Human intestinal biopsy gene expression after infection with Salmonella enterica serovar Typhi

This study describes how Salmonella Typhi, the pathogen responsible for typhoid fever, uses similar strategies to escape immune defense responses and survive within its human host. To elucidate the early mechanisms of typhoid fever, we performed studies using healthy human intestinal tissue samples to analyze gene expression changes in human intestinal specimens and bacterial cells both separately and after colonization. Our results showed mechanistic strategies that S. Typhi uses to rearrange the cellular machinery of the host cytoskeleton to successfully invade the intestinal epithelium, promote polarized cytokine release and evade immune system activation by downregulating genes involved in antigen sampling and presentation during infection. mRNA was collected from four control biopsies, five infected biopsies and four control bacterial samples. RNA sequencing was done using 1x50bp SR, HiSeq 2500; rapid run flow cells and analyzed using an Ergatis-based RNA-Seq analysis pipeline.