Septin binding restricts Shigella growth and triggers intracellular tolerance

Pathogen survival relies on their ability to adapt to changing environments, yet how intracellular bacteria tolerate cell-autonomous immunity remains unclear. Septins assemble into cage-like structures around cytoplasmic Shigella targeted by autophagy, but their antibacterial activity was unknown. Using advanced microscopy and cell-free reconstitution, we show that septins polymerize into circumferentially oriented filaments that inhibit bacterial growth. RNA-sequencing reveals that septin binding to Shigella upregulates type III secretion system (T3SS) effectors and triggers a stress response. Underlying this, septin-bound Shigella possess hyperpolarized membranes, but without lethally damaged cell envelope. We show that exposure to septin binding enhances the impact of the cell envelope-targeting antibiotic polymyxin B. During infection, T3SS effector OspC1 prevents septin recruitment, while stress-response regulator cspC protects against septin-mediated changes to membrane potential. Hence, septin binding is intrinsically antibacterial and is sensed by Shigella as a danger signal to promote mechanisms of intracellular tolerance.