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Autophagy, an ancient and highly conserved intracellular degradation process, is viewed as a critical component of innate immunity because of its ability to deliver cytosolic bacteria to the lysosome. However, the role of bacterial autophagy  in vivo  remains poorly understood. The zebrafish ( Danio rerio ) has emerged as a vertebrate model for the study of infections because it is optically accessible at the larval stages when the innate immune system is already functional. Here, we have characterized the susceptibility of zebrafish larvae to  Shigella flexneri , a paradigm for bacterial autophagy, and have used this model to study  Shigella -phagocyte interactions  in vivo . Depending on the dose,  S. flexneri  injected in zebrafish larvae were either cleared in a few days or resulted in a progressive and ultimately fatal infection. Using high resolution live imaging, we found that  S. flexneri  were rapidly engulfed by macrophages and neutrophils; moreover we discovered a scavenger role for neutrophils in eliminating infected dead macrophages and non-immune cell types that failed to control  Shigella  infection. We observed that intracellular  S. flexneri  could escape to the cytosol, induce septin caging and be targeted to autophagy  in vivo . Depletion of p62 (sequestosome 1 or SQSTM1), an adaptor protein critical for bacterial autophagy  in vitro , significantly increased bacterial burden and host susceptibility to infection. These results show the zebrafish larva as a new model for the study of  S. flexneri  interaction with phagocytes, and the manipulation of autophagy for anti-bacterial therapy  in vivo .

The Zebrafish as a New Model for the In Vivo Study of Shigella flexneri Interaction with Phagocytes and Bacterial Autophagy