I. A. Gardner, S. S. Nielsen, R. J. Whittington, M. T. Collins, D. Bakker et al., Consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis in ruminants, Prev Vet Med, vol.101, pp.18-34, 2011.

P. Kostoulas, S. S. Nielsen, A. J. Branscum, W. O. Johnson, N. Dendukuri et al., STARD-BLCM: standards for the reporting of diagnostic accuracy studies that use Bayesian latent class models, Prev Vet Med, vol.138, pp.37-47, 2017.

S. L. Hui and S. D. Walter, Estimating the error rates of diagnostic tests, Biometrics, vol.36, pp.167-71, 1980.

N. Dendukuri and L. Joseph, Bayesian approaches to modeling the conditional dependence between multiple diagnostic tests, Biometrics, vol.57, pp.158-67, 2001.

M. P. Georgiadis, W. O. Johnson, I. A. Gardner, and R. Singh, Correlation-adjusted estimation of sensitivity and specificity of two diagnostic tests, J R Stat Soc Series B Stat Methodol, vol.52, pp.63-76, 2003.

D. Berkvens, N. Speybroeck, N. Praet, A. A. Lesaffre, and E. , Estimating disease prevalence in a Bayesian framework using probabilistic constraints, Epidemiology, vol.17, pp.145-53, 2006.

W. O. Johnson, J. L. Gastwirth, and L. M. Pearson, Screening without a "gold standard": the Hui-Walter paradigm revisited, Am J Epidemiol, vol.153, pp.921-925, 2001.

A. J. Branscum, I. A. Gardner, and W. O. Johnson, Estimation of diagnostic-test sensitivity and specificity through Bayesian modeling, Prev Vet Med, vol.68, pp.145-63, 2005.

P. M. Vacek, The effect of conditional dependence on the evaluation of diagnostic tests, Biometrics, vol.41, pp.959-68, 1985.

I. A. Gardner, H. Stryhn, P. Lind, and M. T. Collins, Conditional dependence between tests affects the diagnosis and surveillance of animal diseases, Prev Vet Med, vol.45, pp.107-129, 2000.

P. Kostoulas, L. Leontides, C. Billinis, and M. Florou, Application of a semi-dependent latent model in the Bayesian estimation of the sensitivity and specificity of two faecal culture methods for diagnosis of paratuberculosis in sub-clinically infected Greek dairy sheep and goats, Prev Vet Med, vol.76, pp.121-155, 2006.

S. J. Wells, M. T. Collins, K. S. Faaberg, C. Wees, S. Tavornpanich et al., Evaluation of a rapid fecal PCR test for detection of Mycobacterium Avium subsp. paratuberculosis in dairy cattle, Clin Vaccine Immunol, vol.13, pp.1125-1155, 2006.

E. Angelidou, P. Kostoulas, and L. Leontides, Bayesian validation of a serum and milk ELISA for antibodies against Mycobacterium Avium subspecies paratuberculosis in Greek dairy goats across lactation, J Dairy Sci, vol.97, pp.819-847, 2014.

C. A. Bauman, A. Jones-bitton, J. Jansen, D. Kelton, and P. Menzies, Evaluation of fecal culture and fecal RT-PCR to detect Mycobacterium Avium Ssp. paratuberculosis fecal shedding in dairy goats and dairy sheep using latent class Bayesian modeling, BMC Vet Res, vol.12, p.212, 2016.

S. Norton, W. O. Johnson, G. Jones, and C. Heuer, Evaluation of diagnostic tests for Johne's disease (Mycobacterium Avium subspecies paratuberculosis) in New Zealand dairy cows, J Vet Diagn Investig, vol.22, pp.341-51, 2010.

P. Kostoulas, L. Leontides, C. Enoe, C. Billinis, M. Florou et al., Bayesian estimation of sensitivity and specificity of serum ELISA and faecal culture for diagnosis of paratuberculosis in Greek dairy sheep and goats, Prev Vet Med, vol.76, pp.56-73, 2006.

M. F. Weber, J. Verhoeff, G. Van-schaik, and C. Van-maanen, Evaluation of Ziehl-Neelsen stained faecal smear and ELISA as tools for surveillance of clinical paratuberculosis in cattle in the Netherlands, Prev Vet Med, vol.92, pp.256-66, 2009.

M. L. Bermingham, I. G. Handel, E. J. Glass, J. A. Woolliams, C. De et al., Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data, Sci Rep, vol.5, p.11861, 2015.

S. S. Nielsen and N. Toft, Age-specific characteristics of ELISA and fecal culture for purpose-specific testing for paratuberculosis, J Dairy Sci, vol.89, pp.569-79, 2006.

N. Toft, E. Jorgensen, and S. Hojsgaard, Diagnosing diagnostic tests: evaluating the assumptions underlying the estimation of sensitivity and specificity in the absence of a gold standard, Prev Vet Med, vol.68, pp.19-33, 2005.

S. S. Nielsen, C. Gronbaek, J. F. Agger, and H. Houe, Maximum-likelihood estimation of sensitivity and specificity of ELISAs and faecal culture for diagnosis of paratuberculosis, Prev Vet Med, vol.53, pp.191-204, 2002.

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

S. Kawaji, D. J. Begg, K. M. Plain, and R. J. Whittington, A longitudinal study to evaluate the diagnostic potential of a direct faecal quantitative PCR test for Johne's disease in sheep, Vet Microbiol, vol.148, pp.35-44, 2011.

E. L. Laurin, M. Chaffer, J. T. Mcclure, S. L. Mckenna, and G. P. Keefe, The association of detection method, season, and lactation stage on identification of fecal shedding in Mycobacterium Avium Ssp. paratuberculosis infectious dairy cows, J Dairy Sci, vol.98, pp.211-231, 2015.

V. J. Timms, H. M. Mitchell, and B. A. Neilan, Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium Avium subsp. paratuberculosis, J Microbiol Methods, vol.112, pp.99-103, 2015.

D. Fock-chow-tho, E. Topp, E. A. Ibeagha-awemu, and N. Bissonnette, Comparison of commercial DNA extraction kits and quantitative PCR systems for better sensitivity in detecting the causative agent of paratuberculosis in dairy cow fecal samples, J Dairy Sci, vol.100, pp.572-81, 2017.

A. N. Spiess and . Qpcr, Modelling and analysis of real-time PCR data. R package version 1.4-0, 2014.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2016.

S. S. Nielsen and N. Toft, Ante mortem diagnosis of paratuberculosis: a review of accuracies of ELISA, interferon-gamma assay and faecal culture techniques, Vet Microbiol, vol.129, pp.217-252, 2008.

R. W. Sweeney, R. H. Whitlock, A. N. Hamir, A. E. Rosenberger, and S. A. Herr, Isolation of mycobacterium paratuberculosis after oral inoculation in uninfected cattle, Am J Vet Res, vol.53, pp.1312-1316, 1992.

B. J. Moloney and R. J. Whittington, Cross species transmission of ovine Johne's disease from sheep to cattle: an estimate of prevalence in exposed susceptible cattle, Aust Vet J, vol.86, pp.117-140, 2008.

L. Joseph, T. W. Gyorkos, and L. Coupal, Bayesian estimation of disease prevalence and the parameters of diagnostic tests in the absence of a gold standard, Am J Epidemiol, vol.141, pp.263-72, 1995.

C. Enoe, M. P. Georgiadis, and W. O. Johnson, Estimation of sensitivity and specificity of diagnostic tests and disease prevalence when the true disease state is unknown, Prev Vet Med, vol.45, pp.61-81, 2000.

D. J. Spiegelhalter, N. G. Best, B. P. Carlin, and A. Van-der-linde, Bayesian measures of model complexity and fit, J R Stat Soc Series B Stat Methodol, vol.64, pp.583-639, 2002.

A. Hope, P. Kluver, S. Jones, and R. Condron, Sensitivity and specificity of two serological tests for the detection of ovine paratuberculosis, Aust Vet J, vol.78, pp.850-856, 2000.

E. S. Sergeant, D. J. Marshall, G. J. Eamens, C. Kearns, and R. J. Whittington, Evaluation of an absorbed ELISA and an agar-gel immuno-diffusion test for ovine paratuberculosis in sheep in Australia, Prev Vet Med, vol.61, pp.235-283, 2003.

S. Gumber, G. Eamens, and R. J. Whittington, Evaluation of a Pourquier ELISA kit in relation to agar gel immunodiffusion (AGID) test for assessment of the humoral immune response in sheep and goats with and without mycobacterium paratuberculosis infection, Vet Microbiol, vol.115, pp.91-101, 2006.

M. Stevenson, EpiR : Tools for the analysis of epidemiological data (Version 0.9-79, 2016.

D. Lunn, D. Spiegelhalter, A. Thomas, and N. Best, The BUGS project: Evolution, critique and future directions, Stat Med, vol.28, pp.3049-67, 2009.

S. Sturtz, U. Ligges, and A. Gelman, R2WinBUGS: a package for running WinBUGS from R, J Stat Softw, vol.12, pp.1-16, 2005.

S. P. Brooks and A. Gelman, General methods for monitoring convergence of iterative simulations, J Comput Graph Stat, vol.7, pp.434-55, 1998.

A. Gelman and D. B. Rubin, Inference from iterative simulation using multiple sequences, Stat Sci, vol.1992, pp.457-72

M. Plummer, N. Best, K. Cowles, and K. Vines, Coda: convergence diagnosis and output analysis for, MCMC. R News, vol.6, issue.1, pp.7-11, 2006.

G. Jones, W. O. Johnson, T. E. Hanson, and R. Christensen, Identifiability of models for multiple diagnostic testing in the absence of a gold standard, Biometrics, vol.66, pp.855-63, 2010.

S. S. Nielsen, N. Toft, E. Jorgensen, and B. M. Bibby, Bayesian mixture models for within-herd prevalence estimates of bovine paratuberculosis based on a continuous ELISA response, Prev Vet Med, vol.81, pp.290-305, 2007.

B. Shinkins, M. Thompson, S. Mallett, and R. Perera, Diagnostic accuracy studies: how to report and analyse inconclusive test results, BMJ, vol.346, p.2778, 2013.

E. Angelidou, P. Kostoulas, and L. Leontides, Bayesian estimation of sensitivity and specificity of a commercial serum/milk ELISA against the Mycobacterium Avium subsp. Paratuberculosis (MAP) antibody response for each lactation stage in Greek dairy sheep, Prev Vet Med, vol.124, pp.102-107, 2016.

S. Englund, G. Bolske, and K. E. Johansson, An IS900-like sequence found in a mycobacterium sp. other than Mycobacterium Avium subsp. paratuberculosis, FEMS Microbiol Lett, vol.209, pp.267-71, 2002.

S. Kawaji, D. L. Taylor, Y. Mori, and R. J. Whittington, Detection of Mycobacterium Avium subsp. paratuberculosis in ovine faeces by direct quantitative PCR has similar or greater sensitivity compared to radiometric culture, Vet Microbiol, vol.125, pp.36-48, 2007.

K. M. Plain, I. B. Marsh, A. M. Waldron, F. Galea, A. M. Whittington et al., High-throughput direct fecal PCR assay for detection of Mycobacterium Avium subsp. paratuberculosis in sheep and cattle, J Clin Microbiol, vol.52, pp.745-57, 2014.

J. L. Ellingson, C. A. Bolin, and J. R. Stabel, Identification of a gene unique to Mycobacterium Avium subspecies paratuberculosis and application to diagnosis of paratuberculosis, Mol Cell Probes, vol.12, pp.133-175, 1998.

