Many pathogens infect the host via the intestine. We use a combination of whole animal imaging approaches together with defined tissue-based assays to investigate how virulence factors integrate during colonisation and infection. While remaining extracellular the human pathogens enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC respectively) and the mouse pathogen Citrobacter rodentium establish direct links with the cytoskeleton of the target epithelial cell leading to formation of actin- and cytokeratin-rich pedestals underneath attached bacteria. In these microorganisms effector proteins are translocated to the cytosol of the host cell through a type III secretion system (TTSS). TTSS is common among human, animal and plant pathogens and consists of a multi protein assembly, referred to as the needle complex, which spans the bacterial cell wall. The TTSS of EPEC, EHEC and C. rodentium is unique as one of the translocator proteins, EspA, form a filamentous extension to the needle complex. By expressing EspAEHEC in EPEC we have now demonstrated the mechanism by which monomeric EspA subunits are polymerised to form a hollow filament. Recently, a number of new type III effector proteins were identified in EHEC, EPEC and C. rodentium; their contribution to infection and colonisation will be discussed