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Front Microbiol. 2015 Sep 29;6:1036. doi: 10.3389/fmicb.2015.01036. eCollection 2015.

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

Author information

1
Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada.
2
Institute of Infection and Global Health, University of Liverpool Liverpool, UK.
3
Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada.
4
Ottawa Hospital Research Institute Ottawa, ON, Canada.
5
Faculté de Médecine Dentaire, Université de Montréal Montréal, QC, Canada.
6
QIMR Berghofer Medical Research Institute Brisbane, QLD, Australia.
7
Seattle Children's Research Institute, University of Washington School of Medicine Seattle, WA, USA.
8
School of Life Sciences, University of Nottingham Nottingham, UK.
9
Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada.
10
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.
11
Department of Human Genetics, McGill University Montreal, QC, Canada.
12
INRS Institut Armand Frappier Laval, QC, Canada.
13
School of Medicine, Griffith University Gold Coast, QLD, Australia.
14
Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada.
15
Biological Sciences, University of Calgary Calgary, AB, Canada.
16
Department of Systems Biology, Technical University of Denmark Lyngby, Denmark.
17
M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada.
18
Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK.
19
Child Health Research Centre, The University of Queensland Brisbane, QLD, Australia ; Centre for Infection and Immunity, Queen's University Belfast Belfast, UK.
20
Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany.
21
Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada.
22
Department of Biochemistry, University of Otago Dunedin, New Zealand.
23
Institute for Microbiology and Infection, University of Birmingham Birmingham, UK.
24
Department of Infectious Diseases and Immunology, The University of Sydney Sydney, NSW, Australia.
25
Department of Pneumology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval Quebec, QC, Canada.
26
Department of Human Genetics, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology and Department of Experimental Medicine, McGill University Montreal, QC, Canada.
27
Department of Biology, Bard College, Annandale-On-Hudson NY, USA.
28
Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels, Belgium.
29
New Zealand Institute for Advanced Study, Massey University Albany, New Zealand ; Max Planck Institute for Evolutionary Biology Plön, Germany.
30
Department of Biology, University of Minho Braga, Portugal.
31
St. Michael's Hospital Toronto, ON, Canada.
32
Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK.

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.

KEYWORDS:

Pseudomonas aeruginosa; antibiotic resistance; bacterial genome; clinical microbiology; cystic fibrosis; database; next-generation sequencing; phylogeny

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