P. S. Albert and L. E. Dodd, A Cautionary Note on the Robustness of Latent Class Models for Estimating Diagnostic Error without a Gold Standard, Biometrics, vol.60, issue.2, pp.427-435, 2004.

E. S. Allman, C. Matias, and J. A. Rhodes, Identifiability of parameters in latent structure models with many observed variables, The Annals of Statistics, vol.37, issue.6A, pp.3099-3132, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00591202

D. Berkvens, N. Speybroeck, N. Praet, A. Adel, and E. Lesaffre, Estimating disease prevalence in a Bayesian framework using probabilistic constraints, Epidemiology, vol.17, issue.2, pp.145-153, 2006.

A. J. Branscum, I. A. Gardner, J. , and W. O. , Estimation of diagnostictest sensitivity and specificity through Bayesian modeling, Preventive Veterinary Medicine, vol.68, issue.2-4, pp.145-163, 2005.

A. P. Dempster, N. M. Laird, and D. B. Rubin, Maximum Likelihood from Incomplete Data via the EM Algorithm, 1976.

N. Dendukuri and L. Joseph, Bayesian approaches to modeling the conditional dependence between multiple diagnostic tests, Biometrics, vol.57, issue.1, pp.158-167, 2001.

J. Frössling, B. Bonnett, A. Lindberg, and C. Björkman, Validation of a Neospora caninum iscom ELISA without a gold standard, Preventive Veterinary Medicine, vol.57, issue.3, pp.141-153, 2003.

M. P. Georgiadis, W. O. Johnson, I. A. Gardner, and R. Singh, Correlation-adjusted estimation of sensitivity and specificity of two diagnostic tests, Journal of the Royal Statistical Society: Series C (Applied Statistics), vol.52, issue.1, pp.63-76, 2003.

S. L. Hui and S. D. Walter, Estimating the Error Rates of Diagnostic Tests, Biometrics, vol.36, issue.1, p.167, 1980.

G. Jones, W. O. Johnson, T. E. Hanson, and R. Christensen, Identifiability of Models for Multiple Diagnostic Testing in the Absence of a Gold Standard, Biometrics, vol.66, issue.3, pp.855-863, 2010.

Y. Mathevon, G. Foucras, R. Falguières, C. , and F. , Estimation of the sensitivity and specificity of two serum ELISAs and one fecal qPCR for diagnosis of paratuberculosis in sub-clinically infected young-adult French sheep using latent class Bayesian modeling, BMC Veterinary Research, vol.13, p.230, 2017.

M. S. Pepe and H. Janes, Insights into latent class analysis of diagnostic test performance, Biostatistics, vol.8, issue.2, pp.474-484, 2007.

Y. Qu, M. Tan, and M. H. Kutner, Random effects models in latent class analysis for evaluating accuracy of diagnostics tests, Biometrics, vol.52, issue.3, pp.797-810, 1996.

A. W. Rutjes, J. B. Reitsma, A. Coomarasamy, K. S. Khan, and P. M. Bossuyt, Evaluation of diagnostic tests when there is no gold standard. A review of methods, Health Technology Assessment, vol.11, issue.50, p.51, 2007.

, ARTICLE 2 : ESTIMATION PAR UNE APPROCHE FRÉQUENTISTE

J. H. Shih and P. S. Albert, Latent model for correlated binary data with diagnostic error, Biometrics, vol.55, issue.4, pp.1232-1235, 1999.

N. Toft, G. T. Innocent, G. Gettinby, R. , and S. W. , Assessing the convergence of Markov Chain Monte Carlo methods: An example from evaluation of diagnostic tests in absence of a gold standard, Preventive Veterinary Medicine, vol.79, issue.2-4, pp.244-256, 2007.

P. M. Vacek, The Effect of Conditional Dependence on the Evaluation of Diagnostic Tests, Biometrics, vol.41, issue.4, pp.959-968, 1985.

. Chapitre-3, . Performances, . Tests-À-l'échelle, and . Individuelle,

R. Dorfman, The Detection of Defective Members of Large Populations. The Annals of Mathematical 361 Statistics, vol.14, pp.436-440, 1943.

C. Kalis, J. W. Hesselink, H. W. Barkema, and M. T. Collins, Culture of Strategically Pooled Bovine Fecal 363

, Samples as a Method to Screen Herds for Paratuberculosis, Journal of Veterinary Diagnostic, vol.364

, Investigation, vol.12, pp.547-551, 2000.

M. F. Weber, H. Groenendaal, H. Van-roermund, and M. Nielen, Simulation of alternatives for the Dutch 366

, Johne's disease certification-and-monitoring program, Preventive Veterinary Medicine, vol.62, issue.1, pp.1-17, 2004.

R. J. Whittington, S. Fell, D. Walker, S. Mcallister, I. Marsh et al., , p.369

, Culture for Sensitive and Economic Detection of Mycobacterium avium subsp. 370 paratuberculosisInfection in Flocks of Sheep, Journal of clinical microbiology, vol.38, issue.7, pp.2550-2556, 2000.

G. J. Eamens, R. J. Whittington, M. J. Turner, S. L. Austin, S. A. Fell et al., , p.372

G. Eamens, D. Walker, N. Porter, and S. Fell, Pooled faecal culture for the detection of Mycobacterium 376

, Australian Veterinary Journal, vol.85, issue.6, pp.243-251, 2007.

S. S. Aly, B. L. Mangold, R. H. Whitlock, R. W. Sweeney, R. J. Anderson et al., , p.379

, Herrold Egg Yolk Medium Culture and Real-Time Quantitative Polymerase Chain Reaction Results 380 for Mycobacterium Avium Subspecies Paratuberculosis in Pooled Fecal and Environmental Samples. 381 Journal of Veterinary Diagnostic Investigation, vol.22, pp.677-683, 2010.

S. S. Nielsen, S. M. Thamsborg, H. Houe, and V. Bitsch, Bulk-tank milk ELISA antibodies for estimating the 383 prevalence of paratuberculosis in Danish dairy herds, Preventive Veterinary Medicine, vol.44, issue.1, pp.1-7, 2000.

J. R. Stabel, Transitions in immune responses to Mycobacterium paratuberculosis, Veterinary, vol.386

, Microbiology, vol.77, issue.3, pp.465-473, 2000.

I. Slana, M. Liapi, M. Moravkova, A. Kralova, and I. Pavlik, Mycobacterium avium subsp. paratuberculosis in 388 cow bulk tank milk in Cyprus detected by culture and quantitative IS900 and F57 real-time PCR

, Preventive Veterinary Medicine, vol.89, issue.3, pp.223-226, 2009.

E. A. Raizman, S. J. Wells, S. M. Godden, R. F. Bey, M. J. Oakes et al., , p.391

, Mycobacterium avium ssp. paratuberculosis in the Environment Surrounding Minnesota Dairy Farms, Journal of Dairy Science, vol.392, issue.9, pp.2959-2966, 2004.

R. Whittington, I. Marsh, P. Taylor, D. Marshall, C. Taragel et al., Isolation of Mycobacterium 394 avium subsp paratuberculosis from environmental samples collected from farms before and after 395 destocking sheep with paratuberculosis, Australian Veterinary Journal, vol.81, issue.9, pp.559-563, 2003.

G. Van-schaik, C. Rossiter, S. Stehman, S. Shin, and Y. Schukken, Longitudinal study to investigate 398 dairy herds. American journal of veterinary research, vol.64, pp.479-84, 2003.

R. J. Whittington, A. M. Whittington, A. Waldron, D. J. Begg, K. De-silva et al., Development 402 and Validation of a Liquid Medium (M7H9C) for Routine Culture of Mycobacterium avium subsp

, paratuberculosis To Replace Modified Bactec 12B Medium, vol.404, pp.3993-4000, 2013.

G. Van-schaik, F. Pradenas, N. Mella, and V. Kruze, , p.449

, Mycobacterium avium subsp. paratuberculosis. Preventive Veterinary Medicine, vol.82, 2007.

R. J. Whittington and H. Mcgregor, Epidemiology of ovine Johne's disease 2 -pasture contamination level 453 and age susceptibility, p.454

F. Boelaert, P. Biront, B. Soumare, M. Dispas, E. Vanopdenbosch et al., Prevalence of 456 bovine herpesvirus-1 in the Belgian cattle population, Preventive Veterinary Medicine, vol.457, issue.3, pp.285-295, 2000.

N. Speybroeck, C. J. Williams, K. B. Lafia, B. Devleesschauwer, and D. Berkvens, Estimating the prevalence of 459 infections in vector populations using pools of samples, Medical and Veterinary Entomology, vol.460, issue.4, pp.361-371, 2012.

J. A. Toribio and E. Sergeant, A comparison of methods to estimate the prevalence of ovine Johne's infection 462 from pooled faecal samples, Australian Veterinary Journal, vol.85, issue.8, 2007.

B. Devleesschauwer, P. Torgerson, J. Charlier, B. Levecke, N. Praet et al., prevalence: Tools 465 for Prevalence Assessment Studies, p.466, 2015.

R. Team, R: A Language and Environment for Statistical Computing, p.468, 2017.

W. Gu, R. Lampman, and R. J. Novak, Assessment of arbovirus vector infection rates using variable size 470 pooling, Medical and Veterinary Entomology, vol.18, issue.2, pp.200-204, 2004.

H. Brenner and O. Gefeller, Variation of sensitivity, specificity, likelihood ratios and predictive values with 473 disease prevalence, Statistics in Medicine, vol.16, issue.9, pp.981-991, 1997.

M. Leeflang, P. Bossuyt, and L. Irwig, Diagnostic test accuracy may vary with prevalence: 475 implications for evidence-based diagnosis, Journal of Clinical Epidemiology, vol.62, issue.1, 2009.

H. Barkema, K. Orsel, S. Nielsen, A. Koets, V. P. Rutten et al., , p.478

, Transboundary and Emerging Diseases, 2017.

. Chapitre-4, . Stratégies-de-dépistage-À-l'échelle, and . Collective, Nous tenons à remercier les éleveurs d'Ovilot, les techniciens d'élevage, les vétérinaires et les étudiants vétérinaires ayant contribué à la réalisation de cette étude. Cette étude bénéficie du financement conjoint de l'INRA (Métaprogramme GISA, projet PICSAR) et de la région

F. Bastida and R. A. Juste, Journal of immune based therapies and vaccines, vol.9, issue.1, p.8, 2011.

N. K. Dhand, O. Wesley, J. Johnson, R. J. Eppleston, P. A. Whittington et al., Preventive Veterinary Medicine, vol.111, issue.1-2, pp.81-91, 2013.

. Kawaji, D. J. Satoko, K. M. Begg, R. J. Plain, and . Whittington, Veterinary Microbiology, vol.148, issue.1, pp.35-44, 2011.

S. S. Nielsen and N. Toft, Veterinary Microbiology, vol.129, issue.3-4, pp.217-252, 2008.

L. Reddacliff, P. Eppleston, R. Windsor, . Whittington, and . Jones, Veterinary Microbiology, vol.115, pp.77-90, 2006.

P. Windsor, N. Eppleston, . Dhand, R. Et, and . Whittington, Australian Veterinary Journal, vol.92, issue.7, pp.263-68, 2014.

. Contrairement-À-l'étude-de-reddacliff, nos résultats indiquent clairement, 2006.

A. La-naissance-le-système-immunitaire-n'est and . Chase, ) conseillent, chez les bovins, une vaccination tardive pour obtenir une meilleure efficacité, Nous pou, 2008.

