Erratum: The role of bacteria and pattern-recognition receptors in Crohn's disease (Nature Reviews Gastroenterology and Hepatology (2011) 8 (152-168) DOI:10.1038/nrgastro.2011.3);The role of bacteria and pattern-recognition receptors in Crohn's disease

Nature Reviews Gastroenterology and Hepatology

Volumn 8, Issue 3, 2011, Pages 152-168

  Man, Si Ming ^a   Kaakoush, Nadeem O ^b   Mitchell, Hazel M ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CASPASE RECRUITMENT DOMAIN PROTEIN 15; CASPASE RECRUITMENT DOMAIN PROTEIN 4; CRYOPYRIN; DEFENSIN; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR; PATTERN RECOGNITION RECEPTOR; TOLL LIKE RECEPTOR 10; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR 9;

BACTERIAL COLONIZATION; BACTERIAL VIRULENCE; BACTERICIDAL ACTIVITY; BACTERIUM ADHERENCE; BACTEROIDETES; CAMPYLOBACTER; CAMPYLOBACTER CONCISUS; CHRONIC INFLAMMATION; CROHN DISEASE; DISEASE PREDISPOSITION; ENTEROINVASIVE ESCHERICHIA COLI; FIRMICUTES; GENE MUTATION; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; HELICOBACTER; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; MOLECULAR PATHOLOGY; MOLECULAR RECOGNITION; MYCOBACTERIUM PARATUBERCULOSIS; NONHUMAN; ONSET AGE; PRIORITY JOURNAL; PROTEOBACTERIA; PSEUDOMONAS; QUORUM SENSING; REVIEW;

EID: 79952445703     PISSN: 17595045     EISSN: 17595053     Source Type: Journal    
DOI: 10.1038/nrgastro.2011.56     Document Type: Erratum

References (196)

1. Sartor, R. B. Enteric microflora in IBD: pathogens or commensals? Inflamm. Bowel Dis. 3, 230-235 (1997). (Pubitemid 127726448)
2. Yamamoto, T., Allan, R. N. & Keighley, M. R. Effect of fecal diversion alone on perianal Crohn's disease. World J. Surg. 24, 1258-1262 (2000).
3. Rutgeerts, P et al. Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum. Lancet 338, 771-774 (1991).
4. Zelas, P & Jagelman, D. G. Loop illeostomy in the management of Crohn's colitis in the debilitated patient. Ann. Surg. 191, 164-168 (1980). (Pubitemid 10141735)
5. McIlrath, D. C Diverting ileostomy or colostomy in the management of Crohn's disease of the colon. Arch. Surg. 103, 308-310 (1971).
6. D'Haens, G. R. et al. Early lesions of recurrent Crohn's disease caused by infusion of intestinal contents in excluded ileum. Gastroenterology 114, 262-267 (1998). (Pubitemid 28093532)
7. Shafran, I. & Burgunder, P Adjunctive antibiotic therapy with rifaximin may help reduce Crohn's disease activity. Dig. Dis. Sci. 55, 1079-1084 (2010).
8. Prantera, C et al. Antibiotic treatment of Crohn's disease: results of a multicentre, double blind, randomized, placebo-controlled trial with rifaximin. Aliment Pharmacol. Ther. 23, 1117-1125 (2006). (Pubitemid 43779351)
9. Arnold, G. L., Beaves, M. R., Pryjdun, V O. & Mook, W. J. Preliminary study of ciprofloxacin in active Crohn's disease. Inflamm. Bowel Dis. 8, 10-15 (2002). (Pubitemid 34130123)
10. Steinhart, A. H. et al. Combined budesonide and antibiotic therapy for active Crohn's disease: a randomized controlled trial. Gastroenterology 123, 33-40 (2002). (Pubitemid 34747523)
11. Colombel, J. F. et al. A controlled trial comparing ciprofloxacin with mesalazine for the treatment of active Crohn's disease. Groupe d'Etudes Therapeutiques des Affections Inflammatoires Digestives (GETAID). Am. J. Gastroenterol. 94, 674-678 (1999).
12. Prantera, C et al. An antibiotic regimen for the treatment of active Crohn's disease: a randomized, controlled clinical trial of metronidazole plus ciprofloxacin. Am. J. Gastroenterol. 91, 328-332 (1996). (Pubitemid 26067343)
13. Greenbloom, S. L., Steinhart, A. H. & Greenberg, G. R. Combination ciprofloxacin and metronidazole for active Crohn's disease. Can. J. Gastroenterol. 12, 53-56 (1998). (Pubitemid 28105540)
14. Sutherland, L. et al. Double blind, placebo controlled trial of metronidazole in Crohn's disease. Gut 32, 1071-1075 (1991).
