H. pylori clinical isolates show extensive heterogeneity in both sequence and the presence and absence of whole genes. Even in the context of a single human stomach there exist multiple clones with unique gene complements. We are currently investigating how this diversity is generated and the consequences of this diversity on bacterial properties related to pathogenesis and patient outcome. This includes efforts to track genetic changes that accumulate during chronic infection of humans using noninvasive samples (like stool), which we test with molecular methods (like ddPCR) to track virulence and antibiotic resistance genes.
Shape mutants (straight or slightly curved rods instead of helical rods) have stomach colonization defects in our mouse infection model. Most of these cell shape factors alter the peptide content of the peptidoglycan cell wall. We are testing motility in viscous solutions, susceptibility to various stresses and peptidoglycan-mediated innate immune signaling to tease out how these specific proteins, as well as cell morphology more broadly, contribute to survival in the stomach. To understand how changes in cell wall peptides drive shape changes at size scale of the cell, we are using super-resolution microscopy of cell shape proteins and cell wall synthesis probes combined with mathematical modeling to understand how H. pylori builds its helical shape.
We have developed several bacterial mutant libraries, including random transposon mutant libraries and a sequenced-defined mutant library encompassing most non-essential genes. We are using these libraries in a variety of in vitro and in vivo systems to probe H. pylori phenotypes important for pathogenesis. We use gastric epithelial tissue culture cells and primary gastric tissue organoids to monitor wild-type and mutant bacteria binding to host cells and stimulation of host cell signaling pathways, including those activating innate immunity and host cell morphological changes. To understand bacterial-host interactions in the complex environment of the stomach, which includes many cell types, we employ a mouse model of infection, testing both wild-type mice and genetically modified mice with altered immune pathways or stomach epithelial differentiation. This allows us to look at the relative fitness of different bacterial mutants, their location within the gastric epithelium, and their ability to induce host inflammation and pathology associated with gastric cancer.