, ELISA DIVA), comme c'est le cas dans le cadre de l'IBR chez les bovins (Muratore et al., 2017), serait une avancée majeure. Nous avons exclu de nos analyses un élevage dont seulement la moitié des agnelles de renouvellement était vaccinée, l'autre moitié étant constituée d'agnelles non vaccinées achetées, Le suivi sanitaire des troupeaux vaccinés par l'utilisation de la sérologie n'apparaît troupeaux vaccinés, l'élaboration d'un test ELISA différenciant les animaux infectés des animaux vaccinés

K. R. Acharya, D. N. Whittington, R. Et-plain, and K. M. , PCR Inhibition of a Quantitative PCR for Detection of Mycobacterium avium Subspecies Paratuberculosis DNA in Feces : Diagnostic Implications and Potential Solutions, Frontiers in Microbiology, vol.8, 2017.

. Aeema, Définition d'une espèce réservoir, 2017.

. Afssa, Rapport sur la paratuberculose des ruminants, 2009.

A. P. Et-dodd and L. E. , A Cautionary Note on the Robustness of Latent Class Models for Estimating Diagnostic Error without a Gold Standard, Biometrics, vol.60, issue.2, pp.427-435, 2004.

A. D. Turenne, C. Et-behr, and M. A. , Insertion and Deletion Events That Define the Pathogen Mycobacterium avium subsp. paratuberculosis, Journal of Bacteriology, vol.191, issue.3, 2009.

E. S. Allman, M. C. Rhodes, and J. A. , Identifiability of parameters in latent structure models with many observed variables, The Annals of Statistics, vol.37, issue.6A, pp.3099-3132, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00591202

S. S. Aly, M. B. Whitlock, R. H. Sweeney, R. W. , A. R. Jiang et al., Correlation between Herrold Egg Yolk Medium Culture and Real-Time Quantitative Polymerase Chain Reaction Results for Mycobacterium Avium Subspecies Paratuberculosis in Pooled Fe-BIBLIOGRAPHIE cal and Environmental Samples, Journal of Veterinary Diagnostic Investigation, vol.22, issue.5, pp.677-683, 2010.

S. Aly, R. Anderson, R. Whitlock, T. Fyock, S. Mcadams et al., Reliability of environmental sampling to quantify Mycobacterium avium subspecies paratuberculosis on California free-stall dairies, Journal of Dairy Science, vol.92, issue.8, pp.3634-3642, 2009.

H. M. Alzuherri, C. Woodall, and C. J. Et-clarke, Increased intestinal TNF-?, IL-1? and IL-6 expression in ovine paratuberculosis, Veterinary Immunology and Immunopathology, vol.49, issue.4, pp.331-345, 1996.

A. J. , M. J. , K. J. , C. D. , R. R. Nolden et al., Mycobacterium avium subsp. paratuberculosis in Scavenging Mammals in Wisconsin, Journal of Wildlife Diseases, vol.43, issue.2, pp.302-308, 2007.

E. Angelidou, P. Kostoulas, and L. Leontides, Bayesian estimation of sensitivity and specificity of a commercial serum/milk ELISA against the Mycobacterium avium subsp. Paratuberculosis (MAP) antibody response for each lactation stage in Greek dairy sheep, Preventive Veterinary Medicine, vol.124, pp.102-105, 2016.

J. C. Arango-sabogal, G. Côté, J. Paré, O. Labrecque, J. Roy et al., Detection of Mycobacterium avium subspecies paratuberculosis in tie-stall dairy herds using a standardized environmental sampling technique and targeted pooled samples, Canadian Journal of Veterinary Research, vol.80, issue.3, pp.175-182, 2016.

R. J. Arsenault, P. Maattanen, J. Daigle, A. Potter, P. Griebel et al., From mouth to macrophage : mechanisms of innate immune subversion by Mycobacterium avium subsp. paratuberculosis, Veterinary Research, vol.45, issue.1, p.54, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01290568

R. Atreya, M. Bülte, G. Gerlach, R. Goethe, M. W. Hornef et al.,

S. Weiss, Facts, myths and hypotheses on the zoonotic nature of Mycobacterium avium subspecies paratuberculosis, International Journal of Medical Microbiology, vol.304, issue.7, pp.858-867, 2014.

W. Y. Ayele, M. Bartos, P. Svastova, and I. Pavlik, Distribution of Mycobacterium avium subsp. paratuberculosis in organs of naturally infected bull-calves and breeding bulls, Veterinary Microbiology, vol.103, issue.3, pp.209-217, 2004.

J. P. Bannantine, C. Wu, C. Hsu, S. Zhou, D. C. Schwartz et al., Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association, BMC genomics, vol.13, issue.1, p.89, 2012.

J. P. Bannantine, E. G. Laval, F. Stabel, J. R. Lemassu, A. Daffé et al., Cell wall peptidolipids of Mycobacterium avium : from genetic prediction to exact structure of a nonribosomal peptide, Molecular Microbiology, vol.105, issue.4, pp.525-539, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607730

R. A. Bastida-f-et-juste, Paratuberculosis control : a review with a focus on vaccination, Journal of immune based therapies and vaccines, vol.9, issue.1, p.8, 2011.

C. A. Bauman, A. Jones-bitton, J. Jansen, D. Kelton, and P. Menzies, Evaluation of fecal culture and fecal RT-PCR to detect Mycobacterium avium ssp. paratuberculosis fecal shedding in dairy goats and dairy sheep using latent class Bayesian modeling, BMC Veterinary Research, vol.12, issue.1, 2016.

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

D. J. Begg, K. De-silva, C. N. Plain, K. M. , P. A. Whittington et al., Does a Th1 over Th2 dominancy really exist in the early stages of Mycobacterium avium subspecies paratuberculosis infections ?, Immunobiology, vol.216, issue.7, pp.840-846, 2011.

D. J. Begg, P. A. De-silva, K. , D. N. Plain, K. Et-whittington et al., Variation in susceptibility of different breeds of sheep to Mycobacterium avium subspecies paratuberculosis following experimental inoculation, Veterinary Research, vol.48, p.36, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01541136

R. Ben-romdhane, G. Beaunée, G. Camanes, R. Guatteo, C. Fourichon et al., Which phenotypic traits of resistance should be improved in cattle to control paratuberculosis dynamics in a dairy herd : a modelling approach, Veterinary Research, vol.48, issue.1, p.62, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01621477

G. Benedictus, J. Verhoeff, Y. Schukken, and J. W. Et-hesselink, Dutch paratuberculosis programme history, principles and development, Veterinary microbiology, vol.77, issue.3, pp.399-413, 2000.

R. D. Berghaus, T. B. Farver, A. R. Jaravata, C. C. Gardner, and I. A. , Environmental Sampling for Detection of< i> Mycobacterium avium</i> ssp.< i> paratuberculosis</i> on Large California Dairies, Journal of dairy science, vol.89, issue.3, pp.963-970, 2006.

R. D. Berghaus, T. B. Farver, A. R. Adaska, J. M. Gardner, and I. A. , Use of age and milk production data to improve the ability of enzyme-linked immunosorbent assay test results to predict Mycobacterium avium ssp. paratuberculosis fecal culture status, Journal of veterinary diagnostic investigation, vol.18, issue.3, pp.233-242, 2006.

M. L. Bermingham, H. I. Glass, E. J. , W. J. Bronsvoort, B. M. Mcbride et al., Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data : a latent model for latent data, Scientific Reports, vol.5, p.11861, 2015.

B. Bhattarai, G. T. Fosgate, O. J. Fossler, C. P. , P. S. Et-roussel et al., Comparison of calf weaning weight and associated economic variables between beef cows with and without serum antibodies against or isolation from feces of Mycobacterium avium subsp paratuberculosis, Journal of the American Veterinary Medical Association, vol.243, issue.11, pp.1609-1615, 2013.

P. M. Bossuyt, R. J. Bruns, D. E. Gatsonis, C. A. Glasziou, P. P. Irwig et al., Standards for Reporting of Diagnostic Accuracy. 2003. The STARD statement for reporting studies of diagnostic accuracy : explanation and elaboration, Annals of Internal Medicine, vol.138, issue.1, pp.1-12
URL : https://hal.archives-ouvertes.fr/inserm-01327683

G. Botsaris, B. M. Swift, I. Slana, M. Liapi, M. Christodoulou et al., Detection of viable Mycobacterium avium subspecies paratuberculosis in powdered infant formula by phage-PCR and confirmed by culture, International Journal of Food Microbiology, vol.216, pp.91-94, 2016.

H. Brenner and O. Gefeller, Variation of sensitivity, specificity, likelihood ratios and predictive values with disease prevalence, Statistics in Medicine, vol.16, issue.9, pp.981-991, 1997.

J. M. Bibliographie-brinkhof, D. J. Houwers, and C. Et-van-maanen, Development of a sample pooling strategy for the serodiagnosis of small, 2007.

, Small Ruminant Research, vol.70, issue.2-3, pp.194-199

T. Carta, J. Álvarez, P. De-la-lastra, J. Et-gortázar, and C. , Wildlife and paratuberculosis : A review, Research in Veterinary Science, vol.94, issue.2, pp.191-197, 2013.

B. A. Catton, Paucibacillary paratuberculosis in a goat, The Canadian Veterinary Journal, vol.43, issue.10, pp.8-5286, 2002.

W. Chamberlin and S. A. Et-naser, Integrating theories of the etiology of Crohn's disease. On the etiology of Crohn's disease : questioning the hypotheses, Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, vol.12, issue.2, pp.27-33, 2006.

C. C. Chase, H. D. Et-reber, and A. J. , Neonatal Immune Development in the Calf and Its Impact on Vaccine Response, Veterinary Clinics of North America : Food Animal Practice, vol.24, issue.1, pp.87-104, 2008.

R. Chiodini, History of Paratuberculosis. International Association for Paratuberculosis, p.658, 1992.

R. Chiodini and J. Et-hermon-taylor, The thermal resistance of Mycobacterium paratuberculosis in raw milk under conditions simulating pasteurization, Journal of Veterinary Diagnostic Investigation, vol.5, issue.4, pp.629-631, 1993.

C. , D. M. Weeks, S. R. Epperson, W. B. Singh, S. N. Steinlicht et al., Comparison of Two DNA Extractions and Nested PCR, Real-Time PCR, a New Commercial PCR Assay, and Bacterial Culture for Detection of Mycobacterium Avium Subsp. Paratuberculosis in Bovine Feces, Journal of Veterinary Diagnostic Investigation, vol.15, issue.2, pp.87-93, 2003.

C. J. Clarke, The pathology and pathogenesis of paratuberculosis in ruminants and other species, Journal of comparative pathology, vol.116, issue.3, pp.217-261, 1997.

C. Clarke and D. Et-little, The pathology of ovine paratuberculosis : Gross and histological changes in the intestine and other tissues, Journal of Comparative Pathology, vol.114, issue.4, pp.419-437, 1996.

,

C. D. Gabric, D. Et-de-lisle, and G. W. , Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization, Journal of Clinical Microbiology, vol.28, issue.7, pp.95-1137, 1990.

C. D. Gabric, D. Et-de-lisle, and G. W. , Identification of a repetitive DNA sequence specific to Mycobacterium paratuberculosis, FEMS Microbiology Letters, vol.60, issue.2, pp.175-178, 1989.

J. Collins and M. Huynh, Estimation of diagnostic test accuracy without full verification : a review of latent class methods, Statistics in medicine, vol.33, issue.24, pp.4141-4169, 2014.

