Extended Data Fig. 9. Flow cytometry gating strategy.

Single cells were selected by gating on FSC-A and FSC-H. Debris and bacteria were subsequently excluded by gating out the FSC-A^low, SSC-A^low population. The remaining population was analyzed for UPEC (GFP) and annexin V (Pacific Blue) or caspase-3 activity (Pacific Blue). Because we are interested in quantifying cell death, dead cells were not specifically excluded from analyses. Each dot represents one cell. Relative population density is represented by a color spectrum (red indicates regions of high cell density, blue indicates regions of low cell density).