922
Views
112
CrossRef citations to date
0
Altmetric
Review Article

Crohn’s disease and the mycobacterioses: A quarter century later. Causation or simple association?

, , &
Pages 52-93 | Received 17 Sep 2011, Accepted 02 Nov 2011, Published online: 14 Jan 2012

References

  • Abubakar I, Myhill D, Aliyu SH, Hunter PR. (2008). Detection of Mycobacterium avium subspecies paratuberculosis from patients with Crohn’s disease using nucleic acid-based techniques: a systematic review and meta-analysis. Inflamm Bowel Dis, 14, 401–410.
  • Adams RJ, Heazlewood SP, Gilshenan KS, O’Brien M, McGuckin MA, Florin TH. (2008). IgG antibodies against common gut bacteria are more diagnostic for Crohn’s disease than IgG against mannan or flagellin. Am J Gastroenterol, 103, 386–396.
  • Afdhal NH, Long A, Lennon J, Crowe J, O’Donoghue DP. (1991). Controlled trial of antimycobacterial therapy in Crohn’s disease. Clofazimine versus placebo. Dig Dis Sci, 36, 449–453.
  • Ahrens P, Giese SB, Klausen J, Inglis NF. (1995). Two markers, IS901-IS902 and p40, identified by PCR and by using monoclonal antibodies in Mycobacterium avium strains. J Clin Microbiol, 33, 1049–1053.
  • Al-Shamali M, Khan I, Al-Nakib B, Al-Hassan F, Mustafa AS. (1997). A multiplex polymerase chain reaction assay for the detection of Mycobacterium paratuberculosis DNA in Crohn’s disease tissue. Scand J Gastroenterol, 32, 819–823.
  • Allen AJ, Park KT, Barrington GM, Lahmers KK, Abdellrazeq GS, Rihan HM, Sreevatsan S, Davies C, Hamilton MJ, Davis WC. (2011). Experimental infection of a bovine model with human isolates of Mycobacterium avium subsp. paratuberculosis. Vet Immunol Immunopathol, 141, 258–266.
  • Anonymous. (2011). Continuing medical education: supplement 1, April 2011. An evidence-based systematic review on medical therapies for inflammatory bowel diseases. Am J Gastroenterol, 106 Suppl 1, S1.
  • Arnott ID, Satsangi J. (2003). Crohn’s disease or Crohn’s diseases? Gut, 52, 460–461.
  • Autschbach F, Eisold S, Hinz U, Zinser S, Linnebacher M, Giese T, Löffler T, Büchler MW, Schmidt J. (2005). High prevalence of Mycobacterium avium subspecies paratuberculosis IS900 DNA in gut tissues from individuals with Crohn’s disease. Gut, 54, 944–949.
  • Bach H, Ko HH, Raizman EA, Attarian R, Cho B, Biet F, Enns R, Bressler B. (2011). Immunogenicity of Mycobacterium avium subsp. paratuberculosis proteins in Crohn’s disease patients. Scand J Gastroenterol, 46, 30–39.
  • Baelden MC, Bouckaert AE, Grégoire D, van de Poele M, Coene M. (1994). Comparison of thermostable macromolecular antigens from leprosy-associated bacteria. Can J Microbiol, 40, 508–512.
  • Baker PI, Love DR, Ferguson LR. (2009). Role of gut microbiota in Crohn’s disease. Expert Rev Gastroenterol Hepatol, 3, 535–546.
  • Baksh FK, Finkelstein SD, Ariyanayagam-Baksh SM, Swalsky PA, Klein EC, Dunn JC. (2004). Absence of Mycobacterium avium subsp. paratuberculosis in the microdissected granulomas of Crohn’s disease. Mod Pathol, 17, 1289–1294.
  • Bannantine JP, Zhang Q, Li LL, Kapur V. (2003). Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. BMC Microbiol, 3, 10.
  • Bannantine JP, Baechler E, Zhang Q, Li L, Kapur V. (2002). Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J Clin Microbiol, 40, 1303–1310.
  • Barnich N, Darfeuille-Michaud A. (2007). Adherent-invasive Escherichia coli and Crohn’s disease. Curr Opin Gastroenterol, 23, 16–20.
  • Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ; NIDDK IBD Genetics Consortium; Belgian-French IBD Consortium; Wellcome Trust Case Control Consortium. (2008). Genome-wide association defines more than 30 distinct susceptibility loci for Crohn’s disease. Nat Genet, 40, 955–962.
  • Barry CE 3rd, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ, Young D. (2009). The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nat Rev Microbiol, 7, 845–855.
  • Barta Z, Csipo I, Mekkel G, Zeher M, Majoros L. (2004). Seroprevalence of Mycobacterium paratuberculosis in patients with Crohn’s Disease. J Clin Microbiol, 42, 5432; author reply 5432–5432; author reply 5433.
  • Basilisco G, Ranzi T, Campanini C, Piodi L, Bianci PA. (1989). Controlled trial of rifabutin in Crohn’s disease. Curr Ther Res, 6, 245–250.
  • Bataille F, Klebl F, Rümmele P, Schroeder J, Farkas S, Wild PJ, Fürst A, Hofstädter F, Schölmerich J, Herfarth H, Rogler G. (2004). Morphological characterisation of Crohn’s disease fistulae. Gut, 53, 1314–1321.
  • Beckler DR, Elwasila S, Ghobrial G, Valentine JF, Naser SA. (2008). Correlation between rpoB gene mutation in Mycobacterium avium subspecies paratuberculosis and clinical rifabutin and rifampicin resistance for treatment of Crohn’s disease. World J Gastroenterol, 14, 2723–2730.
  • Behr MA, Schurr E. (2006). Mycobacteria in Crohn’s disease: a persistent hypothesis. Inflamm Bowel Dis, 12, 1000–1004.
  • Behr MA, Kapur V. (2008). The evidence for Mycobacterium paratuberculosis in Crohn’s disease. Curr Opin Gastroenterol, 24, 17–21.
  • Behr MA, Hanley J. (2008). Antimycobacterial therapy for Crohn’s disease: a reanalysis. Lancet Infect Dis, 8, 344.
  • Belsheim MR, Darwish RZ, Watson WC, Schieven B. (1983). Bacterial L-form isolation from inflammatory bowel disease patients. Gastroenterology, 85, 364–369.
  • Benedictus G, Kalis CJ. (2003). Paratuberculosis: eradication, control and diagnostic methods. Acta Vet Scand, 44, 231–241.
  • Bentley RW, Keenan JI, Gearry RB, Kennedy MA, Barclay ML, Roberts RL. (2008). Incidence of Mycobacterium avium subspecies paratuberculosis in a population-based cohort of patients with Crohn’s disease and control subjects. Am J Gastroenterol, 103, 1168–1172.
  • Beran V, Havelkova M, Kaustova J, Dvorska L, Pavlik I. (2006). Cell wall deficient forms of mycobacteria: a review. Veterinarni Medicina, 51, 365–389.
  • Bermudez LE, Petrofsky M, Sommer S, Barletta RG. (2010). Peyer’s patch-deficient mice demonstrate that Mycobacterium avium subsp. paratuberculosis translocates across the mucosal barrier via both M cells and enterocytes but has inefficient dissemination. Infect Immun, 78, 3570–3577.
  • Bernstein CN, Nayar G, Hamel A, Blanchard JF. (2003). Study of animal-borne infections in the mucosas of patients with inflammatory bowel disease and population-based controls. J Clin Microbiol, 41, 4986–4990.
  • Bernstein CN, Blanchard JF, Rawsthorne P, Collins MT. (2004). Population-based case control study of seroprevalence of Mycobacterium paratuberculosis in patients with Crohn’s disease and ulcerative colitis. J Clin Microbiol, 42, 1129–1135.
  • Bernstein CN, Wang MH, Sargent M, Brant SR, Collins MT. (2007). Testing the interaction between NOD-2 status and serological response to Mycobacterium paratuberculosis in cases of inflammatory bowel disease. J Clin Microbiol, 45, 968–971.
  • Beumer A, King D, Donohue M, Mistry J, Covert T, Pfaller S. (2010). Detection of Mycobacterium avium subsp. paratuberculosis in drinking water and biofilms by quantitative PCR. Appl Environ Microbiol, 76, 7367–7370.
  • Bhide M, Chakurkar E, Tkacikova L, Barbuddhe S, Novak M, Mikula I. (2006). IS900-PCR-based detection and characterization of Mycobacterium avium subsp. paratuberculosis from buffy coat of cattle and sheep. Vet Microbiol, 112, 33–41.
  • Bhide MR, Mucha R, Mikula I Jr, Kisova L, Skrabana R, Novak M, Mikula I Sr. (2009). Novel mutations in TLR genes cause hyporesponsiveness to Mycobacterium avium subsp. paratuberculosis infection. BMC Genet, 10, 21.
  • Blaser MJ, Miller RA, Lacher J, Singleton JW. (1984). Patients with active Crohn’s disease have elevated serum antibodies to antigens of seven enteric bacterial pathogens. Gastroenterology, 87, 888–894.
  • Borgaonkar MR, MacIntosh DG, Fardy JM. (2000). A meta-analysis of antimycobacterial therapy for Crohn’s disease. Am J Gastroenterol, 95, 725–729.
  • Borody TJ, Leis S, Warren EF, Surace R. (2002). Treatment of severe Crohn’s disease using antimycobacterial triple therapy–approaching a cure? Dig Liver Dis, 34, 29–38.
  • Borody TJ, Bilkey S, Wettstein AR, Leis S, Pang G, Tye S. (2007). Anti-mycobacterial therapy in Crohn’s disease heals mucosa with longitudinal scars. Dig Liver Dis, 39, 438–444.
  • Brunello F, Pera A, Martini S, Marino L, Astegiano M, Barletti C, Gastaldi P, Verme G, Emanuelli G. (1991). Antibodies to Mycobacterium paratuberculosis in patients with Crohn’s disease. Dig Dis Sci, 36, 1741–1745.
  • Bull TJ, McMinn EJ, Sidi-Boumedine K, Skull A, Durkin D, Neild P, Rhodes G, Pickup R, Hermon-Taylor J. (2003). Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn’s disease. J Clin Microbiol, 41, 2915–2923.
  • Burnham WR, Lennard-Jones JE, Stanford JL, Bird RG. (1978). Mycobacteria as a possible cause of inflammatory bowel disease. Lancet, 2, 693–696.
  • Cani PD, Delzenne NM. (2009). Interplay between obesity and associated metabolic disorders: new insights into the gut microbiota. Curr Opin Pharmacol, 9, 737–743.
  • Cartun RW, Van Kruiningen HJ, Pedersen CA, Berman MM. (1993). An immunocytochemical search for infectious agents in Crohn’s disease. Mod Pathol, 6, 212–219.
  • Cattell RB, Mosely CH. (1946). The surgical treatment of tuberculosis of the bowel. Lahey Clin Bull, 5, 6–9.
  • Cellier C, De Beenhouwer H, Berger A, Penna C, Carbonnel F, Parc R, Cugnenc PH, Le Quintrec Y, Gendre JP, Barbier JP, Portaels F. (1998). Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum DNA cannot be detected by PCR in Crohn’s disease tissue. Gastroenterol Clin Biol, 22, 675–678.
  • Cerf O, Griffiths M, Aziza F. (2007). Assessment of the prevalence of Mycobacterium avium subsp. paratuberculosis in commercially pasteurized milk. Foodborne Pathog Dis, 4, 433–447.
  • Chamberlin W. (2007). Importance of the Australian Crohn’s disease antibiotic study. Gastroenterology, 133, 1744–5; author reply 1745.
  • Chamberlin W, Ghobrial G, Chehtane M, Naser SA. (2007). Successful treatment of a Crohn’s disease patient infected with bacteremic Mycobacterium paratuberculosis. Am J Gastroenterol, 102, 689–691.
  • Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. (2010). Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS ONE, 5, e15216.
