Abstract
There are 29 E. coli genome sequences available, mostly related to studies of species diversity or mode of pathogenicity, including two genomes of the well-known O157:H7 clone. However, there have been no genome studies of closely related clones aimed at exposing the details of evolutionary change. Here we sequenced the genome of an O55:H7 strain, closely related to the major pathogenic O157:H7 clone, with published genome sequences, and undertook comparative genomic and proteomic analysis. We were able to allocate most differences between the genomes to individual mutations, recombination events, or lateral gene transfer events, in specific lineages. Major differences include a type II secretion system present only in the O55:H7 chromosome, fewer type III secretion system effectors in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared to 23 in O157:H7, with only three common to both. Many other changes were found in both O55:H7 and O157:H7 lineages, but in general there has been more change in the O157:H7 lineages. For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7. The two strains also diverged at the proteomic level. Mutational synonymous SNPs were used to estimate a divergence time of 400 years using a new clock rate, in contrast to 14,000 to 70,000 years using the traditional clock rates. The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found. This study revealed for the first time the full range of events involved in the evolution of the O157:H7 clone from its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our findings also suggest that E. coli has a much lower frequency of recombination relative to mutation than was observed in a comparable study of a Vibrio cholerae lineage.
Highlights
Escherichia coli has as its primary niche the large intestine and lower part of the small intestine of mammals, larger birds and reptiles [1,2], and has been well studied in humans and domestic animals
We were able to define putative recombinant segments, as done previously [6,13], using the very different distribution of single nucleotide polymorphisms (SNPs) introduced by recombination from those arising by mutation
Divergence within the O157:H7 and O55:H7 Lineages The CB9615 genome sequence gives us a good outgroup for allocating the SNPs between the two O157:H7 genomes, and we find that the two branches within the O157:H7 lineage, for Sakai and EDL933, are very short
Summary
Escherichia coli has as its primary niche the large intestine and lower part of the small intestine of mammals, larger birds and reptiles [1,2], and has been well studied in humans and domestic animals. It is a diverse species with both commensal forms and pathogenic forms, many of the latter falling into welldefined pathovars [3]. Most genes in the auxiliary genome are found in only a small proportion of strains [5], and it is not yet possible to predict the total number of genes in the pan genome, as there is still much E. coli diversity to be explored. In the most recent study [5] the pan genome for 20 strains had reached about 10,000, of which about 8,000 are in the auxiliary genome
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