.. Méthodes-de-détection-des-résistances, 24 1.7.2.1 -Méthodes phénotypiques, p.24

.. Typage-de-campylobacter, 29 1.9.1 -Généralités sur le typage bactérien 29 1.9.2 -Méthodes de typage de Campylobacter, ., p.33

M. Matériels, 34 2.1 -Isolats bactériens, culture et extraction nucléique 34 2.1.1 -Isolats d'origine humaine, p.35

.. Génotypage-de-campylobacter and .. Hrm-de-flaa, 35 2.2.1 -Génotypage par PCR, p.37

P. Détection-des-mutations-de-gyra-par, 41 2.3.1 -Profils de résistance phénotypiques des isolats testés, p.42

R. Génotypage-de-campylobacter and .. , 44 3.1.2 -Détermination des zones de pré-melt et post-melt, ., p.52

P. Détection-des-mutations-de-gyra-par, 53 3.2.1 -Profils de résistance phénotypiques des isolats testés, p.56

P. Détection-des-mutations-de-gyra-par, 60 4.2.1 -Méthode de détection des mutations gyrA 60 4.2.2 -Résultats des travaux de détection des mutations gyrA, p.62

J. Freney, F. Renaud, R. Leclercq, P. Riegel, and C. , Précis de bactériologie clinique. 2e édition. Paris: Editions Eska, 2007.

K. Danis, D. Renzi, M. , O. Neill, W. Smyth et al., Risk factors for sporadic Campylobacter infection: an all-Ireland case-control study, Euro Surveill, vol.14, issue.7, 2009.

C. Friedman, R. Hoekstra, M. Samuel, R. Marcus, J. Bender et al., Infection in the United States: A Case???Control Study in FoodNet Sites, Clinical Infectious Diseases, vol.38, issue.s3, pp.285-296, 2004.
DOI : 10.1086/381598

H. Lindmark, S. Boqvist, M. Ljungström, P. Agren, B. Björkholm et al., Risk Factors for Campylobacteriosis: an Epidemiological Surveillance Study of Patients and Retail Poultry, Journal of Clinical Microbiology, vol.47, issue.8, pp.2616-2625, 2009.
DOI : 10.1128/JCM.00826-09

A. Studahl and Y. Andersson, Risk factors for indigenous campylobacter infection: a Swedish case-control study, Epidemiology and Infection, vol.125, issue.2, pp.269-75, 2000.
DOI : 10.1017/S0950268899004562

T. Humphrey, O. Brien, S. Madsen, and M. , Campylobacters as zoonotic pathogens: A food production perspective, International Journal of Food Microbiology, vol.117, issue.3
DOI : 10.1016/j.ijfoodmicro.2007.01.006

D. Van-cauteren, D. Valk, H. Sommen, C. King, L. et al., Community Incidence of Campylobacteriosis and Nontyphoidal Salmonellosis, France, 2008???2013, Foodborne Pathogens and Disease, vol.12, issue.8, pp.664-673, 2008.
DOI : 10.1089/fpd.2015.1964

J. Roberts, P. Cumberland, P. Sockett, J. Wheeler, L. Rodrigues et al., The study of infectious intestinal disease in England: socio-economic impact, Epidemiology and Infection, vol.130, issue.1, pp.1-11, 2003.
DOI : 10.1017/S0950268802007690

I. Henry, J. Reichardt, M. Denis, and E. Cardinale, Prevalence and risk factors for Campylobacter spp. in chicken broiler flocks in Reunion Island (Indian Ocean), Preventive Veterinary Medicine, vol.100, issue.1, pp.64-70, 2011.
DOI : 10.1016/j.prevetmed.2011.03.007

C. Tessier, P. Atiana, L. Mathis, J. Bernard, C. Zemali et al., Risk factors associated with high prevalence of Salmonella spp. and Campylobacter spp

S. Vacher, A. Menard, E. Bernard, A. Santos, and F. Megraud, spp. by Real-Time PCR, Microbial Drug Resistance, vol.11, issue.1, pp.40-47, 2005.
DOI : 10.1089/mdr.2005.11.40

G. Garrity, J. Bell, and T. Lilburn, Epsilonproteobacteria class. nov. [Internet] In: Bergey's Manual of Systematics of Archaea and Bacteria, p.2015, 2016.

K. Diker, O. Esendal, and M. Akan, Epidemiology of ovine Campylobacter infection determined by numerical analysis of electrophoretic protein profiles, J Vet Med B Infect Dis Vet Public Health, vol.47, issue.10, pp.739-782, 2000.