15. Leiper, K., Morris, A. I. & Rhodes, J. M. Open label trial of oral clarithromycin in active Crohn's disease. Aliment Pharmacol. Ther. 14, 801-806 (2000). (Pubitemid 30352748)
16. Rahimi, R., Nikfar, S., Rezaie, A. & Abdollahi, M. A meta-analysis of broad-spectrum antibiotic therapy in patients with active Crohn's disease. Clin. Ther. 28, 1983-1988 (2006). (Pubitemid 46215747)
17. Nell, S., Suerbaum, S. & Josenhans, C The mpact of the microbiota on the pathogenesis of BD: lessons from mouse infection models. Nat Rev. Microbiol. 8, 564-577 (2010).
18. Guarner, F. The intestinal flora in inflammatory bowel disease: normal or abnormal? Curr. Opin. Gastroenterol. 21, 414-418 (2005). (Pubitemid 40961166)
19. Hooper, L. V., Midtvedt, T & Gordon, J. I. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22, 283-307 (2002). (Pubitemid 35221463)
20. Tamboli, C P., Neut, C., Desreumaux, P & Colombel, J. F. Dysbiosis in inflammatory bowel disease. Gut 53, 1-4 (2004). (Pubitemid 38082999)
21. Tannock, G. W. Analysis of the intestinal microflora using molecular methods. Eur. J. Clin. Nutr. 56 (Suppl. 4), S44-S49 (2002). (Pubitemid 36163803)
22. Zoetendal, E. G., Rajilic-Stojanovic, M. & de Vos, W. M. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57, 1605-1615 (2008).
23. Packey, C D. & Sartor, R. B. Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr. Opin. Infect. Dis. 22, 292-301 (2009).
24. Rehman, A. et al. Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J. Med. Microbiol. 59, 1114-1122 (2010).
25. Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community mbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780-13785 (2007). (Pubitemid 350003397)
26. Baumgart, M. et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J. 1, 403-418 (2007). (Pubitemid 47373247)
27. Kotlowski, R., Bernstein, C N., Sepehri, S. & Krause, D. O. High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 56, 669-675 (2007). (Pubitemid 46662933)
28. Gophna, U., Sommerfeld, K., Gophna, S., Doolittle, W. F. & Veldhuyzen van Zanten, S. J. Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J. Clin. Microbiol. 44, 4136-4141 (2006). (Pubitemid 44737260)
29. Martinez-Medina, M., Aldeguer, X., Gonzalez-Huix, F., Acero, D. & Garcia-Gil, L J. Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm. Bowel Dis. 12, 1136-1145 (2006). (Pubitemid 44847471)
30. Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P & Lochs, H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J. Clin. Microbiol. 43, 3380-3389 (2005). (Pubitemid 40981351)
31. Ott, S. J. et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53, 685-693 (2004). (Pubitemid 38561447)
32. Prindiville, T, Cantrell, M. & Wilson, K. H. Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease. Inflamm. Bowel Dis. 10, 824-833 (2004). (Pubitemid 39545228)
33. Swidsinski, A. et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 122, 44-54 (2002). (Pubitemid 34049193)
34. Kleessen, B., Kroesen, A. J., Buhr, H. J. & Blaut, M. Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand. J. Gastroenterol. 37, 1034-1041 (2002).
35. Conte, M. P et al. Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut 55, 1760-1767 (2006). (Pubitemid 44893575)
36. Bibiloni, R., Mangold, M., Madsen, K. L., Fedorak, R. N. & Tannock, G. W. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J. Med. Microbiol. 55, 1141-1149 (2006). (Pubitemid 44215574)
37. Kang, S. et al. Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray Inflamm. Bowel Dis. 16, 2034-2042 (2010).
38. Mondot, S. et al. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm. Bowel Dis. 17, 185-192 (2011).
39. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
40. Dicksved, J. et al. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J. 2, 716-727 (2008). (Pubitemid 351951567)
41. Takaishi, H. et al. Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease. Int J. Med. Microbiol. 298, 463-472 (2008). (Pubitemid 351734793)
42. Manichanh, C et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55, 205-211 (2006). (Pubitemid 43117279)
43. Sokol, H. et al. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm. Bowel Dis. 12, 106-111 (2006).
44. Seksik, P et al. Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 52, 237-242 (2003). (Pubitemid 36115065)
45. Lupp, C et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 204 (2007). (Pubitemid 47355207)
46. Garrett, W. S. et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8, 292-300 (2010).
47. Kirkwood, C D. et al. Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease. Inflamm. Bowel Dis. 15, 1643-1655 (2009).
48. Di Sabatino, A. et al. Detection of Mycobacterium avium subsp. paratuberculosis (MAP)-specific IS900 DNA and antibodies against MAP peptides and lysate in the blood of Crohn's disease patients. Inflamm. Bowel Dis. doi:10.1002/ibd.21461.
49. Mendoza, J. L. et al. High prevalence of viable Mycobacterium avium subspecies paratuberculosis in Crohn's disease. World J. Gastroenterol. 16, 4558-4563 (2010).
