To date we focused our efforts on the third biovariant of C. trachomatis, lymphogranuloma venereum (LGV), which infect monocytes and disseminate to the local lymph nodes, where they can cause large swellings characteristic of bubonic diseases, Although rare in the UK LGV serovars are endemic in parts of Africa, South East Asia, South America and the Caribbean. Recently an ‘epidemic’ clinical LGV isolate causing proctitis had emerged and spread globally in the men who have sex with men (MSM) community. It had been speculated that this isolate was a new more infectious form on LGV. We have shown that epidemic strain was simply a classical LGV isolate that had been circulating in the human population for a long time and was in fact an old strain causing a new disease.

Recent work has focused on a new variant of the genital tract C. trachomatis (nvCT) emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain meant it 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. We defined the evolutionary relationship between the chromosome and plasmid and since the PCR diagnostic test remains the method of choice for routine diagnosis we also identified more robust diagnostic markers located on plasmid. Current work focuses on the global diversity of C. trachomatis.

Collaborators

Professor Clarke Molecular Microbiology Group, University Medical School Southampton General Hospital, Southampton, United Kingdom.

Dr Hamid Jalal, Addenbrooke’s Hospital, Hills Road, Cambridge, UK.

Brian Spratt, Department of Infectious Disease Epidemiology, Imperial College, London, UK.

Published Genome Data

The Sanger Institute has been funded by Wellcome Trust to sequence the genome of Chlamydia trachomatis strains serovar A and serovar B in collaboration with Dr. Grant McClarty of the National Microbiology Laboratory, Health Canada, Winnipeg, Canada, Professor Harlan Caldwell of the Rocky Mountain Laboratory, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA, Professor David Maybey of the London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. and Prof. Ian N. Clarke of the School of Medicine, University of Southampton, U.K.

Chlamydia trachomatis (serovar A)

• Status: Finished
• Assembly/Annotation: 2 contigs >1kb (2 contigs >2kb); total size 1.052 Mb
• Shotgun: 19830 reads totalling 14.30 Mb, theoretical genome coverage of 99.99%

Chlamydia trachomatis (serovar B)

• Strain B/TZ1A828/OT
  • Assembly/Annotation: The finished and annotated genome is 1044282 BP. in length and is available from the EMBL database with accession number FM872307.
  • The plasmid is 7502 BP in length and is similarly available with accession FM865437.
  • Shotgun: 17,594 reads totalling 10.901 Mb, theoretical genome coverage of 99.99%
• Strain Jali20
  • Assembly/Annotation: The finished and annotated genome is 1044352 BP. in length and is available from the EMBL database with accession number FM872308.
  • The plasmid is 7506 BP in length and is similarly available with accession FM865438.
  • Shotgun: 16,858 reads totalling 10.404 Mb, theoretical genome coverage of 99.99%

Shotgun and assembly data from these projects are available from our FTP site.

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

  Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A, Bignell A, Bjartling C, Clark L, Cutcliffe LT, Lambden PR, Lennard N, Lockey SJ, Quail MA, Salim O, Skilton RJ, Wang Y, Holland MJ, Parkhill J, Thomson NR and Clarke IN

  BMC genomics2009;10;239

  PUBMED: 19460133; PMC: 2693142; DOI: 10.1186/1471-2164-10-239

• Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates.

  Thomson NR, Holden MT, Carder C, Lennard N, Lockey SJ, Marsh P, Skipp P, O'Connor CD, Goodhead I, Norbertzcak H, Harris B, Ormond D, Rance R, Quail MA, Parkhill J, Stephens RS and Clarke IN

  Genome research2008;18;1;161-71

  PUBMED: 18032721; PMC: 2134780; DOI: 10.1101/gr.7020108