Chlamydia trachomatis

C. trachomatis is the major cause of sexually transmitted infections (STI) in the UK and globally accounts for > 89 million STI cases. Complications caused by the genital tract C. trachomatis biovariants include pelvic inflammatory disease, ectopic pregnancy and infertility in women, and epididymitis in men. Ocular biovariants of C. trachomatis are also the leading cause of preventable blindness (trachoma) in the developing world causing acute or sub-acute follicular conjunctivitis (inclusion conjunctivitis), which may progress to punctate keratitis, scarring and trachoma.

We have also studied 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 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.


Data Downloads

[Genome Research Limited]

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:

Studies

Chlamydia trachomatis global diversity project

Sample

Strain

Run Accession

Ct_L2_b1Ct_L2_b1ERR021951
Ct_L2_b2Ct_L2_b2ERR021952
Ct_L2_b3Ct_L2_b3ERR021953
Ct_L2_b4Ct_L2_b4ERR021954
RS1RS1ERR008581
RS2RS2ERR008587
RS2RS2ERR021957
RS3RS3ERR008593
RS3RS3ERR021958
RS4RS4ERR008580
RS4RS4ERR021959
RS5RS5ERR008579
RS5RS5ERR021960
RS6RS6ERR008592
RS6RS6ERR021961
RS7RS7ERR021962
RS7RS7ERR008595
RS8RS8ERR021955
RS8RS8ERR021965
RS8RS8ERR008583
SW3SW3ERR008589
SW2SW2ERR021963
SW2SW2ERR008596
SW4SW4ERR008588
SW5SW5ERR021956
SW5SW5ERR008582
046294-M046294-MERR021964
046294-M046294-MERR008585
049287-B049287-BERR008591
BourBourERR018602
BourBourERR008578
SWFPSWFPERR018603
SWFPSWFPERR008598
D4D4ERR018604
D4D4ERR008590
D6D6ERR018605
D6D6ERR008584
D7D7ERR018606
D7D7ERR008594
D8D8ERR008597
D8D8ERR018607
D10D10ERR018608
D10D10ERR008599
Fr4Fr4ERR008586
L2P-L2P-ERR042039
BY331p3BY331p3ERR071988
LGV173p4LGV173p4ERR071989
LGV98p5LGV98p5ERR071990
LGV913p1LGV913p1ERR071991
LGV1339LGV1339ERR071992
BY170ulcBY170ulcERR071993
Rb1392Rb1392ERR071994
Rb1392MDARb1392MDAERR071995
ASA1IMSASA1IMSERR071996
BIP2405BIP2405ERR071997
BIP1586BIP1586ERR071998
BIP2366BIP2366ERR071999
M31M31ERR072000
Jali16MDAJali16MDAERR111553
D230D230ERR111554
Soton17Soton17ERR111555
Soton53Soton53ERR111556
Soton107Soton107ERR111557
Soton116Soton116ERR111558
Soton120Soton120ERR111559
Soton145Soton145ERR111560
Soton159Soton159ERR111561
26833IM26833IMERR111562
32100IM32100IMERR111563
32840IM32840IMERR111564
28017IM28017IMERR111565
27091IM27091IMERR111566
35067IM35067IMERR111567
526IM526IMERR111568
30591IM30591IMERR111569
36176IM36176IMERR111570
3059IM3059IMERR111571
33512IM33512IMERR111572
4175IM4175IMERR111573
3285IM3285IMERR111574
1519IM1519IMERR111575
297IM297IMERR111576
S2526S2526ERR111577
S3929S3929ERR111578
S3024S3024ERR111579
S2384S2384ERR111580
S2956S2956ERR111581
S3122S3122ERR111582
S2430S2430ERR111583
S4229S4229ERR111584
S1086S1086ERR111585
S2130S2130ERR111586
S1824S1824ERR111587
S3270MDAS3270MDAERR111588
S3489MDAS3489MDAERR111589
S3257MDAS3257MDAERR111590
S3344MDAS3344MDAERR111591
S2459MDAS2459MDAERR111592
S4410MDAS4410MDAERR111593
R28044R28044ERR111594
R23736R23736ERR111595
R25114R25114ERR111596
R28312R28312ERR111597
R28979R28979ERR111598
R27887R27887ERR111599
R30444R30444ERR111600
