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:BackgroundMost cancers in sub-Saharan Africa (SSA) are diagnosed at advanced stages, with limited treatment options and poor outcomes. Part of this may be linked to various events occurring in patients' journey to diagnosis. Using the model of pathways to treatment, we examined the evidence regarding the routes to cancer diagnosis in SSA.Design and settingsA systematic review of available literature was performed.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. Between 30 September and 30 November 2019, seven electronic databases were searched using terms relating to SSA countries, cancer and routes to diagnosis comprising the population, exposure and outcomes, respectively. Citation lists of included studies were manually searched to identify relevant studies. Furthermore, ProQuest Dissertations & Theses Global was searched to identify appropriate grey literature on the subject.Results18 of 5083 references identified met the inclusion criteria: eight focused on breast cancer; three focused on cervical cancer; two each focused on lymphoma, Kaposi's sarcoma and childhood cancers; and one focused on colorectal cancer. With the exception of Kaposi's sarcoma, definitive diagnoses were made in tertiary healthcare centres, including teaching and regional hospitals. The majority of participants initially consulted within primary care, although a considerable proportion first used complementary medicine before seeking conventional medical help. The quality of included studies was a major concern, but their findings provided important insight into the pathways to cancer diagnosis in the region.ConclusionThe proportion of patients who initially use complementary medicine in their cancer journey may explain a fraction of advanced-stage diagnosis and poor survival of cancer in SSA. However, further research would be necessary to fully understand the exact role (or activities) of primary care and alternative care providers in patient cancer journeys.

Dataset Information

LAMP-enabled diagnosis of Kaposi's sarcoma for sub-Saharan Africa.

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LAMP-enabled diagnosis of Kaposi's sarcoma for sub-Saharan Africa.

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