L. King and F. Mégraud, Surveillance des infections à Campylobacter chez l'Homme en France de, BEH, pp.11-14, 2003.

S. Rémic, Référentiel en microbiologie médicale Tomes 1 et 2. 5e édition. Société Française de Microbiologie -SFM, 2015.

C. Friedman, J. Neimann, H. Wegener, and R. Tauxe, Epidemiology of Campylobacter jejuni infections in the United States and other industrialized nations, In: Campylobacter. ASM International, pp.121-159, 2000.

N. Kaakoush, N. Castaño-rodríguez, H. Mitchell, and S. Man, Global Epidemiology of Campylobacter Infection, Clinical Microbiology Reviews, vol.28, issue.3, pp.687-720, 2015.
DOI : 10.1128/CMR.00006-15

M. Helms, P. Vastrup, P. Gerner-smidt, and K. Mølbak, Short and long term mortality associated with foodborne bacterial gastrointestinal infections: registry based study * Commentary: matched cohorts can be useful, BMJ, vol.326, issue.7385, p.357, 2003.
DOI : 10.1136/bmj.326.7385.357

K. Prasad, A. Dixit, and A. Ayyagari, Campylobacter species associated with diarrhoea in patients from a tertiary care centre of north India, Indian J Med Res, vol.114, pp.12-19, 2001.

D. Van-cauteren, P. Lehours, E. Bessede, D. Valk, H. Mégraud et al., Bilan de la surveillance des infections à Campylobacter chez l'Homme en France en 2015, 2015.

E. Bessède, P. Lehours, L. Labadi, S. Bakiri, and F. Mégraud, Comparison of Characteristics of Patients Infected by Campylobacter jejuni, Campylobacter coli, and Campylobacter fetus, Journal of Clinical Microbiology, vol.52, issue.1, pp.328-358, 2014.
DOI : 10.1128/JCM.03029-13

A. Havelaar, S. Ivarsson, M. Löfdahl, and M. Nauta, Estimating the true incidence of campylobacteriosis and salmonellosis in the European Union, 2009, Epidemiology and Infection, vol.8, issue.02, pp.293-302, 2009.
DOI : 10.1186/1471-2334-4-54

I. Gillespie, O. Brien, S. Frost, J. Adak, G. Horby et al., Infection: A Tool for Generating Hypotheses, Emerging Infectious Diseases, vol.8, issue.9, pp.937-979, 2002.
DOI : 10.3201/eid0809.010817

E. Food and S. Authority, Trends and sources of zoonoses and zoonotic agents in the European Union, The EFSA Journal, issue.223, pp.109-144, 2007.

B. Guzman-herrador, L. Vold, and K. Nygard, Surveillance of travel-associated gastrointestinal infections in Norway, 2009-2010: are they all actually imported?, Euro Surveill, vol.17, issue.41, p.20294, 2012.

N. Strachan, O. Rotariu, A. Smith-palmer, J. Cowden, S. Sheppard et al., Identifying the seasonal origins of human campylobacteriosis, Epidemiology and Infection, vol.155, issue.06, pp.1267-75, 2013.
DOI : 10.1017/S0950268804003188

J. Lawes, A. Vidal, F. Clifton-hadley, R. Sayers, J. Rodgers et al., Investigation of prevalence and risk factors for Campylobacter in broiler flocks at slaughter: results from a UK survey, Epidemiology and Infection, vol.82, issue.10, pp.1725-1762, 2012.
DOI : 10.3201/eid1406.071008

J. Platts-mills, S. Babji, L. Bodhidatta, J. Gratz, R. Haque et al., Pathogen-specific burdens of community diarrhoea in developing countries: a multisite birth cohort study (MAL-ED), The Lancet Global Health, vol.3, issue.9, pp.564-575, 2015.
DOI : 10.1016/S2214-109X(15)00151-5

M. Chemaly, C. Magras, J. Madec, J. Santolini, and M. Denis, Campylobacter dans les filières de production animale, BEH, pp.17-26, 2012.

W. Jacobs-reitsma, in poultry, Veterinary Quarterly, vol.58, issue.3, pp.113-120, 1997.
DOI : 10.3109/00365549209054659

S. Payot, S. Dridi, M. Laroche, M. Federighi, and C. Magras, Prevalence and antimicrobial resistance of Campylobacter coli isolated from fattening pigs in France, Veterinary Microbiology, vol.101, issue.2, pp.91-100, 2004.
DOI : 10.1016/j.vetmic.2004.03.014

A. Trimoulinard, C. Tessier, M. Beral, L. Atiana, I. Henry et al., Prevalence and risk factors susceptibility of Salmonella spp., Campylobacter spp. and Listeria spp. isolated from pork and poultry sausages, Reunion Island, France. International Conference on the Epidemiology and Control of Biological, Chemical and Physical Hazards in Pigs and Pork, p.33, 2013.

