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Journal of Clinical Microbiology
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Epidemiology

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

Katrine Grimstrup Joensen, Flemming Scheutz, Ole Lund, Henrik Hasman, Rolf S. Kaas, Eva M. Nielsen, Frank M. Aarestrup
K. C. Carroll, Editor
Katrine Grimstrup Joensen
aNational Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
bDepartment of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
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Flemming Scheutz
bDepartment of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
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Ole Lund
cCenter for Biological Sequence Analysis, Department of System Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Henrik Hasman
aNational Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
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Rolf S. Kaas
aNational Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
cCenter for Biological Sequence Analysis, Department of System Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Eva M. Nielsen
bDepartment of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
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Frank M. Aarestrup
aNational Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
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K. C. Carroll
Roles: Editor
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DOI: 10.1128/JCM.03617-13
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ABSTRACT

Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens.

FOOTNOTES

    • Received 3 January 2014.
    • Returned for modification 5 February 2014.
    • Accepted 18 February 2014.
    • Accepted manuscript posted online 26 February 2014.
  • Supplemental material for this article may be found at http://dx.doi.org/10.1128/JCM.03617-13.

  • Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The authors have paid a fee to allow immediate free access to this article.

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Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
Katrine Grimstrup Joensen, Flemming Scheutz, Ole Lund, Henrik Hasman, Rolf S. Kaas, Eva M. Nielsen, Frank M. Aarestrup
Journal of Clinical Microbiology Apr 2014, 52 (5) 1501-1510; DOI: 10.1128/JCM.03617-13

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Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
Katrine Grimstrup Joensen, Flemming Scheutz, Ole Lund, Henrik Hasman, Rolf S. Kaas, Eva M. Nielsen, Frank M. Aarestrup
Journal of Clinical Microbiology Apr 2014, 52 (5) 1501-1510; DOI: 10.1128/JCM.03617-13
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