Targeting the microbiome in Crohn’s disease

References

• Crohn BB, Ginzburg L, Oppenheimer GD. Regional ileitis: a pathological and clinical entity. JAMA. 1932;99(16):1323–1329.
   Google Scholar
• Dalziel TK. Chronic interstitial enteritis. Br Med J (Clin Res). 1913;2:1068.
   Google Scholar
• Van Kruiningen HJ, Chiodini RJ, Thayer WR, et al. Experimental disease in infant goats induced by a Mycobacterium isolated from a patient with Crohn’s disease. A preliminary report. Dig Dis Sci. 1986;31(12):1351–1360.
   PubMed Web of Science ®Google Scholar
• Chiodini RJ, Van Kruiningen HJ, Merkal RS, et al. Characteristics of an unclassified Mycobacterium species isolated from patients with Crohn’s disease. J Clin Microbiol. 1984;20(5):966–971.
   PubMed Web of Science ®Google Scholar
• Chamberlin W, Borody T, Naser S. MAP-associated Crohn’s disease MAP, Koch’s postulates, causality and Crohn’s disease. Dig Liver Dis. 2007;39(8):792–794.
   PubMedGoogle Scholar
• Greenstein RJ. Is Crohn’s disease caused by a mycobacterium? Comparisons with leprosy, tuberculosis, and Johne’s disease. Lancet Infect Dis. 2003;3(8):507–514.
   PubMed Web of Science ®Google Scholar
• Hermon-Taylor J. Mycobacterium avium subspecies paratuberculosis is a cause of Crohn’s disease. Gut. 2001;49(6):755–757.
   PubMedGoogle Scholar
• Sanderson JD, Moss MT, Tizard ML, et al. Mycobacterium paratuberculosis DNA in Crohn’s disease tissue. Gut. 1992;33(7):890–896.
   PubMed Web of Science ®Google Scholar
• Moss MT, Sanderson JD, Tizard ML, et al. Polymerase chain reaction detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp silvaticum in long term cultures from Crohn’s disease and control tissues. Gut. 1992;33(9):1209–1213.
   PubMed Web of Science ®Google Scholar
• Naser SA, Sagramsingh SR, Naser AS, et al. Mycobacterium avium subspecies paratuberculosis causes Crohn’s disease in some inflammatory bowel disease patients. World J Gastroenterol. 2014;20(23):7403–7415.
   PubMed Web of Science ®Google Scholar
• Axelrad JE, Olén O, Askling J, et al. Gastrointestinal infection increases odds of inflammatory bowel disease in a nationwide case-control study. Clin Gastroenterol Hepatol. 2019;17(7):1311–22.e7.
   PubMed Web of Science ®Google Scholar
• Borody TJ, Leis SM, Warren EF, et al. Treatment of severe Crohn’s disease using antimycobacterial triple therapy—Approaching a cure. Dig Liver Dis. 2002;34(1):29–38.
   PubMedGoogle Scholar
• Liu TC, Stappenbeck TS. Genetics and pathogenesis of inflammatory bowel disease. Annu Rev Pathol. 2016;11(1):127–148.
   PubMedGoogle Scholar
• Sidiq T, Yoshihama S, Downs I, et al. Nod2: a critical regulator of ileal microbiota and Crohn’s disease. Front Immunol. 2016;7:367.
   PubMed Web of Science ®Google Scholar
• Kersse K, Bertrand MJ, Lamkanfi M, et al. NOD-like receptors and the innate immune system: coping with danger, damage and death. Cytokine Growth Factor Rev. 2011;22(5–6):257–276.
   PubMed Web of Science ®Google Scholar
• Abraham C, Cho JH. Inflammatory bowel disease. N Engl J Med. 2009;361(21):2066–2078.
   PubMed Web of Science ®Google Scholar
• Salzman NH. Paneth cell defensins and the regulation of the microbiome: détente at mucosal surfaces. Gut Microbes. 2010;1(6):401–406.
   PubMed Web of Science ®Google Scholar
• Lauro ML, Burch JM, Grimes CL. The effect of NOD2 on the microbiota in Crohn’s disease. Curr Opin Biotechnol. 2016;40:97–102.
