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Growth kinetics of Chlamydia trachomatis in primary human Sertoli cells.

Filardo S, Skilton RJ, O'Neill CE, Di Pietro M, Sessa R, Clarke IN.

Sci Rep. 2019 Apr 10;9(1):5847. doi: 10.1038/s41598-019-42396-3.


Genetic Transformation of a C. trachomatis Ocular Isolate With the Functional Tryptophan Synthase Operon Confers an Indole-Rescuable Phenotype.

O'Neill CE, Skilton RJ, Pearson SA, Filardo S, Andersson P, Clarke IN.

Front Cell Infect Microbiol. 2018 Dec 14;8:434. doi: 10.3389/fcimb.2018.00434. eCollection 2018.


The Genetic Transformation of Chlamydia pneumoniae.

Shima K, Wanker M, Skilton RJ, Cutcliffe LT, Schnee C, Kohl TA, Niemann S, Geijo J, Klinger M, Timms P, Rattei T, Sachse K, Clarke IN, Rupp J.

mSphere. 2018 Oct 10;3(5). pii: e00412-18. doi: 10.1128/mSphere.00412-18.


The Chlamydia muridarum plasmid revisited : new insights into growth kinetics.

Skilton RJ, Wang Y, O'Neill C, Filardo S, Marsh P, Bénard A, Thomson NR, Ramsey KH, Clarke IN.

Wellcome Open Res. 2018 Mar 8;3:25. doi: 10.12688/wellcomeopenres.13905.1. eCollection 2018.


Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ.

Genome Med. 2018 Feb 26;10(1):15. doi: 10.1186/s13073-018-0521-x.


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

Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, Morré SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Genome Res. 2017 Jul;27(7):1220-1229. doi: 10.1101/gr.212647.116. Epub 2017 Jun 6.


Development and evaluation of an enzyme-linked immunosorbent assay for the detection of antibodies to a common urogenital derivative of Chlamydia trachomatis plasmid-encoded PGP3.

Winstanley CE, Ramsey KH, Marsh P, Clarke IN.

J Immunol Methods. 2017 Jun;445:23-30. doi: 10.1016/j.jim.2017.03.002. Epub 2017 Mar 7.


Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.

Andersson P, Harris SR, Smith HMBS, Hadfield J, O'Neill C, Cutcliffe LT, Douglas FP, Asche LV, Mathews JD, Hutton SI, Sarovich DS, Tong SYC, Clarke IN, Thomson NR, Giffard PM.

Nat Commun. 2016 Feb 25;7:10688. doi: 10.1038/ncomms10688.


Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis.

Skipp PJ, Hughes C, McKenna T, Edwards R, Langridge J, Thomson NR, Clarke IN.

PLoS One. 2016 Feb 12;11(2):e0149011. doi: 10.1371/journal.pone.0149011. eCollection 2016.


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.

Labiran C, Marsh P, Zhou J, Bannister A, Clarke IN, Goubet S, Soni S.

Sex Transm Infect. 2016 Jun;92(4):299-304. doi: 10.1136/sextrans-2015-052261. Epub 2015 Oct 20.


Rapid detection of diagnostic targets using isothermal amplification and HyBeacon probes--a homogenous system for sequence-specific detection.

Howard RL, French DJ, Richardson JA, O'Neill CE, Andreou MP, Brown T, Clark D, Clarke IN, Holloway JW, Marsh P, Debenham PG.

Mol Cell Probes. 2015 Apr;29(2):92-8. doi: 10.1016/j.mcp.2014.12.001. Epub 2014 Dec 24.


Structure-based design and functional studies of novel noroviral 3C protease chimaeras offer insights into substrate specificity.

Herod MR, Prince CA, Skilton RJ, Ward VK, Cooper JB, Clarke IN.

Biochem J. 2014 Dec 15;464(3):461-72. doi: 10.1042/BJ20140959.


Plasmid CDS5 influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection.

Ramsey KH, Schripsema JH, Smith BJ, Wang Y, Jham BC, O'Hagan KP, Thomson NR, Murthy AK, Skilton RJ, Chu P, Clarke IN.

Infect Immun. 2014 Aug;82(8):3341-9. doi: 10.1128/IAI.01795-14. Epub 2014 May 27.


The genetic basis of plasmid tropism between Chlamydia trachomatis and Chlamydia muridarum.

Wang Y, Cutcliffe LT, Skilton RJ, Ramsey KH, Thomson NR, Clarke IN.

Pathog Dis. 2014 Oct;72(1):19-23. doi: 10.1111/2049-632X.12175. Epub 2014 May 8.


Expression of the murine norovirus (MNV) ORF1 polyprotein is sufficient to induce apoptosis in a virus-free cell model.

Herod MR, Salim O, Skilton RJ, Prince CA, Ward VK, Lambden PR, Clarke IN.

