S. Balzer, K. Malde, and I. Jonassen, Systematic exploration of error sources in pyrosequencing flowgram data, Bioinformatics, vol.27, issue.13, pp.304-309, 2011.
DOI : 10.1093/bioinformatics/btr251

J. Blázquez, Hypermutation as a factor contributing to the acquisition of antimicrobial resistance, Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am, vol.37, pp.1201-1209, 2003.

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-1403, 2004.
DOI : 10.1101/gr.2289704

C. Ewers, F. Dematheis, H. D. Singamaneni, N. Nandanwar, A. Fruth et al., Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation, Gut Pathogens, vol.9, issue.1, p.37, 2014.
DOI : 10.1186/s13099-014-0037-x

F. C. Fang, S. J. Libby, N. A. Buchmeier, P. C. Loewen, J. Switala et al., The alternative sigma factor katF (rpoS) regulates Salmonella virulence., Proceedings of the National Academy of Sciences, vol.89, issue.24, 1992.
DOI : 10.1073/pnas.89.24.11978

S. L. Fink and B. T. Cookson, Pyroptosis and host cell death responses during Salmonella infection, Cellular Microbiology, vol.165, issue.11, pp.2562-2570, 2007.
DOI : 10.1152/ajpgi.00273.2005

S. L. Fink and B. T. Cookson, Apoptosis, Pyroptosis, and Necrosis: Mechanistic Description of Dead and Dying Eukaryotic Cells, Infection and Immunity, vol.73, issue.4, pp.1907-1916, 2005.
DOI : 10.1128/IAI.73.4.1907-1916.2005

H. Häcker, C. Fürmann, H. Wagner, and G. Häcker, Caspase-9/-3 Activation and Apoptosis Are Induced in Mouse Macrophages upon Ingestion and Digestion of Escherichia coli Bacteria, The Journal of Immunology, vol.169, issue.6, pp.3172-3179, 1950.
DOI : 10.4049/jimmunol.169.6.3172

D. Hersh, D. M. Monack, M. R. Smith, N. Ghori, S. Falkow et al., The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1, Proceedings of the National Academy of Sciences, vol.96, issue.5, 1999.
DOI : 10.1073/pnas.96.5.2396

V. Jesenberger, K. J. Procyk, J. Yuan, S. Reipert, and M. Baccarini, -Induced Caspase-2 Activation in Macrophages, The Journal of Experimental Medicine, vol.67, issue.7, pp.1035-1046, 2000.
DOI : 10.1099/00221287-125-1-173

A. Jolivet-gougeon, B. Kovacs, L. Gall-david, S. , L. Bars et al., Bacterial hypermutation: clinical implications, Journal of Medical Microbiology, vol.60, issue.5, pp.563-573, 2011.
DOI : 10.1099/jmm.0.024083-0
URL : https://hal.archives-ouvertes.fr/hal-00752580

L. A. Knodler and B. B. Finlay, Salmonella and apoptosis: to live or let die? Microbes Infect, Inst. Pasteur, vol.3, pp.1321-1326, 2001.

M. L. Kotewicz, B. Li, D. D. Levy, J. E. Leclerc, A. W. Shifflet et al., Evolution of multi-gene segments in the mutS???rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2 a, Microbiology, vol.148, issue.8, pp.2531-2540, 2002.
DOI : 10.1099/00221287-148-8-2531

L. Bars, H. Bonnaure-mallet, M. Barloy-hubler, F. Jolivet-gougeon, A. Bousarghin et al., Strong mutator phenotype drives faster adaptation from growth on glucose to growth on acetate in Salmonella, Microbiology, vol.160, issue.Pt_10, 2014.
DOI : 10.1099/mic.0.079244-0
URL : https://hal.archives-ouvertes.fr/hal-01064588

L. Bars, H. Bousarghin, L. Bonnaure-mallet, M. Jolivet-gougeon, A. Barloy-hubler et al., Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182, Journal of Bacteriology, vol.194, issue.13, pp.3537-3538, 2012.
DOI : 10.1128/JB.00498-12
URL : https://hal.archives-ouvertes.fr/inserm-00716851

