C. Akimana, S. Al-khodor, A. Kwaik, and Y. , Host factors required for modulation of phagosome biogenesis and proliferation of Francisella tularensis within the cytosol, PLoS ONE, vol.5, 2010.

A. Allaoui, R. Ménard, P. J. Sansonetti, P. , and C. , Characterization of the Shigella flexneri ipgD and ipgF genes, which are located in the proximal part of the mxi locus, Infect. Immun, vol.61, pp.1707-1714, 1993.

M. A. Bakowski, V. Braun, G. Y. Lam, T. Yeung, W. Heo et al., The phosphoinositide phosphatase SopB manipulates membrane surface charge and trafficking of the Salmonella-containing vacuole, Cell Host Microbe, vol.7, pp.453-462, 2010.

J. R. Barker, A. Chong, T. D. Wehrly, J. Yu, S. A. Rodriguez et al., The Francisella tularensis pathogenicity island encodes a secretion system that is required for phagosome escape and virulence, Mol. Microbiol, vol.74, pp.1459-1470, 2009.
DOI : 10.1111/j.1365-2958.2009.06947.x
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2009.06947.x

C. R. Beuzón, S. Méresse, K. E. Unsworth, J. Ruíz-albert, S. Garvis et al., Salmonella maintains the integrity of its intracellular vacuole through the action of SifA, EMBO J, vol.19, pp.3235-3249, 2000.

A. Blocker, P. Gounon, E. Larquet, K. Niebuhr, V. Cabiaux et al., The tripartite type III secreton of Shigella flexneri inserts IpaB and IpaC into host membranes, J. Cell Biol, vol.147, pp.683-693, 1999.
DOI : 10.1083/jcb.147.3.683
URL : http://jcb.rupress.org/content/jcb/147/3/683.full.pdf

F. Boal, R. Mansour, M. Gayral, E. Saland, G. Chicanne et al., TOM1 is a PI5P effector involved in the regulation of endosomal maturation, J. Cell Sci, vol.128, pp.815-827, 2015.

E. Boucrot, T. Henry, J. Borg, J. Gorvel, M. et al., The intracellular fate of Salmonella depends on the recruitment of kinesin, Science, vol.308, pp.1174-1178, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00165696

E. Brombacher, S. Urwyler, C. Ragaz, S. S. Weber, K. Kami et al., Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila, J. Biol. Chem, vol.284, pp.4846-4856, 2009.

J. H. Brumell and M. A. Scidmore, Manipulation of rab GTPase function by intracellular bacterial pathogens. Microbiol, Mol. Biol. Rev, vol.71, pp.636-652, 2007.

J. H. Brumell, P. Tang, M. L. Zaharik, and B. B. Finlay, Disruption of the Salmonella-containing vacuole leads to increased replication of Salmonella enterica serovar typhimurium in the cytosol of epithelial cells, Infect. Immun, vol.70, pp.3264-3270, 2002.

F. Campbell-valois, M. Sachse, P. J. Sansonetti, P. , and C. , Escape of actively secreting Shigella flexneri from ATG8/LC3-positive vacuoles formed during cell-to-cell spread is facilitated by IcsB and VirA, MBio, vol.6, pp.2567-02514, 2015.

N. Carayol, T. Van-nhieu, and G. , The inside story of Shigella invasion of intestinal epithelial cells, Cold Spring Harb. Perspect. Med, vol.3, p.16717, 2013.

N. Carayol, T. Van-nhieu, and G. , Tips and tricks about Shigella invasion of epithelial cells, Curr. Opin. Microbiol, vol.16, pp.32-37, 2013.

A. Chong, T. D. Wehrly, V. Nair, E. R. Fischer, J. R. Barker et al., The early phagosomal stage of Francisella tularensis determines optimal phagosomal escape and Francisella pathogenicity island protein expression, Infect. Immun, vol.76, pp.5488-5499, 2008.

D. L. Clemens, B. Lee, and M. A. Horwitz, Francisella tularensis phagosomal escape does not require acidification of the phagosome, Infect. Immun, vol.77, pp.1757-1773, 2009.

B. Coburn, I. Sekirov, and B. B. Finlay, Type III secretion systems and disease, Clin. Microbiol. Rev, vol.20, pp.535-549, 2007.

