Sequence information from complete genomes, and from multiple loci of strains within species, is transforming the way that we investigate the evolution of bacteria. Such large-scale assessments of bacterial genomes have provided evidence of extensive gene transfer and exchange. Except in rare cases, these two processes do not seem to be coupled: certain species, such as Escherichia coli, undergo relatively low levels of gene exchange; but the emergence of pathogenic strains is associated with the acquisition of numerous virulence factors by lateral gene transfer.