R26833R26833ERR111601
R32100R32100ERR111602
R28017R28017ERR111603
R27091R27091ERR111604
R31458R31458ERR111605
R31975R31975ERR111606
R33420R33420ERR111607
R34962R34962ERR111608
R34345R34345ERR111609
R35506R35506ERR111610
R36176R36176ERR111611
R3059R3059ERR111612
R33512R33512ERR111613
R4175R4175ERR111614
R4159R4159ERR111615
R25308R25308ERR111616
R459R459ERR111617
R4609R4609ERR111618
R9892R9892ERR111619
R2247R2247ERR111620
R1430R1430ERR111621
R2084R2084ERR111622
R27757R27757ERR111623
R6004R6004ERR111624
R9069R9069ERR111625
R26881MR26881MERR111626
R32840MR32840MERR111627
R35248MR35248MERR111628
R27128MR27128MERR111629
R29005MR29005MERR111630
R33358MR33358MERR111631
ND12899MND12899MERR111632
BY331p3MBY331p3MERR111633
Ar5MAr5MERR111634
Ar112MAr112MERR111635
Ar152Ar152ERR111636
Ar152MAr152MERR108272
Ar182Ar182ERR108273
Ar182MAr182MERR108274
Ar246Ar246ERR108275
Ar246MAr246MERR108276
Ar250MAr250MERR108277
Ar427Ar427ERR108278
Ar427MAr427MERR108279
Ar7218Ar7218ERR108280
Ar7218MAr7218MERR108281
S3732S3732ERR108282
S2595S2595ERR108283
S2491S2491ERR108284
S4471S4471ERR108285
S1736S1736ERR108286
S1879S1879ERR108287
S4324S4324ERR108288
S1886S1886ERR108289
S1618S1618ERR108290
S1471S1471ERR108291
S1470S1470ERR108292
S4247S4247ERR108293
S4828S4828ERR108294
S4658S4658ERR108295
S1314S1314ERR108296
HPA314314ERR108297
688IMSMDA688IMSMDAERR108298
S3107S3107ERR108299
S4281S4281ERR108300
S1026S1026ERR108301
S1254S1254ERR108302
S1432S1432ERR108303
S143S143ERR108304
It246It246ERR108305
It307AIt307AERR108306
It769It769ERR108307
It807It807ERR140752
BIP1599BIP1599ERR140753
S276IS276IERR140754
S3580IS3580IERR140755
R15108IR15108IERR140756
FMA3FMA3ERR140757
FMCFMCERR140758
FMDpFMDpERR140759
S2384MDAS2384MDAERR140760
ATCCBIMSATCCBIMSERR140761
ATCCBaIMSATCCBaIMSERR140762
ATCCFIMSATCCFIMSERR140763
It688IMSIt688IMSERR140764
It769IMSIt769IMSERR140765
HPA017HPA017ERR140766
HPA021HPA021ERR140767
T4T4ERR140768
T11T11ERR140769
T3pT3pERR140770
T4pT4pERR140771
T5pT5pERR140772
T7pT7pERR140773
T9pT9pERR140774
T11pT11pERR140775
T12pT12pERR140776
T3pMDAT3pMDAERR140777
T4pMDAT4pMDAERR140778
T5pMDAT5pMDAERR140779
T8pMDAT8pMDAERR140780
T9pMDAT9pMDAERR140781
T10pMDAT10pMDAERR140782
T11pMDAT11pMDAERR140783
T12pMDAT12pMDAERR140784
T4qT4qERR140785
T9qT9qERR140786
T11qT11qERR140787
T3qMDaT3qMDaERR140788
T4qMDAT4qMDAERR140789
T5qMDaT5qMDaERR140790
T9qMDAT9qMDAERR140791
T10qMDAT10qMDAERR140792
T11qMDAT11qMDAERR140793
T12qMDAT12qMDAERR140794
R4663IMR4663IMERR140795
R4195IMR4195IMERR140796
S4773IMS4773IMERR140797
R7369IMR7369IMERR140798
R12921IMR12921IMERR140799
S3948S3948ERR140800
S3073S3073ERR140801
S4306S4306ERR140802
S4106S4106ERR140803
S4093S4093ERR140804
S1227S1227ERR140805
S1614S1614ERR140806
S1846S1846ERR140807
S1019S1019ERR140808
S1528S1528ERR140809
S1148S1148ERR140810
S1494S1494ERR140811
S1613S1613ERR140812
S4641S4641ERR140813
S2477S2477ERR140814
S3695S3695ERR140815
S3724S3724ERR140816
S4007S4007ERR140817
S42MDAS42MDAERR140818
Soton42Soton42ERR140819
Soton48Soton48ERR140820
Soton49Soton49ERR140821
Soton54Soton54ERR140822
Soton83Soton83ERR140823
Soton106Soton106ERR140824
Soton118Soton118ERR140825
