K. Al-hasani, I. Henderson, H. Sakellaris, K. Rajakumar, T. Grant et al., The sigA Gene Which Is Borne on the she Pathogenicity Island of Shigella flexneri 2a Encodes an Exported Cytopathic Protease Involved in Intestinal Fluid Accumulation, Infection and Immunity, vol.68, issue.5, pp.2457-2463, 2000.
DOI : 10.1128/IAI.68.5.2457-2463.2000

G. Allison and N. Verma, Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri, Trends in Microbiology, vol.8, issue.1, pp.17-23, 2000.
DOI : 10.1016/S0966-842X(99)01646-7

P. Ashton, K. Baker, A. Gentle, D. Wooldridge, N. Thomson et al., Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence, Gut Pathogens, vol.6, issue.1, pp.7-10, 2014.
DOI : 10.1371/journal.pone.0070238

K. Baker, T. Dallman, P. Ashton, M. Day, G. Hughes et al., Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. The Lancet. Infectious Diseases, pp.10-1016, 2015.

K. Baker, A. Mather, H. Mcgregor, P. Coupland, G. Langridge et al., The extant World War 1 dysentery bacillus NCTC1: a genomic analysis, The Lancet, vol.384, issue.9955, pp.1691-1697, 2014.
DOI : 10.1016/S0140-6736(14)61789-X

L. Cheng, T. Connor, D. Aanensen, B. Spratt, and J. Corander, Bayesian semi-supervised classification of bacterial samples using MLST databases, BMC Bioinformatics, vol.12, issue.1, pp.302-312, 2011.
DOI : 10.1186/1471-2105-9-421

URL : http://doi.org/10.1186/1471-2105-12-302

L. Cheng, T. Connor, J. Siren, D. Aanensen, and J. Corander, Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software, Molecular Biology and Evolution, vol.30, issue.5, pp.1224-1228, 2013.
DOI : 10.1093/molbev/mst028

S. Choi, Y. Jeon, J. Lee, B. Choi, S. Moon et al., Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries, Journal of Medical Microbiology, vol.56, issue.11, pp.1460-1466, 2007.
DOI : 10.1099/jmm.0.47322-0

J. Corander, P. Marttinen, J. Siren, and J. Tang, Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinformatics, vol.9, issue.1, pp.539-549, 2008.
DOI : 10.1186/1471-2105-9-539

J. Corander, P. Waldmann, P. Marttinen, and M. Sillanpaa, BAPS 2: enhanced possibilities for the analysis of genetic population structure, Bioinformatics, vol.20, issue.15, pp.2363-2369, 2004.
DOI : 10.1093/bioinformatics/bth250

N. Croucher, A. Page, T. Connor, A. Delaney, J. Keane et al., Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Research, vol.43, issue.3, 2014.
DOI : 10.1093/nar/gku1196

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, 1471.
DOI : 10.1186/1471-2148-7-214

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2247476

P. Edwards and W. Ewing, Edwards and Ewing's identification of enterobacteriaceae, p.536, 1986.

M. Emch, M. Ali, and M. Yunus, Risk areas and neighborhood-level risk factors for Shigella dysenteriae 1 and Shigella flexneri, Health & Place, vol.14, issue.1, pp.96-105, 2008.
DOI : 10.1016/j.healthplace.2007.05.004

S. Esrey, R. Feachem, and J. Hughes, Interventions for the control of diarrheal diseases among young-children - Improving water-supplies and excreta disposal facilities, Bulletin of the World Health Organization, vol.63, pp.757-772, 1985.

S. Faruque, R. Khan, M. Kamruzzaman, S. Yamasaki, Q. Ahmad et al., Isolation of Shigella dysenteriae Type 1 and S. flexneri Strains from Surface Waters in Bangladesh: Comparative Molecular Analysis of Environmental Shigella Isolates versus Clinical Strains, Applied and Environmental Microbiology, vol.68, issue.8, pp.3908-3913, 2002.
DOI : 10.1128/AEM.68.8.3908-3913.2002

A. Fasano, F. Noriega, F. Liao, W. Wang, and M. Levine, Effect of shigella enterotoxin 1 (ShET1) on rabbit intestine in vitro and in vivo., Gut, vol.40, issue.4, pp.505-511, 1997.
DOI : 10.1136/gut.40.4.505

M. Gray, K. Lampel, N. Strockbine, R. Fernandez, A. Melton-celsa et al., with an Epidemiological Link to Recent Travel to Hispa??iola, Emerging Infectious Diseases, vol.20, issue.10, pp.1669-1677, 2014.
DOI : 10.3201/eid2010.140292

URL : http://doi.org/10.3201/eid2010.140292

F. He, K. Han, L. Liu, W. Sun, L. Zhang et al., Shigellosis outbreak associated with contaminated well water in a rural elementary school, PLOS ONE, vol.7, 2009.

M. He, F. Miyajima, P. Roberts, L. Ellison, D. Pickard et al., Emergence and global spread of epidemic healthcare-associated Clostridium difficile, Nature Genetics, vol.377, issue.1, pp.109-113, 2013.
DOI : 10.1093/molbev/msi103

I. Henderson, J. Czeczulin, C. Eslava, F. Noriega, and J. Nataro, Characterization of pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli, Infection and Immunity, vol.67, pp.5587-5596, 1999.

