases in Urban Environments of Sub-Saharan Africa: A Systematic Review and Critical Appraisal of Evidence.

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