A. Mamun, A. A. Tominaga, A. Enomoto, and M. , Detection and characterization of the flagellar master operon in the four Shigella subgroups., Journal of Bacteriology, vol.178, issue.13, pp.3722-3726, 1996.
DOI : 10.1128/jb.178.13.3722-3726.1996

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, pp.1-11, 2006.
DOI : 10.1038/msb4100050

M. Barbagallo, D. Martino, M. L. Marcocci, L. Pietrangeli, P. De-carolis et al., A New Piece of the Shigella Pathogenicity Puzzle: Spermidine Accumulationby Silencing of the speG Gene, PLoS ONE, vol.6, issue.11, 2011.
DOI : 10.1371/journal.pone.0027226.s003

K. A. Bliven and A. T. Maurelli, Antivirulence Genes: Insights into Pathogen Evolution through Gene Loss, Infection and Immunity, vol.80, issue.12, pp.406-4070, 2012.
DOI : 10.1128/IAI.00740-12

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497401

M. Casalino, M. W. Yusuf, M. Nicoletti, P. Bazzicalupo, A. Coppo et al., A two-year study of enteric infections associated with diarrhoeal diseases in children in urban Somalia, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.82, issue.4, pp.637-641, 1988.
DOI : 10.1016/0035-9203(88)90542-1

M. Casalino, M. Nicoletti, A. Salvia, B. Colonna, C. Pazzani et al., Characterization of endemic Shigella flexneri strains in Somalia: antimicrobial resistance, plasmid profiles, and serotype correlation, J. Clin. Microbiol, vol.32, pp.1179-1183, 1994.

M. Casalino, M. C. Latella, G. Prosseda, and B. Colonna, CadC Is the Preferential Target of a Convergent Evolution Driving Enteroinvasive Escherichia coli toward a Lysine Decarboxylase-Defective Phenotype, Infection and Immunity, vol.71, issue.10, pp.5472-5479, 2003.
DOI : 10.1128/IAI.71.10.5472-5479.2003

M. Casalino, M. C. Latella, G. Prosseda, P. Ceccarini, F. Grimont et al., Molecular evolution of the lysine decarboxylase-defective phenotype in, International Journal of Medical Microbiology, vol.294, issue.8, pp.503-512, 2005.
DOI : 10.1016/j.ijmm.2004.11.001

M. Casalino, G. Prosseda, M. Barbagallo, A. Iacobino, P. Ceccarini et al., Interference of the CadC regulator in the arginine-dependent acid resistance system of Shigella and enteroinvasive E. coli, International Journal of Medical Microbiology, vol.300, issue.5, pp.289-295, 2010.
DOI : 10.1016/j.ijmm.2009.10.008

D. Carolis, E. Posteraro, B. Florio, A. R. Colonna, B. Prosseda et al., Analysis of heat-induced changes in protein expression of Stenotrophomonas maltophilia K279a reveals a role for GroEL in the host-temperature adaptation, International Journal of Medical Microbiology, vol.301, issue.4, pp.273-281, 2011.
DOI : 10.1016/j.ijmm.2010.10.001

D. Martino, M. L. Campilongo, R. Casalino, M. Micheli, G. Colonna et al., Polyamines: Emerging players in bacteria???host interactions, International Journal of Medical Microbiology, vol.303, issue.8, 2013.
DOI : 10.1016/j.ijmm.2013.06.008

URL : https://hal.archives-ouvertes.fr/pasteur-01044932

U. Dobrindt and J. Hacker, Whole genome plasticity in pathogenic bacteria, Current Opinion in Microbiology, vol.4, issue.5, pp.550-557, 2001.
DOI : 10.1016/S1369-5274(00)00250-2

Y. Feng, Z. Chen, and S. L. Liu, Gene Decay in Shigella as an Incipient Stage of Host-Adaptation, PLoS ONE, vol.6, issue.11, 2011.
DOI : 10.1371/journal.pone.0027754.s005

G. Jr, P. Formal, S. B. Baron, and L. S. , Identification of two widely separated loci conferring nicotinic acid dependence on wild-type Shigella flexneri 2a, Infect. Immun, vol.3, pp.500-503, 1971.

