M. J. Keeling and K. Eames, Networks and epidemic models, J R Soc Interface, vol.2, pp.295-307, 2005.

V. V. Volkova, R. Howey, N. J. Savill, and M. Woolhouse, Potential for transmission of infections in networks of cattle farms, Epidemics, vol.2, pp.116-122, 2010.

L. Danon, A. P. Ford, T. House, C. P. Jewell, M. J. Keeling et al., Networks and the epidemiology of infectious disease, Interdiscip Perspect Infect Dis, p.284909, 2011.

M. G. Buhnerkempe, M. J. Tildesley, T. Lindström, D. A. Grear, K. Portacci et al., The impact of movements and animal density on continental scale cattle disease outbreaks in the United States, PLoS One, vol.9, p.91724, 2014.

B. L. Dutta, P. Ezanno, and E. Vergu, Characteristics of the spatio-temporal network of cattle movements in France over a 5-year period, Prev Vet Med, vol.117, pp.79-94, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02635459

C. Dubé, C. Ribble, D. Kelton, and B. Mcnab, A review of network analysis terminology and its application to foot-and-mouth disease modelling and policy development, Transbound Emerg Dis, vol.56, pp.73-85, 2009.

R. R. Kao, L. Danon, D. M. Green, and I. Z. Kiss, Demographic structure and pathogen dynamics on the network of livestock movements in Great Britain, Proc Biol Sci, vol.273, pp.1999-2007, 2006.

M. Nöremark, N. Håkansson, S. S. Lewerin, A. Lindberg, and A. Jonsson, Network analysis of cattle and pig movements in Sweden: measures relevant for disease control and risk based surveillance, Prev Vet Med, vol.99, pp.78-90, 2011.

S. Rautureau, B. Dufour, and B. Durand, Vulnerability of animal trade networks to the spread of infectious diseases: a methodological approach applied to evaluation and emergency control strategies in cattle, Transbound Emerg Dis, vol.58, pp.110-120, 2005.

P. Bajardi, A. Barrat, F. Natale, L. Savini, and V. Colizza, Dynamical patterns of cattle trade movements, PLoS One, vol.6, p.19869, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00594746

M. C. Vernon, Demographics of cattle movements in the United Kingdom, BMC Vet Res, vol.7, p.31, 2011.

M. M. Mweu, G. Fournié, T. Halasa, N. Toft, and S. S. Nielsen, Temporal characterisation of the network of Danish cattle movements and its implication for disease, Prev Vet Med, vol.110, pp.379-387, 2013.

E. Brooks-pollock, G. O. Roberts, and M. J. Keeling, A dynamic model of bovine tuberculosis spread and control in Great Britain, Nature, vol.511, pp.228-231, 2014.

M. A. Behr and D. M. Collins, Paratuberculosis: Organism, Disease, Control. CABI, 2010.

S. S. Nielsen and N. Toft, A review of prevalences of paratuberculosis in farmed animals in Europe, Prev Vet Med, vol.88, pp.1-14, 2009.

M. Guicharnaud, Description de la prevalence de la paratuberculose chez les bovins laitiers dans le monde : revue et analyse, 2009.

S. L. Ott, S. J. Wells, and B. A. Wagner, Herd-level economic losses associated with Johne's disease on US dairy operations, Prev Vet Med, vol.40, pp.179-192, 1999.

J. E. Lombard, F. B. Garry, B. J. Mccluskey, and B. A. Wagner, Risk of removal and effects on milk production associated with paratuberculosis status in dairy cows, J Am Vet Med Assoc, vol.227, pp.1975-1981, 2005.

P. A. Windsor and R. J. Whittington, Evidence for age susceptibility of cattle to Johne's disease, Vet J, vol.184, pp.37-44, 2010.

R. J. Whittington and P. A. Windsor, In utero infection of cattle with Mycobacterium avium subsp. paratuberculosis: a critical review and metaanalysis, Vet J, vol.179, pp.60-69, 2009.

H. Van-roermund, D. Bakker, P. Willemsen, and M. De-jong, Horizontal transmission of Mycobacterium avium subsp. paratuberculosis in cattle in an experimental setting: calves can transmit the infection to other calves, Vet Microbiol, vol.122, pp.270-279, 2007.

C. Marcé, P. Ezanno, M. F. Weber, H. Seegers, D. U. Pfeiffer et al., Invited review: Modeling within-herd transmission of Mycobacterium avium subspecies paratuberculosis in dairy cattle: a review, J Dairy Sci, vol.93, pp.4455-4470, 2010.

R. W. Humphry, A. W. Stott, C. Adams, and G. J. Gunn, A model of the relationship between the epidemiology of Johne's disease and the environment in suckler-beef herds, Vet J, vol.172, pp.432-445, 2006.

D. A. Bibliographie-abernethy, J. Moscard-costello, E. Dickson, R. Harwood, K. Burns et al., Epidemiology and management of a bovine brucellosis cluster in Northern Ireland, Preventive Veterinary Medicine, vol.98, issue.4, pp.223-229, 2011.

J. M. Adaska and R. J. Anderson, Seroprevalence of Johne's-disease infection in dairy cattle in California, USA. Preventive veterinary medicine, vol.60, pp.255-261, 2003.

S. Altizer, A. Dobson, P. Hosseini, P. Hudson, M. Pascual et al., Seasonality and the dynamics of infectious diseases, Ecology Letters, vol.9, issue.4, pp.467-484, 2006.

J. Álvarez, L. De-juan, V. Briones, B. Romero, A. Aranaz et al., Mycobacterium avium subspecies paratuberculosis in fallow deer and wild boar in Spain, Veterinary Record, vol.156, issue.7, pp.212-213, 2005.

J. L. Anderson, J. K. Meece, J. J. Koziczkowski, D. L. Clark, R. P. Radcliff et al., Mycobacterium avium subsp. paratuberculosis in scavenging mammals in Wisconsin, Journal of Wildlife Diseases, vol.43, issue.2, pp.302-308, 2007.

R. M. Anderson, C. A. Donnelly, N. M. Ferguson, M. Woolhouse, C. J. Watt et al., Transmission dynamics and epidemiology of BSE in British cattle, Nature, vol.382, issue.6594, pp.779-788, 1996.

R. M. Anderson and W. Trewhella, Population Dynamics of the Badger (Meles meles) and the Epidemiology of Bovine Tuberculosis (Mycobacterium bovis), Philosophical Transactions of the Royal Society B : Biological Sciences, vol.310, pp.327-381, 1145.

P. Bajardi, A. Barrat, F. Natale, L. Savini, and V. Colizza, Dynamical patterns of cattle trade movements, PLoS ONE, vol.6, issue.5, p.19869, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00594746

P. Bajardi, A. Barrat, L. Savini, and V. Colizza, Optimizing surveillance for livestock disease spreading through animal movements, Journal of The Royal Society Interface, vol.9, issue.76, pp.2814-2825, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00766126

F. M. Baptista and T. Nunes, Spatial analysis of cattle movement patterns in Portugal, Veterinaria italiana, vol.43, issue.3, pp.611-619, 2007.

F. Bastida and R. A. Juste, Paratuberculosis control : a review with a focus on vaccination, Journal of Immune Based Therapies and Vaccines, vol.9, issue.1, p.8, 2011.

P. M. Beard, M. J. Daniels, D. Henderson, A. Pirie, K. Rudge et al., Paratuberculosis infection of nonruminant wildlife in Scotland, Journal of Clinical Microbiology, vol.39, issue.4, pp.1517-1521, 2001.

B. Beaudeau and F. , Review of culling and replacement practices in dairy cattle herds, 1999.

M. A. Beaumont, Approximate Bayesian Computation in Evolution and Ecology, Evolution, and Systematics, vol.41, pp.379-406, 2010.

M. A. Beaumont, J. Cornuet, J. Marin, and C. P. Robert, Adaptive approximate Bayesian computation, Biometrika, vol.96, issue.4, pp.983-990, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00280461

M. A. Beaumont, W. Zhang, and D. J. Balding, Approximate Bayesian computation in population genetics, Genetics, vol.162, issue.4, pp.2025-2035, 2002.

G. Beaunée, E. Gilot-fromont, M. Garel, and P. Ezanno, A novel epidemiological model to better understand and predict the observed seasonal spread of Pestivirus in Pyrenean chamois populations, Veterinary Research, vol.46, issue.1, p.86, 2015.

G. Beaunée, E. Vergu, and P. Ezanno, Controlling the spread of Mycobacterium avium subsp. paratuberculosis at a regional scale based on internal biosecurity and animal movements, SVEPM, 2015.

G. Beaunée, E. Vergu, and P. Ezanno, Modelling of paratuberculosis spread between dairy cattle farms at a regional scale, Veterinary Research, vol.46, pp.1-13, 2015.

G. Beaunée, E. Vergu, and P. Ezanno, Benefit of epidemiological data in the understanding of Map spread

G. Beaunée, E. Vergu, A. Joly, and P. Ezanno, Controlling bovine paratuberculosis at a regional scale : towards a decision modeling tool

D. J. Begg and R. J. Whittington, Experimental animal infection models for Johne's disease, an infectious enteropathy caused by Mycobacterium avium subsp. paratuberculosis. The Veterinary, Journal, vol.176, issue.2, pp.129-145, 2008.

M. Begon, M. Bennett, R. G. Bowers, N. P. French, S. M. Hazel et al., A clarification of transmission terms in host-microparasite models : numbers, densities and areas, Epidemiology and Infection, vol.129, issue.1, pp.147-153, 2002.

M. A. Behr and D. M. Collins, , 2010.

M. A. Behr and V. Kapur, The evidence for Mycobacterium paratuberculosis in Crohn's disease, Current Opinion in Gastroenterology, vol.24, issue.1, pp.17-21, 2008.

