S. D. Alcaine, Y. Soyer, L. D. Warnick, W. L. Su, S. Sukhnananda et al., Multilocus Sequence Typing Supports the Hypothesis that Cow- and Human-Associated Salmonella Isolates Represent Distinct and Overlapping Populations, Applied and Environmental Microbiology, vol.72, issue.12, pp.7575-7585, 2006.
DOI : 10.1128/AEM.01174-06

S. D. Alcaine, S. S. Sukhnanand, L. D. Warnick, W. L. Su, P. Mcgann et al., Ceftiofur-Resistant Salmonella Strains Isolated from Dairy Farms Represent Multiple Widely Distributed Subtypes That Evolved by Independent Horizontal Gene Transfer, Antimicrobial Agents and Chemotherapy, vol.49, issue.10, pp.4061-4067, 2005.
DOI : 10.1128/AAC.49.10.4061-4067.2005

G. Arlet, T. J. Barrett, P. Butaye, A. Cloeckaert, M. R. Mulvey et al., Salmonella resistant to extended-spectrum cephalosporins: prevalence and epidemiology. Microbes Infect, pp.1945-1954, 2006.

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval et al., CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1712, 2007.
DOI : 10.1126/science.1138140

P. Beltran, J. M. Musser, R. Helmuth, J. J. Farmer, I. et al., Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. choleraesuis, S. derby, S. dublin, S. enteritidis, S. heidelberg, S. infantis, S. newport, and S. typhimurium., Proceedings of the National Academy of Sciences, vol.85, issue.20, pp.7753-7757, 1988.
DOI : 10.1073/pnas.85.20.7753

E. F. Boyd, F. S. Wang, P. Beltran, S. A. Plock, K. Nelson et al., Salmonella reference collection B (SARB): strains of 37 serovars of subspecies I, Journal of General Microbiology, vol.139, issue.6, pp.1125-1132, 1993.
DOI : 10.1099/00221287-139-6-1125

E. W. Brown, M. K. Mammel, J. E. Leclerc, and T. A. Cebula, Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens, Proceedings of the National Academy of Sciences, vol.100, issue.26, pp.15676-15681, 2003.
DOI : 10.1073/pnas.2634406100

T. C. Bruen, H. Philippe, and D. Bryant, A Simple and Robust Statistical Test for Detecting the Presence of Recombination, Genetics, vol.172, issue.4, pp.2665-2681, 2006.
DOI : 10.1534/genetics.105.048975

D. Bryant and V. Moulton, Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks, Molecular Biology and Evolution, vol.21, issue.2, pp.255-265, 2004.
DOI : 10.1093/molbev/msh018

L. R. Bullas, C. Colson, and B. Neufeld, Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes, J. Bacteriol, vol.141, pp.275-292, 1980.

A. Carattoli, F. Tosini, W. P. Giles, M. E. Rupp, S. H. Hinrichs et al., Characterization of Plasmids Carrying CMY-2 from Expanded-Spectrum Cephalosporin-Resistant Salmonella Strains Isolated in the United States between 1996 and 1998, Antimicrobial Agents and Chemotherapy, vol.46, issue.5, pp.1269-1272, 1996.
DOI : 10.1128/AAC.46.5.1269-1272.2002

R. N. Cobbold, D. H. Rice, M. A. Davis, T. E. Besser, and D. D. Hancock, serovar Newport in two dairy herds, Journal of the American Veterinary Medical Association, vol.228, issue.4, pp.585-591, 2006.
DOI : 10.2460/javma.228.4.585

R. A. Devasia, J. K. Varma, J. Whichard, S. Gettner, A. B. Cronquist et al., Antimicrobial use and outcomes in patients with multidrugresistant and pansusceptible Salmonella Newport infections, Microb . Drug Resist, vol.11, pp.2002-2003371, 2005.