D. Bolton, Campylobacter virulence and survival factors, Food Microbiology, vol.48, pp.99-108, 2015.
DOI : 10.1016/j.fm.2014.11.017

M. Blaser, P. Smith, J. Repine, and K. Joiner, Pathogenesis of Campylobacter fetus infections. Failure of encapsulated Campylobacter fetus to bind C3b explains serum and phagocytosis resistance., Journal of Clinical Investigation, vol.81, issue.5, pp.1434-1478, 1988.
DOI : 10.1172/JCI113474

D. Newell, K. Elvers, D. Dopfer, I. Hansson, P. Jones et al., Biosecurity-Based Interventions and Strategies To Reduce Campylobacter spp. on Poultry Farms, Applied and Environmental Microbiology, vol.77, issue.24, pp.8605-8619, 2011.
DOI : 10.1128/AEM.01090-10

C. Riedel, L. Brøndsted, H. Rosenquist, S. Haxgart, and B. Christensen, Chemical Decontamination of Campylobacter jejuni on Chicken Skin and Meat, Journal of Food Protection, vol.72, issue.6, pp.1173-80, 2009.
DOI : 10.4315/0362-028X-72.6.1173

R. Spier, M. Saxena, B. John, M. Mu, T. Van et al., Strategies to reduce Campylobacter colonisation in chickens, Procedia in Vaccinology, vol.7, pp.40-43, 2013.

M. Youssef, G. Corthier, H. Goossens, C. Tancrede, M. Henry-amar et al., Comparative translocation of enteropathogenic Campylobacter spp. and Escherichia coli from the intestinal tract of gnotobiotic mice, Infect Immun, vol.55, issue.4, pp.1019-1040, 1987.

I. Nachamkin, B. Allos, and T. Ho, Campylobacter species and Guillain-Barré syndrome, Clin Microbiol Rev, vol.11, issue.3, pp.555-67, 1998.

J. Lindsay, Chronic Sequelae of Foodborne Disease, Emerging Infectious Diseases, vol.3, issue.4, pp.443-52, 1997.
DOI : 10.3201/eid0304.970405

B. Jacobs, A. Belkum, . Van, and H. Endtz, Guillain-Barr?? Syndrome and Campylobacter Infection, pp.245-61, 2008.
DOI : 10.1128/9781555815554.ch13

D. Briscoe, J. Mcmenamin, O. Donohoe, and N. , Prognosis in Guillain-Barre syndrome., Archives of Disease in Childhood, vol.62, issue.7, pp.733-738, 1987.
DOI : 10.1136/adc.62.7.733

R. Spiller, D. Jenkins, J. Thornley, J. Hebden, T. Wright et al., Increased rectal mucosal enteroendocrine cells, T lymphocytes, and increased gut permeability following acute Campylobacter enteritis and in post-dysenteric irritable bowel syndrome, Gut, vol.47, issue.6, pp.804-815, 2000.
DOI : 10.1136/gut.47.6.804

S. Futagami, T. Itoh, and C. Sakamoto, Systematic review with meta-analysis: post-infectious functional dyspepsia, Alimentary Pharmacology & Therapeutics, vol.107, issue.Suppl., pp.177-88, 2015.
DOI : 10.1111/apt.13006

K. Kamata and Y. Tokuda, Rapid diagnosis of Campylobacter jejuni by stool Gram stain examination, Case Reports, vol.2014, issue.jan28 1, 3912396.
DOI : 10.1136/bcr-2013-202876

M. Skirrow, Campylobacter enteritis: a "new" disease., BMJ, vol.2, issue.6078, pp.9-11, 1977.
DOI : 10.1136/bmj.2.6078.9

M. Karmali, A. Simor, M. Roscoe, P. Fleming, S. Smith et al., Evaluation of a blood-free, charcoal-based, selective medium for the isolation of Campylobacter organisms from feces, J Clin Microbiol, vol.23, issue.3, pp.456-465, 1986.

