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: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:Housing is essential to human well-being but neglected in global health. Today, housing in Africa is rapidly improving alongside economic development, creating an urgent need to understand how these changes can benefit health. We hypothesised that improved housing is associated with better health in children living in sub-Saharan Africa (SSA). We conducted a cross-sectional analysis of housing conditions relative to a range of child health outcomes in SSA. METHODS AND FINDINGS:Cross-sectional data were analysed for 824,694 children surveyed in 54 Demographic and Health Surveys, 21 Malaria Indicator Surveys, and two AIDS Indicator Surveys conducted in 33 countries between 2001 and 2017 that measured malaria infection by microscopy or rapid diagnostic test (RDT), diarrhoea, acute respiratory infections (ARIs), stunting, wasting, underweight, or anaemia in children aged 0-5 years. The mean age of children was 2.5 years, and 49.7% were female. Housing was categorised into a binary variable based on a United Nations definition comparing improved housing (with improved drinking water, improved sanitation, sufficient living area, and finished building materials) versus unimproved housing (all other houses). Associations between house type and child health outcomes were determined using conditional logistic regression within surveys, adjusting for prespecified covariables including age, sex, household wealth, insecticide-treated bed net use, and vaccination status. Individual survey odds ratios (ORs) were pooled using random-effects meta-analysis. Across surveys, improved housing was associated with 8%-18% lower odds of all outcomes except ARI (malaria infection by microscopy: adjusted OR [aOR] 0.88, 95% confidence intervals [CIs] 0.80-0.97, p = 0.01; malaria infection by RDT: aOR 0.82, 95% CI 0.77-0.88, p < 0.001; diarrhoea: aOR 0.92, 95% CI 0.88-0.97, p = 0.001; ARI: aOR 0.96, 95% CI 0.87-1.07, p = 0.49; stunting: aOR 0.83, 95% CI 0.77-0.88, p < 0.001; wasting: aOR 0.90, 95% CI 0.83-0.99, p = 0.03; underweight: aOR 0.85, 95% CI 0.80-0.90, p < 0.001; any anaemia: aOR 0.87, 95% CI 0.82-0.92, p < 0.001; severe anaemia: aOR 0.89, 95% CI 0.84-0.95, p < 0.001). In comparison, insecticide-treated net use was associated with 16%-17% lower odds of malaria infection (microscopy: aOR 0.83, 95% CI 0.78-0.88, p < 0.001; RDT: aOR 0.84, 95% CI 0.79-0.88, p < 0.001). Drinking water source and sanitation facility alone were not associated with diarrhoea. The main study limitations are the use of self-reported diarrhoea and ARI, as well as potential residual confounding by socioeconomic position, despite adjustments for household wealth and education. CONCLUSIONS:In this study, we observed that poor housing, which includes inadequate drinking water and sanitation facility, is associated with health outcomes known to increase child mortality in SSA. Improvements to housing may be protective against a number of important childhood infectious diseases as well as poor growth outcomes, with major potential to improve children's health and survival across SSA.

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Health technology assessment in sub-Saharan Africa: a descriptive analysis and narrative synthesis.

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