A. Benedictus, R. M. Mitchell, M. Linde-widmann, R. Sweeney, T. Fyock et al., Transmission parameters of Mycobacterium avium subspecies paratuberculosis infections in a dairy herd going through a control program, Preventive Veterinary Medicine, vol.83, issue.3-4, pp.215-227, 2008.

G. Benedictus, J. Verhoeff, Y. H. Schukken, and J. W. Hesselink, Dutch paratuberculosis programme history, principles and development, Veterinary Microbiology, vol.77, issue.3-4, pp.399-413, 2000.

R. Bennett, The 'direct costs' of livestock disease : the development of a system of models for the analysis of 30 endemic livestock diseases in great britain, Journal of Agricultural Economics, vol.54, issue.1, pp.55-71, 2003.

A. J. Beulens, D. Broens, P. Folstar, and G. J. Hofstede, Food safety and transparency in food chains and networks Relationships and challenges, Food Control, vol.16, issue.6, pp.481-486, 2005.

, Bibliographie 217

K. B. Bicknell, J. E. Wilen, and R. E. Howitt, Public Policy and Private Incentives for Livestock Disease Control, Australian Journal of Agricultural and Resource Economics, vol.43, issue.4, pp.501-521, 1999.

M. Bigras-poulin, R. A. Thompson, M. Chriél, S. Mortensen, and M. Greiner, Network analysis of Danish cattle industry trade patterns as an evaluation of risk potential for disease spread, Preventive veterinary medicine, vol.76, issue.1-2, pp.11-39, 2006.

A. Blake, M. T. Sinclair, and G. Sugiyarto, Quantifying the impact of foot and mouth disease on tourism and the UK economy, Tourism Economics, vol.9, issue.4, pp.449-465, 2003.

M. G. Blum and O. François, Non-linear regression models for Approximate Bayesian Computation, Statistics and Computing, vol.20, issue.1, pp.63-73, 2010.

I. I. Bogoch, M. I. Creatore, M. S. Cetron, J. S. Brownstein, N. Pesik et al., Assessment of the potential for international dissemination of Ebola virus via commercial air travel during the 2014 west African outbreak, Lancet, issue.9962, pp.29-35, 2015.

M. L. Brennan and R. M. Christley, Biosecurity on Cattle Farms : A Study in North-West England, PLoS ONE, vol.7, issue.1, p.28139, 2012.

T. Britton and F. Giardina, Introduction to statistical inference for infectious diseases

E. Brooks-pollock, M. C. De-jong, M. J. Keeling, D. Klinkenberg, and J. L. Wood, Eight challenges in modelling infectious livestock diseases, Epidemics, vol.10, pp.1-5, 2015.

E. Brooks-pollock and M. Keeling, Herd size and bovine tuberculosis persistence in cattle farms in Great Britain, Preventive Veterinary Medicine, vol.92, issue.4, pp.360-365, 2009.

E. Brooks-pollock, G. O. Roberts, M. J. Keeling, and M. J. Keeling, A dynamic model of bovine tuberculosis spread and control in Great Britain, Nature, vol.511, issue.7508, pp.228-231, 2014.

E. Brooks-pollock and J. L. Wood, Eliminating bovine tuberculosis in cattle and badgers : insight from a dynamic model, Proceedings of the Royal Society of London B : Biological Sciences, p.282, 1808.

M. G. Buhnerkempe, M. J. Tildesley, T. Lindström, D. A. Grear, K. Portacci et al., The impact of movements and animal density on continental scale cattle disease outbreaks in the United States, PLoS ONE, vol.9, issue.3, p.91724, 2014.

E. Burban, Cinétique et variabilité de l'excrétion de Mycobactérium avium paratuberculosis chez les bovins : étude longitudinale et typologie des profils d'excrétion, 2011.

V. Caporale, A. Giovannini, C. Di-francesco, and P. Calistri, Importance of the traceability of animals and animal products in epidemiology. Revue scientifique et technique (International Office of Epizootics, vol.20, pp.372-378, 2001.

T. Carpenter, S. Berry, G. , and J. , Economics of brucella ovis control in sheep : epidemiologic simulation model, Journal of the American Veterinary Medical Association, vol.190, issue.8, pp.977-982, 1987.

D. Bibliographie-carslake, W. Grant, L. E. Green, J. Cave, J. Greaves et al., Endemic cattle diseases : comparative epidemiology and governance, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.366, pp.1975-1986, 1573.

M. Carstensen, D. J. O'brien, and S. M. Schmitt, Public acceptance as a determinant of management strategies for bovine tuberculosis in free-ranging U.S. wildlife, Veterinary Microbiology, vol.151, issue.1-2, pp.200-204, 2011.

M. V. Charron, T. Balenghien, H. Seegers, M. Langlais, and P. Ezanno, How Much Can Diptera-Borne Viruses Persist over Unfavourable Seasons ?, PLoS ONE, vol.8, issue.9, p.74213, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00992684

M. V. Charron, H. Seegers, M. Langlais, and P. Ezanno, Seasonal spread and control of Bluetongue in cattle, Journal of theoretical biology, vol.291, pp.1-9, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00710404

J. Chi, J. A. Vanleeuwen, A. Weersink, and G. P. Keefe, Direct production losses and treatment costs from bovine viral diarrhoea virus, bovine leukosis virus, Mycobacterium avium subspecies paratuberculosis, and Neospora caninum, Preventive Veterinary Medicine, vol.55, issue.2, pp.137-153, 2002.

J. Chi, J. A. Vanleeuwen, A. Weersink, and G. P. Keefe, Management factors related to seroprevalences to bovine viral-diarrhoea virus, bovine-leukosis virus, Mycobacterium avium subspecies paratuberculosis, and Neospora caninum in dairy herds in the Canadian Maritimes, Preventive veterinary medicine, vol.55, issue.1, pp.57-68, 2002.

J. Cho, L. W. Tauer, Y. H. Schukken, M. I. Gómez, R. L. Smith et al., Economic analysis of Mycobacterium avium subspecies paratuberculosis vaccines in dairy herds, Journal of Dairy Science, vol.95, issue.4, pp.1855-1872, 2012.

J. Cho, L. W. Tauer, Y. H. Schukken, R. L. Smith, Z. Lu et al., Compartment Model for Controlling Infectious Livestock Disease : Cost-Effective Control Strategies for Johne's Disease In Dairy Herds. Agricultural & Applied Economics Association's, 2011.

, AAEA & NAREA Joint Annual Meeting

M. Choisy, P. Rohani, and J. F. Guégan, Mathematical Modeling of Infectious Diseases Dynamics, Encyclopedia of Infectious Diseases : Modern Methodologies, pp.379-404, 2007.

V. Colizza, A. Barrat, M. Barthelemy, A. Valleron, and A. Vespignani, Modeling the worldwide spread of pandemic influenza : baseline case and containment interventions, PLoS medicine, vol.4, issue.1, p.95, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00126956

V. Colizza and A. Vespignani, Epidemic modeling in metapopulation systems with heterogeneous coupling pattern : Theory and simulations, Journal of Theoretical Biology, vol.251, issue.3, pp.450-467, 2008.

D. M. Collins, D. M. Gabric, and G. W. De-lisle, Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization, Journal of Clinical Microbiology, vol.28, issue.7, pp.1591-1596, 1990.

M. Collins and I. Morgan, Epidemiological model of paratuberculosis in dairy cattle, Preventive Veterinary Medicine, vol.11, issue.2, pp.131-146, 1991.

M. T. Collins, V. Eggleston, and E. J. Manning, Successful control of Johne's disease in nine dairy herds : Results of a six-year field trial, Journal of Dairy Science, vol.93, issue.4, pp.1638-1643, 2010.

, Bibliographie 219

M. T. Collins and I. R. Morgan, Simulation model of paratuberculosis control in a dairy herd, Preventive Veterinary Medicine, vol.14, issue.1-2, pp.21-32, 1992.

M. T. Collins, D. C. Sockett, W. J. Goodger, T. A. Conrad, C. B. Thomas et al., Herd prevalence and geographic distribution of, and risk factors for, bovine paratuberculosis in Wisconsin, Journal of the American Veterinary Medical Association, vol.204, issue.4, pp.636-641, 1994.

J. L. Corn, E. J. Manning, S. Sreevatsan, and J. R. Fischer, Isolation of Mycobacterium avium subsp. paratuberculosis from free-ranging birds and mammals on livestock premises, Applied and Environmental Microbiology, vol.71, issue.11, pp.6963-6967, 2005.

L. D. Costa, F. A. Rodrigues, G. Travieso, and P. R. Boas, Characterization of complex networks : A survey of measurements, Advances in Physics, vol.56, issue.1, pp.167-242, 2007.

A. Courcoul and P. Ezanno, Modelling the spread of Bovine Viral Diarrhoea Virus (BVDV) in a managed metapopulation of cattle herds, Veterinary Microbiology, vol.142, issue.1-2, pp.119-128, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00578408

A. Courcoul, L. Hogerwerf, D. Klinkenberg, M. Nielen, E. Vergu et al., Modelling effectiveness of herd level vaccination against Q fever in dairy cattle, Veterinary Research, vol.42, issue.1, p.68, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02648249

A. Courcoul, E. Vergu, J. B. Denis, and F. Beaudeau, Spread of Q fever within dairy cattle herds : key parameters inferred using a Bayesian approach, Proceedings of the Royal Society B : Biological Sciences, vol.277, pp.2857-2865, 1695.
URL : https://hal.archives-ouvertes.fr/hal-02752511

S. Coursaget, Etat des lieux de l'offre des actions de maitrise de la paratuberculose bovine dans le grand ouest, 2009.

B. M. Crossley, F. J. Zagmutt-vergara, T. L. Fyock, R. H. Whitlock, and I. A. Gardner, Fecal shedding of Mycobacterium avium subsp. paratuberculosis by dairy cows, Veterinary Microbiology, vol.107, issue.3-4, pp.257-263, 2005.

