Y. Shi, Y. Wu, W. Zhang, J. Qi, and G. Gao, Enabling the 'host jump': structural determinants of receptor-binding specificity in influenza A viruses, Nature Reviews Microbiology, vol.337, issue.12, pp.822-831, 2014.
DOI : 10.1038/nrmicro3362

M. De-graaf and R. A. Fouchier, Role of receptor binding specificity in influenza A virus transmission and pathogenesis, The EMBO Journal, vol.33, issue.8, pp.823-841, 2014.
DOI : 10.1002/embj.201387442

S. Spano and J. E. Galan, A Rab32-Dependent Pathway Contributes to Salmonella Typhi Host Restriction, Science, vol.338, issue.6109, pp.960-963, 2012.
DOI : 10.1126/science.1229224
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693731

R. R. Chaudhuri, Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals, PLoS Genetics, vol.11, issue.4, p.1003456, 2013.
DOI : 10.1371/journal.pgen.1003456.s011

L. Deng, Host Adaptation of a Bacterial Toxin from the Human Pathogen Salmonella Typhi, Cell, vol.159, issue.6, pp.1290-1299, 2014.
DOI : 10.1016/j.cell.2014.10.057

A. E. Mather, 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

M. Mcclelland, Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid, Nature Genetics, vol.60, issue.12, pp.1268-1274, 2004.
DOI : 10.1128/JB.184.9.2411-2419.2002

G. C. Langridge, Patterns of genome evolution that have accompanied host adaptation in Salmonella, Proc. Natl Acad. Sci. USA, pp.863-868, 2015.

D. Viana, A single natural nucleotide mutation alters bacterial pathogen host tropism, Nature Genetics, vol.8, issue.4, pp.361-366, 2015.
DOI : 10.1038/ng.3219
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824278

M. Yue and D. M. Schifferli, Allelic variation in Salmonella: an underappreciated driver of adaptation and virulence, Frontiers in Microbiology, vol.4, p.419, 2014.
DOI : 10.3389/fmicb.2013.00419

R. A. Kingsley, Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar, mBio, vol.4, issue.5, pp.565-578, 2013.
DOI : 10.1128/mBio.00565-13

C. K. Okoro, 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

B. N. Parsons, Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens, PLoS Neglected Tropical Diseases, vol.18, issue.10, p.2487, 2013.
DOI : 10.1371/journal.pntd.0002487.t002

M. Yue, Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes, Applied and Environmental Microbiology, vol.78, issue.20, pp.7480-7482, 2012.
DOI : 10.1128/AEM.01703-12

W. N. Venables and B. D. Ripley, Exploratory Multivariate Analysis in Modern Applied Statistics with S, pp.301-330, 2002.

O. Reilly and P. F. , MultiPhen: joint model of multiple phenotypes can increase discovery in GWAS, PLoS ONE, vol.7, p.34861, 2012.

A. Guo, FimH alleles direct preferential binding of Salmonella to distinct mammalian cells or to avian cells, Microbiology, vol.155, issue.5, pp.1623-1633, 2009.
DOI : 10.1099/mic.0.026286-0

K. Grzymajlo, FimH adhesin from host unrestricted Salmonella Enteritidis binds to different glycoprotein ligands expressed by enterocytes from sheep, pig and cattle than FimH adhesins from host restricted Salmonella Abortus-ovis, Salmonella Choleraesuis and Salmonella Dublin, Veterinary Microbiology, vol.166, issue.3-4, pp.550-557, 2013.
DOI : 10.1016/j.vetmic.2013.07.004

Y. Soyer, R. H. Orsi, L. D. Rodriguez-rivera, Q. Sun, and M. Wiedmann, Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes, BMC Evolutionary Biology, vol.9, issue.1, p.264, 2009.
DOI : 10.1186/1471-2148-9-264

D. I. Kisiela, Allosteric Catch Bond Properties of the FimH Adhesin from Salmonella enterica Serovar Typhimurium, Journal of Biological Chemistry, vol.286, issue.44, pp.38136-38147, 2011.
DOI : 10.1074/jbc.M111.237511

M. Yue, Diversification of the Salmonella Fimbriae: A Model of Macro- and Microevolution, PLoS ONE, vol.26, issue.6, p.38596, 2012.
DOI : 10.1371/journal.pone.0038596.s014

D. Kisiela, Characterization of FimH Adhesins Expressed by Salmonella enterica Serovar Gallinarum Biovars Gallinarum and Pullorum: Reconstitution of Mannose-Binding Properties by Single Amino Acid Substitution, Infection and Immunity, vol.73, issue.9, pp.6187-6190, 2005.
DOI : 10.1128/IAI.73.9.6187-6190.2005

R. M. Tsolis, Identification of a putative Salmonella enterica serotype typhimurium host range factor with homology to IpaH and YopM by signature-tagged mutagenesis, Infect. Immun, vol.67, pp.6385-6393, 1999.