L. Bars, H. , L. Gall-david, S. Renoux, V. M. Bonnaure-mallet et al., Impact of a mutator phenotype on motility and cell adherence in Salmonella Heidelberg, Veterinary Microbiology, vol.159, issue.1-2, pp.99-106, 2012.
DOI : 10.1016/j.vetmic.2012.03.025
URL : https://hal.archives-ouvertes.fr/hal-00796481

L. Gall, S. Desbordes, L. Gracieux, P. Saffroy, S. Bousarghin et al., Distribution of mutation frequencies among Salmonella enterica isolates from animal and human sources and genetic characterization of a Salmonella Heidelberg hypermutator, Veterinary Microbiology, vol.137, issue.3-4, pp.306-312, 2009.
DOI : 10.1016/j.vetmic.2009.01.023

X. Li and Y. He, Caspase-2-Dependent Dendritic Cell Death, Maturation, and Priming of T Cells in Response to Brucella abortus Infection, PLoS ONE, vol.7, issue.8, p.43512, 2012.
DOI : 10.1371/journal.pone.0043512.t001

S. E. Majowicz, J. Musto, E. Scallan, F. J. Angulo, M. Kirk et al., The global burden of nontyphoidal Salmonella gastroenteritis, International Collaboration on Enteric Disease " Burden of Illness Studies, 2010.

S. M. Man, P. Tourlomousis, L. Hopkins, T. P. Monie, K. A. Fitzgerald et al., Salmonella Infection Induces Recruitment of Caspase-8 to the Inflammasome To Modulate IL-1?? Production, The Journal of Immunology, vol.191, issue.10, pp.5239-5246, 2013.
DOI : 10.4049/jimmunol.1301581

K. A. Mcfarland, S. Lucchini, J. C. Hinton, and C. J. Dorman, The Leucine-Responsive Regulatory Protein, Lrp, Activates Transcription of the fim Operon in Salmonella enterica Serovar Typhimurium via the fimZ Regulatory Gene, Journal of Bacteriology, vol.190, issue.2, pp.602-612, 2008.
DOI : 10.1128/JB.01388-07

D. Mérino, H. Réglier-poupet, P. Berche, and A. Charbit, A hypermutator phenotype attenuates the virulence of Listeria monocytogenes in a mouse model, Molecular Microbiology, vol.67, issue.3, pp.877-887, 2002.
DOI : 10.1046/j.1365-2958.2002.02929.x

E. A. Miao, C. M. Alpuche-aranda, M. Dors, A. E. Clark, M. W. Bader et al., Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1?? via Ipaf, Nature Immunology, vol.48, issue.6, pp.569-575, 2006.
DOI : 10.1038/ni1344

E. A. Miao, I. A. Leaf, P. M. Treuting, D. P. Mao, M. Dors et al., Caspase-1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria, Nature Immunology, vol.180, issue.12, pp.1136-1142, 2010.
DOI : 10.1016/S1286-4579(01)01496-4

M. E. Ohl and S. I. Miller, Salmonella: A Model for Bacterial Pathogenesis, Annual Review of Medicine, vol.52, issue.1, pp.259-274, 2001.
DOI : 10.1146/annurev.med.52.1.259

A. Oliver, R. Cantón, P. Campo, F. Baquero, and J. Blázquez, High Frequency of Hypermutable Pseudomonas aeruginosa in Cystic Fibrosis Lung Infection, Science, vol.288, issue.5469, pp.1251-1254, 2000.
DOI : 10.1126/science.288.5469.1251

G. Paesold, D. G. Guiney, L. Eckmann, and M. F. Kagnoff, -induced apoptosis in intestinal epithelial cells, Cellular Microbiology, vol.113, issue.11, pp.771-781, 2002.
DOI : 10.1046/j.1462-5822.2002.00233.x
URL : https://hal.archives-ouvertes.fr/hal-00415798

P. Wilmshurst and H. Sutcliffe, Splenic Abscess Due to Salmonella Heidelberg, Clinical Infectious Diseases, vol.21, issue.4, 1065.
DOI : 10.1093/clinids/21.4.1065

S. Wu, Y. Chu, Y. Yang, Y. Li, P. He et al., Inhibition of macrophage autophagy induced by Salmonella enterica serovar typhi plasmid, Frontiers in Bioscience, vol.19, issue.3, pp.490-503, 2014.
DOI : 10.2741/4220