An analytical journey from pathogen genetics to epidemiology
Recent years have seen a fantastic increase in the feasibility of sequencing whole bacterial genomes from many isolates. The availability of this data has huge potential to help us learn more about the evolution and epidemiology of bacterial pathogens, but the analytical methodology has been lacking behind the sequencing technology. Here we present a scalable approach for such analysis, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. We will describe how dated phylogenies can be constructed, and how they can be used for both fine-scale and large-scale epidemiological analysis.