L. Barquist, A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium, Nucleic Acids Research, vol.41, issue.8, pp.4549-4564, 2013.
DOI : 10.1093/nar/gkt148

K. Karlsson, J. Ångström, J. Bergström, and B. Lanne, Microbial interaction with animal cell surface carbohydrates, APMIS, vol.100, pp.71-83, 1992.

J. D. Boddicker, N. A. Ledeboer, J. Jagnow, B. D. Jones, and S. Clegg, Differential binding to and biofilm formation on, HEp-2 cells by Salmonella enterica Serovar Typhimurium is dependent upon allelic variation in the fimH gene of the fim gene cluster, Molecular Microbiology, vol.25, issue.5, pp.1255-1265, 2002.
DOI : 10.1046/j.1365-2958.2002.03121.x

B. E. Dwyer, K. L. Newton, D. Kisiela, E. V. Sokurenko, and S. Clegg, Single nucleotide polypmorphisms of fimH associated with adherence and biofilm formation by serovars of Salmonella enterica, Microbiology, vol.157, issue.11, pp.3162-3171, 2011.
DOI : 10.1099/mic.0.051425-0

D. I. Kisiela, Evolution of Salmonella enterica Virulence via Point Mutations in the Fimbrial Adhesin, PLoS Pathogens, vol.19, issue.6, p.1002733, 2012.
DOI : 10.1371/journal.ppat.1002733.s007

B. Misselwitz, Salmonella enterica Serovar Typhimurium Binds to HeLa Cells via Fim-Mediated Reversible Adhesion and Irreversible Type Three Secretion System 1-Mediated Docking, Infection and Immunity, vol.79, issue.1, pp.330-341, 2011.
DOI : 10.1128/IAI.00581-10

K. Grzymajlo, M. Kuzminska-bajor, J. Jaworski, P. Dobryszycki, and M. Ugorski, The high-adhesive properties of the FimH adhesin of Salmonella enterica serovar Enteritidis are determined by a single F118S substitution, Microbiology, vol.156, issue.6, pp.1738-1748, 2010.
DOI : 10.1099/mic.0.039206-0

M. Kuzminska-bajor, Decreased colonization of chicks by Salmonella enterica serovar Gallinarum expressing mannose-sensitive FimH adhesin from Salmonella enterica serovar Enteritidis, Veterinary Microbiology, vol.158, issue.1-2, pp.205-210, 2012.
DOI : 10.1016/j.vetmic.2012.01.029

R. L. Wilson, J. Elthon, S. Clegg, and B. D. Jones, Salmonella enterica Serovars Gallinarum and Pullorum Expressing Salmonella enterica Serovar Typhimurium Type 1 Fimbriae Exhibit Increased Invasiveness for Mammalian Cells, Infection and Immunity, vol.68, issue.8, pp.4782-4785, 2000.
DOI : 10.1128/IAI.68.8.4782-4785.2000

E. V. Sokurenko, V. Vogel, and W. Thomas, Catch-Bond Mechanism of Force-Enhanced Adhesion: Counterintuitive, Elusive, but ??? Widespread?, Cell Host & Microbe, vol.4, issue.4, pp.314-323, 2008.
DOI : 10.1016/j.chom.2008.09.005

P. Aprikian, Interdomain Interaction in the FimH Adhesin of Escherichia coli Regulates the Affinity to Mannose, Journal of Biological Chemistry, vol.282, issue.32, pp.23437-23446, 2007.
DOI : 10.1074/jbc.M702037200

F. Liu, Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), Applied and Environmental Microbiology, vol.77, issue.13, pp.4520-4526, 2011.
DOI : 10.1128/AEM.00468-11

F. Liu, Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica, Applied and Environmental Microbiology, vol.77, issue.6, pp.1946-1956, 2011.
DOI : 10.1128/AEM.02625-10

M. Dimarzio, N. Shariat, S. Kariyawasam, R. Barrangou, and E. G. Dudley, Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type, Antimicrobial Agents and Chemotherapy, vol.57, issue.9, pp.4282-4289, 2013.
DOI : 10.1128/AAC.00913-13

N. Shariat, Subtyping of Salmonella enterica Serovar Newport Outbreak Isolates by CRISPR-MVLST and Determination of the Relationship between CRISPR-MVLST and PFGE Results, Journal of Clinical Microbiology, vol.51, issue.7, pp.2328-2336, 2013.
DOI : 10.1128/JCM.00608-13