A. Damman, A. Viet, S. Arnoux, M. Guerrier-chatellet, E. Petit et al., Modelling the spread of bovine viral diarrhea virus (BVDV) in a beef cattle herd and its impact on herd productivity, Veterinary Research, vol.46, issue.1, p.12, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01290663

L. Danon, A. P. Ford, T. House, C. P. Jewell, M. J. Keeling et al., Networks and the Epidemiology of Infectious Disease, Interdisciplinary Perspectives on Infectious Diseases, issue.11, pp.1-28, 2011.

P. Del-moral, A. Doucet, and A. Jasra, Sequential Monte Carlo samplers, Journal of the Royal Statistical Society : Series B (Statistical Methodology), vol.68, pp.411-436, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01593880

Y. Delbrouck, Valeur informative d'outils utilisables à grande échelle pour déterminer le statut des troupeaux bovins laitiers vis-à-vis de l'infection par Mycobacterium avium ssp paratuberculosis, 2008.

O. Diekmann, J. Heesterbeek, and J. A. Metz, On the definition and the computation of the basic reproduction ratio r 0 in models for infectious diseases in heterogeneous populations, Journal of mathematical biology, vol.28, issue.4, pp.365-382, 1990.

C. Dubé, C. Ribble, D. Kelton, and B. Mcnab, Comparing network analysis measures to determine potential epidemic size of highly contagious exotic diseases in fragmented monthly networks of dairy cattle movements in Ontario, Canada. Transboundary and Emerging Diseases, vol.55, issue.9, pp.382-392, 2008.

C. Dubé, C. Ribble, D. Kelton, and B. Mcnab, A Review of Network Analysis Terminology and its Application to Foot-and-Mouth Disease Modelling and Policy Development, Transboundary and Emerging Diseases, vol.56, issue.3, pp.73-85, 2009.

B. Dufour, R. Pouillot, D. , and B. , A cost/benefit study of paratuberculosis certification in French cattle herds, Veterinary Research, vol.35, issue.1, pp.69-81, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00902819

A. J. Duncan, G. J. Gunn, F. I. Lewis, C. Umstatter, and R. W. Humphry, The influence of empirical contact networks on modelling diseases in cattle, Epidemics, vol.4, issue.3, pp.117-123, 2012.

B. L. Dutta, P. Ezanno, and E. Vergu, Characteristics of the spatio-temporal network of cattle movements in France over a 5-year period, Preventive Veterinary Medicine, vol.117, issue.1, pp.79-94, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02635459

A. R. Elbers, A. N. Van-der-spek, and P. A. Van-rijn, Epidemiologic characteristics of bluetongue virus serotype 8 laboratory-confirmed outbreaks in The Netherlands in 2007 and a comparison with the situation in 2006, Preventive veterinary medicine, vol.92, issue.1-2, pp.1-8, 2009.

J. Eppleston, D. J. Begg, N. K. Dhand, B. Watt, and R. J. Whittington, Environmental Survival of Mycobacterium avium subsp paratuberculosis in Different Climatic Zones of Eastern Australia, Applied and Environmental Microbiology, vol.80, issue.8, pp.2337-2342, 2014.

A. K. Ersbøll, B. K. Ersboll, H. Houe, L. Alban, and A. M. Kjeldsen, Spatial modelling of the between-herd infection dynamics of bovine virus diarrhoea virus (BVDV) in dairy herds in Denmark, Preventive Veterinary Medicine, vol.97, issue.2, pp.83-89, 2010.

L. A. Espejo, S. Godden, W. L. Hartmann, and S. J. Wells, Reduction in incidence of Johne's disease associated with implementation of a disease control program in Minnesota demonstration herds, Journal of dairy science, vol.95, issue.7, pp.4141-4152, 2012.

P. Ezanno, M. Aubry-kientz, S. Arnoux, P. Cailly, G. L'ambert et al., A generic weather-driven model to predict mosquito population dynamics applied to species of Anopheles, Culex and Aedes genera of southern France. Preventive veterinary medicine, vol.120, pp.39-50, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02636104

P. Ezanno, C. Fourichon, F. Beaudeau, and H. Seegers, Between-herd movements of cattle as a tool for evaluating the risk of introducing infected animals, Animal Research, vol.55, issue.3, pp.189-208, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00890064

P. Ezanno, C. Fourichon, and H. Seegers, Influence of herd structure and type of virus introduction on the spread of bovine viral diarrhoea virus (BVDV) on the spread of bovine viral diarrhoea virus (BVDV) within a dairy herd, Veterinary Research, vol.39, issue.5, pp.39-51, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00902929

P. Ezanno, G. Van-schaik, M. F. Weber, and J. A. Heesterbeek, A modeling study on the sustainability of a certification-and-monitoring program for paratuberculosis in cattle, Veterinary Research, vol.36, issue.5-6, pp.811-826, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00903000

P. Ezanno, E. Vergu, M. Langlais, and E. Gilot-fromont, Modelling the Dynamics of Host-Parasite Interactions : Basic Principles, New Frontiers of Molecular Epidemiology of Infectious Diseases, pp.79-101, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00992716

N. H. Fefferman and K. L. Ng, How disease models in static networks can fail to approximate disease in dynamic networks, Physical Review E, vol.76, issue.3, pp.31919-31930, 2007.

N. M. Ferguson, C. A. Donnelly, A. , and R. M. , The foot-and-mouth epidemic in Great Britain : pattern of spread and impact of interventions, Science, vol.292, issue.5519, pp.1155-1160, 2001.

, Bibliographie 221

C. Ferrouillet, S. J. Wells, W. L. Hartmann, S. M. Godden, and J. Carrier, Decrease of Johne's disease prevalence and incidence in six Minnesota, USA, dairy cattle herds on a long-term management program, Preventive Veterinary Medicine, vol.88, issue.2, pp.128-137, 2009.

E. M. Fèvre, B. M. Bronsvoort, K. A. Hamilton, and S. Cleaveland, Animal movements and the spread of infectious diseases, Trends in microbiology, vol.14, issue.3, pp.125-131, 2006.

W. E. Fitzgibbon, M. Langlais, and J. J. Morgan, A mathematical model for indirectly transmitted diseases, Mathematical biosciences, vol.206, issue.2, pp.233-248, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00195426

A. Flahault, E. Vergu, and P. Boëlle, Potential for a global dynamic of Influenza A (H1N1), BMC Infectious Diseases, vol.9, issue.1, pp.129-140, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00663615

O. Flaten, G. Lien, M. Koesling, P. S. Valle, and M. Ebbesvik, Comparing risk perceptions and risk management in organic and conventional dairy fanning : empirical results from Norway, Livestock Production Science, vol.95, issue.1-2, pp.11-25, 2005.

N. P. French, L. Kelly, R. Jones, C. , and D. , Dose-response relationships for foot and mouth disease in cattle and sheep, Epidemiology and Infection, vol.128, issue.2, pp.325-332, 2002.

A. B. Garcia and L. Shalloo, Invited review : The economic impact and control of paratuberculosis in cattle, Journal of Dairy Science, vol.98, issue.8, pp.1-21, 2015.

G. P. Garnett, S. Cousens, T. B. Hallett, R. Steketee, and N. Walker, Mathematical models in the evaluation of health programmes, The Lancet, vol.378, issue.9790, pp.515-525, 2011.

J. M. Garrido, P. Vazquez, E. Molina, J. M. Plazaola, I. A. Sevilla et al., Paratuberculosis vaccination causes only limited crossreactivity in the skin test for diagnosis of bovine tuberculosis, PLoS One, vol.8, issue.11, p.80985, 2013.

M. C. Gates, V. V. Volkova, and M. E. Woolhouse, Impact of changes in cattle movement regulations on the risks of bovine tuberculosis for Scottish farms, Preventive Veterinary Medicine, vol.108, issue.2-3, pp.125-136, 2013.

M. C. Gates and M. E. Woolhouse, Suboptimal Herd Performance Amplifies the Spread of Infectious Disease in the Cattle Industry, PLoS ONE, vol.9, issue.3, pp.93410-93420, 2014.

M. C. Gates and M. E. Woolhouse, Controlling infectious disease through the targeted manipulation of contact network structure, Epidemics, vol.12, pp.11-19, 2015.

H. Gerritsmann, G. L. Stalder, J. Spergser, F. Hoelzl, A. Deutz et al., Multiple strain infections and high genotypic diversity among Mycobacterium avium subsp. paratuberculosis field isolates from diseased wild and domestic ruminant species in the eastern Alpine region of Austria, Infection, Genetics and Evolution, vol.21, issue.C, pp.244-251, 2014.

A. H. Ghadiali, M. Strother, S. A. Naser, E. J. Manning, and S. Sreevatsan, Mycobacterium avium subsp. paratuberculosis Strains Isolated from Crohn's Disease Patients and Animal Species Exhibit Similar Polymorphic Locus Patterns, Journal of Clinical Microbiology, vol.42, issue.11, pp.5345-5348, 2004.

P. Ghosh, C. Hsu, E. J. Alyamani, M. M. Shehata, M. A. Al-dubaib et al., Genome-Wide Analysis of the Emerging Infection with Mycobacterium avium Subspecies paratuberculosis in the Arabian Camels (Camelus dromedarius), PLoS ONE, vol.7, issue.2, pp.31947-31958, 2012.

