Clostridium difficile

Clostridium difficile is a major nosocomial pathogen world-wide causing disease ranging from antibiotic-associated diarrhoea to life-threatening pseudomembranous colitis.

Data Downloads

[Genome Research Limited]

We have completed the genome sequencing of Clostridium difficile strain 630. Strain 630 is multi-drug resistant, and was isolated from a patient with severe PMC that had spread to dozens of other patients on the same ward in Zurich, Switzerland in 1982. Thus strain 630 has the genetic attributes of a fully virulent, highly transmissible, drug resistant strain. This work was carried out in collaboration with Brendan Wren of the London School of Hygiene and Tropical Medicine, Neil Fairweather and Gordon Dougan of the Centre for Molecular Microbiology and Infection, Imperial College, London and Peter Mullany of the Eastman Dental Institute, London.

We have also sequenced several other strains of C. difficile, including C. difficile strain R20291 (SM), C. difficile strain 196, C. difficile strain BI1, C. difficile strain M120 and C. difficile strain M68.

Published Genome Data

Published Reference Genome

The Sanger Institute completed the sequencing of Clostridium difficile strain 630 (epidemic type X) in 2006. The genome consists of a circular chromosome of 4,290,252 bp with a G+C content of 29.06%, and a circular plasmid of 7,881 bp with a G+C content of 27.9%. The fully annotated chromosome and plasmid are available from the EMBL/GenBank databases with accession numbers AM180355 and AM180356 respectively. Using a combined transcriptomic and proteomic approach the annotation of Clostridium difficile strain 630 has been updated in 2014 and is available as an embl file. This embl file contains functional class and colour annotation characterising genes into broad functional groups that is not present on the updated EMBL/GenBank version. The embl file along with the key to the colour and class annotation is available from our FTP site. The original shotgun and assembly data can also still be accessed here. The embl file can be interrogated using Artemis which is available as a free download from the Related links on this page.


Other Published Genomes

The Sanger Institute has completed sequencing and assembly of several further strains of C. difficile as follows :

C. difficile strain 196

  • Isolated: France, 1985 (Ribotype 027)
  • Shotgun: 33,509 reads totalling 20.887 Mb, theoretical genome coverage of 99.26%
  • Assembly/Annotation: FN538970

C. difficile strain BI1

  • Isolated: USA, 1988 (Ribotype 027)
  • Shotgun: 34,428 reads totalling 21.622 Mb, theoretical genome coverage of 99.33%
  • Assembly/Annotation: FN668941, FN668942, FN668943

C. difficile strain M120

  • Isolated: UK, 2007 (Ribotype 078)
  • Shotgun: 32,381 reads totalling 21.754 Mb, theoretical genome coverage of 99.33%
  • Assembly/Annotation: FN665653

C. difficile strain M68

  • Isolated: Ireland, 2006 (Ribotype 017)
  • Shotgun: 29,958 reads totalling 18.975 Mb, theoretical genome coverage of 98.77%
  • Assembly/Annotation: FN668375

C. difficile strain SM (R20291)

  • Isolated: UK, 2006 (Ribotype 027)
  • Shotgun: 34,018 reads totalling 22.599 Mb, theoretical genome coverage of 99.45%
  • Assembly/Annotation: FN545816

C. difficile strain CF5

  • Isolated: Belgium, 1995 (Ribotype 017)
  • Shotgun: 34,226 reads totalling 23.359 Mb, theoretical genome coverage of 99.99%
  • Assembly/Annotation: FN665652

C. difficile strain 855

  • Isolated: USA, 2007 (Ribotype 027)
  • Shotgun: 33,918 reads totalling 22.907 Mb, theoretical genome coverage of 99.99%
  • Assembly/Annotation: FN665654

