Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2006 Jun;16(6):757-67.
doi: 10.1101/gr.4759706. Epub 2006 Apr 10.

Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms

Wei Zhang  1 , Weihong Qi, Thomas J Albert, Alifiya S Motiwala, David Alland, Eija K Hyytia-Trees, Efrain M Ribot, Patricia I Fields, Thomas S Whittam, Bala Swaminathan
Affiliations
Comparative Study

Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms

Wei Zhang et al. Genome Res. 2006 Jun.

Abstract

Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous protein-coding genes, limiting the use of nucleotide sequences to study the evolution and epidemiology of this bacterial pathogen. To systematically examine single nucleotide polymorphisms (SNPs) at a genome scale, we designed comparative genome sequencing microarrays and analyzed 1199 chromosomal genes (a total of 1,167,948 bp) and 92,721 bp of the large virulence plasmid (pO157) of eleven outbreak-associated STEC O157 strains. We discovered 906 SNPs in 523 chromosomal genes and observed a high level of DNA polymorphisms among the pO157 plasmids. Based on a uniform rate of synonymous substitution for Escherichia coli and Salmonella enterica (4.7x10(-9) per site per year), we estimate that the most recent common ancestor of the contemporary beta-glucuronidase-negative, non-sorbitolfermenting STEC O157 strains existed ca. 40 thousand years ago. The phylogeny of the STEC O157 strains based on the informative synonymous SNPs was compared to the maximum parsimony trees inferred from pulsed-field gel electrophoresis and multilocus variable numbers of tandem repeats analysis. The topological discrepancies indicate that, in contrast to the synonymous mutations, parts of STEC O157 genomes have evolved through different mechanisms with highly variable divergence rates. The SNP loci reported here will provide useful genetic markers for developing high-throughput methods for fine-resolution genotyping of STEC O157. Functional characterization of nucleotide polymorphisms should shed new insights on the evolution, epidemiology, and pathogenesis of STEC O157 and related pathogens.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Circular map of 1199 protein-coding genes and newly identified 906 SNPs relative to Sakai chromosome. The outer circle shows the genome scale. Triangles on the second circle show locations of virulence-related loci analyzed, including fimbrial biosynthesis loci (green), adhesin and invasin loci (rose), Shiga toxin loci (purple), and locus of enterocyte effacement (yellow). The third circle shows all chromosomal genes analyzed, including 823 backbone genes (blue) and 376 S-loop genes (red). Genes on the forward strand are shown outside the baseline; genes on the reverse strand are shown inside the baseline. Inner circles show all synonymous SNPs (dark blue) and nonsynonymous SNPs (orange) identified in 10 test STEC O157 strains—493/89, G5101, F8768, 01-577, F6141, N0587, F5733, N0303, G5289, and N0436, respectively. The figure was created by GenVision from DNASTAR.
Figure 2.
Figure 2.
Summary of single nucleotide polymorphisms in STEC O157 strains. The total number of SNPs in each strain is given in parentheses. The bars show the percentage of strain-specific SNPs, backbone SNPs, synonymous SNPs, and transversions of all SNPs identified in each strain.
Figure 3.
Figure 3.
Compatibility matrix of 109 PI synonymous SNPs. The upper triangle (blue) is a plot of pairwise comparison of the phylogenetic compatibility of 76 PI sites in backbone loci. The lower triangle (yellow) is a plot of pairwise comparison of 33 PI sites in S-loop loci. The left corner rectangle (green) is a plot of pairwise comparison of 109 PI sites between backbone and S-loop loci. Highly incompatible sites are indicated by black squares.
Figure 4.
Figure 4.
Split decomposition graph of the relationship of STEC O157 strains based on 109 PI synonymous SNPs.
Figure 5.
Figure 5.
(A) Maximum parsimony tree based on 109 PI synonymous SNPs. Branch lengths are measured in terms of the number of synonymous changes per 100 synonymous sites (dS × 100). Bootstrap values are based on 1000 bootstrap replicates for the consensus tree. (B) Maximum parsimony tree based on XbaI PFGE macrorestriction patterns. (C) Maximum parsimony tree based on variable copy numbers at nine VNTR loci by MLVA.
Figure 6.
Figure 6.
Linearized minimum evolution tree based on 389,316 allelic codons of the STEC O157 strains. The bottom scale shows the divergence time frame (thousands of years) and the number of synonymous substitutions per nucleotide site.
See this image and copyright information in PMC

References

    1. Albert T.J., Norton J., Ott M., Richmond T., Nuwaysir K., Nuwaysir E.F., Stengele K.P., Green R.D., Norton J., Ott M., Richmond T., Nuwaysir K., Nuwaysir E.F., Stengele K.P., Green R.D., Ott M., Richmond T., Nuwaysir K., Nuwaysir E.F., Stengele K.P., Green R.D., Richmond T., Nuwaysir K., Nuwaysir E.F., Stengele K.P., Green R.D., Nuwaysir K., Nuwaysir E.F., Stengele K.P., Green R.D., Nuwaysir E.F., Stengele K.P., Green R.D., Stengele K.P., Green R.D., Green R.D. Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays. Nucleic Acids Res. 2003;31:35–44. - PMC - PubMed
    1. Albert T.J., Dailidiene D., Dailide G., Norton J.E., Kalia A., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Dailidiene D., Dailide G., Norton J.E., Kalia A., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Dailide G., Norton J.E., Kalia A., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Norton J.E., Kalia A., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Kalia A., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Richmond T.A., Molla M., Singh J., Green R.D., Berg D.E., Molla M., Singh J., Green R.D., Berg D.E., Singh J., Green R.D., Berg D.E., Green R.D., Berg D.E., Berg D.E. Mutation discovery in bacterial genomes: Metronidazole resistance in Helicobacter pylori. Nat. Methods. 2005;2:951–953. - PubMed
    1. Alderborn A., Kristofferson A., Hammerling U., Kristofferson A., Hammerling U., Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 2000;10:1249–1258. - PMC - PubMed
    1. Bandelt H., Dress A.W.M., Dress A.W.M. Split decomposition: A new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol. 1992;1:242–252. - PubMed
    1. Bitzan M., Ludwig K., Klemt M., Konig H., Buren J., Muller-Wiefel D.E., Ludwig K., Klemt M., Konig H., Buren J., Muller-Wiefel D.E., Klemt M., Konig H., Buren J., Muller-Wiefel D.E., Konig H., Buren J., Muller-Wiefel D.E., Buren J., Muller-Wiefel D.E., Muller-Wiefel D.E. The role of Escherichia coli O157 infections in the classical (enteropathic) hemolytic uraemic syndrome: Results of a central European, multicentre study. Epidemiol. Infect. 1993;110:183–196. - PMC - PubMed

Publication types

Substances