X. Didelot, M. Barker, D. Falush, and F. G. Priest, Evolution of pathogenicity in the Bacillus cereus group, Systematic and Applied Microbiology, vol.32, issue.2, pp.81-90, 2009.
DOI : 10.1016/j.syapm.2009.01.001

X. Didelot and D. Falush, Inference of Bacterial Microevolution Using Multilocus Sequence Data, Genetics, vol.175, issue.3, pp.1251-1266, 2007.
DOI : 10.1534/genetics.106.063305

K. E. Dingle, F. M. Colles, D. Falush, and M. C. Maiden, Sequence Typing and Comparison of Population Biology of Campylobacter coli and Campylobacter jejuni, Journal of Clinical Microbiology, vol.43, issue.1, pp.340-347, 2005.
DOI : 10.1128/JCM.43.1.340-347.2005

B. Doublet, K. Praud, F. Weill, and A. Cloeckaert, Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1, Journal of Antimicrobial Chemotherapy, vol.63, issue.2, pp.282-289, 2009.
DOI : 10.1093/jac/dkn500

B. Doublet, F. Weill, L. Fabre, E. Chaslus-dancla, and A. Cloeckaert, Variant Salmonella Genomic Island 1 Antibiotic Resistance Gene Cluster Containing a Novel 3'-N-Aminoglycoside Acetyltransferase Gene Cassette, aac(3)-Id, in Salmonella enterica Serovar Newport, Antimicrobial Agents and Chemotherapy, vol.48, issue.10, pp.3806-3812, 2004.
DOI : 10.1128/AAC.48.10.3806-3812.2004

E. F. Dunne, P. D. Fey, P. Kludt, R. Reporter, F. Mostashari et al., Emergence of Domestically Acquired Ceftriaxone-Resistant <EMPH TYPE="ITAL">Salmonella</EMPH> Infections Associated With AmpC ??-Lactamase, JAMA, vol.284, issue.24, pp.3151-3156, 2000.
DOI : 10.1001/jama.284.24.3151

S. Egorova, L. Kaftyreva, P. A. Grimont, and F. X. , Isolates in Adults in Saint Petersburg, Russia (2002???2005), Microbial Drug Resistance, vol.13, issue.2, pp.102-107, 2002.
DOI : 10.1089/mdr.2007.712

S. Egorova, M. Timinouni, M. Demartin, S. A. Granier, J. M. Whichard et al., Serotype Newport, France, Emerging Infectious Diseases, vol.14, issue.6, pp.954-957, 2008.
DOI : 10.3201/eid1406.071168

URL : http://doi.org/10.3201/eid1406.071168

M. C. Enright, D. A. Robinson, G. Randle, E. J. Feil, H. Grundmann et al., The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA), Proceedings of the National Academy of Sciences, vol.99, issue.11, pp.7687-7692, 2002.
DOI : 10.1073/pnas.122108599

E. Centre and D. Prevention, Enter-net quarterly Salmonella reports European Centre for Disease Prevention and Control (ECDC), 2009.

D. Falush, M. Torpdahl, X. Didelot, D. F. Conrad, D. J. Wilson et al., Mismatch induced speciation in Salmonella: model and data, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.140, issue.3, pp.2045-2053, 2006.
DOI : 10.1073/pnas.94.18.9786

E. J. Feil, J. E. Cooper, H. Grundmann, D. A. Robinson, M. C. Enright et al., How Clonal Is Staphylococcus aureus?, Journal of Bacteriology, vol.185, issue.11, pp.3307-3316, 2003.
DOI : 10.1128/JB.185.11.3307-3316.2003

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155367

E. J. Feil, E. C. Holmes, D. E. Bessen, M. Chan, N. P. Day et al., Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences, Proc. Natl. Acad. Sci. U. S. A. 98, pp.182-187, 2001.
DOI : 10.1073/pnas.98.1.182

E. J. Feil, B. C. Li, D. M. Aanensen, W. P. Hanage, and B. G. Spratt, eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data, Journal of Bacteriology, vol.186, issue.5, pp.1518-1530, 2004.
DOI : 10.1128/JB.186.5.1518-1530.2004

E. J. Feil, M. C. Maiden, M. Achtman, and B. G. Spratt, The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis, Molecular Biology and Evolution, vol.16, issue.11, pp.1496-1502, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026061

E. J. Feil, J. M. Smith, M. C. Enright, and B. G. Spratt, Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data, Genetics, vol.154, pp.1439-1450, 2000.

