A. Ablordey, J. Swings, C. Hubans, K. Chemlal, C. Locht et al., Multilocus Variable-Number Tandem Repeat Typing of Mycobacterium ulcerans, Journal of Clinical Microbiology, vol.43, issue.4, pp.1546-1551, 2005.
DOI : 10.1128/JCM.43.4.1546-1551.2005

URL : http://jcm.asm.org/content/43/4/1546.full.pdf

M. Achtman, Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens, Annual Review of Microbiology, vol.62, issue.1, pp.53-70, 2008.
DOI : 10.1146/annurev.micro.62.081307.162832

E. Alm, D. Oerther, N. Larsen, D. Stahl, and L. Raskin, The oligonucleotide probe database, Applied and Environmental Microbiology, vol.62, pp.3557-3559, 1996.

A. Amonsin, L. Li, Q. Zhang, J. Bannantine, A. Motiwala et al., Multilocus Short Sequence Repeat Sequencing Approach for Differentiating among Mycobacterium avium subsp. paratuberculosis Strains, Journal of Clinical Microbiology, vol.42, issue.4, pp.1694-1702, 2004.
DOI : 10.1128/JCM.42.4.1694-1702.2004

URL : http://jcm.asm.org/content/42/4/1694.full.pdf

S. Arnaud-haond, A. F. Teixeira, S. Procaccini, G. Serrao, E. Duarte et al., Assessing Genetic Diversity in Clonal Organisms: Low Diversity or Low Resolution? Combining Power and Cost Efficiency in Selecting Markers, Journal of Heredity, vol.76, issue.4, pp.434-440, 2005.
DOI : 10.1038/hdy.1996.83

URL : https://academic.oup.com/jhered/article-pdf/96/4/434/6455694/esi043.pdf

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.272, issue.5269, pp.573-580, 1999.
DOI : 10.1126/science.272.5269.1755

URL : https://academic.oup.com/nar/article-pdf/27/2/573/6268426/27-2-573.pdf

A. Bühlmann, T. Dreo, F. Rezzonico, J. Pothier, T. Smits et al., inferred using minisatellites, Environmental Microbiology, vol.63, issue.7, pp.2112-2125, 2014.
DOI : 10.1099/mic.0.28184-0

J. Castillo and J. Greenberg, Evolutionary Dynamics of Ralstonia solanacearum, Applied and Environmental Microbiology, vol.73, issue.4, pp.1225-1238, 2007.
DOI : 10.1128/AEM.01253-06

URL : http://aem.asm.org/content/73/4/1225.full.pdf

J. Coloma and E. Harris, Molecular Genomic Approaches to Infectious Diseases in Resource-Limited Settings, PLoS Medicine, vol.4, issue.10, 2009.
DOI : 10.1371/journal.pmed.1000142.g001

URL : https://doi.org/10.1371/journal.pmed.1000142

I. Comas, S. Homolka, S. Niemann, and S. Gagneux, Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies, PLoS ONE, vol.18, issue.11, 2009.
DOI : 10.1371/journal.pone.0007815.s006

B. Coupat, F. Chaumeille-dole, S. Fall, P. Prior, P. Simonet et al., Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred, FEMS Microbiology Ecology, vol.140, issue.1, pp.14-24, 2008.
DOI : 10.1111/j.1574-6976.1998.tb00362.x

URL : https://hal.archives-ouvertes.fr/hal-00338013

J. Elphinstone, J. Hennessy, J. Wilson, and D. Stead, Sensitivity of different methods for the detection of Ralstonia solanacearum in potato tuber extracts, EPPO Bulletin, vol.39, issue.1996, pp.663-678, 1996.
DOI : 10.1111/j.1348-0421.1995.tb03275.x

A. Estoup, P. Jarne, and J. Cornuet, Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis, Molecular Ecology, vol.92, issue.9, 2002.
DOI : 10.1073/pnas.92.25.11549

URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294X.2002.01576.x/pdf

M. Fegan and P. Prior, How complex is the Ralstonia solanacearum species complex, Bacterial wilt disease and the Ralstonia solanacearum species complex, pp.449-461, 2005.

R. Fox and H. Narra, Plant disease diagnosis The epidemiology of plant diseases, pp.1-42, 2006.

A. Francisco, C. Vaz, P. Monteiro, J. Melo-cristino, M. Ramirez et al., PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods, BMC Bioinformatics, vol.13, issue.1, pp.87-97, 2012.
DOI : 10.1093/oxfordjournals.molbev.a026082

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-87?site=bmcbioinformatics.biomedcentral.com

M. Gillings and P. Fahy, Genetic diversity of Pseudomonas solanacearum biovars 2 and N2 assessed using restriction endonuclease analysis of total genomic DNA, Plant Pathology, vol.20, issue.13, pp.744-753, 1993.
DOI : 10.1080/00221589.1969.11514322

J. Goudet, hierfstat: estimation and tests of hierarchical F-statistics Available at https:// cran.r-project, 2014.

S. Harrington, J. Francis, W. Bishai, and K. Carroll, Molecular epidemiology and infectious diseases, Infectious disease epidemiology theory and practice. Third. Sudbury: Jones & Bartlett Learning, pp.219-245, 2014.