   PubMed Web of Science ®Google Scholar
• Frank DN, Robertson CE, Hamm CM, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17(1):179–184.
   PubMed Web of Science ®Google Scholar
• Ventura M, Canchaya C, Tauch A, et al. Genomics of actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev. 2007;71(3):495–548.
   PubMed Web of Science ®Google Scholar
• Coulombe F, Divangahi M, Veyrier F, et al. Increased NOD2-mediated recognition of N-glycolyl muramyl dipeptide. J Exp Med. 2009;206(8):1709–1716.
   PubMed Web of Science ®Google Scholar
• Philpott DJ, Sorbara MT, Robertson SJ, et al. NOD proteins: regulators of inflammation in health and disease. Nat Rev Immunol. 2014;14(1):9–23.
   PubMed Web of Science ®Google Scholar
• Clancy R, Ren Z, Turton J, et al. Molecular evidence for Mycobacterium avium subspecies paratuberculosis (MAP) in Crohn’s disease correlates with enhanced TNF-alpha secretion. Dig Liver Dis. 2007;39(5):445–451.
   PubMedGoogle Scholar
• Ren Z, Turton J, Borody T, et al. Selective Th2 pattern of cytokine secretion in Mycobacterium avium subsp. paratuberculosis infected Crohn’s disease. J Gastroenterol Hepatol. 2008;23(2):310–314.
   PubMed Web of Science ®Google Scholar
• Friswell M, Campbell B, Rhodes J. The role of bacteria in the pathogenesis of inflammatory bowel disease. Gut Liver. 2010;4(3):295–306.
   PubMed Web of Science ®Google Scholar
• McNees AL, Markesich D, Zayyani NR, et al. Mycobacterium paratuberculosis as a cause of Crohn’s disease. Expert Rev Gastroenterol Hepatol. 2015;9(12):1523–1534.
   PubMed Web of Science ®Google Scholar
• Gui GPH, Thomas PRS, Tizard MLV, et al. Two-year-outcomes analysis of Crohn’s disease treated with rifabutin and macrolide antibiotics. J Antimicrob Chemother. 1997;39(3):393–400.
   PubMed Web of Science ®Google Scholar
• Hampson SJ, Parker MC, Saverymuttu SH, et al. Quadruple antimycobacterial therapy in Crohn’s disease: results at 9 months of a pilot study in 20 patients. Aliment Pharmacol Therap. 1989;3(4):343–352.
   PubMed Web of Science ®Google Scholar
• Campbell J, Borody TJ, Leis S. The many faces of Crohn’s Disease: latest concepts in etiology. Open J of Internal Med. 2012;2(2):107–115
   Google Scholar
• Collyer R, Clancy A, Agrawal G, et al. Crohn’s strictures open with anti-mycobacterial antibiotic therapy: a retrospective review. World J Gastrointest Endosc. 2020;12(12):542–554.
   PubMed Web of Science ®Google Scholar
• Borody TJ, Pearce L, Bampton PA, et al. Treatment of severe Crohn’s disease (CD) using rifabutin-macrolide-clofazimine combination: interim report. Gastroenterology. 1998;114:A938.
   Web of Science ®Google Scholar
• Borody TJ, Leis S, Surace R, et al. Treatment of severe Crohn’s disease (CD) using rifabutin-macrolide-clofazimine combination: results at 30-37 months. Gastroenterology. 2000;118(4):A1334.
   Web of Science ®Google Scholar
• Borody TJ, Leis S, Surace R, et al. Treatment of severe Crohn’s disease using rifabutin- macrolide-clofazimine combination – results at 38-43 months. J Gastroenterol Hepatol. 2000;15:J102.
   Google Scholar
• Jaworski A, Borody TJ, Ramrakha S, et al. Antibiotic therapy for treatment-naïve Crohn’s disease patients. Am J Gastroenterol. 2016;111:S272.
   Google Scholar
• Agrawal G, Clancy A, Huynh R, et al. Profound remission in Crohn’s disease requiring no further treatment for 3–23 years: a case series. Gut Pathog. 2020;12(1):16.
