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:BackgroundHuman myiasis is a parasitic dipteran fly infestation that infects humans and vertebrates worldwide. However, the disease is endemic in Sub-Saharan Africa and Latin America. In Sub-Saharan Africa, it is under-reported and therefore its prevalence is unknown. This systematic review aims to elucidate the prevalence of human myiasis, factors that influence the infection, and myiasis-causing fly species in SSA. The review also dwelled on the common myiasis types and treatment methods of human myiasis.MethodsHere, we collect cases of human myiasis in Sub-Saharan Africa based on literature retrieved from PubMed, Google Scholar and Science Direct from 1959 to 2022. A total of 75 articles and 157 cases were included in the study. The recommendations of PRISMA 2020 were used for the realization of this systematic review.ResultsIn total, 157 cases of human myiasis in SSA were reviewed. Eleven fly species (Cordylobia anthropophaga, Cordylobia rodhaini, Dermatobia hominis, Lucilia cuprina, Lucilia sericata, Oestrus ovis, Sarcophaga spp., Sarcophaga nodosa, Chrysomya megacephala, Chrysomya chloropyga and Clogmia albipuntum) were found to cause human myiasis in SSA. Cordylobia anthropophaga was the most prevalent myiasis-causing species of the reported cases (n = 104, 66.2%). More than half of the reported cases were from travelers returning from SSA (n = 122, 77.7%). Cutaneous myiasis was the most common clinical presentation of the disease (n = 86, 54.7%). Females were more infected (n = 78, 49.6%) than males, and there was a higher infestation in adults than young children.ConclusionThe findings of this study reveals that international travelers to Sub-Saharan Africa were mostly infested therefore, we recommend that both international travelers and natives of SSA be enlightened by public health officers about the disease and its risk factors at entry points in SSA and the community level respectively. Clinicians in Sub-Saharan Africa often misdiagnose the disease and most of them lack the expertise to properly identify larvae, so we recommend the extensive use of molecular identification methods instead.

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Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.

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Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.

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