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:IntroductionSub-Saharan Africa has the highest under-five mortality rate and is among the regions where people have the least access to adequate Water, Sanitation, and Hygiene (WASH) services. The work aimed to investigate the effects of WASH conditions faced by children on under-five mortality in Sub-Saharan Africa.MethodsWe carried out secondary analyses using the Demographic and Health Survey datasets of 30 countries in Sub-Saharan Africa. The study population consisted of children born within 5 years preceding the selected surveys. The dependent variable was the child's status (1 = deceased versus 0 = alive) on the survey day. The individual WASH conditions in which children live were assessed in their immediate environment, i.e., at the level of their households of residence. The other explanatory variables were related to the child, mother, household, and environment. Following a description of the study variables, we identified the predictors of under-five mortality using a mixed logistic regression.ResultsThe analyses involved 303,985 children. Overall, 6.36% (95% CI = 6.24-6.49) of children died before their fifth birthday. The percentage of children living in households with access to individual basic WASH services was 58.15% (95% CI = 57.51-58.78), 28.18% (95% CI = 27.74-28.63), and 17.06% (95% CI = 16.71-17.41), respectively. Children living in households using unimproved water facilities (aOR = 1.10; 95% CI = 1.04-1.16) or surface water (aOR = 1.11; 95% CI = 1.03-1.20) were more likely to die before five than those coming from households with basic water facilities. The risk of under-five mortality was 11% higher for children living in households with limited sanitation facilities (aOR = 1.11; 95% CI = 1.04-1.18) than for those with basic sanitation services. We found no evidence to support a relationship between household access to hygiene services and under-five mortality.ConclusionInterventions to reduce under-five mortality should focus on strengthening access to basic water and sanitation services. Further studies are needed to investigate the contribution of access to basic hygiene services on under-five mortality.

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

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Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa.

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Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa.

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