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:Introduction: For the COVID-19 (SARS-CoV-2) response, COVID-19 antigen (Ag), and antibody (Ab) rapid diagnostic tests (RDTs) are expected to complement central molecular testing particularly in low-resource settings. The present review assesses requirements for implementation of COVID-19 RDTs in sub-Saharan Africa. Methods: Review of PubMed-published articles assessing COVID-19 RDTs complemented with Instructions for Use (IFU) of products. Results: In total 47 articles on two COVID-19 Ag RDTs and 54 COVID-19 Ab RDTs and IFUs of 20 COVID-19 Ab RDTs were retrieved. Only five COVID-19 Ab RDTs (9.3%) were assessed with capillary blood sampling at the point-of-care; none of the studies were conducted in sub-Saharan Africa. Sampling: Challenges for COVID-19 Ag RDTs include nasopharyngeal sampling (technique, biosafety) and sample stability; for COVID-19 Ab RDTs equivalence of whole blood vs. plasma/serum needs further validation (assessed for only eight (14.8%) products). Sensitivity-Specificity: sensitivity of COVID-19 Ag and Ab RDTs depend on viral load (antigen) and timeframe (antibody), respectively; COVID-19 Ab tests have lower sensitivity compared to laboratory test platforms and the kinetics of IgM and IgG are very similar. Reported specificity was high but has not yet been assessed against tropical pathogens. Kit configuration: For COVID-19 Ag RDTs, flocked swabs should be added to the kit; for COVID-19 Ab RDTs, finger prick sampling materials, transfer devices, and controls should be added (currently only supplied in 15, 5, and 1/20 products). Usability and Robustness: some COVID-19 Ab RDTs showed high proportions of faint lines (>40%) or invalid results (>20%). Shortcomings were reported for buffer vials (spills, air bubbles) and their instructions for use. Stability: storage temperature was ≤ 30°C for all but one RDT, in-use and result stability were maximal at 1 h and 30 min, respectively. Integration in the healthcare setting requires a target product profile, landscape overview of technologies, certified manufacturing capacity, a sustainable market, and a stringent but timely regulation. In-country deployment depends on integration in the national laboratory network. Discussion/Conclusion: Despite these limitations, successful implementation models in triage, contact tracing, and surveillance have been proposed, in particular for COVID-19 Ab RDTs. Valuable experience is available from implementation of other disease-specific RDTs in sub-Saharan Africa.

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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Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa.

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Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa.

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