The evolution of mobile genetic elements in Gram-negative bacteria

Bacterial genomes can adapt by small changes in individual genes and by structural rearrangements, including new genes which travel between genomes on mobile genetic elements. Structural variation is of particular importance for antimicrobial resistance (AMR). With older DNA sequencing technologies, genomes were incomplete and fragmented. Now, complete genomes are common: the challenge is to understand structural variation. I will use structural variation in bacterial genomes to help us understand their recent evolutionary history. I have developed a promising approach to extract shared sequence patterns from diverse regions around AMR genes. I will extend this and develop models of the underlying processes. I will test specific hypotheses about natural selection in bacterial genomes: between mobile 'parasites' and their genome 'hosts'. By using my computational methods for clinically relevant examples, I will help to understand the evolution and spread of AMR. Making software freely available will allow others to do the same.