EXCELLGEN · What to expect of ExPEC: is the success of extraintestinal pathogenic E. coli linked to specific genomic and cellular properties?

Extraintestinal pathogenic E. coli (ExPEC) are one of the greatest challenges for the healthcare system, with a frightening prognosis for the future. Despite being heavily studied in recent years, no unifying principle explaining their success has been identified. Only limited attention has been paid to the additional genomic properties of ExPEC strains that are not virulence factors or antimicrobial resistance genes. I aim to demonstrate that these additional genomic features lead to alterations in cellular features (related to physiology, growth ability and metabolism) that contribute to ExPEC (pathogenic) success. To do so, I will first setup a database of ExPEC specific regions and use this to perform an unbiased large-scale screen comparing them to publicly available E. coli genomes. This analysis will yield specific genomic regions that can be confidently assigned to ExPEC or ExPEC subgroups. To further demonstrate the biological significance of these regions, high-throughput single-cell phenomics will be employed to quantitatively examine specific strains of interest across different growth conditions and identify the genes or groups of genes present in the ExPEC specific regions associated with specific phenotypic alterations. Finally, the identified genomic regions will be further characterized using a deep mutational scanning approach to uncover the exact molecular mechanisms that underlie phenotypic alterations of pathogenic strains in comparison to their non-pathogenic counterparts. I expect this project to bring much-needed insights into ExPEC physiology, linking it with its specific genomic background. Such fundamental knowledge will contribute to managing ExPEC more effectively in the future.