Comparative genomics of Crohn's disease-associated adherent, invasive E. coli

TitleComparative genomics of Crohn's disease-associated adherent, invasive E. coli
Brief TitleGenomics of adherent, invasive E. coli
Collection TypeRepository
Access PrivilegesResearch School of Biology
DOI - Digital Object Identifier10.4225/13/56F08C5B5F0FE
Metadata LanguageEnglish
Data LanguageEnglish
Significance StatementThis study represents the most comprehensive genome comparison of adherent, invasive Escherichia coli strains to-date.
Brief DescriptionAdherent invasive E. coli (AIEC) and non-AIEC genomes were compared.
Full DescriptionObjective

Adherent-invasive E. coli (AIEC) are a leading candidate bacterial trigger for Crohn’s disease (CD). The AIEC pathovar is defined by in vitro cell-line assays examining specific bacteria/cell interactions. No molecular marker exists for their identification. Our aim was to identify a molecular property common to the AIEC phenotype.


41 B2 phylogroup E. coli strains were isolated from 36 Australian subjects: 19 patients with inflammatory bowel disease (IBD) and 17 without. Adherence/invasion assays were conducted using the I-407 epithelial cell line and survival/replication assays using the THP-1 macrophage cell line. Cytokine secretion (TNF-α, IL-6, IL-8, and IL-10) was measured using ELISA. The genomes were assembled and annotated, and cluster analysis performed using CD-HIT. The resulting matrices were analysed to identify genes unique/more frequent in AIEC strains compared to non-AIEC strains. Base composition differences and CRISPR analyses were conducted.


Of all B2 phylogroup strains assessed, 79% could survive and replicate in macrophages. Among them, 11/41 strains (5 CD, 2 ulcerative colitis, 5 non-IBD) also adhere to and invade epithelial cells, a phenotype assigning them to the AIEC pathovar. The AIEC strains were phylogenetically heterogeneous. We did not identify a gene (or nucleic acid base composition differences) common to all, or the majority of, AIEC. Cytokine secretion and CRISPRs were not associated with the AIEC phenotype.


Comparative genomic analysis of AIEC and non-AIEC strains did not identify a molecular property exclusive to the AIEC phenotype. We recommend a broader approach to the identification of the bacteria-host interactions that are important in the pathogenesis of Crohn’s disease.

Contact AddressLvl 5, Bldg 10, Canberra Hospital
Yamba Drive, Garran
ACT 2605
Contact Phone Number0406687565
Principal InvestigatorDr Claire O'Brien
Fields of Research110899 - Medical Microbiology not elsewhere classified
119999 - Medical and Health Sciences not elsewhere classified
KeywordsCrohn's disease
Genome, Microbial
Escherichia coli
Date Coverage
Date FromDate To
Date of data creation2015
Year of data publication2016
Creator(s) for Citation
Given NameSurname
Publisher for CitationGut
Access RightsContact Chief Investigator if you wish to use the data. Cite the relevant publication.
Embargo Date2016-01-01
Retention Period10 years
Disposal Date2026
Extent or Quantity42
Data Size404 MB
Status: Published
Published To:
- Australian National University
Identifier: anudc:5410


  • Files: 42
  • Size: 404 MB

Data Files

Updated:  07 February 2019/ Responsible Officer:  University Librarian/ Page Contact:  Library Systems & Web Coordinator