Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Prokaryotes

Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains

Rebecca L. Lindsey, Eija Trees, Scott Sammons, Vladimir Loparev, Mike Frace, Nancy Strockbine, Ashley L. Sabol, Evan Sowers, Devon Stripling, Haley Martin, Kristen Knipe, Lori Rowe, Peter Gerner-Smidt
Rebecca L. Lindsey
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eija Trees
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Scott Sammons
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vladimir Loparev
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mike Frace
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nancy Strockbine
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ashley L. Sabol
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Evan Sowers
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Devon Stripling
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Haley Martin
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kristen Knipe
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lori Rowe
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter Gerner-Smidt
Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.00501-14
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen. Here, we report the draft whole-genome sequences of nine STEC strains isolated from clinical cases in the United States. This is the first report of such information for STEC of serotypes O69, H11, O145:H25, O118:H16, O91:H21, O146:H21, O45:H2, O128:H2, and O121:H19.

GENOME ANNOUNCEMENT

Shiga toxin-producing Escherichia coli (STEC) is a common cause of food-borne illness. An estimated 265,000 STEC infections occur each year in the United States. Non-O157 STEC strains cause about 64% of these infections, and O157 STEC causes the rest (http://www.cdc.gov/ecoli/general/index.html). The symptoms of STEC infection range from mild, watery to bloody diarrhea, gastroenteritis, hemolytic-uremic syndrome, to death. Most STEC infections are caused by seven serotypes, but >100 STEC serotypes are known to cause illness in humans (1, 2). Only five closed non-O157 STEC genome sequences are publicly available. Four of them (O103, O111, O26, and O145) belong to the most common non-O157 STEC serogroups, and one (O55) is much rarer in prevalence. Here, we report the availability of high-quality draft whole-genome sequences for nine STEC strains that are among the top 15 most common STEC serotypes in prevalence related to human infection in the United States (CDC reference laboratory surveillance, unpublished data). Eight of these draft genome sequences represent STEC serotypes that did not previously have any genome sequences publicly available.

E. coli genomic DNA was extracted according to the manufacturer's protocol (ArchivePure, 5 Prime, Gaithersburg, MD). DNAs were sheared to 10 kbp or 20 kbp utilizing g-Tubes (Covaris, Inc., Woburn, MA). The 20-kbp sheared products were further size selected utilizing BluePippin size selection (Sage Science, Beverly, MA). The sheared DNAs were used to generate large SMRTbell libraries using the standard library protocols of the Pacific Biosciences DNA template preparation kit (Menlo Park, CA). The finished libraries were bound to proprietary P4 polymerase and sequenced on a PacBio RSII sequencer using C2 chemistry for 120-min movies. The sequence reads were filtered and assembled de novo utilizing the PacBio Hierarchical Genome Assembly Process (3) or a modified Celera Assembler (4). The resulting assemblies were confirmed using OpGen (Gaithersburg, MD) whole-genome maps (WGM). WGM were generated according to the OpGen protocol. The sequences were annotated with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (5).

A detailed report on further analysis of the draft genome sequences will be included in a future publication.

Nucleotide sequence accession numbers.The annotated whole-genome E. coli sequences have been deposited in DDBJ/ENA/GenBank under the accession no. JASN00000000 to JASV00000000. The versions described in this paper are the first versions, under the accession no. listed in Table 1.

View this table:
  • View inline
  • View popup
TABLE 1

Accession numbers and assembly metrics of the annotated STEC draft whole-genome sequences

ACKNOWLEDGMENTS

R.L.L. is a recipient of an ORISE/CDC Postdoctoral Research Fellowship.

The findings and conclusions of this article are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention.

FOOTNOTES

    • Received 12 May 2014.
    • Accepted 23 June 2014.
    • Published 10 July 2014.
  • Copyright © 2014 Lindsey et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

REFERENCES

  1. 1.↵
    1. Gould LH,
    2. Bopp C,
    3. Strockbine N,
    4. Atkinson R,
    5. Baselski V,
    6. Body B,
    7. Carey R,
    8. Crandall C,
    9. Hurd S,
    10. Kaplan R,
    11. Neill M,
    12. Shea S,
    13. Somsel P,
    14. Tobin-D'Angelo M,
    15. Griffin PM,
    16. Gerner-Smidt P,
    17. Centers for Disease C
    , Prevention. 2009. Recommendations for diagnosis of Shiga toxin-producing Escherichia coli infections by clinical laboratories. MMWR Recomm. Rep. 58(RR-12):1–14.
    OpenUrlPubMed
  2. 2.↵
    1. Johnson KE,
    2. Thorpe CM,
    3. Sears CL
    . 2006. The emerging clinical importance of non-O157 Shiga toxin-producing Escherichia coli. Clin. Infect. Dis. 43:1587–1595. doi:10.1086/509573.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Chin CS,
    2. Alexander DH,
    3. Marks P,
    4. Klammer AA,
    5. Drake J,
    6. Heiner C,
    7. Clum A,
    8. Copeland A,
    9. Huddleston J,
    10. Eichler EE,
    11. Turner SW,
    12. Korlach J
    . 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563–569. doi:10.1038/nmeth.2474.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    1. Koren S,
    2. Schatz MC,
    3. Walenz BP,
    4. Martin J,
    5. Howard JT,
    6. Ganapathy G,
    7. Wang Z,
    8. Rasko DA,
    9. McCombie WR,
    10. Jarvis ED,
    11. Phillippy AM
    . 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30:693–700. doi:10.1038/nbt.2280.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Klimke W,
    2. Agarwala R,
    3. Badretdin A,
    4. Chetvernin S,
    5. Ciufo S,
    6. Fedorov B,
    7. Kiryutin B,
    8. O'Neill K,
    9. Resch W,
    10. Resenchuk S,
    11. Schafer S,
    12. Tolstoy I,
    13. Tatusova T
    . 2009. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res. 37:D216–D223. doi:10.1093/nar/gkn734.
    OpenUrlCrossRefPubMedWeb of Science
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains
Rebecca L. Lindsey, Eija Trees, Scott Sammons, Vladimir Loparev, Mike Frace, Nancy Strockbine, Ashley L. Sabol, Evan Sowers, Devon Stripling, Haley Martin, Kristen Knipe, Lori Rowe, Peter Gerner-Smidt
Genome Announcements Jul 2014, 2 (4) e00501-14; DOI: 10.1128/genomeA.00501-14

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains
Rebecca L. Lindsey, Eija Trees, Scott Sammons, Vladimir Loparev, Mike Frace, Nancy Strockbine, Ashley L. Sabol, Evan Sowers, Devon Stripling, Haley Martin, Kristen Knipe, Lori Rowe, Peter Gerner-Smidt
Genome Announcements Jul 2014, 2 (4) e00501-14; DOI: 10.1128/genomeA.00501-14
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X