  • Chassaing B, Darfeuille-Michaud A. (2011). The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology, 140, 1720–1728.
  • Chassaing B, Rolhion N, de Vallée A, Salim SY, Prorok-Hamon M, Neut C, Campbell BJ, Söderholm JD, Hugot JP, Colombel JF, Darfeuille-Michaud A. (2011). Crohn disease–associated adherent-invasive E. coli bacteria target mouse and human Peyer’s patches via long polar fimbriae. J Clin Invest, 121, 966–975.
  • Chen W, Li D, Paulus B, Wilson I, Chadwick VS. (2000). Detection of Listeria monocytogenes by polymerase chain reaction in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls. J Gastroenterol Hepatol, 15, 1145–1150.
  • Chermesh I, Azriel A, Alter-Koltunoff M, Eliakim R, Karban A, Levi BZ. (2007). Crohn’s disease and SLC11A1 promoter polymorphism. Dig Dis Sci, 52, 1632–1635.
  • Chiang CY, Centis R, Migliori GB. (2010). Drug-resistant tuberculosis: past, present, future. Respirology, 15, 413–432.
  • Chiba M, Fukushima T, Horie Y, Iizuka M, Masamune O. (1998). No Mycobacterium paratuberculosis detected in intestinal tissue, including Peyer’s patches and lymph follicles, of Crohn’s disease. J Gastroenterol, 33, 482–487.
  • Chiodini RJ. (1986). Biochemical characteristics of various strains of Mycobacterium paratuberculosis. Am J Vet Res, 47, 1442–1445.
  • Chiodini RJ. (1988). Identification of mycobacteria from Crohn’s disease by restriction polymorphism of the 5s ribosomal DNA genes. In: MacDermott RP, ed. Inflammatory bowel disease. Current status and future approach. Amsterdam: Elsevier Science Publishing, Inc, 509–514.
  • Chiodini RJ. (1989). Crohn’s disease and the mycobacterioses: a review and comparison of two disease entities. Clin Microbiol Rev, 2, 90–117.
  • Chiodini RJ. (1990a). Bactericidal activities of various antimicrobial agents against human and animal isolates of Mycobacterium paratuberculosis. Antimicrob Agents Chemother, 34, 366–367.
  • Chiodini RJ. (1990b). Characterization of Mycobacterium paratuberculosis and organisms of the Mycobacterium avium complex by restriction polymorphism of the rRNA gene region. J Clin Microbiol, 28, 489–494.
  • Chiodini RJ. (1991). Antimicrobial activity of rifabutin in combination with two and three other antimicrobial agents against strains of Mycobacterium paratuberculosis. J Antimicrob Chemother, 27, 171–176.
  • Chiodini RJ. (1998). Antimicrobial agents and Crohn’s disease: do they have a therapeutic role? Ital J Gastroenterol Hepatol, 30, 593–598.
  • Chiodini RJ, Buergelt CD. (1993). Susceptibility of Balb/c, C57/B6 and C57/B10 mice to infection with Mycobacterium paratuberculosis. J Comp Pathol, 109, 309–319.
  • Chiodini RJ, Hermon-Taylor J. (1993). The thermal resistance of Mycobacterium paratuberculosis in raw milk under conditions simulating pasteurization. J Vet Diagn Invest, 5, 629–631.
  • Chiodini RJ, Chamberlin WM, Pfaller S. (2011). What is Mycobacterium avium subsp. paratuberculosis? Appl Environ Microbiol, 77, 1923–4; author reply 1923.
  • Chiodini RJ, Van Kruiningen HJ, Merkal RS. (1984a). Ruminant paratuberculosis (Johne’s disease): the current status and future prospects. Cornell Vet, 74, 218–262.
  • Chiodini RJ, Kreeger JM, Thayer WR. (1993). Use of rifabutin in treatment of systemic Mycobacterium paratuberculosis infection in mice. Antimicrob Agents Chemother, 37, 1645–1648.
  • Chiodini RJ, Van Kruiningen HJ, Thayer WR, Coutu JA. (1986). Spheroplastic phase of mycobacteria isolated from patients with Crohn’s disease. J Clin Microbiol, 24, 357–363.
  • Chiodini RJ, Van Kruiningen HJ, Merkal RS, Thayer WR Jr, Coutu JA. (1984b). Characteristics of an unclassified Mycobacterium species isolated from patients with Crohn’s disease. J Clin Microbiol, 20, 966–971.
  • Chiodini RJ, Van Kruiningen HJ, Thayer WR, Coutu JA, Merkal RS. (1984c). In vitro antimicrobial susceptibility of a Mycobacterium sp. isolated from patients with Crohn’s disease. Antimicrob Agents Chemother, 26, 930–932.
  • Chiodini RJ, Van Kruiningen HJ, Thayer WR, Merkal RS, Coutu JA. (1984d). Possible role of mycobacteria in inflammatory bowel disease. I. An unclassified Mycobacterium species isolated from patients with Crohn’s disease. Dig Dis Sci, 29, 1073–1079.
  • Cho SN, Brennan PJ, Yoshimura HH, Korelitz BI, Graham DY. (1986). Mycobacterial aetiology of Crohn’s disease: serologic study using common mycobacterial antigens and a species-specific glycolipid antigen from Mycobacterium paratuberculosis. Gut, 27, 1353–1356.
  • Clancy R, Ren Z, Turton J, Pang G, Wettstein A. (2007). Molecular evidence for Mycobacterium avium subspecies paratuberculosis (MAP) in Crohn’s disease correlates with enhanced TNF-alpha secretion. Dig Liver Dis, 39, 445–451.
  • Clark DL Jr, Anderson JL, Koziczkowski JJ, Ellingson JL. (2006). Detection of Mycobacterium avium subspecies paratuberculosis genetic components in retail cheese curds purchased in Wisconsin and Minnesota by PCR. Mol Cell Probes, 20, 197–202.
  • Clark RG, Griffin JF, Mackintosh CG. (2010). Johne’s disease caused by Mycobacterium avium subsp. paratuberculosis infection in red deer (Cervus elaphus): an histopathological grading system, and comparison of paucibacillary and multibacillary disease. N Z Vet J, 58, 90–97.
  • Clarkston WK, Presti ME, Petersen PF, Zachary PE Jr, Fan WX, Leonardi CL, Vernava AM 3rd, Longo WE, Kreeger JM. (1998). Role of Mycobacterium paratuberculosis in Crohn’s disease: a prospective, controlled study using polymerase chain reaction. Dis Colon Rectum, 41, 195–199.
  • Cleaveland S, Shaw DJ, Mfinanga SG, Shirima G, Kazwala RR, Eblate E, Sharp M. (2007). Mycobacterium bovis in rural Tanzania: risk factors for infection in human and cattle populations. Tuberculosis (Edinb), 87, 30–43.
  • Click RE, Van Kampen CL. (2010). Assessment of Dietzia subsp. C79793-74 for treatment of cattle with evidence of paratuberculosis. Virulence, 1, 145–155.
  • Collins DM, Gabric DM, De Lisle GW. (1989). Identification of a repetitive DNA sequence specific to Mycobacterium paratuberculosis. FEMS Microbiol Lett, 51, 175–178.
  • Collins DM, Gabric DM, de Lisle GW. (1990). Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization. J Clin Microbiol, 28, 1591–1596.
  • Collins JD, Wall PG. (2004). Food safety and animal production systems: controlling zoonoses at farm level. Rev – Off Int Epizoot, 23, 685–700.
  • Collins MT, Lisby G, Moser C, Chicks D, Christensen S, Reichelderfer M, Høiby N, Harms BA, Thomsen OO, Skibsted U, Binder V. (2000). Results of multiple diagnostic tests for Mycobacterium avium subsp. paratuberculosis in patients with inflammatory bowel disease and in controls. J Clin Microbiol, 38, 4373–4381.
  • Cook JL. (2010). Nontuberculous mycobacteria: opportunistic environmental pathogens for predisposed hosts. Br Med Bull, 96, 45–59.
  • Cook KL, Britt JS, Bolster CH. (2010). Survival of Mycobacterium avium subsp. paratuberculosis in biofilms on livestock watering trough materials. Vet Microbiol, 141, 103–109.
  • Cooney R, Jewell D. (2009). The genetic basis of inflammatory bowel disease. Dig Dis, 27, 428–442.
  • Corti M, Palmero D. (2008). Mycobacterium avium complex infection in HIV/AIDS patients. Expert Rev Anti Infect Ther, 6, 351–363.
  • Cossu D, Cocco E, Paccagnini D, Masala S, Ahmed N, Frau J, Marrosu MG, Sechi LA. (2011). Association of Mycobacterium avium subsp. paratuberculosis with multiple sclerosis in Sardinian patients. PLoS ONE, 6, e18482.
  • Cousins DV, Whittington R, Marsh I, Masters A, Evans RJ, Kluver P. (1999). Mycobacteria distenct from Mycobacterium avium subsp. paratuberculosis isolated from the faeces of ruminants possess IS900-like sequences detectable IS900 polymerase chain reaction: implications for diagnosis. Mol Cell Probes, 13, 431–442.
  • Crawford NP, Eichenberger MR, Colliver DW, Lewis RK, Cobbs GA, Petras RE, Galandiuk S. (2005). Evaluation of SLC11A1 as an inflammatory bowel disease candidate gene. BMC Med Genet, 6, 10.
  • Cremon C, Carini G, De Giorgio R, Stanghellini V, Corinaldesi R, Barbara G. (2010). Intestinal dysbiosis in irritable bowel syndrome: etiological factor or epiphenomenon? Expert Rev Mol Diagn, 10, 389–393.
  • da Silva Rabello MC, de Oliveira RS, Silva RM, Leao SC. (2010). Natural occurrence of horizontal transfer of Mycobacterium avium–specific insertion sequence IS1245 to Mycobacterium kansasii. J Clin Microbiol, 48, 2257–2259.
  • Dalton HR, Hoang P, Jewell DP. (1992). Antigen induced suppression in peripheral blood and lamina propria mononuclear cells in inflammatory bowel disease. Gut, 33, 324–330.
  • Daly AK. (2010). Genome-wide association studies in pharmacogenomics. Nat Rev Genet, 11, 241–246.
  • Dalziel TK. (1913). Chronic interstitial enteritis. Br Med J, 2, 1068–1070.
  • de la Rua-Domenech R. (2006). Human Mycobacterium bovis infection in the United Kingdom: Incidence, risks, control measures and review of the zoonotic aspects of bovine tuberculosis. Tuberculosis (Edinb), 86, 77–109.
  • De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y. (2010). Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol, 10, 63.
  • Dell’Isola B, Poyart C, Goulet O, Mougenot JF, Sadoun-Journo E, Brousse N, Schmitz J, Ricour C, Berche P. (1994). Detection of Mycobacterium paratuberculosis by polymerase chain reaction in children with Crohn’s disease. J Infect Dis, 169, 449–451.
  • Doherty TM, Wallis RS, Zumla A. (2009). Biomarkers of disease activity, cure, and relapse in tuberculosis. Clin Chest Med, 30, 783–96, x.
  • Douarre PE, Cashman W, Buckley J, Coffey A, O’Mahony JM. (2010). Isolation and detection of Mycobacterium avium subsp. paratuberculosis (MAP) from cattle in Ireland using both traditional culture and molecular based methods. Gut Pathog, 2, 11.
  • Dow CT, Ellingson JL. (2011). Detection of Mycobacterium avium ss. paratuberculosis in Blau Syndrome tissues. Autoimmune Dis, 2011, 127692.
  • Dumonceau JM, Van Gossum A, Adler M, Fonteyne PA, Van Vooren JP, Deviere J, Portaels F. (1996). No Mycobacterium paratuberculosis found in Crohn’s disease using polymerase chain reaction. Dig Dis Sci, 41, 421–426.