M. T. Collins, Update on paratuberculosis : 1. Epidemiology of Johne's disease and the biology of Mycobacterium paratuberculosis, Irish Veterinary Journal, vol.56, issue.11, pp.565-574, 2003.

M. Collins and I. R. Et-morgan, Simulation model of paratuberculosis control in a dairy herd, Preventive Veterinary Medicine, vol.14, issue.1, p.90081, 1992.

M. Collins, V. Eggleston, and E. 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.

D. Cousins, R. Whittington, I. Marsh, A. Masters, . Evans-r et al., Mycobacteria distinct from Mycobacterium avium subsp. paratuberculosis isolated from the faeces of ruminants possess IS 900 -like sequences detectable by IS 900 polymerase chain reaction : implications for diagnosis, Molecular and Cellular Probes, vol.13, issue.6, pp.431-442, 1999.

P. M. Coussens, N. Verman, C. M. Elftman, M. Et-mcnulty, and A. M. , Cytokine Gene Expression in Peripheral Blood Mononuclear Cells and Tissues of Cattle Infected with Mycobacterium avium subsp. paratuberculosis : Evidence for an Inherent Proinflammatory BIBLIOGRAPHIE Gene Expression Pattern, Infection and Immunity, vol.72, issue.3, pp.1409-1422, 2004.

D. W. Cowling, G. I. Et-johnson, and W. O. , Comparison of methods for estimation of individual-level prevalence based on pooled samples, Preventive veterinary medicine, vol.39, issue.3, pp.211-225, 1999.

T. K. Dalziel, Chronic interstitial enteritis, Diseases of the Colon and Rectum, vol.32, issue.12, pp.12-3706, 1989.

H. L. David and F. Clement, Adsorption and growth of the bacteriophage D29 in selected mycobacteria, Annales de l'Institut Pasteur, vol.131, issue.2, pp.90031-90034, 1980.

H. L. David, S. Clavel, F. Clement, and J. Moniz-pereira, Effects of antituberculosis and antileprosy drugs on mycobacteriophage D29 growth, Antimicrobial Agents and Chemotherapy, vol.18, issue.2, pp.357-359, 1980.

K. De-silva, D. Begg, and R. Whittington, The interleukin 10 response in ovine Johne's disease, Veterinary Immunology and Immunopathology, vol.139, issue.1, pp.10-16, 2011.

K. De-silva, D. J. Begg, K. M. Plain, P. A. Kawaji, S. Dhand et al., Can early host responses to mycobacterial infection predict eventual disease outcomes ? Preventive Veterinary Medicine, vol.112, pp.203-212, 2013.

K. De-silva, K. Plain, A. Purdie, D. Begg, and R. Whittington, Defining resilience to mycobacterial disease : Characteristics of survivors of ovine paratuberculosis, Veterinary Immunology and Immunopathology, vol.195, pp.56-64, 2018.

Y. Delbrouck, Valeur informative d'outils utilisables à grande échelle pour déterminer le statut de troupeaux bovins laitiers vis-à-vis de l'infection à Mycobactérium avium spp paratuberculosis

. Thèse-pour-le-doctorat and . Vétérinaire, , 2008.

N. Dendukuri and L. Joseph, Bayesian approaches to modeling the conditional dependence between multiple diagnostic tests, Biometrics, vol.57, issue.1, pp.158-167, 2001.

N. K. Dhand, J. W. Et-toribio, and J. L. , A Bayesian Approach to Estimate OJD Prevalence From Pooled Fecal Samples of Variable Pool Size, Journal of Agricultural, Biological and Environmental Statistics, vol.15, issue.4, pp.1537-2693, 2010.

N. K. Dhand, S. E. Toribio, J. Et-whittington, and R. J. , Estimation of sensitivity and flock-sensitivity of pooled faecal culture for Mycobacterium avium subsp. paratuberculosis in sheep, Preventive Veterinary Medicine, vol.95, issue.3-4, pp.248-257, 2010.

N. K. Dhand, J. W. Eppleston, J. Whittington, R. Et-windsor, and P. A. , Comparison of preand post-vaccination ovine Johne's disease prevalence using a Bayesian approach, Preventive Veterinary Medicine, vol.111, issue.1-2, pp.81-91, 2013.

N. K. Dhand, J. Eppleston, R. Whittington, and P. A. Et-windsor, Changes in prevalence of ovine paratuberculosis following vaccination with Gudair® : Results of a longitudinal study conducted over a decade, Vaccine, vol.34, issue.42, pp.5107-5113, 2016.

F. J. Diéguez, G. A. Menéndez, S. Vilar, M. J. Sanjuán, M. L. et al., Evaluation of four commercial serum ELISAs for detection of Mycobacterium avium subsp. paratuberculosis infection in dairy cows, The Veterinary Journal, vol.180, issue.2, pp.231-235, 2009.

K. Donat, N. Hahn, T. Eisenberg, K. Schlez, H. Köhler et al., Within-herd prevalence thresholds for the detection of Mycobacterium avium subspecies paratuberculosis-positive dairy herds using boot swabs and liquid manure samples, Epidemiology and infection, 2015.

R. Dorfman, The Detection of Defective Members of Large Populations, The Annals of Mathematical Statistics, vol.14, issue.4, pp.436-440, 1943.

G. Eamens, M. I. Plain, K. Et-whittington, and R. Paratuberculosis, Johne's Disease), 2015.

G. J. Eamens, R. J. Whittington, T. M. , A. S. Fell, S. Et-marsh et al., Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium BIBLIOGRAPHIE subsp. paratuberculosis in cattle, Veterinary Microbiology, vol.125, issue.1-2, pp.22-35, 2007.

S. W. Eisenberg, M. Nielen, J. Hoeboer, V. Rutten, D. Heederik et al., Environmental contamination with Mycobacterium avium subspecies paratuberculosis within and around a dairy barn under experimental conditions, Journal of Dairy Science, vol.95, issue.11, pp.6477-6482, 2012.

S. W. Eisenberg, R. Chuchaisangrat, M. Nielen, and A. P. Koets, Relationship between Presence of Cows with Milk Positive for Mycobacterium avium subsp. paratuberculosis-Specific Antibody by Enzyme-Linked Immunosorbent Assay and Viable M. avium subsp. paratuberculosis in Dust in Cattle Barns, Applied and Environmental Microbiology, vol.79, issue.18, pp.5458-5464, 2013.

J. L. Ellingson, C. Bolin, and J. R. Et-stabel, Identification of a gene unique toMycobacterium aviumsubspeciesparatuberculosisand application to diagnosis of paratuberculosis, Molecular and Cellular Probes, vol.12, issue.3, pp.133-142, 1998.

J. L. Ellingson, A. J. , K. J. , R. R. , S. S. et al., Detection of viable Mycobacterium avium subsp. paratuberculosis in retail pasteurized whole milk by two culture methods and PCR, Journal of Food Protection, vol.68, issue.5, pp.966-972, 2005.

R. Elmore and A. Hall-p-et-neeman, An application of classical invariant theory to identifiability in nonparametric mixtures, Annales de l'institut Fourier, vol.55, issue.1, pp.1-28, 2005.

S. Englund and K. Bölske-g-et-johansson, An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis, FEMS Microbiology Letters, vol.209, issue.2, pp.267-271, 2002.

J. Eppleston and R. Whittington, Isolation of Mycobacterium avium subsp paratuberculosis from the semen of rams with clinical Johne's disease, Australian Veterinary Journal, vol.79, issue.11, pp.776-777, 2001.

J. Eppleston and P. A. Windsor, Lesions attributed to vaccination of sheep with Gudair for BIBLIOGRAPHIE the control of ovine paratuberculosis : post farm economic impacts at slaughter, Australian Veterinary Journal, vol.85, issue.4, pp.129-133, 2007.

J. Eppleston, D. J. Begg, D. N. Watt, B. Whittington, and R. J. , 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.

J. O. Falkinham, Mycobacterial Aerosols and Respiratory Disease, vol.9, pp.763-767, 2003.

M. Fecteau, E. Hovingh, R. H. Whitlock, and R. W. Sweeney, Persistence of Mycobacterium avium subsp. paratuberculosis in soil, crops, and ensiled feed following manure spreading on infected dairy farms, The Canadian Veterinary Journal, vol.54, issue.11, pp.8-5286, 2013.

M. Fernández, J. Benavides, I. A. Sevilla, M. Fuertes, P. Castaño et al., Experimental infection of lambs with C and S-type strains of Mycobacterium avium subspecies paratuberculosis : immunological and pathological findings, Veterinary Research, vol.45, issue.1, 2014.

. J. Fernández-silva, N. Correa-valencia, and N. F. Et-ramírez, Systematic review of the prevalence of paratuberculosis in cattle, sheep, and goats in Latin America and the Caribbean, 2014.

, Tropical Animal Health and Production, vol.46, issue.8, pp.1321-1340

D. Fock-chow-tho, E. Topp, E. Ibeagha-awemu, and N. Bissonnette, Comparison of commercial DNA extraction kits and quantitative PCR systems for better sensitivity in detecting the causative agent of paratuberculosis in dairy cow fecal samples, Journal of Dairy Science, 2016.

A. Foddai and I. Grant, Sensitive and specific detection of viable Mycobacterium avium subsp. paratuberculosis in raw milk by the peptide-mediated magnetic separation-phage assay, Journal of Applied Microbiology, vol.122, issue.5, pp.1357-1367, 2017.

T. E. Foley-, D. L. Whipple, L. E. Bermudez, and R. G. Barletta, Phage infection, transfection and transformation of Mycobacterium avium complex and Mycobacterium paratuberculosis, Microbiology, vol.141, issue.5, pp.1173-1181, 1995.

E. Bibliographie-frederic, Informative value of environmental and pooled samples to evaluate the within-herd prevalence of mycobacterium avium subspecies paratuberculosis in g, 2016.

J. Frössling, B. Bonnett, A. Lindberg, and C. Björkman, Validation of a Neospora caninum iscom ELISA without a gold standard, Preventive Veterinary Medicine, vol.57, issue.3, pp.141-153, 2003.

G. I. Nielsen, S. S. Whittington, R. J. , C. M. Bakker, D. Harris et al., Consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis in ruminants, Preventive Veterinary Medicine, vol.101, issue.1-2, pp.18-34, 2011.

J. M. Garrido, P. Vazquez, E. Molina, J. M. Plazaola, I. A. Sevilla et al., Paratuberculosis Vaccination Causes Only Limited Cross-Reactivity in the Skin Test for Diagnosis of Bovine Tuberculosis, PLOS ONE, vol.8, issue.11, 2013.

M. P. Georgiadis, J. W. , G. I. Et-singh, and R. , Correlation-adjusted estimation of sensitivity and specificity of two diagnostic tests, Journal of the Royal Statistical Society : Series C (Applied Statistics), vol.52, issue.1, pp.63-76, 2003.

S. Gillan, R. O&apos;brien, A. Hughes, and J. F. Et-griffin, Identification of Immune Parameters To Differentiate Disease States among Sheep Infected with Mycobacterium avium subsp. paratuberculosis. Clinical and Vaccine Immunology : CVI, vol.17, pp.108-117, 2010.

M. Gonda, Y. Chang, G. Shook, C. M. Kirkpatrick, and B. , Effect of Mycobacterium paratuberculosis infection on production, reproduction, and health traits in US Holsteins, Preventive Veterinary Medicine, vol.80, issue.2-3, pp.103-119, 2007.

