References
- Chassaing, B & Darfeuille-Michaud, A. The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology 2011;140:1720–1728.
- Kaser, A, Zeissig, S & Blumberg, RS. Inflammatory Bowel Disease. Annu. Rev. Immunol. 2010;28:573.
- Xavier, RJ & Podolsky, DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature 2007;448:427–434.
- Barnich, N & Darfeuille-Michaud, A. Role of bacteria in the etiopathogenesis of inflammatory bowel disease. World J. Gastroenterol. WJG 2007;13:5571.
- Darfeuille-Michaud, A, et al. Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 1998;115:1405–1413.
- Bevins, CL & Salzman, NH. Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nat. Rev. Microbiol. 2011;9:356–368.
- Mantis, NJ & Forbes, SJ. Secretory IgA: Arresting Microbial Pathogens at Epithelial Borders. Immunol. Invest. 2010;39:383.
- Cadwell, K, et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 2008;456:259–263.
- Liu, B, et al. Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 2013;305:G573–584.
- Kaser, A, et al. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell 2008;134:743–756.
- Hugot, JP, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001;411:599–603.
- Ogura, Y, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001;411:603–606.
- Wehkamp, J, et al. NOD2 (CARD15) mutations in Crohn's disease are associated with diminished mucosal α-defensin expression. Gut 2004;53:1658.
- Abraham, C & Cho, JH. Inflammatory bowel disease. N. Engl. J. Med. 2009;361:2066–2078.
- Vazeille, E, et al. Role of meprins to protect ileal mucosa of Crohn's disease patients from colonization by adherent-invasive E. coli. PloS One 2011;6:e21199.
- 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;. 5:213–227.
- O'Brien, CL, et al. Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli. Gut 2016; (). doi:10.1136/gutjnl-2015-311059.
- McPhee, JB, et al. Host defense peptide resistance contributes to colonization and maximal intestinal pathology by Crohn's disease-associated adherent-invasive Escherichia coli. Infect. Immun 2014; 82:3383–3393.
- Gibold, L, et al. The Vat-AIEC protease promotes crossing of the intestinal mucus layer by Crohn's disease-associated Escherichia coli. Cell. Microbiol 2015;n/a-n/a. doi:10.1111/cmi.12539.
- 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;20:1919–1932.
- Claret, L, et al. The Flagellar Sigma Factor FliA Regulates Adhesion and Invasion of Crohn Disease-associated Escherichia coli via a Cyclic Dimeric GMP-dependent Pathway. J. Biol. Chem. 2007;282:33275–33283.
- 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;48:781–794.
- Carvalho, FA, et al. Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM. J. Exp. Med. 2009;206:2179.
- Gewirtz, AT, Navas, TA, Lyons, S, Godowski, PJ & Madara, JL. Cutting Edge Bacterial Flagellin Activates Basolaterally Expressed TLR5 to Induce Epithelial Proinflammatory Gene Expression. J. Immunol. 2001;167:1882–1885.
- Carvalho, FA, et al. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 2012;12:139–152.
- Chassaing, B, Koren, O, Carvalho, FA, Ley, RE & Gewirtz, AT. AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut 2013. doi:10.1136/gutjnl-2013-304909.
- Zhao, Y & Shao, F. The NAIP-NLRC4 inflammasome in innate immune detection of bacterial flagellin and type III secretion apparatus. Immunol. Rev. 2015;265:85–102.
- 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;63:1684–1700.
- Chassaing, B, Etienne-Mesmin, L, Bonnet, R & Darfeuille-Michaud, A. Bile salts induce long polar fimbriae expression favouring Crohn's disease-associated adherent-invasive Escherichia coli interaction with Peyer's patches. Environ. Microbiol. 2013;15:355–371.
- Pope, LM, Reed, KE & Payne, SM. Increased protein secretion and adherence to HeLa cells by Shigella spp. following growth in the presence of bile salts. Infect. Immun 1995;. 63:3642–3648.
- Wibbenmeyer, JA, Provenzano, D, Landry, CF, Klose, KE & Delcour, AH. Vibrio cholerae OmpU and OmpT porins are differentially affected by bile. Infect. Immun. 2002;70:121–126.
- Johansson, M. E. V., et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut 2014;63:281–291.
- Petersson, J, et al. Importance and regulation of the colonic mucus barrier in a mouse model of colitis. Am. J. Physiol. – Gastrointest. Liver Physiol. 2011;300:G327.
- Schreiber, O, et al. iNOS-Dependent Increase in Colonic Mucus Thickness in DSS-Colitic Rats. PLoS ONE 2013;8.
- 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;. 1:403–418.
- Conte, MP, et al. Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn's disease patients: phenotypic and genetic pathogenic features. BMC Res. Notes 2014;7:748.
- Darfeuille-Michaud, A, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004;127:412–421.
- 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. 2009;15:872–882.
- Sepehri, S, Kotlowski, R, Bernstein, CN & Krause, DO. Phylogenetic analysis of inflammatory bowel disease associated Escherichia coli and the fimH virulence determinant. Inflamm. Bowel Dis. 2009;15:1737–1745.
- Harrington, SM, et al. The Pic protease of enteroaggregative Escherichia coli promotes intestinal colonization and growth in the presence of mucin. Infect. Immun. 2009;77:2465–2473.
- Kobayashi, RK, Gaziri, LC & Vidotto, MC. Functional activities of the Tsh protein from avian pathogenic Escherichia coli (APEC) strains. J. Vet. Sci. 2010;11:315–319.