Soton128Soton128ERR140826
Soton137Soton137ERR140827
Soton144Soton144ERR140828
S178S178ERR140829
S581S581ERR140830
S2699S2699ERR140831
S2713S2713ERR140832
S3085S3085ERR140833
S3711S3711ERR140834
R4528R4528ERR140835
R13207R13207ERR140836
R16965R16965ERR140837
R14876R14876ERR140838
R11642R11642ERR140839
R15212R15212ERR140840
S3066IMS3066IMERR140841
CC15CC15ERR140842
CC35CC35ERR140843
CC37CC37ERR140844
CC15MDACC15MDAERR140845
CC35MDACC35MDAERR140846
CC37MDACC37MDAERR140847
NL35IMSUnknownERR164692
NL34IMSUnknownERR164691
NL30IMSUnknownERR164690
NL28IMSUnknownERR164689
NL27IMSUnknownERR164688
NL26IMSUnknownERR164687
NL22IMSUnknownERR164686
NL21IMSUnknownERR164685
NL19IMSUnknownERR164684
NL18IMSUnknownERR164683
NL17IMSUnknownERR164682
NL15IMSUnknownERR164681
NL14IMSUnknownERR164680
NL13IMSUnknownERR164679
NL12IMSUnknownERR164678
NL11IMSUnknownERR164677
NL10IMSUnknownERR164676
NL9IMSUnknownERR164675
NL8IMSUnknownERR164674
NL7IMSUnknownERR164673
NL6IMSUnknownERR164672
NL5IMSUnknownERR164671
NL4IMSUnknownERR164670
NL2IMSUnknownERR164669
Tig1IMSUnknownERR164668
2075pM2UnknownERR164667
B11IMSUnknownERR164666
HPA34UnknownERR164665
HPA32UnknownERR164664
HPA31UnknownERR164663
HPA29UnknownERR164662
HPA27UnknownERR164661
HPA10UnknownERR164660
HPA1UnknownERR164659
ATCCGUnknownERR164658
L2GastonUnknownERR164657
R6004MUnknownERR164656
R33420MUnknownERR164655
R13670UnknownERR164654
R16983IMUnknownERR164653
R180IMUnknownERR164652
R15893IMUnknownERR164651
R18418IMUnknownERR164650
S4821UnknownERR164649
S4377UnknownERR164648
S4034UnknownERR164647
S269IMUnknownERR164646
S13IMUnknownERR164645
Sou37IMUnknownERR189773
Sou24IMUnknownERR189772
Sou9IMUnknownERR189771
Aus8pUnknownERR189770
Au10pMDAUnknownERR189769
Aus9pMDAUnknownERR189768
Au12pMDAUnknownERR189767
Aus6pMDAUnknownERR189766
NL59pUnknownERR189765
NL39pUnknownERR189764
NL32pUnknownERR189763
NL31pUnknownERR189762
Aus13pUnknownERR189761
Aus19pUnknownERR189760
Aus18pUnknownERR189759
NL29UnknownERR189758
NL24UnknownERR189757
NL23UnknownERR189756
Sou114IMUnknownERR189755
Aus20IMUnknownERR189754
Aus18IMUnknownERR189753
Aus17IMUnknownERR189752
Aus16IMUnknownERR189751
Aus15IMUnknownERR189750
Aus14IMUnknownERR189749
Aus13IMUnknownERR189748
Aus11IMUnknownERR189747
Aus10IMUnknownERR189746
Aus5IMUnknownERR189745
Aus4IMUnknownERR189744
Aus3IMUnknownERR189743
Aus2IMUnknownERR189742
Aus1IMUnknownERR189741
HPA27QGUnknownERR189740
C194QGUnknownERR189739
Jali16M2UnknownERR189738
S581MDAUnknownERR189737
ATCCB2UnknownERR189736
NL73IMSUnknownERR189735
NL43IMSUnknownERR189730
NL40IMSUnknownERR189729
NL38IMSUnknownERR189728
NL37IMSUnknownERR189727
NL36IMSUnknownERR189726
NL48IMSUnknownERR189734
NL46IMSUnknownERR189733
NL45IMSUnknownERR189732
NL44IMSUnknownERR189731
Sou46IUnknownERR210998
Sou42IUnknownERR210997
Sou40IUnknownERR210996
Sou34IUnknownERR210995
Aus10UnknownERR210994
Aus9UnknownERR210993
Aus8UnknownERR210992
NL85UnknownERR210991
NL78UnknownERR210990
NL76UnknownERR210989
NL71UnknownERR210988
NL70UnknownERR210987
NL67UnknownERR210986
NL63UnknownERR210985
NL61UnknownERR210984
NL60UnknownERR210983
NL58UnknownERR210982
NL56UnknownERR210981
