Previous work focused on a new variant of the genital tract C. trachomatis (nvCT) which 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.

Magnus Unemo, Department of Laboratory Medicine and Clinical Microbiology, National Reference Laboratory for Pathogenic Neisseria, Örebro University Hospital, Örebro, Sweden.

David Lewis, Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, 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)

• Strain A2497
  • Assembly/Annotation: The finished and annotated genome is 1044325 BP. in length and is available from the EMBL database with accession number FM872306.
  • The plasmid is 7480 BP in length and is similarly available with accession FM865436.
  • 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%

Chlamydia trachomatis (serovar L2)

• Strain L2 434 Bu
  • Assembly/Annotation: The finished and annotated genome is 1038842 BP. in length and is available from the EMBL database with accession number AM884176.
  • Plasmid pL2 is 7499 BP in length and is similarly available with accession AM886278.

• Strain L2b UCH1 proctitis
  • Assembly/Annotation: The finished and annotated genome is 1038863 BP. in length and is available from the EMBL database with accession number AM884177.
  • Plasmid p-UCH1 is 7500 BP in length and is similarly available with accession AM886279.

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

Whole Genome Sequencing Of Diverse Strains Of Chlamydia trachomatis

The following strains were sequenced to a high quality draft level to identify phylogenetic relationships:

• Chlamydia trachomatis A/363. Chromosome: HE601796 Plasmid: HE603209
• Chlamydia trachomatis A/5291. Chromosome: HE601810 Plasmid: HE603210
• Chlamydia trachomatis A/7249. Chromosome: HE601797 Plasmid: HE603211
• Chlamydia trachomatis D/SotonD1. Chromosome: HE601798 Plasmid: HE603229
• Chlamydia trachomatis D/SotonD5. Chromosome: HE601799 Plasmid: HE603230
• Chlamydia trachomatis D/SotonD6. Chromosome: HE601800 Plasmid: HE603231
• Chlamydia trachomatis E/Bour. Chromosome: HE601870 Plasmid: HE603212
• Chlamydia trachomatis E/SotonE4. Chromosome: HE601802 Plasmid: HE603232
• Chlamydia trachomatis E/SotonE8. Chromosome: HE601803 Plasmid: HE603233
• Chlamydia trachomatis E/SW2. Chromosome: FN652779 Plasmid: FM865439
• Chlamydia trachomatis E/SW3. Chromosome: HE601801 Plasmid: FM865440
• Chlamydia trachomatis F/SotonF3. Chromosome: HE601806 Plasmid: HE603234
• Chlamydia trachomatis F/SW4. Chromosome: HE601804 Plasmid: FM865441
• Chlamydia trachomatis F/SW5. Chromosome: HE601805 Plasmid: FM865442
• Chlamydia trachomatis G/SotonG1. Chromosome: HE601807 Plasmid: HE603235
• Chlamydia trachomatis I/SotonIa1. Chromosome: HE601808 Plasmid: HE603236
• Chlamydia trachomatis I/SotonIa3. Chromosome: HE601809 Plasmid: HE603237
• Chlamydia trachomatis K/SotonK1. Chromosome: HE601794 Plasmid: HE603238
• Chlamydia trachomatis L1/115. Chromosome: HE601952 Plasmid: HE603218
• Chlamydia trachomatis L1/1322/p2. Chromosome: HE601951 Plasmid: HE603219
• Chlamydia trachomatis L1/224. Chromosome: HE601953 Plasmid: HE603220
• Chlamydia trachomatis L1/440/LN. Chromosome: HE601950
• Chlamydia trachomatis L2/25667R. Chromosome: HE601954
• Chlamydia trachomatis L2b/795. Chromosome: HE601949 Plasmid: HE603221
• Chlamydia trachomatis L2b/8200/07. Chromosome: HE601795 Plasmid: HE603222
• Chlamydia trachomatis L2b/Ams1. Chromosome: HE601959 Plasmid: HE603213
• Chlamydia trachomatis L2b/Ams2. Chromosome: HE601961 Plasmid: HE603214
• Chlamydia trachomatis L2b/Ams3. Chromosome: HE601962 Plasmid: HE603215
• Chlamydia trachomatis L2b/Ams4. Chromosome: HE601964 Plasmid: HE603216
• Chlamydia trachomatis L2b/Ams5. Chromosome: HE601965 Plasmid: HE603217
• Chlamydia trachomatis L2b/Canada1. Chromosome: HE601963 Plasmid: HE603223
• Chlamydia trachomatis L2b/Canada2. Chromosome: HE601957 Plasmid: HE603224
• Chlamydia trachomatis L2b/CV204. Chromosome: HE601960 Plasmid: HE603225
• Chlamydia trachomatis L2b/LST. Chromosome: HE601958 Plasmid: HE603226
• Chlamydia trachomatis L2b/UCH-2. Chromosome: HE601956 Plasmid: HE603227
• Chlamydia trachomatis L3/404. Chromosome: HE601955 Plasmid: HE603228

• Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.

  Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJ, Morré SA, Speksnijder A, Bébéar CM, Clerc M, de Barbeyrac B, Parkhill J and Thomson NR

  Nature genetics 2012;44;4;413-9, S1

  PUBMED: 22406642; PMC: 3378690; DOI: 10.1038/ng.2214

• The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization.

  Unemo M, Seth-Smith HM, Cutcliffe LT, Skilton RJ, Barlow D, Goulding D, Persson K, Harris SR, Kelly A, Bjartling C, Fredlund H, Olcén P, Thomson NR and Clarke IN

  Microbiology (Reading, England) 2010;156;Pt 5;1394-404

  PUBMED: 20093289; PMC: 3541825; DOI: 10.1099/mic.0.036830-0

• 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 genomics 2009;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 research 2008;18;1;161-71

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