N. Shariat, The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis, Food Microbiology, vol.34, issue.1, pp.164-173, 2013.
DOI : 10.1016/j.fm.2012.11.012

A. E. Darling, B. Mau, and N. Perna, progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement, PLoS ONE, vol.15, issue.6, p.11147, 2010.
DOI : 10.1371/journal.pone.0011147.s005
URL : http://doi.org/10.1371/journal.pone.0011147

R. Overbeek, The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Research, vol.42, issue.D1, pp.206-214, 2014.
DOI : 10.1093/nar/gkt1226

Y. Zhou, Y. Liang, K. H. Lynch, J. J. Dennis, and D. S. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.39, issue.suppl, pp.347-352, 2011.
DOI : 10.1093/nar/gkr485
URL : http://doi.org/10.1093/nar/gkr485

S. V. Angiuoli, CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing, BMC Bioinformatics, vol.12, issue.1, p.356, 2011.
DOI : 10.1371/journal.pcbi.1000352

J. Song, Y. Xu, S. White, K. W. Miller, and M. Wolinsky, SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes, Bioinformatics, vol.21, issue.9, pp.2083-2084, 2005.
DOI : 10.1093/bioinformatics/bti176

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

R. L. Borowsky, Estimating Nucleotide Diversity From Random Amplified Polymorphic DNA and Amplified Fragment Length Polymorphism Data, Molecular Phylogenetics and Evolution, vol.18, issue.1, pp.143-148, 2001.
DOI : 10.1006/mpev.2000.0865

W. Delport, A. F. Poon, S. D. Frost, and S. L. Kosakovsky-pond, Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology, Bioinformatics, vol.26, issue.19, pp.2455-2457, 2010.
DOI : 10.1093/bioinformatics/btq429

K. A. Jolley, E. J. Feil, M. S. Chan, and M. Maiden, Sequence type analysis and recombinational tests (START), Bioinformatics, vol.17, issue.12, pp.1230-1231, 2001.
DOI : 10.1093/bioinformatics/17.12.1230

J. A. Carrico, Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes, Journal of Clinical Microbiology, vol.44, issue.7, pp.2524-2532, 2006.
DOI : 10.1128/JCM.02536-05

A. Roy, A. Kucukural, and Y. Zhang, I-TASSER: a unified platform for automated protein structure and function prediction, Nature Protocols, vol.59, issue.4, pp.725-738, 2010.
DOI : 10.1038/nprot.2010.5
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849174

S. Wu and Y. Zhang, LOMETS: A local meta-threading-server for protein structure prediction, Nucleic Acids Research, vol.35, issue.10, pp.3375-3382, 2007.
DOI : 10.1093/nar/gkm251

J. Yang, A. Roy, and Y. Zhang, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, vol.29, issue.20, pp.2588-2595, 2013.
DOI : 10.1093/bioinformatics/btt447
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789548

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

I. C. Blomfield, M. S. Mcclain, and B. Eisenstein, Type 1 fimbriae mutants of Escherichia coli K12: characterization of recognized afimbriate strains and construction of new fim deletion mutants, Molecular Microbiology, vol.53, issue.6, pp.1439-1445, 1991.
DOI : 10.1016/0378-1119(86)90010-7

J. M. Rhoads, L-glutamine and L-asparagine stimulate Na þ -H þ exchange in porcine jejunal enterocytes, Am. J. Physiol, vol.266, pp.828-838, 1994.

R. Gonzalez-vallina, Lipoprotein and apolipoprotein secretion by a newborn piglet intestinal cell line (IPEC-1), Am. J. Physiol, vol.271, pp.249-259, 1996.

D. Rusu, S. Loret, O. Peulen, J. Mainil, and G. Dandrifosse, Immunochemical biomolecular and biochemical characterization of bovine epithelial intestinal primocultures, BMC Cell Biology, vol.6, issue.1, p.42, 2005.
DOI : 10.1186/1471-2121-6-42

S. Loret, Preliminary characterization of jejunocyte and colonocyte cell lines isolated by enzymatic digestion from adult and young cattle, Research in Veterinary Science, vol.87, issue.1, pp.123-132, 2009.
DOI : 10.1016/j.rvsc.2008.12.002

N. Perreault and J. Beaulieu, Primary Cultures of Fully Differentiated and Pure Human Intestinal Epithelial Cells, Experimental Cell Research, vol.245, issue.1, pp.34-42, 1998.
DOI : 10.1006/excr.1998.4221