Identification of Pathogenicity Island Genes Associated with Loss of Type IV Secretion Function during Murine Infection with Helicobacter pylori.

Chronic colonization in animal models often leads to downregulation of the type IV secretion system (T4SS), typically by recombination in , which is an essential T4SS gene. However, 17 other pathogenicity island (PAI) genes, as well as some non-PAI genes, are also essential for T4SS function. To get a more complete picture of how regulates the T4SS during animal colonization, we examined in 534 mouse-passaged isolates that lost T4SS function, defined as a normalized interleukin-8 (IL-8) value of <0.3 relative to the input strain PMSS1. In order to analyze the genetic changes in the strains with unchanged , we sequenced the entire pathogenicity island of 60 such isolates using single-molecule, real-time (SMRT) sequencing technology (PacBio, Menlo Park, CA), and we compared the results to the PMSS1 wild type (WT). Of the 534 strains, 271 (51%) showed evidence of recombination in , but we also found indels or nonsynonymous changes in 13 other essential PAI genes implicated in T4SS function, most commonly , , and While recombination is the most common mechanism by which downregulates T4SS function during murine infection, loss of function is also associated with changes in other essential PAI genes.