ORIGINAL ARTICLE Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation Belgin Dogan, PhD,* Haruo Suzuki, PhD, † ,‡ Deepali Herlekar, DVM,* R. Balfour Sartor, MD, §,k Barry J. Campbell, PhD, ¶ Carol L. Roberts, PhD, ¶ Katrina Stewart, DVM,* Ellen J. Scherl, MD,** Yasemin Araz, MA, MEd,* Paulina P. Bitar, BA, † Tristan Lefébure, PhD, † Brendan Chandler, BS,* Ynte H. Schukken, DVM, PhD, † Michael J. Stanhope, PhD, † and Kenneth W. Simpson, BVM&S, PhD* Background: Perturbations of the intestinal microbiome, termed dysbiosis, are linked to intestinal inflammation. Isolation of adherent-invasive Escherichia coli (AIEC) from intestines of patients with Crohn’s disease (CD), dogs with granulomatous colitis, and mice with acute ileitis suggests these bacteria share pathoadaptive virulence factors that promote inflammation. Methods: To identify genes associated with AIEC, we sequenced the genomes of phylogenetically diverse AIEC strains isolated from people with CD (4), dogs with granulomatous colitis (2), and mice with ileitis (2) and 1 non-AIEC strain from CD ileum and compared them with 38 genome sequences of E. coli and Shigella. We then determined the prevalence of AIEC-associated genes in 49 E. coli strains from patients with CD and controls and correlated genotype with invasion of intestinal epithelial cells, persistence within macrophages, AIEC pathotype, and growth in standardized conditions. Results: Genes encoding propanediol utilization (pdu operon) and iron acquisition (yersiniabactin, chu operon) were overrepresented in AIEC relative to nonpathogenic E. coli. PduC (propanediol dehydratase) was enriched in CD-derived AIEC, correlated with increased cellular invasion, and persistence in vitro and was increasingly expressed in fucose-containing media. Growth of AIEC required iron, and the presence of chuA (heme acquisition) correlated with persistence in macrophages. CD-associated AIEC with lpfA 154 (long polar fimbriae) demonstrated increased invasion of epithelial cells and translocation across M cells. Conclusions: Our findings provide novel insights into the genetic basis of the AIEC pathotype, supporting the concept that AIEC are equipped to exploit and promote intestinal inflammation and reveal potential targets for intervention against AIEC and inflammation-associated dysbiosis. (Inflamm Bowel Dis 2014;0:1–14) Key Words: comparative genomics, inflammatory bowel disease, Crohn’s disease, dysbiosis, long polar fimbriae P erturbations in the intestinal microbiome, termed dysbiosis, are increasingly implicated in the development of chronic intestinal inflammation, exemplified by Crohn’s disease (CD) and ulcerative colitis, but the specific components of the complex polymicrobial enteric environment driving the inflammatory response are unre- solved. Numerous studies using conventional and culture- independent microbial analyses have revealed an overabundance of Escherichia coli and a correlation between mucosal colonization Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal’s Web site (www.ibdjournal.org). Received for publication July 9, 2014; Accepted July 9, 2014. From the Departments of *Clinical Sciences, and † Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York; ‡ Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi, Japan; § Departments of Medicine, and k Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina; ¶ Department of Gastroenterology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom; and **Department of Medicine, Jill Roberts Center for Inflammatory Bowel Disease, Weill Medical College of Cornell University, New York, New York. Dr. T. Lefébure is now with the Université de Lyon and Université Lyon 1, Centre National de la Recherche Scientifique, Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France. Supported by grants from the Crohn’s Colitis Foundation (Senior Research Award to K. W. Simpson), NIH R01 DK53347 (R. B. Sartor and K. W. Simpson), and the Jill Roberts Center for Inflammatory Bowel Disease, Weill Medical College of Cornell University, New York. C. L. Roberts and B. J. Campbell were supported by grants from the Wellcome Trust UK (074949/Z/04/Z) and the National Institute of Health Research Specialist Biomedical Research Centre in Microbial Disease (01CD1). B. J. Campbell is also supported by a Crohn’s & Colitis UK award (M/13/2). The authors have no conflicts of interest to disclose. Reprints: Kenneth W. Simpson, BVM&S, PhD, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853 (e-mail: kws5@cornell.edu). Copyright © 2014 Crohn’s & Colitis Foundation of America, Inc. DOI 10.1097/MIB.0000000000000183 Published online. Inflamm Bowel Dis  Volume 0, Number 0, Month 2014 www.ibdjournal.org | 1 Copyright © 2014 Crohn’s & Colitis Foundation of America, Inc. Unauthorized reproduction of this article is prohibited.