S. B. Bibliographie-giese and P. Ahrens, Detection of Mycobacterium avium subsp paratuberculosis in milk from clinically affected cows by PCR and culture, Veterinary Microbiology, vol.77, issue.3-4, pp.291-297, 2000.

M. Gilbert, A. Mitchell, D. Bourn, J. Mawdsley, R. Clifton-hadley et al., Cattle movements and bovine tuberculosis in Great Britain, Nature, vol.435, issue.7041, pp.491-496, 2005.

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.

D. T. Gillespie, Approximate accelerated stochastic simulation of chemically reacting systems, The Journal of Chemical Physics, vol.115, issue.4, p.1716, 2001.

H. C. Godfray, J. R. Beddington, I. R. Crute, L. Haddad, D. Lawrence et al., Food security : the challenge of feeding 9 billion people, Science, vol.327, issue.5967, pp.812-818, 2010.

N. S. Gollnick, R. M. Mitchell, M. Baumgart, H. K. Janagama, S. Sreevatsan et al., Survival of Mycobacterium avium subsp. paratuberculosis in bovine monocytederived macrophages is not affected by host infection status but depends on the infecting bacterial genotype, Veterinary immunology and immunopathology, vol.120, issue.3-4, pp.93-105, 2007.

M. G. Gonda, Y. M. Chang, G. E. Shook, M. T. Collins, and B. W. Kirkpatrick, Genetic variation of Mycobacterium avium ssp. paratuberculosis infection in US Holsteins, Journal of Dairy Science, vol.89, issue.5, pp.1804-1812, 2006.

M. G. Gonda, B. W. Kirkpatrick, G. E. Shook, and M. T. Collins, Identification of a QTL on BTA20 affecting susceptibility to Mycobacterium avium ssp. paratuberculosis infection in US Holsteins, Animal genetics, vol.38, issue.4, pp.389-396, 2007.

R. F. Grais, J. H. Ellis, and G. E. Glass, Assessing the impact of airline travel on the geographic spread of pandemic influenza, European journal of epidemiology, vol.18, issue.11, pp.1065-1072, 2003.

M. Grandjean, Etude longitudinale des profils d'excretion de Mycobacterium avium subspecies paratuberculosis existants chez des bovins en troupeaux laitiers infectés, 2013.

L. E. Green and G. F. Medley, Mathematical modelling of the foot and mouth disease epidemic of 2001 : strengths and weaknesses, Research in veterinary science, vol.73, issue.3, pp.201-205, 2002.

M. Greenwood, On the Statistical Measure of Infectiousness, The Journal of hygiene, vol.31, issue.3, pp.336-351, 1931.

A. Greig, K. Stevenson, D. Henderson, V. Perez, V. Hughes et al., Epidemiological study of paratuberculosis in wild rabbits in Scotland, Journal of Clinical Microbiology, vol.37, issue.6, pp.1746-1751, 1999.

B. Grenfell, O. N. Bjørnstad, and J. Kappey, Travelling waves and spatial hierarchies in measles epidemics, Nature, vol.414, issue.6865, pp.716-723, 2001.

B. Grenfell and J. Harwood, (meta) population dynamics of infectious diseases, Trends in ecology & evolution, vol.12, issue.10, pp.395-399, 1997.

J. M. Griffin, D. H. Williams, G. E. Kelly, T. A. Clegg, I. O'boyle et al., The impact of badger removal on the control of tuberculosis in cattle herds in Ireland, Preventive veterinary medicine, vol.67, issue.4, pp.237-266, 2005.

H. Groenendaal and D. T. Galligan, Economic consequences of control programs for paratuberculosis in midsize dairy farms in the United States, Journal of the American Veterinary Medical Association, vol.223, issue.12, pp.1757-1763, 2003.

H. Groenendaal, M. Nielen, A. W. Jalvingh, S. H. Horst, D. T. Galligan et al., A simulation of Johne's disease control, Preventive Veterinary Medicine, vol.54, issue.3, pp.225-245, 2002.

R. Guatteo, A. Joly, and F. Beaudeau, Evaluation of combined environmental and pooled animals sampling to determine dairy cattle herd infection status for Mycobacterium avium subspecies paratuberculosis (MAP), 11th International Colloquium on Paratuberculosis, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02745751

M. Guicharnaud, Description de la prévalence de la paratuberculose chez les bovins laitiers dans le monde : revue et analyse, 2009.

R. Guy, C. Larédo, and E. Vergu, Approximation of epidemic models by diffusion processes and their statistical inference, Journal of Mathematical Biology, vol.70, issue.3, pp.621-646, 2015.
URL : https://hal.archives-ouvertes.fr/hal-00823193

W. A. Hagan, Age as a Factor in Susceptibility to Johne's Disease, Cornell Veterinarian, vol.28, pp.34-40, 1938.

T. J. Hagenaars, C. A. Donnelly, and N. M. Ferguson, Spatial heterogeneity and the persistence of infectious diseases, Journal of Theoretical Biology, vol.229, issue.3, pp.349-359, 2004.

J. E. Halliday, M. E. Chase-topping, M. C. Pearce, I. J. Mckendrick, L. Allison et al., Herd-level risk factors associated with the presence of Phage type 21/28 E. coli O157 on Scottish cattle farms, BMC Microbiology, vol.6, issue.1, p.99, 2006.

I. Hanski, Metapopulation dynamics, Nature, vol.396, issue.6706, pp.41-49, 1998.

F. Hartig, J. M. Calabrese, B. Reineking, T. Wiegand, and A. Huth, Statistical inference for stochastic simulation models -theory and application, Ecology letters, vol.14, issue.8, pp.816-827, 2011.

J. Heesterbeek and M. G. Roberts, The type-reproduction number T in models for infectious disease control, Mathematical biosciences, 2007.

J. A. Heesterbeek, A Brief History of R 0 and a Recipe for its Calculation, Acta Biotheoretica, vol.50, issue.3, pp.189-204, 2002.

J. Heffernan, R. Smith, and L. Wahl, Perspectives on the basic reproductive ratio, Journal of the Royal Society Interface, vol.2, issue.4, pp.281-293, 2005.

G. Hess, Disease in metapopulation models : implications for conservation, Ecology, pp.1617-1632, 1996.

T. Hoch, C. Fourichon, A. Viet, and H. Seegers, Influence of the transmission function on a simulated pathogen spread within a population, Epidemiology and Infection, vol.136, issue.10, pp.1374-1382, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02662416

P. Holme, Modern temporal network theory : a colloquium, The European Physical Journal B, vol.88, issue.9, pp.1-30, 2015.

P. Holme and J. Saramäki, Temporal networks, Physics Reports, vol.519, issue.3, pp.97-125, 2012.

B. Hsu, C. Wu, C. Talaat, and A. M. , Genome-Wide Sequence Variation among Mycobacterium avium Subspecies paratuberculosis Isolates : A Better Understanding of Johne's Disease Transmission Dynamics, Frontiers in microbiology, vol.2, p.236, 2011.

R. W. Humphry, A. W. Stott, C. Adams, G. , and G. J. , A model of the relationship between the epidemiology of Johne's disease and the environment in suckler-beef herds, The Veterinary Journal, vol.172, issue.3, pp.432-445, 2006.

M. Jesse, P. Ezanno, S. Davis, and J. A. Heesterbeek, A fully coupled, mechanistic model for infectious disease dynamics in a metapopulation : Movement and epidemic duration, Journal of Theoretical Biology, vol.254, issue.2, pp.331-338, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02658793

M. Jesse and H. Heesterbeek, Divide and conquer ? Persistence of infectious agents in spatial metapopulations of hosts, Journal of Theoretical Biology, vol.275, issue.1, pp.12-20, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00676094

B. A. Jones, D. Grace, R. Kock, S. Alonso, J. Rushton et al., Zoonosis emergence linked to agricultural intensification and environmental change, Proceedings of the National Academy of Sciences, vol.110, issue.21, pp.8399-8404, 2013.

J. B. Jørgensen, Survival of Mycobacterium paratuberculosis in slurry, Nordisk Veterinaer Medicin, vol.29, issue.6, pp.267-270, 1977.

J. B. Jørgensen, An improved medium for culture of Mycobacterium paratuberculosis from bovine faeces, Acta veterinaria Scandinavica, vol.23, issue.3, pp.325-335, 1982.

R. A. Juste, Current strategies for eradication of paratuberculosis and issues in public health, Veterinary Immunology and Immunopathology, vol.148, issue.1-2, pp.16-22, 2012.

V. Jégou, J. Porhiel, and P. Brunschwig, Risk management factors affecting mortality among dairy calves herds in 80 herds in Brittany, Proc. Journées Bovines Nantaises, 2006.

C. H. Kalis, M. T. Collins, H. W. Barkema, and J. W. Hesselink, Certification of herds as free of Mycobacterium paratuberculosis infection : actual pooled faecal results versus certification model predictions, Preventive veterinary medicine, vol.65, issue.3-4, pp.189-204, 2004.

R. R. Kao, The role of mathematical modelling in the control of the 2001 FMD epidemic in the UK, Trends in microbiology, vol.10, issue.6, pp.279-286, 2002.

R. R. Kao, L. Danon, D. M. Green, and I. Z. Kiss, Demographic structure and pathogen dynamics on the network of livestock movements in Great Britain, Proceedings of the Royal Society B : Biological Sciences, vol.273, pp.1999-2007, 1597.

R. R. Kao, D. M. Green, J. Johnson, and I. Z. Kiss, Disease dynamics over very different time-scales : foot-and-mouth disease and scrapie on the network of livestock movements in the UK, Journal of The Royal Society Interface, vol.4, issue.16, pp.907-916, 2007.

M. Keeling, The implications of network structure for epidemic dynamics, Theoretical Population Biology, vol.67, issue.1, pp.1-8, 2005.

