Publications Details
Predictive Pathogen Biology: Genome-Based Prediction of Pathogenic Potential and Countermeasures Targets
Bacterial pathogens have numerous processes by which their genomic DNA is acquired or rearranged as part of their normal physiology (e.g., exchange of plasmids through conjugation) or by bacteriophage that parasitize bacteria and often insert into the bacterial genome as prophages. These processes occur with relatively high probability/frequency, and may lead to sudden changes in virulence, as new genetic material is added to the chromosome, or structural changes in the chromosome affect gene expression. We set out to devise methods to measure the rates of these processes in bacteria using next generation DNA sequencing. Using very deep sequencing on genomes we had assembled, using library preparation methods and bioinformatics tools designed to help find mobile elements and signs of their insertion, we were able to find numerous examples of attempted novel genome arrangements, revealing data that can be used to calculate rates of different mechanisms of genome change.