Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC), particularly sepsis-associated E. coli (SEPEC), is a major cause of bloodstream infections and neonatal sepsis worldwide, yet its genomic landscape in sub-Saharan Africa (sSA) remains poorly understood. We hypothesize that the genomic diversity of SEPEC strains circulating in sSA is distinct from that observed in other regions and from non-SEPEC strains. To address this, we will perform a comprehensive genomic characterization of SEPEC and neonatal SEPEC isolates from sSA within the context of global SEPEC, diarrhoeal, and community strains. Leveraging publicly available sequence data, previously generated datasets from the CABU-EICU project in DR Congo and Burkina Faso, and newly curated collections, our study will: (i) describe the genomic diversity of SEPEC in sSA compared to global SEPEC and non-SEPEC strains using state-of-the-art genomic epidemiology approaches; (ii) investigate genetic determinants of pathogenicity and antimicrobial resistance, including O-antigen diversity, virulence factors, AMR genes, and plasmid replicons, to elucidate their genomic context and co-occurrence patterns; and (iii) enhance resolution of bacterial evolutionary dynamics by incorporating in silico analyses of understudied recombination events, such as tandem repeats. This work will provide critical insights into the evolution and adaptation of SEPEC in sSA, informing global strategies for surveillance, prevention, and treatment of E. coli infections.
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