M. Keeling and P. Rohani, Modeling Infectious Diseases in Humans and Animals, 2008.

M. J. Keeling, Models of foot-and-mouth disease, Proceedings of the Royal Society B : Biological Sciences, vol.272, pp.1195-1202, 1569.

M. J. Keeling, L. Danon, M. C. Vernon, and T. A. House, Individual identity and movement networks for disease metapopulations, Proceedings of the National Academy of Sciences, vol.107, issue.19, pp.8866-8870, 2010.

M. J. Keeling and K. T. Eames, Networks and epidemic models, Journal of The Royal Society Interface, vol.2, issue.4, pp.295-307, 2005.

M. J. Keeling, M. E. Woolhouse, D. J. Shaw, L. Matthews, M. Chase-topping et al., Dynamics of the 2001 UK Foot and Mouth Epidemic : Stochastic Dispersal in a Heterogeneous Landscape, Science, vol.294, issue.5543, pp.813-817, 2001.

D. J. Kennedy and M. B. Allworth, Progress in national control and assurance programs for bovine Johne's disease in Australia, Veterinary Microbiology, vol.77, issue.3-4, pp.443-451, 2000.

D. J. Kennedy and G. Benedictus, Control of Mycobacterium avium subsp. paratuberculosis infection in agricultural species, Rev Sci Tech Off Int Epiz, vol.20, pp.151-179, 2001.

W. O. Kermack and A. G. Mckendrick, A Contribution to the Mathematical Theory of Epidemics, Proceedings of the Royal Society A : Mathematical, Physical and Engineering Sciences, vol.115, issue.772, pp.700-721, 1927.

R. P. Kitching, M. Thrusfield, and N. M. Taylor, Use and abuse of mathematical models : an illustration from the 2001 foot and mouth disease epidemic in the United Kingdom, Revue scientifique et technique (International Office of Epizootics), vol.25, issue.1, pp.293-311, 2006.

A. S. Klovdahl, Social networks and the spread of infectious diseases : the AIDS example, Social science & medicine, vol.21, issue.11, pp.1203-1216, 1982.

A. S. Klovdahl, J. J. Potterat, D. E. Woodhouse, J. B. Muth, S. Q. Muth et al., Social networks and infectious disease : the Colorado Springs Study, Social science & medicine, vol.38, issue.1, pp.79-88, 1982.

A. P. Koets, G. Adugna, L. L. Janss, H. J. Van-weering, C. H. Kalis et al., Genetic variation of susceptibility to Mycobacterium avium subsp. paratuberculosis infection in dairy cattle, Journal of Dairy Science, vol.83, issue.11, pp.2702-2708, 2000.

K. Krogh, S. S. Nielsen, and L. Trier, Certification programme to reduce risk of between-herd transmission of paratuberculosis in the Danish dairy industry, 2012.

A. B. Kudahl, S. S. Nielsen, and S. Østergaard, Economy, Efficacy, and Feasibility of a Risk-Based Control Program Against Paratuberculosis, Journal of Dairy Science, vol.91, issue.12, pp.4599-4609, 2008.

A. B. Kudahl, S. S. Nielsen, and S. Østergaard, Strategies for time of culling in control of paratuberculosis in dairy herds, Journal of Dairy Science, vol.94, issue.8, pp.3824-3834, 2011.

A. B. Kudahl, S. Østergaard, J. T. Sørensen, and S. S. Nielsen, A stochastic model simulating paratuberculosis in a dairy herd, Preventive Veterinary Medicine, vol.78, issue.2, pp.97-117, 2007.

A. B. Larsen, M. Rs, R. C. , and C. , Age of cattle as related to resistance to infection with Mycobacterium paratuberculosis, American Journal of Veterinary Research, vol.36, issue.3, pp.255-257, 1975.

M. A. Bibliographie-leibold, M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase et al., The metacommunity concept : a framework for multi-scale community ecology, Ecology Letters, vol.7, issue.7, pp.601-613, 2004.

A. Lemenach, J. Legrand, R. F. Grais, C. Viboud, A. Valleron et al., Modeling spatial and temporal transmission of foot-and-mouth disease in France : identification of high-risk areas, Veterinary Research, vol.36, issue.5-6, pp.699-712, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00902993

L. L. Li, J. P. Bannantine, Q. Zhang, A. Amonsin, B. J. May et al., The complete genome sequence of Mycobacterium avium subspecies paratuberculosis, Proceedings of the National Academy of Sciences, vol.102, issue.35, pp.12344-12349, 2005.

W. Liu, L. Matthews, M. Chase-topping, N. J. Savill, D. J. Shaw et al., Metapopulation dynamics of Escherichia coli O157 in cattle : an exploratory model, Journal of The Royal Society Interface, vol.4, issue.16, pp.917-924, 2007.

A. L. Lloyd and V. A. Jansen, Spatiotemporal dynamics of epidemics : synchrony in metapopulation models, Mathematical Biosciences, vol.188, issue.1-2, pp.1-16, 2004.

J. E. Lombard, I. A. Gardner, S. R. Jafarzadeh, C. P. Fossler, B. Harris et al., Herd-level prevalence of Mycobacterium avium subsp. paratuberculosis infection in United States dairy herds in 2007, Preventive veterinary medicine, vol.108, issue.2-3, pp.234-238, 2013.

J. E. Lombard, F. B. Garry, F. B. Garry, B. J. Mccluskey, B. J. Mccluskey et al., Risk of removal and effects on milk production associated with paratuberculosis status in dairy cows, Journal of the American Veterinary Medical Association, vol.227, issue.12, pp.1975-1981, 2005.

Z. Lu, R. M. Mitchell, R. L. Smith, J. S. Van-kessel, P. P. Chapagain et al., The importance of culling in Johne's disease control, Journal of Theoretical Biology, vol.254, issue.1, pp.135-146, 2008.

Z. Lu, Y. H. Schukken, R. L. Smith, and Y. T. Grohn, Stochastic simulations of a multi-group compartmental model for Johne's disease on US dairy herds with test-based culling intervention, Journal of Theoretical Biology, vol.264, issue.4, pp.1190-1201, 2010.

Z. Lu, Y. H. Schukken, R. L. Smith, and Y. T. Grohn, Using vaccination to prevent the invasion of Mycobacterium avium subsp. paratuberculosis in dairy herds : A stochastic simulation study, Preventive Veterinary Medicine, vol.110, issue.3-4, pp.335-345, 2013.

Z. Lu, Y. H. Schukken, R. L. Smith, R. M. Mitchell, and Y. T. Grohn, Impact of imperfect Mycobacterium avium subsp. paratuberculosis vaccines in dairy herds : a mathematical modeling approach, Preventive Veterinary Medicine, vol.108, issue.2-3, pp.148-158, 2013.

A. Lurette, C. Belloc, S. Touzeau, T. Hoch, P. Ezanno et al., Modelling Salmonella spread within a farrow-to-finish pig herd, Veterinary Research, vol.39, issue.5, p.49, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00902934

M. Magnusson, A. Christiansson, B. Svensson, and C. Kolstrup, Effect of Different Premilking Manual Teat-Cleaning Methods on Bacterial Spores in Milk, Journal of Dairy Science, vol.89, issue.10, pp.3866-3875, 2006.

G. Magombedze, G. Magombedze, C. N. Ngonghala, and C. Lanzas, Evaluation [corrected] of the "Iceberg Phenomenon" in Johne's disease through mathematical modelling, PLoS ONE, vol.8, issue.10, p.76636, 2013.

C. Marcé, Modelling the transmission of and effectiveness of control measures for Mycobacterium avium subsp. paratuberculosis in dairy herds, 2010.

C. Marcé, P. Ezanno, H. Seegers, D. U. Pfeiffer, and C. Fourichon, Predicting fadeout versus persistence of paratuberculosis in a dairy cattle herd for management and control purposes : a modelling study, Veterinary Research, issue.36, p.42, 2011.

C. Marcé, P. Ezanno, H. Seegers, D. U. Pfeiffer, and C. Fourichon, Within-herd contact structure and transmission of Mycobacterium avium subspecies paratuberculosis in a persistently infected dairy cattle herd, Preventive Veterinary Medicine, vol.100, issue.2, pp.116-125, 2011.

C. Marcé, P. Ezanno, M. F. Weber, H. Seegers, D. U. Pfeiffer et al., Invited review : Modeling within-herd transmission of Mycobacterium avium subspecies paratuberculosis in dairy cattle : A review, Journal of Dairy Science, vol.93, issue.10, pp.4455-4470, 2010.

C. Marcé, R. Guatteo, N. Bareille, and C. Fourichon, Dairy calf housing systems across Europe and risk for calf infectious diseases, vol.4, pp.1588-1596, 2010.

M. H. Mars, C. J. Bruschke, and J. T. Van-oirschot, Airborne transmission of BHV1, BRSV, and BVDV among cattle is possible under experimental conditions, Veterinary Microbiology, vol.66, issue.3, pp.197-207, 1999.

M. Marsot, S. Rautureau, B. Dufour, D. , and B. , Impact of Stakeholders Influence, Geographic Level and Risk Perception on Strategic Decisions in Simulated Foot and Mouth Disease Epizootics in France, PLoS ONE, vol.9, issue.1, pp.86323-86339, 2014.

B. Martínez-lópez, A. M. Perez, and J. M. Sánchez-vizcaíno, Combined application of social network and cluster detection analyses for temporal-spatial characterization of animal movements in Salamanca, Spain. Preventive veterinary medicine, vol.91, pp.29-38, 2009.

T. Massaro, S. Lenhart, M. Spence, C. Drakes, G. Yang et al., Modeling for cost analysis of johne's disease control based on evelisa testing, Journal of Biological Systems, issue.4, p.41, 2013.

