Open Access Highly Accessed Open Badges Research article

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

John HE Nash1, Andre Villegas1, Andrew M Kropinski2, Renan Aguilar-Valenzuela3, Paulina Konczy2, Mariola Mascarenhas2, Kim Ziebell2, Alfredo G Torres3, Mohamed A Karmali12 and Brian K Coombes4*

Author Affiliations

1 Office of Biotechnology, Genomics and Population Health, Public Health Agency of Canada, 180 Queen Street West, Toronto, Ontario M5V 3L7, Canada

2 Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, Ontario N1G 3W4, Canada

3 Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, 77555-1070, USA

4 Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada

For all author emails, please log on.

BMC Genomics 2010, 11:667  doi:10.1186/1471-2164-11-667

Published: 25 November 2010



Adherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated E. coli pathotype.


We sequenced the complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal E. coli allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype.


Up to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease.