Dense genomic sampling identifies highways of pneumococcal recombination

Claire Chewapreecha; Simon R. Harris; Nicholas J. Croucher; Claudia Turner; Pekka Marttinen; Lu Cheng; Alberto Pessia; David M. Aanensen; Alison E. Mather; Andrew J. Page; Susannah J. Salter; David Harris; Francois Nosten; David Goldblatt; Jukka Corander; Julian Parkhill; Paul Turner; Stephen D. Bentley

doi:10.1038/ng.2895

Dense genomic sampling identifies highways of pneumococcal recombination

Claire Chewapreecha, Simon R. Harris, Nicholas J. Croucher, Claudia Turner, Pekka Marttinen, Lu Cheng, Alberto Pessia, David M. Aanensen, Alison E. Mather, Andrew J. Page, Susannah J. Salter, David Harris, Francois Nosten, David Goldblatt, Jukka Corander, Julian Parkhill, Paul Turner, Stephen D. Bentley

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Abstract

Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. We report whole-genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4-km² refugee camp. This sequencing provides unprecedented resolution of the process of recombination and its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends, demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may have a major role in genetic exchange and the adaptation of the species as a whole. These findings advance understanding of pneumococcal population dynamics and provide information for the design of future intervention strategies.

Original language	English
Pages (from-to)	305-309
Number of pages	5
Journal	Nature Genetics
Volume	46
Issue number	3
Early online date	9 Feb 2014
DOIs	https://doi.org/10.1038/ng.2895
Publication status	Published - 1 Mar 2014

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Cite this

Chewapreecha, C., Harris, S. R., Croucher, N. J., Turner, C., Marttinen, P., Cheng, L., Pessia, A., Aanensen, D. M., Mather, A. E., Page, A. J., Salter, S. J., Harris, D., Nosten, F., Goldblatt, D., Corander, J., Parkhill, J., Turner, P., & Bentley, S. D. (2014). Dense genomic sampling identifies highways of pneumococcal recombination. Nature Genetics, 46(3), 305-309. https://doi.org/10.1038/ng.2895

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title = "Dense genomic sampling identifies highways of pneumococcal recombination",

abstract = "Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. We report whole-genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4-km2 refugee camp. This sequencing provides unprecedented resolution of the process of recombination and its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends, demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may have a major role in genetic exchange and the adaptation of the species as a whole. These findings advance understanding of pneumococcal population dynamics and provide information for the design of future intervention strategies.",

author = "Claire Chewapreecha and Harris, {Simon R.} and Croucher, {Nicholas J.} and Claudia Turner and Pekka Marttinen and Lu Cheng and Alberto Pessia and Aanensen, {David M.} and Mather, {Alison E.} and Page, {Andrew J.} and Salter, {Susannah J.} and David Harris and Francois Nosten and David Goldblatt and Jukka Corander and Julian Parkhill and Paul Turner and Bentley, {Stephen D.}",

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Chewapreecha, C, Harris, SR, Croucher, NJ, Turner, C, Marttinen, P, Cheng, L, Pessia, A, Aanensen, DM, Mather, AE, Page, AJ, Salter, SJ, Harris, D, Nosten, F, Goldblatt, D, Corander, J, Parkhill, J, Turner, P & Bentley, SD 2014, 'Dense genomic sampling identifies highways of pneumococcal recombination', Nature Genetics, vol. 46, no. 3, pp. 305-309. https://doi.org/10.1038/ng.2895

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AU - Chewapreecha, Claire

AU - Harris, Simon R.

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AU - Turner, Claudia

AU - Marttinen, Pekka

AU - Cheng, Lu

AU - Pessia, Alberto

AU - Aanensen, David M.

AU - Mather, Alison E.

AU - Page, Andrew J.

AU - Salter, Susannah J.

AU - Harris, David

AU - Nosten, Francois

AU - Goldblatt, David

AU - Corander, Jukka

AU - Parkhill, Julian

AU - Turner, Paul

AU - Bentley, Stephen D.

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AB - Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. We report whole-genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4-km2 refugee camp. This sequencing provides unprecedented resolution of the process of recombination and its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends, demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may have a major role in genetic exchange and the adaptation of the species as a whole. These findings advance understanding of pneumococcal population dynamics and provide information for the design of future intervention strategies.

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