Host-associated niche metabolism enhances the expression of type 3 secretion and a co-ordinated suite of effector proteins during enteric infection

The integration of host-associated metabolism with bacterial virulence regulation dictates niche colonization by pathogens. Here, we employed in vivo RNA-seq to decipher the transcriptome of an attaching and effacing pathogen during infection. Citrobacter rodentium relies on a type 3 secretion system and a suite of effector proteins to colonize the host. The in vivo transcriptome was defined by the unique expression pattern of virulence factors essential for infection. We also describe the host-associated transcription of the operon for 1,2-propanediol metabolism, a microbiota fermentation product, and its role in enhancing expression of the type 3 secretion system via endogenous breakdown to propionate. Furthermore, we identified the co-ordinated expression profile of the effector repertoire in response to host signals such as 1,2-propanediol and reveal a novel function for one such effector in vivo. This study affirms the unprecedented power of in vivo transcriptomics for identifying novel links between host metabolism and virulence.