H. T. Matthews, On Johne's disease. The Veterinary Record, vol.59, pp.397-401, 1947.

H. Mccallum, N. Barlow, and J. Hone, How should pathogen transmission be modelled ? Trends in ecology & evolution, vol.16, pp.295-300, 2001.

S. L. Mckenna, G. P. Keefe, A. Tiwari, J. Vanleeuwen, and H. W. Barkema, Johne's disease in Canada part II : disease impacts, risk factors, and control programs for dairy producers. The Canadian veterinary journal. La revue vétérinaire canadienne, vol.47, pp.1089-1099, 2006.

G. J. Medema, P. Teunis, A. H. Havelaar, and C. N. Haas, Assessment of the doseresponse relationship of Campylobacter jejuni, International Journal of Food Microbiology, vol.30, issue.1-2, pp.101-111, 1996.

J. F. Mee, T. Geraghty, R. O'neill, and S. J. More, Bioexclusion of diseases from dairy and beef farms : Risks of introducing infectious agents and risk reduction strategies, The Veterinary Journal, vol.194, issue.2, pp.143-150, 2012.

M. Meuwissen, R. Huirne, and J. B. Hardaker, Risk and risk management : an empirical analysis of Dutch livestock farmers, 2001.

M. Bibliographie-miraglia, H. J. Marvin, G. A. Kleter, P. Battilani, C. Brera et al., Climate change and food safety : An emerging issue with special focus on Europe, Food and Chemical Toxicology, vol.47, issue.5, pp.1009-1021, 2009.

R. M. Mitchell, G. F. Medley, M. T. Collins, and Y. H. Schukken, A meta-analysis of the effect of dose and age at exposure on shedding of Mycobacterium avium subspecies paratuberculosis (MAP) in experimentally infected calves and cows, Epidemiology and Infection, vol.140, issue.2, pp.231-246, 2012.

R. M. Mitchell, Y. Schukken, A. Koets, M. Weber, D. Bakker et al., Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle, Veterinary Research, vol.46, issue.1, p.66, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333711

R. M. Mitchell, R. H. Whitlock, Y. T. Groehn, and Y. H. Schukken, Back to the real world : Connecting models with data. Preventive veterinary medicine, vol.118, pp.215-225, 2015.

R. M. Mitchell, R. H. Whitlock, S. M. Stehman, A. Benedictus, P. P. Chapagain et al., Simulation modeling to evaluate the persistence of Mycobacterium avium subsp. paratuberculosis (MAP) on commercial dairy farms in the United States, Preventive Veterinary Medicine, vol.83, issue.3-4, pp.360-380, 2008.

D. A. Moore, M. L. Merryman, M. L. Hartman, and D. J. Klingborg, Comparison of published recommendations regarding biosecurity practices for various production animal species and classes, Journal of the American Veterinary Medical Association, vol.233, issue.2, pp.249-256, 2008.

C. Moriceau, Evaluation de la valeur informative d'outils diagnostiques utilisés seuls ou en combinaisons pour définir le statut des troupeaux bovins vis-à-vis de l'infection par Mycobacterium avium subspecies paratuberculosis, 2013.

H. Mortensen, S. S. Nielsen, and P. Berg, Genetic Variation and Heritability of the Antibody Response to Mycobacterium avium subspecies paratuberculosis in Danish Holstein Cows, Journal of Dairy Science, vol.87, issue.7, pp.2108-2113, 2004.

M. Moslonka-lefebvre, C. Gilligan, H. Monod, C. Belloc, P. Ezanno et al., Market analyses of livestock trade networks to inform the prevention of joint economic and epidemiological risk

A. S. Motiwala, A. Amonsin, M. Strother, E. Manning, V. Kapur et al., Molecular epidemiology of Mycobacterium avium subsp paratuberculosis isolates recovered from wild animal species, Journal of Clinical Microbiology, vol.42, issue.4, pp.1703-1712, 2004.

J. Muskens, H. W. Barkema, E. Russchen, K. Van-maanen, Y. H. Schukken et al., Prevalence and regional distribution of paratuberculosis in dairy herds in The Netherlands, Veterinary Microbiology, vol.77, issue.3-4, pp.253-261, 2000.

J. Muskens, A. R. Elbers, H. J. Van-weering, and J. P. Noordhuizen, Herd Management Practices Associated with Paratuberculosis Seroprevalence in Dutch Dairy Herds, Journal of Veterinary Medicine, Series B, vol.50, issue.8, pp.372-377, 2003.

M. M. Mweu, G. Fournié, T. Halasa, N. Toft, and S. S. Nielsen, Temporal characterisation of the network of Danish cattle movements and its implication for disease, Preventive Veterinary Medicine, vol.110, issue.3-4, pp.379-387, 2013.

F. Natale, A. Giovannini, L. Savini, D. Palma, L. Possenti et al., Network analysis of Italian cattle trade patterns and evaluation of risks for potential disease spread, Preventive veterinary medicine, vol.92, issue.4, pp.341-350, 2009.

S. S. Nielsen, Danish control programme for bovine paratuberculosis, Cattle Practice, vol.15, pp.161-168, 2007.

S. S. Nielsen, Transitions in diagnostic tests used for detection of Mycobacterium avium subsp. paratuberculosis infections in cattle, Veterinary Microbiology, vol.132, issue.3-4, pp.274-282, 2008.

S. S. Nielsen, Programmes on paratuberculosis in Europe, Tenth International Colloquium on Paratuberculosis, 2009.

S. S. Nielsen, H. Bjerre, and N. Toft, Colostrum and Milk as Risk Factors for Infection with Mycobacterium avium subspecies paratuberculosis in Dairy Cattle, Journal of dairy science, vol.91, issue.12, pp.4610-4615, 2008.

S. S. Nielsen, C. Enevoldsen, and N. Toft, Milk production losses associated with bovine paratuberculosis diagnosed from repeated testing, 11th international Symposia of Veterinary Epidemiology and Economics, 2006.

S. S. Nielsen and A. K. Ersbøll, Age at Occurrence of Mycobacterium avium Subspecies paratuberculosis in Naturally Infected Dairy Cows, Journal of Dairy Science, vol.89, issue.12, pp.4557-4566, 2006.

S. S. Nielsen and N. Toft, Ante mortem diagnosis of paratuberculosis : a review of accuracies of ELISA, interferon-gamma assay and faecal culture techniques, Veterinary Microbiology, vol.129, issue.3-4, pp.217-235, 2008.

S. S. Nielsen and N. Toft, A review of prevalences of paratuberculosis in farmed animals in Europe, Preventive Veterinary Medicine, vol.88, issue.1, pp.1-14, 2009.

S. S. Nielsen, N. Toft, L. Alban, and L. A. Kelly, Management practices reducing the test-prevalence of paratuberculosis in Danish dairy herds, Proceedings of the Society for Veterinary Epidemiology and Preventive Medicine, pp.189-200, 2010.

S. S. Nielsen, M. F. Weber, A. B. Kudahl, C. Marcé, and N. Toft, Stochastic models to simulate paratuberculosis in dairy herds. Revue scientifique et technique (International Office of Epizootics), vol.30, pp.615-625, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647355

M. Nöremark, N. Håkansson, S. S. Lewerin, A. Lindberg, J. et al., Network analysis of cattle and pig movements in Sweden : measures relevant for disease control and risk based surveillance, Preventive Veterinary Medicine, vol.99, issue.2-4, pp.78-90, 2011.

R. O'brien, C. G. Mackintosh, D. Bakker, M. Kopecna, I. Pavlik et al., Immunological and Molecular Characterization of Susceptibility in Relationship to Bacterial Strain Differences in Mycobacterium avium subsp. paratuberculosis Infection in the Red Deer (Cervus elaphus), Infection and Immunity, vol.74, issue.6, pp.3530-3537, 2006.

H. Okura, S. S. Nielsen, and N. Toft, Prevalence of Mycobacterium avium subsp. paratuberculosis infection in adult Danish non-dairy cattle sampled at slaughter. Preventive veterinary medicine, vol.94, pp.185-190, 2010.

S. L. Ott, S. J. Wells, and B. A. Wagner, Herd-level economic losses associated with Johne's disease on US dairy operations, Preventive veterinary medicine, vol.40, issue.3-4, pp.179-192, 1999.

B. Pastor-satorras, R. Castellano, C. Van-mieghem, P. Vespignani, and A. , Epidemic processes in complex networks, Rev. Mod. Phys, vol.87, pp.925-979, 2015.

T. N. Petney and R. H. Andrews, Multiparasite communities in animals and humans : frequency, structure and pathogenic significance, International Journal for Parasitology, vol.28, issue.3, pp.377-393, 1998.

R. B. Pillars, D. L. Grooms, J. A. Woltanski, and E. Blair, Prevalence of Michigan dairy herds infected with Mycobacterium avium subspecies paratuberculosis as determined by environmental sampling, Preventive Veterinary Medicine, vol.89, issue.3-4, pp.191-196, 2009.

R. G. Pouillot, B. Dufour, and B. T. Durand, A deterministic and stochastic simulation model for intra-herd paratuberculosis transmission, Veterinary Research, vol.35, issue.1, pp.53-68, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00902820

. R-core-team, R : A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2015.

A. M. Ramírez-villaescusa, G. F. Medley, S. Mason, and L. E. Green, Risk factors for herd breakdown with bovine tuberculosis in 148 cattle herds in the south west of England, Preventive veterinary medicine, vol.95, issue.3-4, pp.224-230, 2010.

J. D. Rankin, The estimation of doses of Mycobacterium johnei suitable for the production of Johne's disease in cattle, The Journal of Pathology and Bacteriology, vol.77, issue.2, pp.638-642, 1959.

