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.
| Language | English |
|---|---|
| Number of pages | 25 |
| Journal | FEMS Microbiology Letters |
| Early online date | 12 Jun 2018 |
| DOIs | |
| Publication status | E-pub ahead of print - 12 Jun 2018 |
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Keywords
- Pseudomonas aeruginosa
- comparative genomics
- antimicrobial resistance
- genomic islands
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}
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 journal › Article
TY - JOUR
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.
AB - 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.
KW - Pseudomonas aeruginosa
KW - comparative genomics
KW - antimicrobial resistance
KW - genomic islands
UR - https://academic.oup.com/femsle
U2 - 10.1093/femsle/fny120
DO - 10.1093/femsle/fny120
M3 - Article
JO - FEMS Microbiology Letters
T2 - FEMS Microbiology Letters
JF - FEMS Microbiology Letters
SN - 0378-1097
ER -