Genome analysis of E. coli isolated from Crohn's disease patients

Abstract

Background: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related.

Results: We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons.

Conclusions: Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.

Keywords: Crohn’s disease; E. coli; Genome; Propanediol.

Fig. 1

Genomic similarity of E. coli from individual colonies. Heatmap colors represent the number of SNPs per nucleotide (all-vs-all method). Lighter colors mean higher sequence similarity

Fig. 2

Phylogenetic analysis of E. coli strains. The phylogenetic tree of all universal single-copy genes was constructed by the maximum-likelihood algorithm with 100 bootstrap replicates for E. coli isolates from ten patients (this study), 32 E. coli and Shigella strains from [42] from phylogroups A (yellow), B1(light green), B2 (green), D(cyan), E (blue), S (violet), previously published [–30] CD-associated strains (red), and uropathogenic strain JJ1886. Escherichia albertii KF1 and Escherichia fergusonii ECD227 were used as outgroups

Fig. 3

Genomic comparison of 14 CD-associated strains with pathogenic and non-pathogenic E. coli genomes. Maximum likelihood unrooted tree is based on the core genes. Strains from this study are colored black (here and on the images below indicated as Crohn); previously published CDEC (here and on the images below indicated as CrohnLit) are grey; nonpathogenic, green; pathogenic, pink; strains of undetermined pathogenicity, white. Derivatives of one laboratory strain are merged. Strains containing a plasmid homologous to plLF82 and pJJ1886 are indicated. Pdu operons from LF82 are marked with red

Fig. 4

Full-length alignment of plasmids shared by CDEC strains from the present study: E. coli LF82 plasmid (a), and JJ1886 plasmid 4 (b). The first row in each case represents the plasmid map; other rows show homologous regions and rearrangments (MAUVE 2.4.0, default parameters) between the plasmid of interest and meta-assemblies for specific patients. Each homologous region is shown by a specific color

Fig. 5

Multidimensional scaling plot of distances between the PFAM-domain content in CDEC, pathogenic, non pathogenic, and commensal E. coli. The colors of strains are as in Fig. 3

Fig. 6

Functions of overrepresented OGs (Fisher’s test p-value <0.05 prior to Holm’s correction). The number of overrepresented OGs with a given function is shown on the horizontal axis for commensal strains (grey, left panel) and CDEC (yellow, right panel)

Fig. 7

Operons and gene groups enriched in CDEC (yellow) and commensal E. coli (grey) (Fisher test p-value <0.05 prior to Holm’s correction). OGs form horisontal rows, strains – vertical columns. Genomes with similar OG patterns were clustered together using a custom R script (see Methods). that can be achieved at GitHub repository https://github.com/paraslonic/Rakitina_etal_Crohn_paper/tree/master/ogEnrichment [41]. Phylogroups of strains are indicated (A, B2, B1, D)

Fig. 8

Schematic representation of the propanediol and galactitol operons in CDEC genomes. For each operon the reference strain and the percent of genomes containing it is indicated (CDEC vs commensal)