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

Abstract

BackgroundAdherent 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.ResultsWe 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.ConclusionsUp 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.

Molecular and serological investigation of Leptospira and leptospirosis in dogs in Japan

“…This statistical value may be attributable to the small sample numbers in this study, and a larger sample size may be needed to verify the correlation between Leptospira genotypes and virulence. Reduced virulence in a specific genotype has never been reported, and a new insight into leptospiral virulence could be obtained through a comparative genomic analysis of strains of the serogroup Hebdomadis (Gulig et al, 2010;Nash et al, 2010).…”

Pathogenesis of Human Enterovirulent Bacteria: Lessons from Cultured, Fully Differentiated Human Colon Cancer Cell Lines

“…The results indicate that AIEC isolated from IBD patients has not evolved from a single ancestral background but corresponds to a group of bacteria that have been able to take advantage of an "IBD microenvironment" and probably share some common genes with ExPEC (446). Effectively, ExPEC and AIEC strains share similar virulence gene sets, and certain strains are phylogenetically related to the B2 phylogroup, but most ExPEC strains do not behave like AIEC strains (450)(451)(452). Analysis of the genomes of E. coli isolates obtained from patients with UC and CD (453) and of the genomes of AIEC strains LF82 (441), UM146 (452), NRG857c (O83:H1) (451), and HM605 (450) reveals that the genome of AIEC is characterized by the absence of known virulence factors composing the T3SS of enteroinvasive Salmonella, Yersinia, and Shigella strains and by the presence of a number of ExPEC-related virulence determinants such as the pap, sfa, cdt, sat, and hly genes and of the genes of ExPEC-associated genomic islands, but importantly, with little or no evidence of group-specific determinants.…”

“…Analysis of the genomes of E. coli isolates obtained from patients with UC and CD (453) and of the genomes of AIEC strains LF82 (441), UM146 (452), NRG857c (O83:H1) (451), and HM605 (450) reveals that the genome of AIEC is characterized by the absence of known virulence factors composing the T3SS of enteroinvasive Salmonella, Yersinia, and Shigella strains and by the presence of a number of ExPEC-related virulence determinants such as the pap, sfa, cdt, sat, and hly genes and of the genes of ExPEC-associated genomic islands, but importantly, with little or no evidence of group-specific determinants. However, it is impossible to exclude the possibility that AIEC expresses so-far-unidentified AIEC-specific genes that could be IBD specific (451). On the basis of what is known about AIEC pathogenesis and the absence of any demonstration that AIEC is directly involved in the development of IBD lesions, so far it seems reasonable to think that AIEC strains constitute a heterogeneous new pathovar of enterovirulent E. coli with genomic profiles that are indistinguishable from those of ExPEC isolates but which display particular proinflammatory virulence traits.…”

Escherichia coli Isolate for Studying Colonization of the Mouse Intestine and Its Application to Two-Component Signaling Knockouts

“…Since this porin gene in MP1 is located in a different region of the chromosome, we have named it nmpD, to avoid confusion with E. coli K-12 nmpC. Several strains closely related to MP1, including CFT073, LF82, and NRG 857C, have both nmpC (without the insertion sequence) and nmpD (32)(33)(34). In particular, NmpD from MP1 has a predicted amino acid sequence that is identical to that of the protein C2348, encoded in the CFT073 genome.…”