Project description:The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the “Coloured" populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5%-7.2%. NB two individuals withdrew consent so this data contains only 75 individuals as compared to the 77 cited in the article.
Project description:The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence. Experimental Design: Whole blood collected in tempus tubes from patients with different spectra of TB disease. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum. Latent TB: LTB - All patients were screened at a tuberculosis clinic. All were positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, or microbiological evidence of active infection and were asymptomatic. Experimental Variables: Patient group: Active PTB; Latent TB. There are no healthy controls in this dataset as it was being used for validation only. Controls: Latent TB individuals are used as a control for PTB in this dataset since there are few to no unexposed adult controls in Cape Town.
Project description:The study aimed to characterize plasmids mediating carbepenem resistance in Klebsiella pneumoniae in Pretoria, South Africa. We analysed 56 K. pneumoniae isolates collected from academic hospital around Pretoria. Based on phenotypic and molecular results of these isolates, 6 representative isolates were chosen for further analysis using long reads sequencing platform. We observed multidrug resistant phenotype in all these isolates, including resistance to aminoglycosides, tetracycline, phenicol, fosfomycin, floroquinolones, and beta-lactams antibiotics. The blaOXA-48/181 and blaNDM-1/7 were manily the plasmid-mediated carbapenemases responsible for carbapenem resistance in the K. pneumoniae isolates in these academic hospitals. These carbapenemase genes were mainly associated with plasmid replicon groups IncF, IncL/M, IncA/C, and IncX3. This study showed plasmid-mediated carbapenemase spread of blaOXA and blaNDM genes mediated by conjugative plasmids in Pretoria hospitals.
Project description:The effects on respiratory health in populations living close to silica-rich gold mine dumps are unknown. This pilot study related respiratory health and exposure to mine dump dust using two measures of exposure: exposure group, based on distance lived from the mine dump-high (n = 93) (home <500 m from a mine dump), moderate (n = 133) (500-1.5 km), and low (n = 84) (>15 km, control group); and cumulative exposure index (CEI) derived from exposure group and number of years of residence in each exposure group. Participants were interviewed about respiratory symptoms and had chest X-rays and spirometry. We adjusted for key respiratory confounders. No subject had radiological features of silicosis. The high relative to low exposure group had significantly elevated adjusted odds ratios (aORs) for upper respiratory symptoms (aOR: 2.76, 95% CI: 1.28-5.97), chest wheezing (aOR: 3.78; 95% CI: 1.60-8.96), and spirometry-diagnosed chronic obstructive pulmonary disease (COPD) (aOR: 8.17; 95%CI: 1.01-65.85). These findings were similar for the high relative to medium exposure group, but no significant associations were found for the medium versus low exposure group. Chronic bronchitis and tuberculosis risks did not differ significantly among groups. CEI and exposure group produced similar results. In conclusion, residents residing <500 m from mine dumps had elevated adverse respiratory health effects.