Bacterial pathogenomics

Genomes from all of the crucial bacterial pathogens of humans, plants and animals have now been sequenced, as have genomes from many of the important commensal, symbiotic and environmental microorganisms. Analysis of these sequences has revealed the forces that shape pathogen evolution and has brought to light unexpected aspects of pathogen biology. The finding that horizontal gene transfer and genome decay have key roles in the evolution of bacterial pathogens was particularly surprising. It has also become evident that even the definitions for ‘pathogen ’ and ‘virulence factor ’ need to be re-evaluated. The sequencing of bacterial genomes (see Glossary) has occurred against the backdrop of an established programme of research on bac-terial pathogenesis. Nonetheless, it has uncovered aspects of pathogen biology that were unexpected before the genomic revolution. Here, we examine the ‘creative clash ’ between genomic research and bac terial pathogenesis research, an encounter that has spawned new technolo-gies and new avenues for applied research. In addition, we discuss the forces that have shaped the evolution of bacterial pathogens, and we reappraise human–pathogen interactions in the light of bacteria