RT Journal
A1 Hadfield, James
A1 Harris, Simon R.
A1 Seth-Smith, Helena M.B.
A1 Parmar, Surendra
A1 Andersson, Patiyan
A1 Giffard, Philip M.
A1 Schachter, Julius
A1 Moncada, Jeanne
A1 Ellison, Louise
A1 Vaulet, María Lucía Gallo
A1 Fermepin, Marcelo Rodríguez
A1 Radebe, Frans
A1 Mendoza, Suyapa
A1 Ouburg, Sander
A1 Morré, Servaas A.
A1 Sachse, Konrad
A1 Puolakkainen, Mirja
A1 Korhonen, Suvi J.
A1 Sonnex, Chris
A1 Wiggins, Rebecca
A1 Jalal, Hamid
A1 Brunelli, Tamara
A1 Casprini, Patrizia
A1 Pitt, Rachel
A1 Ison, Cathy
A1 Savicheva, Alevtina
A1 Shipitsyna, Elena
A1 Hadad, Ronza
A1 Kari, Laszlo
A1 Burton, Matthew J.
A1 Mabey, David
A1 Solomon, Anthony W.
A1 Lewis, David
A1 Marsh, Peter
A1 Unemo, Magnus
A1 Clarke, Ian N.
A1 Parkhill, Julian
A1 Thomson, Nicholas R.
T1 Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
JF Genome Research 
JO Genome Research 
YR 2017 
FD July 01 
VO 27 
IS 7 
SP 1220 
OP 1229 
DO 10.1101/gr.212647.116 
UL http://genome.cshlp.org/content/27/7/1220.abstract 
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.