NL55UnknownERR210980
NL54UnknownERR210979
NL53UnknownERR210978
NL41UnknownERR210971
NL16UnknownERR210970
NL1UnknownERR210969
L694uUnknownERR211064
L809uUnknownERR211063
L115p10UnknownERR211062
L942p1uUnknownERR211061
L867p1UnknownERR211060
L232p1UnknownERR211059
L224p1UnknownERR211058
L82p2UnknownERR211057
SW2p72UnknownERR211056
SW2p36UnknownERR211055
L728UnknownERR211054
L388UUnknownERR211053
L755UnknownERR211052
L115P9UnknownERR211051
L198UnknownERR211050
L224P4UnknownERR211049
L1507UnknownERR211048
L1197UnknownERR211047
L246P3UnknownERR211046
L165P2UnknownERR211045
L146P1UnknownERR211044
L232P2UnknownERR211043
L1291UnknownERR211042
L1286UnknownERR211041
L1069UnknownERR211040
L924UnknownERR211039
L1448UnknownERR211038
L1322UnknownERR211037
L1502UnknownERR211036
L1034UnknownERR211035
L910UnknownERR211034
NL86MDAUnknownERR211033
NL57MDAUnknownERR211032
Aus21UnknownERR211031
NL87MDAUnknownERR211030
NL83MDAUnknownERR211029
NL81MDAUnknownERR211028
NL72MDAUnknownERR211027
NL66MDAUnknownERR211026
NL84UnknownERR211025
NL82UnknownERR211024
NL69UnknownERR211023
NL35UnknownERR211022
NL34UnknownERR211021
NL22UnknownERR211020
NL21UnknownERR211019
NL5UnknownERR211018
NL4UnknownERR211017
NL2UnknownERR211016
Sou111IUnknownERR211015
Sou107IUnknownERR211014
Sou106IUnknownERR211013
Sou105IUnknownERR211012
Sou103IUnknownERR211011
Sou102IUnknownERR211010
Sou100IUnknownERR211009
Sou99IUnknownERR211008
Sou94IUnknownERR211007
Sou89IUnknownERR211006
Sou87IUnknownERR211005
Sou75IUnknownERR211004
Sou70IUnknownERR211003
Sou69IUnknownERR211002
Sou67IUnknownERR211001
Sou64IUnknownERR211000
Sou60IUnknownERR210999
NL52UnknownERR210977
NL51UnknownERR210976
NL50UnknownERR210975
NL49UnknownERR210974
NL47UnknownERR210973
NL42UnknownERR210972
162STDY5437328UnknownERR278225
162STDY5437327UnknownERR278224
162STDY5437326UnknownERR278223
162STDY5437325UnknownERR278222
162STDY5437324UnknownERR278221
162STDY5437323UnknownERR278220
162STDY5437322UnknownERR278219
162STDY5437321UnknownERR278218
162STDY5437320UnknownERR278217
162STDY5437319UnknownERR278216
162STDY5437318UnknownERR278215
162STDY5437317UnknownERR278214
162STDY5437316UnknownERR278213
162STDY5437293UnknownERR278190
162STDY5437292UnknownERR278189
162STDY5437291UnknownERR278188
162STDY5437290UnknownERR278187
162STDY5437289UnknownERR278186
162STDY5437288UnknownERR278185
162STDY5437287UnknownERR278184
162STDY5437286UnknownERR278183
162STDY5437285UnknownERR278182
162STDY5437284UnknownERR278181
162STDY5437283UnknownERR278180
162STDY5437282UnknownERR278179
162STDY5437281UnknownERR278178
162STDY5437280UnknownERR278177
162STDY5437279UnknownERR278176
162STDY5437278UnknownERR278175
162STDY5437277UnknownERR278174
162STDY5437276UnknownERR278173
162STDY5437275UnknownERR278172
162STDY5437274UnknownERR278171
162STDY5437273UnknownERR278170
162STDY5437272UnknownERR278169
162STDY5437271UnknownERR278168
162STDY5437270UnknownERR278167
162STDY5437269UnknownERR278166
162STDY5437268UnknownERR278165
162STDY5437267UnknownERR278164
162STDY5437266UnknownERR278163
162STDY5437265UnknownERR278162
162STDY5437264UnknownERR278161
162STDY5437263UnknownERR278160
