Using whole genome sequencing to understand the evolution of Shigella and enteroinvasive E. coli

Shigella and enteroinvasive E. coli (EIEC) are important human pathogens that cause severe diarrhoea and dysentery. Despite the fact that they are named differently, Shigella species and EIEC belong within the broader Escherichia coli group. Each Shigella species and EIEC lineage have independently acquired very similar disease phenotypes via convergent evolution. A hallmark of this adaptation is the acquisition of a virulence plasmid, gene loss, and as a result, loss of various metabolic pathways. Within Shigella and EIEC, gene loss is often mediated by insertion sequences (IS) – small, transposable elements that are ubiquitous in Shigella and EIEC genomes. Comparative genomic analyses is a powerful approach for understanding how bacterial pathogens evolve. In this project, the student will apply the latest genomics analysis approaches to investigate IS and their role in gene loss and metabolic pathway loss in different Shigella and EIEC lineages, using an existing framework that we have already developed. The student will compare and contrast the lineages to one another and to the broader E. coli group. The outcomes of this project will improve our understanding of the less well-studied Shigella and EIEC lineages. Projects in this space could be refined to accommodate projects of varying length. A student undertaking this project would gain skills in genomics, phylogenetic analysis, and metabolic modelling. This project is best suited for students interested in the application of computational biology approaches (including command-line programs) to analyse and interpret large datasets. Specific analysis approaches will include de novo genome assembly and annotation, reference-based variant detection, BLAST search and phylogenetics.