PLoS One. 2014 Mar 5;9(3):e90679. doi: 10.1371/journal.pone.0090679. eCollection 2014.


Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Nat Protoc. 2013 Dec;8(12):2404-12. doi: 10.1038/nprot.2013.147. Epub 2013 Nov 7.


Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model.

Sigar IM, Schripsema JH, Wang Y, Clarke IN, Cutcliffe LT, Seth-Smith HM, Thomson NR, Bjartling C, Unemo M, Persson K, Ramsey KH.

Pathog Dis. 2014 Feb;70(1):61-9. doi: 10.1111/2049-632X.12086. Epub 2013 Sep 10.


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.

Wang Y, Cutcliffe LT, Skilton RJ, Persson K, Bjartling C, Clarke IN.

Pathog Dis. 2013 Mar;67(2):100-3. doi: 10.1111/2049-632X.12024. Epub 2013 Feb 13.


Genetic transformation of a clinical (genital tract), plasmid-free isolate of Chlamydia trachomatis: engineering the plasmid as a cloning vector.

Wang Y, Kahane S, Cutcliffe LT, Skilton RJ, Lambden PR, Persson K, Bjartling C, Clarke IN.

PLoS One. 2013;8(3):e59195. doi: 10.1371/journal.pone.0059195. Epub 2013 Mar 18.


Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.

Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, Golparian D, Shipitsyna E, Duy PT, Scott P, Cutcliffe LT, O'Neill C, Parmar S, Pitt R, Baker S, Ison CA, Marsh P, Jalal H, Lewis DA, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Genome Res. 2013 May;23(5):855-66. doi: 10.1101/gr.150037.112. Epub 2013 Mar 22.


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.

O'Neill CE, Seth-Smith HM, Van Der Pol B, Harris SR, Thomson NR, Cutcliffe LT, Clarke IN.

Microbiology. 2013 Apr;159(Pt 4):748-56. doi: 10.1099/mic.0.065391-0. Epub 2013 Feb 1.


Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis.

Labiran C, Clarke IN, Cutcliffe LT, Wang Y, Skilton RJ, Persson K, Bjartling C, Herrmann B, Christerson L, Marsh P.

Front Cell Infect Microbiol. 2012 May 17;2:68. doi: 10.3389/fcimb.2012.00068. eCollection 2012.


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, Thomson NR.

Nat Genet. 2012 Mar 11;44(4):413-9, S1. doi: 10.1038/ng.2214.


Inherent structural disorder and dimerisation of murine norovirus NS1-2 protein.

Baker ES, Luckner SR, Krause KL, Lambden PR, Clarke IN, Ward VK.

PLoS One. 2012;7(2):e30534. doi: 10.1371/journal.pone.0030534. Epub 2012 Feb 7.


Evolution of Chlamydia trachomatis.

Clarke IN.

Ann N Y Acad Sci. 2011 Aug;1230:E11-8. doi: 10.1111/j.1749-6632.2011.06194.x. Review.


Development of a transformation system for Chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector.

Wang Y, Kahane S, Cutcliffe LT, Skilton RJ, Lambden PR, Clarke IN.

PLoS Pathog. 2011 Sep;7(9):e1002258. doi: 10.1371/journal.ppat.1002258. Epub 2011 Sep 22.


Infection of calves with bovine norovirus GIII.1 strain Jena virus: an experimental model to study the pathogenesis of norovirus infection.

Otto PH, Clarke IN, Lambden PR, Salim O, Reetz J, Liebler-Tenorio EM.

J Virol. 2011 Nov;85(22):12013-21. doi: 10.1128/JVI.05342-11. Epub 2011 Aug 31.


The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms.

Reed DL, Currier RW, Walton SF, Conrad M, Sullivan SA, Carlton JM, Read TD, Severini A, Tyler S, Eberle R, Johnson WE, Silvestri G, Clarke IN, Lagergård T, Lukehart SA, Unemo M, Shafer WM, Beasley RP, Bergström T, Norberg P, Davison AJ, Sharp PM, Hahn BH, Blomberg J.

Ann N Y Acad Sci. 2011 Aug;1230:74-107. doi: 10.1111/j.1749-6632.2011.06133.x. Review.


Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples.

Wang Y, Skilton RJ, Cutcliffe LT, Andrews E, Clarke IN, Marsh P.

PLoS One. 2011 Feb 11;6(2):e16971. doi: 10.1371/journal.pone.0016971.


Genome sequence of the zoonotic pathogen Chlamydophila psittaci.

Seth-Smith HM, Harris SR, Rance R, West AP, Severin JA, Ossewaarde JM, Cutcliffe LT, Skilton RJ, Marsh P, Parkhill J, Clarke IN, Thomson NR.

J Bacteriol. 2011 Mar;193(5):1282-3. doi: 10.1128/JB.01435-10. Epub 2010 Dec 23.


