Résumé
This chapter does not attempt to provide a comprehensive catalogue of the various methods of analysis and technologies used to characterize pathogens (molecular epidemiology). Rather it argues why molecular epidemiology should not be conceived without an extensive use of the concepts of population genetics and evolutionary biology. Moreover, it stresses that characterizing pathogens should open up to evaluating the impact of pathogens’ genetic diversity on their relevant medical properties (downstream studies). Lastly, it presents the foreseeable future developments in this field, which has been upset by the exponential development of megatechnologies (massive sequencing, postgenomic studies, and bioinformatics).