L. A. Goodman, Exploratory latent structure analysis using both identifiable and unidentifiable models, Biometrika, vol.61, issue.2, pp.215-231, 1974.

G. I. Foddai, A. C. , T. J. Kunkel, B. Hartmann, F. A. Mcguirk et al., Viable Mycobacterium avium ssp. paratuberculosis isolated from calf milk replacer, Journal of Dairy Science, 2017.

E. P. Green, M. L. Tizard, J. Thompson, W. D. Mcfadden, J. Et-hermontaylor et al., Sequence and characteristics or IS900, an insertion element identified in a human Crohn's disease isolate or Mycobacterium paratuberculosis, Nucleic Acids Research, vol.17, issue.22, pp.9063-9073, 1989.

S. K. Grewal, R. S. Sreevatsan, S. Michel, and F. C. , Persistence of Mycobacterium avium subsp. paratuberculosis and Other Zoonotic Pathogens during Simulated Composting, Manure Packing, and Liquid Storage of Dairy Manure, Applied and Environmental Microbiology, vol.72, issue.1, pp.565-574, 2006.

K. Graesbøll, A. L. Halasa, T. Toft, and N. , Opportunities and challenges when pooling milk samples using ELISA, Preventive Veterinary Medicine, vol.139, pp.93-98, 2017.

R. Guatteo, A. Joly, F. Beaudeau, and C. Chognard-t-et-fourichon, EVALUATION OF COMBI-NED ENVIRONMENTAL AND POOLED ANIMALS SAMPLING TO DETERMINE DAIRY CATTLE HERD INFECTION STATUS FOR MYCOBACTERIUM AVIUM SUBSPECIES PARATUBERCULO-SIS (MAP), Proceedings of the 11th International Colloquium on Paratuberculosis, pp.349-351, 2012.

M. Guescini, D. Sisti, M. B. Rocchi, L. Stocchi, and V. Stocchi, A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition, BMC Bioinformatics, vol.9, issue.1, p.326, 2008.

N. Hahn, K. Failing, T. Eisenberg, K. Schlez, P. Zschöck et al., Evaluation of different diagnostic methods for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples, BMC Veterinary Research, vol.13, 2017.

C. A. Heid, J. Stevens, K. J. Livak, and P. M. Williams, Real time quantitative PCR, Genome Research, vol.6, issue.10, pp.986-994, 1996.

D. Bibliographie-herthnek, N. S. Lindberg, A. Bölske, and G. , A robust method for bacterial lysis and DNA purification to be used with real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in milk, Journal of Microbiological Methods, vol.75, issue.2, pp.335-340, 2008.

S. Hickey, C. Morris, J. Dobbie, and D. Lake, Heritability of Johne's disease and survival data from Romney and Merino sheep, Proceedings of the New Zealand Society of Animal Production, vol.63, pp.179-182, 2003.

F. Hilbink and D. West, The antibody response of sheep to vaccination against Johne's disease, New Zealand Veterinary Journal, vol.38, issue.4, pp.168-169, 1990.

M. E. Hines, J. R. Stabel, R. W. Sweeney, G. F. Talaat, A. M. Bakker et al., Experimental challenge models for Johne's disease : A review and proposed international guidelines, Veterinary Microbiology, vol.122, issue.3, pp.197-222, 2007.

K. Hoogendam and J. Richardson-e-et-mee, Paratuberculosis sero-status and milk production, SCC and calving interval in Irish dairy herds, Irish Veterinary Journal, vol.62, pp.265-271, 2009.

,

J. Hostetter, . Kagan-r, and E. Steadham, Opsonization Effects on Mycobacterium avium subsp. paratuberculosis-Macrophage Interactions, Clinical and Diagnostic Laboratory Immunology, vol.12, issue.6, pp.793-796, 2005.

S. L. Hui and S. D. Walter, Estimating the Error Rates of Diagnostic Tests, Biometrics, vol.36, issue.1, 1980.

J. Y. , K. J. , G. J. , L. J. Sprecher, D. Et-coe et al., The Effect of Subclinical Mycobacterium paratuberculosis Infection on Milk Production in Michigan Dairy Cows, Journal of Dairy Science, vol.84, issue.10, pp.74665-74671, 2001.

G. Jones, J. W. , H. T. Et-christensen, and R. , Identifiability of Models for Multiple Diagnostic Testing in the Absence of a Gold Standard, Biometrics, vol.66, issue.3, pp.855-863, 2010.

W. Jones and H. L. Et-david, Inhibition by Rifampin of Mycobacteriophage D29 Replication in its Drug-Resistant Host, Mycobacterium smegmatis ATCC 607, American Review of Respiratory Disease, vol.103, issue.5, pp.618-624, 1971.

J. Judge, D. R. , M. G. White, P. Et-hutchings, and M. R. , Persistence of Mycobacterium avium subspecies paratuberculosis in rabbits : the interplay between horizontal and vertical transmission, Journal of Applied Ecology, vol.44, issue.2, pp.302-311, 2007.

G. Jungersen, H. Mikkelsen, and S. N. Grell, Use of the johnin PPD interferon-gamma assay in control of bovine paratuberculosis, Veterinary Immunology and Immunopathology, vol.148, issue.1, pp.48-54, 2012.

M. Kaevska, S. Lvoncik, I. Slana, P. Kulich, and P. Kralik, Microscopy, Culture, and Quantitative Real-Time PCR Examination Confirm Internalization of Mycobacteria in Plants, Applied and Environmental Microbiology, vol.80, issue.13, pp.3888-3894, 2014.

C. Kalis, M. Collins, H. Barkema, and J. Hesselink, Certification of herds as free of Mycobacterium paratuberculosis infection : actual pooled faecal results versus certification model predictions, 2004.

, Preventive Veterinary Medicine, vol.65, issue.3-4, pp.189-204

S. Kawaji, T. D. Mori, Y. Whittington, and R. J. , Detection of Mycobacterium avium subsp. paratuberculosis in ovine faeces by direct quantitative PCR has similar or greater sensitivity compared to radiometric culture, Veterinary Microbiology, vol.125, issue.1-2, pp.36-48, 2007.

S. Kawaji, D. J. Begg, K. Plain, and R. J. Et-whittington, A longitudinal study to evaluate the diagnostic potential of a direct faecal quantitative PCR test for Johne's disease in sheep, Veterinary Microbiology, vol.148, issue.1, pp.35-44, 2011.

S. Khare, A. L. Osterstock, J. Roussel, A. David, and L. , Effects of Shipping and Storage BIBLIOGRAPHIE Conditions of Fecal Samples on Viability of Mycobacterium paratuberculosis, Journal of Clinical Microbiology, vol.46, issue.4, pp.1561-1562, 2008.

S. Khare, D. K. , L. S. Nunes, F. J. , R. C. Gull et al., Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections, PLOS ONE, vol.11, issue.9, 2016.

B. W. Kirkpatrick, X. Shi, G. E. Shook, and M. T. Collins, Whole-Genome association analysis of susceptibility to paratuberculosis in Holstein cattle, Animal Genetics, vol.42, issue.2, pp.149-160, 2011.

B. W. Kirkpatrick and G. E. Shook, Genetic Susceptibility to Paratuberculosis, Veterinary Clinics of North America : Food Animal Practice, vol.27, issue.3, pp.559-571, 2011.

J. N. Kiser, M. Neupane, S. White, and H. L. Et-neibergs, Identification of genes associated with susceptibility to <Emphasis Type="Italic">Mycobacterium avium</Emphasis> ssp, 2017.

, Italic">Map</Emphasis>) tissue infection in Holstein cattle using gene set enrichment analysis-SNP, Type="Italic">paratuberculosis</Emphasis> (<Emphasis Type=, pp.1432-1777

B. Klanicova, I. Slana, P. Roubal, I. Pavlik, and P. Kralik, Mycobacterium avium subsp. paratuberculosis survival during fermentation of soured milk products detected by culture and quantitative real time PCR methods, International Journal of Food Microbiology, vol.157, issue.2, pp.150-155, 2012.

A. P. Koets, E. S. Sreevatsan, and S. , The within host dynamics of Mycobacterium avium ssp. paratuberculosis infection in cattle : where time and place matter, Veterinary Research, vol.46, issue.1, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333708

P. Kostoulas, L. Leontides, C. Billinis, G. Amiridis, and M. Florou, The association of sub-clinical paratuberculosis with the fertility of Greek dairy ewes and goats varies with parity, Preventive Veterinary Medicine, vol.74, issue.2-3, pp.226-238, 2006.

P. Kostoulas, L. Leontides, C. Billinis, and M. Florou, Application of a semi-dependent latent model in the Bayesian estimation of the sensitivity and specificity of two faecal culture methods for diagnosis of paratuberculosis in sub-clinically infected Greek dairy sheep and goats, Preventive Veterinary Medicine, vol.76, issue.1-2, pp.121-134, 2006.

P. Kostoulas, L. Leontides, C. Enøe, C. Billinis, M. Florou et al., Bayesian estimation of sensitivity and specificity of serum ELISA and faecal culture for diagnosis of paratuberculosis in Greek dairy sheep and goats, Preventive Veterinary Medicine, vol.76, issue.1-2, pp.56-73, 2006.

P. Kostoulas, S. S. Nielsen, A. J. Branscum, J. W. Dendukuri, N. et al., STARD-BLCM : Standards for the Reporting of Diagnostic accuracy studies that use Bayesian Latent Class Models, Preventive Veterinary Medicine, vol.138, pp.37-47, 2017.

P. Kralik, V. Babak, and R. Dziedzinska, Repeated cycles of chemical and physical disinfection and their influence on Mycobacterium avium subsp. paratuberculosis viability measured by propidium monoazide F57 quantitative real time PCR, The Veterinary Journal, vol.201, issue.3, pp.359-364, 2014.

M. Y. Krishnan, E. J. Manning, and M. T. Et-collins, Comparison of three methods for susceptibility testing of Mycobacterium avium subsp. paratuberculosis to 11 antimicrobial drugs, Journal of Antimicrobial Chemotherapy, vol.64, issue.2, pp.310-316, 2009.

J. Kruze, G. Monti, F. Schulze, M. A. Leiva, and S. , Herd-level prevalence of Map infection in dairy herds of southern Chile determined by culture of environmental fecal samples and bulktank milk qPCR, Preventive Veterinary Medicine, vol.111, issue.3, pp.319-324, 2013.

J. Kruze, M. Salgado, E. Paredes, M. A. Collins, and M. T. , Goat Paratuberculosis in Chile : First Isolation and Confirmation of Mycobacterium Avium Subspecies Paratuberculosis Infection in a Dairy Goat, Journal of Veterinary Diagnostic Investigation, vol.18, issue.5, pp.476-479, 2006.

S. Kudahl-a-et-nielsen, Effect of paratuberculosis on slaughter weight and slaughter value of dairy cows, Journal of Dairy Science, vol.92, issue.9, pp.4340-4346, 2009.

J. T. Kuenstner, S. Naser, W. Chamberlin, T. Borody, G. D. Mcnees et al., The Consensus from the Mycobacterium avium ssp, Frontiers in Public Health, vol.5, 2017.

C. Lambeth, L. Reddacliff, P. Windsor, K. Abbott, H. Mcgregor et al., Intrauterine and transmammary transmission of Mycobacterium avium subsp paratuberculosis in sheep, 2004.

