Genome-scale analysis of pathogenic Escherichia coli (360G-Wellcome-099830_Z_12_Z)

The aim of this project is to identify Escherichia coli gene signatures which can be used to classify pathogenic strains. Recent outbreaks have shown that there is a need for rapid identification and subtyping of pathogenic strains in real time. We will construct and leverage the power of the E. coli pan genome by grouping all genes across the available E. coli genomes (environmental, pathogenic and commensal strains) into core, accessory and distributed gene sets. This will define an E. coli species-wide gene pool which will facilitate the detection of gene combinations associated with pathogenic strains. The incorporation of genome data from other species that display similar modes of infection or inhabit similar environments will generate corss species correlog information and widen the scope of our findings. In addition to the pan genomic approach, the methylation profile of E. coli serotypes will be determined using SMRT sequencing to provide insights into the role methylation plays in virulence. The project will mostly consist of bioinformatics analysis with lab work including the preparation of samples and validation of bioinformatics findings.