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
Genome Sequences

Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract

Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
John J. Dennehy, Editor
Natalia Purta
aNeuroscience Program, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Taylor Miller-Ensminger
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adelina Voukadinova
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alan J. Wolfe
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catherine Putonti
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
dDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
eDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Catherine Putonti
John J. Dennehy
Queens College
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00407-20
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Here, we introduce the 2.8-Mbp draft genome of Enterococcus faecalis strain UMB0843, isolated from the female urinary tract. E. faecalis is a leading cause of nosocomial infections, and many strains are often resistant to multiple antibiotics. We focus our genome analysis on the multiple genes involved in antibiotic resistance in this strain.

ANNOUNCEMENT

Enterococcus faecalis lives in the gastrointestinal tract of many organisms (1) and has recently emerged as a leading cause of nosocomial infections due to its increased resistance to many antibiotics (2, 3). E. faecalis is often a primary cause of surgical infections, infections within the bloodstream, and urinary tract infections (UTIs) (3, 4). Recently, we isolated E. faecalis strain UMB0843 from a urine sample obtained from a pregnant female. Here, we present the draft genome sequence of this isolate and the antibiotic resistance genes found within the genome.

E. faecalis UMB0843 was collected as part of a previous institutional review board (IRB)-approved study (5) and cultured using the expanded quantitative urine culture (EQUC) protocol (6). To determine the genus and species of each isolate, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry was used, following a protocol detailed previously (6), prior to storage of the isolates at −80°C. From the freezer stocks, E. faecalis was streaked onto a Columbia nalidixic acid (CNA) agar plate and incubated at 35°C in 5% CO2 for 24 h. A single colony was selected, inoculated in brain heart infusion (BHI) broth (premixed BBL brain heart infusion; BD), and incubated under the same conditions described above. DNA was extracted using the Qiagen DNeasy blood and tissue kit and quantified using the fluorescence-based Qubit. The Gram-positive extraction protocol was followed with the following exception: 230 μl of lysis buffer was used (180 μl of 20 mM Tris-Cl, 2 mM sodium EDTA, and 1.2% Triton X-100 and 50 μl of lysozyme). The extracted DNA was sent to the Microbial Genome Sequencing Center (MiGS) at the University of Pittsburgh for sequencing. The DNA was first enzymatically fragmented using the Illumina tagmentation enzyme, and then indices were attached using PCR. Sequencing was performed using an Illumina NextSeq 550 flow cell, and 1,590,783 pairs of 150-bp reads were generated. The raw reads were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle) and assembled using SPAdes v3.13.0 with the “only-assembler” option for k values of 55, 77, 99, and 127 (7). BBMap v38.47 (https://sourceforge.net/projects/bbmap/) was used to calculate the genome coverage. Genome sequences were annotated using PATRIC v3.6.3 (8), while the publicly available genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.11 (9). Unless stated otherwise, default parameters were used for all software.

The E. faecalis UMB0843 draft genome is 2,805,168 bp long, assembled into 20 contigs with a genome coverage of 147× and an N50 score of 284,798 bp. The genome has a GC content of 38%, similar to that of other genomes of the species. PGAP identified 2,611 protein-coding regions. Both annotation tools found 51 tRNAs and 5 complete rRNA gene sequences (3 5S, 1 16S, and 1 23S). While resistance of this strain was not experimentally tested, PATRIC reported 39 genes associated with antibiotic resistance. Upon further investigation using ResFinder v3.2 (10), only antibiotic resistance to macrolides was detected [resistance gene, lsa(A)]. Our analysis suggests that this strain is susceptible to vancomycin, commonly used as the last line of defense. Vancomycin-resistant strains of E. faecalis emerged in the United States first in 1989 (11) and have become a significant concern for UTI treatment (12).

Data availability.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. JAAUWL000000000. The version described in this paper is the first version, JAAUWL010000000. The raw sequencing reads have been deposited in the SRA under the accession no. SRR11441019.

ACKNOWLEDGMENTS

This work was conducted as part of the Bacterial Genomics course at Loyola University Chicago’s Department of Biology. For prior patient recruitment, we acknowledge the Loyola Urinary Education and Research Collaborative (LUEREC) and the patients who provided the samples for this study.