E. Bessède, O. Solecki, E. Sifré, L. Labadi, and F. Mégraud, Identification of Campylobacter species and related organisms by matrix assisted laser desorption ionization???time of flight (MALDI-TOF) mass spectrometry, Clinical Microbiology and Infection, vol.17, issue.11, pp.1735-1744, 2011.
DOI : 10.1111/j.1469-0691.2011.03468.x

G. Mcauliffe, T. Anderson, M. Stevens, J. Adams, R. Coleman et al., Systematic application of multiplex PCR enhances the detection of bacteria, parasites, and viruses in stool samples, Journal of Infection, vol.67, issue.2, pp.122-131, 2013.
DOI : 10.1016/j.jinf.2013.04.009

A. Ménard, F. Dachet, V. Prouzet-mauleon, M. Oleastro, and F. Mégraud, Development of a real-time fluorescence resonance energy transfer PCR to identify the main pathogenic Campylobacter spp., Clinical Microbiology and Infection, vol.11, issue.4, pp.281-288, 2005.
DOI : 10.1111/j.1469-0691.2005.01072.x

P. Floch, J. Goret, E. Bessède, P. Lehours, and F. Mégraud, Evaluation of the positive predictive value of a rapid Immunochromatographic test to detect Campylobacter in stools, Gut Pathogens, vol.4, issue.1, p.17, 2012.
DOI : 10.1111/j.1469-0691.2005.01072.x

H. Rautelin and T. Kosunen, An acid extract as a common antigen in Campylobacter coli and Campylobacter jejuni strains, J Clin Microbiol, vol.17, issue.4, pp.700-701, 1983.

K. Wieczorek and J. Osek, Antimicrobial resistance mechanisms among Campylobacter, Biomed Res Int, vol.2013, p.340605, 2013.

A. Mérens and A. Servonnet, M??canismes et ??pid??miologie de la r??sistance aux fluoroquinolones en 2010, Revue Francophone des Laboratoires, vol.2010, issue.422, pp.33-41, 2010.
DOI : 10.1016/S1773-035X(10)70508-6

B. Ge, P. Mcdermott, D. White, and J. Meng, Role of Efflux Pumps and Topoisomerase Mutations in Fluoroquinolone Resistance in Campylobacter jejuni and Campylobacter coli, Antimicrobial Agents and Chemotherapy, vol.49, issue.8, pp.3347-54, 2005.
DOI : 10.1128/AAC.49.8.3347-3354.2005

N. Luo, O. Sahin, J. Lin, L. Michel, and Q. Zhang, In Vivo Selection of Campylobacter Isolates with High Levels of Fluoroquinolone Resistance Associated with gyrA Mutations and the Function of the CmeABC Efflux Pump, Antimicrobial Agents and Chemotherapy, vol.47, issue.1, pp.390-394, 2003.
DOI : 10.1128/AAC.47.1.390-394.2003

J. Han, O. Sahin, Y. Barton, and Q. Zhang, Key Role of Mfd in the Development of Fluoroquinolone Resistance in Campylobacter jejuni, PLoS Pathogens, vol.37, issue.6, p.1000083, 2008.
DOI : 10.1371/journal.ppat.1000083.t002

Y. Wang, W. Huang, and D. Taylor, Cloning and nucleotide sequence of the Campylobacter jejuni gyrA gene and characterization of quinolone resistance mutations., Antimicrobial Agents and Chemotherapy, vol.37, issue.3, pp.457-63, 1993.
DOI : 10.1128/AAC.37.3.457

M. Hänninen and M. Hannula, Spontaneous mutation frequency and emergence of ciprofloxacin resistance in Campylobacter jejuni and Campylobacter coli, Journal of Antimicrobial Chemotherapy, vol.60, issue.6, pp.1251-1258, 2007.
DOI : 10.1093/jac/dkm345

R. Alonso, E. Mateo, C. Girbau, E. Churruca, I. Martinez et al., PCR-Restriction Fragment Length Polymorphism Assay for Detection of gyrA Mutations Associated with Fluoroquinolone Resistance in Campylobacter coli, Antimicrobial Agents and Chemotherapy, vol.48, issue.12, pp.4886-4894, 2004.
DOI : 10.1128/AAC.48.12.4886-4888.2004

L. Beckmann, M. Müller, P. Luber, C. Schrader, E. Bartelt et al., Analysis of gyrA mutations in quinolone-resistant and -susceptible Campylobacter jejuni isolates from retail poultry and human clinical isolates by non-radioactive single-strand conformation polymorphism analysis and DNA sequencing, Journal of Applied Microbiology, vol.37, issue.1, pp.1040-1047, 2004.
DOI : 10.1016/S0378-1097(00)00306-2

L. Piddock, V. Ricci, L. Pumbwe, M. Everett, and D. Griggs, Fluoroquinolone resistance in Campylobacter species from man and animals: detection of mutations in topoisomerase genes, Journal of Antimicrobial Chemotherapy, vol.51, issue.1, pp.19-26, 2003.
DOI : 10.1093/jac/dkg033