K. E. Holt, S. Baker, F. X. Weill, E. C. Holmes, A. Kitchen et al., Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nature Genetics, vol.28, issue.9, pp.1056-1059, 2012.
DOI : 10.1186/1471-2164-9-75

URL : https://hal.archives-ouvertes.fr/pasteur-01117702

Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen et al., Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K-12 and O157, pp.4432-4441, 2002.
DOI : 10.1093/nar/gkf566

J. B. Kaper, J. P. Nataro, and H. L. Mobley, Pathogenic Escherichia coli, Nature Reviews Microbiology, vol.63, issue.2, pp.123-140, 2004.
DOI : 10.1128/IAI.69.1.315-324.2001

D. K. Karaolis, R. Lan, and P. R. Reeves, Sequence variation in Shigella sonnei (Sonnei ), a pathogenic clone of Escherichia coli, over four continents and 41 years, J. Clin. Microbiol, vol.32, pp.796-802, 1994.

R. Lan and P. R. Reeves, Escherichia coli in disguise: molecular origins of Shigella, Microbes and Infection, vol.4, issue.11, pp.1125-1132, 2002.
DOI : 10.1016/S1286-4579(02)01637-4

R. Lan, M. C. Alles, K. Donohoe, M. B. Martinez, and P. R. Reeves, Molecular Evolutionary Relationships of Enteroinvasive Escherichia coli and Shigella spp., Infection and Immunity, vol.72, issue.9, pp.5080-5088, 2004.
DOI : 10.1128/IAI.72.9.5080-5088.2004

K. J. Livak and T. D. Schmittgen, Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2???????CT Method, Methods, vol.25, issue.4, pp.402-408, 2001.
DOI : 10.1006/meth.2001.1262

L. Loiseau, S. Ollagnier-de-choudens, D. Lascoux, E. Forest, M. Fontecave et al., Analysis of the Heteromeric CsdA-CsdE Cysteine Desulfurase, Assisting Fe-S Cluster Biogenesis in Escherichia coli, Journal of Biological Chemistry, vol.280, issue.29, pp.26760-26769, 2005.
DOI : 10.1074/jbc.M504067200

N. J. Mantis and P. J. Sansonetti, The nadB gene of Salmonella typhimurium complement the nicotinic acid auxotrophy of Shigella flexneri, Mol. Gen. Genet, vol.252, pp.626-629, 1996.

I. Marinoni, S. Nonnis, C. Monteferrante, P. Heathcote, E. Härtig et al., Characterization of l-aspartate oxidase and quinolinate synthase from Bacillus???subtilis, FEBS Journal, vol.66, issue.20, pp.5090-5107, 2008.
DOI : 10.1111/j.1742-4658.2008.06641.x

A. T. Maurelli, Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens, FEMS Microbiology Letters, vol.267, issue.1, pp.1-8, 2007.
DOI : 10.1111/j.1574-6968.2006.00526.x

N. Nakata, T. Tobe, I. Fukuda, T. Suzuki, K. Komatsu et al., The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci, Molecular Microbiology, vol.3, issue.3, pp.459-468, 1993.
DOI : 10.1038/357257a0

H. Nie, F. Yang, X. Zhang, J. Yang, L. Chen et al., Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a, BMC Genomics, vol.7, issue.1, p.173, 2006.
DOI : 10.1186/1471-2164-7-173

N. T. Onodera, J. Ryu, T. Durbic, C. Nislow, J. M. Archibald et al., Genome Sequence of Shigella flexneri Serotype 5a Strain M90T Sm, Journal of Bacteriology, vol.194, issue.11, p.3022, 2012.
DOI : 10.1128/JB.00393-12

A. Osterman, I. Curtiss, R. Kaper, J. B. Squires, C. L. Karp et al., Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor, EcoSal, 2009.
DOI : 10.1128/ecosalplus.3.6.3.10

J. Peng, J. Yang, and Q. Jin, The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli, Infection, Genetics and Evolution, vol.9, issue.1, pp.147-152, 2009.
DOI : 10.1016/j.meegid.2008.10.003

T. Penfound and J. W. Foster, NAD-dependent DNA-binding activity of the bifunctional NadR regulator of Salmonella typhimurium, J. Bacteriol, vol.181, pp.648-655, 1999.

