Applying Rapid Genome Sequencing Technologies To Characterize Pathogen Genomes

R ecent predictions of the worldwide burden of diseases under a variety of scenarios sug-gest that infectious diseases will continue to negatively impact the health of human populations well into the fu-ture (1). Although economic, social, and technological developments will surely influence these projections, the impact of the constantly changing interaction between hosts and infectious agents is rarely considered. Throughout evolutionary history, human populations were selected to develop immune responses to micro-bial challenges. The resulting human adaptations then caused pathogen populations to develop resistance via mechanisms such as antigenic variation to evade the immune system. The human host, in turn, coun-teradapted to the pathogens, not only with genetic changes but also with technologies, such as vaccines and therapeutics, that better recognize and combat the more virulent pathogens. This pattern of host–pathogen coevolution, where changes in allele frequencies in one population exert selection pressures af-fecting allele frequencies in the other population, creates a complex evolutionary arms race whose course may be difficult to predict (2). Analyzing pathogen and host genomes can elucidate the mecha-nisms underlying novel adaptations that arise as a consequence of this ongoing evolutionary arms race. Pathogen genomes, because of their relatively small size, were the first to be completely sequenced and have provided researchers fundamental insights into the biology of the organisms, evolutionary relationships, and the determinants of virulence (3)