, Australian Veterinary Journal, vol.82, issue.8, pp.504-508

J. Landis and G. G. Et-koch, The Measurement of Observer Agreement for Categorical Data, 1977.

, Biometrics, vol.33, issue.1, p.159

H. Lee, J. Stabel, and M. E. Et-kehrli, Cytokine gene expression in ileal tissues of cattle infected with Mycobacterium paratuberculosis, Veterinary Immunology and Immunopathology, vol.82, issue.1, pp.73-85, 2001.

M. M. Leeflang, P. M. Bossuyt, and L. Et-irwig, Diagnostic test accuracy may vary with prevalence : implications for evidence-based diagnosis, Journal of Clinical Epidemiology, vol.62, issue.1, pp.5-12, 2009.

,

M. M. Leeflang, R. A. , R. J. Hooft, L. Bossuyt, and P. M. , Variation of a test's sensitivity and specificity with disease prevalence, CMAJ : Canadian Medical Association Journal, vol.185, issue.11, 2013.

L. H. Lefrançois, Etude des adhésines HBHA et LBP impliquées dans l'interaction de Mycobac-BIBLIOGRAPHIE terium avium ssp. paratuberculosis avec les cellules épithéliales intestinales, cibles privilégiées de la bactérie in vivo, 2012.

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

J. G. Lijmer, M. B. Heisterkamp, S. Bonsel, G. J. , P. M. Meulen et al., Empirical Evidence of Design-Related Bias in Studies of Diagnostic Tests, JAMA, vol.282, issue.11, pp.1061-1066, 1999.

E. Litvak, T. X. Et-pagano, and M. , Screening for the Presence of a Disease by Pooling Sera Samples, Journal of the American Statistical Association, vol.89, issue.426, pp.424-434, 1994.

J. E. Lombard, B. A. Wagner, S. R. Mccluskey, B. J. , H. B. et al., Evaluation of Environmental Sampling and Culture to Determine Mycobacterium avium subspecies paratuberculosis Distribution and Herd Infection Status on US Dairy Operations, Journal of Dairy Science, vol.89, issue.11, pp.4163-4171, 2006.

J. E. Lombard, G. F. Mccluskey, B. J. Wagner, and B. A. , 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, 1975.

V. Luu-the, N. Paquet, C. E. Cumps, and J. , Improved real-time RT-PCR method for highthroughput measurements using second derivative calculation and double correction, BioTechniques, vol.38, pp.287-93, 2005.

E. Maio, T. Carta, A. Balseiro, I. A. Sevilla, A. Romano et al., Paratuberculosis in European wild rabbits from the Iberian Peninsula, BIBLIOGRAPHIE Manning E. J et Collins M. T. 2001. Mycobacterium avium subsp. paratuberculosis : pathogen, pathogenesis and diagnosis, vol.91, pp.133-150, 2011.

C. Marcé, P. Ezanno, H. Seegers, D. Pfeiffer, and C. Et-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.

Y. Mathevon, G. Foucras, and F. Falguières-r-et-corbiere, Estimation of the sensitivity and specificity of two serum ELISAs and one fecal qPCR for diagnosis of paratuberculosis in sub-clinically infected young-adult French sheep using latent class Bayesian modeling. BMC Veterinary Research, vol.13, p.230, 2017.

P. Möbius, H. Hotzel, A. Raßbach, and H. Köhler, Comparison of 13 single-round and nested PCR assays targeting IS900, ISMav2, f57 and locus 255 for detection of Mycobacterium avium subsp. paratuberculosis, Veterinary Microbiology, vol.126, issue.4, pp.324-333, 2008.

H. Mcgregor, N. K. Dhand, O. Dhungyel, and R. J. Et-whittington, Transmission of Mycobacterium avium subsp. paratuberculosis : Dose-response and age-based susceptibility in a sheep model, Preventive Veterinary Medicine, vol.107, issue.1-2, pp.76-84, 2012.

H. Mcgregor, A. K. Et-whittington, and R. J. , Effects of Mycobacterium avium subsp. paratuberculosis infection on serum biochemistry, body weight and wool growth in Merino sheep : A longitudinal study, Small Ruminant Research, vol.125, pp.146-153, 2015.

P. Mercier, C. Baudry, F. Beaudeau, H. Seegers, and X. Malher, Estimated prevalence of Mycobacterium avium subspecies paratuberculosis infection in herds of dairy goats in France, Veterinary Record, vol.167, issue.11, pp.412-415, 2010.

R. G. Merwe, P. D. Helden, M. Warren, R. , L. Sampson-s-et-pittius et al., Phage-based detection of bacterial pathogens, Analyst, vol.139, issue.11, pp.2617-2626, 2014.

G. Minozzi, W. J. Stella, A. Strozzi, F. Luini, M. Settles et al., Meta-Analysis of Two Genome-Wide Association Studies of Bovine Paratuberculosis, PLOS ONE, vol.7, issue.3, 2012.

A. Mita, Y. Mori, T. Nakagawa, T. Tasaki, K. Utiyama et al., Comparison of fecal pooling methods and DNA extraction kits for the detection of Mycobacterium avium subspecies paratuberculosis, vol.5, pp.134-142, 2015.

M. R. Schukken, Y. Koets, A. Weber, M. Bakker, D. Stabel 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, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333711

P. Münster, I. Völkel, W. Wemheuer, D. Schwarz, S. Döring et al., Blood and Faeces of a Naturally Infected Bull by IS 900 Semi-Nested and Quantitative Real-Time PCR, Transboundary and Emerging Diseases, vol.60, issue.2, pp.175-187, 2013.

R. Moloney-b-et-whittington, Cross species transmission of ovine Johne's disease from sheep to cattle : an estimate of prevalence in exposed susceptible cattle, Australian Veterinary Journal, vol.86, issue.4, pp.117-123, 2008.

E. Momotani, D. L. Whipple, A. Thiermann, and N. F. Et-cheville, Role of M Cells and Macrophages in the Entrance of Mycobacterium paratuberculosis into Domes of Ileal Peyer's Patches in Calves, Veterinary Pathology, vol.25, issue.2, pp.131-137, 1988.

M. Moravkova, V. Babak, A. Kralova, I. Pavlik, and I. Slana, Culture-and Quantitative IS900 RealTime PCR-Based Analysis of the Persistence of Mycobacterium avium subsp. paratuberculosis in a Controlled Dairy Cow Farm Environment, Applied and Environmental Microbiology, vol.78, issue.18, pp.6608-6614, 2012.

R. A. Mortier, H. W. Barkema, J. M. Bystrom, O. Illanes, K. Orsel et al., Evaluation of age-dependent susceptibility in calves infected with two doses of Mycobacterium BIBLIOGRAPHIE avium subspecies paratuberculosis using pathology and tissue culture, Veterinary Research, vol.44, issue.1, 2013.

R. A. Mortier, H. W. Barkema, K. Orsel, R. Wolf, D. Buck et al., Shedding patterns of dairy calves experimentally infected with Mycobacterium avium subspecies paratuberculosis, Veterinary Research, vol.45, issue.1, p.71, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01290571

M. Muñoz, G. Marin, J. Garcia-pariente, C. Reyes, L. Verna et al., IAP : 2005 : Efficacy of a killed vaccine (SILIRUM®) in calves challenged with Map, 2005.

E. Muratore, L. Bertolotti, C. Nogarol, C. Caruso, L. Lucchese et al., Surveillance of Infectious Bovine Rhinotracheitis in markervaccinated dairy herds : Application of a recombinant gE ELISA on bulk milk samples. Veterinary Immunology and Immunopathology, vol.185, pp.1-6, 2017.

P. Nebbia, P. Robino, S. Zoppi, and D. D. Meneghi, Detection and excretion pattern of Mycobacterium avium subspecies paratuberculosis in milk of asymptomatic sheep and goats by Nested-PCR, Small Ruminant Research, vol.66, issue.1, pp.116-120, 2006.

S. S. Nielsen, T. S. Houe, H. Bitsch, and V. , Bulk-tank milk ELISA antibodies for estimating the prevalence of paratuberculosis in Danish dairy herds, vol.44, pp.1-7, 2000.

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. Grønbaek, J. Agger, and H. Et-houe, Maximum-likelihood estimation of sensitivity and specificity of ELISAs and faecal culture for diagnosis of paratuberculosis, Preventive Veterinary Medicine, vol.53, issue.3, pp.191-204, 2002.

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

N. Nielsen-s-et-toft, Ante mortem diagnosis of paratuberculosis : A review of accuracies of ELISA, interferon-? assay and faecal culture techniques, Veterinary Microbiology, vol.129, issue.3-4, pp.217-235, 2008.

N. Nielsen-s-et-toft, Effect of management practices on paratuberculosis prevalence in Danish dairy herds, Journal of Dairy Science, vol.94, issue.4, pp.1849-1857, 2011.

S. Nielsen, N. Toft, J. E. Bibby, and B. , Bayesian mixture models for within-herd prevalence estimates of bovine paratuberculosis based on a continuous ELISA response, Preventive Veterinary Medicine, vol.81, issue.4, pp.290-305, 2007.

S. Norton, C. Heuer, and R. Jackson, A questionnaire-based cross-sectional study of clinical Johne's disease on dairy farms in New Zealand, New Zealand Veterinary Journal, vol.57, issue.1, pp.34-43, 2009.

,

L. M. O&apos;brien, M. C. , S. L. Strain, S. A. Et-grant, and I. R. , Diagnostic potential of the peptide-mediated magnetic separation (PMS)-phage assay and PMS-culture to detect Mycobacterium avium subsp. paratuberculosis in bovine milk samples. Transboundary and Emerging Diseases

. Oie and . Système, Mondial d'Information Zoosanitaire, ?disease_type_ hidden=&disease_id_hidden=&selected_disease_name_hidden=&disease_type=0& disease_id_terrestrial=24&species_t=2&disease_id_aquatic=-999&species_a= 0&sta_method=semesterly&selected_start_year=2016&selected_report_period=1& selected_start_month=2&date_submit=OK, 2017.

J. B. Okuni, Occurence of Paratuberculosis in African Countries : a, Review. Journal of Veterinary Advances, vol.3, issue.1, pp.1-8, 2013.

J. E. Olsen, J. Jørgensen, and P. Et-nansen, On the reduction of Mycobacterium paratuberculosis in bovine slurry subjected to batch mesophilic or thermophilic anaerobic digestion, Agricultural Wastes, vol.13, issue.4, pp.90052-90058, 1985.

. Bibliographie-oms, Lignes directrices de l'OMS pour l'utilisation chez les animaux de rentes destinés à l'alimentation humaine des antimicrobiens importants pour la médecine humaine, 2017.

N. Parrish, A. Vadlamudi, and N. Goldberg, Anaerobic adaptation of Mycobacterium avium subspecies paratuberculosis in vitro : similarities to M. tuberculosis and differential susceptibility to antibiotics. Gut Pathogens, 9, 2017.

I. Pavlík, L. Bej?ková, M. Pavlas, Z. Rozsypalová, and S. Kosková, Characterization by restriction endonuclease analysis and DNA hybridization using IS900 of bovine, ovine, caprine and human dependent strains of Mycobacterium paratuberculosis isolated in various localities, Veterinary Microbiology, vol.45, issue.4, pp.311-318, 1995.

M. Pepe and H. Et-janes, Insights into latent class analysis of diagnostic test performance, 2007.

, Biostatistics, vol.8, issue.2, pp.474-484

M. N. Pesqueira, E. Yus, C. Factor, I. Mato, M. L. Sanjuán et al., Short communication : Correlation between within-herd antibody-prevalence and bulk tank milk antibody levels to Mycobacterium avium ssp. paratuberculosis using 2 commercial immunoassays, Journal of Dairy Science, vol.100, issue.9, pp.7544-7548, 2017.

