Nielsen SS, Toft N (2009) A review of prevalences of paratuberculosis in farmed animals in Europe. Prev Vet Med 88:1–14
Article
PubMed
Google Scholar
Whittington RJ, Windsor PA (2009) In utero infection of cattle with Mycobacterium avium subsp. paratuberculosis: a critical review and meta-analysis. Vet J 179:60–69
Article
PubMed
Google Scholar
Mortier R, Orsel K, Barkema HW, Atkins G, De Buck J (2011) Age and dose dependent susceptibility to Mycobacterium avium subsp. paratuberculosis in dairy cattle. WCDS Adv Dairy Technol 23:375
Google Scholar
Good M, Clegg T, Sheridan H, Yearsely D, O’Brien T, Egan J, Mullowey P (2009) Prevalence and distribution of paratuberculosis (Johne’s disease) in cattle herds in Ireland. Ir Vet J 62:597–606
Article
CAS
PubMed
PubMed Central
Google Scholar
Raizman EA, Wells SJ, Muñoz-Zanzi CA, Tavornpanich S (2011) Estimated within-herd prevalence (WHP) of Mycobacterium avium subsp. paratuberculosis in a sample of Minnesota dairy herds using bacterial culture of pooled fecal samples. Can J Vet Res 75:112–116
PubMed
PubMed Central
Google Scholar
Mortier RA, Barkema HW, Orsel K, Wolf R, De Buck J (2014) Shedding patterns of dairy calves experimentally infected with Mycobacterium avium subspecies paratuberculosis. Vet Res 45:71
Article
PubMed
PubMed Central
Google Scholar
Mortier RA, Barkema HW, De Buck J (2015) Susceptibility to and diagnosis of Mycobacterium avium subspecies paratuberculosis infection in dairy calves: a review. Prev Vet Med 121:189–198
Article
PubMed
Google Scholar
Stewart DJ, Vaughan JA, Stiles PL, Noske PJ, Tizard ML, Prowse SJ, Michalski WP, Butler KL, Jones SL (2007) A long-term bacteriological and immunological study in Holstein-Friesian cattle experimentally infected with Mycobacterium avium subsp. paratuberculosis and necropsy culture results for Holstein-Friesian cattle, Merino sheep and Angora goats. Vet Microbiol 122:83–96
Article
CAS
PubMed
Google Scholar
van Roermund HJW, Bakker D, Willemsen PTJ, de Jong MC (2007) Horizontal transmission of Mycobacterium avium subsp. paratuberculosis in cattle in an experimental setting: calves can transmit the infection to other calves. Vet Microbiol 122:270–279
Article
PubMed
Google Scholar
Mitchell RM, Medley GF, Collins MT, Schukken YH (2012) 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. Epidemiol Infect 140:231–246
Article
CAS
PubMed
Google Scholar
Nielsen SS (2008) Transitions in diagnostic tests used for detection of Mycobacterium avium subsp. paratuberculosis infections in cattle. Vet Microbiol 132:274–282
Article
CAS
PubMed
Google Scholar
Matthews HT (1947) On Johne’s disease. Vet Rec 59:397–401
CAS
PubMed
Google Scholar
Ezanno P, van Schaik G, Weber MF, Heesterbeek JA (2005) A modeling study on the sustainability of a certification-and-monitoring program for paratuberculosis in cattle. Vet Res 36:811–826
Article
PubMed
Google Scholar
Bastida F, Juste RA (2011) Paratuberculosis control: a review with a focus on vaccination. J Immune Based Ther Vaccines 9:8
Article
CAS
PubMed
PubMed Central
Google Scholar
Beaunée G, Vergu E, Ezanno P (2015) Modelling of paratuberculosis spread between dairy cattle farms at a regional scale. Vet Res 46:111
Article
PubMed
PubMed Central
Google Scholar
Kalis CH, Hesselink JW, Barkema HW, Collins MT (2001) Use of long-term vaccination with a killed vaccine to prevent fecal shedding of Mycobacterium avium subsp. paratuberculosis in dairy herds. Am J Vet Res 62:270–274
