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Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation

Nature Microbiology volume 2, Article number: 16190 (2016) | Download Citation

Abstract

Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK). TprK demonstrated remarkable variability and redundancy, intra- and interpatient, suggesting ongoing parallel adaptive diversification during human infection. Some bacterial functions (for example, flagella- and chemotaxis-associated) were systematically targeted by both inter- and intrastrain single nucleotide polymorphisms, as well as by ongoing within-patient phase variation events. Finally, patient-derived genomes possess mutations targeting a penicillin-binding protein coding gene (mrcA) that had never been reported, unveiling it as a candidate target to investigate the impact on the susceptibility to penicillin. Our findings decode the major genetic mechanisms by which T. pallidum promotes immune evasion and survival, and demonstrate the exceptional power of characterizing evolving pathogen subpopulations during human infection.

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Acknowledgements

This study was partially supported by grant EXPL/BIA-MIC/0309/2013 from the Fundação para a Ciência e a Tecnologia (FCT).

Author information

Author notes

    • Miguel Pinto
    •  & Vítor Borges

    These authors contributed equally to this work.

Affiliations

  1. Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal

    • Miguel Pinto
    • , Vítor Borges
    • , Minia Antelo
    • , Alexandra Nunes
    • , Maria José Borrego
    •  & João Paulo Gomes
  2. Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal

    • Miguel Pinto
    • , Vítor Borges
    • , Alexandra Nunes
    •  & João Paulo Gomes
  3. School of Medicine, University of St Andrews, KY16 9TF, UK

    • Miguel Pinheiro
  4. Sexually Transmitted Diseases Clinic, Lapa Health Centre, 1200-831 Lisbon, Portugal

    • Jacinta Azevedo
  5. Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, 1649-016 Lisbon, Portugal

    • Joana Mendonça
    • , Dina Carpinteiro
    •  & Luís Vieira

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Contributions

J.P.G. conceived the study. M.Pint., V.B. and J.P.G. designed the study. M.Pint., M.A., J.M., D.C. and L.V. performed the wet lab experiments. M.Pint. and V.B. performed bioinformatics and comparative genomics analyses. M.Pint., V.B., M.A., A.N., M.J.B., J.M., D.C., L.V. and J.P.G. performed research and analysed data. J.A. performed sample collection and clinical diagnostics. M.Pinh. provided bioinformatics support. M.Pint., V.B. and J.P.G. wrote the manuscript. All authors read and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to João Paulo Gomes.

Supplementary information

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    Supplementary information

    Supplementary Figures 1-6, Supplementary Tables 1 and 2, legends for Supplementary Tables 3 and 4, Supplementary References

Excel files

  1. 1.

    Supplementary Table 3

    Poly(G/C) tracts in T. pallidum pallidum genomes analysed for the presence of in-length genetic heterogeneity within clinical samples

  2. 2.

    Supplementary Table 4

    Sequence diversity within the seven variable regions (V1-V7) of tprK captured directly from 24 T. pallidum pallidum clinical samples.

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DOI

https://doi.org/10.1038/nmicrobiol.2016.190

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