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Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

Author

Listed:
  • P. M. Ashton

    (Oxford University Clinical Research Unit
    University of Oxford)

  • L. T. Thanh

    (Oxford University Clinical Research Unit)

  • P. H. Trieu

    (Oxford University Clinical Research Unit)

  • D. Anh

    (Oxford University Clinical Research Unit)

  • N. M. Trinh

    (Oxford University Clinical Research Unit)

  • J. Beardsley

    (Oxford University Clinical Research Unit
    University of Oxford
    University of Sydney)

  • F. Kibengo

    (MRC/UVRI and LSHTM Uganda Research Unit)

  • W. Chierakul

    (Mahidol Oxford Tropical Medicine Research Unit)

  • D. A. B. Dance

    (University of Oxford
    Lao–Oxford–Mahosot Hospital–Wellcome Trust Research Unit
    London School of Hygiene and Tropical Medicine)

  • S. Rattanavong

    (Lao–Oxford–Mahosot Hospital–Wellcome Trust Research Unit)

  • V. Davong

    (Lao–Oxford–Mahosot Hospital–Wellcome Trust Research Unit)

  • L. Q. Hung

    (Cho Ray Hospital)

  • N. V. V. Chau

    (Hospital for Tropical Diseases)

  • N. L. N. Tung

    (Hospital for Tropical Diseases)

  • A. K. Chan

    (University of Toronto
    Dignitas International)

  • G. E. Thwaites

    (Oxford University Clinical Research Unit
    University of Oxford)

  • D. G. Lalloo

    (Liverpool School of Tropical Medicine)

  • C. Anscombe

    (Oxford University Clinical Research Unit
    University of Oxford)

  • L. T. H. Nhat

    (Oxford University Clinical Research Unit)

  • J. Perfect

    (Duke University)

  • G. Dougan

    (Wellcome Trust-Cambridge Centre for Global Health Research
    The Wellcome Trust Sanger Institute
    University of Cambridge)

  • S. Baker

    (Oxford University Clinical Research Unit
    University of Oxford
    Wellcome Trust-Cambridge Centre for Global Health Research
    University of Cambridge)

  • S. Harris

    (The Wellcome Trust Sanger Institute)

  • J. N. Day

    (Oxford University Clinical Research Unit
    University of Oxford)

Abstract

Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.

Suggested Citation

  • P. M. Ashton & L. T. Thanh & P. H. Trieu & D. Anh & N. M. Trinh & J. Beardsley & F. Kibengo & W. Chierakul & D. A. B. Dance & S. Rattanavong & V. Davong & L. Q. Hung & N. V. V. Chau & N. L. N. Tung & , 2019. "Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10092-5
    DOI: 10.1038/s41467-019-10092-5
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