  • Dunn JR, Kaneene JB, Grooms DL, Bolin SR, Bolin CA, Bruning-Fann CS. (2005). Effects of positive results for Mycobacterium avium subsp paratuberculosis as determined by microbial culture of feces or antibody ELISA on results of caudal fold tuberculin test and interferon-gamma assay for tuberculosis in cattle. J Am Vet Med Assoc, 226, 429–435.
  • Dvorak AM, Dickersin GR. (1979). Crohn’s disease: electron microscopic studies. Pathol Annu, 14 Pt 2, 259–306.
  • Dvorska L, Bull TJ, Bartos M, Matlova L, Svastova P, Weston RT, Kintr J, Parmova I, Van Soolingen D, Pavlik I. (2003). A standardised restriction fragment length polymorphism (RFLP) method for typing Mycobacterium avium isolates links IS901 with virulence for birds. J Microbiol Methods, 55, 11–27.
  • Eamens GJ, Whittington RJ, Marsh IB, Turner MJ, Saunders V, Kemsley PD, Rayward D. (2000). Comparative sensitivity of various faecal culture methods and ELISA in dairy cattle herds with endemic Johne’s disease. Vet Microbiol, 77, 357–367.
  • Ebert EC, Bhatt BD, Liu S, Das KM. (1991). Induction of suppressor cells by Mycobacterium paratuberculosis antigen in inflammatory bowel disease. Clin Exp Immunol, 83, 320–325.
  • Economou M, Zambeli E, Michopoulos S. (2009). Incidence and prevalence of Crohn’s disease and its etiological influences. Ann Gastroenterol, 22, 158–167.
  • Ellingson JL, Cheville JC, Brees D, Miller JM, Cheville NF. (2003). Absence of Mycobacterium avium subspecies paratuberculosis components from Crohn’s disease intestinal biopsy tissues. Clin Med Res, 1, 217–226.
  • Ellingson JL, Anderson JL, Koziczkowski JJ, Radcliff RP, Sloan SJ, Allen SE, Sullivan NM. (2005). Detection of viable Mycobacterium avium subsp. paratuberculosis in retail pasteurized whole milk by two culture methods and PCR. J Food Prot, 68, 966–972.
  • Elsaghier A, Prantera C, Moreno C, Ivanyi J. (1992). Antibodies to Mycobacterium paratuberculosis–specific protein antigens in Crohn’s disease. Clin Exp Immunol, 90, 503–508.
  • Eltholth MM, Marsh VR, Van Winden S, Guitian FJ. (2009). Contamination of food products with Mycobacterium avium paratuberculosis: a systematic review. J Appl Microbiol, 107, 1061–1071.
  • Engel MA, Neurath MF. (2010). New pathophysiological insights and modern treatment of IBD. J Gastroenterol, 45, 571–583.
  • Englund S, Bölske G, Johansson KE. (2002). An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis. FEMS Microbiol Lett, 209, 267–271.
  • Euzéby JP. (2011). List of prokaryotic names with standing in nomenclature. Available at: http://www.bacterio.cict.fr/
  • Feller M, Huwiler K, Schoepfer A, Shang A, Furrer H, Egger M. (2010). Long-term antibiotic treatment for Crohn’s disease: systematic review and meta-analysis of placebo-controlled trials. Clin Infect Dis, 50, 473–480.
  • Feller M, Huwiler K, Stephan R, Altpeter E, Shang A, Furrer H, Pfyffer GE, Jemmi T, Baumgartner A, Egger M. (2007). Mycobacterium avium subspecies paratuberculosis and Crohn’s disease: a systematic review and meta-analysis. Lancet Infect Dis, 7, 607–613.
  • Ferrouillet C, Wells SJ, Hartmann WL, Godden SM, Carrier J. (2009). Decrease of Johne’s disease prevalence and incidence in six Minnesota, USA, dairy cattle herds on a long-term management program. Prev Vet Med, 88, 128–137.
  • Fidler HM, Thurrell W, Johnson NM, Rook GA, McFadden JJ. (1994). Specific detection of Mycobacterium paratuberculosis DNA associated with granulomatous tissue in Crohn’s disease. Gut, 35, 506–510.
  • Flores LL, Pai M, Colford JM Jr, Riley LW. (2005). In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression. BMC Microbiol, 5, 55.
  • Franchi L, Warner N, Viani K, Nuñez G. (2009). Function of Nod-like receptors in microbial recognition and host defense. Immunol Rev, 227, 106–128.
  • Frank DN, Pace NR. (2008). Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol, 24, 4–10.
  • Frank TS, Cook SM. (1996). Analysis of paraffin sections of Crohn’s disease for Mycobacterium paratuberculosis using polymerase chain reaction. Mod Pathol, 9, 32–35.
  • Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S, Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, Wijmenga C, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Cohen A, Colombel JF, Cottone M, Stronati L, Denson T, De Vos M, D’Inca R, Dubinsky M, Edwards C, Florin T, Franchimont D, Gearry R, Glas J, Van Gossum A, Guthery SL, Halfvarson J, Verspaget HW, Hugot JP, Karban A, Laukens D, Lawrance I, Lemann M, Levine A, Libioulle C, Louis E, Mowat C, Newman W, Panés J, Phillips A, Proctor DD, Regueiro M, Russell R, Rutgeerts P, Sanderson J, Sans M, Seibold F, Steinhart AH, Stokkers PC, Torkvist L, Kullak-Ublick G, Wilson D, Walters T, Targan SR, Brant SR, Rioux JD, D’Amato M, Weersma RK, Kugathasan S, Griffiths AM, Mansfield JC, Vermeire S, Duerr RH, Silverberg MS, Satsangi J, Schreiber S, Cho JH, Annese V, Hakonarson H, Daly MJ, Parkes M. (2010). Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat Genet, 42, 1118–1125.
  • Fraune S, Abe Y, Bosch TC. (2009). Disturbing epithelial homeostasis in the metazoan Hydra leads to drastic changes in associated microbiota. Environ Microbiol, 11, 2361–2369.
  • Friswell M, Campbell B, Rhodes J. (2010). The role of bacteria in the pathogenesis of inflammatory bowel disease. Gut Liver, 4, 295–306.
  • Fujikane T, Fujiuchi S, Yamazaki Y, Sato M, Yamamoto Y, Takeda A, Nishigaki Y, Fujita Y, Shimizu T. (2005). Efficacy and outcomes of clarithromycin treatment for pulmonary MAC disease. Int J Tuberc Lung Dis, 9, 1281–1287.
  • Fujita H, Eishi Y, Ishige I, Saitoh K, Takizawa T, Arima T, Koike M. (2002). Quantitative analysis of bacterial DNA from Mycobacteria spp., Bacteroides vulgatus, and Escherichia coli in tissue samples from patients with inflammatory bowel diseases. J Gastroenterol, 37, 509–516.
  • Gill CO, Saucier L, Meadus WJ. (2011). Mycobacterium avium subsp. paratuberculosis in dairy products, meat, and drinking water. J Food Prot, 74, 480–499.
  • Gillevet P, Sikaroodi M, Keshavarzian A, Mutlu EA. (2010). Quantitative assessment of the human gut microbiome using multitag pyrosequencing. Chem Biodivers, 7, 1065–1075.
  • Gitlin L, Biesecker J. (2007). Australian Crohn’s antibiotic study opens new horizons. Gastroenterology, 133, 1743–4; author reply 1745.
  • Glanemann B, Schönenbrücher H, Bridger N, Abdulmawjood A, Neiger R, Bülte M. (2008). Detection of Mycobacterium avium subspecies paratuberculosis–specific DNA by PCR in intestinal biopsies of dogs. J Vet Intern Med, 22, 1090–1094.
  • Glassroth J. (2008). Pulmonary disease due to nontuberculous mycobacteria. Chest, 133, 243–251.
  • Golan L, Livneh-Kol A, Gonen E, Yagel S, Rosenshine I, Shpigel NY. (2009). Mycobacterium avium paratuberculosis invades human small-intestinal goblet cells and elicits inflammation. J Infect Dis, 199, 350–354.
  • Golden MP, Vikram HR. (2005). Extrapulmonary tuberculosis: an overview. Am Fam Physician, 72, 1761–1768.
  • Goodgame RW, Kimball K, Akram S, Ike E, Ou CN, Sutton F, Graham D. (2001). Randomized controlled trial of clarithromycin and ethambutol in the treatment of Crohn’s disease. Aliment Pharmacol Ther, 15, 1861–1866.
  • Gordon SV, Bottai D, Simeone R, Stinear TP, Brosch R. (2009). Pathogenicity in the tubercle bacillus: molecular and evolutionary determinants. Bioessays, 31, 378–388.
  • Graham DY, Markesich DC, Yoshimura HH. (1988). Letter. Digestive Diseases and Sciences, 33.
  • Grant IR. (2005). Zoonotic potential of Mycobacterium avium ssp. paratuberculosis: the current position. J Appl Microbiol, 98, 1282–1293.
  • Greco S, Girardi E, Navarra A, Saltini C. (2006). Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis. Thorax, 61, 783–790.
  • Green EP, Tizard ML, Moss MT, Thompson J, Winterbourne DJ, McFadden JJ, Hermon-Taylor J. (1989). Sequence and characteristics of IS900, an insertion element identified in a human Crohn’s disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res, 17, 9063–9073.
  • Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, Holland SM, Horsburgh R, Huitt G, Iademarco MF, Iseman M, Olivier K, Ruoss S, von Reyn CF, Wallace RJ Jr, Winthrop K; ATS Mycobacterial Diseases Subcommittee; American Thoracic Society; Infectious Disease Society of America. (2007). An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med, 175, 367–416.
  • Gui GP, Thomas PR, Tizard ML, Lake J, Sanderson JD, Hermon-Taylor J. (1997). Two-year-outcomes analysis of Crohn’s disease treated with rifabutin and macrolide antibiotics. J Antimicrob Chemother, 39, 393–400.
  • Gwozdz JM, Thompson KG, Manktelow BW. (2001). Lymphocytic neuritis of the ileum in sheep with naturally acquired and experimental paratuberculosis. J Comp Pathol, 124, 317–320.
  • Hampson SJ, Parker MC, Saverymuttu SH, Joseph AE, McFadden JJ, Hermon-Taylor J. (1989). Quadruple antimycobacterial chemotherapy in Crohn’s disease: results at 9 months of a pilot study in 20 patients. Aliment Pharmacol Ther, 3, 343–352.
  • Hampson SJ, Portaels F, Thompson J, Green EP, Moss MT, Hermon-Taylor J, McFadden JJ. (1989). DNA probes demonstrate a single highly conserved strain of Mycobacterium avium infecting AIDS patients. Lancet, 1, 65–68.
  • Hansen R, Thomson JM, El-Omar EM, Hold GL. (2010). The role of infection in the aetiology of inflammatory bowel disease. J Gastroenterol, 45, 266–276.
  • Harada A, Ohkusa T, Kushima K, Sakamoto M, Benno Y, Beppu K, Shibuya T, Sakamoto N, Watanabe S. (2008). Identification of bacteria from blood in febrile patients with ulcerative colitis by terminal restriction fragment length polymorphism profile analysis of 16S rRNA gene. Scand J Gastroenterol, 43, 423–430.
  • Harris NB, Barletta RG. (2001). Mycobacterium avium subsp. paratuberculosis in veterinary medicine. Clin Microbiol Rev, 14, 489–512.
  • Hendrick SH, Kelton DF, Leslie KE, Lissemore KD, Archambault M, Bagg R, Dick P, Duffield TF. (2006). Efficacy of monensin sodium for the reduction of fecal shedding of Mycobacterium avium subsp. paratuberculosis in infected dairy cattle. Prev Vet Med, 75, 206–220.
  • Hermon-Taylor J, Barnes N, Clarke C, Finlayson C. (1998). Mycobacterium paratuberculosis cervical lymphadenitis, followed five years later by terminal ileitis similar to Crohn’s disease. BMJ, 316, 449–453.
