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 Moores, Geoffrey L. Winsor, Shawn D. Aaron, Jean Barbeau, Scott C. Bell, Jane L. Burns, Miguel Camara, André Cantin, Steve J. Charette, Ken Dewar, Éric Déziel & 38 others Keith Grimwood, Robert E. W. Hancock, Joe J. Harrison, Stephan Heeb, Lars Jelsbak, Baofeng Jia, Dervla T. Kenna, Timothy J. Kidd, Jens Klockgether, Joseph S. Lam, Iain L. Lamont, Shawn Lewenza, Nick Loman, François Malouin, Jim Manos, Andrew G. McArthur, Josie McKeown, Julie Milot, Hardeep Naghra, Dao Nguyen, Sheldon K. Pereira, Gabriel G. Perron, Jean-Paul Pirnay, Paul B. Rainey, Simon Rousseau, Pedro M. Santos, Anne Stephenson, Véronique Taylor, Jane F. Turton, Nicholas Waglechner, Paul Williams, Sandra W. Thrane, Gerard D. Wright, Fiona S. L. Brinkman, Nicholas P. Tucker, Burkhard Tümmler, Craig Winstanley, Roger C. Levesque

Research output: Contribution to journalArticle

50 Citations (Scopus)

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.
LanguageEnglish
Article number1036
Number of pages8
JournalFrontiers in Microbiology
Volume6
DOIs
Publication statusPublished - 29 Sep 2015

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Genomics
Pseudomonas aeruginosa
Genome
Microbial Drug Resistance
Pseudomonas
Infection
Virulence
Patient Care
Databases
Genes

Keywords

  • infectious diseases
  • pseudomonas genomes
  • P. aeruginosa
  • genome comparison

Cite this

Freschi, L., Jeukens, J., Kukavica-Ibrulj, I., Boyle, B., Dupont, M-J., Laroche, J., ... Levesque, R. C. (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. ; Moores, Matthew ; Winsor, Geoffrey L. ; Aaron, Shawn D. ; Barbeau, Jean ; Bell, Scott C. ; Burns, Jane L. ; Camara, Miguel ; Cantin, André ; Charette, Steve J. ; Dewar, Ken ; Déziel, Éric ; Grimwood, Keith ; Hancock, Robert E. W. ; Harrison, Joe J. ; Heeb, Stephan ; Jelsbak, Lars ; Jia, Baofeng ; Kenna, Dervla T. ; Kidd, Timothy J. ; Klockgether, Jens ; Lam, Joseph S. ; Lamont, Iain L. ; Lewenza, Shawn ; Loman, Nick ; Malouin, François ; Manos, Jim ; McArthur, Andrew G. ; McKeown, Josie ; Milot, Julie ; Naghra, Hardeep ; Nguyen, Dao ; Pereira, Sheldon K. ; Perron, Gabriel G. ; Pirnay, Jean-Paul ; Rainey, Paul B. ; Rousseau, Simon ; Santos, Pedro M. ; Stephenson, Anne ; Taylor, Véronique ; Turton, Jane F. ; Waglechner, Nicholas ; Williams, Paul ; Thrane, Sandra W. ; Wright, Gerard D. ; Brinkman, Fiona S. L. ; Tucker, Nicholas P. ; Tümmler, Burkhard ; Winstanley, Craig ; Levesque, Roger C. / Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. In: Frontiers in Microbiology. 2015 ; Vol. 6.
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Freschi, L, Jeukens, J, Kukavica-Ibrulj, I, Boyle, B, Dupont, M-J, Laroche, J, Larose, S, Maaroufi, H, Fothergill, JL, Moores, M, Winsor, GL, Aaron, SD, Barbeau, J, Bell, SC, Burns, JL, Camara, M, Cantin, A, Charette, SJ, Dewar, K, Déziel, É, Grimwood, K, Hancock, REW, Harrison, JJ, Heeb, S, Jelsbak, L, Jia, B, Kenna, DT, Kidd, TJ, Klockgether, J, Lam, JS, Lamont, IL, Lewenza, S, Loman, N, Malouin, F, Manos, J, McArthur, AG, McKeown, J, Milot, J, Naghra, H, Nguyen, D, Pereira, SK, Perron, GG, Pirnay, J-P, Rainey, PB, Rousseau, S, Santos, PM, Stephenson, A, Taylor, V, Turton, JF, Waglechner, N, Williams, P, Thrane, SW, Wright, GD, Brinkman, FSL, Tucker, NP, Tümmler, B, Winstanley, C & Levesque, RC 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.; Moores, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; Camara, Miguel; Cantin, André; Charette, Steve J.; Dewar, Ken; Déziel, Éric; Grimwood, Keith; Hancock, Robert E. W.; Harrison, Joe J.; Heeb, Stephan; Jelsbak, Lars; Jia, Baofeng; Kenna, Dervla T.; Kidd, Timothy J.; Klockgether, Jens; Lam, Joseph S.; Lamont, Iain L.; Lewenza, Shawn; Loman, Nick; Malouin, François; Manos, Jim; McArthur, Andrew G.; McKeown, Josie; Milot, Julie; Naghra, Hardeep; Nguyen, Dao; Pereira, Sheldon K.; Perron, Gabriel G.; Pirnay, Jean-Paul; Rainey, Paul B.; Rousseau, Simon; Santos, Pedro M.; Stephenson, Anne; Taylor, Véronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S. L.; Tucker, Nicholas P.; Tümmler, Burkhard; Winstanley, Craig; Levesque, Roger C.