162STDY5437262UnknownERR278159
162STDY5437261UnknownERR278158
162STDY5437260UnknownERR278157
162STDY5437259UnknownERR278156
162STDY5437258UnknownERR278155
162STDY5437257UnknownERR278154
162STDY5437256UnknownERR278153
162STDY5437255UnknownERR278152
162STDY5437254UnknownERR278151
162STDY5437253UnknownERR278150
162STDY5437252UnknownERR278149
162STDY5437251UnknownERR278148
162STDY5437250UnknownERR278147
162STDY5437249UnknownERR278146
162STDY5437248UnknownERR278145
162STDY5437247UnknownERR278144
162STDY5437246UnknownERR278143
162STDY5437245UnknownERR278142
162STDY5437244UnknownERR278141
162STDY5437243UnknownERR278140
162STDY5437242UnknownERR278139
162STDY5437241UnknownERR278138
162STDY5437240UnknownERR278137
162STDY5437239UnknownERR278136
162STDY5437238UnknownERR278135
162STDY5437237UnknownERR278134
162STDY5437236UnknownERR278133
162STDY5437235UnknownERR278132
162STDY5437234UnknownERR278131
162STDY5532010UnknownERR348861
162STDY5532009UnknownERR348860
162STDY5532008UnknownERR348859
162STDY5532007UnknownERR348858
162STDY5532006UnknownERR348857
162STDY5532005UnknownERR348856
162STDY5532004UnknownERR348855
162STDY5532003UnknownERR348854
162STDY5532002UnknownERR348853
162STDY5532001UnknownERR348852
162STDY5532000UnknownERR348851
162STDY5531999UnknownERR348850
162STDY5531998UnknownERR348849
162STDY5531997UnknownERR348848
162STDY5531914UnknownERR351535
162STDY5531913UnknownERR351534
162STDY5531912UnknownERR351533
162STDY5531911UnknownERR351532
162STDY5531910UnknownERR351531
162STDY5531909UnknownERR351530
162STDY5531908UnknownERR351529
162STDY5531907UnknownERR351528
162STDY5531906UnknownERR351527
162STDY5531905UnknownERR351526
162STDY5531904UnknownERR351525
162STDY5531903UnknownERR351524
162STDY5531902UnknownERR351523
162STDY5531901UnknownERR351522
162STDY5531817UnknownERR348847
162STDY5531816UnknownERR348846
162STDY5531815UnknownERR348845
162STDY5531814UnknownERR348844
162STDY5531813UnknownERR348843
162STDY5531812UnknownERR348842
162STDY5531811UnknownERR348841
162STDY5531810UnknownERR348840
162STDY5531809UnknownERR348839
162STDY5531808UnknownERR348838
162STDY5531807UnknownERR348837
162STDY5531806UnknownERR348836
162STDY5531805UnknownERR348835
162STDY5592966UnknownERR386233
162STDY5592958UnknownERR386232
162STDY5591721UnknownERR386231
162STDY5591720UnknownERR386230
162STDY5591719UnknownERR386229
162STDY5591717UnknownERR386228
162STDY5591716UnknownERR386227
162STDY5591714UnknownERR386225
162STDY5591713UnknownERR386224
162STDY5591712UnknownERR386223
162STDY5591711UnknownERR386222
162STDY5669675UnknownERR459472
162STDY5669674UnknownERR459471
162STDY5669673UnknownERR459470
162STDY5669672UnknownERR459469
162STDY5669671UnknownERR459468
162STDY5669670UnknownERR459467
162STDY5669669UnknownERR459466
162STDY5669668UnknownERR459465
162STDY5669667UnknownERR459464
162STDY5669666UnknownERR459463
162STDY5669665UnknownERR459462
162STDY5669664UnknownERR459461
162STDY5669663UnknownERR459460
162STDY5669662UnknownERR459459
162STDY5669680UnknownERR516394
162STDY5669679UnknownERR516393
162STDY5669678UnknownERR516392
162STDY5669677UnknownERR516391
162STDY5669676UnknownERR516390