P. Cossart, R. , and C. R. , Manipulation of host membrane machinery by bacterial pathogens, Curr. Opin. Cell Biol, vol.22, pp.547-554, 2010.

E. A. Creasey and R. R. Isberg, The protein SdhA maintains the integrity of the Legionella-containing vacuole, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.3481-3486, 2012.

E. A. Creasey and R. R. Isberg, Maintenance of vacuole integrity by bacterial pathogens, Curr. Opin. Microbiol, vol.17, pp.46-52, 2014.

C. De-geyter, B. Vogt, Z. Benjelloun-touimi, P. J. Sansonetti, J. M. Ruysschaert et al., Purification of IpaC, a protein involved in entry of Shigella flexneri into epithelial cells and characterization of its interaction with lipid membranes, FEBS Lett, vol.400, pp.149-154, 1997.

C. De-geyter, R. Wattiez, P. Sansonetti, P. Falmagne, J. M. Ruysschaert et al., Characterization of the interaction of IpaB and IpaD, proteins required for entry of Shigella flexneri into epithelial cells, with a lipid membrane, Eur. J. Biochem, vol.267, pp.5769-5776, 2000.

I. Derré, M. Pypaert, A. Dautry-varsat, A. , and H. , RNAi screen in Drosophila cells reveals the involvement of the Tom complex in Chlamydia infection, PLoS Pathog, vol.3, 2007.

N. E. Dickenson, S. P. Choudhari, P. R. Adam, R. M. Kramer, S. B. Joshi et al., Oligomeric states of the Shigella translocator protein IpaB provide structural insights into formation of the type III secretion translocon, Protein Sci, vol.22, pp.614-627, 2013.

A. Dumont, E. Boucrot, S. Drevensek, V. Daire, J. Gorvel et al., SKIP, the host target of the Salmonella virulence factor SifA, promotes kinesin-1-dependent vacuolar membrane exchanges, Traffic, vol.11, pp.899-911, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00503009

N. Dupont, S. Lacas-gervais, J. Bertout, I. Paz, B. Freche et al., Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy, Cell Host Microbe, vol.6, pp.137-149, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02109149

S. Ehsani, J. C. Santos, C. D. Rodrigues, R. Henriques, L. Audry et al., Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion, Infect. Immun, vol.80, pp.2548-2557, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01899474

R. G. Fehon, A. I. Mcclatchey, and A. Bretscher, Organizing the cell cortex: the role of ERM proteins, Nat. Rev. Mol. Cell Biol, vol.11, pp.276-287, 2010.

C. M. Fernandez-prada, D. L. Hoover, B. D. Tall, A. Hartman, B. Kopelowitz et al., Shigella flexneri IpaH(7.8) facilitates escape of virulent bacteria from the endocytic vacuoles of mouse and human macrophages, Infect. Immun, vol.68, pp.3608-3619, 2000.

R. A. Fratti, J. Chua, I. Vergne, and V. Deretic, Mycobacterium tuberculosis glycosylated phosphatidylinositol causes phagosome maturation arrest, Proc. Natl. Acad. Sci. U.S.A, vol.100, pp.5437-5442, 2003.

J. Fredlund and J. Enninga, Cytoplasmic access by intracellular bacterial pathogens, Trends Microbiol, vol.22, pp.128-137, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01113445

A. Guichard, V. Nizet, and E. Bier, RAB11-mediated trafficking in host-pathogen interactions, Nat. Rev. Microbiol, vol.12, pp.624-634, 2014.

S. Håkansson, K. Schesser, C. Persson, E. E. Galyov, R. Rosqvist et al., The YopB protein of Yersinia pseudotuberculosis is essential for the translocation of Yop effector proteins across the target cell plasma membrane and displays a contact-dependent membrane disrupting activity, EMBO J, vol.15, pp.5812-5823, 1996.

L. D. Hernandez, K. Hueffer, M. R. Wenk, and J. E. Galán, Salmonella modulates vesicular traffic by altering phosphoinositide metabolism, Science, vol.304, pp.1805-1807, 2004.

N. High, J. Mounier, M. C. Prévost, and P. J. Sansonetti, IpaB of Shigella flexneri causes entry into epithelial cells and escape from the phagocytic vacuole, EMBO J, vol.11, pp.1991-1999, 1992.

