The interactions between pathogens and host cells reflect millions of years of co-evolution. For intracellular pathogens, their trafficking and the formation of their niche within targeted cells takes place through the subversion of host pathways. Furthermore, the host has evolved means to sense the incoming pathogen depending on its precise localization. The underlying host-pathogen interactions are generally very dynamic and tightly regulated. Therefore, it has been difficult to establish methodologies that can capture this crosstalk. With the “Endosubvert” project, we have developed a combination of novel approaches to monitor the dynamic host-pathogen interactions with the aim to uncover key features of the intracellular niche formation of invasive microbial pathogens. “Endosubvert” has employed microscopy-based single-cell/single-microbe analysis of the dynamics during the infection of host cells with enteroinvasive bacteria. During the project period, the “Endosubvert” project has revealed molecular links between the intracellular niche formation of the pathogens and the impact on the course of infection. We demonstrated that host cell subversion (for example through Rab GTPases of the host) is key to change the intracellular pathogen localization of Shigella and Salmonella through regulated cytosolic access. Furthermore, we identified through “Endosubvert” in situ formed host compartments that we named “infection associated macropinosomes (IAMs)”, and that play a major role for the intracellular pathogen lifecycle. We were able to compare IAMs formed during different infection processes with macropinosomes formed in the absence of pathogens. Through the “Endosubvert” project, we were able to propose a new concept, “the conditioned niche hypothesis” stating that the intracellular localization of a pathogen is not only dependent on pathogen factors, but is also driven by host cell pathways and the intracellular environment. We have made major efforts to render our toolbox of new methods available to the scientific community.
