Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • 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 Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AAC
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • AAC Podcast
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • 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 Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Antimicrobial Agents and Chemotherapy
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AAC
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • AAC Podcast
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Epidemiology and Surveillance

Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group

Timothy J. Johnson, Ehud Elnekave, Elizabeth A. Miller, Jeannette Munoz-Aguayo, Cristian Flores Figueroa, Brian Johnston, Daniel W. Nielson, Catherine M. Logue, James R. Johnson
Timothy J. Johnson
aDepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
bMid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ehud Elnekave
cDepartment of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elizabeth A. Miller
aDepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
cDepartment of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeannette Munoz-Aguayo
bMid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cristian Flores Figueroa
bMid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brian Johnston
dMinneapolis Veterans Health Care System, Minneapolis, Minnesota, USA
eDepartment of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel W. Nielson
fDepartment of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catherine M. Logue
gDepartment of Population Health, University of Georgia, Athens, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James R. Johnson
dMinneapolis Veterans Health Care System, Minneapolis, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AAC.01913-18
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    FIG 1

    Phylogenetic tree of ST1193 (n = 355) and non-ST1193 STc14 (n = 72) isolates based on single-nucleotide polymorphisms in nonrecombinant core genome regions. In the tree, bright green is ST1193 with IncF-:A1:B1 plasmids, red is ST1193 with IncF-:A1:B10 plasmids, pink is ST1193 with IncF-:A1:B20 plasmids, and black is non-ST1193, STc14. Blue-colored circles indicate the presence of specific capsular types, and purple-colored squares indicate presence of F-plasmid alleles. Isolate names colored green indicate the ST1193 isolates sequenced in this study.

  • FIG 2
    • Open in new tab
    • Download powerpoint
    FIG 2

    Phylogenetic distribution of accessory traits in representative ST1193 and non-ST1193 STc14 isolates. Squares, colored by trait category, represent the presence of a trait examined. Mutations refer to mutations conferring fluoroquinolone resistance. Year (green to red, older to recent) and ST are categorically colored for comparison. Plasmid mapping refers to the presence of a region (>95% similarity and >80% length) relative to plasmid p1ESCUM.

  • FIG 3
    • Open in new tab
    • Download powerpoint
    FIG 3

    Mapping of sequencing reads from ST1193 and non-ST1193 STc14 isolates against plasmid pNMEC-O75A in the context of F-plasmid replicon. In the sequencing maps, black peaks indicate regions with exact matches, colored peaks indicate matching regions with nucleotide variation, and white regions indicate areas with no mapping of reads.

  • FIG 4
    • Open in new tab
    • Download powerpoint
    FIG 4

    Time-scaled phylogenetic analysis of 111 ST1193 isolates collected in the U.S. between 2008 and 2018. Red node bars indicate the 95% highest posterior density interval of the node position. Purple circles indicate nodes with at least 70% posterior support. Brown bars at the right indicate the presence of capsular types K1 and K5, and purple bars at right indicate presence of F plasmid alleles.

  • FIG 5
    • Open in new tab
    • Download powerpoint
    FIG 5

    Heatmap presence or absence of non-core-predicted proteins across STc14 isolates sequenced in this study. Red, presence of predicted protein presence; cream, absence of predicted protein. Heatmap was generated using Ward two-way hierarchical clustering with the Euclidean distance method.

  • FIG 6
    • Open in new tab
    • Download powerpoint
    FIG 6

    Enterobase GrapeTree of 484 STc14 isolates, generated using core genome multilocus sequence typing (cgMLST). Using the Achtman 7-gene MLST scheme in Enterobase, a search for ST14 with a mismatch setting of 1 allele resulted in a database of 483 STc14 strains. cgMLST was used in the experimental data setting to generate GrapeTree (minimal spanning tree) images. The upper image is colored according to ST, and the lower image is colored according to predicted serogroup. In the keys, the numbers in brackets represent number of isolates.

  • FIG 7
    • Open in new tab
    • Download powerpoint
    FIG 7

    Postulated key events leading to the currently circulating ST1193 fluoroquinolone-resistant clonal group. RepFIB alleles B1, B10, and B20 are depicted as boxes at the lower right.

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Escherichia coli isolates used in this study (n = 427)

    STNo. of isolatesSourceNo. of isolates per sourceYrCountry(ies) of isolation
    Non-ST1193, STc1472This study91980–2008USA and Australia
    Enterobasea63UnknownUnknown
    ST1193355This study1092008–2018USA and Australia
    Enterobasea246UnknownUnknown
    Total427Both4271980–2018
    • ↵a Enterobase isolates existed as sequence reads only, not physical isolates. While most of these isolates were sequenced in Europe, it is unclear if they were isolated in Europe.