  • Hill AB. (1965). the environment and disease: association or causation? Proc R Soc Med, 58, 295–300.
  • Hornick DB, Dayton CS, Bedell GN, Fick RB Jr. (1988). Nontuberculous mycobacterial lung disease. Substantiation of a less aggressive approach. Chest, 93, 550–555.
  • Hottat F, Coene M, Cocito C. (1988). DNA methylation in leprosy-associated bacteria: Mycobacterium leprae and Corynebacterium tuberculostearicum. Med Microbiol Immunol, 177, 33–45.
  • Huatian G, Qin O, Hong B. (1997). Mycobacterium paratuberculosis in the intestine of patients with Crohn’s disease. Chin J Intern Med, 36, 228–230.
  • Hulten K, Karttunen TJ, El-Zimaity HM, Naser SA, Collins MT, Graham DY, El-Zaatari FA. (2000). Identification of cell wall deficient forms of M. avium subsp. paratuberculosis in paraffin embedded tissues from animals with Johne’s disease by in situ hybridization. J Microbiol Methods, 42, 185–195.
  • Hulten K, Karttunen TJ, El-Zimaity HM, Naser SA, Almashhrawi A, Graham DY, El-Zaatari FA. (2000). In situ hybridization method for studies of cell wall deficient M. paratuberculosis in tissue samples. Vet Microbiol, 77, 513–518.
  • Hulten K, El-Zimaity HM, Karttunen TJ, Almashhrawi A, Schwartz MR, Graham DY, El-Zaatari FA. (2001). Detection of Mycobacterium avium subspecies paratuberculosis in Crohn’s diseased tissues by in situ hybridization. Am J Gastroenterol, 96, 1529–1535.
  • Hume G, Radford-Smith GL. (2002). The pathogenesis of Crohn’s disease in the 21st century. Pathology, 34, 561–567.
  • Ibbotson JP, Lowes JR, Chahal H, Gaston JS, Life P, Kumararatne DS, Sharif H, Alexander-Williams J, Allan RN. (1992). Mucosal cell-mediated immunity to mycobacterial, enterobacterial and other microbial antigens in inflammatory bowel disease. Clin Exp Immunol, 87, 224–230.
  • Imirzalioglu C, Dahmen H, Hain T, Billion A, Kuenne C, Chakraborty T, Domann E. (2011). Highly specific and quick detection of Mycobacterium avium subsp. paratuberculosis in feces and gut tissue of cattle and humans by multiple real-time PCR assays. J Clin Microbiol, 49, 1843–1852.
  • Jaravata CV, Smith WL, Rensen GJ, Ruzante J, Cullor JS. (2007). Survey of ground beef for the detection of Mycobacterium avium paratuberculosis. Foodborne Pathog Dis, 4, 103–106.
  • Jayarao B, Shreekumar P. (1999). A meta-analytic study of the detection of Mycobacterium avium subsp. paratuberculosis from patients with Crohn’s disease. Internet Med J, Available at: http://www.medjournal.com/archives/1999/19990726-crohns.htm
  • Jeyanathan M, Alexander DC, Turenne CY, Girard C, Behr MA. (2006). Evaluation of in situ methods used to detect Mycobacterium avium subsp. paratuberculosis in samples from patients with Crohn’s disease. J Clin Microbiol, 44, 2942–2950.
  • Jeyanathan M, Boutros-Tadros O, Radhi J, Semret M, Bitton A, Behr MA. (2007). Visualization of Mycobacterium avium in Crohn’s tissue by oil-immersion microscopy. Microbes Infect, 9, 1567–1573.
  • Johansen TB, Djønne B, Jensen MR, Olsen I. (2005). Distribution of IS1311 and IS1245 in Mycobacterium avium subspecies revisited. J Clin Microbiol, 43, 2500–2502.
  • John LJ, Fromm M, Schulzke JD. (2011). Epithelial barriers in intestinal inflammation. Antioxid Redox Signal, 15, 1255–1270.
  • Johnson CS, Wannemuehler MJ, Hostetter JM. (2011). Persistent enteric mycobacterial infection enhances sensitivity to acute mucosal injury. Exp Biol Med (Maywood), 236, 36–43.
  • Jones PH, Farver TB, Beaman B, Cetinkaya B, Morgan KL. (2006). Crohn’s disease in people exposed to clinical cases of bovine paratuberculosis. Epidemiol Infect, 134, 49–56.
  • Juarez E, Nuñez C, Sada E, Ellner JJ, Schwander SK, Torres M. (2010). Differential expression of Toll-like receptors on human alveolar macrophages and autologous peripheral monocytes. Respir Res, 11, 2.
  • Juste RA, Garrido JM, Geijo M, Elguezabal N, Aduriz G, Atxaerandio R, Sevilla I. (2005). Comparison of blood polymerase chain reaction and enzyme-linked immunosorbent assay for detection of Mycobacterium avium subsp. paratuberculosis infection in cattle and sheep. J Vet Diagn Invest, 17, 354–359.
  • Juste RA, Elguezabal N, Pavón A, Garrido JM, Geijo M, Sevilla I, Cabriada JL, Tejada A, García-Campos F, Casado R, Ochotorena I, Izeta A. (2009). Association between Mycobacterium avium subsp. paratuberculosis DNA in blood and cellular and humoral immune response in inflammatory bowel disease patients and controls. Int J Infect Dis, 13, 247–254.
  • Juste RA, Elguezabal N, Garrido JM, Pavon A, Geijo MV, Sevilla I, Cabriada JL, Tejada A, García-Campos F, Casado R, Ochotorena I, Izeta A, Greenstein RJ. (2008). On the prevalence of M. avium subspecies paratuberculosis DNA in the blood of healthy individuals and patients with inflammatory bowel disease. PLoS ONE, 3, e2537.
  • Kallinowski F, Wassmer A, Hofmann MA, Harmsen D, Heesemann J, Karch H, Herfarth C, Buhr HJ. (1998). Prevalence of enteropathogenic bacteria in surgically treated chronic inflammatory bowel disease. Hepatogastroenterology, 45, 1552–1558.
  • Kanazawa K, Haga Y, Funakoshi O, Nakajima H, Munakata A, Yoshida Y. (1999). Absence of Mycobacterium paratuberculosis DNA in intestinal tissues from Crohn’s disease by nested polymerase chain reaction. J Gastroenterol, 34, 200–206.
  • Kappelman MD, Rifas-Shiman SL, Kleinman K, Ollendorf D, Bousvaros A, Grand RJ, Finkelstein JA. (2007). The prevalence and geographic distribution of Crohn’s disease and ulcerative colitis in the United States. Clin Gastroenterol Hepatol, 5, 1424–1429.
  • Kappelman MD, Porter CQ, Galanko JA, Rifas-Shiman SL, Ollendorf DA, Sandler RS, Finkelstein JA. (2011). Utilization of healthcare resources by U.S. children and adults with inflammatory bowel disease. Inflamm Bowel Dis, 17, 62–68.
  • Kar HK, Sharma P, Bhardwaj M. (2009). Borderline tuberculoid leprosy with upgrading Type 1 reaction in a HIV seropositive patient, after antiretroviral therapy: an immune reconstitution inflammatory syndrome. Lepr Rev, 80, 85–88.
  • Kasperbauer SH, Daley CL. (2008). Diagnosis and treatment of infections due to Mycobacterium avium complex. Semin Respir Crit Care Med, 29, 569–576.
  • Kawai T, Akira S. (2009). The roles of TLRs, RLRs and NLRs in pathogen recognition. Int Immunol, 21, 317–337.
  • Keller AP, Beggs ML, Amthor B, Bruns F, Meissner P, Haas WH. (2002). Evidence of the presence of IS1245 and IS1311 or closely related insertion elements in nontuberculous mycobacteria outside of the Mycobacterium avium complex. J Clin Microbiol, 40, 1869–1872.
  • Kennedy KJ, Tetlow L. (2008). Test and teach. Chronic soft tissue inflammation following accidental inoculation with a sheep vaccine. Diagnosis: Immune response to mineral oil and Mycobacterium antigens in vaccine strain (Gudair) of Mycobacterium avium subsp. paratuberculosis. Pathology, 40, 711–713.
  • Khan KJ, Ullman TA, Ford AC, Abreu MT, Abadir A, Abadir A, Marshall JK, Talley NJ, Moayyedi P. (2011). Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol, 106, 661–673.
  • Kirkpatrick BW, Shi X, Shook GE, Collins MT. (2010). Whole-Genome association analysis of susceptibility to paratuberculosis in holstein cattle. Anim Genet, 42, 149–160.
  • Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, Catto-Smith AG, Cameron DJ, Bishop RF. (2009). Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn’s disease. Inflamm Bowel Dis, 15, 1643–1655.
  • Klanicova B, Slana I, Vondruskova H, Kaevska M, Pavlik I. (2011). Real-time quantitative PCR detection of Mycobacterium avium subspecies in meat products. J Food Prot, 74, 636–640.
  • Kluge JP, Merkal RS, Monlux WS, Larsen AB, Kopecky KE, Ramsey FK, Lehmann RP. (1968). Experimental paratuberculosis in sheep after oral, intratracheal, or intravenous inoculation lesions and demonstration of etiologic agent. Am J Vet Res, 29, 953–962.
  • Knösel T, Schewe C, Petersen N, Dietel M, Petersen I. (2009). Prevalence of infectious pathogens in Crohn’s disease. Pathol Res Pract, 205, 223–230.
  • Koch R. (1884). Die Aetiologie der Tuberkulose. Mittheilungen aus den Kaiserlichen Gesundheitsamte, 2, 1–88.
  • Koets A, Santema W, Mertens H, Oostenrijk D, Keestra M, Overdijk M, Labouriau R, Franken P, Frijters A, Nielen M, Rutten V. (2010). Susceptibility to paratuberculosis infection in cattle is associated with single nucleotide polymorphisms in Toll-like receptor 2 which modulate immune responses against Mycobacterium avium subspecies paratuberculosis. Prev Vet Med, 93, 305–315.
  • Korou LM, Liandris E, Gazouli M, Ikonomopoulos J. (2010). Investigation of the association of the SLC11A1 gene with resistance/sensitivity of goats (Capra hircus) to paratuberculosis. Vet Microbiol, 144, 353–358.
  • Krishnan MY, Manning EJ, Collins MT. (2009). Comparison of three methods for susceptibility testing of Mycobacterium avium subsp. paratuberculosis to 11 antimicrobial drugs. J Antimicrob Chemother, 64, 310–316.
  • Laffineur G, Lescut D, Vincent P, Quandalle P, Wurtz A, Colombel JF. (1992). [Bacterial translocation in Crohn disease]. Gastroenterol Clin Biol, 16, 777–781.
  • Lamont EA, Sreevatsan S. (2010). Paradigm redux–Mycobacterium avium subspecies paratuberculosis-macrophage interactions show clear variations between bovine and human physiological body temperatures. Microb Pathog, 48, 143–149.
  • Lawlor G, Moss AC. (2010). Cytomegalovirus in inflammatory bowel disease: pathogen or innocent bystander? Inflamm Bowel Dis, 16, 1620–1627.
  • Lee A, Griffiths TA, Parab RS, King RK, Dubinsky MC, Urbanski SJ, Wrobel I, Rioux KP. (2011). Association of Mycobacterium avium subspecies paratuberculosis with Crohn Disease in pediatric patients. J Pediatr Gastroenterol Nutr, 52, 170–174.
  • Lee TW, Fedorak RN. (2010). Tumor necrosis factor-a monoclonal antibodies in the treatment of inflammatory bowel disease: clinical practice pharmacology. Gastroenterol Clin North Am, 39, 543–557.
  • Lees CW, Satsangi J. (2009). Genetics of inflammatory bowel disease: implications for disease pathogenesis and natural history. Expert Rev Gastroenterol Hepatol, 3, 513–534.
