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The chlamydia research group

The Chlamydia Biobank is part of the Chlamydia Research Group in the Faculty of Medicine at the University of Southampton. The ability to diagnose accurately and rapidly treat chlamydia infections is necessary to reduce the burden of this disease. The chlamydia research group, headed by Professor Ian Clarke, is involved in a major programme to define the nature and extent of diversity in C. trachomatis with the overall research goal of understanding the role of C. trachomatis in complications of infection such as infertility and pelvic inflammatory disease. The genomics programme and Biobank are supported by the Wellcome Trust and are performed in partnership with Professor Nicholas Thomson of the Sanger Institute. The group also has funding from Public Health England (PHE) for investigating the epidemiology of C. trachomatis in the UK and works in close partnership with Dr Peter Marsh of the Southampton-based PHE laboratory.

The chlamydia research group has made many significant advances in the field including the recent development of the first chlamydia transformation protocol. Current research activities in the group will be enhanced by our access to diverse strains through the Biobank, and we hope that collaborations old and new will be reinvigorated through this venture.

Labiran, C., Rowan, D., Clarke, I.N. and Marsh, P. Detailed molecular epidemiology of Chlamydia trachomatis in the population of Southampton attending the genitourinary medicine clinic in 2012-13 reveals the presence of long established genotypes and transitory sexual networks. PLoS One. 2017; 12(9): e0185059.(PMCID: PMC5612685)

Andersson, P., Harris, S.R., Seth-Smith, H.M., Hadfield, J., O'Neill, C., Cutcliffe, L.T., Douglas, F.P., Asche, L.V., Mathews, J.D., Hutton, S.I., Sarovich, D.S., Tong, S.Y., Clarke, I.N., Thomson, N.R. and Giffard, P.M. Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages. Nat Commun. 2016 Feb;7:10688. doi: 10.1038/ncomms10688 (PMID: 26871455)

Labiran, C., Marsh, P., Zhou, J., Bannister, A., Clarke, I.N., Goubet, S. and Soni, S. Highly diverse MLVA-ompA genotypes of rectal Chlamydia trachomatis among men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network. Sex Transm Infect 2016 Jun; 92(4):299-304 doi: 10.1136/sextrans-2015-052261. (PMID: 25542839)

Ramsey, K., Schripsema, J.H., Smith, B.J., Wang, Y., Jham, B.C., O'Hagan, K.P., Thomson, N.R., Murthy, A.K., Skilton, R.J., Chu, P and Clarke, I.N. Plasmid coding sequence-five influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection. 2014 May; doi10.1128/IAI.01795-14 [Epub ahead of print] (PMID:24866804)

Wang, Y., Cutcliffe, L.T., Skilton, R.J., Ramsey, K.H., Thomson, N.R., Clarke, I.N. The genetic basis of plasmid tropism between Chlamydia trachomatis and Chlamydia muridarum. Pathog Dis. 2014 Apr; doi: 10.1111/2049-632X.12175. [Epub ahead of print] (PMID: 24700815)

Sigar, I.M., Schripsema, J.H., Wang, Y., Clarke, I.N., Cutcliffe, L.T., Seth-Smith, H.M., Thomson, N.R., Bjartling, C., Unemo, M., Persson, K., Ramsey, K.H. Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model. Pathog Dis. 2014 Feb;70(1):61-9. doi: 10.1111/2049-632X.12086 (PMID: 24022847).

Seth-Smith, H.M., Harris, S.R., Scott, P., Parmar, S., Marsh, P., Unemo, M., Clarke, I.N., Parkhill, J., Thomson, N.R. Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA. Nat Protoc. 2013 Dec;8(12):2404-12. doi: 10.1038/nprot.2013.147 (PMID: 24202554)

Seth-Smith, H.M., Harris, S.R., Skilton, R.J., Radebe, F.M., Golparian, D., Shipitsyna, E., Duy, P.T., Scott, P., Cutcliffe, L.T., O'Neill, C.E., Parmar, S., Pitt, R., Baker, S., Ison, C.A., Marsh, P., Jalal, H., Lewis, D.A., Unemo, M., Clarke, I.N., Parkhill, J., Thomson, N.R. Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome Res. 2013 May;23(5):855-66. doi: 10.1101/gr.150037.112 (PMID: 23525359).

