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

Luca Freschi, Claire Bertelli, Julie Jeukens, Matthew P. Moore, Irena Kukavica-Ibrulj, Jean-Guillaume Emond-Rheault, Jérémie Hamel, Joanne L Fothergill, Nicholas P. Tucker, Siobhán McClean, Jens Klockgether, Anthony de Soyza, Fiona S.L. Brinkman, Roger C. Levesque, Craig Winstanley

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

LanguageEnglish
Number of pages25
JournalFEMS Microbiology Letters
Early online date12 Jun 2018
DOIs
Publication statusE-pub ahead of print - 12 Jun 2018

Fingerprint

Gene Pool
Pseudomonas aeruginosa
Genome
Genomic Islands
Cystic Fibrosis
Prophages
Phylogeny
Microbial Drug Resistance
Respiratory Tract Infections
Cluster Analysis
Nucleotides
Databases
Mutation
Infection
Population
Genes

Keywords

  • Pseudomonas aeruginosa
  • comparative genomics
  • antimicrobial resistance
  • genomic islands

Cite this

Freschi, Luca ; Bertelli, Claire ; Jeukens, Julie ; Moore, Matthew P. ; Kukavica-Ibrulj, Irena ; Emond-Rheault, Jean-Guillaume ; Hamel, Jérémie ; Fothergill, Joanne L ; Tucker, Nicholas P. ; McClean, Siobhán ; Klockgether, Jens ; de Soyza, Anthony ; Brinkman, Fiona S.L. ; Levesque, Roger C. ; Winstanley, Craig. / Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools. In: FEMS Microbiology Letters . 2018.
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abstract = "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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Freschi, L, Bertelli, C, Jeukens, J, Moore, MP, Kukavica-Ibrulj, I, Emond-Rheault, J-G, Hamel, J, Fothergill, JL, Tucker, NP, McClean, S, Klockgether, J, de Soyza, A, Brinkman, FSL, Levesque, RC & Winstanley, C 2018, 'Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools' FEMS Microbiology Letters . https://doi.org/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. / Freschi, Luca; Bertelli, Claire; Jeukens, Julie; Moore, Matthew P.; Kukavica-Ibrulj, Irena; Emond-Rheault, Jean-Guillaume; Hamel, Jérémie; Fothergill, Joanne L; Tucker, Nicholas P.; McClean, Siobhán; Klockgether, Jens; de Soyza, Anthony; Brinkman, Fiona S.L.; Levesque, Roger C.; Winstanley, Craig.

In: FEMS Microbiology Letters , 12.06.2018.

Research output: Contribution to journalArticle

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T1 - Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools

AU - Freschi, Luca

AU - Bertelli, Claire

AU - Jeukens, Julie

AU - Moore, Matthew P.

AU - Kukavica-Ibrulj, Irena

AU - Emond-Rheault, Jean-Guillaume

AU - Hamel, Jérémie

AU - Fothergill, Joanne L

AU - Tucker, Nicholas P.

AU - McClean, Siobhán

AU - Klockgether, Jens

AU - de Soyza, Anthony

AU - Brinkman, Fiona S.L.

AU - Levesque, Roger C.

AU - Winstanley, Craig

PY - 2018/6/12

Y1 - 2018/6/12

N2 - 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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KW - comparative genomics

KW - antimicrobial resistance

KW - genomic islands

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DO - 10.1093/femsle/fny120

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