50. Shin, A. R. et al. 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 (2010).
51. Bach, H. et al. Immunogenicity of Mycobacterium avium subsp. paratuberculosis proteins in Crohn's disease patients. Scand. J. Gastroenterol. doi:10.3109/00365521.
52. Hermon-Taylor, J. Mycobacterium avium subspecies paratuberculosis, Crohn's disease and the Doomsday scenario. Gut Pathog. 1, 15 (2009).
53. Sibartie, S. et al. Mycobacterium avium subsp. paratuberculosis (MAP) as a modifying factor in Crohn's disease. Inflamm. Bowel Dis. 16, 296-304 (2010).
54. Feller, M. et al. Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis. Lancet Infect Dis. 7, 607-613 (2007). (Pubitemid 47268226)
55. Abubakar, I., Myhill, D., Aliyu, S. H. & Hunter, P R. 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 (2008). (Pubitemid 351441331)
56. Boudeau, J., Glasser, A. L., Masseret, E., Joly, B. & Darfeuille-Michaud, A. Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease. Infect. Immun. 67, 4499-4509 (1999). (Pubitemid 29400425)
57. Glasser, A. L et al. Adherent invasive Escherichia coli strains from patients with Crohn's disease survive and replicate within macrophages without inducing host cell death. Infect Immun. 69, 5529-5537 (2001).
58. Darfeuille-Michaud, A. et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127, 412-421 (2004). (Pubitemid 39091889)
59. Martin, H. M. et al. Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer. Gastroenterology 127, 80-93 (2004). (Pubitemid 38962277)
60. Martinez-Medina, M. et al. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease. Inflamm. Bowel Dis. 15, 872-882 (2009).
61. Meconi, S. et al. Adherent-invasive Escherichia coli isolated from Crohn's disease patients induce granulomas in vitro. Cell. Microbiol. 9, 1252-1261 (2007). (Pubitemid 46547142)
62. Rolhion, N., Carvalho, F. A. & Darfeuille-Michaud, A. OmpC and the sigma(E) regulatory pathway are involved in adhesion and invasion of the Crohn's disease-associated Escherichia coli strain LF82. Mol. Microbiol. 63, 1684-1700 (2007). (Pubitemid 46426710)
63. Bringer, M. A., Rolhion, N., Glasser, A. L. & Darfeuille-Michaud, A. The oxidoreductase DsbA plays a key role in the ability of the Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 to resist macrophage killing. J. Bacteriol. 189, 4860-4871 (2007). (Pubitemid 47025598)
64. Rolhion, N. et al. Abnormally expressed ER stress response chaperone Gp96 in CD favours adherent-invasive Escherichia coli invasion. Gut 59, 1355-1362 (2010).
65. Barnich, N. et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, Supporting ileal mucosa colonization in Crohn disease. J. Clin. Invest 117, 1566-1574 (2007). (Pubitemid 46871341)
66. Carvalho, F. A. et al. Crohn's disease-associated Escherichia coli LF82 aggravates colitis in injured mouse colon via signaling by flagellin. Inflamm. Bowel Dis. 14, 1051-1060 (2008).
67. Zhang, L. et al. Detection and isolation of Campylobacter species other than C. jejuni from children with Crohn's disease. J. Clin. Microbiol. 47, 453-455 (2009).
68. Man, S. M. et al. Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn's disease. Inflamm. Bowel Dis. 16, 1008-1016 (2010).
69. Man, S. M. et al. Host attachment, invasion, and stimulation of proinflammatory cytokines by Campylobacter concisus and other non-Campylobacter jejuni Campylobacter species. J. Infect Dis. 202, 1855-1865 (2010).
70. Istivan, T. S., Coloe, P J., Fry, B. N., Ward, P & Smith, S. C Characterization of a haemolytic phospholipase A(2) activity in clinical isolates of Campylobacter concisus. J. Med. Microbiol. 53, 483-493 (2004). (Pubitemid 38803041)
71. Istivan, T. S., Smith, S. C., Fry, B. N. & Coloe, P J. Characterization of Campylobacter concisus hemolysins. FEMS Immunol. Med. Microbiol. 54, 224-235 (2008).
72. Kaakoush, N. O. et al. The secretome of Campylobacter concisus. FEBS J. 277, 1606-1617 (2010).
73. Engberg, J. et al. Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics. Clin. Microbiol. Infect. 11, 288-295 (2005). (Pubitemid 40443834)
74. Aabenhus, R., Stenram, U., Andersen, L. P, Permin, H. & Ljungh, A. First attempt to produce experimental Campylobacter concisus infection in mice. World J. Gastroenterol. 14, 6954-6959 (2008).
75. Hansen, R., Thomson, J. M., Fox, J. G., El-Omar, E. M. & Hold, G. L Could Helicobacter organisms cause inflammatory bowel disease? FEMS Immunol. Med. Microbiol. doi:10.1111/j.1574-695X.2010.00744.x.