W. F. Fricke, T. J. Welsh, P. F. Mcdermott, M. K. Mammel, J. E. Leclerc et al., Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family, Journal of Bacteriology, vol.191, issue.15, pp.4750-4757, 2009.
DOI : 10.1128/JB.00189-09

M. Guibourdenche, P. Roggentin, M. Mikoleit, P. I. Fields, J. Bockemuhl et al., Supplement 2003???2007 (No. 47) to the White-Kauffmann-Le Minor scheme, Research in Microbiology, vol.161, issue.1, pp.26-29, 2003.
DOI : 10.1016/j.resmic.2009.10.002

A. Gupta, J. Fontana, C. Crowe, B. Bolstroff, A. Stout et al., Serotype Newport Infections Resistant to Expanded???Spectrum Cephalosporins in the United States, The Journal of Infectious Diseases, vol.188, issue.11, pp.1707-1716, 2003.
DOI : 10.1086/379668

W. P. Hanage, C. Fraser, and B. G. Spratt, The impact of homologous recombination on the generation of diversity in bacteria, Journal of Theoretical Biology, vol.239, issue.2, pp.210-219, 2006.
DOI : 10.1016/j.jtbi.2005.08.035

W. P. Hanage, B. G. Spratt, K. M. Turner, and C. Fraser, Modelling bacterial speciation, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.94, issue.18, pp.2039-2044, 2006.
DOI : 10.1073/pnas.94.18.9763

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764933

H. Harbottle, D. G. White, P. F. Mcdermott, R. D. Walker, and S. Zhao, Comparison of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Typing for Characterization of Salmonella enterica Serotype Newport Isolates, Journal of Clinical Microbiology, vol.44, issue.7, pp.2449-2457, 2006.
DOI : 10.1128/JCM.00019-06

K. E. Holt, J. Parkhill, C. J. Mazzoni, P. Roumagnac, F. Weill et al., High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics, vol.149, issue.8, pp.987-993, 2008.
DOI : 10.1186/gb-2004-5-2-r12

E. Honsa, T. Fricke, A. J. Stephens, D. Ko, F. Kong et al., Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms, BMC Microbiology, vol.8, issue.1, p.140, 2008.
DOI : 10.1186/1471-2180-8-140

D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006.
DOI : 10.1093/molbev/msj030

I. B. Jakobsen and S. Easteal, A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences, Bioinformatics, vol.12, issue.4, pp.291-295, 1996.
DOI : 10.1093/bioinformatics/12.4.291

C. Kidgell, U. Reichard, J. Wain, B. Linz, M. Torpdahl et al., Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old, Infection, Genetics and Evolution, vol.2, issue.1, pp.39-45, 2002.
DOI : 10.1016/S1567-1348(02)00089-8

R. A. Kingsley, C. L. Msefula, N. R. Thomson, S. Kariuki, K. E. Holt et al., Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype, Genome Research, vol.19, issue.12, pp.2279-2287, 2009.
DOI : 10.1101/gr.091017.109

G. Morelli, X. Didelot, B. Kusecek, S. Schwarz, D. Falush et al., Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families, PLoS Genetics, vol.323, issue.7, p.1001036, 2010.
DOI : 10.1371/journal.pgen.1001036.s006

S. Octavia and R. Lan, Frequent recombination and low level of clonality within Salmonella enterica subspecies I, Microbiology, vol.152, issue.4, pp.1099-1108, 2006.
DOI : 10.1099/mic.0.28486-0

C. Poppe, L. Martin, A. Muckle, M. Archambault, S. Mcewen et al., Characterization of antimicrobial resistance of Salmonella Newport isolated from animals, the environment, and animal food products in Canada, Can. J. Vet. Res, vol.70, pp.105-114, 2006.