  • TABLE 2

    Prevalence of plasmid-associated replicons and F-plasmid alleles among Escherichia coli ST1193 and non-ST1193, STc14 isolates

    Category and specific traitTrait prevalencea (%)
    Non-ST1193, STc14 (n = 72)All ST1193 (n = 355)ST1193, green clades (n = 46)ST1193, pink clade (n = 27)ST1193, red clade (n = 282)
    Capsular type
        K10.092.7100.00.0100.0
        K5100.07.30.0100.00.0
    Virulence genes
        gad64.9100.0100.0100.0100.0
        iha97.499.4100.0100.099.3
        ireA72.24.50.00.05.7
        sat94.495.895.796.395.7
        senB61.186.573.985.288.7
        vat100.093.8100.0100.092.2
    Plasmid types
        IncF-:A1:B11.410.769.67.41.4
        IncF-:A1:B105.668.22.20.085.5
        IncF-:A1:B201.43.90.051.90.0
        IncF4:A-:B524.20.00.00.00.0
        IncF29:A-:B1029.20.30.00.00.4
        IncF52:A-:B1016.70.00.00.00.0
        IncI12.828.728.33.731.2
    • ↵a Clade color refers to clade coloring from Fig. 1.

  • TABLE 3

    Prevalence of antimicrobial resistance genes among ST1193 and non-ST1193, STc14 isolates

    Resistance gene and drug classPrevalence of gene (%)
    Non-ST1193, STc14 (n = 72)All ST1193 (n = 355)ST1193, green clades (n = 46)ST1193, pink clade (n = 27)ST1193, red clade (n = 282)
    Beta-lactam
        blaTEM-1B31.969.984.874.167.0
        blaCMY-20.08.20.00.010.3
        blaCTX-M-151.49.015.23.78.5
        blaOXA-14.22.30.03.72.5
        blaCTX-M-270.015.210.90.017.4
        blaCTX-M-550.02.56.53.71.8
    Aminoglycoside
        strAB38.974.982.670.474.1
        aac(3)-IId2.832.723.955.631.9
        aadA54.240.839.170.438.3
    Sulfonamide
        sul118.141.141.370.438.3
        sul240.374.178.370.473.8
    Macrolide
        mphA8.363.980.463.061.3
        ermB1.49.610.90.010.3
    Folate antagonist
        dfrA148.36.245.70.00.4
        dfrA176.961.741.363.064.9
    Tetracycline
        tetA4.241.739.170.439.4
        tetB29.227.947.83.727.0
    Quinolone
        aac6'Ib_cr0.02.50.03.72.8

Additional Files

  • Figures
  • Tables
  • Supplemental material

    • Supplemental file 1 -

      Supplemental Data Set S1

      XLSX, 63K

    • Supplemental file 2 -

      Supplemental Data Set S1

      XLSX, 270K

PreviousNext
Back to top
Download PDF
Citation Tools
Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group
Timothy J. Johnson, Ehud Elnekave, Elizabeth A. Miller, Jeannette Munoz-Aguayo, Cristian Flores Figueroa, Brian Johnston, Daniel W. Nielson, Catherine M. Logue, James R. Johnson
Antimicrobial Agents and Chemotherapy Dec 2018, 63 (1) e01913-18; DOI: 10.1128/AAC.01913-18

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 Antimicrobial Agents and Chemotherapy 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.
Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group
(Your Name) has forwarded a page to you from Antimicrobial Agents and Chemotherapy
(Your Name) thought you would be interested in this article in Antimicrobial Agents and Chemotherapy.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group
Timothy J. Johnson, Ehud Elnekave, Elizabeth A. Miller, Jeannette Munoz-Aguayo, Cristian Flores Figueroa, Brian Johnston, Daniel W. Nielson, Catherine M. Logue, James R. Johnson
Antimicrobial Agents and Chemotherapy Dec 2018, 63 (1) e01913-18; DOI: 10.1128/AAC.01913-18
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • MATERIALS AND METHODS
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

ExPEC
ST1193
antimicrobial resistance
fluoroquinolone
plasmid

Related Articles

Cited By...

About

  • About AAC
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • AAC Podcast
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AACJournal

@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

Print ISSN: 0066-4804; Online ISSN: 1098-6596