T. Jesse, M. Englen, L. Pittenger-alley, and P. Fedorka-cray, Two distinct mutations in gyrA lead to ciprofloxacin and nalidixic acid resistance in Campylobacter coli and Campylobacter jejuni isolated from chickens and beef cattle*, Journal of Applied Microbiology, vol.37, issue.4, pp.682-690, 2006.
DOI : 10.1111/j.1574-6968.2000.tb09253.x

J. Parkhill, B. Wren, K. Mungall, J. Ketley, C. Churcher et al., The genome sequence of the foodborne pathogen Campylobacter jejuni reveals hypervariable sequences, Nature, vol.403, issue.6770, pp.665-673, 2000.
DOI : 10.1038/35001088

J. Lin, L. Michel, and Q. Zhang, CmeABC Functions as a Multidrug Efflux System in Campylobacter jejuni, Antimicrobial Agents and Chemotherapy, vol.46, issue.7, pp.2124-2155, 2002.
DOI : 10.1128/AAC.46.7.2124-2131.2002

L. Pumbwe and L. Piddock, multidrug efflux pump, FEMS Microbiology Letters, vol.206, issue.2, pp.185-194, 2002.
DOI : 10.1111/j.1574-6968.2002.tb11007.x

M. Yan, O. Sahin, J. Lin, and Q. Zhang, Role of the CmeABC efflux pump in the emergence of fluoroquinolone-resistant Campylobacter under selection pressure, Journal of Antimicrobial Chemotherapy, vol.58, issue.6, pp.1154-1163, 2006.
DOI : 10.1093/jac/dkl412

B. Wretlind, A. Strömberg, L. Ostlund, E. Sjögren, and B. Kaijser, Rapid Emergence of Quinolone Resistance in Campylobacter jejuni in Patients Treated with Norfloxacin, Scandinavian Journal of Infectious Diseases, vol.35, issue.5, pp.685-691, 1992.
DOI : 10.3109/00365549209054659

S. Française-de-microbiologie, EUropean Committee on Antimicrobial Susceptibility Testing. Recommandations 2016 -V 1.0 -CASFM -EUCAST -Février, 2016.

E. Sifré, B. Salha, A. Ducournau, P. Floch, H. Chardon et al., EUCAST recommendations for antimicrobial susceptibility testing applied to the three main Campylobacter species isolated in humans, Journal of Microbiological Methods, vol.119, pp.206-219, 2015.
DOI : 10.1016/j.mimet.2015.10.018

R. Slinger, D. Bellfoy, M. Desjardins, and F. Chan, High-resolution melting assay for the detection of gyrA mutations causing quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi, Diagnostic Microbiology and Infectious Disease, vol.57, issue.4, pp.455-463, 2007.
DOI : 10.1016/j.diagmicrobio.2006.09.011

A. Lee, D. Ong, J. Wong, G. Siu, and W. Yam, High-Resolution Melting Analysis for the Rapid Detection of Fluoroquinolone and Streptomycin Resistance in Mycobacterium tuberculosis, PLoS ONE, vol.55, issue.2, p.31934, 2012.
DOI : 10.1371/journal.pone.0031934.t004

P. Luber, J. Wagner, H. Hahn, and E. Bartelt, Antimicrobial Resistance in Campylobacter jejuni and Campylobacter coli Strains Isolated in 1991 and 2001-2002 from Poultry and Humans in Berlin, Germany, Antimicrobial Agents and Chemotherapy, vol.47, issue.12, pp.3825-3855, 2003.
DOI : 10.1128/AAC.47.12.3825-3830.2003

D. Mevius, W. B. Pelt, W. Van, L. Puister-jansen, N. Bondt et al., Monitoring of antimicrobial resistance and antibiotic usage in animals in the Netherlands, 2006.

S. Boonmar, Y. Morita, M. Fujita, L. Sangsuk, K. Suthivarakom et al., Isolates from Humans and Chickens in Thailand, Microbiology and Immunology, vol.37, issue.5, pp.531-538, 2007.
DOI : 10.1111/j.1348-0421.2007.tb03941.x

J. Engberg, J. Neimann, E. Nielsen, F. Aarestrup, and V. Fussing, Infections: Risk Factors and Clinical Consequences1, Emerging Infectious Diseases, vol.10, issue.6, pp.1056-63, 2004.
DOI : 10.3201/eid1006.030669