G. Prosseda, P. A. Fradiani, D. Lorenzo, M. Falconi, M. Micheli et al., A role for H-NS in the regulation of the virF gene of Shigella and enteroinvasive Escherichia coli, Research in Microbiology, vol.149, issue.1, pp.15-25, 1998.
DOI : 10.1016/S0923-2508(97)83619-4

G. Prosseda, M. Falconi, M. Nicoletti, M. Casalino, G. Micheli et al., Histone-like proteins and the Shigella invasivity regulon, Research in Microbiology, vol.153, issue.7, pp.461-468, 2002.
DOI : 10.1016/S0923-2508(02)01346-3

G. Prosseda, M. C. Latella, M. Barbagallo, M. Nicoletti, A. Kassas et al., The two-faced role of cad genes in the virulence of pathogenic Escherichia coli, Research in Microbiology, vol.158, issue.6, pp.487-493, 2007.
DOI : 10.1016/j.resmic.2007.05.001

G. Prosseda, D. Martino, M. L. Campilongo, R. Fioravanti, R. Micheli et al., Shedding of genes that interfere with the pathogenic lifestyle: the Shigella model, Research in Microbiology, vol.163, issue.6-7, pp.399-406, 2012.
DOI : 10.1016/j.resmic.2012.07.004

URL : https://hal.archives-ouvertes.fr/pasteur-00947763

A. L. Prunier, R. Schuch, R. E. Fernández, K. L. Mumy, H. Kohler et al., nadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity, Microbiology, vol.153, issue.7, pp.2363-2372, 2007.
DOI : 10.1099/mic.0.2007/006916-0

A. L. Prunier, R. Schuch, R. E. Fernández, and A. T. Maurelli, Genetic Structure of the nadA and nadB Antivirulence Loci in Shigella spp., Journal of Bacteriology, vol.189, issue.17, pp.6482-6486, 2007.
DOI : 10.1128/JB.00525-07

G. M. Pupo, R. Lan, and P. R. Reeves, Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics, Proceedings of the National Academy of Sciences, vol.97, issue.19, pp.10567-10572, 2000.
DOI : 10.1073/pnas.180094797

C. Rousset, M. Fontecave, and S. Ollagnier-de-choudens, : Investigation of cluster ligands, FEBS Letters, vol.96, issue.19, pp.2937-2944, 2008.
DOI : 10.1016/j.febslet.2008.07.032

P. J. Sansonetti, H. Hauteville, S. B. Formal, and M. Toucas, Plasmid-mediated invasiveness of Shigella-like Escherichia coli, Ann. Microbiol. (Inst. Pasteur), vol.132, pp.351-355, 1982.

G. N. Schroeder and H. Hilbi, Molecular Pathogenesis of Shigella spp.: Controlling Host Cell Signaling, Invasion, and Death by Type III Secretion, Clinical Microbiology Reviews, vol.21, issue.1, pp.134-156, 2008.
DOI : 10.1128/CMR.00032-07

C. N. Tran, M. Giangrossi, G. Prosseda, A. Brandi, D. Martino et al., A multifactor regulatory circuit involving H-NS, VirF and an antisense RNA modulates transcription of the virulence gene icsA of Shigella flexneri, Nucleic Acids Research, vol.39, issue.18, pp.8122-8134, 2011.
DOI : 10.1093/nar/gkr521

URL : https://hal.archives-ouvertes.fr/pasteur-00975905

F. Yang, J. Yang, X. Zhang, L. Chen, Y. Jiang et al., Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery, Differentiation between Shigella, enteroinvasive Escherichia coli (EIEC) and noninvasive Escherichia coli, pp.6445-6458, 2005.
DOI : 10.1093/nar/gki954

J. Wei, M. B. Goldberg, V. Burland, M. M. Venkatesan, W. Deng et al., Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T, Infection and Immunity, vol.71, issue.5, pp.2775-2786, 2003.
DOI : 10.1128/IAI.71.5.2775-2786.2003

C. Zagaglia, M. Casalino, B. Colonna, C. Conti, A. Calconi et al., Virulence plasmids of enteroinvasive Escherichia coli and Shigella flexneri integrate into a specific site on the host chromosome: integration greatly reduces expression of plasmid-carried virulence genes, Infect. Immun, vol.59, pp.792-799, 1991.

G. Zhao, L. Zhu, E. Feng, X. Cao, N. Shang et al., A novel anti-virulence gene revealed by proteomic analysis in Shigella flexneri 2a, Proteome Science, vol.8, issue.1, p.30, 2010.
DOI : 10.1186/1477-5956-8-30