S. Rautureau, B. Dufour, D. , and B. , Vulnerability of Animal Trade Networks to The Spread of Infectious Diseases : A Methodological Approach Applied to Evaluation and Emergency Control Strategies in Cattle, Transboundary and Emerging Diseases, vol.58, issue.2, pp.110-120, 2005.

S. Rautureau, B. Dufour, D. , and B. , Structuring the Passive Surveillance Network Improves Epizootic Detection and Control Efficacy : A Simulation Study on Foot-and-Mouth Disease in France, Transboundary and Emerging Diseases, vol.59, issue.4, pp.311-322, 2012.

F. J. Reviriego-gordejo and J. P. Vermeersch, Towards eradication of bovine tuberculosis in the European Union, Veterinary Microbiology, vol.112, issue.2-4, pp.101-109, 2006.

S. E. Ridge, I. M. Baker, and M. Hannah, Effect of compliance with recommended calf-rearing practices on control of bovine Johne's disease, Australian veterinary journal, vol.83, issue.1-2, pp.85-90, 2005.

S. Riley, Large-Scale Spatial-Transmission Models of Infectious Disease, Science, vol.316, issue.5829, pp.1298-1301, 2007.

O. Rio, Frequency and risks of mortality and health disorders of calves in dairy cattle herds, 1999.

M. G. Roberts and J. A. Heesterbeek, A new method for estimating the effort required to control an infectious disease, Proceedings of the Royal Society B : Biological Sciences, vol.270, pp.1359-1364, 1522.

J. Robins, S. Bogen, A. Francis, A. Westhoek, A. Kanarek et al., Agent-based model for Johne's disease dynamics in a dairy herd, Veterinary Research, vol.46, issue.1, p.68, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333714

S. E. Robinson and R. M. Christley, Identifying temporal variation in reported births, deaths and movements of cattle in Britain, BMC Veterinary Research, vol.2, issue.1, p.11, 2006.

S. E. Robinson and R. M. Christley, Exploring the role of auction markets in cattle movements within Great Britain. Preventive veterinary medicine, vol.81, pp.21-37, 2007.

S. E. Robinson, M. G. Everett, and R. M. Christley, Recent network evolution increases the potential for large epidemics in the British cattle population, Journal of the Royal Society, Interface / the Royal Society, vol.4, issue.15, pp.669-674, 2007.

W. J. Rogan and B. Gladen, Estimating prevalence from the results of a screening test, American Journal of Epidemiology, vol.107, issue.1, pp.71-76, 1978.

C. A. Rossiter and W. S. Burhans, Farm-specific approach to paratuberculosis (Johne's disease) control. The Veterinary clinics of North America, Food animal practice, vol.12, issue.2, pp.383-415, 1996.

W. Rossmanith, R. Janacek, W. , and E. , Control of BVDV-infection on common grassland-The key for successful BVDV-eradication in Lower Austria. Preventive veterinary medicine, vol.72, pp.133-137, 2005.

D. Schley, S. Gubbins, P. , and D. J. , Quantifying the Risk of Localised Animal Movement Bans for Foot-and-Mouth Disease, PLoS ONE, vol.4, issue.5, pp.5481-5487, 2009.

Y. H. Schukken, R. H. Whitlock, D. Wolfgang, Y. Grohn, A. Beaver et al., Longitudinal data collection of Mycobacterium avium subspecies Paratuberculosis infections in dairy herds : the value of precise field data, Veterinary Research, vol.46, issue.1, p.65, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333712

L. A. Sechi and C. T. Dow, Mycobacterium avium ss. paratuberculosis zoonosis-the hundred year war-beyond crohn's disease, Frontiers in immunology, vol.6, 2015.

U. Sorge, D. Kelton, K. Lissemore, A. Godkin, S. Hendrick et al., Attitudes of Canadian dairy farmers toward a voluntary Johne's disease control program, Journal of dairy science, vol.93, issue.4, pp.1491-1499, 2010.

J. R. Stabel, S. Hurd, L. Calvente, and R. F. Rosenbusch, Destruction of Mycobacterium paratuberculosis, Salmonella spp., and Mycoplasma spp. in Raw Milk by a Commercial On-Farm High-Temperature, Short-Time Pasteurizer, Journal of dairy science, vol.87, issue.7, pp.2177-2183, 2004.

K. Stahl, A. Lindberg, H. Rivera, C. Ortiz, and J. Moreno-lopez, Self-clearance from BVDV infections -A frequent finding in dairy herds in an endemically infected region in Peru, Preventive Veterinary Medicine, vol.83, issue.3-4, pp.285-296, 2008.

K. Stevenson, Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis : a review, Veterinary Research, vol.46, issue.1, p.64, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333713

K. Stevenson, J. Alvarez, D. Bakker, F. Biet, L. De-juan et al., Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants, BMC Microbiology, issue.212, p.9, 2009.

A. W. Stott, R. W. Humphry, and G. J. Gunn, Modelling the effects of previous infection and re-infection on the costs of bovine viral diarrhoea outbreaks in beef herds, The Veterinary Journal, vol.185, issue.2, pp.138-143, 2010.

R. N. Streeter, G. F. Hoffsis, S. Bechnielsen, W. P. Shulaw, and M. Rings, Isolation of Mycobacterium-Paratuberculosis From Colostrum and Milk of Subclinically Infected Cows, American Journal of Veterinary Research, vol.56, issue.10, pp.1322-1324, 1995.

R. W. Sweeney, Transmission of paratuberculosis. The Veterinary clinics of North America, Food animal practice, vol.12, issue.2, pp.305-312, 1996.

R. W. Sweeney, R. H. Whitlock, and A. E. Rosenberger, Mycobacterium paratuberculosis isolated from fetuses of infected cows not manifesting signs of the disease, American Journal of Veterinary Research, vol.53, issue.4, pp.477-480, 1992.

D. Taisne, Description d'un plan de maitrise de la paratuberculose en troupeau infecte : exemple de l'ille-et-vilaine, 2009.

D. Thompson, P. Muriel, D. Russell, P. Osborne, A. Bromley et al., Economic costs of the foot and mouth disease outbreak in the United Kingdom in 2001. Revue scientifique et technique, International Office of Epizootics), vol.21, issue.3, pp.675-687, 2002.

J. G. Thorne and L. E. Hardin, Estimated prevalence of paratuberculosis in Missouri, USA cattle, Preventive Veterinary Medicine, vol.31, issue.1-2, pp.51-57, 1997.

P. K. Thornton, Livestock production : recent trends, future prospects, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.365, pp.2853-2867, 1554.

T. Tiensin, M. Nielen, H. Vernooij, T. Songserm, W. Kalpravidh et al., Transmission of the Highly Pathogenic Avian Influenza Virus H5N1 within Flocks during the 2004 Epidemic in Thailand, The Journal of Infectious Diseases, vol.196, issue.11, pp.1679-1684, 2007.

M. J. Tildesley, P. R. Bessell, M. J. Keeling, and M. E. Woolhouse, The role of pre-emptive culling in the control of foot-and-mouth disease, Proceedings of the Royal Society B : Biological Sciences, vol.276, pp.3239-3248, 1671.

M. J. Tildesley, N. J. Savill, D. J. Shaw, R. Deardon, S. P. Brooks et al., Optimal reactive vaccination strategies for a foot-and-mouth outbreak in the UK, Nature, vol.440, issue.7080, pp.83-86, 2006.

M. J. Tildesley, V. V. Volkova, and M. E. Woolhouse, Potential for epidemic take-off from the primary outbreak farm via livestock movements, BMC veterinary research, vol.7, p.76, 2011.

A. Tiwari, J. A. Vanleeuwen, I. R. Dohoo, G. P. Keefe, J. P. Haddad et al., Production Effects of Pathogens Causing Bovine Leukosis, Bovine Viral Diarrhea, Paratuberculosis, and Neosporosis, Journal of dairy science, vol.90, issue.2, pp.659-669, 2007.

A. Tiwari, J. A. Vanleeuwen, I. R. Dohoo, H. Stryhn, G. P. Keefe et al., Effects of seropositivity for bovine leukemia virus, bovine viral diarrhoea virus, Mycobacterium avium subspecies paratuberculosis, and Neospora caninum on culling in dairy cattle in four Canadian provinces, Veterinary Microbiology, vol.109, issue.3-4, pp.147-158, 2005.

A. Tiwari, J. A. Vanleeuwen, S. L. Mckenna, G. P. Keefe, and H. W. Barkema, , 2006.

, Johne's disease in Canada Part I : clinical symptoms, pathophysiology, diagnosis, and prevalence in dairy herds. The Canadian veterinary journal. La revue vétérinaire canadienne, vol.47, pp.874-882

T. Toni, D. Welch, N. Strelkowa, A. Ipsen, and M. P. Stumpf, Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems, Journal of The Royal Society Interface, vol.6, issue.31, pp.187-202, 2009.

S. Touzeau, M. E. Chase-topping, L. Matthews, D. Lajous, F. Eychenne et al., Modelling the spread of scrapie in a sheep flock : evidence for increased transmission during lambing seasons, Archives of Virology, vol.151, issue.4, pp.735-751, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02665309

P. R. Tozer and A. J. Heinrichs, What Affects the Costs of Raising Replacement Dairy Heifers : A Multiple-Component Analysis, Journal of dairy science, vol.84, issue.8, pp.1836-1844, 2001.

J. Turner, R. G. Bowers, D. Clancy, M. C. Behnke, and R. M. Christley, A network model of E. coli O157 transmission within a typical UK dairy herd : The effect of heterogeneity and clustering on the prevalence of infection, Journal of theoretical biology, vol.254, issue.1, pp.45-54, 2008.