S. Porwollik, E. F. Boyd, C. Choy, P. Cheng, L. Florea et al., Characterization of Salmonella enterica Subspecies I Genovars by Use of Microarrays, Journal of Bacteriology, vol.186, issue.17, pp.5883-5898, 2004.
DOI : 10.1128/JB.186.17.5883-5898.2004

D. Posada and K. A. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

M. W. Reeves, G. M. Evins, A. A. Heiba, B. D. Plikaytis, J. J. Farmer et al., Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov, J. Clin. Microbiol, vol.27, pp.313-320, 1989.

A. M. Ridley, P. Punia, L. R. Ward, B. Rowe, and E. J. , Plasmid characterization and pulsed-field electrophoretic analysis demonstrate that ampicillin-resistant strains of Salmonella enteritidis phage type 6a are derived from Salm. enteritidis phage type 4, J. Appl. Bacteriol, vol.81, pp.613-618, 1996.

J. Rozas, J. C. Sanchez-delbarrio, X. Messeguer, and R. Rozas, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359

R. K. Selander, P. Beltran, N. H. Smith, R. M. Barker, P. B. Crichton et al., Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B, Infect. Immun, vol.58, pp.1891-1901, 1990.

R. K. Selander, P. Beltran, N. H. Smith, F. A. Helmuth, D. J. Rubin et al., Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers, Infect. Immun, vol.58, pp.2262-2275, 1990.

N. H. Smith, S. V. Gordon, R. Rua-domenech, R. S. Clifton-hadley, and R. G. Hewinson, Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis, Nature Reviews Microbiology, vol.51, issue.9, pp.670-681, 2006.
DOI : 10.1038/nrmicro1472

B. G. Spratt, Exploring the Concept of Clonality in Bacteria, Methods Mol. Biol, vol.266, pp.323-352, 2004.
DOI : 10.1385/1-59259-763-7:323

S. Sukhnanand, S. Alcaine, L. D. Warnick, W. Su, J. Hof et al., DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected Salmonella enterica Serotypes, Journal of Clinical Microbiology, vol.43, issue.8, pp.3688-3698, 2005.
DOI : 10.1128/JCM.43.8.3688-3698.2005

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092

URL : http://mbe.oxfordjournals.org/cgi/content/short/24/8/1596

M. Torpdahl, M. N. Skov, D. Sandvang, and D. L. Baggesen, Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism, Journal of Microbiological Methods, vol.63, issue.2, pp.173-184, 2005.
DOI : 10.1016/j.mimet.2005.03.006

T. J. Welch, W. F. Fricke, P. F. Mcdermott, D. G. White, M. L. Rosso et al., Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk, PLoS ONE, vol.189, issue.1, p.309, 2007.
DOI : 10.1371/journal.pone.0000309.s001

M. Wiesner, M. B. Zaidi, E. Calva, M. Fernandez-mora, J. J. Clava et al., Association of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains, BMC Microbiology, vol.9, issue.1, p.131, 2009.
DOI : 10.1186/1471-2180-9-131

P. L. Winokur, A. Brueggemann, D. L. Desalvo, L. Hoffmann, M. D. Apley et al., Animal and Human Multidrug-Resistant, Cephalosporin-Resistant Salmonella Isolates Expressing a Plasmid-Mediated CMY-2 AmpC beta -Lactamase, Antimicrobial Agents and Chemotherapy, vol.44, issue.10, pp.2777-2783, 2000.
DOI : 10.1128/AAC.44.10.2777-2783.2000

S. D. Zhao, D. G. White, P. F. Mcdermott, S. Friedman, L. English et al., Identification and Expression of Cephamycinase blaCMY Genes in Escherichia coli and Salmonella Isolates from Food Animals and Ground Meat, Antimicrobial Agents and Chemotherapy, vol.45, issue.12, pp.3647-3650, 2001.
DOI : 10.1128/AAC.45.12.3647-3650.2001