@article{dcf0aeab8acd4f2a8681a5ea33d118a9,
title = "Comprehensive global genome dynamics of 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.",
keywords = "Chlamydia trachomatis/genetics, Drug Resistance, Bacterial/genetics, Ecotype, Evolution, Molecular, Female, Genome, Bacterial, Humans, Male",
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}",
note = "{\textcopyright} 2017 Hadfield et al.; Published by Cold Spring Harbor Laboratory Press.",
year = "2017",
month = jul,
doi = "10.1101/gr.212647.116",
language = "English",
volume = "27",
pages = "1220--1229",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "7",
}