Chlamydia trachomatis Sure Select V1

Sample

Strain

Run Accession

SC_CTRAC5363715L2b/UCH-1/proctitisERR164847
SC_CTRAC5363714L2b/UCH-1/proctitisERR164846
SC_CTRAC5363707L2b/UCH-1/proctitisERR164844
SC_CTRAC5363706L2b/UCH-1/proctitisERR164843
SC_CTRAC5363705L2b/UCH-1/proctitisERR164842
SC_CTRAC5363704L2b/UCH-1/proctitisERR164841
SC_CTRAC5363703L2b/UCH-1/proctitisERR164840
SC_CTRAC5363702L2b/UCH-1/proctitisERR164839
SC_CTRAC5363701L2b/UCH-1/proctitisERR164838
SC_CTRAC5363700L2b/UCH-1/proctitisERR164837
SC_CTRAC5363699L2b/UCH-1/proctitisERR164836
SC_CTRAC5363698L2b/UCH-1/proctitisERR164835
SC_CTRAC5363708L2b/UCH-1/proctitisERR164845

Chlamydia trachomatis pilot

Sample

Strain

Run Accession

sw1_1507swab1_150710ERR024694
sw2_1507swab2_150710ERR024698
sw3_1507swab3_150710ERR024699
sw5_1507swab5_150710ERR024700
sw6_1507swab6_150710ERR024701
sw7_1507swab7_150710ERR024702
sw8_1507swab8_150710ERR024703
Fr4_10_3Fr4_10_3ERR024704
Fr4_10_4Fr4_10_4ERR024705
Fr4_10_5Fr4_10_5ERR024695
Fr4_10_6Fr4_10_6ERR024696
Fr4_10_7Fr4_10_7ERR024697
U3IM2311U3IM2311ERR034208
B11IM23B11IM23ERR034212
363MDA363MDAERR034213
5291MDA5291MDAERR034214
7249MDA7249MDAERR034215
25a50425a504ERR034216
25D501625D5016ERR034217
25a501625a5016ERR034218
1000038710000387ERR034219
16H45sp16H45spERR034209
16TT30sp16TT30spERR034210
16TT45sp16TT45spERR034211
MH858MH858ERR175560
MH2145MH2145ERR175561
MH2497MH2497ERR175562
MH5368MH5368ERR175563
MH5786MH5786ERR175564
MH12023MH12023ERR175565
MH13849MH13849ERR175566
MH14553MH14553ERR175567
MH16005MH16005ERR175568
MH18843MH18843ERR175569
MH19657MH19657ERR175570
MH23527MH23527ERR175571
MH24673MH24673ERR175572
MH25256MH25256ERR175573
MH47300MH47300ERR175574
MH1364MH1364ERR175575
MH3234MH3234ERR175576
MH4510MH4510ERR175577
MH6446MH6446ERR175578
MH7205MH7205ERR175579
MH8910MH8910ERR175580
MH9922MH9922ERR175581
MH10549MH10549ERR175582
MH10648MH10648ERR175583
MH10901MH10901ERR175584
MH11715MH11715ERR175585
MH11979MH11979ERR175586
MH15048MH15048ERR175587
MH15741MH15741ERR175588
MH16170MH16170ERR175589
MH16665MH16665ERR175590
MH17127MH17127ERR175591
MH18876MH18876ERR175592
MH19679MH19679ERR175593
MH20130MH20130ERR175594
MH20933MH20933ERR175595
MH21571MH21571ERR175596
MH24519MH24519ERR175597
MH24640MH24640ERR175598
MH25883MH25883ERR175599