, World Population Prospects : The 2015 Revision, Key Findings and Advance Tables, United Nations, 2015.

E. Valdano, L. Ferreri, C. Poletto, and V. Colizza, Analytical Computation of the Epidemic Threshold on Temporal Networks, Physical Review X, vol.5, issue.2, pp.21005-21014, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01275250

A. Valleron, Les rôles de la modélisation en épidémiologie, Comptes Rendus de l'Académie des Sciences-Series III-Sciences de la Vie, vol.323, pp.429-433, 2000.

P. Van-den-driessche and J. Watmough, Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission, Mathematical biosciences, vol.180, pp.29-48, 2002.

K. J. Van-hulzen, H. C. Heuven, M. Nielen, J. Hoeboer, W. J. Santema et al., Different Mycobacterium avium subsp. paratuberculosis MIRUâ?"VNTR patterns coexist within cattle herds, Veterinary Microbiology, vol.148, issue.2-4, pp.419-424, 2011.

K. J. Van-hulzen, A. P. Koets, M. Nielen, H. C. Heuven, J. A. Van-arendonk et al., The effect of genetic selection for Johne's disease resistance in dairy cattle : Results of a genetic-epidemiological model, Journal of Dairy Science, vol.97, issue.3, pp.1762-1773, 2014.

H. Van-roermund, A. M. Van-vos, and M. C. Jong, Within-herd transmission of paratuberculosis and the possible role of infectious calves, Proceedings of the Seventh International Colloquium on Paratuberculosis, 2002.

H. Van-roermund, M. Weber, A. De-koeijer, A. Velthuis, and M. Jong, Development of a milk quality assurance program for paratuberculosis : from within-and between herd dynamics to economic decision analysis, Proceedings of the Eight Internarional Colloquium on Paratuberculosis, pp.51-59, 2005.

H. Van-roermund, M. F. Weber, . Bilbao, . Spain, H. J. Van-roermund et al., Horizontal transmission of Mycobacterium avium subsp. paratuberculosis in cattle in an experimental setting : Calves can transmit the infection to other calves, Seventh International Colloquium on Paratuberculosis, vol.122, pp.270-279, 2002.

B. Verdugo, C. Pleydell, E. Price-carter, M. Prattley, D. Collins et al., Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms, Preventive veterinary medicine, vol.117, issue.3-4, pp.436-446, 2014.

E. Vergu, H. Busson, and P. Ezanno, Impact of the infection period distribution on the epidemic spread in a metapopulation model, PLoS One, vol.5, issue.2, pp.9371-9387, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668470

M. C. Vernon, Demographics of cattle movements in the United Kingdom, BMC Veterinary Research, vol.7, issue.31, p.31, 2011.

M. C. Vernon and M. J. Keeling, Representing the UK's cattle herd as static and dynamic networks, Proceedings of the Royal Society B : Biological Sciences, vol.276, pp.469-476, 1656.

M. M. Vissers, F. Driehuis, M. C. Te-giffel, P. De-jong, and J. M. Lankveld, Improving Farm Management by Modeling the Contamination of Farm Tank Milk with Butyric Acid Bacteria, Journal of Dairy Science, vol.89, issue.3, pp.850-858, 2006.

V. V. Volkova, R. Howey, N. J. Savill, and M. E. Woolhouse, Potential for transmission of infections in networks of cattle farms, Epidemics, vol.2, issue.3, pp.116-122, 2010.

L. A. Waddell, A. Raji?, K. D. Stärk, and S. A. Mcewen, The zoonotic potential of Mycobacterium avium ssp. paratuberculosis : a systematic review and meta-analyses of the evidence, Epidemiology and infection, pp.1-23, 2015.

X. Wang, R. Gautam, P. J. Pinedo, L. J. Allen, and R. Ivanek, A stochastic model for transmission, extinction and outbreak of Escherichia coli O157 :H7 in cattle as affected by ambient temperature and cleaning practices, Journal of Mathematical Biology, vol.69, issue.2, pp.501-532, 2014.

M. F. Weber, H. Groenendaal, H. J. Van-roermund, and M. Nielen, Simulation of alternatives for the Dutch Johne's disease certification-and-monitoring program, Preventive Veterinary Medicine, vol.62, issue.1, pp.1-17, 2004.

R. H. Whitlock and C. Buergelt, Preclinical and clinical manifestations of paratuberculosis (including pathology), Veterinary Clinics of North America-Food Animal Practice, vol.12, issue.2, pp.345-356, 1996.

R. H. Whitlock, S. J. Wells, R. W. Sweeney, and J. Van-tiem, ELISA and fecal culture for paratuberculosis (Johne's disease) : sensitivity and specificity of each method, Veterinary Microbiology, vol.77, issue.3-4, pp.387-398, 2000.

R. J. Whittington, D. J. Marshall, P. J. Nicholls, I. B. Marsh, and L. A. Reddacliff, Survival and dormancy of Mycobacterium avium subsp. paratuberculosis in the environment, Applied and Environmental Microbiology, vol.70, issue.5, pp.2989-3004, 2004.

R. J. Whittington, L. A. Reddacliff, I. Marsh, S. Mcallister, and V. Saunders, Temporal patterns and quantification of excretion of Mycobacterium avium subsp paratuberculosis in sheep with Johne's disease, Australian Veterinary Journal, vol.78, issue.1, pp.34-37, 2000.

R. J. Whittington, C. A. Taragel, S. Ottaway, I. Marsh, J. Seaman et al., Molecular epidemiological confirmation and circumstances of occurrence of sheep (S) strains of Mycobacterium avium subsp. paratuberculosis in cases of paratuberculosis in cattle in Australia and sheep and cattle in Iceland, Veterinary Microbiology, vol.79, issue.4, pp.311-322, 2001.

R. J. Whittington and P. A. Windsor, In utero infection of cattle with Mycobacterium avium subsp. paratuberculosis : A critical review and meta-analysis, The Veterinary Journal, vol.179, issue.1, pp.60-69, 2009.

P. A. Windsor and R. J. Whittington, Evidence for age susceptibility of cattle to Johne's disease, The Veterinary Journal, vol.184, issue.1, pp.37-44, 2010.

R. Wolf, H. W. Barkema, J. Buck, M. Slomp, J. Flaig et al., High herd-level prevalence of Mycobacterium avium subspecies paratuberculosis in Western Canadian dairy farms, based on environmental sampling, Journal of Dairy Science, vol.97, issue.10, pp.6250-6259, 2014.

R. Wolf, K. Orsel, J. De-buck, and H. W. Barkema, Calves shedding Mycobacterium avium subspecies paratuberculosis are common on infected dairy farms, Veterinary Research, vol.46, issue.1, p.71, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333718

M. Woolhouse, M. Ward, B. Van-bunnik, and J. Farrar, Antimicrobial resistance in humans, livestock and the wider environment, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.370, pp.20140083-20140083, 1670.

M. Wraight, Compliance of Victorian dairy farmers with current calf rearing recommendations for control of Johne's disease, Veterinary Microbiology, vol.77, issue.3-4, pp.429-442, 2000.

J. L. Wylie and A. Jolly, Patterns of chlamydia and gonorrhea infection in sexual networks in Manitoba, Canada. Sexually transmitted diseases, vol.28, issue.1, pp.14-24, 2001.

J. W. Wynne, T. J. Bull, T. Seemann, D. M. Bulach, J. Wagner et al., Exploring the zoonotic potential of Mycobacterium avium subspecies paratuberculosis through comparative genomics, PLoS ONE, vol.6, issue.7, p.22171, 2011.

Y. Xiao, D. Clancy, N. P. French, and R. G. Bowers, A semi-stochastic model for Salmonella infection in a multi-group herd, Mathematical Biosciences, vol.200, issue.2, pp.214-233, 2006.

G. Beaunée, E. Vergu, A. Joly, and P. Ezanno, Controlling bovine paratuberculosis at a regional scale : towards a decision modeling tool

G. Beaunée, E. Vergu, and P. Ezanno, Modelling of paratuberculosis spread between dairy cattle farms at a regional scale, Veterinary Research, vol.46, p.111, 2015.

G. Beaunée, E. Vergu, and P. Ezanno, Controlling the spread of Mycobacterium avium subsp. paratuberculosis at a regional scale based on internal biosecurity and animal movements, Pages 97-107 in Society for Veterinary Epidemiology and Preventive Medicine (SVEPM), pp.97-107, 2015.

G. Beaunée, E. Vergu, and P. Ezanno, Modeling of the spread and control of Mycobacterium avium subsp. paratuberculosis in a metapopulation of cattle herds, European Conference on Mathematical and Theoretical Biology, issue.9, 2014.

G. Beaunée, E. Vergu, and P. Ezanno, Spread and control of Mycobacterium avium subsp. paratuberculosis (Map) in a metapopulation of cattle herds, 12. International Colloquium on Paratuberculosis (ICP), 2014.

G. Beaunée, E. Vergu, and P. Ezanno, Modeling the impact of age-dependent shedding on paratuberculosis transmission in dairy cattle, 4. International Conference on Infectious Disease Dynamics (Epidemics), 2013.

, Gael Beaunée 1?, Elisabeta Vergu 2 and Pauline Ezanno 1

O. Inra and L. Bioepar, France Author for correspondence : gael.beaunee@jouy.inra.fr References, vol.2, p.44307

C. Marcé, P. Ezanno, H. Seegers, D. U. Pfeiffer, C. Fourichon et al., Epidemiology and infection, vol.42, issue.2, pp.37-44, 2010.

-. Mia-;-2-inra and O. Université, UMR1300 BioEpAR, 44307 Nantes, France author for correspondence : gael.beaunee@jouy.inra.fr, vol.78350