H. Hilbi and A. Haas, Secretive bacterial pathogens and the secretory pathway, Traffic, vol.13, pp.1187-1197, 2012.

H. Hilbi, J. E. Moss, D. Hersh, Y. Chen, J. Arondel et al., , 1998.

, Shigella-induced apoptosis is dependent on caspase-1 which binds to IpaB, J. Biol. Chem, vol.273, pp.32895-32900

C. Hoffmann, I. Finsel, A. Otto, G. Pfaffinger, E. Rothmeier et al., Functional analysis of novel Rab GTPases identified in the proteome of purified Legionella-containing vacuoles from macrophages, Cell. Microbiol, vol.16, pp.1034-1052, 2014.

P. J. Hume, E. J. Mcghie, R. D. Hayward, and V. Koronakis, The purified Shigella IpaB and Salmonella SipB translocators share biochemical properties and membrane topology, Mol. Microbiol, vol.49, pp.425-439, 2003.

R. R. Isberg, T. J. O'connor, and M. Heidtman, The Legionella pneumophila replication vacuole: making a cosy niche inside host cells, Nat. Rev. Microbiol, vol.7, pp.13-24, 2009.

C. Keller, N. Mellouk, A. Danckaert, R. Simeone, R. Brosch et al., Single cell measurements of vacuolar rupture caused by intracellular pathogens, J. Vis. Exp. e50116, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01113507

S. Kreibich, M. Emmenlauer, J. Fredlund, P. Rämö, C. Münz et al., Autophagy proteins promote repair of endosomal membranes damaged by the salmonella type three secretion system 1, Cell Host Microbe, vol.18, pp.527-537, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01899446

Y. Kumar and R. Valdivia, Leading a sheltered life: intracellular pathogens and maintenance of vacuolar compartments, Cell Host Microbe, vol.5, pp.593-601, 2009.

Y. Kumar and R. H. Valdivia, Actin and intermediate filaments stabilize the Chlamydia trachomatis vacuole by forming dynamic structural scaffolds, Cell Host Microbe, vol.4, pp.159-169, 2008.

N. S. Lossi, N. Rolhion, A. I. Magee, C. Boyle, and D. W. Holden, The Salmonella SPI-2 effector SseJ exhibits eukaryotic activator-dependent phospholipase A and glycerophospholipid : cholesterol acyltransferase activity, Microbiology, vol.154, pp.2680-2688, 2008.

M. P. Machner and R. R. Isberg, Targeting of host Rab GTPase function by the intravacuolar pathogen Legionella pneumophila, Dev. Cell, vol.11, pp.47-56, 2006.

G. V. Mallo, M. Espina, A. C. Smith, M. R. Terebiznik, A. Alemán et al., SopB promotes phosphatidylinositol 3-phosphate formation on Salmonella vacuoles by recruiting Rab5 and Vps34, J. Cell Biol, vol.182, pp.741-752, 2008.
DOI : 10.1083/jcb.200804131
URL : http://jcb.rupress.org/content/jcb/182/4/741.full.pdf

S. L. Marcus, M. R. Wenk, O. Steele-mortimer, and B. B. Finlay, A synaptojanin-homologous region of Salmonella typhimurium SigD is essential for inositol phosphatase activity and Akt activation, FEBS Lett, vol.494, pp.201-207, 2001.

R. Ménard, P. J. Sansonetti, P. , and C. , Nonpolar mutagenesis of the ipa genes defines IpaB, IpaC, and IpaD as effectors of Shigella flexneri entry into epithelial cells, J. Bacteriol, vol.175, pp.5899-5906, 1993.

N. Mellouk, A. Weiner, N. Aulner, C. Schmitt, M. Elbaum et al., Shigella subverts the host recycling compartment to rupture its vacuole, Cell Host Microbe, vol.16, pp.517-530, 2014.
DOI : 10.1016/j.chom.2014.09.005
URL : https://hal.archives-ouvertes.fr/pasteur-01113365

S. Méresse, K. E. Unsworth, A. Habermann, G. Griffiths, F. Fang et al., Remodelling of the actin cytoskeleton is essential for replication of intravacuolar Salmonella, Cell. Microbiol, vol.3, pp.567-577, 2001.