76. Solnick, J. V & Schauer, D. B. Emergence of diverse Helicobacter species in the pathogenesis of gastric and enterohepatic diseases. Clin. Microbiol. Rev. 14, 59-97 (2001). (Pubitemid 32096207)
77. Bohr, U. R. et al. Identification of enterohepatic Helicobacter species in patients suffering from inflammatory bowel disease. J. Clin. Microbiol. 42, 2766-2768 (2004). (Pubitemid 38747533)
78. Zhang, L., Day A., McKenzie, G. & Mitchell, H. Nongastric Helicobacter species detected in the intestinal tract of children. J. Clin. Microbiol. 44, 2276-2279 (2006). (Pubitemid 43902194)
79. Man, S. M., Zhang, L., Day A. S., Leach, S. & Mitchell, H. Detection of enterohepatic and gastric Helicobacter species in fecal specimens of children with Crohn's disease. Helicobacter 13, 234-238 (2008).
80. Kaakoush, N. O. et al. Detection of Helicobacteraceae in intestinal biopsies of children with Crohn's disease. Helicobacter 15, 549-557 (2010).
81. Laharie, D. et al. Association between entero-hepatic Helicobacter species and Crohn's disease: a prospective cross-sectional study Aliment Pharmacol. Ther. 30, 283-293 (2009).
82. Varon, C et al. Study of Helicobacter pullorum proinflammatory properties on human epithelial cells in vitro. Gut 58, 629-635 (2009).
83. Bell, S. J., Chisholm, S. A., Owen, R. J., Borriello, S. P & Kamm, M. A. Evaluation of Helicobacter species in inflammatory bowel disease. Aliment. Pharmacol. Ther. 18, 481-486 (2003). (Pubitemid 37152288)
84. Grehan, M., Danon, S., Lee, A., Daskalopoulos, G. & Mitchell, H. Absence of mucosa-associated colonic Helicobacters in an Australian urban population. J. Clin. Microbiol. 42, 874-876 (2004). (Pubitemid 38222686)
85. Wagner, J. et al. Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease. PLoS ONE 3, e3578 (2008).
86. Wei, B. et al. Pseudomonas fluorescens encodes the Crohn's disease-associated I2 sequence and T-cell superantigen. Infect. Immun. 70, 6567-6575 (2002). (Pubitemid 35387882)
87. Spivak, J. et al. Antibodies to I2 predict clinical response to fecal diversion in Crohn's disease. Inflamm. Bowel Dis. 12, 1122-1130 (2006). (Pubitemid 44847469)
88. Ashorn, S. et al. Fecal calprotectin levels and serological responses to microbial antigens among children and adolescents with inflammatory bowel disease. Inflamm. Bowel Dis. 15, 199-205 (2009).
89. Lamps, L. W. et al. Pathogenic Yersinia DNA is detected in bowel and mesenteric lymph nodes from patients with Crohn's disease. Am. J. Surg. Pathol. 27, 220-227 (2003). (Pubitemid 36152232)
90. Safa, G., Loppin, M., Tisseau, L. & Lamoril, J. Cutaneous aseptic neutrophilic abscesses and Yersinia enterocolitica infection in a case subsequently diagnosed as Crohn's disease. Dermatology 217, 340-342 (2008).
91. Zippi, M. et al. Mesenteric adenitis caused by Yersinia pseudotubercolosis in a patient subsequently diagnosed with Crohn's disease of the terminal ileum. World J. Gastroenterol. 12, 3933-3935 (2006). (Pubitemid 44028413)
92. Saebo, A., Vik, E., Lange, O. J. & Matuszkiewicz, L. Inflammatory bowel disease associated with Yersinia enterocolitica O:3 infection. Eur. J. Intern. Med. 16, 176-182 (2005). (Pubitemid 40828255)
93. Goodman, M. J., Pearson, K. W., McGhie, D., Dutt, S. & Deodhar, S. G. Campylobacter and Giardia lamblia causing exacerbation of inflammatory bowel disease. Lancet 2, 1247 (1980). (Pubitemid 11250872)
94. Newman, A. & Lambert, J. R. Campylobacter jejuni causing flare-up in inflammatory bowel disease. Lancet 2, 919 (1980). (Pubitemid 10014333)
95. Gradel, K. O. et al. Increased short-and long-term risk of inflammatory bowel disease after Salmonella or Campylobacter gastroenteritis. Gastroenterology 137, 495-501 (2009).
96. Ternhag, A., Torner, A., Svensson, A., Ekdahl, K. & Giesecke, J. Short-and long-term effects of bacterial gastrointestinal infections. Emerg. Infect Dis. 14, 143-148 (2008).
97. Hugot, J. P et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411, 599-603 (2001).
98. Ogura, Y et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411, 603-606 (2001). (Pubitemid 32531409)
99. Leulier, F & Lemaitre, B. Toll-like receptors-taking an evolutionary approach. Nat Rev. Genet 9, 165-178 (2008).
100. Silva, M. A. et al. Dendritic cells and toll-like receptors 2 and 4 in the ileum of Crohn's disease patients. Dig. Dis. Sci. 53, 1917-1928 (2008).
