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

被引:515
作者
Baumgart, Martin
Dogan, Belgin
Rishniw, Mark
Weitzman, Gil
Bosworth, Brian
Yantiss, Rhonda
Orsi, Renato H.
Wiedmann, Martin
McDonough, Patrick
Kim, Sung Guk
Berg, Douglas
Schukken, Ynte
Scherl, Ellen
Simpson, Kenneth W.
机构
[1] Cornell Univ, Coll Vet Med, Dept Clin Sci, Ithaca, NY 14850 USA
[2] Cornell Univ, Weill Cornell Med Coll, Jill Roberts Inflammatory Bowel Dis Ctr, Div Gastroenterol & Hepatol, Ithaca, NY 14850 USA
[3] Cornell Univ, Coll Agr & Life Sci, Dept Food Sci, Div Gastroenterol & Hepatol, Ithaca, NY 14850 USA
[4] Cornell Univ, Coll Vet Med, Dept Populat Med & Diagnost Sci, Ithaca, NY 14850 USA
[5] Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63130 USA
关键词
adherent and invasive E. coli; dysbiosis; genome subtraction; inflammatory bowel disease; 16S rDNA; INFLAMMATORY-BOWEL-DISEASE; GRADIENT GEL-ELECTROPHORESIS; ULCERATIVE-COLITIS; BACTERIAL INVASION; VIRULENCE FACTORS; FECAL MICROBIOTA; HIGH PREVALENCE; RIBOSOMAL-RNA; IDENTIFICATION; ADHERENT;
D O I
10.1038/ismej.2007.52
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071301 [植物生态学];
摘要
Intestinal bacteria are implicated increasingly as a pivotal factor in the development of Crohn's disease, but the specific components of the complex polymicrobial enteric environment driving the inflammatory response are unresolved. This study addresses the role of the ileal mucosa-associated microflora in Crohn's disease. A combination of culture-independent analysis of bacterial diversity (16S rDNA library analysis, quantitative PCR and fluorescence in situ hybridization) and molecular characterization of cultured bacteria was used to examine the ileal mucosa-associated flora of patients with Crohn's disease involving the ileum (13), Crohn's disease restricted to the colon (CCD) (8) and healthy individuals (7). Analysis of 16S rDNA libraries constructed from ileal mucosa yielded nine clades that segregated according to their origin (P<0.0001). 16S rDNA libraries of ileitis mucosa were enriched in sequences for Escherichia coli (P<0.001), but relatively depleted in a subset of Clostridiales (P<0.05). PCR of mucosal DNA was negative for Mycobacterium avium subspecies paratuberculosis, Shigella and Listeria. The number of E. coli in situ correlated with the severity of ileal disease (rho 0.621, P<0.001) and invasive E. coli was restricted to inflamed mucosa. E. coli strains isolated from the ileum were predominantly novel in phylogeny, displayed pathogen-like behavior in vitro and harbored chromosomal and episomal elements similar to those described in extraintestinal pathogenic E. coli and pathogenic Enterobacteriaceae. These data establish that dysbiosis of the ileal mucosa-associated flora correlates with an ileal Crohn's disease (ICD) phenotype, and raise the possibility that a selective increase in a novel group of invasive E. coli is involved in the etiopathogenesis to Crohn's disease involving the ileum.
引用
收藏
页码:403 / 418
页数:16
相关论文
共 57 条
[1]
The molecular classification of the clinical manifestations of Crohn's disease [J].
Ahmad, T ;
Armuzzi, A ;
Bunce, M ;
Mulcahy-Hawes, K ;
Marshall, SE ;
Orchard, TR ;
Crawshaw, J ;
Large, O ;
De Silva, A ;
Cook, JT ;
Barnardo, M ;
Cullen, S ;
Welsh, KI ;
Jewell, DP .
GASTROENTEROLOGY, 2002, 122 (04) :854-866
[2]
PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori [J].
Akopyants, NS ;
Fradkov, A ;
Diatchenko, L ;
Hill, JE ;
Siebert, PD ;
Lukyanov, SA ;
Sverdlov, ED ;
Berg, DE .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (22) :13108-13113
[3]
Sero-reactivity to microbial components in Crohn's disease is associated with disease severity and progression, but not NOD2/CARD15 genotype [J].
Arnott, IDR ;
Landers, CJ ;
Nimmo, EJ ;
Drummond, HE ;
Smith, BKR ;
Targan, SR ;
Satsangi, J .
AMERICAN JOURNAL OF GASTROENTEROLOGY, 2004, 99 (12) :2376-2384
[4]
Adherent-invasive Escherichia coli and Crohn's disease [J].
Barnich, Nicolas ;
Darfeuille-Michaud, Arlette .
CURRENT OPINION IN GASTROENTEROLOGY, 2007, 23 (01) :16-20
[5]
Supplementation of total parenteral nutrition with butyrate acutely increases structural aspects of intestinal adaptation after an 80% jejunoileal resection in neonatal piglets [J].
Bartholome, AL ;
Albin, DM ;
Baker, DH ;
Holst, JJ ;
Tappenden, KA .
JOURNAL OF PARENTERAL AND ENTERAL NUTRITION, 2004, 28 (04) :210-222
[6]
Boudeau J, 2001, MOL MICROBIOL, V39, P1272, DOI 10.1046/j.1365-2958.2001.02315.x
[7]
Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease [J].
Boudeau, J ;
Glasser, AL ;
Masseret, E ;
Joly, B ;
Darfeuille-Michaud, A .
INFECTION AND IMMUNITY, 1999, 67 (09) :4499-4509
[8]
How to become a uropathogen:: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains [J].
Brzuszkiewicz, Elzbieta ;
Brueggemann, Holger ;
Liesegang, Heiko ;
Emmerth, Melanie ;
Oeschlaeger, Tobias ;
Nagy, Gabor ;
Albermann, Kaj ;
Wagner, Christian ;
Buchrieser, Carmen ;
Emody, Levente ;
Gottschalk, Gerhard ;
Hackert, Joerg ;
Dobrindt, Ulrich .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (34) :12879-12884
[9]
Rapid and simple determination of the Escherichia coli phylogenetic group [J].
Clermont, O ;
Bonacorsi, S ;
Bingen, E .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2000, 66 (10) :4555-4558
[10]
Bacterial invasion: The paradigms of enteroinvasive pathogens [J].
Cossart, P ;
Sansonetti, PJ .
SCIENCE, 2004, 304 (5668) :242-248