Abstract

Bacterial genomes are around 1,000 times smaller than vertebrate genomes, which suggests that we should be able to use current sequencing technologies to produce 1,000 times more bacterial genomes per run. Although this is not yet logistically feasible, using indexing protocols, deep coverage of 96 genomes per run is possible. This data can provide phylogenetic and epidemiological data at unprecedented levels of detail, allowing us to study bacterial populations at the genomic level. I will present recent data from experiments sampling collections of several hundred bacteria at global and local levels, within specific, highly related bacterial clades. These data allow us to study transmission pathways between continents and between patients, but they also give insights into population parameters such as rates of mutation and recombination within these clades. Full analysis of these data sets, and many more like them, will require novel high-throughput analysis tools.