A. Gupta, J. Nelson, T. Barrett, R. Tauxe, S. Rossiter et al., Strains, United States, 1997???2001, Emerging Infectious Diseases, vol.10, issue.6, pp.1102-1111, 1997.
DOI : 10.3201/eid1006.030635

D. Isenbarger, C. Hoge, A. Srijan, C. Pitarangsi, N. Vithayasai et al., Comparative Antibiotic Resistance of Diarrheal Pathogens from Vietnam and Thailand, 1996-1999, Emerging Infectious Diseases, vol.8, issue.2, pp.175-80, 1996.
DOI : 10.3201/eid0802.010145

K. Smith, J. Besser, C. Hedberg, F. Leano, J. Bender et al., Infections in Minnesota, 1992???1998, New England Journal of Medicine, vol.340, issue.20, pp.1525-1557, 1999.
DOI : 10.1056/NEJM199905203402001

I. Nachamkin, H. Ung, and M. Li, Pennsylvania, USA,1982???20011, Emerging Infectious Diseases, vol.8, issue.12, pp.1501-1504, 1982.
DOI : 10.3201/eid0812.020115

F. Mégraud, E. Bessède, and P. Lehours, Infections ?? Campylobacter, EMC - Maladies infectieuses, vol.7, issue.3, 2016.
DOI : 10.1016/S1166-8598(10)43985-X

H. Endtz, G. Ruijs, B. Van-klingeren, W. Jansen, T. Van-der-reyden et al., Quinolone resistance in campylobacter isolated from man and poultry following the introduction of fluoroquinolones in veterinary medicine, Journal of Antimicrobial Chemotherapy, vol.27, issue.2, pp.199-208, 1991.
DOI : 10.1093/jac/27.2.199

P. Mcdermott, S. Bodeis, L. English, D. White, R. Walker et al., Evolves Rapidly in Chickens Treated with Fluoroquinolones, The Journal of Infectious Diseases, vol.185, issue.6, pp.837-877, 2002.
DOI : 10.1086/339195

M. Van-boven, K. Veldman, M. De-jong, and D. Mevius, Rapid selection of quinolone resistance in Campylobacter jejuni but not in Escherichia coli in individually housed broilers, Journal of Antimicrobial Chemotherapy, vol.52, issue.4, pp.719-742, 2003.
DOI : 10.1093/jac/dkg402

I. Kempf, G. Mourand, P. Châtre, M. Haenni, J. Santolini et al., Antibiorésistance de Campylobacter dans différentes filières animales en France : pincipales tendances, BEH, pp.15-21, 2012.

J. Nelson, K. Smith, D. Vugia, T. Rabatsky-ehr, S. Segler et al., Infection, The Journal of Infectious Diseases, vol.190, issue.6, pp.1150-1157, 2004.
DOI : 10.1086/423282

URL : https://hal.archives-ouvertes.fr/inserm-00493685

M. Helms, J. Simonsen, K. Olsen, and K. Mølbak, Species: A Registry???Based Cohort Study, The Journal of Infectious Diseases, vol.191, issue.7, pp.1050-1055, 2005.
DOI : 10.1086/428453

T. Wassenaar, M. Kist, and A. De-jong, Re-analysis of the risks attributed to ciprofloxacin-resistant Campylobacter jejuni infections, International Journal of Antimicrobial Agents, vol.30, issue.3, pp.195-201, 2007.
DOI : 10.1016/j.ijantimicag.2007.01.019

F. Feodoroff, A. Lauhio, S. Sarna, M. Hänninen, and H. Rautelin, Severe diarrhoea caused by highly ciprofloxacin-susceptible Campylobacter isolates, Clinical Microbiology and Infection, vol.15, issue.2, pp.188-92, 2009.
DOI : 10.1111/j.1469-0691.2008.02657.x

E. Salazar-lindo, R. Sack, E. Chea-woo, B. Kay, Z. Piscoya et al., Early treatment with erythromycin of Campylobacter jejuni-associated dysentery in children, The Journal of Pediatrics, vol.109, issue.2, pp.355-60, 1986.
DOI : 10.1016/S0022-3476(86)80404-8

A. Ternhag, T. Asikainen, J. Giesecke, and K. Ekdahl, A Meta-Analysis on the Effects of Antibiotic Treatment on Duration of Symptoms Caused by Infection with Campylobacter Species, Clinical Infectious Diseases, vol.44, issue.5, pp.696-700, 2007.
DOI : 10.1086/509924

C. Rapp, C. Pulcini, C. , and T. P. , Pilly 2016 : Maladies infectieuses et tropicales. 25e édition. Paris: Alinéa Plus, 2015.