The Swedish new variant of Chlamydia trachomatis.

Unemo M, Clarke IN.

Curr Opin Infect Dis. 2011 Feb;24(1):62-9. doi: 10.1097/QCO.0b013e32834204d5. Review.


A structural study of norovirus 3C protease specificity: binding of a designed active site-directed peptide inhibitor.

Hussey RJ, Coates L, Gill RS, Erskine PT, Coker SF, Mitchell E, Cooper JB, Wood S, Broadbridge R, Clarke IN, Lambden PR, Shoolingin-Jordan PM.

Biochemistry. 2011 Jan 18;50(2):240-9. Epub 2010 Dec 15.


Crystallization and preliminary X-ray diffraction analysis of the protease from Southampton norovirus complexed with a Michael acceptor inhibitor.

Hussey RJ, Coates L, Gill RS, Wright JN, Sarwar M, Coker S, Erskine PT, Cooper JB, Wood S, Clarke IN, Lambden PR, Broadbridge R, Shoolingin-Jordan PM.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Nov 1;66(Pt 11):1544-8. doi: 10.1107/S1744309110039059. Epub 2010 Oct 29.


Chlamydia trachomatis: small genome, big challenges.

Thomson NR, Clarke IN.

Future Microbiol. 2010 Apr;5(4):555-61. doi: 10.2217/fmb.10.31. Review.


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, Clarke IN.

Microbiology. 2010 May;156(Pt 5):1394-404. doi: 10.1099/mic.0.036830-0. Epub 2010 Jan 21.


Penicillin induced persistence in Chlamydia trachomatis: high quality time lapse video analysis of the developmental cycle.

Skilton RJ, Cutcliffen LT, Barlow D, Wang Y, Salim O, Lambden PR, Clarke IN.

PLoS One. 2009 Nov 6;4(11):e7723. doi: 10.1371/journal.pone.0007723.


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, Clarke IN.

BMC Genomics. 2009 May 21;10:239. doi: 10.1186/1471-2164-10-239.


Behind the chlamydial cloak: the replication cycle of chlamydiaphage Chp2, revealed.

Salim O, Skilton RJ, Lambden PR, Fane BA, Clarke IN.

Virology. 2008 Aug 1;377(2):440-5. doi: 10.1016/j.virol.2008.05.001.


Functional analysis of the 5' genomic sequence of a bovine norovirus.

Salim O, Clarke IN, Lambden PR.

PLoS One. 2008 May 14;3(5):e2169. doi: 10.1371/journal.pone.0002169.


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, Clarke IN.

Genome Res. 2008 Jan;18(1):161-71. Epub 2007 Nov 21.


Serotype 1 and 2 bovine noroviruses are endemic in cattle in the United kingdom and Germany.

Oliver SL, Wood E, Asobayire E, Wathes DC, Brickell JS, Elschner M, Otto P, Lambden PR, Clarke IN, Bridger JC.

J Clin Microbiol. 2007 Sep;45(9):3050-2. Epub 2007 Jun 27.


Recovery of infectious murine norovirus using pol II-driven expression of full-length cDNA.

Ward VK, McCormick CJ, Clarke IN, Salim O, Wobus CE, Thackray LB, Virgin HW 4th, Lambden PR.

Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):11050-5. Epub 2007 Jun 20.


Intracellular parasitism of chlamydiae: specific infectivity of chlamydiaphage Chp2 in Chlamydophila abortus.

Skilton RJ, Cutcliffe LT, Pickett MA, Lambden PR, Fane BA, Clarke IN.

J Bacteriol. 2007 Jul;189(13):4957-9. Epub 2007 Apr 27.


The effect of penicillin on Chlamydia trachomatis DNA replication.

Lambden PR, Pickett MA, Clarke IN.

Microbiology. 2006 Sep;152(Pt 9):2573-8.


Characterization of a cross-reactive linear epitope in human genogroup I and bovine genogroup III norovirus capsid proteins.

Batten CA, Clarke IN, Kempster SL, Oliver SL, Bridger JC, Lambden PR.

Virology. 2006 Dec 5-20;356(1-2):179-87. Epub 2006 Aug 24.


Quest for complete proteome coverage.

O'Connor CD, Clarke IN, Skipp P.

Methods Biochem Anal. 2006;49:27-38. Review. No abstract available.


Genotype 1 and genotype 2 bovine noroviruses are antigenically distinct but share a cross-reactive epitope with human noroviruses.

Oliver SL, Batten CA, Deng Y, Elschner M, Otto P, Charpilienne A, Clarke IN, Bridger JC, Lambden PR.

J Clin Microbiol. 2006 Mar;44(3):992-8.


Shotgun proteomic analysis of Chlamydia trachomatis.

Skipp P, Robinson J, O'Connor CD, Clarke IN.

Proteomics. 2005 Apr;5(6):1558-73.


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