, PFGE: Pulsed-field gel electrophoresis 641 QRDR: Quinolone resistance-determining region 642 SGI: Salmonella Genomic Island 643 SNV: Single-nucleotide variant 644 WHO: World Health Organisation 645 WGS: Whole-genome sequencing

F. Weill, S. Bertrand, F. Guesnier, S. Baucheron, A. Cloeckaert et al.,

, Ciprofloxacin-resistant Salmonella Kentucky in travelers, Emerg Infect Dis, vol.653, issue.10, pp.1611-1613, 2006.

L. Hello, S. Hendriksen, R. S. Doublet, B. Fisher, I. Nielsen et al., International spread of an epidemic population of Salmonella enterica 656 serotype Kentucky ST198 resistant to ciprofloxacin, J Infect Dis, vol.204, issue.5, pp.675-84, 2011.

L. Hello, S. Bekhit, A. Granier, S. A. Barua, H. Beutlich et al., The 659 global establishment of a highly-fluoroquinolone resistant Salmonella enterica 660 serotype Kentucky ST198 strain, Front Microbiol. Frontiers, vol.4, p.395, 2013.

L. Hello, S. Harrois, D. Bouchrif, B. Sontag, L. Elhani et al., Highly 662 drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a 663 microbiological study, Lancet Infect Dis, vol.13, issue.8, pp.672-681, 2013.

T. Westrell, D. L. Monnet, C. Gossner, O. Heuer, and J. Takkinen, , p.665

, Salmonella enterica serotype Kentucky in Europe, Lancet Infect Dis, vol.666, issue.4, pp.270-271, 2014.

L. Hello, S. Weill, F. Guibert, V. Praud, K. Cloeckaert et al., Early 668 strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence 669 type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants 670 with a novel insertion sequence, Antimicrob Agents Chemother. American 671 Society for Microbiology, vol.56, issue.10, pp.5096-102, 2012.

D. Boyd, G. A. Peters, A. Cloeckaert, K. S. Boumedine, and E. Chaslus-dancla, , p.673

H. Imberechts, Complete nucleotide sequence of a 43-kilobase genomic 674 island associated with the multidrug resistance region of Salmonella enterica 675 serovar Typhimurium DT104 and its identification in phage type DT120 and 676 serovar Agona, J Bacteriol, vol.183, pp.5725-5757, 2019.

D. Boyd, A. Cloeckaert, E. Chaslus-dancla, and M. R. Mulvey, Characterization of 679 variant Salmonella genomic island 1 multidrug resistance regions from serovars 680

T. Dt104 and A. , Antimicrobial Agents and Chemotherapy, vol.681, issue.6, pp.1714-1736, 2002.

E. Siebor and C. Neuwirth, Emergence of Salmonella genomic island, vol.1, issue.SGI1, p.683

, Proteus mirabilis clinical isolates

B. Doublet, D. Boyd, M. R. Mulvey, and A. Cloeckaert, The Salmonella genomic island 686 1 is an integrative mobilizable element, Mol Microbiol, vol.55, issue.6, p.11, 2005.

N. Carraro, D. Matteau, P. Luo, S. Rodrigue, and V. Burrus, , p.689

, IncA/C conjugative plasmids stimulates genomic islands and multidrug 690 resistance dissemination, PLoS Genet, vol.10, issue.10, p.1004714, 2014.

G. Douard, K. Praud, A. Cloeckaert, and B. Doublet, The Salmonella Genomic Island 1 693 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid 694 family, vol.5, p.15302, 2010.

R. M. Hall, Salmonella genomic islands and antibiotic resistance in Salmonella 697 enterica, Future Microbiol, vol.5, issue.10, pp.1525-1563, 2010.

E. Siebor and C. Neuwirth, Proteus genomic island 1 (PGI1), a new resistance 699 genomic island from two Proteus mirabilis French clinical isolates, J Antimicrob, p.700
DOI : 10.1093/jac/dku314
URL : https://academic.oup.com/jac/article-pdf/69/12/3216/2457975/dku314.pdf

. Chemother, , vol.701, p.15, 2014.

R. S. Levings, S. P. Djordjevic, and R. M. Hall, SGI2, a relative of Salmonella genomic 702 island SGI1 with an independent origin, Antimicrob Agents Chemother

B. Doublet, K. Praud, F. Weill, and A. Cloeckaert, Association of IS26-composite 705 transposons and complex In4-type integrons generates novel multidrug 706 resistance loci in Salmonella genomic island 1, J Antimicrob Chemother, vol.63, issue.2, pp.282-291, 2009.

B. Doublet, K. Praud, S. Bertrand, J. M. Collard, F. X. Weill et al., , vol.709, pp.3745-54

R. S. Levings, S. R. Partridge, S. P. Djordjevic, and R. M. Hall, SGI1-K, a variant of the 711 SGI1 genomic island carrying a mercury resistance region, in Salmonella 712 enterica serovar Kentucky, Antimicrob Agents Chemother. American Society 713 for Microbiology, vol.51, issue.1, pp.317-340, 2007.