  • Leiper K, Morris AI, Rhodes JM. (2000). Open label trial of oral clarithromycin in active Crohn’s disease. Aliment Pharmacol Ther, 14, 801–806.
  • Leong RW, Armuzzi A, Ahmad T, Wong ML, Tse P, Jewell DP, Sung JJ. (2003). NOD2/CARD15 gene polymorphisms and Crohn’s disease in the Chinese population. Aliment Pharmacol Ther, 17, 1465–1470.
  • Levesque BG, Pai R, Cartwright CA. (2009). Crohn’s colitis complicated by cytomegalovirus infection. Dig Dis Sci, 54, 1864–1867.
  • Lewis K, Lutgendorff F, Phan V, Söderholm JD, Sherman PM, McKay DM. (2010). Enhanced translocation of bacteria across metabolically stressed epithelia is reduced by butyrate. Inflamm Bowel Dis, 16, 1138–1148.
  • Li L, Bannantine JP, Zhang Q, Amonsin A, May BJ, Alt D, Banerji N, Kanjilal S, Kapur V. (2005). The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA, 102, 12344–12349.
  • Lidar M, Langevitz P, Shoenfeld Y. (2009). The role of infection in inflammatory bowel disease: initiation, exacerbation and protection. Isr Med Assoc J, 11, 558–563.
  • Lipton JE, Barash DP. (2007). Flawed Australian CD study does not end MAP controversy. Gastroenterology, 133, 1742; author reply 1745–1742; author reply 1746.
  • Lisby G, Andersen J, Engbaek K, Binder V. (1994). Mycobacterium paratuberculosis in intestinal tissue from patients with Crohn’s disease demonstrated by a nested primer polymerase chain reaction. Scand J Gastroenterol, 29, 923–929.
  • Liu Y, van Kruiningen HJ, West AB, Cartun RW, Cortot A, Colombel JF. (1995). Immunocytochemical evidence of Listeria, Escherichia coli, and Streptococcus antigens in Crohn’s disease. Gastroenterology, 108, 1396–1404.
  • Loftus EV Jr, Silverstein MD, Sandborn WJ, Tremaine WJ, Harmsen WS, Zinsmeister AR. (1998). Crohn’s disease in Olmsted County, Minnesota, 1940–1993: incidence, prevalence, and survival. Gastroenterology, 114, 1161–1168.
  • Lowe AM, Yansouni CP, Behr MA. (2008). Causality and gastrointestinal infections: Koch, Hill, and Crohn’s. Lancet Infect Dis, 8, 720–726.
  • Lozano-Leon A, Barreiro-de Acosta M, Domínguez-Munoz JE. (2006). Absence of Mycobacterium avium subspecies paratuberculosis in Crohn’s disease patients. Inflamm Bowel Dis, 12, 1190–1192.
  • Lund BM, Gould GW, Rampling AM. (2002). Pasteurization of milk and the heat resistance of Mycobacterium avium subsp. paratuberculosis: a critical review of the data. Int J Food Microbiol, 77, 135–145.
  • Macpherson A, Khoo UY, Forgacs I, Philpott-Howard J, Bjarnason I. (1996). Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria. Gut, 38, 365–375.
  • Man SM, Kaakoush NO, Mitchell HM. (2011). The role of bacteria and pattern-recognition receptors in Crohn’s disease. Nat Rev Gastroenterol Hepatol, 8, 152–168.
  • Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J. (2006). Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut, 55, 205–211.
  • Manning EJ, Collins MT. (2001). Mycobacterium avium subsp. paratuberculosis: pathogen, pathogenesis and diagnosis. Rev - Off Int Epizoot, 20, 133–150.
  • Markesich DC, Graham DY, Yoshimura HH. (1988). Progress in culture and subculture of spheroplasts and fastidious acid-fast bacilli isolated from intestinal tissues. J Clin Microbiol, 26, 1600–1603.
  • Marks DJ, Rahman FZ, Sewell GW, Segal AW. (2010). Crohn’s disease: an immune deficiency state. Clin Rev Allergy Immunol, 38, 20–31.
  • Marshall BJ. (2002). The discovery that Helicobacter pylori, a spiral bacterium, caused peptic ulcer disease. Carlton, Victoria, Australia: Blackwell Science Asia.
  • Marshall BJ, Armstrong JA, McGechie DB, Glancy RJ. (1985). Attempt to fulfil Koch’s postulates for pyloric Campylobacter. Med J Aust, 142, 436–439.
  • Marteau P. (2009). Bacterial flora in inflammatory bowel disease. Dig Dis, 27 Suppl 1, 99–103.
  • Martineau AR, Honecker FU, Wilkinson RJ, Griffiths CJ. (2007). Vitamin D in the treatment of pulmonary tuberculosis. J Steroid Biochem Mol Biol, 103, 793–798.
  • Mayer L. (2010). Evolving paradigms in the pathogenesis of IBD. J Gastroenterol, 45, 9–16.
  • McClure HM, Chiodini RJ, Anderson DC, Swenson RB, Thayer WR, Coutu JA. (1987). Mycobacterium paratuberculosis infection in a colony of stumptail macaques (Macaca arctoides). J Infect Dis, 155, 1011–1019.
  • McFadden JJ, Fidler HM. (1996). Mycobacteria as possible causes of sarcoidosis and Crohn’s disease. Soc Appl Bacteriol Symp Ser, 25, 47S–52S.
  • McFadden JJ, Butcher PD, Chiodini R, Hermon-Taylor J. (1987). Crohn’s disease-isolated mycobacteria are identical to Mycobacterium paratuberculosis, as determined by DNA probes that distinguish between mycobacterial species. J Clin Microbiol, 25, 796–801.
  • McGrath EE, Blades Z, McCabe J, Jarry H, Anderson PB. (2010). Nontuberculous mycobacteria and the lung: from suspicion to treatment. Lung, 188, 269–282.
  • McGuckin MA, Eri R, Simms LA, Florin TH, Radford-Smith G. (2009). Intestinal barrier dysfunction in inflammatory bowel diseases. Inflamm Bowel Dis, 15, 100–113.
  • Mendoza JL, San-Pedro A, Culebras E, Cíes R, Taxonera C, Lana R, Urcelay E, de la Torre F, Picazo JJ, Díaz-Rubio M. (2010). High prevalence of viable Mycobacterium avium subspecies paratuberculosis in Crohn’s disease. World J Gastroenterol, 16, 4558–4563.
  • Merkal RS, Larsen AB. (1973). Clofazimine treatment of cows naturally infected with Mycobacterium paratuberculosis. Am J Vet Res, 34, 27–28.
  • Merkal RS, Kopecky KE, Larsen AB. (1970). Immunologic mechanisms in bovine paratuberculosis. Am J Vet Res, 31, 475–485.
  • Merkal RS, Kluge JP, Monlux WS, Larsen AB, Kopecky KE, Quinn LY, Lehmann RP. (1968). Experimental paratuberculosis in sheep after oral, intratracheal, or intravenous inoculation: histochemical localization of hydrolase activities. Am J Vet Res, 29, 985–994.
  • Merkal RS, Larsen AB, Kopecky KE, Kluge JP, Monlux WS, Lehmann RP, Quinn LY. (1968). Experimental paratuberculosis in sheep after oral, intratracheal, or intravenous inoculation: serologic and intradermal tests. Am J Vet Res, 29, 963–969.
  • Mijs W, de Haas P, Rossau R, Van der Laan T, Rigouts L, Portaels F, van Soolingen D. (2002). Molecular evidence to support a proposal to reserve the designation Mycobacterium avium subsp. avium for bird-type isolates and ‘M. avium subsp. hominissuis’ for the human/porcine type of M. avium. Int J Syst Evol Microbiol, 52, 1505–1518.
  • Mikula C. (2000). Measles vaccination a risk factor for inflammatory bowel disease? Gastroenterol Nurs, 23, 168–171.
  • Millar D, Ford J, Sanderson J, Withey S, Tizard M, Doran T, Hermon-Taylor J. (1996). IS900 PCR to detect Mycobacterium paratuberculosis in retail supplies of whole pasteurized cows’ milk in England and Wales. Appl Environ Microbiol, 62, 3446–3452.
  • Minozzi G, Buggiotti L, Stella A, Strozzi F, Luini M, Williams JL. (2010). Genetic loci involved in antibody response to Mycobacterium avium ssp. paratuberculosis in cattle. PLoS ONE, 5, e11117.
  • Misch EA, Berrington WR, Vary JC Jr, Hawn TR. (2010). Leprosy and the human genome. Microbiol Mol Biol Rev, 74, 589–620.
  • Mishina D, Katsel P, Brown ST, Gilberts EC, Greenstein RJ. (1996). On the etiology of Crohn disease. Proc Natl Acad Sci USA, 93, 9816–9820.
  • Möbius P, Luyven G, Hotzel H, Köhler H. (2008). High genetic diversity among Mycobacterium avium subsp. paratuberculosis strains from German cattle herds shown by combination of IS900 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing. J Clin Microbiol, 46, 972–981.
  • Möbius P, Lentzsch P, Moser I, Naumann L, Martin G, Köhler H. (2006). Comparative macrorestriction and RFLP analysis of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. hominissuis isolates from man, pig, and cattle. Vet Microbiol, 117, 284–291.
  • Modlin RL. (2010). The innate immune response in leprosy. Curr Opin Immunol, 22, 48–54.
  • Möller M, Hoal EG. (2010). Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis. Tuberculosis (Edinb), 90, 71–83.
  • Molodecky NA, Soon IS, Rabi DM, Ghali WA, Ferris M, Chernoff G, Benchimol EI, Panaccione R, Ghosh S, Barkema HW, Kaplan GG. (2011). Increasing Incidence and Prevalence of the Inflammatory Bowel Diseases with Time, Based on Systematic Review. Gastroenterology [Epub ahead of print]. DOI: 10.1053/j.gastr.2011.10.001
  • Momotani E, Whipple DL, Thiermann AB, Cheville NF. (1988). Role of M cells and macrophages in the entrance of Mycobacterium paratuberculosis into domes of ileal Peyer’s patches in calves. Vet Pathol, 25, 131–137.
  • Montoya D, Modlin RL. (2010). Learning from leprosy: insight into the human innate immune response. Adv Immunol, 105, 1–24.
  • Moss MT, Sanderson JD, Tizard ML, Hermon-Taylor J, el-Zaatari FA, Markesich DC, Graham DY. (1992). Polymerase chain reaction detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp silvaticum in long term cultures from Crohn’s disease and control tissues. Gut, 33, 1209–1213.
  • Müller S, Arni S, Varga L, Balsiger B, Hersberger M, Maly F, Seibold F. (2006). Serological and DNA-based evaluation of Chlamydia pneumoniae infection in inflammatory bowel disease. Eur J Gastroenterol Hepatol, 18, 889–894.
  • Murray A, Oliaro J, Schlup MM, Chadwick VS. (1995). Mycobacterium paratuberculosis and inflammatory bowel disease: frequency distribution in serial colonoscopic biopsies using the polymerase chain reaction. Microbios, 83, 217–228.
  • Nacy C, Buckley M. (2008). A report from the American Academy of Microbiology. Mycobacterium avium paratuberculosis: Infrequent Human Pathogen or Public Health Threat? Available at: http://academy.asm.org/images/stories/documents/mycobacteriumaviumparatuberculosis.pdf
  • Nakase H, Nishio A, Tamaki H, Matsuura M, Asada M, Chiba T, Okazaki K. (2006). Specific antibodies against recombinant protein of insertion element 900 of Mycobacterium avium subspecies paratuberculosis in Japanese patients with Crohn’s disease. Inflamm Bowel Dis, 12, 62–69.
  • Naser SA, Ghobrial G, Romero C, Valentine JF. (2004). Culture of Mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn’s disease. Lancet, 364, 1039–1044.
