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Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

Nature Genetics volume 46, pages 82–87 (2014)Cite this article

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Abstract

Advances in sequencing technologies have enabled the identification of mutations acquired by bacterial pathogens during infection1,2,3,4,5,6,7,8,9,10. However, it remains unclear whether adaptive mutations fix in the population or lead to pathogen diversification within the patient11,12. Here we study the genotypic diversity of Burkholderia dolosa within individuals with cystic fibrosis by resequencing individual colonies and whole populations from single sputum samples. We find extensive intrasample diversity, suggesting that mutations rarely fix in a patient's pathogen population—instead, diversifying lineages coexist for many years. Under strong selection, multiple adaptive mutations arise, but none of these sweep to fixation, generating lasting allele diversity that provides a recorded signature of past selection. Genes involved in outer-membrane components, iron scavenging and antibiotic resistance all showed this signature of within-patient selection. These results offer a general and rapid approach for identifying the selective pressures acting on a pathogen in individual patients based on single clinical samples.

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Figure 1: Alternative models of within-patient evolution.
Figure 2: Two methods for studying genomic intraspecies diversity.
Figure 3: Within-patient evolution leads to diversification not substitution.
Figure 4: Sublineages coexist within a patient for many years after divergence.
Figure 5: Coexistence of alternative adaptive mutations in the same sample highlights specific genes as drivers of within-host evolution.

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Sequence Read Archive

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NCBI Reference Sequence

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Acknowledgements

We are grateful to J.-B. Michel and members of the Kishony laboratory for insightful discussions and support, to the team at the Partners HealthCare Center for Personalized Genetic Medicine (PCPGM) for Illumina sequencing, to L. Williams and A. Palmer for discussions and technical assistance, and to Y. Gerardin, J. Meyer, L. Stone and R. Ward for their comments on the manuscript. T.D.L. and G.P.P. were supported in part by grants from the Cystic Fibrosis Foundation (LIEBER12H0 to T.D.L. and PRIEBE1310 to G.P.P.). This work was funded in part by the US National Institutes of Health (GM081617 to R.K.), the New England Regional Center of Excellence for Biodefense and Emerging Infectious Diseases (NERCE; U54 AI057159 to R.K.) and Hoffman-LaRoche.

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Authors and Affiliations

  1. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

    Tami D Lieberman & Roy Kishony

  2. Department of Medicine, Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Kelly B Flett & Gregory P Priebe

  3. Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel

    Idan Yelin & Roy Kishony

  4. Department of Medicine, Division of Respiratory Diseases, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Thomas R Martin

  5. Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Alexander J McAdam

  6. Department of Anesthesiology, Division of Critical Care Medicine, Perioperative and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Gregory P Priebe

  7. Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Gregory P Priebe

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Contributions

T.D.L., A.J.M., G.P.P. and R.K. designed the study. A.J.M. and T.R.M. collected clinical samples. K.B.F., T.R.M., A.J.M. and G.P.P. conducted chart review and provided medical information. T.D.L. performed experiments. T.D.L., I.Y. and R.K. wrote the sequence analysis scripts. T.D.L. and R.K. analyzed the data. T.D.L., A.J.M., G.P.P. and R.K. interpreted the results and wrote the manuscript.

Corresponding authors

Correspondence to Alexander J McAdam, Gregory P Priebe or Roy Kishony.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1–4 and Supplementary Note (PDF 2544 kb)

Supplementary Table 5

Mutations found in isolates (XLSX 63 kb)

Supplementary Table 6

Mutations found in deep population sequencing (XLSX 126 kb)

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Lieberman, T., Flett, K., Yelin, I. et al. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat Genet 46, 82–87 (2014). https://doi.org/10.1038/ng.2848

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