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Longitudinal expression analysis during acquisition of Mycobacterium tuberculosis infection in adolescents from South Africa

ABSTRACT: Longitudinal expression analysis during acquisition of Mycobacterium tuberculosis infection in adolescents from South Africa

PROVIDER: PRJNA476788 | ENA |

REPOSITORIES: ENA

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Longitudinal expression analysis during acquisition of Mycobacterium tuberculosis infection in adolescents from South Africa

Project description:Time-course expression analysis profiling whole blood samples collected from healthy South African adolescents while monitoring their potential acquisition of a Mycobacterium tuberculosis infection.

2018-08-18 | GSE116014 | GEO

Genotyping of 75 individuals from the Afrikaner population of South Africa

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.

2020-01-28 | E-MTAB-8757 | biostudies-arrayexpress

Soil South Africa

Project description:Soil South Africa Raw sequence reads

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paediatric atopic dermatitis in South Africa

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Mukandavire2020 - SEIR model of early COVID-19 transmission in South Africa

Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.

2024-09-02 | BIOMD0000000978 | BioModels

Characterization of plasmids mediating carbapenem resistance in Klebsiella pneumoniae in Pretoria, South Africa

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.

2019-10-17 | GSE138949 | GEO

Carbapenem-resistant Klebsiella pneumoniae South Africa

Project description:Carbapenem-resistant Klebsiella pneumoniae South Africa

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Isoniazid resistant TB in South Africa

Project description:Isoniazid resistant TB in South Africa

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mRNA expression changes in chicken livers associated with field exposure to DDTs in KwaZulu-Natal, South Africa

Project description:Free-range chickens were sampled from homesteads in South Africa where DDT is sprayed for malaria control. The purpose was to detect potential effects associated with contamination. Livers were sampled post-mortem & analysed for DDTs (DDT and metabolites) contamination. Samples from two birds were further processed by microarray analysis – one with a relatively low (1,116.0 ng/g wet weight; sample SA1) and one with a relatively high (1,938.0 ng/g wet weight; sample SA2) level of contamination by DDTs.

2018-10-16 | E-MTAB-7130 | biostudies-arrayexpress

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