Sartor RB. Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006;3:390–407.
Molodecky NA, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142:46–54.
Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134:577–94.
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. 2007;1:403–18.
Dogan B, Simpson KW. Microflora in Crohn’s disease: the emergence of adherent and invasive Escherichia coli. Expert Rev Clin Immunol. 2008;4:133–7.
Frank DN, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA. 2007;104:13780–5.
Darfeuille-Michaud A, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004;127:412–21.
Craven M, et al. Inflammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn’s disease. PLoS One. 2012;7:e41594.
Dogan B, et al. Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation. Inflamm Bowel Dis. 2014;20:1919–32.
Barnich N, Boudeau J, Claret L, Darfeuille-Michaud A. Regulatory and functional co-operation of flagella and type 1 pili in adhesive and invasive abilities of AIEC strain LF82 isolated from a patient with Crohn’s disease. Mol Microbiol. 2003;48:781–94.
DuPont HL. Biologic properties and clinical uses of rifaximin. Expert Opin Pharmacother. 2011;12:293–302.
Prantera C, et al. Rifaximin-extended intestinal release induces remission in patients with moderately active Crohn’s disease. Gastroenterology. 2012;142:473.e4
Calanni F, Renzulli C, Barbanti M, Viscomi GC. Rifaximin: beyond the traditional antibiotic activity. J Antibiot. 2014;67:667–70.
Kothary V, et al. Rifaximin resistance in Escherichia coli associated with inflammatory bowel disease correlates with prior rifaximin use, mutations in rpoB, and activity of Phe-Arg-β-naphthylamide-inhibitable efflux pumps. Antimicrob Agents Chemother. 2013;57:811–7.
Soldi S, et al. Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach. Clin Exp Gastroenterol. 2015;8:309–25.
Brigidi P, Swennen E, Rizzello F, Bozzolasco M, Matteuzzi D. Effects of rifaximin administration on the intestinal microbiota in patients with ulcerative colitis. J Chemother. 2002;14:290–5.
Huang DB, DuPont HL. Rifaximin-a novel antimicrobial for enteric infections. J Infect. 2005;50:97–106.
Jiang ZD, Ke S, Dupont HL. Rifaximin-induced alteration of virulence of diarrhoea-producing Escherichia coli and Shigella sonnei. Int J Antimicrob Agents. 2010;35:278–81.
Debbia EA, Maioli E, Roveta S, Marchese A. Effects of rifaximin on bacterial virulence mechanisms at supra- and sub-inhibitory concentrations. J Chemother. 2008;20:186–94.
Brown EL, Xue Q, Jiang ZD, Xu Y, Dupont HL. Pretreatment of epithelial cells with rifaximin alters bacterial attachment and internalization profiles. Antimicrob Agents Chemother. 2010;54:388–96.
Barnich N, Bringer MA, Claret L, Darfeuille-Michaud A. Involvement of lipoprotein NlpI in the virulence of adherent invasive Escherichia coli strain LF82 isolated from a patient with Crohn’s disease. Infect Immun. 2004;72:2484–93.
Bringer MA, Barnich N, Glasser AL, Bardot O, Darfeuille-Michaud A. HtrA stress protein is involved in intramacrophagic replication of adherent and invasive Escherichia coli strain LF82 isolated from a patient with Crohn’s disease. Infect Immun. 2005;73:712–21.
Bringer MA, Rolhion N, Glasser AL, 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. 2007;189:4860–71.
Rolhion N, Barnich N, Claret L, Darfeuille-Michaud A. Strong decrease in invasive ability and outer membrane vesicle release in Crohn’s disease-associated adherent-invasive Escherichia coli strain LF82 with the yfgL gene deleted. J Bacteriol. 2005;187:2286–96.
Rolhion N, Carvalho FA, 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. 2007;63:1684–700.
Jiang ZD, Ke S, Palazzini E, Riopel L, Dupont H. In vitro activity and fecal concentration of rifaximin after oral administration. Antimicrob Agents Chemother. 2000;44:2205–6.
Nitzan O, Elias M, Peretz A, Saliba W. Role of antibiotics for treatment of inflammatory bowel disease. World J Gastroenterol. 2016;22:1078–87.
Dogan B, et al. Multidrug resistance is common in Escherichia coli associated with ileal Crohn’s disease. Inflamm Bowel Dis. 2013;19:141–50.
Carvalho FA, et al. Crohn’s disease-associated Escherichia coli LF82 aggravates colitis in injured mouse colon via signaling by flagellin. Inflamm Bowel Dis. 2008;14:1051–60.
Barnich N, et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease. J Clin Invest. 2007;117:1566–74.
Schrodt C, McHugh EE, Gawinowicz MA, Dupont HL, Brown EL. Rifaximin-mediated changes to the epithelial cell proteome: 2-D gel analysis. PLoS One. 2013;8:e68550.
Simpson KW, et al. Adherent and invasive Escherichia coli is associated with granulomatous colitis in Boxer dogs. Infect Immun. 2006;74:4778–92.
Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol. 2014;5:213–27.
Ma X, et al. Rifaximin is a gut-specific human pregnane X receptor activator. J Pharmacol Exp Ther. 2007;322:391–8.
Cheng J, Shah YM, Gonzalez FJ. Pregnane X receptor as a target for treatment of inflammatory bowel disorders. Trends Pharmacol Sci. 2012;33:323–30.
Dring MM, et al. The pregnane X receptor locus is associated with susceptibility to inflammatory bowel disease. Gastroenterology. 2006;130:341–8.
Haslam IS, Jones K, Coleman T, Simmons NL. Rifampin and digoxin induction of MDR1 expression and function in human intestinal (T84) epithelial cells. Br J Pharmacol. 2008;154:246–55.
Habano W, et al. Involvement of promoter methylation in the regulation of Pregnane X receptor in colon cancer cells. BMC Cancer. 2011;11:81.
Langmann T, et al. Loss of detoxification in inflammatory bowel disease: dysregulation of pregnane X receptor target genes. Gastroenterology. 2004;127:26–40.
Glasser AL, 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. 2001;69:5529–37.
Bringer MA, Billard E, Glasser AL, Colombel JF, Darfeuille-Michaud A. Replication of Crohn’s disease-associated AIEC within macrophages is dependent on TNF-alpha secretion. Lab Invest. 2012;92:411–9.