T. L. Bannerman, G. A. Hancock, F. C. Tenover, and J. M. Miller, Pulsed-®eld gel electrophoresis as a replacement for bacteriophage typing of Staphylococcus aureus, J. Clin. Microbiol, vol.33, pp.551-555, 1995.

H. Hadrys, M. Balick, and B. Schierwater, Applications of random ampli®ed polymorphic DNA (RAPD) in molecular ecology, Mol. Ecol, vol.1, pp.55-63, 1992.

W. Dabrowski, U. Czekajlo-kolodziej, D. Medrala, and S. Giedrys-kalemba, Optimisation of AP-PCR ®ngerprinting discriminatory power for clinical isolates of Pseudomonas aeruginosa, FEMS Microbiol. Lett, vol.218, pp.51-57, 2003.

B. N. Kreiswirth, S. M. Lutwick, E. K. Chapnick, J. D. Gradon, L. I. Lutwick et al., Tracing the spread of methicillin-resistant Staphylococcus aureus by Southern blot hybridization using gene-speci®c probes of mec and Tn554, Microb. Drug Resist, vol.1, pp.307-313, 1995.

D. Schneider, E. Duperchy, J. Depeyrot, E. Coursange, R. Lenski et al., Genomic comparisons among Escherichia coli strains B, K-12 and O157:H7 using IS elements as molecular markers, BMC Microbiol, vol.2, pp.18-25, 2002.

M. C. Enright and B. G. Spratt, Multilocus sequence typing, Trends Microbiol, vol.7, pp.482-487, 1999.

M. C. Enright, N. P. Day, C. E. Davies, S. J. Peacock, and B. G. Spratt, Multilocus sequence typing for characterization of methicillinresistant and methicillin-susceptible clones of Staphylococcus aureus, J. Clin. Microbiol, vol.38, pp.1008-1015, 2000.

M. C. Enright, D. A. Robinson, G. Randle, E. J. Feil, H. Grundmann et al., The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA), Proc. Natl Acad. Sci. USA, 99, pp.7687-7692, 2002.

J. R. Fitzgerald and J. M. Musser, Evolutionary genomics of pathogenic bacteria, Trends Microbiol, vol.9, pp.547-553, 2001.

J. R. Fitzgerald, D. E. Sturdevant, S. M. Mackie, S. R. Gill, and J. M. Musser, Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic, Proc. Natl Acad. Sci. USA, 98, pp.8821-8826, 2001.

I. Tamas, L. Klasson, B. Canback, A. K. Naslund, A. S. Eriksson et al., million years of genomic stasis in endosymbiotic bacteria, Science, pp.2376-2379, 2002.

D. C. Oliveira, A. Tomasz, and H. De-lencastre, Secrets of success of a human pathogen: molecular evolution of pandemic clones of methicillin-resistant Staphylococcus aureus, Lancet Infect. Dis, vol.2, pp.180-189, 2002.

Y. Leloir, F. Baron, and M. Gautier, Staphylococcus aureus and food poisoning, Genet. Mol. Res, vol.2, pp.63-76, 2003.

M. Kuroda, T. Ohta, I. Uchiyama, T. Baba, H. Yuzawa et al., Whole genome sequencing of meticillin-resistant Staphylococcus aureus, Lancet, vol.357, pp.1225-1240, 2001.

T. Baba, F. Takeuchi, M. Kuroda, H. Yuzawa, K. Aoki et al., Genome and virulence determinants of high virulence community-acquired MRSA, Lancet, pp.1819-1827, 2002.

M. Ohnishi, J. Terajima, K. Kurokawa, K. Nakayama, T. Murata et al., Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning, Proc. Natl Acad. Sci. USA, pp.17043-17048, 2002.

A. Lapidus, N. Galleron, J. T. Andersen, P. L. Jorgensen, S. D. Ehrlich et al., Co-linear scaffold of the Bacillus licheniformis and Bacillus subtilis genomes and its use to compare their competence genes, FEMS Microbiol. Lett, vol.209, pp.23-30, 2002.

S. Rozen and H. Skaletsky, Primer3 on the WWW for general users and for biologist programmers, Methods Mol. Biol, vol.132, pp.365-386, 2000.

S. Haas, M. Vingron, A. Poutska, and S. Wiemann, Primer design for large-scale sequencing, Nucleic Acids Res, vol.26, pp.3006-3012, 1998.

P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans et al., PRIMO: a primer design program that applies base quality statistics for automated large-scale DNA sequencing, Genomics, vol.40, pp.476-485, 1997.

W. Rychlik, Selection of primers for polymerase chain reaction, Mol. Biotechnol, vol.3, pp.129-134, 1995.

S. V. Suggs, T. Hirose, E. H. Myoke, M. J. Kawashima, K. I. Johnson et al., ICN-UCLA Symposium for Developmental Biology Using Puri®ed Gene, vol.23, pp.683-693, 1981.

K. J. Breslauer, R. Frank, H. Blaker, and L. A. Marky, Predicting DNA duplex stability from the base sequence, Proc. Natl Acad. Sci. USA, vol.83, pp.3746-3750, 1986.

M. J. Blommers, J. A. Walters, C. A. Haasnoot, J. M. Aelen, G. A. Van-der-marel et al., Effects of base sequence on the loop folding in DNA hairpins, Biochemistry, vol.28, pp.7491-7498, 1989.

B. W. Kernighan and D. M. Ritchie, The C Programming (ANSI C) Language (2nd Edn), 1988.

J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz et al., The Bioperl Toolkit: Perl modules for the life sciences, Genome Res, vol.12, pp.1161-1168, 2002.

P. Weis, M. V. Aponte, A. Laville, M. Mauny, and A. Suarez, The CAML Reference Manual, 1990.
URL : https://hal.archives-ouvertes.fr/inria-00070046

S. F. Altschul, W. Gish, W. Miller, W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990.

R. Andonov, N. Yanev, D. Lavenier, and P. Veber, Combinatorial approaches for segmenting bacterial genomes, 2003.

S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye et al., REPuter: the manifold applications of repeat analysis on a genomic scale, Nucleic Acids Res, vol.29, pp.4633-4642, 2001.

J. M. Yarwood, J. K. Mccormick, M. L. Paustian, P. M. Orwin, V. Kapur et al., Characterization and expression analysis of Staphylococcus aureus pathogenicity island 3. Implications for the evolution of staphylococcal pathogenicity islands, J. Biol. Chem, vol.277, pp.13138-13147, 2002.

C. Ubeda, M. A. Tormo, C. Cucarella, P. Trotonda, T. J. Foster et al., Sip, an integrase protein with excision, circularization and integration activities, de®nes a new family of mobile Staphylococcus aureus pathogenicity islands, Mol. Microbiol, vol.49, pp.193-210, 2003.

I. Chambaud, R. Heilig, S. Ferris, V. Barbe, D. Samson et al., The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis, Nucleic Acids Res, vol.29, pp.2145-2153, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02679458

R. D. Fleischmann, D. Alland, J. A. Eisen, L. Carpenter, O. White et al., Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains, J. Bacteriol, vol.184, pp.5479-5490, 2002.