Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69

Abstract

Enteropathogenic Escherichia coli (EPEC) was the first pathovar of E. coli to be implicated in human disease; however, no EPEC strain has been fully sequenced until now. Strain E2348/69 (serotype O127:H6 belonging to E. coli phylogroup B2) has been used worldwide as a prototype strain to study EPEC biology, genetics, and virulence. Studies of E2348/69 led to the discovery of the locus of enterocyte effacement-encoded type III secretion system (T3SS) and its cognate effectors, which play a vital role in attaching and effacing lesion formation on gut epithelial cells. In this study, we determined the complete genomic sequence of E2348/69 and performed genomic comparisons with other important E. coli strains. We identified 424 E2348/69-specific genes, most of which are carried on mobile genetic elements, and a number of genetic traits specifically conserved in phylogroup B2 strains irrespective of their pathotypes, including the absence of the ETT2-related T3SS, which is present in E. coli strains belonging to all other phylogroups. The genome analysis revealed the entire gene repertoire related to E2348/69 virulence. Interestingly, E2348/69 contains only 21 intact T3SS effector genes, all of which are carried on prophages and integrative elements, compared to over 50 effector genes in enterohemorrhagic E. coli O157. As E2348/69 is the most-studied pathogenic E. coli strain, this study provides a genomic context for the vast amount of existing experimental data. The unexpected simplicity of the E2348/69 T3SS provides the first opportunity to fully dissect the entire virulence strategy of attaching and effacing pathogens in the genomic context. Escherichia coli is important because it is biology's premier model organism, is a common commensal of the vertebrate gut, and is a versatile pathogen of humans and animals. Molecular epidemiological studies have classified E. coli strains into a number of phylogroups (phylogroups A, B1, B2, D, and E) (13, 42), which are estimated to have diverged in the last 5 to 9 million years (37, 42). Commensal E. coli strains are beneficial to the host and rarely cause disease. However, several clones of E. coli are responsible for a spectrum of diseases, including urinary tract infection, sepsis/meningitis, and diarrhea (for a review, see reference 15). Diarrheagenic E. coli strains are divided into enterotoxigenic E. coli (ETEC), en-

Quantitative Proteomic Analysis of Type III Secretome of Enteropathogenic Escherichia coli Reveals an Expanded Effector Repertoire for Attaching/Effacing Bacterial Pathogens

“…Type III-secreted Proteins by the Effector Hypersecreting sepD Mutant of EPEC-Several known EPEC effectors were absent from the list of proteins secreted by WT EPEC (Table I and supplemental Table S2) (10), suggesting that WT EPEC is not an ideal source for cataloguing the effector inventory by proteomics under our experimental conditions because of its strong bias toward secretion of the translocators. To identify additional EPEC effectors, we next analyzed the secreted proteins from EPEC ⌬lysA⌬argH⌬sepD and ⌬lysA-⌬argH⌬sepD⌬escN by SILAC, because EPEC sepD and sepL mutants have been shown to hypersecrete effectors in DMEM (25).…”

“…The prototypical EPEC O127:H6 strain E2348/69, an isolate from a human patient, and EHEC O157:H7 strain EDL933, and C. rodentium strain DBS100, all with sequenced genomes (10,15,22,23), were used in this study. The bacteria were grown in LB broth or agar plates.…”

“…The genome of the prototypical human EPEC strain E2348/69 has been sequenced, and based on bioinformatic analyses of the genome and its comparison with other A/E pathogens, it was estimated that this EPEC strain encodes 21 functional effectors (10). This is a relatively small effector repertoire compared with that of EHEC and C. rodentium (10 -16).…”

In Vitro and In Vivo Model Systems for Studying Enteropathogenic Escherichia coli Infections

“…Adult volunteers have been used to verify the roles of intimin, EspB, and bundle-forming pili (BFP) in EPEC pathogenesis (Donnenberg et al 1993;Bieber et al 1998;Tacket et al 2000). BFP is an EPEC-specific virulence factor but intimin and EspB are found in the genomes of diverse A/E pathogen species (Tauschek et al 2002;Iguchi et al 2009;Ogura et al 2009;Petty et al 2010). Intimin and EspB are essential for A/E lesion formation in tissue culture (Foubister et al 1994;Abe et al 1997) and intestinal damage in rabbits and mice infected with REPEC (Abe et al 1998;Marchès et al 2000) or C. rodentium, respectively (Schauer and Falkow 1993;Newman et al 1999;Deng et al 2004).…”

“…In addition to Tir, the T3SS translocates an assortment of effector proteins into host cells, which subvert cellular processes to promote A/E pathogen infection (Kenny 2002;Dean et al 2005;. To date, several LEE-encoded effectors, as well as a number of non-LEE (Nle)-encoded effectors , have been identified in the genomes of EPEC and EHEC (Tobe et al 2006;Coburn et al 2007;Iguchi et al 2009). …”