MH26862MH26862ERR175600
MH27137MH27137ERR175601
MH34496MH34496ERR175602
MH35739MH35739ERR175603
MH53658MH53658ERR175604
BIP39BIP39ERR175605
BIP195BIP195ERR175606
BIP312BIP312ERR175607
swab6swab6ERR175608
Mol39MDAMol39MDAERR558490
BIP403MDABIP403MDAERR558491
BIP780MMBIP780MMERR558492
SotU3SotU3ERR558493
DIOL1883DIOL1883ERR558494
EDK20EDK20ERR558495
GIOL238GIOL238ERR558496
HUW4HUW4ERR558497
ASA1ASA1ERR558498
CTW3CTW3ERR558499
IU824IU824ERR558500
IU888IU888ERR558501
ASA1MDAASA1MDAERR558502
CTW3MDACTW3MDAERR558503
JUW36MDAJUW36MDAERR558504
KUW31MDAKUW31MDAERR558505
CUW1OTMDACUW1OTMDAERR558506
Syn1ASyn1AERR558507
U3IMS13U3IMS13ERR558508
B1IMS13B1IMS13ERR173901
B11IMS13B11IMS13ERR173902
12_2MDA12_2MDAERR173903
12_3MDA12_3MDAERR173904
12_4MDA12_4MDAERR173905
12_5MDA12_5MDAERR173906
24_2MDA24_2MDAERR173907
24_3MDA24_3MDAERR173908
24_4MDA24_4MDAERR173909
24_5MDA24_5MDAERR173910
SOTONE2SOTONE2ERR175612
IMSDB11UnknownERR175613
IMSDU4UnknownERR175614
B4_7JunUnknownERR175615
B8_7JunUnknownERR175616
C4IMSUnknownERR175617
C5IMSUnknownERR175618
C7IMSUnknownERR175619
C8IMSUnknownERR175620
C32IMSUnknownERR175621
C33IMSUnknownERR175622
C37IMSUnknownERR175623
C38IMSUnknownERR175624
C55IMSUnknownERR175625
C58IMSUnknownERR175626
C75IMSUnknownERR175627
C79IMSUnknownERR175628
C114IMSUnknownERR175629
CUW1OTUnknownERR175630
M48UnknownERR175631
9922UnknownERR175632
RB10392UnknownERR175633
UB2UnknownERR175634
UB4UnknownERR175635
C133UnknownERR175636
C153UnknownERR175637
C194UnknownERR175638
C195UnknownERR175639
C208aUnknownERR175640
C224UnknownERR175641
C230UnknownERR175642
C236UnknownERR175643
C237UnknownERR175644
C239UnknownERR175645
C258UnknownERR175646
C261UnknownERR175647
C266UnknownERR175648
CUW1newUnknownERR175649
NI1UnknownERR175650
M48newUnknownERR175651
D213UnknownERR175652
363UnknownERR175653
9922newUnknownERR175654
  • 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

  • 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

  • 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

  • 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

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.

Sequencing enquiries

Please address all sequencing enquiries to: pathinfo@sanger.ac.uk

* quick link - http://q.sanger.ac.uk/j7rt8oo5