G. M. Blackstone, J. L. Nordstrom, M. C. Vickery, M. D. Bowen, R. F. Meyer et al., Detection of pathogenic Vibrio parahaemolyticus in oyster enrichments by real time PCR, Journal of Microbiological Methods, vol.53, issue.2, pp.149-155, 2003.
DOI : 10.1016/S0167-7012(03)00020-4

M. G. Bondad-reantaso, R. P. Subasinghe, J. R. Arthur, K. Ogawa, S. Chinabut et al., Disease and health management in Asian aquaculture, Veterinary Parasitology, vol.132, issue.3-4, pp.249-272, 2005.
DOI : 10.1016/j.vetpar.2005.07.005

K. H. Boström, K. Simu, Å. Hagström, and L. Riemann, Optimization of DNA extraction for quantitative marine bacterioplankton community analysis, Limnology and Oceanography: Methods, vol.2, issue.11, pp.365-373, 2004.
DOI : 10.4319/lom.2004.2.365

D. J. Brenner, A. F. Kaufmann, K. R. Sulzer, A. G. Steigerwalt, F. C. Rogers et al., Further determination of DNA relatedness between serogroups and serovars in the family Leptospiraceae with a proposal for Leptospira alexanderi sp. nov. and four new Leptospira genomospecies, International Journal of Systematic Bacteriology, vol.49, issue.2, pp.839-858, 1999.
DOI : 10.1099/00207713-49-2-839

V. Burrus and M. K. Waldor, Shaping bacterial genomes with integrative and conjugative elements, Research in Microbiology, vol.155, issue.5, pp.376-386, 2004.
DOI : 10.1016/j.resmic.2004.01.012

J. E. Cooper and E. J. Feil, Multilocus sequence typing -what is resolved? Trends Microbiol, pp.373-377, 2004.

R. Costa, I. Mermoud, S. Koblavi, B. Morlet, P. Haffner et al., Isolation and characterization of bacteria associated with a Penaeus stylirostris disease (Syndrome 93) in New Caledonia, Aquaculture, vol.164, issue.1-4, pp.297-309, 1998.
DOI : 10.1016/S0044-8486(98)00195-1

U. Dobrindt and J. Hacker, Whole genome plasticity in pathogenic bacteria, Current Opinion in Microbiology, vol.4, issue.5, pp.550-557, 2001.
DOI : 10.1016/S1369-5274(00)00250-2

M. C. Enright and B. G. Spratt, Multilocus sequence typing, Trends in Microbiology, vol.7, issue.12, pp.482-487, 1999.
DOI : 10.1016/S0966-842X(99)01609-1

M. J. Espy, J. R. Uhl, L. M. Sloan, S. P. Buckwalter, M. F. Jones et al., Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing, Clinical Microbiology Reviews, vol.19, issue.1, pp.165-256, 2006.
DOI : 10.1128/CMR.19.1.165-256.2006

E. J. Feil and M. C. Enright, Analyses of clonality and the evolution of bacterial pathogens, Current Opinion in Microbiology, vol.7, issue.3, pp.308-313, 2004.
DOI : 10.1016/j.mib.2004.04.002

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543

URL : https://hal.archives-ouvertes.fr/hal-00435028

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1987.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

C. Goarant and F. Mérien, Quantification of Vibrio penaeicida, the etiological agent of Syndrome 93 in New Caledonian shrimp, by real-time PCR using SYBR Green I chemistry, Journal of Microbiological Methods, vol.67, issue.1, pp.27-35, 2006.
DOI : 10.1016/j.mimet.2006.02.013

URL : https://hal.archives-ouvertes.fr/pasteur-00498909

C. Goarant, D. Ansquer, J. Herlin, D. Domalain, F. Imbert et al., ???Summer Syndrome??? in Litopenaeus stylirostris in New Caledonia: Pathology and epidemiology of the etiological agent, Vibrio nigripulchritudo, Aquaculture, vol.253, issue.1-4, pp.105-113, 2006.
DOI : 10.1016/j.aquaculture.2005.07.031

C. Goarant, F. Mérien, F. Berthe, I. Mermoud, and P. Pérolat, Arbitrarily primed PCR to type Vibrio spp. pathogenic for shrimp, Appl. Environ. Microbiol, vol.65, pp.1145-1151, 1999.
URL : https://hal.archives-ouvertes.fr/pasteur-00498910

C. Goarant, Y. Reynaud, D. Ansquer, S. De-decker, D. Saulnier et al., Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia, Systematic and Applied Microbiology, vol.29, issue.7, pp.570-580, 2006.
DOI : 10.1016/j.syapm.2005.12.005

B. G. Hall and M. Barlow, Phylogenetic Analysis as a Tool in Molecular Epidemiology of Infectious Diseases, Annals of Epidemiology, vol.16, issue.3, pp.157-169, 2006.
DOI : 10.1016/j.annepidem.2005.04.010

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser, vol.41, pp.95-98, 1999.

