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

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

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.

1088-9051
1220-1229
Hadfield, James
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Harris, Simon R.
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Seth-Smith, Helena M.B.
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Andersson, Patiyan
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Giffard, Philip M.
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Schachter, Julius
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Moncada, Jeanne
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Ellison, Louise
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Vaulet, María Lucía Gallo
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Fermepin, Marcelo Rodríguez
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Radebe, Frans
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Mendoza, Suyapa
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Ouburg, Sander
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Sachse, Konrad
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Puolakkainen, Mirja
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Korhonen, Suvi J.
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Sonnex, Chris
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Wiggins, Rebecca
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Jalal, Hamid
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Pitt, Rachel
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Ison, Cathy
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Savicheva, Alevtina
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Shipitsyna, Elena
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Kari, Laszlo
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Burton, Matthew J.
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Mabey, David
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Solomon, Anthony W.
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Lewis, David
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Marsh, Peter
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Unemo, Magnus
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Clarke, Ian N.
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Parkhill, Julian
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Thomson, Nicholas R.
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Hadfield, James
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Harris, Simon R.
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Seth-Smith, Helena M.B.
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Parmar, Surendra
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Andersson, Patiyan
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Giffard, Philip M.
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Schachter, Julius
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Moncada, Jeanne
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Ellison, Louise
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Vaulet, María Lucía Gallo
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Fermepin, Marcelo Rodríguez
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Radebe, Frans
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Mendoza, Suyapa
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Sachse, Konrad
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Puolakkainen, Mirja
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Korhonen, Suvi J.
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Sonnex, Chris
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Wiggins, Rebecca
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Jalal, Hamid
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Casprini, Patrizia
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Ison, Cathy
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Savicheva, Alevtina
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Shipitsyna, Elena
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Hadad, Ronza
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Kari, Laszlo
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Burton, Matthew J.
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Mabey, David
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Solomon, Anthony W.
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Lewis, David
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Marsh, Peter
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Unemo, Magnus
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Clarke, Ian N.
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Parkhill, Julian
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Thomson, Nicholas R.
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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 and Thomson, Nicholas 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. (doi:10.1101/gr.212647.116).

Record type: Article

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.

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Genome Res.-2017-Hadfield-1220-9 - Version of Record
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Accepted/In Press date: 27 April 2017
e-pub ahead of print date: 6 June 2017
Published date: 1 July 2017

Identifiers

Local EPrints ID: 412768
URI: https://eprints.soton.ac.uk/id/eprint/412768
ISSN: 1088-9051
PURE UUID: b8e43b9e-7e47-4eec-96ae-3928fbb83783
ORCID for Ian N. Clarke: ORCID iD orcid.org/0000-0002-4938-1620

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Date deposited: 01 Aug 2017 16:31
Last modified: 03 Dec 2019 02:08

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Contributors

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

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