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Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

Helena MB Seth-Smith2, Simon R Harris2, Kenneth Persson3, Pete Marsh4, Andrew Barron2, Alexandra Bignell2, Carina Bjartling5, Louise Clark2, Lesley T Cutcliffe1, Paul R Lambden1, Nicola Lennard2, Sarah J Lockey1, Michael A Quail2, Omar Salim1, Rachel J Skilton1, Yibing Wang1, Martin J Holland6, Julian Parkhill2, Nicholas R Thomson2 and Ian N Clarke17*

Author Affiliations

1 Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK

2 The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

3 Department of Clinical Microbiology, Malmo University Hospital, SE 205 02 Malmo, Sweden

4 Health Protection Agency South East, Southampton General Hospital, Southampton, SO16 6YD, UK

5 Department of Obstetrics and Gynaecology, Malmo University Hospital, SE 205 02, Malmo, Sweden

6 Viral Diseases Programme, Medical Research Council PO Box 273, Banjul, The Gambia

7 Clinical Research Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

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BMC Genomics 2009, 10:239  doi:10.1186/1471-2164-10-239

Published: 21 May 2009



Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C. trachomatis: 'trachoma', causing ocular and genital tract infections, and the invasive 'lymphogranuloma venereum' strains. Recently, a new variant of the genital tract C. trachomatis emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain has meant it has spread rapidly across the country provoking a worldwide alert. In addition to being a key diagnostic target, the plasmid has been linked to chlamydial virulence. Analysis of chlamydial plasmids and their cognate chromosomes was undertaken to provide insights into the evolutionary relationship between chromosome and plasmid. This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis.


The genomes of two new C. trachomatis strains were sequenced, together with plasmids from six C. trachomatis isolates, including the new variant strain from Sweden. The plasmid from the new Swedish variant has a 377 bp deletion in the first predicted coding sequence, abolishing the site used for PCR detection, resulting in negative diagnosis. In addition, the variant plasmid has a 44 bp duplication downstream of the deletion. The region containing the second predicted coding sequence is the most highly conserved region of the plasmids investigated. Phylogenetic analysis of the plasmids and chromosomes are fully congruent. Moreover this analysis also shows that ocular and genital strains diverged from a common C. trachomatis progenitor.


The evolutionary pathways of the chlamydial genome and plasmid imply that inheritance of the plasmid is tightly linked with its cognate chromosome. These data suggest that the plasmid is not a highly mobile genetic element and does not transfer readily between isolates. Comparative analysis of the plasmid sequences has revealed the most conserved regions that should be used to design future plasmid based nucleic acid amplification tests, to avoid diagnostic failures.