D. Ed, The Sanford guide to antimicrobial therapy 2016. 46 Poc, Antimicrobial Therapy, 2016.

A. Van-belkum, P. Tassios, L. Dijkshoorn, S. Haeggman, B. Cookson et al., Guidelines for the validation and application of typing methods for use in bacterial epidemiology, Clinical Microbiology and Infection, vol.13, pp.1-46, 2007.
DOI : 10.1111/j.1469-0691.2007.01786.x

M. Ahmed, L. Dunn, and E. Ivanova, Strains, Foodborne Pathogens and Disease, vol.9, issue.5, pp.375-85, 2012.
DOI : 10.1089/fpd.2011.0988

URL : https://hal.archives-ouvertes.fr/hal-01005074

E. Taboada, C. Clark, E. Sproston, and C. Carrillo, Current methods for molecular typing of Campylobacter species, Journal of Microbiological Methods, vol.95, issue.1, pp.24-31, 2013.
DOI : 10.1016/j.mimet.2013.07.007

R. Meinersmann, L. Helsel, P. Fields, and K. Hiett, Discrimination of Campylobacter jejuni isolates by fla gene sequencing, J Clin Microbiol, vol.35, issue.11, pp.2810-2814, 1997.

R. Alm, P. Guerry, and T. Trust, Significance of Duplicated Flagellin Genes in Campylobacter, Journal of Molecular Biology, vol.230, issue.2, pp.359-63, 1993.
DOI : 10.1006/jmbi.1993.1151

S. Merchant-patel, P. Blackall, J. Templeton, E. Price, S. Tong et al., Campylobacter jejuni and Campylobacter coli Genotyping by High-Resolution Melting Analysis of a flaA Fragment, Applied and Environmental Microbiology, vol.76, issue.2, pp.493-502, 2010.
DOI : 10.1128/AEM.01164-09

K. Dingle, F. Colles, D. Wareing, R. Ure, A. Fox et al., Multilocus Sequence Typing System for Campylobacter jejuni, Journal of Clinical Microbiology, vol.39, issue.1, pp.14-23, 2001.
DOI : 10.1128/JCM.39.1.14-23.2001

S. Tong and P. Giffard, Microbiological Applications of High-Resolution Melting Analysis, Journal of Clinical Microbiology, vol.50, issue.11, pp.3418-3439, 2012.
DOI : 10.1128/JCM.01709-12

F. Mao, W. Leung, and X. Xin, Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications, BMC Biotechnology, vol.7, issue.1, p.76, 2007.
DOI : 10.1186/1472-6750-7-76

N. Fang, High Resolution Melting -From assay to analysis, Qiagen Données commerciales

S. Lévesque, S. Michaud, R. Arbeit, and E. Frost, High-Resolution Melting System to Perform Multilocus Sequence Typing of Campylobacter jejuni, PLoS ONE, vol.42, issue.1, p.16167, 2011.
DOI : 10.1371/journal.pone.0016167.t009

V. Reja, A. Kwok, G. Stone, L. Yang, A. Missel et al., ScreenClust: Advanced statistical software for supervised and unsupervised high resolution melting (HRM) analysis, Methods, vol.50, issue.4, pp.10-14, 2010.
DOI : 10.1016/j.ymeth.2010.02.006

. Qiagen, . Rotor-gene, H. Screenclust, and . Software-user-guide, Available from: https://www.qiagen.com/resources/download.aspx?, pp.33-38, 2009.

M. Yu, A. Hillebrand, P. Tewarie, J. Meier, B. Van-dijk et al., Hierarchical clustering in minimum spanning trees, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.25, issue.2, p.23107, 2015.
DOI : 10.1063/1.4908014

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, p.87, 2012.
DOI : 10.1093/oxfordjournals.molbev.a026082

S. Thakur, W. Morrow, J. Funk, P. Bahnson, and W. Gebreyes, Molecular Epidemiologic Investigation of Campylobacter coli in Swine Production Systems, Using Multilocus Sequence Typing, Applied and Environmental Microbiology, vol.72, issue.8, pp.5666-5675, 2006.
DOI : 10.1128/AEM.00658-06

P. Hunter, Reproducibility and indices of discriminatory power of microbial typing methods, J Clin Microbiol, vol.28, issue.9, pp.1903-1908, 1990.

