The imaging of intracellular pathogens inside host cells is complicated due to low resolution and sensitivity of conventional fluorescence microscopy and the lack of ultrastructural information. Here we present a new method to visualize pathogenic bacteria during infection that circumvents these problems. By using a metabolic hijacking approach the intracellular pathogen Salmonella Typhimurium was bio-orthogonally labelled in a stochastic optical reconstruction microscopy (STORM) and correlative light electron microscopy (CLEM) compatible manner, allowing the imaging of the Salmonella-pathogen within the ultrastructural cellular context of its host cell with a resolution of 20 nm. This STORM-CLEM approach represents a new tool to understand the lifecycle of pathogenic bacteria during host cell invasion.
doi: 10.1002/cbic.201800230.