Single-cell analysis of genetically minimized Salmonella reveals effector gene cooperation in vivo

Abstract

Bacterial pathogens such as Salmonella Typhimurium (S.Tm) can deliver large repertoires of effector proteins directly into host cells. Due to the genetic and functional redundancies found in these systems, it has been difficult to determine how individual effector proteins cooperate with one another to elicit pathogenic phenotypes in vivo. To overcome this challenge, targeted genome minimization has been used to identify small effector protein networks sufficient for S.Tm colonization of complex tissues. Here we used mass cytometry to generate a comprehensive map of minimal effector network functions at single-cell resolution. This approach revealed the temporal progression of S.Tm transmission and uncovered a CD62L+ monocyte population as a major bottleneck to cell-to-cell dissemination in the spleen. We further show how cooperation between two effector gene networks acquired during distinct episodes of bacterial evolution has shaped the cellular and tissue tropism of non-typhoidal Salmonella species. A minimal effector subset enables Salmonella Typhimurium to overcome bottlenecks regulated by the early innate immune response and establish infection within a CD62L+ monocyte niche in the spleen.