Dual RNA-seq of zebrafish larvae infected with Shigella sonnei

Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet the closely-related Shigella sonnei is replacing S. flexneri, especially in developing countries. The underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) model of Shigella infection, we discover that S. sonnei is more virulent than S. flexneri in vivo. Whole animal dual-RNAseq and testing of bacterial mutants suggest that S. sonnei virulence depends on its O-antigen oligosaccharide (which is unique among Shigella species). We show in vivo using zebrafish and ex vivo using human neutrophils that S. sonnei O-antigen can mediate neutrophil tolerance. Consistent with this, we demonstrate that O-antigen enables S. sonnei to resist phagolysosome acidification and promotes neutrophil cell death. Chemical inhibition or promotion of phagolysosome maturation respectively decreases and increases neutrophil control of S. sonnei and zebrafish survival. Strikingly, larvae primed with a sublethal dose of S. sonnei are protected against a secondary lethal dose of S. sonnei in an O-antigen-dependent manner, indicating that exposure to O-antigen can train the innate immune system against S. sonnei. Collectively, these findings reveal O-antigen as an important therapeutic target against bacillary dysentery, and may explain the rapidly increasing S. sonnei burden in developing countries. Overall design: Profiling of host and pathogen transcriptome for zebrafish larvae infected with Shigella sonnei at 24 hours post infection and comparison to transcriptome of control injected larvae and control bacteria grown in liquid culture Grant: H2020-MSCA-IF-2015 700088; Grantee: Vincenzo Torraca; Type: European Union's Horizon 2020 research and innovation program Grant: 772853 - ENTRAPMENT; Grantee: Serge Mostowy; Type: European Research Council Consolidator Grant Grant: 206444/Z/17/Z; Grantee: Serge Mostowy; Type: Wellcome Trust Senior Research Fellowship Grant: WT097411MA; Grantee: Serge Mostowy; Type: Wellcome Trust Research Career Development Fellowship Grant: No code given; Grantee: Serge Mostowy; Type: Lister Institute of Preventive Medicine