H. Petit, Résultats d'une enquête GDS sur la paratuberculose. Le point vétérinaire, 2006.

R. W. Pickup, G. Rhodes, S. Arnott, K. Sidi-boumedine, T. J. Bull et al., Mycobacterium avium subsp. paratuberculosis in the Catchment Area and Water of the River Taff in South Wales, United Kingdom, and Its Potential Relationship to Clustering of Crohn's Disease Cases in the City of Cardiff, Applied and Environmental Microbiology, vol.71, issue.4, pp.2130-2139, 2005.

R. W. Pickup, G. Rhodes, T. J. Bull, S. Arnott, K. Sidi-boumedine et al., Mycobacterium avium subsp. paratuberculosis in Lake Catchments, in River Water Abstracted for Domestic Use, and in Effluent from Domestic Sewage Treatment Works : Diverse Opportunities for Environmental Cycling and Human Exposure, Applied and Environmental Microbiology, vol.72, issue.6, pp.1098-5336, 2006.

S. Pillai and B. M. Et-jayarao, Application of IS900 PCR for Detection of Mycobacterium avium subsp. paratuberculosis Directly from Raw Milk, Journal of Dairy Science, vol.85, issue.5, pp.1052-1057, 2002.

,

R. B. Pillars, D. Grooms, and J. B. Et-kaneene, Longitudinal study of the distribution of Mycobacterium avium subsp. paratuberculosis in the environment of dairy herds in the Michigan Johne's disease control demonstration herd project, The Canadian Veterinary Journal, vol.50, issue.10, pp.8-5286, 2009.

S. R. Portaels-f-et-pattyn, Growth of mycobacteria in relation to the pH of the medium, 1982.

, Annales De Microbiologie, vol.133, issue.2, pp.213-221

P. Poupart, M. Coene, H. Heuverswyn, and C. Et-cocito, Preparation of a specific RNA probe for detection of Mycobacterium paratuberculosis and diagnosis of Johne's disease, Journal of Clinical Microbiology, vol.31, issue.6, pp.1098-660, 1993.

V. Pérez, J. García-marín, and J. J. Et-badiola, Description and classification of different types of lesion associated with natural paratuberculosis infection in sheep, Journal of Comparative Pathology, vol.114, issue.2, pp.107-122, 1996.

A. C. Purdie, K. M. Plain, D. J. Begg, and R. J. De-silva-k-et-whittington, Candidate gene and genomewide association studies of Mycobacterium avium subsp. paratuberculosis infection in cattle and sheep : A review, Comparative Immunology, Microbiology and Infectious Diseases, vol.34, issue.3, pp.197-208, 2011.

Y. Qu, M. Tan, and M. H. Kutner, Random effects models in latent class analysis for evaluating accuracy of diagnostics tests, Biometrics, vol.52, issue.3, pp.797-810, 1996.

R. E. , W. S. Muñoz-zanzi, C. Et-tavornpanich, and S. , Estimated within-herd prevalence (WHP) of Mycobacterium avium subsp. paratuberculosis in a sample of Minnesota dairy herds using bacterial culture of pooled fecal samples, Canadian Journal of Veterinary Research, vol.75, issue.2, p.112, 2011.

L. Reddacliff, J. Eppleston, P. Windsor, R. Whittington, and S. Jones, Efficacy of a killed vaccine for the control of paratuberculosis in Australian sheep flocks, Veterinary Microbiology, vol.115, issue.1-3, pp.77-90, 2006.

C. Bibliographie-ritz and A. Spiess, qpcR : an R package for sigmoidal model selection in quantitative realtime polymerase chain reaction analysis, Bioinformatics, vol.24, issue.13, pp.1549-1551, 2008.

S. Robbe-austerman, Evaluation of cell mediated immune diagnostic tests to detect Mycobacterium avium subspecies paratuberculosis, 2007.

S. Robbe-austerman, G. I. Thomsen, B. V. , D. G. , M. B. et al., Sensitivity and specificity of the agar-gel-immunodiffusion test, ELISA and the skin test for detection of paratuberculosis in United States Midwest sheep populations, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00903040

, Veterinary Research, vol.37, issue.4, pp.1297-9716

G. Rossi, G. Nigro, I. Tattoli, S. Vincenzetti, P. Mariani et al., Adhesion molecules and cytokine profile in ileal tissue of sheep infected with Mycobacterium avium subsp, paratuberculosis. Microbes and Infection, vol.11, issue.6, pp.698-706, 2009.

J. Rothel, S. Jones, L. Corner, J. Cox, and P. Wood, A sandwich enzyme immunoassay for bovine interferon-? and its use for the detection of tuberculosis in cattle, Australian Veterinary Journal, vol.67, issue.4, pp.134-137, 1990.

A. Rovira, J. Cano, and C. Et-muñoz-zanzi, Feasibility of pooled-sample testing for the detection of porcine reproductive and respiratory syndrome virus antibodies on serum samples by ELISA, Veterinary Microbiology, vol.130, issue.1, pp.60-68, 2008.

R. M. Grant and I. , Mycobacterium avium ssp. paratuberculosis and its potential survival tactics, Letters in Applied Microbiology, vol.42, issue.4, pp.305-311, 2006.

A. W. Rutjes, A. Coomarasamy, K. Khan, and P. M. Et-bossuyt, Evaluation of diagnostic tests when there is no gold standard. A review of methods, Health Technology Assessment, vol.11, issue.50, 2007.

S. L. Mckenna, D. C. Sockett, G. P. Keefe, J. Mcclure, J. A. Vanleeuwen et al., Comparison of Two Enzyme-Linked Immunosorbent Assays for Diagnosis of Mycobacterium Avium Subsp, Paratuberculosis. Journal of Veterinary Diagnostic Investigation, vol.17, issue.5, pp.463-466, 2005.

A. Saah and D. R. Et-hoover, Sensitivity" and "specificity" reconsidered : the meaning of these terms in analytical and diagnostic settings, Annals of Internal Medicine, vol.126, issue.1, pp.91-94, 1997.

R. K. Saiki, S. Scharf, F. Faloona, K. B. Mullis, G. T. Horn et al., Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia, Science, vol.230, issue.4732, pp.1350-1354, 1985.

D. G. Schwarz, M. C. Lima, M. Barros, F. L. Valente, T. M. Scatamburlo et al.,

S. A. Oliveira, L. Et-moreira, and M. A. , Short communication : Passive shedding of Mycobacterium avium ssp. paratuberculosis in commercial dairy goats in Brazil, Journal of Dairy Science, vol.100, issue.10, pp.8426-8429, 2017.

E. S. Sergeant, R. Whittington, and S. J. Et-more, Sensitivity and specificity of pooled faecal culture and serology as flock-screening tests for detection of ovine paratuberculosis in Australia, 2002.

, Preventive Veterinary Medicine, vol.52, issue.3, pp.199-211

S. E. Baldock and F. , The estimated prevalence of Johne's disease infected sheep flocks in Australia, Australian Veterinary Journal, vol.80, issue.12, pp.762-768, 2002.

M. Serrano, N. Elguezabal, I. A. Sevilla, M. V. Geijo, E. Molina et al., Tuberculosis Detection in Paratuberculosis Vaccinated Calves : New Alternatives against Interference, PLOS ONE, vol.12, issue.1, 2017.

L. J. Shaughnessy, S. L. Evans, J. Anderson, D. Caldow, G. et al., High prevalence of paratuberculosis in rabbits is associated with difficulties in controlling the disease in cattle, The Veterinary Journal, vol.198, issue.1, pp.267-270, 2013.

I. Slana, R. Pribylova, A. Kralova, and I. Pavlik, Persistence of Mycobacterium avium subsp. paratuberculosis at a Farm-Scale Biogas Plant Supplied with Manure from Paratuberculosis-Affected BIBLIOGRAPHIE Dairy Cattle, Applied and Environmental Microbiology, vol.77, issue.9, pp.3115-3119, 2011.

J. A. Smeed, C. A. Watkins, S. M. Rhind, and J. Hopkins, Differential cytokine gene expression profiles in the three pathological forms of sheep paratuberculosis, BMC Veterinary Research, vol.3, issue.18, 2007.

N. Speybroeck, W. C. , L. K. Devleesschauwer, B. Berkvens, and D. , Estimating the prevalence of infections in vector populations using pools of samples, Medical and Veterinary Entomology, vol.26, issue.4, pp.361-371, 2012.

J. R. Stabel, Transitions in immune responses to Mycobacterium paratuberculosis, Veterinary Microbiology, vol.77, issue.3, pp.465-473, 2000.

J. R. Stabel, Host responses to <span class="italic">Mycobacterium avium</span> subsp. <span class="italic">paratuberculosis</span> : a complex arsenal, Animal Health Research Reviews, vol.7, issue.1-2, pp.61-70, 2006.

J. Stabel and S. Et-robbe-austerman, Early Immune Markers Associated with Mycobacterium avium subsp. paratuberculosis Infection in a Neonatal Calf Model. Clinical and Vaccine Immunology : CVI, vol.18, pp.393-405, 2011.

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, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01333713

,

R. Sting, M. Hrubenja, J. Mandl, G. Seemann, A. Salditt et al., Detection of Mycobacterium avium subsp. paratuberculosis in faeces using different procedures of pre-treatment for realtime PCR in comparison to culture, The Veterinary Journal, vol.199, issue.1, pp.138-142, 2014.

B. Strommenger, K. Stevenson, and G. Gerlach, Isolation and diagnostic potential of ISMav2, a novel insertion sequence-like element from Mycobacterium avium subspecies paratuberculosis, FEMS Microbiology Letters, vol.196, issue.1, pp.31-37, 2001.

S. N. Collins and M. T. , Thermal Tolerance of Mycobacterium paratuberculosis, Applied and Environmental Microbiology, vol.64, issue.3, pp.999-1005, 1998.

R. W. Sweeney, R. H. Whitlock, A. N. Hamir, A. E. Rosenberger, and S. A. Herr, Isolation of Mycobacterium paratuberculosis after oral inoculation in uninfected cattle, American Journal of Veterinary Research, vol.53, issue.8, pp.1312-1314, 1992.

R. W. Sweeney, R. Whitlock, and A. E. Et-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.

R. W. Sweeney, J. Uzonna, R. H. Whitlock, P. L. Habecker, P. Chilton et al., Tissue predilection sites and effect of dose on Mycobacterium avium subs. paratuberculosis organism recovery in a short-term bovine experimental oral infection model, Research in Veterinary Science, vol.80, issue.3, pp.253-259, 2006.

B. M. Swift, D. E. , M. S. Huxley, J. Et-rees, and C. E. , Development of a rapid phage-based method for the detection of viable Mycobacterium avium subsp. paratuberculosis in blood within 48 h, Journal of Microbiological Methods, vol.94, issue.3, pp.175-179, 2013.

B. M. Swift, J. N. Huxley, K. M. Plain, D. J. Begg, K. De-silva et al.,

E. D. , Evaluation of the limitations and methods to improve rapid phage-based detection of viable Mycobacterium avium subsp. paratuberculosis in the blood of experimentally infected cattle, BMC Veterinary Research, vol.12, 2016.

S. Tavornpanich, C. A. Muñoz-zanzi, W. S. , R. E. Carpenter, T. E. et al., Simulation model for evaluation of testing strategies for detection of paratuberculosis in Midwestern US dairy herds, Preventive Veterinary Medicine, vol.83, issue.1, pp.65-82, 2008.

