Raw dataset: Molecular epidemiology of extraintestinal pathogenic Escherichia coli causing bloodstream infections in hospitalised patients in the healthcare sectors in Gauteng, South Africa

A total of 466 <i>E. coli</i> isolates collected from public and private healthcare facilities between 2021 and 2022 were analysed.</p><p dir="ltr">The study characterised ST131 and non-ST131 <i>E. coli</i> isolates using PCR-based methods, including ST131 clade and subclade assignment, 7-SNP-qPCR clonotyping and multiplex PCR for major sequence types.

Antimicrobial susceptibility testing and assessment of extended-spectrum beta-lactamase (ESBL) production were also performed. Selected non-ST131 isolates underwent whole genome sequencing to investigate sequence types, antimicrobial resistance genes, virulence genes, plasmid content and genetic relatedness.</p><p dir="ltr">The dataset contains the laboratory, antimicrobial susceptibility and molecular characterisation data generated during the study and provides data for investigating ExPEC lineages, antimicrobial resistance and molecular epidemiology in healthcare settings in Gauteng, South Africa.</p>