  • Naser SA, Collins MT, Crawford JT, Valentine JF. (2009). Culture of Mycobacterium avium subspecies paratuberculosis (MAP) from the Blood of Patients with Crohn’s disease: A Follow-Up Blind Multi Center Investigation. Open Inflamm J, 2, 22–23.
  • Naser SA, Hulten K, Shafran I, Graham DY, El-Zaatari FA. (2000). Specific seroreactivity of Crohn’s disease patients against p35 and p36 antigens of M. avium subsp. paratuberculosis. Vet Microbiol, 77, 497–504.
  • Naser SA, Shafran I, Schwartz D, El-Zaatari F, Biggerstaff J. (2002). In situ identification of mycobacteria in Crohn’s disease patient tissue using confocal scanning laser microscopy. Mol Cell Probes, 16, 41–48.
  • Naser SA, Felix J, Liping H, Romero C, Naser N, Walsh A, Safranek W. (1999). Occurrence of the IS900 gene in Mycobacterium avium complex derived from HIV patients. Mol Cell Probes, 13, 367–372.
  • Nerich V, Jantchou P, Boutron-Ruault MC, Monnet E, Weill A, Vanbockstael V, Auleley GR, Balaire C, Dubost P, Rican S, Allemand H, Carbonnel F. (2011). Low exposure to sunlight is a risk factor for Crohn’s disease. Aliment Pharmacol Ther, 33, 940–945.
  • Nielsen SS, Toft N. (2008). Ante mortem diagnosis of paratuberculosis: a review of accuracies of ELISA, interferon-gamma assay and faecal culture techniques. Vet Microbiol, 129, 217–235.
  • NIH Consensus Conference. (1994). Helicobacter pylori in peptic ulcer disease. NIH Consensus Development Panel on Helicobacter pylori in Peptic Ulcer Disease. JAMA, 272, 65–69.
  • Norman G. (2011). Chaos, complexity and complicatedness: lessons from rocket science. Med Educ, 45, 549–559.
  • Ohkusa T, Sato N. (2005). Antibacterial and antimycobacterial treatment for inflammatory bowel disease. J Gastroenterol Hepatol, 20, 340–351.
  • Olsen I, Wiker HG, Johnson E, Langeggen H, Reitan LJ. (2001). Elevated antibody responses in patients with Crohn’s disease against a 14-kDa secreted protein purified from Mycobacterium avium subsp. paratuberculosis. Scand J Immunol, 53, 198–203.
  • Olsen I, Tollefsen S, Aagaard C, Reitan LJ, Bannantine JP, Andersen P, Sollid LM, Lundin KE. (2009). Isolation of Mycobacterium avium subspecies paratuberculosis reactive CD4 T cells from intestinal biopsies of Crohn’s disease patients. PLoS ONE, 4, e5641.
  • Onwuamaegbu ME, Belcher RA, Soare C. (2005). Cell wall-deficient bacteria as a cause of infections: a review of the clinical significance. J Int Med Res, 33, 1–20.
  • Osterstock JB, Fosgate GT, Norby B, Manning EJ, Collins MT, Roussel AJ. (2007). Contribution of environmental mycobacteria to false-positive serum ELISA results for paratuberculosis. J Am Vet Med Assoc, 230, 896–901.
  • Packey CD, Sartor RB. (2009). Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis, 22, 292–301.
  • Pagnini C, Corleto VD, Mangoni ML, Pilozzi E, Torre MS, Marchese R, Carnuccio A, Giulio ED, Delle Fave G. (2011). Alteration of local microflora and a-defensins hyper-production in colonic adenoma mucosa. J Clin Gastroenterol, 45, 602–610.
  • Panés J, Gomollón F, Taxonera C, Hinojosa J, Clofent J, Nos P. (2007). Crohn’s disease: a review of current treatment with a focus on biologics. Drugs, 67, 2511–2537.
  • Parent K, Mitchell PD. (1976). Bacterial variants: etiologic agent in Crohn’s disease? Gastroenterology, 71, 365–368.
  • Parrish NM, Radcliff RP, Brey BJ, Anderson JL, Clark DL Jr, Koziczkowski JJ, Ko CG, Goldberg ND, Brinker DA, Carlson RA, Dick JD, Ellingson JL. (2009). Absence of mycobacterium avium subsp. paratuberculosis in Crohn’s patients. Inflamm Bowel Dis, 15, 558–565.
  • Patterson CJ, LaVenture M, Hurley SS, Davis JP. (1988). Accidental self-inoculation with Mycobacterium paratuberculosis bacterin (Johne’s bacterin) by veterinarians in Wisconsin. J Am Vet Med Assoc, 192, 1197–1199.
  • Pavlik I, Svastova P, Bartl J, Dvorska L, Rychlik I. (2000). Relationship between IS901 in the Mycobacterium avium complex strains isolated from birds, animals, humans, and the environment and virulence for poultry. Clin Diagn Lab Immunol, 7, 212–217.
  • Persson S, Danielsson D. (1979). On the occurrence of serum antibodies to Bacteroides fragilis and serogroups of E. coli in patients with Crohn’s disease. Scand J Infect Dis Suppl, 19, 61–67.
  • Peyrin-Biroulet L, Lémann M. (2011). Review article: remission rates achievable by current therapies for inflammatory bowel disease. Aliment Pharmacol Ther, 33, 870–879.
  • Peyrin-Biroulet L, Neut C, Colombel JF. (2007). Antimycobacterial therapy in Crohn’s disease: game over? Gastroenterology, 132, 2594–2598.
  • Pickup RW, Rhodes G, Arnott S, Sidi-Boumedine K, Bull TJ, Weightman A, Hurley M, Hermon-Taylor J. (2005). 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. Appl Environ Microbiol, 71, 2130–2139.
  • Pinedo PJ, Buergelt CD, Donovan GA, Melendez P, Morel L, Wu R, Langaee TY, Rae DO. (2009). Association between CARD15/NOD2 gene polymorphisms and paratuberculosis infection in cattle. Vet Microbiol, 134, 346–352.
  • Prantera C, Kohn A, Mangiarotti R, Andreoli A, Luzi C. (1994). Antimycobacterial therapy in Crohn’s disease: results of a controlled, double-blind trial with a multiple antibiotic regimen. Am J Gastroenterol, 89, 513–518.
  • Primm TP, Lucero CA, Falkinham JO 3rd. (2004). Health impacts of environmental mycobacteria. Clin Microbiol Rev, 17, 98–106.
  • 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.
  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J; MetaHIT Consortium. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59–65.
  • Qual DA, Kaneene JB, Varty TJ, Miller R, Thoen CO. (2010). Lack of association between the occurrence of Crohn’s disease and occupational exposure to dairy and beef cattle herds infected with Mycobacterium avium subspecies paratuberculosis. J Dairy Sci, 93, 2371–2376.
  • Quesniaux VF, Jacobs M, Allie N, Grivennikov S, Nedospasov SA, Garcia I, Olleros ML, Shebzukhov Y, Kuprash D, Vasseur V, Rose S, Court N, Vacher R, Ryffel B. (2010). TNF in host resistance to tuberculosis infection. Curr Dir Autoimmun, 11, 157–179.
  • Radomski N, Thibault VC, Karoui C, de Cruz K, Cochard T, Gutiérrez C, Supply P, Biet F, Boschiroli ML. (2010). Determination of genotypic diversity of Mycobacterium avium subspecies from human and animal origins by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat and IS1311 restriction fragment length polymorphism typing methods. J Clin Microbiol, 48, 1026–1034.
  • Raizman EA, Wells SJ, Godden SM, Bey RF, Oakes MJ, Bentley DC, Olsen KE. (2004). The distribution of Mycobacterium avium ssp. paratuberculosis in the environment surrounding Minnesota dairy farms. J Dairy Sci, 87, 2959–2966.
  • Rankin JD. (1955). An attempt to prevent the establishment of Mycobacterium johnei in calves by means of isoniazid alone and in combination with streptomycin. Vet Rec, 66, 550–551.
  • Rath T, Roderfeld M, Blöcher S, Rhode A, Basler T, Akineden Ö, Abdulmawjood A, Halwe JM, Goethe R, Bülte M, Roeb E. (2011). Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP) DNA is not associated with altered MMP expression in ulcerative colitis. BMC Gastroenterol, 11, 34.
  • Ren Z, Turton J, Borody T, Pang G, Clancy R. (2008). Selective Th2 pattern of cytokine secretion in Mycobacterium avium subsp. paratuberculosis infected Crohn’s disease. J Gastroenterol Hepatol, 23, 310–314.
  • Ricanek P, Lothe SM, Szpinda I, Jorde AT, Brackmann S, Perminow G, Jørgensen KK, Rydning A, Vatn MH, Tønjum T; IBSEN II study group. (2010). Paucity of mycobacteria in mucosal bowel biopsies from adults and children with early inflammatory bowel disease. J Crohns Colitis, 4, 561–566.
  • Roffey DM, Wai EK, Bishop P, Kwon BK, Dagenais S. (2010). Causal assessment of occupational sitting and low back pain: results of a systematic review. Spine J, 10, 252–261.
  • Roiz MP, Palenque E, Guerrero C, Garcia MJ. (1995). Use of restriction fragment length polymorphism as a genetic marker for typing Mycobacterium avium strains. J Clin Microbiol, 33, 1389–1391.
  • Romero C, Hamdi A, Valentine JF, Naser SA. (2005). Evaluation of surgical tissue from patients with Crohn’s disease for the presence of Mycobacterium avium subspecies paratuberculosis DNA by in situ hybridization and nested polymerase chain reaction. Inflamm Bowel Dis, 11, 116–125.
  • Rosu V, Ahmed N, Paccagnini D, Gerlach G, Fadda G, Hasnain SE, Zanetti S, Sechi LA. (2009). Specific immunoassays confirm association of Mycobacterium avium subsp. paratuberculosis with type-1 but not type-2 diabetes mellitus. PLoS ONE, 4, e4386.
  • Rothman KJ, Greenland S. (2005). Causation and causal inference in epidemiology. Am J Public Health, 95 Suppl 1, S144–S150.
  • Rowbotham DS, Howdle PD, Trejdosiewicz LK. (1995). Peripheral cell-mediated immune response to mycobacterial antigens in inflammatory bowel disease. Clin Exp Immunol, 102, 456–461.
  • Rowbotham DS, Mapstone NP, Trejdosiewicz LK, Howdle PD, Quirke P. (1995). Mycobacterium paratuberculosis DNA not detected in Crohn’s disease tissue by fluorescent polymerase chain reaction. Gut, 37, 660–667.
  • Roy E, Lowrie DB, Jolles SR. (2007). Current strategies in TB immunotherapy. Curr Mol Med, 7, 373–386.
  • Ruiz-Larrañaga O, Garrido JM, Iriondo M, Manzano C, Molina E, Koets AP, Rutten VP, Juste RA, Estonba A. (2010a). Genetic association between bovine NOD2 polymorphisms and infection by Mycobacterium avium subsp. paratuberculosis in Holstein-Friesian cattle. Anim Genet, 41, 652–655.
  • Ruiz-Larrañaga O, Garrido JM, Manzano C, Iriondo M, Molina E, Gil A, Koets AP, Rutten VP, Juste RA, Estonba A. (2010b). Identification of single nucleotide polymorphisms in the bovine solute carrier family 11 member 1 (SLC11A1) gene and their association with infection by Mycobacterium avium subspecies paratuberculosis. J Dairy Sci, 93, 1713–1721.
  • Ruiz-Larrañaga O, Garrido JM, Iriondo M, Manzano C, Molina E, Montes I, Vazquez P, Koets AP, Rutten VP, Juste RA, Estonba A. (2010c). SP110 as a novel susceptibility gene for Mycobacterium avium subspecies paratuberculosis infection in cattle. J Dairy Sci, 93, 5950–5958.
