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Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.

Zhou Z, Li X, Liu B, Beutin L, Xu J, Ren Y, Feng L, Lan R, Reeves PR, Wang L - PLoS ONE (2010)

Bottom Line: 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.For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7.The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found.

View Article: PubMed Central - PubMed

Affiliation: Tianjin Economic-Technological Development Area School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.

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.

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Related in: MedlinePlus

Tree showing the relationships of UTI89, S88 and APEC 01 ExPEC strains.The tree topography is for mutational SNPs as allocated by the virtual outgroup analysis (Tables S7 and S8). For each lineage the number of mutations and recombination events is shown in grids as for Figure 1.
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pone-0008700-g004: Tree showing the relationships of UTI89, S88 and APEC 01 ExPEC strains.The tree topography is for mutational SNPs as allocated by the virtual outgroup analysis (Tables S7 and S8). For each lineage the number of mutations and recombination events is shown in grids as for Figure 1.

Mentions: We then undertook an analysis of recombination and mutation for the S88, UTI89 and APEC 01 group (Tables S5, S6, S7, S8, and Figure 4). The omission of recombinant segment SNPs for the phylogenic analysis changed the topology relative to that shown in Figure 3 and by Touchon et al. [5]. There is strong support for the topology shown in Figure 4. The difference arises because the previous study [5] did not distinguish between changes due to mutation and those due to recombination, although there was statistical evaluation of the role of recombination in sequence variation. We suggest that the alternate topology observed earlier [5] is due to inclusion of recombinant regions in the analysis. Analysis of the SNPs involved in that part of the tree (data not shown) showed that most supported the new tree presented in Figure 4 with UTI89 the first to diverge. The SNPS that take S88 to be first to diverge in the original tree are in segments covered by putative recombination events 36 and 40 (Table S8), in which S88 appeared to gain DNA from a K-12 like donor, These two segments have 47% of the SNPs in recombinant segments in this 3 strain alignment, which accounts for their effect on the tree.


Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.

Zhou Z, Li X, Liu B, Beutin L, Xu J, Ren Y, Feng L, Lan R, Reeves PR, Wang L - PLoS ONE (2010)

Tree showing the relationships of UTI89, S88 and APEC 01 ExPEC strains.The tree topography is for mutational SNPs as allocated by the virtual outgroup analysis (Tables S7 and S8). For each lineage the number of mutations and recombination events is shown in grids as for Figure 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2806823&req=5

pone-0008700-g004: Tree showing the relationships of UTI89, S88 and APEC 01 ExPEC strains.The tree topography is for mutational SNPs as allocated by the virtual outgroup analysis (Tables S7 and S8). For each lineage the number of mutations and recombination events is shown in grids as for Figure 1.
Mentions: We then undertook an analysis of recombination and mutation for the S88, UTI89 and APEC 01 group (Tables S5, S6, S7, S8, and Figure 4). The omission of recombinant segment SNPs for the phylogenic analysis changed the topology relative to that shown in Figure 3 and by Touchon et al. [5]. There is strong support for the topology shown in Figure 4. The difference arises because the previous study [5] did not distinguish between changes due to mutation and those due to recombination, although there was statistical evaluation of the role of recombination in sequence variation. We suggest that the alternate topology observed earlier [5] is due to inclusion of recombinant regions in the analysis. Analysis of the SNPs involved in that part of the tree (data not shown) showed that most supported the new tree presented in Figure 4 with UTI89 the first to diverge. The SNPS that take S88 to be first to diverge in the original tree are in segments covered by putative recombination events 36 and 40 (Table S8), in which S88 appeared to gain DNA from a K-12 like donor, These two segments have 47% of the SNPs in recombinant segments in this 3 strain alignment, which accounts for their effect on the tree.

Bottom Line: 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.For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7.The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found.

View Article: PubMed Central - PubMed

Affiliation: Tianjin Economic-Technological Development Area School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.

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.

Show MeSH
Related in: MedlinePlus