Article
CAS
PubMed
Google Scholar
Behr MA, Collins DM (2010) Paratuberculosis: organism, disease. Control, vol 1. CABI, Wallingford, UK, Cambridge, USA, p 1–388
Kirkpatrick BW, Shook GE (2011) Genetic susceptibility to paratuberculosis. Vet Clin N Am Food Anim Pract 27:559–571
Article
Google Scholar
van Hulzen KJ, Nielen M, Koets AP, de Jong G, van Arendonk JA, Heuven HC (2011) Effect of herd prevalence on heritability estimates of antibody response to Mycobacterium avium subspecies paratuberculosis. J Dairy Sci 94:992–997
Article
PubMed
Google Scholar
Küpper J, Brandt H, Donat K, Erhardt G (2012) Heritability estimates for Mycobacterium avium subspecies paratuberculosis status of German Holstein cows tested by fecal culture. J Dairy Sci 95:2734–2739
Article
PubMed
Google Scholar
Zare Y, Shook GE, Collins MT, Kirkpatrick BW (2014) Short communication: heritability estimates for susceptibility to Mycobacterium avium subspecies paratuberculosis infection defined by ELISA and fecal culture test results in Jersey cattle. J Dairy Sci 97:4562–4567
Article
CAS
PubMed
Google Scholar
Purdie AC, Plain KM, Begg DJ, de Silva K, Whittington RJ (2011) Candidate gene and genome-wide association studies of Mycobacterium avium subsp. paratuberculosis infection in cattle and sheep: a review. Comp Immunol Microbiol Infect Dis 34:197–208
Article
PubMed
Google Scholar
Kirkpatrick BW, Shi X, Shook GE, Collins MT (2011) Whole-Genome association analysis of susceptibility to paratuberculosis in Holstein cattle. Anim Genet 42:149–160
Article
CAS
PubMed
Google Scholar
van Hulzen KJ, Koets AP, Nielen M, Hoeboer J, van Arendonk JA, Heuven HC (2012) Genetic variation for infection status as determined by a specific antibody response against Mycobacterium avium subspecies paratuberculosis in milk of Dutch dairy goats. J Dairy Sci 95:6145–6151
Article
PubMed
Google Scholar
Alpay F, Zare Y, Kamalludin MH, Huang X, Shi X, Shook GE, Collins MT, Kirkpatrick BW (2014) Genome-wide association study of susceptibility to infection by Mycobacterium avium subspecies paratuberculosis in Holstein cattle. PLoS One 9:e111704
Article
PubMed
PubMed Central
Google Scholar
Zanella R, Settles ML, McKay SD, Schnabel R, Taylor J, Whitlock RH, Schukken Y, Van Kessel JS, Smith JM, Neibergs HL (2011) Identification of loci associated with tolerance to Johne’s disease in Holstein cattle. Anim Genet 42:28–38
Article
CAS
PubMed
Google Scholar
Settles M, Zanella R, McKay SD, Schnabel RD, Taylor JF, Whitlock R, Schukken Y, Van Kessel JS, Smith JM, Neibergs H (2009) A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. paratuberculosis infection status in US holstein cattle. Anim Genet 40:655–662
Article
CAS
PubMed
Google Scholar
Neibergs HL, Settles ML, Whitlock RH, Taylor JF (2010) GSEA-SNP identifies genes associated with Johne’s disease in cattle. Mamm Genome 21:419–425
Article
CAS
PubMed
Google Scholar
van Hulzen KJ, Koets AP, Nielen M, Heuven HC, van Arendonk JA, Klinkenberg D (2014) The effect of genetic selection for Johne’s disease resistance in dairy cattle: results of a genetic-epidemiological model. J Dairy Sci 97:1762–1773
Article
PubMed
Google Scholar
Marcé C, Ezanno P, Weber MF, Seegers H, Pfeiffer DU, Fourichon C (2010) Invited review: modeling within-herd transmission of Mycobacterium avium subspecies paratuberculosis in dairy cattle: a review. J Dairy Sci 93:4455–4470
Article
PubMed
Google Scholar