  • Rutgeerts P, Geboes K, Vantrappen G, Van Isveldt J, Peeters M, Penninckx F, Hiele M. (1992). Rifabutin and ethambutol do not help recurrent Crohn’s disease in the neoterminal ileum. J Clin Gastroenterol, 15, 24–28.
  • Ryan P, Bennett MW, Aarons S, Lee G, Collins JK, O’Sullivan GC, O’Connell J, Shanahan F. (2002). PCR detection of Mycobacterium paratuberculosis in Crohn’s disease granulomas isolated by laser capture microdissection. Gut, 51, 665–670.
  • Salonen A, de Vos WM, Palva A. (2010). Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology (Reading, Engl), 156, 3205–3215.
  • Sanderson JD, Moss MT, Tizard ML, Hermon-Taylor J. (1992). Mycobacterium paratuberculosis DNA in Crohn’s disease tissue. Gut, 33, 890–896.
  • Sasikala M, Reddy DN, Pratap N, Sharma SK, Balkumar PR, Sekaran A, Banerjee R, Reddy DB. (2009). Absence of Mycobacterium avium ss paratuberculosis–specific IS900 sequence in intestinal biopsy tissues of Indian patients with Crohn’s disease. Indian J Gastroenterol, 28, 169–174.
  • Scanu AM, Bull TJ, Cannas S, Sanderson JD, Sechi LA, Dettori G, Zanetti S, Hermon-Taylor J. (2007). Mycobacterium avium subspecies paratuberculosis infection in cases of irritable bowel syndrome and comparison with Crohn’s disease and Johne’s disease: common neural and immune pathogenicities. J Clin Microbiol, 45, 3883–3890.
  • Schirbel A, Fiocchi C. (2010). Inflammatory bowel disease: Established and evolving considerations on its etiopathogenesis and therapy. J Dig Dis, 11, 266–276.
  • Schuller JL, Piket-van Ulsen J, Veeken IV, Michel MF, Stolz E. (1979). Antibodies against Chlamydia of lymphogranuloma-venereum type in Crohn’s disease. Lancet, 1, 19–20.
  • Schulzke JD, Ploeger S, Amasheh M, Fromm A, Zeissig S, Troeger H, Richter J, Bojarski C, Schumann M, Fromm M. (2009). Epithelial tight junctions in intestinal inflammation. Ann N Y Acad Sci, 1165, 294–300.
  • Schurr E, Gros P. (2009). A common genetic fingerprint in leprosy and Crohn’s disease? N Engl J Med, 361, 2666–2668.
  • Schwartz D, Shafran I, Romero C, Piromalli C, Biggerstaff J, Naser N, Chamberlin W, Naser SA. (2000). Use of short-term culture for identification of Mycobacterium avium subsp. paratuberculosis in tissue from Crohn’s disease patients. Clin Microbiol Infect, 6, 303–307.
  • Scollard DM, Joyce MP, Gillis TP. (2006). Development of leprosy and type 1 leprosy reactions after treatment with infliximab: a report of 2 cases. Clin Infect Dis, 43, e19–e22.
  • Scollard DM, Adams LB, Gillis TP, Krahenbuhl JL, Truman RW, Williams DL. (2006). The continuing challenges of leprosy. Clin Microbiol Rev, 19, 338–381.
  • Sechi LA, Mura M, Tanda E, Lissia A, Fadda G, Zanetti S. (2004). Mycobacterium avium sub. paratuberculosis in tissue samples of Crohn’s disease patients. New Microbiol, 27, 75–77.
  • Sechi LA, Mura M, Tanda F, Lissia A, Solinas A, Fadda G, Zanetti S, Manuela M, Francesco T, Amelia L, Antonello S, Giovanni F, Stefania Z. (2001). Identification of Mycobacterium avium subsp. paratuberculosis in biopsy specimens from patients with Crohn’s disease identified by in situ hybridization. J Clin Microbiol, 39, 4514–4517.
  • Sechi LA, Scanu AM, Molicotti P, Cannas S, Mura M, Dettori G, Fadda G, Zanetti S. (2005). Detection and Isolation of Mycobacterium avium subspecies paratuberculosis from intestinal mucosal biopsies of patients with and without Crohn’s disease in Sardinia. Am J Gastroenterol, 100, 1529–1536.
  • Sechi LA, Gazouli M, Ikonomopoulos J, Lukas JC, Scanu AM, Ahmed N, Fadda G, Zanetti S. (2005). Mycobacterium avium subsp. paratuberculosis, genetic susceptibility to Crohn’s disease, and Sardinians: the way ahead. J Clin Microbiol, 43, 5275–5277.
  • Sechi LA, Gazouli M, Sieswerda LE, Molicotti P, Ahmed N, Ikonomopoulos J, Scanu AM, Paccagnini D, Zanetti S. (2006). Relationship between Crohn’s disease, infection with Mycobacterium avium subspecies paratuberculosis and SLC11A1 gene polymorphisms in Sardinian patients. World J Gastroenterol, 12, 7161–7164.
  • Selby W, Pavli P, Crotty B, Florin T. (2007). Author’s reply. Gastroenterol, 133, 1745–1746.
  • Selby W, Pavli P, Crotty B, Florin T, Radford-Smith G, Gibson P, Mitchell B, Connell W, Read R, Merrett M, Ee H, Hetzel D; Antibiotics in Crohn’s Disease Study Group. (2007). Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology, 132, 2313–2319.
  • Seldenrijk CA, Drexhage HA, Meuwissen SG, Meijer CJ. (1990). T-cellular immune reactions (in macrophage inhibition factor assay) against Mycobacterium paratuberculosis, Mycobacterium kansasii, Mycobacterium tuberculosis, Mycobacterium avium in patients with chronic inflammatory bowel disease. Gut, 31, 529–535.
  • Semret M, Turenne CY, Behr MA. (2006). Insertion sequence IS900 revisited. J Clin Microbiol, 44, 1081–1083.
  • Shaffer JL, Hughes S, Linaker BD, Baker RD, Turnberg LA. (1984). Controlled trial of rifampicin and ethambutol in Crohn’s disease. Gut, 25, 203–205.
  • Shafran I, Kugler L, El-Zaatari FA, Naser SA, Sandoval J. (2002). Open clinical trial of rifabutin and clarithromycin therapy in Crohn’s disease. Dig Liver Dis, 34, 22–28.
  • Shaoul R, Karban A, Weiss B, Reif S, Wasserman D, Pacht A, Eliakim R, Wardi J, Shirin H, Wine E, Leshinsky-Silver E, Levine A. (2004). NOD2/CARD15 mutations and presence of granulomas in pediatric and adult Crohn’s disease. Inflamm Bowel Dis, 10, 709–714.
  • Shin AR, Kim HJ, Cho SN, Collins MT, Manning EJ, Naser SA, Shin SJ. (2010). Identification of seroreactive proteins in the culture filtrate antigen of Mycobacterium avium ssp. paratuberculosis human isolates to sera from Crohn’s disease patients. FEMS Immunol Med Microbiol, 58, 128–137.
  • Sidoti F, Banche G, Astegiano S, Allizond V, Cuffini AM, Bergallo M. (2011). Validation and standardization of IS900 and F57 real-time quantitative PCR assays for the specific detection and quantification of Mycobacterium avium subsp. paratuberculosis. Can J Microbiol, 57, 347–354.
  • Sigurdardóttir OG, Bakke-McKellep AM, Djønne B, Evensen O. (2005). Mycobacterium avium subsp. paratuberculosis enters the small intestinal mucosa of goat kids in areas with and without Peyer’s patches as demonstrated with the everted sleeve method. Comp Immunol Microbiol Infect Dis, 28, 223–230.
  • Singh PK, Singh SV, Singh AV, Sohal JS. (2008). Evaluation of four methods of DNA recovery from Mycobacterium avium subspecies paratuberculosis present in intestine tissue of goats and comparative sensitivity of IS900 PCR with respect to culture for diagnosis of Johne’s disease. Indian J Exp Biol, 46, 579–582.
  • Sisto M, Cucci L, D’Amore M, Dow TC, Mitolo V, Lisi S. (2010). Proposing a relationship between Mycobacterium avium subspecies paratuberculosis infection and Hashimoto’s thyroiditis. Scand J Infect Dis, 42, 787–790.
  • Smego RA, Ahmed N. (2003). A systematic review of the adjunctive use of systemic corticosteroids for pulmonary tuberculosis. Int J Tuberc Lung Dis, 7, 208–213.
  • Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, Corthier G, Tran Van Nhieu J, Furet JP. (2011). Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS ONE, 6, e16393.
  • Sohal JS, Singh SV, Singh AV, Singh PK. (2010). Strain diversity within Mycobacterium avium subspecies paratuberculosis—a review. Indian J Exp Biol, 48, 7–16.
  • St-Jean G, Jernigan AD. (1991). Treatment of Mycobacterium paratuberculosis infection in ruminants. Vet Clin North Am Food Anim Pract, 7, 793–804.
  • Stainsby KJ, Lowes JR, Allan RN, Ibbotson JP. (1993). Antibodies to Mycobacterium paratuberculosis and nine species of environmental mycobacteria in Crohn’s disease and control subjects. Gut, 34, 371–374.
  • Steingart KR, Henry M, Laal S, Hopewell PC, Ramsay A, Menzies D, Cunningham J, Weldingh K, Pai M. (2007). Commercial serological antibody detection tests for the diagnosis of pulmonary tuberculosis: a systematic review. PLoS Med, 4, e202.
  • Stephan R, Schumacher S, Tasara T, Grant IR. (2007). Prevalence of Mycobacterium avium subspecies paratuberculosis in Swiss raw milk cheeses collected at the retail level. J Dairy Sci, 90, 3590–3595.
  • Stevenson K. (2010). Diagnosis of Johne’s Disease: Current limitations and prospects. Cattle Pract, 18, 104–109.
  • Stewart LC, Day AS, Pearson J, Barclay ML, Gearry RB, Roberts RL, Bentley RW. (2010). SLC11A1 polymorphisms in inflammatory bowel disease and Mycobacterium avium subspecies paratuberculosis status. World J Gastroenterol, 16, 5727–5731.
  • Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C, Clarke K, Cronin A, Davis P, Goodhead I, Holroyd N, Jagels K, Lord A, Moule S, Mungall K, Norbertczak H, Quail MA, Rabbinowitsch E, Walker D, White B, Whitehead S, Small PL, Brosch R, Ramakrishnan L, Fischbach MA, Parkhill J, Cole ST. (2008). Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res, 18, 729–741.
  • Subramanian S, Campbell BJ, Rhodes JM. (2006). Bacteria in the pathogenesis of inflammatory bowel disease. Curr Opin Infect Dis, 19, 475–484.
  • Suenaga K, Yokoyama Y, Okazaki K, Yamamoto Y. (1995). Mycobacteria in the intestine of Japanese patients with inflammatory bowel disease. Am J Gastroenterol, 90, 76–80.
  • Suenaga K, Yokoyama Y, Nishimori I, Sano S, Morita M, Okazaki K, Onishi S. (1999). Serum antibodies to Mycobacterium paratuberculosis in patients with Crohn’s disease. Dig Dis Sci, 44, 1202–1207.
  • Swift GL, Srivastava ED, Stone R, Pullan RD, Newcombe RG, Rhodes J, Wilkinson S, Rhodes P, Roberts G, Lawrie BW. (1994). Controlled trial of anti-tuberculous chemotherapy for two years in Crohn’s disease. Gut, 35, 363–368.
  • Tabaqchali S, O’Donoghue DP, Bettelheim KA. (1978). Escherichia coli antibodies in patients with inflammatory bowel disease. Gut, 19, 108–113.
  • Taddei S, Robbi C, Cesena C, Rossi I, Schiano E, Arrigoni N, Vicenzoni G, Cavirani S. (2004). Detection of Mycobacterium avium subsp. paratuberculosis in bovine fecal samples: comparison of three polymerase chain reaction-based diagnostic tests with a conventional culture method. J Vet Diagn Invest, 16, 503–508.