M. Molmeret, D. M. Bitar, L. Han, and Y. A. Kwaik, Disruption of the phagosomal membrane and egress of Legionella pneumophila into the cytoplasm during the last stages of intracellular infection of macrophages and Acanthamoeba polyphaga, Infect. Immun, vol.72, pp.4040-4051, 2004.

J. Mounier, V. Laurent, A. Hall, P. Fort, M. F. Carlier et al., Rho family GTPases control entry of Shigella flexneri into epithelial cells but not intracellular motility, J. Cell Sci, vol.112, pp.2069-2080, 1999.

K. Niebuhr, S. Giuriato, T. Pedron, D. J. Philpott, F. Gaits et al., Conversion of PtdIns(4,5)P(2) into PtdIns(5)P by the S. flexneri effector IpgD reorganizes host cell morphology, EMBO J, vol.21, pp.5069-5078, 2002.

K. Niebuhr, N. Jouihri, A. Allaoui, P. Gounon, P. J. Sansonetti et al., IpgD, a protein secreted by the type III secretion machinery of Shigella flexneri, is chaperoned by IpgE and implicated in entry focus formation, Mol. Microbiol, vol.38, pp.8-19, 2000.

T. J. O'connor, D. Boyd, M. S. Dorer, and R. R. Isberg, Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen, Science, vol.338, pp.1440-1444, 2012.

M. B. Ohlson, K. Fluhr, C. L. Birmingham, H. Brumell, S. I. Miller et al., SseJ deacylase activity by Salmonella enterica serovar typhimurium promotes virulence in mice, Infect. Immun, vol.73, pp.6249-6259, 2005.
DOI : 10.1128/iai.73.10.6249-6259.2005
URL : https://iai.asm.org/content/73/10/6249.full.pdf

I. Paz, M. Sachse, N. Dupont, J. Mounier, C. Cederfur et al., , 2010.

, Galectin-3, a marker for vacuole lysis by invasive pathogens, Cell. Microbiol, vol.12, pp.530-544

C. Pendaries, H. Tronchère, L. Arbibe, J. Mounier, O. Gozani et al., PtdIns5P activates the host cell PI3-kinase/Akt pathway during Shigella flexneri infection, EMBO J, vol.25, pp.1024-1034, 2006.

J. Pizarro-cerdá, A. Kühbacher, C. , and P. , Entry of Listeria monocytogenes in mammalian epithelial cells: an updated view. Cold Spring Harb, Perspect. Med, vol.2, pp.1-17, 2012.

A. Prada-delgado, E. Carrasco-marín, C. Peña-macarro, E. Del-cerro-vadillo, M. Fresno-escudero et al., Inhibition of Rab5a exchange activity is a key step for Listeria monocytogenes survival, Traffic, vol.6, pp.252-265, 2005.

A. L. Radtke, K. L. Anderson, M. J. Davis, M. J. Dimagno, J. A. Swanson et al., Listeria monocytogenes exploits cystic fibrosis transmembrane conductance regulator (CFTR) to escape the phagosome, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.1633-1638, 2011.

M. S. Rahman, J. J. Gillespie, S. J. Kaur, K. T. Sears, S. M. Ceraul et al., Rickettsia typhi possesses phospholipase A2 enzymes that are involved in infection of host cells, PLoS Pathog, vol.9, p.1003399, 2013.

D. Ramel, F. Lagarrigue, V. Pons, J. Mounier, S. Dupuis-coronas et al., Shigella flexneri infection generates the lipid PI5P to alter endocytosis and prevent termination of EGFR signaling, Sci. Signal, vol.4, p.61, 2011.

E. Ramond, G. Gesbert, M. Rigard, J. Dairou, M. Dupuis et al., Glutamate utilization couples oxidative stress defense and the tricarboxylic acid cycle in francisella phagosomal escape, PLoS Pathog, vol.10, p.1003893, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00972072

K. Ray, A. Bobard, A. Danckaert, I. Paz-haftel, C. Clair et al., Tracking the dynamic interplay between bacterial and host factors during pathogen-induced vacuole rupture in real time, Cell. Microbiol, vol.12, pp.545-556, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01899489

K. Ray, B. Marteyn, P. J. Sansonetti, and C. M. Tang, Life on the inside: the intracellular lifestyle of cytosolic bacteria, Nat. Rev. Microbiol, vol.7, pp.333-340, 2009.