Lu Z, Schukken YH, Smith RL, Grohn YT (2010) Stochastic simulations of a multi-group compartmental model for Johne’s disease on US dairy herds with test-based culling intervention. J Theor Biol 264:1190–1201
Article
PubMed
Google Scholar
Marcé C, Ezanno P, Seegers H, Pfeiffer DU, Fourichon C (2011) Predicting fadeout versus persistence of paratuberculosis in a dairy cattle herd for management and control purposes: a modelling study. Vet Res 42:36
Article
PubMed
PubMed Central
Google Scholar
Marcé C, Ezanno P, Seegers H, Pfeiffer DU, Fourichon C (2011) Within-herd contact structure and transmission of Mycobacterium avium subspecies paratuberculosis in a persistently infected dairy cattle herd. Prev Vet Med 100:116–125
Article
PubMed
Google Scholar
Robins J, Bogen S, Francis A, Westhoek A, Kanarek A, Lenhart S, Eda S (2015) Agent-based model for Johne’s disease dynamics in a dairy herd. Vet Res 46:68
Article
PubMed
PubMed Central
Google Scholar
Martcheva M, Lenhart S, Eda S, Klinkenberg D, Momotani E, Stabel J (2015) An immuno-epidemiological model for Johne’s disease in cattle. Vet Res 46:69
Article
PubMed
PubMed Central
Google Scholar
Smith RL, Schukken YH, Gröhn YT (2015) A new compartmental model of Mycobacterium avium subsp. paratuberculosis infection dynamics in cattle. Prev Vet Med 122:298–305
Article
PubMed
PubMed Central
Google Scholar
Koets AP, Gröhn YT (2015) Within- and between-host mathematical modeling of Mycobacterium avium subspecies paratuberculosis (MAP) infections as a tool to study the dynamics of host–pathogen interactions in bovine paratuberculosis. Vet Res 46:60
Article
PubMed
PubMed Central
Google Scholar
Al-Mamun MA, Smith RL, Schukken YH, Gröhn YT (2016) Modeling of Mycobacterium avium subsp. paratuberculosis dynamics in a dairy herd: an individual based approach. J Theor Biol 408:105–117
Article
PubMed
Google Scholar
Pradhan AK, Mitchell RM, Kramer AJ, Zurakowski MJ, Fyock TL, Whitlock RH, Smith JM, Hovingh E, Van Kessel JA, Karns JS, Schukken YH (2011) Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis in a longitudinal study of three dairy herds. J Clin Microbiol 49:893–901
Article
PubMed
PubMed Central
Google Scholar
Råberg L, Sim D, Read AF (2007) Disentangling genetic variation for resistance and tolerance to infectious diseases in animals. Science 318:812–814
Article
PubMed
Google Scholar
Schneider DS, Ayres JS (2008) Two ways to survive infection: what resistance and tolerance can teach us about treating infectious diseases. Nat Rev Immunol 8:889–895
Article
CAS
PubMed
PubMed Central
Google Scholar
R Core Team (2016) R: A language and environment for statistical computing. Vienna, Austria. R Foundation for Statistical. http://www.R-project.org/
Everitt BS, Hothorn T (2010) Cluster analysis: classifying Romano-British pottery and exoplanets. In: A handbook of statistical analyses using R, 2nd ed. CRC Press, Taylor and Francis Group edition, Boca Raton, p 315–348. http://www.bagualu.net/wordpress/wp-content/uploads/2015/10/A_Handbook_of_Statistical_Analyses_Using_R__Second_Edition.pdf
Thinsungnoen T, Kaoungku N, Durongdumronchai P, Kerdprasop K, Kerdprasop N (2015) The clustering validity with silhouette and sum of squared errors. In: Proceedings of the 3rd international conference on industrial application engineering, p 44–51. https://www2.ia-engineers.org/iciae/index.php/iciae/iciae2015/paper/viewFile/576/380
