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 Wiggins & 18 others Hamid 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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    Chlamydia trachomatis
    History
    Genome
    Ecotype
    Blindness
    Sexually Transmitted Diseases

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    Hadfield, James ; Harris, Simon R. ; Seth-Smith, Helena M.B. ; Parmar, Surendra ; Andersson, Patiyan ; Giffard, Philip M. ; Schachter, Julius ; Moncada, Jeanne ; Ellison, Louise ; Vaulet, María Lucía Gallo ; Fermepin, Marcelo Rodríguez ; Radebe, Frans ; Mendoza, Suyapa ; Ouburg, Sander ; Morré, Servaas A. ; Sachse, Konrad ; Puolakkainen, Mirja ; Korhonen, Suvi J. ; Sonnex, Chris ; Wiggins, Rebecca ; Jalal, Hamid ; Brunelli, Tamara ; Casprini, Patrizia ; Pitt, Rachel ; Ison, Cathy ; Savicheva, Alevtina ; Shipitsyna, Elena ; Hadad, Ronza ; Kari, Laszlo ; Burton, Matthew J. ; Mabey, David ; Solomon, Anthony W. ; Lewis, David ; Marsh, Peter ; Unemo, Magnus ; Clarke, Ian N. ; Parkhill, Julian ; Thomson, Nicholas R. / Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. In: Genome Research. 2017 ; Vol. 27, No. 7. pp. 1220-1229.
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    title = "Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion",
    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.",
    author = "James Hadfield and Harris, {Simon R.} and Seth-Smith, {Helena M.B.} and Surendra Parmar and Patiyan Andersson and Giffard, {Philip M.} and Julius Schachter and Jeanne Moncada and Louise Ellison and Vaulet, {Mar{\'i}a Luc{\'i}a Gallo} and Fermepin, {Marcelo Rodr{\'i}guez} and Frans Radebe and Suyapa Mendoza and Sander Ouburg and Morr{\'e}, {Servaas A.} and Konrad Sachse and Mirja Puolakkainen and Korhonen, {Suvi J.} and Chris Sonnex and Rebecca Wiggins and Hamid Jalal and Tamara Brunelli and Patrizia Casprini and Rachel Pitt and Cathy Ison and Alevtina Savicheva and Elena Shipitsyna and Ronza Hadad and Laszlo Kari and Burton, {Matthew J.} and David Mabey and Solomon, {Anthony W.} and David Lewis and Peter Marsh and Magnus Unemo and Clarke, {Ian N.} and Julian Parkhill and Thomson, {Nicholas R.}",
    year = "2017",
    month = "7",
    doi = "10.1101/gr.212647.116",
    language = "English",
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    pages = "1220--1229",
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    Hadfield, J, Harris, SR, Seth-Smith, HMB, Parmar, S, Andersson, P, Giffard, PM, Schachter, J, Moncada, J, Ellison, L, Vaulet, MLG, Fermepin, MR, Radebe, F, Mendoza, S, Ouburg, S, Morré, SA, Sachse, K, Puolakkainen, M, Korhonen, SJ, Sonnex, C, Wiggins, R, Jalal, H, Brunelli, T, Casprini, P, Pitt, R, Ison, C, Savicheva, A, Shipitsyna, E, Hadad, R, Kari, L, Burton, MJ, Mabey, D, Solomon, AW, Lewis, D, Marsh, P, Unemo, M, Clarke, IN, Parkhill, J & Thomson, NR 2017, 'Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion', Genome Research, vol. 27, no. 7, pp. 1220-1229. https://doi.org/10.1101/gr.212647.116

    Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. / Hadfield, James; Harris, Simon R.; Seth-Smith, Helena M.B.; Parmar, Surendra; Andersson, Patiyan; Giffard, Philip M.; Schachter, Julius; Moncada, Jeanne; Ellison, Louise; Vaulet, María Lucía Gallo; Fermepin, Marcelo Rodríguez; Radebe, Frans; Mendoza, Suyapa; Ouburg, Sander; Morré, Servaas A.; Sachse, Konrad; Puolakkainen, Mirja; Korhonen, Suvi J.; Sonnex, Chris; Wiggins, Rebecca; Jalal, Hamid; Brunelli, Tamara; Casprini, Patrizia; Pitt, Rachel; Ison, Cathy; Savicheva, Alevtina; Shipitsyna, Elena; Hadad, Ronza; Kari, Laszlo; Burton, Matthew J.; Mabey, David; Solomon, Anthony W.; Lewis, David; Marsh, Peter; Unemo, Magnus; Clarke, Ian N.; Parkhill, Julian; Thomson, Nicholas R.

    In: Genome Research, Vol. 27, No. 7, 07.2017, p. 1220-1229.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

    AU - Hadfield, James

    AU - Harris, Simon R.

    AU - Seth-Smith, Helena M.B.

    AU - Parmar, Surendra

    AU - Andersson, Patiyan

    AU - Giffard, Philip M.

    AU - Schachter, Julius

    AU - Moncada, Jeanne

    AU - Ellison, Louise

    AU - Vaulet, María Lucía Gallo

    AU - Fermepin, Marcelo Rodríguez

    AU - Radebe, Frans

    AU - Mendoza, Suyapa

    AU - Ouburg, Sander

    AU - Morré, Servaas A.

    AU - Sachse, Konrad

    AU - Puolakkainen, Mirja

    AU - Korhonen, Suvi J.

    AU - Sonnex, Chris

    AU - Wiggins, Rebecca

    AU - Jalal, Hamid

    AU - Brunelli, Tamara

    AU - Casprini, Patrizia

    AU - Pitt, Rachel

    AU - Ison, Cathy

    AU - Savicheva, Alevtina

    AU - Shipitsyna, Elena

    AU - Hadad, Ronza

    AU - Kari, Laszlo

    AU - Burton, Matthew J.

    AU - Mabey, David

    AU - Solomon, Anthony W.

    AU - Lewis, David

    AU - Marsh, Peter

    AU - Unemo, Magnus

    AU - Clarke, Ian N.

    AU - Parkhill, Julian

    AU - Thomson, Nicholas R.

    PY - 2017/7

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    AB - 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.

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