A. Rejman-lipinski, J. Heymann, C. Meissner, A. Karlas, V. Brinkmann et al., Rab6 and Rab11 regulate Chlamydia trachomatis development and golgin-84-dependent Golgi fragmentation, PLoS Pathog, vol.5, p.1000615, 2009.

P. Renesto, P. Dehoux, E. Gouin, L. Touqui, P. Cossart et al., Identification and characterization of a phospholipase D-superfamily gene in rickettsiae, J. Infect. Dis, vol.188, pp.1276-1283, 2003.

J. Saarikangas, H. Zhao, and P. Lappalainen, Regulation of the actin cytoskeleton-plasma membrane interplay by phosphoinositides, Physiol. Rev, vol.90, pp.259-289, 2010.

N. Schroeder, T. Henry, C. De-chastellier, W. Zhao, G. Aude-agnés et al., The virulence protein SopD2 regulates membrane dynamics of Salmonella-containing vacuoles, PLoS Pathog, vol.6, p.1001002, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00610105

L. Senerovic, S. P. Tsunoda, C. Goosmann, V. Brinkmann, A. Zychlinsky et al., Spontaneous formation of IpaB ion channels in host cell membranes reveals how Shigella induces pyroptosis in macrophages, Cell Death Dis, vol.3, 2012.

R. Simeone, A. Bobard, J. Lippmann, W. Bitter, L. Majlessi et al., Phagosomal rupture by Mycobacterium tuberculosis results in toxicity and host cell death, PLoS Pathog, vol.8, p.1002507, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01899479

R. Simeone, F. Sayes, O. Song, M. I. Gröschel, P. Brodin et al., Cytosolic access of Mycobacterium tuberculosis: critical impact of phagosomal acidification control and demonstration of occurrence in vivo, PLOS Pathog, vol.11, 2015.

R. Singh, A. Jamieson, C. , and P. , GILT is a critical host factor for Listeria monocytogenes infection, Nature, vol.455, pp.1244-1247, 2008.

A. C. Smith, Interaction of the Salmonella-containing vacuole with the endocytic recycling system, J. Biol. Chem, vol.280, pp.24634-24641, 2005.

J. Smith, J. Manoranjan, M. Pan, A. Bohsali, J. Xu et al., Evidence for pore formation in host cell membranes by ESX-1-secreted ESAT-6 and its role in Mycobacterium marinum escape from the vacuole, Infect. Immun, vol.76, pp.5478-5487, 2008.

M. R. Terebiznik, O. V. Vieira, S. L. Marcus, A. Slade, C. M. Yip et al., Elimination of host cell PtdIns(4,5)P(2) by bacterial SigD promotes membrane fission during invasion by Salmonella, Nat. Cell Biol, vol.4, pp.766-773, 2002.

T. Van-nhieu, G. Caron, E. Hall, A. Sansonetti, P. J. Van-der-wel et al., IpaC induces actin polymerization and filopodia formation during Shigella entry into epithelial cells, EMBO J, vol.18, pp.1287-1298, 1999.

I. Vergne, J. Chua, H. Lee, M. Lucas, J. Belisle et al., Mechanism of phagolysosome biogenesis block by viable Mycobacterium tuberculosis, Proc. Natl. Acad. Sci. U.S.A, vol.102, pp.4033-4038, 2005.

S. Weber, M. Wagner, and H. Hilbi, Live-cell imaging of phosphoinositide dynamics and membrane architecture during Legionella infection, MBio, vol.5, pp.839-852, 2013.

S. S. Weber, C. Ragaz, and H. Hilbi, Pathogen trafficking pathways and host phosphoinositide metabolism, Mol. Microbiol, vol.71, pp.1341-1352, 2009.

T. Whitworth, V. L. Popov, X. Yu, D. H. Walker, and D. H. Bouyer, Expression of the Rickettsia prowazekii pld or tlyC gene in Salmonella enterica serovar Typhimurium mediates phagosomal escape, Infect. Immun, vol.73, pp.6668-6673, 2005.