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

被引：86

作者：

Hadfield, James ^{[1
]}

Harris, Simon R. ^{[1
]}

Seth-Smith, Helena M. B. ^{[1
,26
,27
]}

Parmar, Surendra ^{[2
]}

Andersson, Patiyan ^{[3
]}

Giffard, Philip M. ^{[3
,4
]}

Schachter, Julius ^{[5
]}

Moncada, Jeanne ^{[5
]}

Ellison, Louise ^{[1
]}

Gallo Vaulet, Maria Lucia ^{[6
]}

Rodriguez Fermepin, Marcelo ^{[6
]}

Radebe, Frans ^{[7
]}

Mendoza, Suyapa ^{[8
]}

Ouburg, Sander ^{[9
]}

Morre, Servaas A. ^{[9
,10
]}

Sachse, Konrad ^{[11
]}

Puolakkainen, Mirja ^{[12
,13
]}

Korhonen, Suvi J. ^{[12
,13
]}

Sonnex, Chris ^{[2
]}

Wiggins, Rebecca ^{[14
]}

Jalal, Hamid

Brunelli, Tamara ^{[15
]}

Casprini, Patrizia ^{[15
]}

Pitt, Rachel ^{[16
]}

Ison, Cathy ^{[16
]}

Savicheva, Alevtina ^{[17
]}

Shipitsyna, Elena ^{[17
,18
]}

Hadad, Ronza ^{[18
]}

Kari, Laszlo ^{[19
]}

Burton, Matthew J. ^{[20
]}

Mabey, David ^{[20
]}

Solomon, Anthony W. ^{[20
]}

Lewis, David ^{[21
,22
]}

Marsh, Peter ^{[23
]}

Unemo, Magnus ^{[18
]}

Clarke, Ian N. ^{[24
]}

Parkhill, Julian ^{[1
]}

Thomson, Nicholas R. ^{[1
,25
]}

机构：

[1] Wellcome Trust Sanger Inst, Pathogen Genom, Wellcome Trust Genome Campus, Cambridge CB10 1SA, England

[2] Addenbrookes Hosp, Publ Hlth Lab Cambridge, Publ Hlth England, Cambridge CB2 0QW, England

[3] Menzies Sch Hlth Res, Darwin, NT 0810, Australia

[4] Charles Darwin Univ, Sch Psychol & Clin Sci, Darwin, NT 0909, Australia

[5] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94110 USA

[6] Univ Buenos Aires, Fac Farm & Bioquim, Dept Bioquim Clin, Microbiol Clin, C1113AAD, Buenos Aires, DF, Argentina

[7] Natl Inst Communicable Dis, Natl Hlth Lab Serv, Ctr HIV & Sexually Transmitted Infect, ZA-2192 Johannesburg, South Africa

[8] Lab Nacl Vigilancia, Jefe Lab ITS, FM1100, Tegucigalpa, Honduras

[9] Vrije Univ Amsterdam Med Ctr, Lab Immunogenet, Dept Med Microbiol & Infect Control, NL-1081 HZ Amsterdam, Netherlands

[10] Univ Maastricht, Fac Hlth Med & Life Sci, Sch Oncol & Dev Biol GROW, Dept Genet & Cell Biol,Inst Publ Hlth Genom, NL-6229 ER Maastricht, Netherlands

[11] Fed Res Inst Anim Hlth, Friedrich Loeffler Inst, Inst Mol Pathogenesis, D-07743 Jena, Germany

[12] Univ Helsinki, Dept Virol, Helsinki 00014, Finland

[13] Univ Helsinki, Helsinki Univ Hosp, Helsinki 00014, Finland

[14] Univ York, Dept Biol, York CB2 2QQ, N Yorkshire, England

[15] Santo Stefano Hosp, Clin Chem & Microbiol Lab, ASL4, I-59100 Prato, Italy

[16] Publ Hlth England, Microbiol Serv, Sexually Transmitted Bacteria Reference Unit, London NW9 5HT, England

[17] DO Ott Res Inst Obstet & Gynecol, Lab Microbiol, St Petersburg 199034, Russia

[18] Orebro Univ Hosp, Fac Med & Hlth, WHO Collaborating Ctr Gonorrhoea & Other STIs, SE-70185 Orebro, Sweden

[19] NIAID, Lab Intracellular Parasites, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA

[20] London Sch Hygiene & Trop Med, Fac Infect & Trop Dis, Clin Res Dept, London, England

[21] Univ Sydney, Westmead Clin Sch, Ctr Infect Dis & Microbiol, Sydney, NSW 2192, Australia

[22] Univ Sydney, Westmead Clin Sch, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW 2192, Australia

[23] Southampton Gen Hosp, Publ Hlth Lab Southampton, Publ Hlth England, Southampton SO16 6YD, Hants, England

[24] Southampton Gen Hosp, Univ Med Sch, Mol Microbiol Grp, Southampton SO16 6YD, Hants, England

[25] London Sch Hyg & Trop Med, Dept Pathogen Mol Biol, London WC1 7HT, England

[26] Univ Basel, Dept Biomed, Appl Microbiol Res, CH-4056 Basel, Switzerland

[27] Univ Hosp Basel, Clin Microbiol, CH-4031 Basel, Switzerland

来源：

GENOME RESEARCH | 2017年 / 27卷 / 07期

基金：

英国医学研究理事会; 英国惠康基金;

关键词：

PHENOTYPIC CHARACTERIZATION; INTRACELLULAR PATHOGEN; ANTIBIOTIC-RESISTANCE; CLINICAL-SAMPLES; HIGH-THROUGHPUT; IN-VITRO; SEQUENCE; RECOMBINATION; EVOLUTION; GENE;

D O I：

10.1101/gr.212647.116

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1220 / 1229

页数：10

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