O'Neill, C.E., Seth-Smith, H.M., Van Der Pol, B., Harris, S.R., Thomson, N.R., Cutcliffe., L.T. and Clarke, I.N. Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes. Microbiology. 2013 Apr;159(Pt 4):748-56. doi: 10.1099/mic.0.065391-0 (PMID: 23378575).

Wang, Y., Cutcliffe, L.T., Skilton, R.J., Persson, K., Bjartling, C., and Clarke, I.N. Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype. Pathog Dis 2013 Mar;67(2):100-3. doi: 10.1111/2049-632X.12024. Epub 2013 Feb 13. (PMID: 23620154)

Labiran, C., Clarke, Ian N., Cutcliffe, Lesley T., Wang, Yibing, Skilton, Rachel J., Persson, Kenneth, Bjartling, Carina, Herrmann, Björn, Christerson, Linus and Marsh, Peter (2012) Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis. Front Cell Infect Microbiol. 2012 May 17;2:68. doi: 10.3389/fcimb.2012.00068 (PMID: 22919659).

Harris, Simon R., Clarke, I., Seth-Smith, Helena M.B., Solomon, Anthony W., Cutcliffe, Lesley T., Marsh, Peter, Skilton, Rachel J., Holland, Martin J., Mabey, David., Peeling, Rosanna W., Lewis, David A., Spratt, Brian G., Unemo, Magnus, Persson, Kenneth, Bjartling, Carina, Brunham, Robert, de Vries, Henry J.C., Morré Servaas A., Speksnijder, Arjen, Bébéar, Cécile M., Clerc, Maïté, de Barbeyrac, Bertille, Parkhill, Julian and Thomson, Nicholas R. (2012) Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet. 2012 Mar 11;44(4):413-9, S1. doi: 10.1038/ng.2214 PMID: 22406642).

Wang, Yibing, Kahane, Simona, Cutcliffe, Lesley T, Skilton, Rachel J, Lambden, Paul R and Clarke, Ian N (2011) Development of a transformation system for chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector. PLoS Pathog. 2011 Sep;7(9):e1002258. doi: 10.1371/journal.ppat.1002258 (PMID: 21966270).

Clarke, I.N. (2011) Evolution of chlamydia trachomatis. In, Nahmias, Andre, Danielsson, Dan and Beckman Nahmais, Susa (eds.) The Evolution of Infectious Agents in Relation to Sex. Chichester, GB, Wiley, E11-E18. Ann N Y Acad Sci. 2011 Aug;1230:E11-8. doi: 10.1111/j.1749-6632.2011.06194.x (PMID: 22239534)

Reed, David L., Currier, Russell W., Walton, Shelley F., Conrad, Melissa, Sullivan, Steven A., Carlton, Jane M., Read, Timothy D., Severini, Alberto, Tyler, Shaun, Eberle, R., Johnson, Welkin E., Silvestri, Guido, Clarke, Ian N., Lagergård, Teresa, Lukehart, Sheila A., Unemo, Magnus, Shafer, William M., Beasley, R. Palmer, Bergström, Tomas, Norberg, Peter, Davison, Andrew J., Sharp, Paul M., Hahn, Beatrice H and Blomberg, Jonas (2011) The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms. Ann N Y Acad Sci. 2011 Aug;1230:74-107. doi: 10.1111/j.1749-6632.2011.06133.x. (PMID: 21824167)

Turner, Katy, Clarke, Ian, Tompson, Nicholas and Horner, Patrick (2011) Chlamydia trachomatis in the age of the genome: application of molecular genotyping to improve our understanding of the immunopathogenesis of Chlamydia genital tract disease. Sexually Transmitted Diseases, 38, (6), 495-498. doi:10.1097/OLQ.0b013e3182185744. (PMID: 22256335)

Seth-Smith, H M B, Harris, S R, Rance, R, West, A, Severin, J, Ossewaarde, J, Cutcliffe, L.T., Skilton, R.J., Marsh, P., Parkhill, J, Clarke, Ian N. and Thomson, N (2011) Genome sequence of the zoonotic pathogen Chlamydophila psittaci. J Bacteriol. 2011 Mar;193(5):1282-3. doi: 10.1128/JB.01435-10. (PMID: 21183672)

Unemo, Magnus and Clarke, Ian (2011) The Swedish new variant of Chlamydia trachomatis. Current Opinion in Infectious Diseases, 24, (1), 62-69. doi: 10.1097/QCO.0b013e32834204d5. (PMID: 21157332).