101. Szebeni, B. et al. Increased expression of Tollike receptor (TLR) 2 and TLR4 in the colonic mucosa of children with inflammatory bowel disease. Clin. Exp. Immunol. 151, 34-41 (2008). (Pubitemid 350230984)
102. Cario, E. & Podolsky, D. K. Differential alteration in intestinal epithelial cell expression of toll-like receptor 3 (TLR3) and TLR4 in inflammatory bowel disease. Infect. Immun. 68, 7010-7017 (2000). (Pubitemid 32463415)
103. Frolova, L., Drastich, P, Rossmann, P., Klimesova, K. & Tlaskalova-Hogenova, H. Expression of Toll-like receptor 2 (TLR2), TLR4, and CD14 in biopsy samples of patients with inflammatory bowel diseases: upregulated expression of TLR2 in terminal ileum of patients with ulcerative colitis. J. Histochem. Cytochem. 56, 267-274 (2008). (Pubitemid 351272998)
104. Bryant, C E., Spring, D. R., Gangloff, M. & Gay, N. J. The molecular basis of the host response to lipopolysaccharide. Nat Rev. Microbiol. 8, 8-14 (2010).
105. Franchimont, D. et al. Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn's disease and ulcerative colitis. Gut 53, 987-992 (2004). (Pubitemid 38824157)
106. Ouburg, S. et al. The toll-like receptor 4 (TLR4) Asp299Gly polymorphism is associated with colonic localisation of Crohn's disease without a major role for the Saccharomyces cerevisiae mannan-LBP-CD14-TLR4 pathway. Gut 54, 439-440 (2005). (Pubitemid 40299106)
107. Hume, G. E. et al. Novel NOD2 haplotype strengthens the association between TLR4 Asp299gly and Crohn's disease in an Australian population. Inflamm. Bowel Dis. 14, 585-590 (2008). (Pubitemid 351742974)
108. Gazouli, M. et al. Association between polymorphisms in the Toll-like receptor 4, CD14, and CARD15/NOD2 and inflammatory bowel disease in the Greek population. World J. Gastroenterol. 11, 681-685 (2005). (Pubitemid 40220757)
109. Zouiten-Mekki, L. et al. Toll-like receptor 4 (TLR4) polymorphisms in Tunisian patients with Crohn's disease: genotype-phenotype correlation. BMC Gastroenterol. 9, 62 (2009).
110. Lakatos, P L. et al. Toll-like receptor 4 and NOD2/CARD15 mutations in Hungarian patients with Crohn's disease: phenotype-genotype correlations. World J. Gastroenterol. 11, 1489-1495 (2005). (Pubitemid 40468084)
111. Hong, J. et al. TLR2, TLR4 and TLR9 polymorphisms and Crohn's disease in a New Zealand Caucasian cohort. J. Gastroenterol. Hepatol. 22, 1760-1766 (2007). (Pubitemid 47525075)
112. Arbour, N. C et al. TLR4 mutations are associated with endotoxin hyporesponsiveness in humans. Nat Genet 25, 187-191 (2000). (Pubitemid 30394990)
113. Lorenz, E., Mira, J. P, Frees, K. L & Schwartz, D. A. Relevance of mutations in the TLR4 receptor in patients with gram-negative septic shock. Arch. Intern. Med. 162, 1028-1032 (2002). (Pubitemid 34492532)
114. Kiechl, S. et al. Toll-like receptor 4 polymorphisms and atherogenesis. N. Engl. J. Med. 347, 185-192 (2002). (Pubitemid 34764822)
115. Hemmi, H. et al. A Toll-like receptor recognizes bacterial DNA. Nature 408, 740-745 (2000). (Pubitemid 32015992)
116. Pedersen, G., Andresen, L., Matthiessen, M. W., Rask-Madsen, J. & Brynskov, J. Expression of Toll-ike receptor 9 and response to bacterial CpG oligodeoxynucleotides in human intestinal epithelium. Clin. Exp. Immunol. 141, 298-306 (2005). (Pubitemid 41003354)
117. Torok, H. P et al. Epistasis between Toll-like receptor-9 polymorphisms and variants in NOD2 and IL23R modulates susceptibility to Crohn's disease. Am. J. Gastroenterol. 104, 1723-1733 (2009).
118. Pierik, M. et al. Toll-like receptor-1,-2, and-6 polymorphisms influence disease extension in inflammatory bowel diseases. Inflamm. Bowel Dis. 12, 1-8 (2006). (Pubitemid 43032444)
119. Steenholdt, C., Andresen, L., Pedersen, G., Hansen, A. & Brynskov, J. Expression and function of toll-like receptor 8 and Tollip in colonic epithelial cells from patients with inflammatory bowel disease. Scand. J. Gastroenterol. 44, 195-204 (2009).