In: Frontiers in Microbiology, Vol. 6, 1036, 29.09.2015.

Research output: Contribution to journalArticle

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 - Moores, Matthew

AU - Winsor, Geoffrey L.

AU - Aaron, Shawn D.

AU - Barbeau, Jean

AU - Bell, Scott C.

AU - Burns, Jane L.

AU - Camara, Miguel

AU - Cantin, André

AU - Charette, Steve J.

AU - Dewar, Ken

AU - Déziel, Éric

AU - Grimwood, Keith

AU - Hancock, Robert E. W.

AU - Harrison, Joe J.

AU - Heeb, Stephan

AU - Jelsbak, Lars

AU - Jia, Baofeng

AU - Kenna, Dervla T.

AU - Kidd, Timothy J.

AU - Klockgether, Jens

AU - Lam, Joseph S.

AU - Lamont, Iain L.

AU - Lewenza, Shawn

AU - Loman, Nick

AU - Malouin, François

AU - Manos, Jim

AU - McArthur, Andrew G.

AU - McKeown, Josie

AU - Milot, Julie

AU - Naghra, Hardeep

AU - Nguyen, Dao

AU - Pereira, Sheldon K.

AU - Perron, Gabriel G.

AU - Pirnay, Jean-Paul

AU - Rainey, Paul B.

AU - Rousseau, Simon

AU - Santos, Pedro M.

AU - Stephenson, Anne

AU - Taylor, Véronique

AU - Turton, Jane F.

AU - Waglechner, Nicholas

AU - Williams, Paul

AU - Thrane, Sandra W.

AU - Wright, Gerard D.

AU - Brinkman, Fiona S. L.

AU - Tucker, Nicholas P.

AU - Tümmler, Burkhard

AU - Winstanley, Craig

AU - Levesque, Roger C.

PY - 2015/9/29

Y1 - 2015/9/29

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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 - infectious diseases

KW - pseudomonas genomes

KW - P. aeruginosa

KW - genome comparison

UR - http://journal.frontiersin.org/article/10.3389/fmicb.2015.01036/full

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DO - 10.3389/fmicb.2015.01036

M3 - Article

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JO - Frontiers in Microbiology

T2 - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

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ER -