. Van-belkum, High-throughput epidemiologic typing in clinical microbiology, Clinical Microbiology and Infection, vol.9, issue.2, pp.86-100, 2003.
DOI : 10.1046/j.1469-0691.2003.00549.x

M. Enright and B. Spratt, Multilocus sequence typing, Trends in Microbiology, vol.7, issue.12, pp.482-489, 1999.
DOI : 10.1016/S0966-842X(99)01609-1

M. Gutacker, J. Smoot, C. Migliaccio, S. Ricklefs, S. Hua et al., Genomewide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains, Genetics, vol.162, pp.1533-1576, 2002.

M. Achtman, K. Zurth, G. Morelli, G. Torrea, A. Guiyoule et al., Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis, Proceedings of the National Academy of Sciences, vol.96, issue.24, pp.14043-85017, 1997.
DOI : 10.1073/pnas.96.24.14043

R. Frothingham and W. Meeker-o-'connell, Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats, Microbiology, vol.144, issue.5, pp.1189-1196, 1998.
DOI : 10.1099/00221287-144-5-1189

P. Supply, E. Mazars, S. Lesjean, V. Vincent, B. Gicquel et al., Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome, Molecular Microbiology, vol.59, issue.3, pp.762-771, 2000.
DOI : 10.1046/j.1365-2958.2000.01905.x

D. Adair, P. Worsham, K. Hill, A. Klevytska, P. Jackson et al., Diversity in a variable-number tandem repeat from Yersinia pestis, J Clin Microbiol, vol.38, pp.1516-1525, 2000.

L. Flèche, P. Hauck, Y. Onteniente, L. Prieur, A. Denoeud et al., A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis, BMC Microbiol, vol.1, issue.2, 2001.

L. Flèche, P. Fabre, M. Denoeud, F. Koeck, J. Vergnaud et al., High resolution , on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing, BMC Microbiology, vol.2, issue.1, p.37, 2002.
DOI : 10.1186/1471-2180-2-37

J. Spanier, S. Jones, and P. Cleary, Small DNA deletions creating avirulence in Streptococcus pyogenes, Science, vol.225, issue.4665, pp.935-943, 1984.
DOI : 10.1126/science.6089334

S. Hollingshead, V. Fischetti, and J. Scott, Size variation in group A streptococcal M protein is generated by homologous recombination between intragenic repeats, MGG Molecular & General Genetics, vol.46, issue.2-3, pp.196-203, 1987.
DOI : 10.1007/BF00331578

P. Keim, A. Kalif, J. Schupp, K. Hill, S. Travis et al., Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers., Journal of Bacteriology, vol.179, issue.3, pp.818-842, 1997.
DOI : 10.1128/jb.179.3.818-824.1997

P. Keim, L. Price, A. Klevytska, K. Smith, J. Schupp et al., Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis, Journal of Bacteriology, vol.182, issue.10, pp.2928-2936, 2000.
DOI : 10.1128/JB.182.10.2928-2936.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC102004

P. Sylvestre, E. Couture-tosi, and M. Mock, Polymorphism in the Collagen-Like Region of the Bacillus anthracis BclA Protein Leads to Variation in Exosporium Filament Length, Journal of Bacteriology, vol.185, issue.5, pp.1555-63, 2003.
DOI : 10.1128/JB.185.5.1555-1563.2003

P. Supply, S. Lesjean, E. Savine, K. Kremer, D. Van-soolingen et al., Automated High-Throughput Genotyping for Study of Global Epidemiology of Mycobacterium tuberculosis Based on Mycobacterial Interspersed Repetitive Units, Journal of Clinical Microbiology, vol.39, issue.10, pp.3563-3571, 2001.
DOI : 10.1128/JCM.39.10.3563-3571.2001

G. Vergnaud and F. Denoeud, Minisatellites: Mutability and Genome Architecture, Genome Research, vol.10, issue.7, pp.899-907, 2000.
DOI : 10.1101/gr.10.7.899
URL : https://hal.archives-ouvertes.fr/hal-01159813

C. Pourcel, Y. Vidgop, F. Ramisse, G. Vergnaud, and C. Tram, Characterization of a Tandem Repeat Polymorphism in Legionella pneumophila and Its Use for Genotyping, Journal of Clinical Microbiology, vol.41, issue.5, pp.1819-1826, 2003.
DOI : 10.1128/JCM.41.5.1819-1826.2003
URL : https://hal.archives-ouvertes.fr/hal-01158324