120. Kanneganti, T. D., Lamkanfi, M. & Nunez, G. Intracellular NOD-like receptors in host defense and disease. Immunity 27, 549-559 (2007). (Pubitemid 47615512)
121. Barnes, P J. & Karin, M. Nuclear factor-kappaB: a pivotal transcription factor in chronic inflammatory diseases. N. Engl. J. Med. 336, 1066-1071 (1997). (Pubitemid 27163860)
122. Salucci, V. et al. Monocyte-derived dendritic cells from Crohn patients show differential NOD2/CARD15-dependent immune responses to bacteria. Inflamm. Bowel Dis. 14, 812-818 (2008). (Pubitemid 351898066)
123. Ferwerda, G. et al. Mycobacterium paratuberculosis is recognized by Toll-like receptors and NOD2. J. Leukoc Biol. 82, 1011-1018 (2007). (Pubitemid 47511061)
124. Brosbol-Ravnborg, A. et al. Toll-like receptor-induced granulocyte-macrophage colony-stimulating factor secretion is impaired in Crohn's disease by nucleotide oligomerization domain 2-dependent and-independent pathways. Clin. Exp. Immunol. 155, 487-495 (2009).
125. Hedl, M., Li, J., Cho, J. H. & Abraham, C Chronic stimulation of Nod2 mediates tolerance to bacterial products. Proc. Natl Acad. Sci. USA 104, 19440-19445 (2007).
126. Kramer, M., Netea, M. G., de Jong, D. J., Kullberg, B. J. & Adema, G. J. Impaired dendritic cell function in Crohn's disease patients with NOD2 3020insC mutation. J. Leukoc Biol. 79, 860-866 (2006). (Pubitemid 44835619)
127. Bonen, D. K. et al. Crohn's disease-associated NOD2 variants share a signaling defect in response to lipopolysaccharide and peptidoglycan. Gastroenterology 124, 140-146 (2003). (Pubitemid 36055347)
128. Homer, C R., Richmond, A. L., Rebert, N. A., Achkar, J. P. & McDonald, C ATG16L1 and NOD2 interact in an autophagy-dependent antibacterial pathway implicated in Crohn's disease pathogenesis. Gastroenterology 139, 1630-1641e2 (2010).
129. Van Beelen, A. J. et al. Stimulation of the intracellular bacterial sensor NOD2 programs dendritic cells to promote interleukin-17 production in human memory T cells. Immunity 27, 660-669 (2007).
130. Perez, L. H. et al. Direct bacterial killing in vitro by recombinant Nod2 is compromised by Crohn's disease-associated mutations. PLoS ONE 5, e10915 (2010).
131. Cooney, R. et al. NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation. Nat Med. 16, 90-97 (2010).
132. Hisamatsu, T. et al. CARD15/NOD2 functions as an antibacterial factor in human intestinal epithelial cells. Gastroenterology 124, 993-1000 (2003). (Pubitemid 36389802)
133. Lipinski, S. et al. DUOX2-derived reactive oxygen species are effectors of NOD2-mediated antibacterial responses. J. Cell Sci. 122, 3522-3530 (2009).
134. Magalhaes, J. G. et al. Nod2-dependent Th2 polarization of antigen-specific immunity J. Immunol. 181, 7925-7935 (2008).
135. Geddes, K. et al. Nod1 and Nod2 regulation of inflammation in the Salmonella colitis model. Infect. Immun. 78, 5107-5115 (2010).
136. Barreau, F. et al. Nod2 regulates the host response towards microflora by modulating T cel function and epithelial permeability in mouse Peyer's patches. Gut 59, 207-217 (2010).
137. Girardin, S. E. et al. Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan. Science 300, 1584-1587 (2003). (Pubitemid 36682892)
138. McGovern, D. P. et al. Association between a complex insertion/deletion polymorphism in NOD1 (CARD4) and susceptibility to inflammatory bowel disease. Hum. Mol. Genet 14, 1245-1250 (2005). (Pubitemid 40744484)
139. Canto, E. et al. Influence of a nucleotide oligomerization domain 1 (NOD1) polymorphism and NOD2 mutant alleles on Crohn's disease phenotype. World J. Gastroenterol. 13, 5446-5453 (2007). (Pubitemid 47610988)
140. Tremelling, M. et al. Complex insertion/deletion polymorphism in NOD1 (CARD4) is not associated with inflammatory bowel disease susceptibility in East Anglia panel. Inflamm. Bowel Dis. 12, 967-971 (2006). (Pubitemid 44498285)
141. Van Limbergen, J. et al. Contribution of the NOD1/CARD4 insertion/deletion polymorphism +32656 to inflammatory bowel disease in Northern Europe. Inflamm. Bowel Dis. 13, 882-889 (2007). (Pubitemid 47203866)
142. Van Limbergen, J. et al. Investigation of NOD1/CARD4 variation in inflammatory bowel disease using a haplotype-tagging strategy. Hum. Mol. Genet 16, 2175-2186 (2007). (Pubitemid 47354900)
143. Lu, W. G. et al. Association of NOD1 (CARD4) insertion/deletion polymorphism with susceptibility to IBD: a meta-analysis. World J. Gastroenterol. 16, 4348-4356 (2010).