S. Baucheron, L. Hello, S. Doublet, B. , G. E. Weill et al., ramR 715 mutations affecting fluoroquinolone susceptibility in epidemic multidrug-716 resistant Salmonella enterica serovar Kentucky ST198. Front Microbiol, vol.4, pp.1-6, 2013717-09-07.
DOI : 10.3389/fmicb.2013.00213
URL : https://www.frontiersin.org/articles/10.3389/fmicb.2013.00213/pdf

M. W. Allard, E. Strain, D. Melka, K. Bunning, S. M. Musser et al.,

, Practical Value of Food Pathogen Traceability through Building a Whole-720

, Genome Sequencing Network and Database

R. E. Timme, H. Rand, M. S. Leon, M. Hoffmann, E. Strain et al.,

, GenomeTrakr proficiency testing for foodborne pathogen surveillance: an 724 exercise from 2015, Microbial Genomics. Microbiology Society, vol.4, issue.7, pp.289-726, 2018.

M. Inouye, H. Dashnow, L. Raven, M. B. Schultz, B. J. Pope et al., SRST2: Rapid genomic surveillance for public health and hospital microbiology 728 labs, Genome Med, vol.6, issue.11, p.90, 2014.
DOI : 10.1101/006627
URL : https://www.biorxiv.org/content/biorxiv/early/2014/07/28/006627.full.pdf

S. Kurtz, A. Phillippy, and A. L. Delcher, Versatile and open software for comparing 730 large genomes, Genome Biology, vol.5, 2004.

K. E. Holt, J. Parkhill, C. J. Mazzoni, P. Roumagnac, F. Weill et al.,

, High-throughput sequencing provides insights into genome variation and 733 evolution in Salmonella Typhi, Nat Genet, vol.40, issue.8, pp.987-93, 2008.

K. E. Holt, S. Baker, F. Weill, E. C. Holmes, A. Kitchen et al., Shigella 736 sonnei genome sequencing and phylogenetic analysis indicate recent 737 global dissemination from Europe, Nat Genet, vol.44, issue.9, pp.1056-1065, 2012738-09.
DOI : 10.1038/ng.2369
URL : http://europepmc.org/articles/pmc3442231?pdf=render

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2. Nat 740 Meth, vol.9, pp.357-366, 2012.
DOI : 10.1038/nmeth.1923
URL : http://europepmc.org/articles/pmc3322381?pdf=render

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The 742 Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf

N. J. Croucher, A. J. Page, T. R. Connor, A. J. Delaney, J. A. Keane et al.,

, Rapid phylogenetic analysis of large samples of recombinant bacterial whole 746 genome sequences using Gubbins, Nucleic Acids Res, vol.747, p.1196, 2014.

R. Bouckaert, J. Heled, D. Kühnert, T. Vaughan, C. Wu et al., BEAST 2: 749 a software platform for Bayesian evolutionary analysis, PLoS Comput Biol, vol.750, issue.4, p.1003537, 2014.
DOI : 10.1371/journal.pcbi.1003537
URL : https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003537&type=printable

A. Rambaut, M. A. Suchard, D. Xie, and A. J. Drummond, Tracer, vol.753, p.31

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by 754 sampling trees, BMC Evol Biol. BioMed Central Ltd, vol.7, issue.1, p.32, 2007.
DOI : 10.1186/1471-2148-7-214
URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-7-214

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-756 analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1315, 2014757-05-01.

, Composition of macro geographical 759 (continental) regions, geographical sub-regions, and selected economic and other 760 groupings, p.761, 2013.

J. P. Bollback, SIMMAP: stochastic character mapping of discrete traits on 763 phylogenies, BMC Bioinformatics. BioMed Central Ltd, vol.7, issue.1, p.35, 2006.

L. J. Revell, phytools: an R package for phylogenetic comparative biology (and 765 other things), vol.766, pp.217-240, 2011.
DOI : 10.1111/j.2041-210x.2011.00169.x
URL : https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2011.00169.x

H. Lab and . Fastxtoolkit, , 2010.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: A flexible trimmer for Illumina 770
DOI : 10.1093/bioinformatics/btu170
URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf

, Sequence Data. Bioinformatics, vol.30, 2014.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., 772 SPAdes: a new genome assembly algorithm and its applications to single-cell 773 sequencing, J Comput Biol, vol.19, issue.5, pp.455-77, 2012.
DOI : 10.1089/cmb.2012.0021
URL : http://europepmc.org/articles/pmc3342519?pdf=render

M. Boetzer, C. V. Henkel, H. J. Jansen, D. Butler, and W. Pirovano, Scaffolding pre-775 assembled contigs using SSPACE, Bioinformatics, vol.776, issue.4, pp.578-587, 2011.
DOI : 10.1093/bioinformatics/btq683
URL : https://academic.oup.com/bioinformatics/article-pdf/27/4/578/16902132/btq683.pdf

M. Boetzer and W. Pirovano, Toward almost closed genomes with GapFiller
DOI : 10.1186/gb-2012-13-6-r56
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2012-13-6-r56

, Genome Biology. BioMed Central, vol.13, issue.6, pp.1-779, 2012.