A. Hayward, Journal of Applied Bacteriology, vol.44, issue.2, pp.265-277, 1964.
DOI : 10.1007/BF02545855

P. Hunter, Reproducibility and indices of discriminatory power of microbial typing methods, Journal of Clinical Microbiology, vol.28, pp.1903-1905, 1990.

P. Hunter and M. Gaston, Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity, Journal of Clinical Microbiology, vol.26, pp.2465-2466, 1988.

A. Jeffreys, Highly variable minisatellites and DNA fingerprints, Biochemical Society Transactions, vol.15, issue.3, pp.309-317, 1987.
DOI : 10.1042/bst0150309

Y. Kashi and D. King, Simple sequence repeats as advantageous mutators in evolution, Trends in Genetics, vol.22, issue.5, pp.253-259, 2006.
DOI : 10.1016/j.tig.2006.03.005

H. Katoh, S. Subandiyah, K. Tomimura, M. Okuda, H. Su et al., ABSTRACT, Applied and Environmental Microbiology, vol.77, issue.5, pp.1910-1917, 1128.
DOI : 10.1128/AEM.01571-10

A. Kelman, The relationship of pathogenicity in pseudomonas solanacearum to colony appearance on a tetrazolium medium, Phytopathology, vol.44, pp.693-695, 1954.

L. Fleche, 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, pp.37-47, 2002.
DOI : 10.1186/1471-2180-2-37

URL : https://hal.archives-ouvertes.fr/hal-01158328

P. Legendre and F. Lapointe, ASSESSING CONGRUENCEAMONG DISTANCE MATRICES: SINGLE-MALT SCOTCH WHISKIES REVISITED, Australian <html_ent glyph="@amp;" ascii="&"/> New Zealand Journal of Statistics, vol.46, issue.4, pp.615-629, 2004.
DOI : 10.1111/j.1467-842X.2004.00357.x

B. Lindstedt, Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria, ELECTROPHORESIS, vol.37, issue.3, pp.2567-2582, 2005.
DOI : 10.1093/clinids/6.Supplement_3.S627

B. Lindstedt, M. Torpdahl, G. Vergnaud, L. Hello, S. Weill et al., Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, Eurosurveillance, vol.18, p.20385, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01111429

M. Somo-toukam, G. Cellier, G. Wicker, E. Guilbaud, C. Kahane et al., Strains in Cameroon, Plant Disease, vol.93, issue.11, pp.1123-1130, 2009.
DOI : 10.1094/PDIS-93-11-1123

M. Maiden, Multilocus Sequence Typing of Bacteria, Annual Review of Microbiology, vol.60, issue.1, pp.561-588, 2006.
DOI : 10.1146/annurev.micro.59.030804.121325

M. Maiden, J. Bygraves, E. Feil, G. Morelli, J. Russell et al., Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms, Proceedings of the National Academy of Sciences, vol.34, issue.2, pp.3140-3145, 1998.
DOI : 10.1007/BF00182389

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Research, vol.27, pp.209-220, 1967.

A. Michael, Molecular approaches to diagnosing and managing infectious diseases: practicality and costs, Emerging Infectious Disease journal, vol.7, pp.312-322, 2001.

N. Guessan, C. Brisse, S. , L. Roux-nio, A. Poussier et al., Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot, Journal of Microbiological Methods, vol.92, issue.3, pp.366-374, 2013.
DOI : 10.1016/j.mimet.2013.01.012

URL : https://hal.archives-ouvertes.fr/hal-01199311

N. Parkinson, R. Bryant, J. Bew, C. Conyers, R. Stones et al., ABSTRACT, Applied and Environmental Microbiology, vol.79, issue.19, pp.6016-6022, 1128.
DOI : 10.1128/AEM.01219-13

R. Peakall and P. Smouse, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update, Bioinformatics, vol.20, issue.6, pp.2537-2539, 2012.
DOI : 10.1111/j.1365-294X.2010.04996.x

C. Pourcel and G. Vergnaud, Strain Typing Using Multiple ???Variable Number of Tandem Repeat??? Analysis and Genetic Element CRISPR, pp.179-197, 2011.
DOI : 10.1128/9781555816834.ch11

S. Poussier, P. Prior, J. Luisetti, C. Hayward, and M. Fegan, Partial Sequencing of the hrpB and Endoglucanase Genes Confirms and Expands the Known Diversity within the Ralstonia solanacearum Species Complex, Systematic and Applied Microbiology, vol.23, issue.4, pp.479-486, 2000.
DOI : 10.1016/S0723-2020(00)80021-1

S. Poussier, D. Trigalet-demery, P. Vandewalle, B. Goffinet, J. Luisetti et al., Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision, Microbiology, vol.47, issue.7, pp.1679-1692, 2000.
DOI : 10.1080/01621459.1963.10500845

S. Poussier, P. Vandewalle, and J. Luisetti, Genetic diversity of african and worldwide strains of Ralstonia solanacearum as determined by PCR-restriction fragment length polymorphism analysis of the hrp gene region, Applied and Environmental Microbiology, vol.65, pp.2184-2194, 1999.

