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.

FIG. 1.

Circular maps of the chromosome and plasmids of EPEC strain E2348/69. (A) EPEC strain E2348/69 chromosome. From the outside in, the first circle shows the locations of PPs and IEs (purple, lambda-like PPs; light blue, other PPs; green, IEs and the LEE element), the second circle shows the nucleotide sequence positions (in Mbp), the third and fourth circles show CDSs transcribed clockwise and anticlockwise, respectively (gray, conserved in all eight other sequenced E. coli strains; red, conserved only in the B2 phylogroup; yellow, variable distribution; blue, E2348/69 specific), the fifth circle shows the tRNA genes (red), the sixth circle shows the rRNA operons (blue), the seventh circle shows the G+C content, and the eighth circle shows the GC skew. (B) EPEC strain E2348/69 plasmids. The boxes in the outer and inner circles represent CDSs transcribed clockwise and anticlockwise, respectively. Pseudogenes are indicated by black boxes, and other CDSs are indicated by the colors described above for panel A.

FIG. 2.

Dot plot presentation of DNA sequence homologies between the chromosomes of E2348/69 and eight sequenced E. coli strains. The chromosome sequence of E2348/69 was compared with the chromosome sequences of eight sequenced E. coli strains. The locations of PPs and IEs on the E2348/69 chromosome are indicated.

FIG. 3.

Genome organizations of four PPs and five IEs carrying E2348/69 virulence-related genes. The four phages are lambda-like phages. Homologous genes in the lambda (accession no. NC_001416) and four PP genomes are indicated by gray shading. T3SS effectors are encoded on three lambda-like phages (PP2, PP4, and PP6) and four IEs (IE2, IE5, IE6, and LEE). Since the NleE family gene on IE2 contains an in-frame 168-bp deletion, it may be nonfunctional.

FIG. 4.

Conservation of E2348/69 genes in the eight sequenced E. coli strains. The numbers of E2348/69 genes conserved in each of the eight sequenced E. coli strains are indicated. Of the 4,492 genes (or multicopy gene families) identified in E2348/69, 3,141 (indicated by gray) were conserved in all the E. coli strains. Other genes were classified into three groups according to their locations in the E2348/69 genome (in plasmids, in PPs and IEs, and in other chromosome regions).