S. Assefa, T. M. Keane, T. D. Otto, C. Newbold, and M. Berriman, ABACAS: algorithm-780 based automatic contiguation of assembled sequences, Bioinformatics, vol.25, issue.15, pp.1968-1977, 2009.
DOI : 10.1093/bioinformatics/btp347
URL : https://academic.oup.com/bioinformatics/article-pdf/25/15/1968/563909/btp347.pdf

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.783
DOI : 10.1093/bioinformatics/btu153
URL : https://academic.oup.com/bioinformatics/article-pdf/30/14/2068/7250406/btu153.pdf

S. K. Gupta, B. R. Padmanabhan, S. M. Diene, R. Lopez-rojas, M. Kempf et al., ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance 786 genes in bacterial genomes, Antimicrob Agents Chemother. American Society 787 for Microbiology, vol.58, issue.1, pp.212-232, 2014.

A. J. Page, C. A. Cummins, M. Hunt, V. K. Wong, S. Reuter et al.,

, Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, issue.22, pp.3691-3694, 2015790-11-15.

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos et al., 792 BLAST+: architecture and applications, BMC Bioinformatics. BioMed Central, vol.793, issue.1, p.421, 2009.
DOI : 10.1186/1471-2105-10-421
URL : https://doi.org/10.1186/1471-2105-10-421

L. Chen, D. Zheng, B. Liu, J. Yang, and J. Q. , VFDB 2016: hierarchical and refined 795 dataset for big data analysis -10 years on, Nucleic Acids Res, vol.44, issue.D1, pp.694-701, 2016.
DOI : 10.1093/nar/gkv1239
URL : https://doi.org/10.1093/nar/gkv1239

J. Hawkey, M. Hamidian, R. R. Wick, D. J. Edwards, H. Billman-jacobe et al., ISMapper: identifying transposase insertion sites in bacterial genomes from 799 short read sequence data, BMC Genomics. BioMed Central Ltd, vol.16, issue.1, p.19, 2015.
DOI : 10.1186/s12864-015-1860-2
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1860-2

R. R. Wick, M. B. Schultz, J. Zobel, and K. E. Holt, Bandage: interactive visualization of 801 de novo genome assemblies, Bioinformatics, vol.31, p.49, 1920.

A. Carattoli, E. Zankari, A. García-fernández, V. Larsen, M. Lund et al., In silico detection and typing of plasmids using PlasmidFinder and plasmid 804 multilocus sequence typing, Antimicrob Agents Chemother. American Society 805 for Microbiology, vol.58, issue.7, pp.3895-903, 2014.

S. J. Hancock, M. D. Phan, K. M. Peters, B. M. Forde, T. M. Chong et al., 807 Identification of IncA/C Plasmid Replication and Maintenance Genes and 808 Development of a Plasmid Multilocus Sequence Typing Scheme. Antimicrob 809 Agents Chemother, vol.61, pp.1740-1756, 2017.

P. Leekitcharoenphon, E. M. Nielsen, R. S. Kaas, O. Lund, and F. M. Aarestrup, Evaluation 811 of whole genome sequencing for outbreak detection of Salmonella enterica, PLoS ONE, vol.812, issue.2, p.87991, 2014.

C. K. Okoro, R. A. Kingsley, T. R. Connor, S. R. Harris, and C. M. Parry,

. Mn, Intracontinental spread of human invasive Salmonella Typhimurium 815 pathovariants in sub-Saharan Africa, Nature 816 Publishing Group, vol.44, issue.11, pp.1215-1236, 2012.

Z. Zhou, A. Mccann, E. Litrup, R. Murphy, M. Cormican et al., , vol.818

, Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica, p.819

, PLoS Genet. Public Library of Science, vol.820, issue.4, p.1003471, 2013.

V. K. Wong, S. Baker, D. J. Pickard, J. Parkhill, A. J. Page et al.,

, Phylogeographical analysis of the dominant multidrug-resistant H58 clade of 823

, Salmonella Typhi identifies inter-and intracontinental transmission events. Nat 824 Genet, vol.47, pp.632-641, 2015.

Z. Zhou, A. Mccann, F. Weill, C. Blin, S. Nair et al., Transient 826 Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years 827 of global spread of enteric fever, Proc Natl Acad Sci, vol.828, issue.33, pp.12199-204, 2014.

S. Duchêne, K. E. Holt, F. Weill, L. Hello, S. Hawkey et al.,

, Genome-scale rates of evolutionary change in bacteria. Microbial Genomics. 831 Microbiology Society, vol.2, 2016.

L. Villa, B. Guerra, S. Schmoger, J. Fischer, R. Helmuth et al., IncA/C 833 Plasmid Carrying bla(NDM-1), bla(CMY-16), and fosA3 in a Salmonella 834 enterica Serovar Corvallis Strain Isolated from a Migratory Wild Bird in, p.835

. Pubmed--ncbi, Antimicrob Agents Chemother, vol.59, issue.10, p.58, 2015.

B. Mollet, S. Iida, J. Shepherd, and W. Arber, Nucleotide sequence of IS26, a new 837 prokaryotic mobile genetic element, Nucleic Acids Res, vol.11, issue.18, pp.6319-6349, 1983.