Once considered to be contained, infectious diseases of bacterial origin ar
e now making a comeback. A lack of innovative therapies and the appearance
of drug-resistant pathogens are becoming increasingly serious problems. A b
etter understanding of pathogen-host interactions at the cellular and molec
ular levels is necessary to define new targets in our fight against microor
ganisms. In the past few years, the merging of cell biology and microbiolog
y has started to yield critical and often surprising new information on the
interactions that occur between various pathogens and their mammalian host
cells. Here we focus on the intracellular routing of vacuoles containing m
icroorganisms, as well as on the bacterial effecters and their host-cell ta
rgets that control vacuole maturation. We also describe new approaches for
isolating microorganism-containing vacuoles and analysing their molecular c
omposition, which will help researchers to define the molecules and mechani
sms governing vacuole biogenesis.