  • Talhari C, Ferreira LC, Araújo JR, Talhari AC, Talhari S. (2008). Immune reconstitution inflammatory syndrome or upgrading type 1 reaction? Report of two AIDS patients presenting a shifting from borderline lepromatous leprosy to borderline tuberculoid leprosy. Lepr Rev, 79, 429–435.
  • Tanaka K, Wilks M, Coates PJ, Farthing MJ, Walker-Smith JA, Tabaqchali S. (1991). Mycobacterium paratuberculosis and Crohn’s disease. Gut, 32, 43–45.
  • Tasara T, Hoelzle LE, Stephan R. (2005). Development and evaluation of a Mycobacterium avium subspecies paratuberculosis (MAP) specific multiplex PCR assay. Int J Food Microbiol, 104, 279–287.
  • Thamer M, Ray NF, Henderson SC, Rinehart CS, Sherman CR, Ferguson JH. (1998). Influence of the NIH Consensus Conference on Helicobacter pylori on physician prescribing among a Medicaid population. Med Care, 36, 646–660.
  • Thayer WR. (1992). The use of antimycobacterial agents in Crohn’s disease. J Clin Gastroenterol, 15, 5–7.
  • Thayer WR Jr, Coutu JA, Chiodini RJ, Van Kruiningen HJ, Merkal RS. (1984). Possible role of mycobacteria in inflammatory bowel disease. II. Mycobacterial antibodies in Crohn’s disease. Dig Dis Sci, 29, 1080–1085.
  • Thia KT, Sandborn WJ, Harmsen WS, Zinsmeister AR, Loftus EV Jr. (2010). Risk factors associated with progression to intestinal complications of Crohn’s disease in a population-based cohort. Gastroenterology, 139, 1147–1155.
  • Thiam S, LeFevre AM, Hane F, Ndiaye A, Ba F, Fielding KL, Ndir M, Lienhardt C. (2007). Effectiveness of a strategy to improve adherence to tuberculosis treatment in a resource-poor setting: a cluster randomized controlled trial. JAMA, 297, 380–386.
  • Thomas Dow C. (2008). Cows, Crohn’s and more: is Mycobacterium paratuberculosis a superantigen? Med Hypotheses, 71, 858–861.
  • Thomas GA, Swift GL, Green JT, Newcombe RG, Braniff-Mathews C, Rhodes J, Wilkinson S, Strohmeyer G, Kreuzpainter G. (1998). Controlled trial of antituberculous chemotherapy in Crohn’s disease: a five year follow up study. Gut, 42, 497–500.
  • Thorel MF, Krichevsky M, Lévy-Frébault VV. (1990). Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of Mycobacterium avium, and description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov. Int J Syst Bacteriol, 40, 254–260.
  • Thornton GF. (1970). The role of corticosteroids in the management of tuberculous infections. In: Johnson JEI, ed., Rational Therapy and Control of Tuberculosis. A Symposium. Gainesville: University of Florida Press.
  • Toracchio S, El-Zimaity HM, Urmacher C, Katz S, Graham DY. (2008). Mycobacterium avium subspecies paratuberculosis and Crohn’s disease granulomas. Scand J Gastroenterol, 43, 1108–1111.
  • Tuci A, Tonon F, Castellani L, Sartini A, Roda G, Marocchi M, Caponi A, Munarini A, Rosati G, Ugolini G, Fuccio L, Scagliarini M, Bazzoli F, Belluzzi A. (2011). Fecal detection of Mycobacterium avium paratuberculosis using the IS900 DNA sequence in crohn’s disease and ulcerative colitis patients and healthy subjects. Dig Dis Sci, 56, 2957–2962.
  • Turenne CY, Wallace R Jr, Behr MA. (2007). Mycobacterium avium in the postgenomic era. Clin Microbiol Rev, 20, 205–229.
  • Turenne CY, Collins DM, Alexander DC, Behr MA. (2008). Mycobacterium avium subsp. paratuberculosis and M. avium subsp. avium are independently evolved pathogenic clones of a much broader group of M. avium organisms. J Bacteriol, 190, 2479–2487.
  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. (2009). The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med, 1, 6ra14.
  • Uematsu S, Fujimoto K. (2010). The innate immune system in the intestine. Microbiol Immunol, 54, 645–657.
  • USDA. (2008). Johne’s disease on U.S. dairies, 1991–2007. Fort Collins, CO: USDA, APHIS, Veterinary Services, Center for Epidemiology and Animal Health.
  • USDA, National Advisory Committee on Microbiological Criteria for Foods. (2010). Assessment of food as a source of exposure to Mycobacterium avium subspecies paratuberculosis (MAP). J Food Prot, 73, 1357–1397.
  • Ustianowski AP, Lawn SD, Lockwood DN. (2006). Interactions between HIV infection and leprosy: a paradox. Lancet Infect Dis, 6, 350–360.
  • Uzoigwe JC, Khaitsa ML, Gibbs PS. (2007). Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn’s disease. Epidemiol Infect, 135, 1057–1068.
  • Van Kruiningen HJ. (1999). Lack of support for a common etiology in Johne’s disease of animals and Crohn’s disease in humans. Inflamm Bowel Dis, 5, 183–191.
  • Van Kruiningen HJ, Chiodini RJ, Thayer WR, Coutu JA, Merkal RS, Runnels PL. (1986). Experimental disease in infant goats induced by a Mycobacterium isolated from a patient with Crohn’s disease. A preliminary report. Dig Dis Sci, 31, 1351–1360.
  • van Vliet MJ, Harmsen HJ, de Bont ES, Tissing WJ. (2010). The role of intestinal microbiota in the development and severity of chemotherapy-induced mucositis. PLoS Pathog, 6, e1000879.
  • Vary PH, Andersen PR, Green E, Hermon-Taylor J, McFadden JJ. (1990). Use of highly specific DNA probes and the polymerase chain reaction to detect Mycobacterium paratuberculosis in Johne’s disease. J Clin Microbiol, 28, 933–937.
  • Vatn MH. (2009). Natural history and complications of IBD. Curr Gastroenterol Rep, 11, 481–487.
  • Verma RK, Jain A. (2007). Antibodies to mycobacterial antigens for diagnosis of tuberculosis. FEMS Immunol Med Microbiol, 51, 453–461.
  • Verna AE, Garcia-Pariente C, Muñoz M, Moreno O, García-Marin JF, Romano MI, Paolicchi F, Pérez V. (2007). Variation in the immuno-pathological responses of lambs after experimental infection with different strains of Mycobacterium avium subsp. paratuberculosis. Zoonoses Public Health, 54, 243–252.
  • Verschoor CP, Pant SD, You Q, Schenkel FS, Kelton DF, Karrow NA. (2010). Polymorphisms in the gene encoding bovine interleukin-10 receptor alpha are associated with Mycobacterium avium ssp. paratuberculosis infection status. BMC Genet, 11, 23.
  • Viazis N, Vlachogiannakos J, Georgiou O, Rodias M, Georgiadis D, Papastamopoulos V, Baraboutis IG, Karamanolis DG, Skoutelis A. (2010). Course of inflammatory bowel disease in patients infected with human immunodeficiency virus. Inflamm Bowel Dis, 16, 507–511.
  • Wagner J, Sim W, Bishop RF, Catto-Smith AG, Cameron DJ, Kirkwood CD. (2011). Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn’s disease: a longitudinal follow-up study. Inflamm Bowel Dis, 17, 1825–1826.
  • Wall S, Kunze ZM, Saboor S, Soufleri I, Seechurn P, Chiodini R, McFadden JJ. (1993). Identification of spheroplast-like agents isolated from tissues of patients with Crohn’s disease and control tissues by polymerase chain reaction. J Clin Microbiol, 31, 1241–1245.
  • Walmsley RS, Ibbotson JP, Chahal H, Allan RN. (1996). Antibodies against Mycobacterium paratuberculosis in Crohn’s disease. QJM, 89, 217–221.
  • Wen Z, Fiocchi C. (2004). Inflammatory bowel disease: autoimmune or immune-mediated pathogenesis? Clin Dev Immunol, 11, 195–204.
  • Whan L, Ball HJ, Grant IR, Rowe MT. (2005). Occurrence of Mycobacterium avium subsp. paratuberculosis in untreated water in Northern Ireland. Appl Environ Microbiol, 71, 7107–7112.
  • Whitlock RH, Wells SJ, Sweeney RW, Van Tiem J. (2000). ELISA and fecal culture for paratuberculosis (Johne’s disease): sensitivity and specificity of each method. Vet Microbiol, 77, 387–398.
  • Whittington RJ, Marshall DJ, Nicholls PJ, Marsh IB, Reddacliff LA. (2004). Survival and dormancy of Mycobacterium avium subsp. paratuberculosis in the environment. Appl Environ Microbiol, 70, 2989–3004.
  • Whittington RJ, Marsh IB, Saunders V, Grant IR, Juste R, Sevilla IA, Manning EJ, Whitlock RH. (2011). Culture phenotypes of genomically and geographically diverse Mycobacterium avium subsp. paratuberculosis isolates from different hosts. J Clin Microbiol, 49, 1822–1830.
  • Windsor PA, Whittington RJ. (2010). Evidence for age susceptibility of cattle to Johne’s disease. Vet J, 184, 37–44.
  • Windsor PA, Bush R, Links I, Eppleston J. (2005). Injury caused by self-inoculation with a vaccine of a Freund’s complete adjuvant nature (Gudair) used for control of ovine paratuberculosis. Aust Vet J, 83, 216–220.
  • Winthrop KL, Chang E, Yamashita S, Iademarco MF, LoBue PA. (2009). Nontuberculous mycobacteria infections and anti-tumor necrosis factor-alpha therapy. Emerging Infect Dis, 15, 1556–1561.
  • Wynne JW, Seemann T, Bulach DM, Coutts SA, Talaat AM, Michalski WP. (2010). Resequencing the Mycobacterium avium subsp. paratuberculosis K10 genome: improved annotation and revised genome sequence. J Bacteriol, 192, 6319–6320.
  • Yim JJ, Selvaraj P. (2010). Genetic susceptibility in tuberculosis. Respirology, 15, 241–256.
  • Zhang FR, Huang W, Chen SM, Sun LD, Liu H, Li Y, Cui Y, Yan XX, Yang HT, Yang RD, Chu TS, Zhang C, Zhang L, Han JW, Yu GQ, Quan C, Yu YX, Zhang Z, Shi BQ, Zhang LH, Cheng H, Wang CY, Lin Y, Zheng HF, Fu XA, Zuo XB, Wang Q, Long H, Sun YP, Cheng YL, Tian HQ, Zhou FS, Liu HX, Lu WS, He SM, Du WL, Shen M, Jin QY, Wang Y, Low HQ, Erwin T, Yang NH, Li JY, Zhao X, Jiao YL, Mao LG, Yin G, Jiang ZX, Wang XD, Yu JP, Hu ZH, Gong CH, Liu YQ, Liu RY, Wang DM, Wei D, Liu JX, Cao WK, Cao HZ, Li YP, Yan WG, Wei SY, Wang KJ, Hibberd ML, Yang S, Zhang XJ, Liu JJ. (2009). Genomewide association study of leprosy. N Engl J Med, 361, 2609–2618.
  • Zhang H, Massey D, Tremelling M, Parkes M. (2008). Genetics of inflammatory bowel disease: clues to pathogenesis. Br Med Bull, 87, 17–30.
  • Zhang MZ, Zhang S. (2011). An efficient DNA extraction method for polymerase chain reaction-based detection of Mycobacterium avium subspecies paratuberculosis in bovine fecal samples. J Vet Diagn Invest, 23, 41–48.
  • Zwick LS, Walsh TF, Barbiers R, Collins MT, Kinsel MJ, Murnane RD. (2002). Paratuberculosis in a mandrill (Papio sphinx). J Vet Diagn Invest, 14, 326–328.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.