A. W. Taylor, The experimental infection of cattle with varieties of Mycobacterium Johnei isolated from sheep, Journal of Comparative Pathology and Therapeutics, vol.63, pp.368-373, 1953.

R. D. Team, R : A Language and Environment for Statistical Computing, 2017.

V. J. Timms, M. H. Et-neilan, and B. A. , Optimisation of DNA extraction and validation of BIBLIOGRAPHIE PCR assays to detect Mycobacterium avium subsp. paratuberculosis, Journal of Microbiological Methods, vol.112, pp.99-103, 2015.

B. Toma, B. Dufour, J. Bénet, M. Sanaa, A. Shaw et al., Epidémiologie appliquée à la lutte collective contre les maladies animales transmissibles majeures, AEEMA, 2010.

J. Toribio and E. Sergeant, A comparison of methods to estimate the prevalence of ovine Johne's infection from pooled faecal samples, Australian Veterinary Journal, vol.85, issue.8, pp.317-324, 2007.

, , pp.1751-0813

J. Tse-c-et-capeau, Quantification des acides nucléiques par PCR quantitative en temps réel, 2003.

, Annales de Biologie Clinique, vol.61, issue.3, pp.279-293

T. X. , L. E. Pagano, and M. , On the Informativeness and Accuracy of Pooled Testing in Estimating Prevalence of a Rare Disease : Application to HIV Screening, Biometrika, vol.82, issue.2, pp.287-297, 1995.

C. Y. Turenne, C. D. , A. D. Et-behr, and M. A. , Mycobacterium avium subsp. paratuberculosis and M. avium subsp. avium Are Independently Evolved Pathogenic Clones of a Much Broader Group of M. avium Organisms, Journal of Bacteriology, vol.190, issue.7, pp.2479-2487, 2008.

F. W. Twort and G. L. Ingram, A Method for Isolating and Cultivating the Mycobacterium enteritidis chronicae pseudotuberculosae bovis, Johne, and some Experiments on the Preparation of a Diagnostic Vaccine for Pseudo-tuberculous Enteritis of Bovines, Proceedings of the Royal Society of London B : Biological Sciences, vol.84, issue.575, pp.517-542, 1912.

P. M. Vacek, The Effect of Conditional Dependence on the Evaluation of Diagnostic Tests, 1985.

, Biometrics, vol.41, issue.4, pp.959-968

G. Van-schaik, F. Haro, M. A. Kruze, and J. , Bayesian analysis to validate a commercial ELISA to detect paratuberculosis in dairy herds of southern Chile, Preventive Veterinary Medicine, vol.79, issue.1, pp.59-69, 2007.

C. Verdugo, G. Jones, W. Johnson, P. Wilson, L. Stringer et al., Estimation of flock/herdlevel true Mycobacterium avium subspecies paratuberculosis prevalence on sheep, beef cattle and deer farms in New Zealand using a novel Bayesian model, Preventive Veterinary Medicine, vol.117, issue.3-4, pp.447-455, 2014.

C. Verdugo, E. Pleydell, M. Price-carter, D. 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, pp.436-446, 2014.

R. Verin, M. Perroni, G. Rossi, D. Grossi, L. Botta et al., Paratuberculosis in sheep : Histochemical, immunohistochemical and in situ hybridization evidence of in utero and milk transmission, Research in Veterinary Science, vol.106, pp.173-179, 2016.

V. A. Garcia-pariente, C. Muñoz, M. Moreno, O. García-marin, J. F. Romano et al., Variation in the Immuno-pathological Responses of Lambs after Experimental Infection with Different Strains of Mycobacterium avium subsp. paratuberculosis, Zoonoses and Public Health, vol.54, issue.6-7, pp.243-252, 2007.

L. Waddell, A. Raji´craji´c, K. Stärk, and S. A. Mcewen, Mycobacterium avium ssp. paratuberculosis detection in animals, food, water and other sources or vehicles of human exposure : A scoping review of the existing evidence, Preventive Veterinary Medicine, vol.132, pp.32-48, 2016.

M. F. Weber, J. Verhoeff, G. Van-schaik, and C. Et-van-maanen, Evaluation of Ziehl-Neelsen stained faecal smear and ELISA as tools for surveillance of clinical paratuberculosis in cattle in the Netherlands, Preventive Veterinary Medicine, vol.92, issue.3, pp.256-266, 2009.

R. J. Bibliographie-whittington, I. Marsh, S. Mcallister, T. M. , M. D. Fraser et al., Evaluation of Modified BACTEC 12b Radiometric Medium and Solid Media for Culture of Mycobacterium avium subsp. paratuberculosis from Sheep, Journal of Clinical Microbiology, vol.37, issue.4, pp.1077-1083, 1999.

R. J. Whittington, S. Fell, D. Walker, S. Mcallister, I. Marsh et al., Use of Pooled Fecal Culture for Sensitive and Economic Detection of Mycobacterium avium subsp. paratuberculosisInfection in Flocks of Sheep, Journal of clinical microbiology, vol.38, issue.7, pp.2550-2556, 2000.

R. J. Whittington, M. I. Et-whitlock, and R. H. , Typing of IS 1311 polymorphisms confirms that bison (Bison bison) with paratuberculosis in Montana are infected with a strain of Mycobacterium avium subsp. paratuberculosis distinct from that occurring in cattle and other domesticated livestock, Molecular and Cellular Probes, vol.15, issue.3, pp.139-145, 2001.

R. J. Whittington, D. J. Begg, K. De-silva, P. A. Dhand, N. Et-plain et al., Case definition terminology for paratuberculosis (Johne's disease), BMC Veterinary Research, vol.13, 2017.
DOI : 10.1186/s12917-017-1254-6
URL : https://bmcvetres.biomedcentral.com/track/pdf/10.1186/s12917-017-1254-6

R. Whittington and P. A. Et-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.

R. J. Whittington, M. D. , N. P. , M. I. Et-reddacliff, and L. A. , 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, M. I. Et-reddacliff, and L. A. , Survival of Mycobacterium avium subsp. paratuberculosis in Dam Water and Sediment, Applied and Environmental Microbiology, vol.71, issue.9, pp.1098-5336, 2005.

R. J. Whittington, A. Whittington, A. Waldron, D. J. Begg, K. De-silva et al., Development and Validation of a Liquid Medium (M7h9c) for Routine Culture of Mycobacterium avium subsp. paratuberculosis To Replace Modified Bactec 12b Medium, Journal of Clinical Microbiology, vol.51, issue.12, pp.3993-4000, 2013.

R. Whittington, L. Reddacliff, I. Marsh, S. Mcallister, and V. Saunders, Temporal patterns and quantification of excretion of Mycobacterium avium subsp paratuberculosis in sheep with, 2000.

, Johne's disease, Australian Veterinary Journal, vol.78, issue.1, pp.34-37

W. D. Rood, K. Biswas, P. Byrem, and T. M. , Herd-level prevalence of Johne's disease in Utah and adjacent areas of the intermountain west as detected by a bulk-tank milk surveillance project, Journal of Dairy Science, vol.93, issue.12, pp.5792-5797, 2010.

P. Windsor, J. Eppleston, N. Dhand, and R. Whittington, Effectiveness of Gudair? vaccine for the control of ovine Johne's disease in flocks vaccinating for at least 5 years, Australian Veterinary Journal, vol.92, issue.7, pp.263-268, 2014.

R. Wolf, H. W. Barkema, D. Buck, and K. Et-orsel, Sampling location, herd size, and season influence Mycobacterium avium ssp. paratuberculosis environmental culture results, Journal of Dairy Science, vol.98, issue.1, pp.275-287, 2015.
DOI : 10.3168/jds.2014-8676

S. Zanetti, P. Molicotti, S. Cannas, S. Ortu, A. N. Sechi et al., In vitro" activities of antimycobacterial agents against Mycobacterium avium subsp. paratuberculosis linked to Crohn's Disease and Paratuberculosis, Annals of Clinical Microbiology and Antimicrobials, vol.5, p.27, 2006.

Y. Zare, G. E. Shook, C. M. Et-kirkpatrick, B. W. Corbiere-f, . Mathevon-y et al., Genome-Wide Association Analysis and Genomic Prediction of Mycobacterium avium Subspecies paratuberculosis Infection in US Jersey Cattle, PLoS ONE, vol.9, issue.2, 2014.

-. and C. Foucras-g, Analyses de mélanges de sérums et de fèces pour le diagnostic de la paratuberculose à l'échelle des troupeaux : premiers résultats chez les ovins. Comité de programmation et d'orientation de l'UMT Santé des Troupeaux de Petits Ruminants, vol.23, p.2017

-. Mathevon and Y. Foucras-g, Analyses de mélanges de fèces pour le diagnostic de la paratuberculose à l'échelle des troupeaux : premiers résultats chez les ovins et caprins

U. Journée, . Spr, and P. Omacap, , pp.27-2017

-. Mathevon and Y. Corbiere-f, Paratuberculose et vaccination. Journée technique sur la paratuberculose caprine, pp.1-2015

-. Mathevon and Y. Corbiere-f, Vaccination contre la paratuberculose : Méca-nismes, conditions de mise en oeuvre et conséquences. GDS France -Commission ovine et caprine -15 novembre, 2016.

-. , L. , T. , G. E. Falguieres-r, . Corbiere-f et al., La vaccination contre la paratuberculose ovine : développements méthodologiques et évaluation de son efficacité, Journées d'animation scientifique du département Santé Animale de l'INRA, 2016.

-. Mathevon and Y. Foucras-g, Paratuberculose et vaccination. Journée technique sur la paratuberculose caprine et ovine, 2016.

-. Mathevon and Y. Foucras-g, Analyses de mélanges de sérums et de fèces pour le diagnostic de la paratuberculose à l'échelle des troupeaux : premiers résultats chez les ovins, 2016.

R. Du-comité-de-pilotage-du-programme, P. Mathevon, and Y. Foucras-g, Programme PICSAR : état d'avancement des travaux chez les ovins .Comité de pilotage du métaprogramme PICSAR, vol.28, 2015.

-. Mathevon and Y. Foucras-g, Paratuberculose ovine : concordances entre tests individuels et premiers résultats des analyses de mélanges. Comité de pilotage du métapro-gramme PICSAR, vol.25, 2016.

-. and F. Corbiere-f, Paratuberculose ovine : estimation des performances diagnostiques des tests à l'échelle individuelle et apports des analyses de mélanges

, Comité de pilotage du métaprogramme PICSAR, pp.26-2017

, Présentations aux éleveurs -Programmes Paratuberculose PICSAR / PAROVLOT : vaccination contre la paratuberculose ovine : premiers résultats dans le Lot. Commission Sanitaire d'Ovilot, Gramat, 26 mars 2015 -Programmes Paratuberculose PICSAR / PAROVLOT : résultats dans le lot, Assemblée géné-rale d'Ovilot, Fontanes du Causse, vol.20, 2016.

. Mathevon-y.-1, . Lafort-m-p.-2, and G. E. Tasca-c.-1,

. Inra-envt, UMR 1225 IHAP, p.31076

, ENVT, 23 chemin des Capelles, p.31076

. Capel-ovilot, France Since 2009, vaccination against paratuberculosis is available in France for sheep. We evaluate the GUDAIR® vaccination effects on individual serological response and faecal shedding of Map in 19 commercial meat sheep holdings. Nine highly infected flocks vaccinated replacement ewes between 4 and 6 months old

, Highly infected flocks Min:2.5% Median:12%, p.19