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EHEC Genomics: Past, Present, and Future

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  • Authors: Shah M. Sadiq1, Tracy H. Hazen2, David A. Rasko3, Mark Eppinger4
  • Editors: Vanessa Sperandio5, Carolyn J. Hovde6
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology, and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249; 2: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201; 3: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201; 4: Department of Biology, and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249; 5: University of Texas Southwestern Medical Center, Dallas, TX; 6: University of Idaho, Moscow, ID
  • Source: microbiolspec July 2014 vol. 2 no. 4 doi:10.1128/microbiolspec.EHEC-0020-2013
  • Received 25 October 2013 Accepted 18 November 2013 Published 31 July 2014
  • Mark Eppinger, mark.eppinger@utsa.edu; David A. Rasko, 33drasko@som.umaryland.edu
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  • Abstract:

    This article examines the role of genomics in the understanding and identification of O157:H7 enterohemorrhagic (EHEC). We highlight the development of novel molecular typing systems that are based on the genomic sequence that has been generated for this pathotype. The genomic comparisons of EHEC to other strains highlight the close relatedness of the O157 and O55 isolates and also identify other non-O157 clades of isolates that appear to have a different genomic history. Analysis within the EHEC isolates must be completed on a fine scale using whole-genome sequence-based approaches to assess both the conserved and lateral acquired gene content. The plethora of genomic data for EHEC isolates has provided the ability to examine this pathotype in detail, which has provided opportunities for novel surveillance, detection, and diagnostics.

  • Citation: Sadiq S, Hazen T, Rasko D, Eppinger M. 2014. EHEC Genomics: Past, Present, and Future. Microbiol Spectrum 2(4):EHEC-0020-2013. doi:10.1128/microbiolspec.EHEC-0020-2013.

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2014-07-31
2017-11-22

Abstract:

This article examines the role of genomics in the understanding and identification of O157:H7 enterohemorrhagic (EHEC). We highlight the development of novel molecular typing systems that are based on the genomic sequence that has been generated for this pathotype. The genomic comparisons of EHEC to other strains highlight the close relatedness of the O157 and O55 isolates and also identify other non-O157 clades of isolates that appear to have a different genomic history. Analysis within the EHEC isolates must be completed on a fine scale using whole-genome sequence-based approaches to assess both the conserved and lateral acquired gene content. The plethora of genomic data for EHEC isolates has provided the ability to examine this pathotype in detail, which has provided opportunities for novel surveillance, detection, and diagnostics.

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FIGURE 1

Figure depicts the molecular differences that define each of the attaching and effacing . The gene encodes the intimin protein on the LEE region; the gene in this case is the presence of the bundle-forming pilus operon, and the gene encodes the Shiga toxin. These three features are classically used to define the pathotypes, including EHEC. doi.10.1128/microbiolspec.EHEC-0020-2013.f1

Source: microbiolspec July 2014 vol. 2 no. 4 doi:10.1128/microbiolspec.EHEC-0020-2013
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FIGURE 2

Phylogeny of reference isolates, including EHEC. The reference used for the SNP calling is HS as a true commensal isolate ( 62 ). The tree is maximum likelihood with 100 bootstraps made using RAxML, as previously described ( 68 ).This figure highlights, as does MLST, that when compared to a large and diverse collection of isolates, EHEC, and specifically the O157 and O55 (in red and purple) and other serotypes (highlighted in yellow), demonstrates a high level of similarity. This high-level of similarity extends within these groups. Only once these clades are examined in detail can one begin to identify regions that are diagnostic in these clades. doi.10.1128/microbiolspec.EHEC-0020-2013.f2

Source: microbiolspec July 2014 vol. 2 no. 4 doi:10.1128/microbiolspec.EHEC-0020-2013
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FIGURE 3

Phylogeny of O157 reference isolates demonstrating that there is variation within the O157 clade that is not observed in the larger genomic comparisons. This multi-whole genome alignment contains 4,093,272 bp of sequence. The tree is maximum likelihood with 100 bootstraps made using RAxML, as previously described ( 68 ). The color indicates distinguishable clades within this selection of 50 EHEC isolates. The additional numbers in parentheses are the clade and LSPA designations, as described in the text. doi.10.1128/microbiolspec.EHEC-0020-2013.f3

Source: microbiolspec July 2014 vol. 2 no. 4 doi:10.1128/microbiolspec.EHEC-0020-2013
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