Determinants of the Divergent Salmonella and Shigella Epithelial Colonization Strategies Resolved in Human Enteroids and Colonoids

Despite close relatedness, the major enteropathogens Salmonella and Shigella differ in infectious dose, pathogenesis, and disease kinetics. The prototype strains Salmonella enterica serovar Typhimurium (Salmonella) and Shigella flexneri (Shigella) use Type-3-secretion-systems (T3SSs) to colonize intestinal epithelial cells (IECs), but have evolved partially unique sets of T3SS effectors and accessory virulence factors. A synthesis of how these differences impact the temporal progression of infection in non-transformed human epithelia is missing. Here, we followed Salmonella and Shigella infections of human enteroids and colonoids by time-lapse imaging to pinpoint virulence factor modules that shape the divergent epithelial colonization strategies. By an apical targeting module that integrates flagella and the SPI-4-encoded adhesin system with T3SS, Salmonella accomplishes appreciable numbers of apical invasion events, promptly terminated by IEC death, and thus fostering a polyclonal iterative epithelial colonization strategy. The lack of a corresponding module in Shigella makes this pathogen reliant on external factors such as preexisting damage for rare apical access to the intraepithelial environment. However, Shigella compensates for this ineptness by an intraepithelial expansion module, where tight coupling of OspC3-dependent temporal delay of cell death and IcsA-mediated lateral spread enables intraepithelial Shigella to outrun the IEC death response, fostering an essentially monoclonal colonization strategy.