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.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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3917-x) contains supplementary material, which is available to authorized users.

Genome Complexity Browser: estimation and visualization of prokaryote genome variability

“…Figures 2 A and B show an example of subgraphs representing the gene context of the hemin uptake locus (hmu) and propanediol utilization operon (pdu) in 326 complete genomes of Escherichia coli from the RefSeq database (downloaded at the September 2017). The presence of E. coli harboring these operons in the intestinal microbiome was previously shown to be associated with Crohn's disease (Dogan et al, 2014;Viladomiu et al, 2017;Rakitina et al, 2017). While hmu operon is preferentially present in B2 phylogroup ( Supplementary Figure 1, retention index = 1), pdu operon can be found in phylogenetically distinct strains of E. coli, and its presence is in low agreement with the phylogenetic tree ( Supplementary Figure 2, retention index = 0.26).…”

Neutrophil activation by Escherichia coli isolates from human intestine: effects of bacterial hydroperoxidase activity and surface hydrophobicity

“… Phylogroups of E. coli isolates were determined from their genomes (sequencing performed in our previous work ). …”

“…References to the genomes of E. coli isolates are given according to Ref. [29] Localization, clinical activity, and endoscopical activity of inflammation were determined according to Ref. [30,31] a The amount of E. coli DNA was measured in feces or aspirate even if some E. coli strains for study were sampled from biopsy.…”

“…Alignment of E. coli genome sequences from different intestine parts of one patient performed earlier [29] revealed only minor heterogeneity and some deletions (usually a deletion of one of the smaller contigs, probably a plasmid). At the same time, sequences of genes identified as encoding catalases and peroxidases of isolates from one patient were identical, since none of the found polymorphisms was located in those genes.…”

Targeted therapy of inflammatory bowel diseases: realities and prospects

“…Таксономические изменения микро-биома у пациентов с ВЗК заключаются в повышении Enterobacteriaceae (преимущественно Escherichia/Shigella) у пациентов с БК и снижении Leuconostocaceae у больных ЯК [13,24,25]. Более того, в ряде работ было показано, что БК-ассоциированные Escherichia coli обладают способно-стями, кумулятивно позволяющими рассматривать их как потенциальный патогенетический фактор при БК (адгезия к эпителиоцитам слизистой; внедрение в эпителиоциты слизистой; активная репликация внутри макрофагов) [26][27][28]. Частота выявления такого фенотипа Escherichia coli у пациентов с БК на 30% выше, чем у здоровых лиц [29].…”