UltraPath – Pipeline for in cellulo ultrastructure determination of dynamic host-pathogen interactions

Pathogens invade host cells to establish niches and propagate via complex pathogen-host cell interaction. The molecular and cellular determinants of these highly dynamic events are mostly studied through high-resolution fluorescent microscopy that cannot resolve individual molecules.

Newly developed cryo-EM pipelines (cryo-FIB/SEM followed by tomography), provide in cellulo ultrastructural information in a close to native state. Cryo-EM projects can be facilitated through 6 specific fluorescent markers by cryo-Correlative Light Electron Microscopy (cryo-CLEM) pipelines that provides structural and functional information of intracellular pathogens in their native cellular environments. High throughput and reproducibility remain the bottleneck for cryo-CLEM projects.

UltraPath uses the intracellular lifestyle of Shigella flexneri and Legionella pneumophila in infected as well as other important pathogen models such as the emerging SARS-CoV-2 and the transport of pathogenic amyloid proteins cells as proof-of-concept model to overcome the main bottlenecks of cryo-CLEM. This will provide the scientific community with a reliable pipeline combining high resolution light microscopy on patterned cells, automated cryo-FIB milling and tomography.