MacQueen J (1967) Some methods for classification and analysis of multivariate observations. In: Proceedings of the fifth berkeley symposium on mathematical statistics and probability, vol 1. University of California Press, Berkeley, California, p 281–297. https://projecteuclid.org/download/pdf_1/euclid.bsmsp/1200512992
Husson F, Josse J, Le S, Mazet J (2016) FactoMineR: multivariate exploratory data analysis and data mining. R package version 1.32. https://CRAN.R-project.org/package=FactoMineR
Zare Y, Shook GE, Collins MT, Kirkpatrick BW (2014) Genome-wide association analysis and genomic prediction of Mycobacterium avium subspecies paratuberculosis infection in US Jersey cattle. PLoS One 9:e88380
Article
PubMed
PubMed Central
Google Scholar
McSpadden K, Caires K, Zanella R (2013) The effect of Mycobacterium avium subspecies paratuberculosis exposure on animal health. Acta Sci Vet 41:1095
Google Scholar
Pauciullo A, Küpper J, Brandt H, Donat K, Iannuzzi L, Erhardt G (2015) Wingless-type MMTV integration site family member 2 (WNT2) gene is associated with resistance to MAP in faecal culture and antibody response in Holstein cattle. Anim Genet 46:122–132
Article
CAS
PubMed
Google Scholar
Carvajal AM, Huircan P, Lepori A (2013) Single nucleotide polymorphisms in immunity-related genes and their association with mastitis in Chilean dairy cattle. Genet Mol Res 12:2702–2711
Article
CAS
PubMed
Google Scholar
Rankin JD (1962) The experimental infection of cattle with Mycobacterium johnei. IV. Adult cattle maintained in an infectious environment. J Comp Pathol 72:113–117
Article
CAS
PubMed
Google Scholar
Hagan WA (1938) Age as a factor in susceptibility to Johne’s disease. Cornell Vet 28:34–40
Google Scholar
Whitlock RH, Buergelt C (1996) Preclinical and clinical manifestations of paratuberculosis (including pathology). Vet Clin N Am Food Anim Pract 12:345–356
Article
CAS
Google Scholar
Windsor PA, Whittington RJ (2010) Evidence for age susceptibility of cattle to Johne’s disease. Vet J 184:37–44
Article
PubMed
Google Scholar
Begg DJ, Whittington RJ (2008) Experimental animal infection models for Johne’s disease, an infectious enteropathy caused by Mycobacterium avium subsp. paratuberculosis. Vet J 176:129–145
Article
PubMed
Google Scholar
Sweeney RW, Whitlock RH, Rosenberger AE (1992) Mycobacterium paratuberculosis isolated from fetuses of infected cows not manifesting signs of the disease. Am J Vet Res 53:477–480
CAS
PubMed
Google Scholar
Giese SB, Ahrens P (2000) Detection of Mycobacterium avium subsp. paratuberculosis in milk from clinically affected cows by PCR and culture. Vet Microbiol 77:291–297
Article
CAS
PubMed
Google Scholar
Rossiter CA, Burhans WS (1996) Farm-specific approach to paratuberculosis (Johne’s disease) control. Vet Clin N Am Food Anim Pract 12:383–415
Article
CAS
Google Scholar
Whittington RJ, Reddacliff LA, Marsh I, McAllister S, Saunders V (2000) Temporal patterns and quantification of excretion of Mycobacterium avium subsp. paratuberculosis in sheep with Johne’s disease. Aust Vet J 78:34–37
Article
CAS
PubMed
Google Scholar
Jørgensen JB (1982) An improved medium for culture of Mycobacterium paratuberculosis from bovine faeces. Acta Vet Scand 23:325–335
PubMed
Google Scholar
Benedictus A, Mitchell RM, Linde-Widmann M, Sweeney R, Fyock T, Schukken YH, Whitlock RH (2008) Transmission parameters of Mycobacterium avium subspecies paratuberculosis infections in a dairy herd going through a control program. Prev Vet Med 83:215–227
Article
CAS
PubMed
Google Scholar