   PubMed Web of Science ®Google Scholar
• Agrawal G, Clancy A, Sharma R, et al. Targeted combination antibiotic therapy induces remission in treatment-naïve Crohn’s disease: a case series. Microorganisms. 2020;8(3):371.
   Web of Science ®Google Scholar
• Selby W, Pavli P, Crotty B, et al. Antibiotics in Crohn’s disease study group. two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology. 2007;132(7):2313–2319.
   PubMed Web of Science ®Google Scholar
• Behr MA, Hanley J. Reflection and reaction antimycobacterial therapy for Crohn’s disease: a reanalysis. Lancet Infect Dis. 2008;8(6):2008.
   Google Scholar
• Graham DY, Hardi R, Welton T, et al. Phase III Randomized, Double Blind, Placebo-Controlled, Multicenter, Parallel Group Study to assess the efficacy and safety of add-on fixed-dose anti-microbial therapy (RHB-104) in moderately to severe active Crohn’s Disease (MAP US). Late breaking abstracts. United European Gastroenterol J. 2018;6:1586–1597.
   Google Scholar
• Khan KJ, Ullman TA, Ford AC, et al. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol. 2011;106(4):661–673.
   PubMed Web of Science ®Google Scholar
• Borody TJ, George L, Andrews P, et al. Bowel flora alteration: a potential cure for inflammatory bowel disease and irritable bowel syndrome? Med J Aust. 1989;150(10):604.
   PubMed Web of Science ®Google Scholar
• Paramsothy S, Paramsothy R, Rubin DT, et al. Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohn’s Colitis. 2017;11(10):1180–1199.
   Google Scholar
• Wei Y, Zhu W, Gong J. Fecal Microbiota Transplantation improves the quality of life in patients with inflammatory bowel disease. Gastroenterol Res Pract. 2015;517597:1–5.
   Google Scholar
• Li Q, Ding X, Liu Y. Fecal microbiota transplantation is a promising switch therapy for patients with prior failure of infliximab in crohn’s disease. Front Pharmacol. 2021;12:658087.
   PubMed Web of Science ®Google Scholar
• Fang H, Fu L, Wang J. Protocol for fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis. Biomed Res Int. 2018;8941340:1–11.
   Google Scholar
• He Z, Li P, Zhu J, et al. Multiple fresh fecal microbiota transplants induces and maintains clinical remission in Crohn’s disease complicated with inflammatory mass. Sci Rep. 2017;7(1):4753.
   PubMedGoogle Scholar
• Caldeira L, Borba HH, Tonin FS, et al. Fecal microbiota transplantation in inflammatory bowel disease patients: a systematic review and metaanalysis. PLoS ONE. 2020;15(9):e0238910.
   PubMed Web of Science ®Google Scholar
• Fehily SR, Basnayake C, Wright EK. Fecal microbiota transplantation therapy in Crohn’s disease: systematic review. J Gastroenterol Hepatol. 2021;36(10):2672–2686.
   PubMed Web of Science ®Google Scholar
• Kamm M. The MIRO II study: microbial restoration in inflammatory bowel diseases [Internet]. clinicaltrials.gov; 2021 Jul [cited 2022 May 1]. Report No.: NCT04970446. Available from: https://clinicaltrials.gov/ct2/show/NCT04970446
   Google Scholar
• Turner D. Manipulating the microbiome in IBD by antibiotics and Fecal Microbiota Transplantation (FMT): a randomized controlled trial [Internet]. clinicaltrials.gov; 2021 Sep [cited 2022 May 1]. Report No.: NCT02033408. Available from: https://clinicaltrials.gov/ct2/show/NCT02033408
   Google Scholar
• Agrawal G, Jayewardene AF, Leis S. Prolonged endoscopic remission with mucosal healing in Crohnʼs patients: treatment cessation for 3-23 years. Am J Gastroenterol. 2017;112:S420.
   Web of Science ®Google Scholar
• Shah RS, Click BH. Medical therapies for postoperative Crohn’s disease. Therap Adv Gastroenterol. 2021;14:1756284821993581.
   Web of Science ®Google Scholar