Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

Luca Freschi, Julie Jeukens, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Jérôme Laroche, Stéphane Larose, Halim Maaroufi, Joanne L. Fothergill, Matthew Moore, Lars Jelsbak, Sandra Wingaard Thrane

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    Abstract

    The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.
    Original languageEnglish
    Article number1036
    JournalFrontiers in Microbiology
    Volume6
    Number of pages8
    ISSN1664-302X
    DOIs
    Publication statusPublished - 2015

    Bibliographical note

    For a complete author list see article.

    This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    Keywords

    • Pseudomonas aeruginosa
    • Antibiotic resistance
    • Bacterial genome
    • Clinical microbiology
    • Cystic fibrosis
    • Database
    • Next-generation sequencing
    • Phylogeny

    Cite this

    Freschi, L., Jeukens, J., Kukavica-Ibrulj, I., Boyle, B., Dupont, M-J., Laroche, J., ... Thrane, S. W. (2015). Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology, 6, [1036]. https://doi.org/10.3389/fmicb.2015.01036
    Freschi, Luca ; Jeukens, Julie ; Kukavica-Ibrulj, Irena ; Boyle, Brian ; Dupont, Marie-Josée ; Laroche, Jérôme ; Larose, Stéphane ; Maaroufi, Halim ; Fothergill, Joanne L. ; Moore, Matthew ; Jelsbak, Lars ; Thrane, Sandra Wingaard. / Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. In: Frontiers in Microbiology. 2015 ; Vol. 6.
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    abstract = "The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.",
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    note = "For a complete author list see article. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.",
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    Freschi, L, Jeukens, J, Kukavica-Ibrulj, I, Boyle, B, Dupont, M-J, Laroche, J, Larose, S, Maaroufi, H, Fothergill, JL, Moore, M, Jelsbak, L & Thrane, SW 2015, 'Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium', Frontiers in Microbiology, vol. 6, 1036. https://doi.org/10.3389/fmicb.2015.01036

    Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. / Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Laroche, Jérôme; Larose, Stéphane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Jelsbak, Lars; Thrane, Sandra Wingaard.

    In: Frontiers in Microbiology, Vol. 6, 1036, 2015.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

    AU - Freschi, Luca

    AU - Jeukens, Julie

    AU - Kukavica-Ibrulj, Irena

    AU - Boyle, Brian

    AU - Dupont, Marie-Josée

    AU - Laroche, Jérôme

    AU - Larose, Stéphane

    AU - Maaroufi, Halim

    AU - Fothergill, Joanne L.

    AU - Moore, Matthew

    AU - Jelsbak, Lars

    AU - Thrane, Sandra Wingaard

    N1 - For a complete author list see article. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    PY - 2015

    Y1 - 2015

    N2 - The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.

    AB - The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.

    KW - Pseudomonas aeruginosa

    KW - Antibiotic resistance

    KW - Bacterial genome

    KW - Clinical microbiology

    KW - Cystic fibrosis

    KW - Database

    KW - Next-generation sequencing

    KW - Phylogeny

    U2 - 10.3389/fmicb.2015.01036

    DO - 10.3389/fmicb.2015.01036

    M3 - Journal article

    VL - 6

    JO - Frontiers in Microbiology

    JF - Frontiers in Microbiology

    SN - 1664-302X

    M1 - 1036

    ER -