A. Pradhan, R. Mitchell, A. Kramer, M. Zurakowski, T. Fyock et al., Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis in a Longitudinal Study of Three Dairy Herds, Journal of Clinical Microbiology, vol.49, issue.3, pp.893-901, 1128.
DOI : 10.1128/JCM.01107-10

P. Prior, C. Allen, and J. Elphinstone, Bacterial wilt disease: molecular and ecological aspects, 1998.
DOI : 10.1007/978-3-662-03592-4

P. Prior and M. Fegan, RECENT DEVELOPMENTS IN THE PHYLOGENY AND CLASSIFICATION OF RALSTONIA SOLANACEARUM, 1st international symposium on tomato diseases. Leuven: International Society for Horticultural Science (ISHS), pp.127-136, 2005.
DOI : 10.17660/ActaHortic.2005.695.14

O. Pruvost, M. Magne, K. Boyer, A. Leduc, C. Tourterel et al., A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage, PLoS ONE, vol.79, issue.6, 2014.
DOI : 10.1371/journal.pone.0098129.s003

URL : https://hal.archives-ouvertes.fr/hal-01456735

R. Team, R: a language and environment for statistical computing . Vienna: the R Foundation for Statistical Computing, 2013.

B. Remenant, B. Coupat-goutaland, A. Guidot, G. Cellier, E. Wicker et al., Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence, BMC Genomics, vol.11, issue.1, pp.379-389, 2010.
DOI : 10.1186/1471-2164-11-379

URL : http://doi.org/10.1186/1471-2164-11-379

J. Reyes, C. Chan, and M. Tanaka, Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis, Infection, Genetics and Evolution, vol.12, issue.4, pp.811-818, 2012.
DOI : 10.1016/j.meegid.2011.05.018

A. Severiano, F. Pinto, M. Ramirez, and J. Carrico, Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods, Journal of Clinical Microbiology, vol.49, issue.11, pp.3997-4000, 1128.
DOI : 10.1128/JCM.00624-11

URL : http://jcm.asm.org/content/49/11/3997.full.pdf

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. Faircloth et al., Primer3???new capabilities and interfaces, Nucleic Acids Research, vol.3, issue.15, pp.115-125, 2012.
DOI : 10.6026/97320630003282

URL : https://academic.oup.com/nar/article-pdf/40/15/e115/16967451/gks596.pdf

A. Van-belkum, S. Scherer, L. Van-alphen, and H. Verbrugh, Short-sequence DNA repeats in prokaryotic genomes, Microbiology and Molecular Biology Reviews, vol.62, pp.275-293, 1998.

G. Vergnaud and C. Pourcel, Multiple locus variable number of tandem repeats analysis Molecular epidemiology of microorganisms: methods and protocols, pp.141-158, 2009.

B. Vinatzer and C. Bull, The impact of genomic approaches on our understanding of diversity and taxonomy of plant pathogenic bacteria Plant pathogenic bacteria: genomics and molecular biology, 2009.

J. Weber, Informativeness of human (dC-dA)n ?? (dG-dT)n polymorphisms, Genomics, vol.7, issue.4, pp.524-530, 1990.
DOI : 10.1016/0888-7543(90)90195-Z

E. Wicker, P. Lefeuvre, D. Cambiaire, J. Lemaire, C. Poussier et al., Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA, The ISME Journal, vol.146, issue.5, pp.961-974, 1038.
DOI : 10.1128/AEM.00180-08

URL : https://hal.archives-ouvertes.fr/hal-01199343

J. Zaluga, P. Stragier, V. Vaerenbergh, J. Maes, M. et al., Multilocus variablenumber-tandem-repeats analysis (MLVA) distinguishes a clonal complex of Clavibacter michiganensis subsp. michiganensis strains isolated from recent outbreaks of bacterial wilt and canker in Belgium, BMC Microbiology, vol.13, pp.1-15, 2013.
DOI : 10.1186/1471-2180-13-126

URL : https://bmcmicrobiol.biomedcentral.com/track/pdf/10.1186/1471-2180-13-126?site=bmcmicrobiol.biomedcentral.com