C. D. Harvell, K. Kim, J. M. Burkholder, R. R. Colwell, P. R. Epstein et al., Emerging Marine Diseases--Climate Links and Anthropogenic Factors, Science, vol.285, issue.5433, pp.1505-1510, 1999.
DOI : 10.1126/science.285.5433.1505

G. Hernandez and J. Olmos, Molecular identification of pathogenic and nonpathogenic strains of Vibrio harveyi using PCR and RAPD, Applied Microbiology and Biotechnology, vol.63, issue.6, pp.722-727, 2004.
DOI : 10.1007/s00253-003-1451-z

M. Hiratsuka, K. Narahara, Y. Kishikawa, S. I. Hamdy, N. Endo et al., A simultaneous LightCycler detection assay for five genetic polymorphisms influencing drug sensitivity, Clinical Biochemistry, vol.35, issue.1, pp.35-40, 2002.
DOI : 10.1016/S0009-9120(02)00269-2

M. Kotetishvili, O. C. Stine, Y. Chen, A. Kreger, A. Sulakvelidze et al., Multilocus Sequence Typing Has Better Discriminatory Ability for Typing Vibrio cholerae than Does Pulsed-Field Gel Electrophoresis and Provides a Measure of Phylogenetic Relatedness, Journal of Clinical Microbiology, vol.41, issue.5, pp.2191-296, 2003.
DOI : 10.1128/JCM.41.5.2191-2196.2003

J. H. Lee, K. H. Han, S. Y. Choi, M. E. Lucas, C. Mondlane et al., Multilocus sequence typing (MLST) analysis of Vibrio cholerae O1 El Tor isolates from Mozambique that harbour the classical CTX prophage, Journal of Medical Microbiology, vol.55, issue.2, pp.165-170, 2006.
DOI : 10.1099/jmm.0.46287-0

D. V. Lightner and D. H. Lewis, A septicemic bacterial disease syndrome of penaeid shrimp, Mar. Fish. Rev, vol.37, pp.25-28, 1975.

B. Lobitz, L. Beck, A. Huq, B. Wood, G. Fuchs et al., Climate and infectious disease: Use of remote sensing for detection of Vibrio cholerae by indirect measurement, Proceedings of the National Academy of Sciences, vol.97, issue.4, pp.1438-1443, 2000.
DOI : 10.1073/pnas.97.4.1438

I. Mermoud, R. Costa, O. Ferré, C. Goarant, and P. Haffner, `Syndrome 93' in New Caledonian outdoor rearing ponds of Penaeus stylirostris: history and description of three major outbreaks, Aquaculture, vol.164, issue.1-4, pp.323-335, 1998.
DOI : 10.1016/S0044-8486(98)00197-5

K. L. Mumy and R. H. Findlay, Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR, Journal of Microbiological Methods, vol.57, issue.2, pp.259-268, 2004.
DOI : 10.1016/j.mimet.2004.01.013

O. Shea, Y. A. Reen, F. J. Quirke, A. M. Boyd, and E. F. , Evolutionary Genetic Analysis of the Emergence of Epidemic Vibrio cholerae Isolates on the Basis of Comparative Nucleotide Sequence Analysis and Multilocus Virulence Gene Profiles, Journal of Clinical Microbiology, vol.42, issue.10, pp.4657-4671, 2004.
DOI : 10.1128/JCM.42.10.4657-4671.2004

H. J. Oakey and L. Owens, A new bacteriophage, VHML, isolated from a toxin-producing strain of Vibrio harveyi in tropical Australia, Journal of Applied Microbiology, vol.272, issue.4, pp.702-709, 2000.
DOI : 10.1016/0042-6822(70)90218-7

L. Overbergh, A. Giuletti, B. Valckx, B. Decallonne, R. Bouillon et al., The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression, J. Biomol. Tech, vol.14, pp.33-43, 2003.

G. Panicker, M. L. Myers, and A. K. Bej, Rapid Detection of Vibrio vulnificus in Shellfish and Gulf of Mexico Water by Real-Time PCR, Applied and Environmental Microbiology, vol.70, issue.1, pp.498-507, 2004.
DOI : 10.1128/AEM.70.1.498-507.2004

D. R. Rañoa and C. T. Hedreyda, Sequence analysis of partial toxR gene from Philippine Vibrio isolates and design of toxR-targeted primers for detection, The Journal of General and Applied Microbiology, vol.51, issue.6, pp.343-351, 2005.
DOI : 10.2323/jgam.51.343

D. Saulnier, P. Haffner, C. Goarant, P. Levy, and D. Ansquer, Experimental infection models for shrimp vibriosis studies: a review, Aquaculture, vol.191, issue.1-3, pp.133-144, 2000.
DOI : 10.1016/S0044-8486(00)00423-3

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-80, 1994.
DOI : 10.1093/nar/22.22.4673

R. Urwin and M. C. Maiden, Multi-locus sequence typing: a tool for global epidemiology, Trends in Microbiology, vol.11, issue.10, pp.479-487, 2003.
DOI : 10.1016/j.tim.2003.08.006

F. Vernel-pauillac, V. Falcot, D. Whiley, and F. Merien, using a real-time PCR assay, FEMS Microbiology Letters, vol.255, issue.1, pp.66-74, 2006.
DOI : 10.1111/j.1574-6968.2005.00053.x

S. A. Whalley, D. Brown, C. G. Teo, G. M. Dusheiko, and N. A. Saunders, Monitoring the Emergence of Hepatitis B Virus Polymerase Gene Variants during Lamivudine Therapy Using the LightCycler, Journal of Clinical Microbiology, vol.39, issue.4, pp.1456-1459, 2001.
DOI : 10.1128/JCM.39.4.1456-1459.2001