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FEMS Microbiol Lett. 2018 Jul 1;365(14). doi: 10.1093/femsle/fny120.

Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools.

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Institute for Integrative and Systems Biology (IBIS), University Laval, Qu├ębec City, QC G1V 0A6, Canada.
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland.
Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK.
Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.
Centre of Microbial Host Interactions, Institute of Technology Tallaght, Tallaght, Dublin D24 FKT9, Ireland.
Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, D-30625, Hannover, Germany.
Institute for Cellular Medicine, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.


Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections of cystic fibrosis (CF). In order to facilitate coordinated study of this pathogen, an international reference panel of P. aeruginosa isolates was assembled. Here we report the genome sequencing and analysis of 33 of these isolates and 7 reference genomes to further characterise this panel. Core genome single nucleotide variant phylogeny demonstrated that the panel strains are widely distributed amongst the P. aeruginosa population. Common loss-of-function mutations reported as adaptive during CF (such as in mucA and mexA) were identified amongst isolates from chronic respiratory infections. From the 40 strains analysed, 37 unique resistomes were predicted, based on the Resistance Gene Identifier method using the Comprehensive Antibiotic Resistance Database. Notably, hierarchical clustering and phylogenetic reconstructions based on the presence/absence of genomic islands (GIs), prophages and other regions of genome plasticity (RGPs) supported the subdivision of P. aeruginosa into two main groups. This is the largest, most diverse analysis of GIs and associated RGPs to date, and the results suggest that, at least at the largest clade grouping level (group 1 vs group 2), each group may be drawing upon distinct mobile gene pools.

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