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 Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection

Mikalina Belmonte, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
David Rasko, Editor
Mikalina Belmonte
aDepartment of Biology, 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
aDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
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 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
David Rasko
University of Maryland School of Medicine
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00437-20
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Escherichia coli is a Gram-negative, motile, rod-shaped bacterium that causes the majority of uncomplicated urinary tract infections (UTIs). Here, we report the draft genome of E. coli strain UMB9246, an isolate from a woman with recurrent UTI.

ANNOUNCEMENT

Pathogenic strains of Escherichia coli can cause intestinal, urinary tract, and internal infections, and E. coli isolates from multiple body sites have been sequenced (1). Specifically, uropathogenic E. coli (UPEC) strains are responsible for the majority of infrequent urinary tract infections (UTIs) in humans (2, 3). Recurrence of UTIs is frequent (4). Recurrent UTIs (rUTIs) are considerably more complicated and nuanced than infrequent UTIs. Here, we isolated E. coli strain UMB9246 from a catheterized urine sample obtained from a woman with an rUTI.

E. coli strain UMB9246 was collected as part of a prior institutional review board (IRB)-approved study (University of California, San Diego, IRB no. 170077AW) using the expanded quantitative urine culture (EQUC) protocol (5). Briefly, 100 μl of urine was spread onto a 5% sheep blood agar plate and incubated overnight at 35°C with 5% CO2 for 24 h. Each morphologically distinct colony was then further purified through successive plating. The genus and species for this isolate were determined via matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry as previously described (5). The isolate was then stored at −80°C until sequencing. From this freezer stock, the sample was streaked onto a Columbia nalidixic acid (CNA) agar plate and incubated at 35°C with 5% CO2 for 24 h. A single colony was selected and incubated in LB broth at 37°C with shaking for 24 h. DNA was extracted using the DNeasy blood and tissue kit following the manufacturer’s protocol for Gram-positive bacteria with the following alterations. We used 230 μl of lysis buffer (180 μl of 20 mM Tris-Cl, 2 mM sodium EDTA, and 1.2% Triton X-100 and 50 μl of lysozyme) in step 2, and in step 5 of the protocol, we incubated the sample at 56°C for 10 min. DNA was quantified using the Qubit fluorometer and sent to the Microbial Genome Sequencing Center (MiGS) at the University of Pittsburgh for sequencing. The DNA was enzymatically fragmented using an Illumina tagmentation enzyme, and indices were attached using PCR. The DNA was sequenced using an Illumina NextSeq 550 flow cell, producing 1,408,737 pairs of 150-bp reads. 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 (6). The genome coverage is 71× and was calculated using BBMap v38.47 (https://sourceforge.net/projects/bbmap/). The genome assembly was first annotated using PATRIC v3.6.3 (7). The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.11 (8) was used to annotate the publicly available genome. The genome assembly was also examined using PHASTER (9) and CRISPRCasFinder (10) to identify prophage sequences and CRISPR spacer arrays, respectively. Default parameters were used for each software tool, unless previously stated.

The E. coli UMB9246 draft genome is 5,057,732 bp long in 90 contigs with an N50 score of 159,145 bp and a GC content of 50.8%. The PGAP annotation identified 4,691 protein-coding genes, 5 rRNA operons, and 77 tRNAs. PHASTER predicted 1 questionable, 2 incomplete, and 1 intact phage for this strain. CRISPRCasFinder found 2 CRISPR arrays. PATRIC identified in the genome assembly both virulence factors and antibiotic resistance genes, including those for tetracycline resistance. Further analysis of this strain and other isolates from individuals suffering from uncomplicated UTIs and rUTIs will give us insight into the mechanisms for recurrence.

Data availability.This whole-genome shotgun project has been deposited in GenBank under the accession no. JAAUVS000000000. The version described in this paper is the first version, JAAUVS010000000. The raw sequencing reads have been deposited in SRA under the accession no. SRR11441020.

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 17 April 2020.
    • Accepted 14 May 2020.
    • Published 4 June 2020.
  • Copyright © 2020 Belmonte 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. Moriel DG,
    2. Tan L,
    3. Goh KGK,
    4. Phan M-D,
    5. Ipe DS,
    6. Lo AW,
    7. Peters KM,
    8. Ulett GC,
    9. Beatson SA,
    10. Schembri MA
    . 2016. A novel protective vaccine antigen from the core Escherichia coli genome. mSphere 1:e00326-16. doi:10.1128/mSphere.00326-16.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Johnson JR
    . 1991. Virulence factors in Escherichia coli urinary tract infection. Clin Microbiol Rev 4:80–128. doi:10.1128/cmr.4.1.80.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    1. Terlizzi ME,
    2. Gribaudo G,
    3. Maffei ME
    . 2017. Uropathogenic Escherichia coli (UPEC) infections: virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Front Microbiol 8:1566. doi:10.3389/fmicb.2017.01566.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Foxman B,
    2. Gillespie B,
    3. Koopman J,
    4. Zhang L,
    5. Palin K,
    6. Tallman P,
    7. Marsh JV,
    8. Spear S,
    9. Sobel JD,
    10. Marty MJ,
    11. Marrs CF
    . 2000. Risk factors for second urinary tract infection among college women. Am J Epidemiol 151:1194–1205. doi:10.1093/oxfordjournals.aje.a010170.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    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
  6. 6.↵
    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
  7. 7.↵
    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
  8. 8.↵
    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
  9. 9.↵
    1. Arndt D,
    2. Grant JR,
    3. Marcu A,
    4. Sajed T,
    5. Pon A,
    6. Liang Y,
    7. Wishart DS
    . 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21. doi:10.1093/nar/gkw387.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Couvin D,
    2. Bernheim A,
    3. Toffano-Nioche C,
    4. Touchon M,
    5. Michalik J,
    6. Néron B,
    7. Rocha EPC,
    8. Vergnaud G,
    9. Gautheret D,
    10. Pourcel C
    . 2018. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46:W246–W251. doi:10.1093/nar/gky425.
    OpenUrlCrossRefPubMed
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection
Mikalina Belmonte, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements Jun 2020, 9 (23) e00437-20; DOI: 10.1128/MRA.00437-20

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 Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection
(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 Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection
Mikalina Belmonte, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements Jun 2020, 9 (23) e00437-20; DOI: 10.1128/MRA.00437-20
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