144. Hoffman, H. M., Mueller, J. L., Broide, D. H., Wanderer, A. A. & Kolodner, R. D. Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. Nat Genet 29, 301-305 (2001). (Pubitemid 33096455)
145. Villani, A. C et al. Common variants in the NLRP3 region contribute to Crohn's disease susceptibility Nat Genet 41, 71-76 (2009).
146. Lewis, G. J. et al. Genetic association between NLRP3 variants and Crohn's disease does not replicate in a large UK panel. Inflamm Bowel Dis. doi:10.1002/ibd.21499.
147. Schoultz, I. et al. Combined polymorphisms in genes encoding the inflammasome components NALP3 and CARD8 confer susceptibility to Crohn's disease in Swedish men. Am. J. Gastroenterol. 104, 1180-1188 (2009).
148. Schreiber, S. et al. Tumour necrosis factor alpha and interleukin 1beta in relapse of Crohn's disease. Lancet 353, 459-461 (1999). (Pubitemid 29067338)
149. Broz, P et al. Redundant roles for inflammasome receptors NLRP3 and NLRC4 in host defense against Salmonella. J. Exp. Med. 207, 1745-1755 (2010).
150. Mariathasan, S. et al. Cryopyrin activates the inflammasome in response to toxins and ATP. Nature 440, 228-232 (2006). (Pubitemid 43372102)
151. Zaki, M. H. et al. The NLRP3 inflammasome protects against loss of epithelial integrity and mortality during experimental colitis. Immunity 32, 379-391 (2010).
152. Mizushima, N., Levine, B., Cuervo, A. M. & Klionsky, D. J. Autophagy fights disease through cellular self-digestion. Nature 451, 1069-1075 (2008). (Pubitemid 351317450)
153. Hampe, J. et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39, 207-211 (2007). (Pubitemid 46184351)
154. Rioux, J. D. et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39, 596-604 (2007). (Pubitemid 46676115)
155. Weersma, R. K. et al. ATG16L1 and IL23R are associated with inflammatory bowel diseases but not with celiac disease in the Netherlands. Am. J. Gastroenterol. 103, 621-627 (2008). (Pubitemid 351405995)
156. Glas, J. et al. The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associated with susceptibility to Crohn's disease in the German population. Am. J. Gastroenterol. 103, 682-691 (2008). (Pubitemid 351406000)
157. Parkes, M. et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility Nat Genet 39, 830-832 (2007). (Pubitemid 47014496)
158. McCarroll, S. A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 40, 1107-1112 (2008).
159. Singh, S. B., Davis, A. S., Taylor, G. A. & Deretic, V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 313, 1438-1441 (2006). (Pubitemid 44360272)
160. Lapaquette, P, Glasser, A. L., Huett, A., Xavier, R. J. & Darfeuille-Michaud, A. Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly. Cell. Microbiol. 12, 99-113 (2010).
161. Intemann, C D. et al. Autophagy gene variant RGM-261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains. PLoS Pathog. 5, e1000577 (2009).
162. Travassos, L. H. et al. Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat Immunol. 11, 55-62 (2009).
163. Perminow, G. et al. Defective paneth cell-mediated host defense in pediatric ileal Crohn's disease. Am. J. Gastroenterol. 105, 452-459 (2010).
164. Wehkamp, J. et al. Reduced Paneth cell alpha-defensins in ileal Crohn's disease. Proc Natl Acad. Sci. USA 102, 18129-18134 (2005). (Pubitemid 41798513)
165. Wehkamp, J. et al. NOD2 (CARD15) mutations in Crohn's disease are associated with diminished mucosal alpha-defensin expression. Gut 53, 1658-1664 (2004). (Pubitemid 39434112)
166. Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259-263 (2008).
167. Sim, W. H. et al. Novel Burkholderiales 23S rRNA genes identified in ileal biopsy samples from children: preliminary evidence that a subtype is associated with perianal Crohn's disease. J. Clin. Microbiol. 48, 1939-1942 (2010).