FOOTNOTES

    • Received 13 April 2020.
    • Accepted 27 April 2020.
    • Published 14 May 2020.
  • Copyright © 2020 Purta et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Lawley TD,
    2. Walker AW
    . 2013. Intestinal colonization resistance. Immunology 138:1–11. doi:10.1111/j.1365-2567.2012.03616.x.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Gilmore MS,
    2. Lebreton F,
    3. van Schaik W
    . 2013. Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol 16:10–16. doi:10.1016/j.mib.2013.01.006.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Jett BD,
    2. Huycke MM,
    3. Gilmore MS
    . 1994. Virulence of enterococci. Clin Microbiol Rev 7:462–478. doi:10.1128/cmr.7.4.462.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Hidron AI,
    2. Edwards JR,
    3. Patel J,
    4. Horan TC,
    5. Sievert DM,
    6. Pollock DA,
    7. Fridkin SK, National Healthcare Safety Network Team, Participating National Healthcare Safety Network Facilities
    . 2008. Antimicrobial-resistant pathogens associated with healthcare-associated infections: annual summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007. Infect Control Hosp Epidemiol 29:996–1011. doi:10.1086/591861.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Jacobs KM,
    2. Thomas-White KJ,
    3. Hilt EE,
    4. Wolfe AJ,
    5. Waters TP
    . 2017. Microorganisms identified in the maternal bladder: discovery of the maternal bladder microbiota. AJP Rep 7:e188–e196. doi:10.1055/s-0037-1606860.
    OpenUrlCrossRef
  6. 6.↵
    1. Hilt EE,
    2. McKinley K,
    3. Pearce MM,
    4. Rosenfeld AB,
    5. Zilliox MJ,
    6. Mueller ER,
    7. Brubaker L,
    8. Gai X,
    9. Wolfe AJ,
    10. Schreckenberger PC
    . 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52:871–876. doi:10.1128/JCM.02876-13.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Wattam AR,
    2. Davis JJ,
    3. Assaf R,
    4. Boisvert S,
    5. Brettin T,
    6. Bun C,
    7. Conrad N,
    8. Dietrich EM,
    9. Disz T,
    10. Gabbard JL,
    11. Gerdes S,
    12. Henry CS,
    13. Kenyon RW,
    14. Machi D,
    15. Mao C,
    16. Nordberg EK,
    17. Olsen GJ,
    18. Murphy-Olson DE,
    19. Olson R,
    20. Overbeek R,
    21. Parrello B,
    22. Pusch GD,
    23. Shukla M,
    24. Vonstein V,
    25. Warren A,
    26. Xia F,
    27. Yoo H,
    28. Stevens RL
    . 2017. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 45:D535–D542. doi:10.1093/nar/gkw1017.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Zankari E,
    2. Hasman H,
    3. Cosentino S,
    4. Vestergaard M,
    5. Rasmussen S,
    6. Lund O,
    7. Aarestrup FM,
    8. Larsen MV
    . 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi:10.1093/jac/dks261.
    OpenUrlCrossRefPubMedWeb of Science
  11. 11.↵
    1. Sahm DF,
    2. Kissinger J,
    3. Gilmore MS,
    4. Murray PR,
    5. Mulder R,
    6. Solliday J,
    7. Clarke B
    . 1989. In vitro susceptibility studies of vancomycin-resistant Enterococcus faecalis. Antimicrob Agents Chemother 33:1588–1591. doi:10.1128/aac.33.9.1588.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Shrestha LB,
    2. Baral R,
    3. Khanal B
    . 2019. Comparative study of antimicrobial resistance and biofilm formation among Gram-positive uropathogens isolated from community-acquired urinary tract infections and catheter-associated urinary tract infections. Infect Drug Resist 12:957–963. doi:10.2147/IDR.S200988.
    OpenUrlCrossRef
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract
Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements May 2020, 9 (20) e00407-20; DOI: 10.1128/MRA.00407-20

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 Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract
(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 Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract
Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements May 2020, 9 (20) e00407-20; DOI: 10.1128/MRA.00407-20
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • 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