2
|
Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore 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 JP, 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. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol 2015; 6:1036. [PMID: 26483767 PMCID: PMC4586430 DOI: 10.3389/fmicb.2015.01036] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/11/2015] [Indexed: 11/24/2022] Open
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.
Collapse
Affiliation(s)
- Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | | | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Jérôme Laroche
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Stéphane Larose
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Halim Maaroufi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Matthew Moore
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Shawn D Aaron
- Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Jean Barbeau
- Faculté de Médecine Dentaire, Université de Montréal Montréal, QC, Canada
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute Brisbane, QLD, Australia
| | - Jane L Burns
- Seattle Children's Research Institute, University of Washington School of Medicine Seattle, WA, USA
| | - Miguel Camara
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - André Cantin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Steve J Charette
- 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
| | - Ken Dewar
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Éric Déziel
- INRS Institut Armand Frappier Laval, QC, Canada
| | - Keith Grimwood
- School of Medicine, Griffith University Gold Coast, QLD, Australia
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Joe J Harrison
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Baofeng Jia
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Dervla T Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Timothy J Kidd
- Child Health Research Centre, The University of Queensland Brisbane, QLD, Australia ; Centre for Infection and Immunity, Queen's University Belfast Belfast, UK
| | - Jens Klockgether
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Iain L Lamont
- Department of Biochemistry, University of Otago Dunedin, New Zealand
| | - Shawn Lewenza
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Nick Loman
- Institute for Microbiology and Infection, University of Birmingham Birmingham, UK
| | - François Malouin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Jim Manos
- Department of Infectious Diseases and Immunology, The University of Sydney Sydney, NSW, Australia
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Josie McKeown
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Julie Milot
- Department of Pneumology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval Quebec, QC, Canada
| | - Hardeep Naghra
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Dao Nguyen
- Department of Human Genetics, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology and Department of Experimental Medicine, McGill University Montreal, QC, Canada
| | - Sheldon K Pereira
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-On-Hudson NY, USA
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels, Belgium
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University Albany, New Zealand ; Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Simon Rousseau
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Pedro M Santos
- Department of Biology, University of Minho Braga, Portugal
| | | | - Véronique Taylor
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Paul Williams
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sandra W Thrane
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK
| | - Burkhard Tümmler
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| |
Collapse
|