168. Van Etterijck, R. et al. Isolation of Campylobacter concisus from feces of children with and without diarrhea. J. Clin. Microbiol. 34, 2304-2306 (1996). (Pubitemid 26272225)
169. Kangro, H. O., Chong, S. K., Hardiman, A., Heath, R. B. & Walker-Smith, J. A. A prospective study of viral and Mycoplasma infections in chronic inflammatory bowel disease. Gastroenterology 98, 549-553 (1990). (Pubitemid 20069688)
170. Schuller, J. L., Piket-van Ulsen, J., Veeken, I. V., Michel, M. F. & Stolz, E. Antibodies against Chlamydia of lymphogranuloma-venereum type in Crohn's disease. Lancet 1, 19-20 (1979). (Pubitemid 9084466)
171. Swidsinski, A., Loening-Baucke, V., Vaneechoutte, M. & Doerffel, Y Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora. Inflamm. Bowel Dis. 14, 147-161 (2008). (Pubitemid 351288036)
172. Willing, B. et al. Twin studies reveal specific mbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm. Bowel Dis. 15, 653-660 (2009).
173. Sokol, H. et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 15, 1183-1189 (2009).
174. Schwiertz, A. et al. Microbiota in pediatric inflammatory bowel disease. J. Pediatr. 157, 240-244e1 (2010).
175. Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA 105, 16731-16736 (2008).
176. Jia, W. et al. Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease? FEMS Microbiol. Lett. 310, 138-144.
177. Luther, J., Dave, M., Higgins, P D. & Kao, J. Y Association between Helicobacter pylori infection and inflammatory bowel disease: a meta-analysis and systematic review of the literature. Inflamm. Bowel Dis. 16, 1077-1084 (2010).
178. Gutierrez, A. et al. Cytokine association with bacterial DNA in serum of patients with inflammatory bowel disease. Inflamm. Bowel Dis. 15, 508-514 (2009).
179. Liu, Y et al. Immunocytochemical evidence of Listeria, Escherichia coli, and Streptococcus antigens in Crohn's disease. Gastroenterology 108, 1396-1404 (1995).
180. Chen, W., Li, D., Paulus, B., Wilson, I. & Chadwick, V S. 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 (2000).
181. Chiba, M. et al. Listeria monocytogenes in Crohn's disease. Scand. J. Gastroenterol. 33, 430-434 (1998). (Pubitemid 28212557)
182. Qual, D. A., Kaneene, J. B., Varty, T. J., Miller, R. & Thoen, C O. 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 (2010).
183. Canto, E. et al. TNF alpha production to TLR2 igands in active IBD patients. Clin. Immunol. 119, 156-165 (2006).
184. Ng, M. T. et al. Increase in NF-kappaB binding affinity of the variant C allele of the toll-like receptor 9-1237T/C polymorphism is associated with Helicobacter pylori-induced gastric disease. Infect. Immun. 78, 1345-1352 (2010).
185. Molnar, T. et al. NOD1 gene E266K polymorphism is associated with disease susceptibility but not with disease phenotype or NOD2/CARD15 in Hungarian patients with Crohn's disease. Dig. Liver Dis. 39, 1064-1070 (2007). (Pubitemid 350131545)
186. Hysi, P et al. NOD1 variation, immunoglobulin E and asthma. Hum. Mol. Genet. 14, 935-941 (2005). (Pubitemid 40533104)
187. Lala, S. et al. Crohn's disease and the NOD2 gene: a role for paneth cells. Gastroenterology 125, 47-57 (2003). (Pubitemid 36799106)
188. Seidelin, J. B., Broom, O. J., Olsen, J. & Nielsen, O. H. Evidence for impaired CARD15 signalling in Crohn's disease without disease inked variants. PLoS ONE 4, e7794 (2009).
189. Lacher, M. et al. Autophagy 16-like 1 rs2241880 G. allele is associated with Crohn's disease in German children. Acta Paediatr. 98, 1835-1840 (2009).
190. Von Kampen, O. et al. Caspase recruitment domain-containing protein 8 (CARD8) negatively regulates NOD2-mediated signaling. J. Biol. Chem. 285, 19921-19926 (2010).
191. McGovern, D. P et al. TUCAN (CARD8) genetic variants and inflammatory bowel disease. Gastroenterology 131, 1190-1196 (2006). (Pubitemid 44515100)
192. Zhernakova, A. et al. Genetic analysis of innate mmunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP Am. J. Hum. Genet 82, 1202-1210 (2008).
193. Klein, W. et al. A polymorphism in the CD14 gene is associated with Crohn disease. Scand. J. Gastroenterol. 37, 189-191 (2002). (Pubitemid 34102256)
194. Yuan, F. F. et al. Clinical relevance of TLR2, TLR4, CD14 and FcgammaRIIA gene polymorphisms in Streptococcus pneumoniae infection. Immunol. Cell Biol. 86, 268-270 (2008). (Pubitemid 351430807)
195. Gibot, S., Cariou, A., Drouet, L., Rossignol, M. & Ripoll, L Association between a genomic polymorphism within the CD14 locus and septic shock susceptibility and mortality rate. Crit Care Med. 30, 969-973 (2002). (Pubitemid 34508015)
196. De Jager, P L. et al. The role of the Toll receptor pathway in susceptibility to inflammatory bowel diseases. Genes Immun. 8, 387-397 (2007). (Pubitemid 47163102)