We aim at detecting the emergence of pathogenic bacterial strains and understanding microevolutionary events, including mobility of genetic elements, which favoured emergence. We investigate population genetic structure and strain diversity within species by combining epidemiological, genomic and phenotypic approaches. We study two main models. The first is Klebsiella pneumoniae, a member of the Enterobacteriaceae family that causes multidrug resistant infections in hospitals and severe invasive infections including liver abscess, pneumonia and meningitis in non-hospitalized persons. The second is Listeria monocytogenes, a food-borne pathogen that causes invasive infections with a high fatality rate in populations at risk including pregnant woman and the elderly.