- Aldhous, MC, Noble, CL & Satsangi, J. Dysregulation of human beta-defensin-2 protein in inflammatory bowel disease. PloS One 2009;4:e6285.
- Meisch, JP, et al. Human β-defensin 3 peptide is increased and redistributed in Crohn's ileitis. Inflamm. Bowel Dis. 2013;19:942–953.
- Lane, MC, Alteri, CJ, Smith, SN & Mobley, H. L. T.. Expression of flagella is coincident with uropathogenic Escherichia coli ascension to the upper urinary tract. Proc. Natl. Acad. Sci. U. S. A. 2007;104:16669.
- Jozwick, A. K. S., Graf, J & Welch, TJ. The flagellar master operon flhDC is a pleiotropic regulator involved in motility and virulence of the fish pathogen Yersinia ruckeri. J. Appl. Microbiol. 2017;122:578–588.
- Giraud, A, et al. Dissecting the genetic components of adaptation of Escherichia coli to the mouse gut. PLoS Genet 2008;. 4:e2.
- Gauger, EJ, et al. Role of motility and the flhDC Operon in Escherichia coli MG1655 colonization of the mouse intestine. Infect. Immun. 2007;75:3315–3324.
- Miquel, S, et al. Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82. PloS One 2010;5.
- Nash, JH, et al. Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes. BMC Genomics 2010;11:667.
- Schippa, S, et al. A potential role of Escherichia coli pathobionts in the pathogenesis of pediatric inflammatory bowel disease. Can. J. Microbiol 2012;. 58:426–432.
- Dreux, N, et al. Point mutations in FimH adhesin of Crohn's disease-associated adherent-invasive Escherichia coli enhance intestinal inflammatory response. PLoS Pathog 2013;. 9:e1003141.
- Hughes, KT & Mathee, K. The anti-sigma factors. Annu. Rev. Microbiol. 1998;52:231–286.
- Alaniz, RC, Cummings, LA, Bergman, MA, Rassoulian-Barrett, SL & Cookson, BT. Salmonella typhimurium coordinately regulates FliC location and reduces dendritic cell activation and antigen presentation to CD4+ T cells. J. Immunol. Baltim. Md 1950 2006;177:3983–3993.
- Cummings, LA, Barrett, S. L. R., Wilkerson, WD, Fellnerova, I & Cookson, BT. FliC-specific CD4+ T cell responses are restricted by bacterial regulation of antigen expression. J. Immunol. Baltim. Md 1950 2005;174:7929–7938.
- Yim, L, et al. Repression of flagella is a common trait in field isolates of Salmonella enterica serovar Dublin and is associated with invasive human infections. Infect. Immun 2014;. 82:1465–1476.
- Curtis, MM, et al. QseC inhibitors as an antivirulence approach for Gram-negative pathogens. mBio 2014;5:e02165.
- Rasko, DA, et al. Targeting QseC Signaling and Virulence for Antibiotic Development. Science 2008;321:1078.
- Shuai-Cheng, W, et al. Subinhibitory concentrations of phloretin repress the virulence of Salmonella typhimurium and protect against Salmonella typhimurium infection. Antonie Van Leeuwenhoek 2016;109:1503–1512.
- Marathe, SA, et al. Curcumin Reduces the Motility of Salmonella enterica serovar Typhimurium by Binding to the Flagella thereby Leading to Flagellar Fragility and Shedding. J. Bacteriol. 2016; JB:00092–16. doi:10.1128/JB.00092-16
- Datsenko, KA & Wanner, BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U. S. A. 2000;97:6640–6645.
- Chaveroche, MK, Ghigo, JM & d'Enfert, C. A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans. Nucleic Acids Res 2000; 28:E97.
- Lesuffleur, T, et al. Differential expression of the human mucin genes MUC1 to MUC5 in relation to growth and differentiation of different mucus-secreting HT-29 cell subpopulations. J. Cell Sci. 1993;106(Pt 3):771–783.
- Bringer, M.-A., Barnich, N, Glasser, A.-L., 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;73:712–721.
- Aldridge, P, Gnerer, J, Karlinsey, JE & Hughes, KT. Transcriptional and Translational Control of the Salmonella fliC Gene. J. Bacteriol. 2006;188:4487–4496.
- Ide, N, Ikebe, T & Kutsukake, K. Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella. Genes Genet. Syst. 1999;74:113–116.
- Simons, RW, Houman, F & Kleckner, N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 1987;53:85–96.
- Miller, J. Experiments in Molecular Genetics. .NY: Cold Spring Harbor Laboratory Press. Cold Spring Harb; 1972.
- Chan, C. H. F. & Stanners, CP. Novel mouse model for carcinoembryonic antigen-based therapy. Mol. Ther. J. Am. Soc. Gene Ther. 2004;9:775–785.
- Dalmasso, G, et al. The PepT1-NOD2 signaling pathway aggravates induced colitis in mice. Gastroenterology 2011;141:1334–1345.
- Brett, PJ, Mah, DC & Woods, DE. Isolation and characterization of Pseudomonas pseudomallei flagellin proteins. Infect. Immun. 1994;62:1914–1919.
- Hecht, G, et al. A simple cage-autonomous method for the maintenance of the barrier status of germ-free mice during experimentation. Lab. Anim. 2014;48:292–297.
- Johansson, M. E. V. & Hansson, GC. Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH. Methods Mol. Biol. Clifton NJ 2012;842:229–235.
- Chassaing, B, et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 2015;519:92.