42 Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet the 43 closely-related Shigella sonnei is replacing S. flexneri, especially in developing countries. The 44 underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) 45 model of Shigella infection, we discover that S. sonnei is more virulent than S. flexneri in vivo. 46 Whole animal dual-RNAseq and testing of bacterial mutants suggest that S. sonnei virulence 47 depends on its O-antigen oligosaccharide (which is unique among Shigella species). We show 48 in vivo using zebrafish and ex vivo using human neutrophils that S. sonnei O-antigen can 49 mediate neutrophil tolerance. Consistent with this, we demonstrate that O-antigen enables S. 50 sonnei to resist phagolysosome acidification and promotes neutrophil cell death. Chemical 51 inhibition or promotion of phagolysosome maturation respectively decreases and increases 52 neutrophil control of S. sonnei and zebrafish survival. Strikingly, larvae primed with a sublethal 3 53 dose of S. sonnei are protected against a secondary lethal dose of S. sonnei in an O-antigen-54 dependent manner, indicating that exposure to O-antigen can train the innate immune system 55 against S. sonnei. Collectively, these findings reveal O-antigen as an important therapeutic 56 target against bacillary dysentery, and may explain the rapidly increasing S. sonnei burden in 57 developing countries. 58 59 60 Author Summary 61 Shigella sonnei is predominantly responsible for dysentery in developed countries, and is 62 replacing Shigella flexneri in areas undergoing economic development and improvements in 63 water quality. Using Shigella infection of zebrafish (in vivo) and human neutrophils (in vitro), 64 we discover that S. sonnei is more virulent than S. flexneri because of neutrophil tolerance 65 mediated by its O-antigen oligosaccharide acquired from the environmental bacteria 66 Plesiomonas shigelloides. To inspire new approaches for S. sonnei control, we show that 67 increased phagolysosomal acidification or innate immune training can promote S. sonnei 68 clearance by neutrophils in vivo. These findings have major implications for our evolutionary 69 understanding of Shigella, and may explain why exposure to P. shigelloides in low and middle-70 income countries (LMICs) can protect against dysentery incidence. 71 72 73 4 80 has been a valuable discovery tool in the field of innate immunity, helping to illuminate the role 81 of neutrophil extracellular traps (NETs) [5], nucleotide-binding oligomerisation domain (NOD)-82 like receptors (NLRs) [6], bacterial autophagy [7], interferon-inducible guanylate-binding 83 proteins (GBPs) [8,9] and septin-mediated cell-autonomous immunity [10,11] in host 84 defence. 85 86 The genus Shigella comprises four different species (S. flexneri, S. sonnei, S. boydii, S. 87 dysenteriae), although DNA sequencing suggests they evolved from convergent evolution of 88 different founders [12]. The most recent strains of S. flexne...