Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium.
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.
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Luca
L
Freschi
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Julie
J
Jeukens
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Irena
I
Kukavica-Ibrulj
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Brian
B
Boyle
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Marie-Josée
MJ
Dupont
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Jérôme
J
Laroche
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Stéphane
S
Larose
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Halim
H
Maaroufi
Institute of Infection and Global Health, University of Liverpool Liverpool, UK.
Joanne L
JL
Fothergill
Institute of Infection and Global Health, University of Liverpool Liverpool, UK.
Matthew
M
Moore
Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada.
Geoffrey L
GL
Winsor
Ottawa Hospital Research Institute Ottawa, ON, Canada.
Shawn D
SD
Aaron
Faculté de Médecine Dentaire, Université de Montréal Montréal, QC, Canada.
Jean
J
Barbeau
QIMR Berghofer Medical Research Institute Brisbane, QLD, Australia.
Scott C
SC
Bell
Seattle Children's Research Institute, University of Washington School of Medicine Seattle, WA, USA.
Jane L
JL
Burns
School of Life Sciences, University of Nottingham Nottingham, UK.
Miguel
M
Camara
Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada.
André
A
Cantin
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec, QC, Canada ; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec, QC, Canada.
Steve J
SJ
Charette
Department of Human Genetics, McGill University Montreal, QC, Canada.
Ken
K
Dewar
INRS Institut Armand Frappier Laval, QC, Canada.
Éric
É
Déziel
School of Medicine, Griffith University Gold Coast, QLD, Australia.
Keith
K
Grimwood
Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada.
Robert E W
RE
Hancock
Biological Sciences, University of Calgary Calgary, AB, Canada.
Joe J
JJ
Harrison
School of Life Sciences, University of Nottingham Nottingham, UK.
Stephan
S
Heeb
Department of Systems Biology, Technical University of Denmark Lyngby, Denmark.
Lars
L
Jelsbak
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
Baofeng
B
Jia
Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK.
Dervla T
DT
Kenna
Child Health Research Centre, The University of Queensland Brisbane, QLD, Australia ; Centre for Infection and Immunity, Queen's University Belfast Belfast, UK.
Timothy J
TJ
Kidd
Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany.
Jens
J
Klockgether
Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada.
Joseph S
JS
Lam
Department of Biochemistry, University of Otago Dunedin, New Zealand.
Iain L
IL
Lamont
Biological Sciences, University of Calgary Calgary, AB, Canada.
Shawn
S
Lewenza
Institute for Microbiology and Infection, University of Birmingham Birmingham, UK.
Nick
N
Loman
Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada.
François
F
Malouin
Department of Infectious Diseases and Immunology, The University of Sydney Sydney, NSW, Australia.
Jim
J
Manos
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
Andrew G
AG
McArthur
School of Life Sciences, University of Nottingham Nottingham, UK.
Josie
J
McKeown
Department of Pneumology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval Quebec, QC, Canada.
Julie
J
Milot
School of Life Sciences, University of Nottingham Nottingham, UK.
Hardeep
H
Naghra
Department of Human Genetics, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology and Department of Experimental Medicine, McGill University Montreal, QC, Canada.
Dao
D
Nguyen
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
Sheldon K
SK
Pereira
Department of Biology, Bard College, Annandale-On-Hudson NY, USA.
Gabriel G
GG
Perron
Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels, Belgium.
Jean-Paul
JP
Pirnay
New Zealand Institute for Advanced Study, Massey University Albany, New Zealand ; Max Planck Institute for Evolutionary Biology Plön, Germany.
Paul B
PB
Rainey
Department of Human Genetics, McGill University Montreal, QC, Canada.
Simon
S
Rousseau
Department of Biology, University of Minho Braga, Portugal.
Pedro M
PM
Santos
St. Michael's Hospital Toronto, ON, Canada.
Anne
A
Stephenson
Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada.
Véronique
V
Taylor
Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK.
Jane F
JF
Turton
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
Nicholas
N
Waglechner
School of Life Sciences, University of Nottingham Nottingham, UK.
Paul
P
Williams
Department of Systems Biology, Technical University of Denmark Lyngby, Denmark.
Sandra W
SW
Thrane
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
Gerard D
GD
Wright
Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada.
Fiona S L
FS
Brinkman
Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK.
Nicholas P
NP
Tucker
Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany.
Burkhard
B
Tümmler
Institute of Infection and Global Health, University of Liverpool Liverpool, UK.
Craig
C
Winstanley
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
Roger C
RC
Levesque
Pseudomonas aeruginosa; antibiotic resistance; bacterial genome; clinical microbiology; cystic fibrosis; database; next-generation sequencing; phylogeny