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

M. Struelens, Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems, Clinical Microbiology and Infection, vol.2, issue.1, pp.2-11, 1996.
DOI : 10.1111/j.1469-0691.1996.tb00193.x

S. Magnússon, S. Guðmundsdóttir, E. Reynisson, A. Rúnarsson, H. Harðardóttir et al., Comparison of Campylobacter jejuni isolates from human, food, veterinary and environmental sources in Iceland using PFGE, MLST and fla-SVR sequencing, Journal of Applied Microbiology, vol.4, issue.4, pp.971-81, 2011.
DOI : 10.1111/j.1365-2672.2011.05100.x

S. Kittl, G. Heckel, B. Korczak, and P. Kuhnert, Source Attribution of Human Campylobacter Isolates by MLST and Fla-Typing and Association of Genotypes with Quinolone Resistance, PLoS ONE, vol.191, issue.11, p.81796, 2013.
DOI : 10.1371/journal.pone.0081796.s005

S. Lévesque, E. Frost, R. Arbeit, and S. Michaud, Multilocus Sequence Typing of Campylobacter jejuni Isolates from Humans, Chickens, Raw Milk, and Environmental Water in Quebec, Canada, Journal of Clinical Microbiology, vol.46, issue.10, pp.3404-3415, 2008.
DOI : 10.1128/JCM.00042-08

Y. Wang and D. Taylor, Natural transformation in Campylobacter species., Journal of Bacteriology, vol.172, issue.2, pp.949-55, 1990.
DOI : 10.1128/jb.172.2.949-955.1990

C. Clark, E. Taboada, C. Grant, C. Blakeston, F. Pollari et al., Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance, Journal of Clinical Microbiology, vol.50, issue.3, pp.798-809, 2012.
DOI : 10.1128/JCM.05733-11

K. Dingle, F. Colles, D. Falush, and M. Maiden, Sequence Typing and Comparison of Population Biology of Campylobacter coli and Campylobacter jejuni, Journal of Clinical Microbiology, vol.43, issue.1, pp.340-347, 2005.
DOI : 10.1128/JCM.43.1.340-347.2005

A. Kinana, E. Cardinale, F. Tall, I. Bahsoun, J. Sire et al., Genetic Diversity and Quinolone Resistance in Campylobacter jejuni Isolates from Poultry in Senegal, Applied and Environmental Microbiology, vol.72, issue.5, pp.3309-3322, 2006.
DOI : 10.1128/AEM.72.5.3309-3313.2006

URL : https://hal.archives-ouvertes.fr/pasteur-00624407

M. Denis, E. Henrique, B. Chidaine, A. Tircot, S. Bougeard et al., Campylobacter from sows in farrow-to-finish pig farms: Risk indicators and genetic diversity, Veterinary Microbiology, vol.154, issue.1-2, pp.163-70, 2011.
DOI : 10.1016/j.vetmic.2011.07.001

F. Colles and M. Maiden, Campylobacter sequence typing databases: applications and future prospects, Microbiology, vol.158, issue.Pt_11, pp.2695-709, 2012.
DOI : 10.1099/mic.0.062000-0

A. Cody, N. Mccarthy, J. Bray, H. Wimalarathna, F. Colles et al., isolates are a consistent source of human disease, in Oxfordshire, United Kingdom, Environmental Microbiology Reports, vol.26, issue.5, pp.782-790, 2015.
DOI : 10.1111/1758-2229.12314

T. Wassenaar, A. Fernández-astorga, R. Alonso, V. Marteinsson, S. Magnússon et al., -SVR genotypes isolated from humans and poultry in three European regions, Letters in Applied Microbiology, vol.110, issue.3, pp.388-95, 2009.
DOI : 10.1111/j.1472-765X.2009.02678.x

URL : https://hal.archives-ouvertes.fr/hal-00955916

X. Chen, F. Kong, Q. Wang, C. Li, J. Zhang et al., Rapid Detection of Isoniazid, Rifampin, and Ofloxacin Resistance in Mycobacterium tuberculosis Clinical Isolates Using High-Resolution Melting Analysis, Journal of Clinical Microbiology, vol.49, issue.10, pp.3450-3457, 2011.
DOI : 10.1128/JCM.01068-11

S. Ngoi and K. Thong, High resolution melting analysis for rapid mutation screening in gyrase and Topoisomerase IV genes in quinolone-resistant Salmonella enterica, Biomed Res Int, vol.2014, p.718084, 2014.

B. Loveless, A. Yermakova, D. Christensen, J. Kondig, H. Heine et al., Identification of ciprofloxacin resistance by SimpleProbe???, High Resolution Melt and Pyrosequencing??? nucleic acid analysis in biothreat agents: Bacillus anthracis, Yersinia pestis and Francisella tularensis, Molecular and Cellular Probes, vol.24, issue.3, pp.154-60, 2010.
DOI : 10.1016/j.mcp.2010.01.003