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Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization


Pathogenic enterobacteria face various oxygen (O2) levels during intestinal colonization from the O2-deprived lumen to oxygenated tissues. Using Shigella flexneri as a model, we have previously demonstrated that epithelium invasion is promoted by O2 in a type III secretion system-dependent manner. However, subsequent pathogen adaptation to tissue oxygenation modulation remained unknown. Assessing single-cell distribution, together with tissue oxygenation, we demonstrate here that the colonic mucosa O2 is actively depleted by S. flexneri aerobic respiration—and not host neutrophils—during infection, leading to the formation of hypoxic foci of infection. This process is promoted by type III secretion system inactivation in infected tissues, favouring colonizers over explorers. We identify the molecular mechanisms supporting infectious hypoxia induction, and demonstrate here how enteropathogens optimize their colonization capacity in relation to their ability to manipulate tissue oxygenation during infection.

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Fig. 1: Hypoxia is specifically induced by Shigella within foci of infection.
Fig. 2: Neutrophils are not essential for O2 depletion in infected tissues, which is mainly caused by Shigella aerobic respiration.
Fig. 3: Aerobic respiration is required for hypoxia induction and efficient colonic mucosa colonization by Shigella in vivo.
Fig. 4: S. flexneri T3SS is inactive in the colonic mucosa, supporting foci of infection extension.

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The datasets generated and/or analysed during the current study are available from the corresponding author on reasonable request.


  1. Marteyn, B. et al. Modulation of Shigella virulence in response to available oxygen in vivo. Nature 465, 355–358 (2010).

    Article  CAS  Google Scholar 

  2. Cramer, T. et al. HIF-1α is essential for myeloid cell-mediated inflammation. Cell 112, 645–657 (2003).

    Article  CAS  Google Scholar 

  3. Peyssonnaux, C. et al. HIF-1α expression regulates the bactericidal capacity of phagocytes. J. Clin. Invest. 115, 1806–1815 (2005).

    Article  CAS  Google Scholar 

  4. Walmsley, S. R. et al. Hypoxia-induced neutrophil survival is mediated by HIF-1α-dependent NF-κB activity. J. Exp. Med. 201, 105–115 (2005).

    Article  CAS  Google Scholar 

  5. Huether, S. E. & McCance, K. L. Understanding Pathophysiology (Elsevier Health Sciences, 2015).

  6. Karhausen, J. et al. Epithelial hypoxia-inducible factor-1 is protective in murine experimental colitis. J. Clin. Invest. 114, 1098–1106 (2004).

    Article  CAS  Google Scholar 

  7. Campbell, E. L. et al. Transmigrating neutrophils shape the mucosal microenvironment through localized oxygen depletion to influence resolution of inflammation. Immunity 40, 66–77 (2014).

    Article  CAS  Google Scholar 

  8. Arena, E. T., Tinevez, J.-Y., Nigro, G., Sansonetti, P. J. & Marteyn, B. S. The infectious hypoxia: occurrence and causes during Shigella infection. Microbes Infect. 19, 157–165 (2017).

    Article  Google Scholar 

  9. Ziemer, L. S. et al. Noninvasive imaging of tumor hypoxia in rats using the 2-nitroimidazole 18F-EF5. Eur. J. Nucl. Med. Mol. Imaging 30, 259–266 (2003).

    Article  CAS  Google Scholar 

  10. Bumann, D. Heterogeneous host–pathogen encounters: act locally, think globally. Cell Host Microbe 17, 13–19 (2015).

    Article  CAS  Google Scholar 

  11. Davis, K. M. & Isberg, R. R. Defining heterogeneity within bacterial populations via single cell approaches. BioEssays 38, 782–790 (2016).

    Article  Google Scholar 

  12. Anderson, M. C. et al. MUB40 binds to lactoferrin and stands as a specific neutrophil marker. Cell Chem. Biol. 25, 483–493 (2018).

    Article  CAS  Google Scholar 

  13. Sheridan, W. G., Lowndes, R. H. & Young, H. L. Intraoperative tissue oximetry in the human gastrointestinal tract. Am. J. Surg. 159, 314–319 (1990).

    Article  CAS  Google Scholar 

  14. Unden, G. & Trageser, M. Oxygen regulated gene expression in Escherichia coli: control of anaerobic respiration by the FNR protein. Antonie Van Leeuwenhoek 59, 65–76 (1991).

    Article  CAS  Google Scholar 

  15. Way, S. S., Sallustio, S., Magliozzo, R. S. & Goldberg, M. B. Impact of either elevated or decreased levels of cytochrome bd expression on Shigella flexneri virulence. J. Bacteriol. 181, 1229–1237 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Campbell-Valois, F.-X. et al. A fluorescent reporter reveals on/off regulation of the Shigella type III secretion apparatus during entry and cell-to-cell spread. Cell Host Microbe 15, 177–189 (2014).

    Article  CAS  Google Scholar 

  17. Davis, K. M., Mohammadi, S. & Isberg, R. R. Community behavior and spatial regulation within a bacterial microcolony in deep tissue sites serves to protect against host attack. Cell Host Microbe 17, 21–31 (2015).

    Article  CAS  Google Scholar 

  18. Hughes, E. R. et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis. Cell Host Microbe 21, 208–219 (2017).

    Article  CAS  Google Scholar 

  19. Nizet, V. & Johnson, R. S. Interdependence of hypoxic and innate immune responses. Nat. Rev. Immunol. 9, 609–617 (2009).

    Article  CAS  Google Scholar 

  20. Taylor, C. T. & Colgan, S. P. Regulation of immunity and inflammation by hypoxia in immunological niches. Nat. Rev. Immunol. 17, 774–785 (2017).

    Article  CAS  Google Scholar 

  21. Light, S. H. et al. A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria. Nature 562, 140–144 (2018).

    Article  CAS  Google Scholar 

  22. Dejean, L., Beauvoit, B., Guérin, B. & Rigoulet, M. Growth of the yeast Saccharomyces cerevisiae on a non-fermentable substrate: control of energetic yield by the amount of mitochondria. Biochim. Biophys. Acta 1457, 45–56 (2000).

    Article  CAS  Google Scholar 

  23. Monceaux, V. et al. Anoxia and glucose supplementation preserve neutrophil viability and function. Blood 128, 993–1002 (2016).

    Article  CAS  Google Scholar 

  24. Arena, E. T. et al. Bioimage analysis of Shigella infection reveals targeting of colonic crypts. Proc. Natl Acad. Sci. USA 112, E3282–E3290 (2015).

    Article  CAS  Google Scholar 

  25. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article  CAS  Google Scholar 

  26. Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).

    Article  CAS  Google Scholar 

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We acknowledge France-BioImaging infrastructure, supported by the French National Research Agency (ANR-10-INBS-04, Imagopole; to J.-Y.T.), ANR JCJC 2017-17-CE15-0012 (to B.S.M.) and the European Research Council (ERC grant 2009-AdG HOMEOPATH; to P.J.S.). E.T.A. was a Pasteur Foundation and Pasteur-Roux fellow.

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B.S.M., J.-Y.T. and E.T.A. designed the experiments, interpreted the data and wrote the paper. M.A. designed the Shigella mutants. G.N., L.I., A.A., M.F. and F.-X.C.-V. contributed to studying the Shigella mutants in vitro and in vivo. J.-Y.T. conducted quantitative analysis of the data. A.D., S.L.S. and P.J.S. contributed to data interpretation.

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Correspondence to Benoit S. Marteyn.

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Tinevez, JY., Arena, E.T., Anderson, M. et al. Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization. Nat Microbiol 4, 2001–2009 (2019).

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