C. Hendricks and S. Morrison, Multiplication and growth of selected enteric bacteria in clear mountain stream water, Water Research, vol.1, issue.8-9, pp.567-576, 1967.
DOI : 10.1016/0043-1354(67)90039-5

K. Holt, S. Baker, F. Weill, E. 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

K. Holt, T. Nga, T. Thanh, D. Vinh, H. Kim et al., Tracking the establishment of local endemic populations of an emergent enteric pathogen, Proceedings of the National Academy of Sciences of, pp.17522-17527, 2013.
DOI : 10.1073/pnas.1308632110

M. Islam, M. Hasan, and S. Khan, Growth and survival of Shigella flexneri in common Bangladeshi foods under various conditions of time and temperature, Applied and Environmental Microbiology, vol.59, pp.652-654, 1993.

M. Islam, F. Rezwan, and S. Khan, Survival of Shigella flexneri in artificial aquatic environment: effects of different physicochemical stress factors, Journal of Diarrhoeal Diseases Research, vol.14, pp.37-40, 1996.

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

K. Kotloff, J. Nataro, W. Blackwelder, D. Nasrin, T. Farag et al., Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study, The Lancet, vol.382, issue.9888, pp.209-222, 1016.
DOI : 10.1016/S0140-6736(13)60844-2

K. Kotloff, J. Winickoff, B. Ivanoff, J. Clemens, D. Swerdlow et al., Global burden of Shigella infections: implications for vaccine development and implementation of control strategies, Bulletin of the World Health Organization, vol.77, pp.651-666, 1999.

K. Lawlor, P. Daskaleros, R. Robinson, and S. Payne, Virulence of iron transport mutants of Shigella flexneri and utilization of host iron compounds, Infection and Immunity, vol.55, pp.594-599, 1987.

S. Livio, N. Strockbine, S. Panchalingam, S. Tennant, E. Barry et al., Shigella Isolates From the Global Enteric Multicenter Study Inform Vaccine Development, Clinical Infectious Diseases, vol.59, issue.7, pp.933-941, 2014.
DOI : 10.1093/cid/ciu468

S. Luck, S. Turner, K. Rajakumar, H. Sakellaris, and B. Adler, Ferric Dicitrate Transport System (Fec) of Shigella flexneri 2a YSH6000 Is Encoded on a Novel Pathogenicity Island Carrying Multiple Antibiotic Resistance Genes, Infection and Immunity, vol.69, issue.10, pp.6012-6021, 2001.
DOI : 10.1128/IAI.69.10.6012-6021.2001

A. Mather, S. Reid, D. Maskell, J. Parkhill, M. Fookes et al., Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts, Science, vol.341, issue.6153, pp.1514-1517, 2013.
DOI : 10.1126/science.1240578

A. Mcnally, L. Cheng, S. Harris, and J. Corander, The evolutionary path to extraintestinal pathogenic, drugresistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome, 2013.

A. Mutreja, D. Kim, N. Thomson, T. Connor, J. Lee et al., Evidence for several waves of global transmission in the seventh cholera pandemic, Nature, vol.7, issue.7365, pp.462-465, 1038.
DOI : 10.1038/nature10392

F. Noriega, F. Liao, S. Formal, A. Fasano, and M. Levine, Prevalence of Shigella Enterotoxin 1 among Shigella Clinical Isolates of Diverse Serotypes, Journal of Infectious Diseases, vol.172, issue.5, 1995.
DOI : 10.1093/infdis/172.5.1408

O. Brien, I. Gibson, and F. , The structure of enterochelin and related 2,3-dihydroxy-N-benzoylserine conjugates from Escherichia coli, Biochimica et Biophysica Acta, vol.21570, pp.393-402, 1970.

C. Okoro, R. Kingsley, T. Connor, S. Harris, C. Parry et al., Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa, Nature Genetics, vol.4, issue.11, pp.1215-1221, 2012.
DOI : 10.1093/bioinformatics/btn529

T. Otto, M. Sanders, M. Berriman, and C. Newbold, Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology, Bioinformatics, vol.26, issue.14, pp.1704-1707, 2010.
DOI : 10.1093/bioinformatics/btq269

G. Pupo, R. Lan, and P. 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 of the USA, pp.10567-10572, 2000.
DOI : 10.1073/pnas.180094797

P. Ram, J. Crump, S. Gupta, M. Miller, and E. Mintz, Part II. Analysis of data gaps pertaining to Shigella infections in low and medium human development index countries, Epidemiology and Infection, vol.136, pp.577-603, 1984.