Wang, Yibing, Skilton, Rachel J., Cutcliffe, Lesley T., Andrews, Emma, Clarke, Ian N. and Marsh, Pete (2011) Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples. PLoS ONE, 6, (2), e16971. (doi:10.1371/journal.pone.0016971). (PMID: 21347295)

Unemo, Magnus, Seth-Smith, Helena M.B., Cutcliffe, Lesley T., Skilton, Rachel J., Barlow, David, Goulding, David, Persson, Kenneth, Harris, Simon, Kelly, Anne, Bjartling, Carina, Fredlund, Hans, Olcén, Per, Thomson, N icholas R. and Clarke, Ian N. (2010) The Swedish new variant of chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization. Microbiology, 156, (5), 1394-404. (doi:10.1099/mic.0.036830-0). (PMID: 20093289)

Thomson, Nicholas R. and Clarke, Ian N. (2010) Chlamydia trachomatis: small genome, big challenges. Future Microbiology, 5, (4), 555-561. (doi:10.2217/fmb.10.31). (PMID: 20353297)

Clarke, Ian N. (2010) Chlamydial transformation: facing up to the challenge. In, Chlamydial Infections. Twelfth International Symposium on Human Chlamydial Infections San Francisco, US, Twelfth International Symposium on Human Chlamydial Infections, 295-304

Skilton, Rachel J., Cutcliffe, Lesley T., Barlow, David, Wang, Yibing, Salim, Omar, Lambden, Paul R. and Clarke, Ian N. (2009) Penicillin induced persistence in Chlamydia trachomatis: high quality time lapse video analysis of the developmental cycle. PloS one, 4, (11), e7723. (doi:10.1371/journal.pone.0007723). (PMID: 19542292).

Seth-Smith, Helena M.B., Harris, Simon R., Persson, Kenneth, Marsh, Pete, Barron, Andrew, Bignell, Alexandra, Bjartling, Carina, Clark, Louise, Cutcliffe, Lesley T., Lambden, Paul R., Lennard, Nicola, Lockey, Sarah J., Quail, Michael A., Salim, Omar, Skilton, Rachel J., Wang, Yibing, Holland, Martin J., Parkhill, Julian, Thomson, Nicholas R. and Clarke, I.N. (2009) Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain. BMC Genomics, 10, (239)(doi:10.1186/1471- 2164-10-239). (PMID: 19460133)

Skilton, R.J., Cutcliffe, L.T., Pickett, M.A., Lambden, P.R., Fane, B.A. and Clarke, I.N. 2007. Intracellular Parasitism of Chlamydiae: Specific Infectivity of Chlamydiaphage Chp2 in Chlamydophila abortus. Journal of Bacteriology, 189(13): 4957-4959. (PMID: 17468245)

Salim, Omar, Skilton, Rachel J., Lambden, Paul R., Fane, Bentley A. and Clarke, Ian N. (2008) Behind the chlamydial cloak: the replication cycle of chlamydiaphage Chp2, revealed. Virology, 377, (2), 440-445. doi:10.1016/j.virol.2008.05.001. (PMID: 18570973)

Thomson, N. R., M. T. Holden, C. Carder, N. Lennard, S. J. Lockey, P. Marsh, P. Skipp, C. D. O'Connor, I. Goodhead, H. Norbertzcak, B. Harris, D. Ormond, R. Rance, M. A. Quail, J. Parkhill, R. S. Stephens, and I. N. Clarke. 2008. Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates. Genome Res. 18:161-171. doi:gr.7020108 [pii];10.1101/gr.7020108 [doi]. (PMID: 18032721)

Skipp, P., J. Robinson, C. D. O'Connor, and I. N. Clarke. 2005. Shotgun proteomic analysis of Chlamydia trachomatis. Proteomics. 5:1558-1573. doi:10.1002/pmic.200401044 [doi]. (PMID: 15838905)

Pickett, M. A., J. S. Everson, P. J. Pead, and I. N. Clarke. 2005. The plasmids of Chlamydia trachomatis and Chlamydophila pneumoniae (N16): accurate determination of copy number and the paradoxical effect of plasmid-curing agents. Microbiology 151:893-903. doi:151/3/893 [pii];10.1099/mic.0.27625-0 [doi] (PMID: 15758234).