L. Onteniente, S. Brisse, P. Tassios, and G. Vergnaud, Evaluation of the Polymorphisms Associated with Tandem Repeats for Pseudomonas aeruginosa Strain Typing, Journal of Clinical Microbiology, vol.41, issue.11, pp.4991-4998, 2003.
DOI : 10.1128/JCM.41.11.4991-4997.2003

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.27, issue.2, pp.573-580, 1999.
DOI : 10.1093/nar/27.2.573

F. Denoeud, G. Vergnaud, and G. Benson, Predicting Human Minisatellite Polymorphism, Genome Research, vol.13, issue.5, pp.856-867, 2003.
DOI : 10.1101/gr.574403
URL : https://hal.archives-ouvertes.fr/hal-01158326

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

J. Parkhill, B. Wren, N. Thomson, R. Titball, M. Holden et al., Genome sequence of Yersinia pestis, the causative agent of plague, Nature, vol.404, issue.6855, pp.523-530, 2001.
DOI : 10.1038/35097083

W. Deng, V. Burland, G. Plunkett, A. Boutin, G. Mayhew et al., Genome Sequence of Yersinia pestis KIM, Journal of Bacteriology, vol.184, issue.16, pp.4601-4612, 2002.
DOI : 10.1128/JB.184.16.4601-4611.2002

L. Radnedge, P. Agron, P. Worsham, and G. Andersen, Genome plasticity in Yersinia pestis, Microbiology, vol.148, issue.6, pp.1687-98, 2002.
DOI : 10.1099/00221287-148-6-1687

R. Fleischmann, D. Alland, J. Eisen, L. Carpenter, O. White et al., Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains, Journal of Bacteriology, vol.184, issue.19, pp.5479-5490, 2002.
DOI : 10.1128/JB.184.19.5479-5490.2002

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii et al., Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12, DNA Research, vol.8, issue.1, pp.11-22, 2001.
DOI : 10.1093/dnares/8.1.11

R. Welch, V. Burland, G. Plunkett, R. P. Roesch, P. Rasko et al., Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proceedings of the National Academy of Sciences, vol.99, issue.26, pp.17020-17024, 2002.
DOI : 10.1073/pnas.252529799

H. Tettelin, V. Masignani, M. Cieslewicz, J. Eisen, S. Peterson et al., Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, Proceedings of the National Academy of Sciences, vol.99, issue.19, pp.12391-12397, 2002.
DOI : 10.1073/pnas.182380799

M. Mcclelland, K. Sanderson, J. Spieth, S. Clifton, P. Latreille et al., Complete genome sequence of Salmonella enterica serovar Typhimurium LT2, Nature, vol.413, issue.6858, pp.852-858, 2001.
DOI : 10.1038/35101614

Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen et al., Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Research, vol.30, issue.20, pp.4432-4473, 2002.
DOI : 10.1093/nar/gkf566

B. Bricker, D. Ewalt, and S. Halling, Brucella 'Hoof-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs), BMC Microbiology, vol.3, issue.1, p.15, 2003.
DOI : 10.1186/1471-2180-3-15

B. Goodner, G. Hinkle, S. Gattung, N. Miller, M. Blanchard et al., Genome Sequence of the Plant Pathogen and Biotechnology Agent Agrobacterium tumefaciens C58, Science, vol.294, issue.5550, pp.2323-2331, 2001.
DOI : 10.1126/science.1066803

D. Wood, J. Setubal, R. Kaul, D. Monks, J. Kitajima et al., The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58, The genome of the natural genetic engineer Agrobacterium tumefaciens C58, pp.2317-2340, 2001.
DOI : 10.1126/science.1066804

G. Benson and L. Dong, Reconstructing the duplication history of a tandem repeat, Proc Int Conf Intell Syst Mol Biol, pp.44-53, 1999.

A. Van-belkum, S. Scherer, L. Van-alphen, and H. Verbrugh, Shortsequence DNA repeats in prokaryotic genomes, Microbiol Mol Biol Rev, vol.62, pp.275-93, 1998.

S. Schumacher, R. Fuchs, and M. Bichara, Two distinct models account for short and long deletions within sequence repeats in Escherichia coli., Journal of Bacteriology, vol.179, issue.20, pp.6512-6519, 1997.
DOI : 10.1128/jb.179.20.6512-6517.1997

X. De-bolle, C. Bayliss, D. Field, T. Van-de-ven, N. Saunders et al., The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases, Molecular Microbiology, vol.146, issue.1, pp.211-233, 2000.
DOI : 10.1046/j.1365-2958.1998.01108.x