S. Reuter, T. Connor, L. Barquist, D. Walker, T. Feltwell et al., Parallel independent evolution of pathogenicity within the genus Yersinia, Proceedings of the National Academy of Sciences of the, pp.6768-6773, 2014.
DOI : 10.1073/pnas.1317161111

L. Rohmer, M. Jacobs, M. Brittnacher, C. Fong, H. Hayden et al., Genomic analysis of the emergence of 20th century epidemic dysentery, BMC Genomics, vol.15, issue.1, pp.355-365, 2014.
DOI : 10.1093/oxfordjournals.molbev.a026236

URL : https://hal.archives-ouvertes.fr/hal-01061621

L. Runyen-janecky, S. Reeves, E. Gonzales, and S. Payne, Contribution of the Shigella flexneri Sit, Iuc, and Feo Iron Acquisition Systems to Iron Acquisition In Vitro and in Cultured Cells, Infection and Immunity, vol.71, issue.4, 1919.
DOI : 10.1128/IAI.71.4.1919-1928.2003

D. Sack, S. Hoque, M. Etheridge, and A. Huq, Is protection against shigellosis induced by natural infection with Plesiomonas shigelloides?, The Lancet, vol.343, issue.8910, pp.1413-1415, 1994.
DOI : 10.1016/S0140-6736(94)92531-3

T. Saha, M. Murhekar, Y. Hutin, and T. Ramamurthy, An urban, water-borne outbreak of diarrhoea and shigellosis in a district town in eastern India, The National Medical Journal of India, vol.22, pp.237-239, 2009.

J. Sahl, C. Morris, J. Emberger, C. Fraser, J. Ochieng et al., Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics, Journal of Clinical Microbiology, vol.53, issue.3, pp.951-960, 2015.
DOI : 10.1128/JCM.03527-14

P. Sansonetti, D. Kopecko, and S. Formal, Involvement of a plasmid in the invasive ability of Shigella flexneri, Infection and Immunity, vol.35, pp.852-860, 1982.

M. Schmitt and S. Payne, Genetics and regulation of enterobactin genes in Shigella flexneri., Journal of Bacteriology, vol.170, issue.12, pp.5579-5587, 1988.
DOI : 10.1128/jb.170.12.5579-5587.1988

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, 2006.
DOI : 10.1093/bioinformatics/btl446

Q. Sun, R. Lan, Y. Wang, A. Zhao, S. Zhang et al., Development of a Multiplex PCR Assay Targeting O-Antigen Modification Genes for Molecular Serotyping of Shigella flexneri, Journal of Clinical Microbiology, vol.49, issue.11, pp.3766-3770, 1128.
DOI : 10.1128/JCM.01259-11

W. Swaddiwudhipong, S. Karintraratana, and S. Kavinum, A common-source outbreak of shigellosis involving a piped public water supply in northern Thai communities, The Journal of Tropical Medicine and Hygiene, vol.98, pp.145-150, 1995.

A. Ud-din, S. Wahid, H. Latif, M. Shahnaij, M. Akter et al., Changing Trends in the Prevalence of Shigella Species: Emergence of Multi-Drug Resistant Shigella sonnei Biotype g in Bangladesh, PLoS ONE, vol.18, issue.12, 2013.
DOI : 10.1371/journal.pone.0082601.t002

M. Uyanik, H. Yazgi, and A. Ayyildiz, Survival of Salmonella typhi and Shigella flexneri in different water samples and at different temperatures, Turkish Journal of Medical Sciences, vol.38, pp.307-310, 2008.

H. Vinh, N. Nhu, T. Nga, P. Duy, J. Campbell et al., A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation, BMC Infectious Diseases, vol.134, issue.6, pp.204-214, 2009.
DOI : 10.1016/0264-410X(95)00102-7

A. Von-mentzer, T. Connor, L. Wieler, T. Semmler, A. Iguchi et al., Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution, Nature Genetics, vol.65, issue.12, pp.1321-1326, 2014.
DOI : 10.1016/j.mimet.2005.03.018

L. Von-seidlein, D. Kim, A. M. Lee, H. Wang, X. Thiem et al., A Multicentre Study of Shigella Diarrhoea in Six Asian Countries: Disease Burden, Clinical Manifestations, and Microbiology, PLoS Medicine, vol.129, issue.9, 2006.
DOI : 10.1371/journal.pmed.0030353.sd001

E. Wyckoff, M. Boulette, and S. Payne, Genetics and environmental regulation of Shigella iron transport systems, BioMetals, vol.33, issue.4, pp.43-51, 2009.
DOI : 10.1007/s10534-008-9188-x

F. Yang, Y. J. Zhang, X. Chen, L. Jiang, Y. Yan et al., Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery, Nucleic Acids Research, vol.33, issue.19, pp.6445-6458, 2005.
DOI : 10.1093/nar/gki954

Y. Yang, M. Song, S. Park, and S. Kim, Direct detection of Shigella flexneri and Salmonella typhimurium in human feces by real-time PCR, Journal of Microbiology and Biotechnology, vol.17, pp.1616-1621, 2007.

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801

N. Zhang, R. Lan, Q. Sun, J. Wang, Y. Wang et al., Genomic Portrait of the Evolution and Epidemic Spread of a Recently Emerged Multidrug-Resistant Shigella flexneri Clone in China, Journal of Clinical Microbiology, vol.52, issue.4, pp.1119-1126, 1128.
DOI : 10.1128/JCM.02669-13