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

James Hadfield, Simon R. Harris, Helena M.B. Seth-Smith, Surendra Parmar, Patiyan Andersson, Philip M. Giffard, Julius Schachter, Jeanne Moncada, Louise Ellison, María Lucía Gallo Vaulet, Marcelo Rodríguez Fermepin, Frans Radebe, Suyapa Mendoza, Sander Ouburg, Servaas A. Morré, Konrad Sachse, Mirja Puolakkainen, Suvi J. Korhonen, Chris Sonnex, Rebecca WigginsHamid Jalal, Tamara Brunelli, Patrizia Casprini, Rachel Pitt, Cathy Ison, Alevtina Savicheva, Elena Shipitsyna, Ronza Hadad, Laszlo Kari, Matthew J. Burton, David Mabey, Anthony W. Solomon, David Lewis, Peter Marsh, Magnus Unemo, Ian N. Clarke, Julian Parkhill, Nicholas R. Thomson

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    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.

    Original languageEnglish
    Pages (from-to)1220-1229
    Number of pages10
    JournalGenome Research
    Volume27
    Issue number7
    DOIs
    Publication statusPublished - Jul 2017

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    Hadfield, J., Harris, S. R., Seth-Smith, H. M. B., Parmar, S., Andersson, P., Giffard, P. M., Schachter, J., Moncada, J., Ellison, L., Vaulet, M. L. G., Fermepin, M. R., Radebe, F., Mendoza, S., Ouburg, S., Morré, S. A., Sachse, K., Puolakkainen, M., Korhonen, S. J., Sonnex, C., ... Thomson, N. R. (2017). Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. Genome Research, 27(7), 1220-1229. https://doi.org/10.1101/gr.212647.116