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Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Author

Listed:
  • Mark G. Young

    (Broad Institute)

  • Timothy J. Straub

    (Broad Institute)

  • Colin J. Worby

    (Broad Institute)

  • Hayden C. Metsky

    (Broad Institute)

  • Andreas Gnirke

    (Broad Institute)

  • Ryan A. Bronson

    (Broad Institute)

  • Lucas R. van Dijk

    (Broad Institute
    Delft University of Technology)

  • Christopher A. Desjardins

    (Broad Institute)

  • Christian Matranga

    (Broad Institute)

  • James Qu

    (Broad Institute)

  • Jesús Bazan Villicana

    (Washington University School of Medicine)

  • Philippe Azimzadeh

    (Washington University School of Medicine)

  • Andrew Kau

    (Washington University School of Medicine
    Washington University School of Medicine
    Washington University School of Medicine)

  • Karen W. Dodson

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Henry L. Schreiber

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Abigail L. Manson

    (Broad Institute)

  • Scott J. Hultgren

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Ashlee M. Earl

    (Broad Institute)

Abstract

Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (

Suggested Citation

  • Mark G. Young & Timothy J. Straub & Colin J. Worby & Hayden C. Metsky & Andreas Gnirke & Ryan A. Bronson & Lucas R. van Dijk & Christopher A. Desjardins & Christian Matranga & James Qu & Jesús Bazan V, 2024. "Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53829-7
    DOI: 10.1038/s41467-024-53829-7
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    References listed on IDEAS

    as
    1. Caitlin N. Spaulding & Roger D. Klein & Ségolène Ruer & Andrew L. Kau & Henry L. Schreiber & Zachary T. Cusumano & Karen W. Dodson & Jerome S. Pinkner & Daved H. Fremont & James W. Janetka & Han Remau, 2017. "Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist," Nature, Nature, vol. 546(7659), pages 528-532, June.
    2. Leland Wilkinson, 2011. "ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H," Biometrics, The International Biometric Society, vol. 67(2), pages 678-679, June.
    3. Michael D. Valentino & Abigail Manson McGuire & Jason W. Rosch & Paulo J. M. Bispo & Corinna Burnham & Christine M. Sanfilippo & Robert A. Carter & Michael E. Zegans & Bernard Beall & Ashlee M. Earl &, 2014. "Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    4. Peter J. Turnbaugh & Ruth E. Ley & Michael A. Mahowald & Vincent Magrini & Elaine R. Mardis & Jeffrey I. Gordon, 2006. "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, Nature, vol. 444(7122), pages 1027-1031, December.
    5. Charles R. Harris & K. Jarrod Millman & Stéfan J. Walt & Ralf Gommers & Pauli Virtanen & David Cournapeau & Eric Wieser & Julian Taylor & Sebastian Berg & Nathaniel J. Smith & Robert Kern & Matti Picu, 2020. "Array programming with NumPy," Nature, Nature, vol. 585(7825), pages 357-362, September.
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