Genome analysis of E. coli isolated from Crohn\u2019s disease patients

Daria V Rakitina,Petr Scherbakov ,Elena S Kostryukova,И Л Халиф ,Elena N Ilina,Dmitry Alexeev ,Vladislav V Babenko,Alexander I Manolov,Roman Gorodnichev ,Eugenia S Lisitsyna,D N Andreev ,V G Ladygina ,И В Маев ,Irina Y Karpova,Sofya K Garushyants,М В Шапина ,Mikhail S Gelfand,Г И Алешкин ,Р К Исмагилова ,Andrei K Larin,Alexandra Kanygina ,Tatiana A Semashko,Sergey Malanin ,Julia Baikova ,Vadim M Govorun

doi:10.1186/s12864-017-3917-x

Abstract

BackgroundEscherichia 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.ResultsWe 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.ConclusionsOur 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.

Highlights

Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD)
E. coli Strains cultivated from an inflamed intestine of a CD patient are closely related Genome assemblies were obtained for 28 E. coli isolates from 10 Crohn’s disease patients (Table 1)
Our findings suggest that CDEC are of diverse phylogeny

Summary

Introduction

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. The histological picture of Crohn’s disease includes thickened submucosa, transmural inflammation, fissuring ulceration, and non-caseating granulomas. Many factors, both genetic and environmental, are regarded to contribute to the CD pathogenesis. It is a general notion that CD is a result of abnormal immune response of genetically susceptible individuals to the imbalance in the intestinal microbiota (reviewed in [1, 2]). Host susceptibility factors include intestinal barrier dysfunctions (decreased levels of antimicrobial peptides defensins, discontinuous tight junctions and aberrant mucin assembly) and defects in innate immunity, autophagy, and phagocytosis. NOD2, ATG16L1, and IRGM) involved in these processes have been reported to be associated with CD

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