Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

  1. Nicholas R. Thomson1,23
  1. 1Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom;
  2. 2Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom;
  3. 3Menzies School of Health Research, Darwin, Northern Territory 0810, Australia;
  4. 4School of Psychological and Clinical Sciences, Charles Darwin University, Darwin 0909, Australia;
  5. 5Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94110, USA;
  6. 6Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Microbiología Clínica, Buenos Aires C1113AAD, Argentina;
  7. 7Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 2192 Johannesburg, South Africa;
  8. 8Jefe Laboratorio de ITS, Laboratorio Nacional de Vigilancia, FM1100, Honduras;
  9. 9Department of Medical Microbiology and Infection Control, Laboratory of Immunogenetics, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands;
  10. 10Department of Genetics and Cell Biology, Institute of Public Health Genomics, School for Oncology & Developmental Biology (GROW), Faculty of Health, Medicine and Life Sciences, University of Maastricht, 6229 ER Maastricht, The Netherlands;
  11. 11Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany;
  12. 12Department of Virology, University of Helsinki and Helsinki University Hospital, University of Helsinki, 00014 Helsinki, Finland;
  13. 13Department of Biology, University of York, York CB2 2QQ, United Kingdom;
  14. 14Clinical Chemistry and Microbiology Laboratory, Santo Stefano Hospital, ASL4, 59100 Prato, Italy;
  15. 15Sexually Transmitted Bacteria Reference Unit, Microbiological Services, Public Health England, London NW9 5HT, United Kingdom;
  16. 16Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynecology, St. Petersburg, Russia 199034;
  17. 17WHO Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85 Örebro, Sweden;
  18. 18Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA;
  19. 19Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom;
  20. 20Centre for Infectious Diseases and Microbiology and Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Clinical School, University of Sydney, Sydney 2192, Australia;
  21. 21Public Health England, Public Health Laboratory Southampton, Southampton General Hospital, Southampton SO16 6YD, United Kingdom;
  22. 22Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom;
  23. 23Department of Pathogen Molecular Biology, The London School of Hygiene and Tropical Medicine, London WC1 7HT, United Kingdom

  • ↵Present addresses: 24Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; 25Clinical Microbiology, University Hospital Basel, 4031 Basel, Switzerland

  • Corresponding author: nrt{at}sanger.ac.uk

    • Abstract

    Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.

    Footnotes

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.212647.116.

    • Freely available online through the Genome Research Open Access option.

    • Received July 11, 2016.
    • Accepted April 27, 2017.

    This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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    1. Published in Advance June 6, 2017, doi: 10.1101/gr.212647.116 Genome Res. 27: 1220-1229 © 2017 Hadfield et al.; Published by Cold Spring Harbor Laboratory Press

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