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A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

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Related in: MedlinePlus

Histogram comparing frequencies of detected recombination sizes in a collection of PMEN1 isolates and in vitro transformants.The algorithm used to detect sequence imports in a sample of PMEN1 genomes was individually applied to each transformant sequence from the first experiment described in this work. In both graphs, the blue bars show the output of the algorithm applied to sequences from this experiment, whereas the red bars represent the data from the PMEN1 strains. (A) Comparison of the ten serotype switching recombinations characterised in PMEN1 with the transformation events spanning the cps locus selected in vitro. (B) Comparison of the unselected secondary transformation events characterised in vitro with the 615 homologous recombinations (i.e. excluding events overlapping prophage or conjugative elements) identified in the PMEN1 isolates.
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ppat-1002745-g008: Histogram comparing frequencies of detected recombination sizes in a collection of PMEN1 isolates and in vitro transformants.The algorithm used to detect sequence imports in a sample of PMEN1 genomes was individually applied to each transformant sequence from the first experiment described in this work. In both graphs, the blue bars show the output of the algorithm applied to sequences from this experiment, whereas the red bars represent the data from the PMEN1 strains. (A) Comparison of the ten serotype switching recombinations characterised in PMEN1 with the transformation events spanning the cps locus selected in vitro. (B) Comparison of the unselected secondary transformation events characterised in vitro with the 615 homologous recombinations (i.e. excluding events overlapping prophage or conjugative elements) identified in the PMEN1 isolates.

Mentions: The lengths of the recombinations changing capsule type in the PMEN1 clinical isolates can be compared with those selected in this work through applying the algorithm used to detect sequence imports in the PMEN1 strains [35] to the in vitro transformants. In these comparable datasets, the distribution of cps-spanning recombination sizes is very similar in both (Figure 8A). Elsewhere in the genome, the distributions of recombination sizes are alike (Figure 8B), but the set detected in the PMEN1 population has fewer short recombinations. This is likely to be due to a reduced power to differentiate such events, which import few SNPs, from the background of point mutations in the clinical isolates, as compared to the near-complete absence of variation outside of transformation events from the isolates in this study. Hence the exponential decline is less clear from the data derived from clinical isolates, and the rate parameter λR is estimated as being artefactually low (1.58×10−4 bp−1; 95% confidence intervals 1.47–1.72×10−4 bp−1).


A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Histogram comparing frequencies of detected recombination sizes in a collection of PMEN1 isolates and in vitro transformants.The algorithm used to detect sequence imports in a sample of PMEN1 genomes was individually applied to each transformant sequence from the first experiment described in this work. In both graphs, the blue bars show the output of the algorithm applied to sequences from this experiment, whereas the red bars represent the data from the PMEN1 strains. (A) Comparison of the ten serotype switching recombinations characterised in PMEN1 with the transformation events spanning the cps locus selected in vitro. (B) Comparison of the unselected secondary transformation events characterised in vitro with the 615 homologous recombinations (i.e. excluding events overlapping prophage or conjugative elements) identified in the PMEN1 isolates.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375284&req=5

ppat-1002745-g008: Histogram comparing frequencies of detected recombination sizes in a collection of PMEN1 isolates and in vitro transformants.The algorithm used to detect sequence imports in a sample of PMEN1 genomes was individually applied to each transformant sequence from the first experiment described in this work. In both graphs, the blue bars show the output of the algorithm applied to sequences from this experiment, whereas the red bars represent the data from the PMEN1 strains. (A) Comparison of the ten serotype switching recombinations characterised in PMEN1 with the transformation events spanning the cps locus selected in vitro. (B) Comparison of the unselected secondary transformation events characterised in vitro with the 615 homologous recombinations (i.e. excluding events overlapping prophage or conjugative elements) identified in the PMEN1 isolates.
Mentions: The lengths of the recombinations changing capsule type in the PMEN1 clinical isolates can be compared with those selected in this work through applying the algorithm used to detect sequence imports in the PMEN1 strains [35] to the in vitro transformants. In these comparable datasets, the distribution of cps-spanning recombination sizes is very similar in both (Figure 8A). Elsewhere in the genome, the distributions of recombination sizes are alike (Figure 8B), but the set detected in the PMEN1 population has fewer short recombinations. This is likely to be due to a reduced power to differentiate such events, which import few SNPs, from the background of point mutations in the clinical isolates, as compared to the near-complete absence of variation outside of transformation events from the isolates in this study. Hence the exponential decline is less clear from the data derived from clinical isolates, and the rate parameter λR is estimated as being artefactually low (1.58×10−4 bp−1; 95% confidence intervals 1.47–1.72×10−4 bp−1).

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

Show MeSH
Related in: MedlinePlus