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Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung.

Diaz Caballero J, Clark ST, Coburn B, Zhang Y, Wang PW, Donaldson SL, Tullis DE, Yau YC, Waters VJ, Hwang DM, Guttman DS - MBio (2015)

Bottom Line: Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection.Pseudomonas aeruginosa is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients.We show that diversity of P. aeruginosa is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood and network-based (neighbor-net) phylogenetic analyses. The phylogenetic structure of 233 P. aeruginosa isolates was characterized based on genome-wide single nucleotide polymorphisms (SNPs) using the maximum likelihood (A) and neighbor-net (B) algorithms. The structure of the resulting tree revealed two populations, clades A (blue) and B (red). The 152 isolates in clade B produce a star phylogeny consistent with a recent expansion of a clonal population, while the 81 isolates in clade A show longer branches with more phylogenetic structure. (A) The scale bar shows genetic distance using the maximum composite distance and all segregating SNPs. The strain names shown on the tree are a composite of the specimen number from which the clone was isolated, an arbitrary clone letter, and the clade designation. (B) Individual strain names at the tips of each branch have been replaced with pie charts indicating the distribution of dates during which the strains were sampled (indicated by the circular legend). The scale bar indicates genetic distances.
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fig2: Maximum likelihood and network-based (neighbor-net) phylogenetic analyses. The phylogenetic structure of 233 P. aeruginosa isolates was characterized based on genome-wide single nucleotide polymorphisms (SNPs) using the maximum likelihood (A) and neighbor-net (B) algorithms. The structure of the resulting tree revealed two populations, clades A (blue) and B (red). The 152 isolates in clade B produce a star phylogeny consistent with a recent expansion of a clonal population, while the 81 isolates in clade A show longer branches with more phylogenetic structure. (A) The scale bar shows genetic distance using the maximum composite distance and all segregating SNPs. The strain names shown on the tree are a composite of the specimen number from which the clone was isolated, an arbitrary clone letter, and the clade designation. (B) Individual strain names at the tips of each branch have been replaced with pie charts indicating the distribution of dates during which the strains were sampled (indicated by the circular legend). The scale bar indicates genetic distances.

Mentions: The data were analyzed by both network-based (neighbor-net) and traditional (maximum likelihood) phylogenetic methods (Fig. 2). For the latter, the position of the root is very similar, regardless of whether it is identified by incorporating P. aeruginosa LESB58 into the analysis, selecting it based on the position of the strains isolated in specimen 1, or through midpoint rooting. Visual inspection of both trees revealed an unusual topology. Approximately one-third of the isolates share more structured relationships with relatively long branches, and these are distinctly separated from another set of isolates that have relatively short branches originating from a very recent common ancestor. Based on this observation, we designate two clades: clades A and B. While the clades are discrete and distinct in the network-based analyses, the rooted phylogenetic analysis shows that clade B is nested inside clade A, making clade A technically paraphyletic since it is not monophyletic without the clade B strains. Despite this, we will refer to the two groups as clades for simplicity. Importantly, all analyses comparing the two clades are performed on discrete sets of strains, where all strains are designated as belonging to either clade A or clade B as determined by the network-based phylogenetic analysis.


Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung.

Diaz Caballero J, Clark ST, Coburn B, Zhang Y, Wang PW, Donaldson SL, Tullis DE, Yau YC, Waters VJ, Hwang DM, Guttman DS - MBio (2015)

Maximum likelihood and network-based (neighbor-net) phylogenetic analyses. The phylogenetic structure of 233 P. aeruginosa isolates was characterized based on genome-wide single nucleotide polymorphisms (SNPs) using the maximum likelihood (A) and neighbor-net (B) algorithms. The structure of the resulting tree revealed two populations, clades A (blue) and B (red). The 152 isolates in clade B produce a star phylogeny consistent with a recent expansion of a clonal population, while the 81 isolates in clade A show longer branches with more phylogenetic structure. (A) The scale bar shows genetic distance using the maximum composite distance and all segregating SNPs. The strain names shown on the tree are a composite of the specimen number from which the clone was isolated, an arbitrary clone letter, and the clade designation. (B) Individual strain names at the tips of each branch have been replaced with pie charts indicating the distribution of dates during which the strains were sampled (indicated by the circular legend). The scale bar indicates genetic distances.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556809&req=5

fig2: Maximum likelihood and network-based (neighbor-net) phylogenetic analyses. The phylogenetic structure of 233 P. aeruginosa isolates was characterized based on genome-wide single nucleotide polymorphisms (SNPs) using the maximum likelihood (A) and neighbor-net (B) algorithms. The structure of the resulting tree revealed two populations, clades A (blue) and B (red). The 152 isolates in clade B produce a star phylogeny consistent with a recent expansion of a clonal population, while the 81 isolates in clade A show longer branches with more phylogenetic structure. (A) The scale bar shows genetic distance using the maximum composite distance and all segregating SNPs. The strain names shown on the tree are a composite of the specimen number from which the clone was isolated, an arbitrary clone letter, and the clade designation. (B) Individual strain names at the tips of each branch have been replaced with pie charts indicating the distribution of dates during which the strains were sampled (indicated by the circular legend). The scale bar indicates genetic distances.
Mentions: The data were analyzed by both network-based (neighbor-net) and traditional (maximum likelihood) phylogenetic methods (Fig. 2). For the latter, the position of the root is very similar, regardless of whether it is identified by incorporating P. aeruginosa LESB58 into the analysis, selecting it based on the position of the strains isolated in specimen 1, or through midpoint rooting. Visual inspection of both trees revealed an unusual topology. Approximately one-third of the isolates share more structured relationships with relatively long branches, and these are distinctly separated from another set of isolates that have relatively short branches originating from a very recent common ancestor. Based on this observation, we designate two clades: clades A and B. While the clades are discrete and distinct in the network-based analyses, the rooted phylogenetic analysis shows that clade B is nested inside clade A, making clade A technically paraphyletic since it is not monophyletic without the clade B strains. Despite this, we will refer to the two groups as clades for simplicity. Importantly, all analyses comparing the two clades are performed on discrete sets of strains, where all strains are designated as belonging to either clade A or clade B as determined by the network-based phylogenetic analysis.

Bottom Line: Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection.Pseudomonas aeruginosa is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients.We show that diversity of P. aeruginosa is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.

No MeSH data available.


Related in: MedlinePlus