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

Studies

Clostridium difficile Ribotype Reference Genome Project

Sample

Strain

Run Accession

cd001001ERR017370
cd002002ERR017368
cd014014ERR017369
cd015015ERR022513
cd023023ERR017367
cd106106ERR017371
clo01UnknownERR125956
clo02UnknownERR125957
clo03UnknownERR125958
clo04UnknownERR125959
clo05UnknownERR125960
clo06UnknownERR125961
clo07UnknownERR125962
clo08UnknownERR125963
clo09UnknownERR125964
clo10UnknownERR125965
clo11UnknownERR125966
clo12UnknownERR125967
clo13UnknownERR125968
clo14UnknownERR125969
clo15UnknownERR125970
clo16UnknownERR125971
clo17UnknownERR125972
clo18UnknownERR125973
clo19UnknownERR125974
clo21UnknownERR125975
clo22UnknownERR125976
clo23UnknownERR125977
clo24UnknownERR125978
clo25UnknownERR125979
clo26UnknownERR125980
clo27UnknownERR125981
clo28UnknownERR125982
clo30UnknownERR125983
clo31UnknownERR125984
clo32UnknownERR125985
clo33UnknownERR125986
clo34UnknownERR125987
clo35UnknownERR125988
clo36UnknownERR125989
clo37UnknownERR125990
clo38UnknownERR125991
clo39UnknownERR125992
clo40UnknownERR125993
clo41UnknownERR125994
clo42UnknownERR125995
lsh01UnknownERR125996
lsh04UnknownERR125997
lsh06UnknownERR125998
lsh07UnknownERR125999
lsh08UnknownERR126000
lsh09UnknownERR126001
lsh10UnknownERR126002
lsh11UnknownERR126003
lsh12UnknownERR125908
lsh13UnknownERR125909
lsh14UnknownERR125910
lsh15UnknownERR125911
lsh16UnknownERR125912
lsh17UnknownERR125913
lsh18UnknownERR125914
lsh20UnknownERR125915
lsh21UnknownERR125916
lsh22UnknownERR125917
lsh23UnknownERR125918
lsh24UnknownERR125919
lsh25UnknownERR125920
lsh26UnknownERR125921
lsh27UnknownERR125922
lsh28UnknownERR125923
lsh29UnknownERR125924
lsh30UnknownERR125925
lsh31UnknownERR125926
lsh32UnknownERR125927
lsh33UnknownERR125928
lsh34UnknownERR125929
lsh35UnknownERR125930
lsh36UnknownERR125931
lsh37UnknownERR125932
lsh38UnknownERR125933
lsh39UnknownERR125934
lsh40UnknownERR125935
lsh41UnknownERR125936
Den001UnknownERR125937
Den002UnknownERR125938
Den003UnknownERR125939
Den004UnknownERR125940
Den005UnknownERR125941
Den006UnknownERR125942
Den007UnknownERR125943
Den008UnknownERR125944
Den009UnknownERR125945
Den010UnknownERR125946
tl291UnknownERR125947
tl292UnknownERR125948
tl293UnknownERR125949
tl294UnknownERR125950
R711UnknownERR125951
TA8UnknownERR125952
TA9UnknownERR125953
TA10UnknownERR125954
TA11UnknownERR125955

Clostridium difficile genomic stability

Sample

Strain

Run Accession

M001BI-7ERR024996
M002BI-7ERR025000
M003BI-7ERR025001
M004BI-7ERR025002
M005BI-7ERR025003
M006BI-7ERR025004
M007BI-7ERR025005
M008BI-7ERR025006
M009BI-7ERR025007
M010BI-7ERR024997
M011BI-7ERR024998
M012BI-7ERR024999
M013BI-7ERR025009
M014BI-7ERR025013
M015BI-7ERR025014
M016BI-7ERR025015
M017BI-7ERR025016
M018BI-7ERR025017
M019BI-7ERR025018
M020BI-7ERR025019
M021BI-7ERR025020
M022BI-7ERR025010
M023BI-7ERR025011
M024BI-7ERR025012
M025BI-7ERR025022
M026BI-7ERR025026
M027BI-7ERR025027
M028BI-7ERR025028
M029BI-7ERR025029
M030BI-7ERR025030
M031BI-7ERR025031
M032BI-7ERR025032
M033BI-7ERR025033
M034BI-7ERR025023
M035BI-7ERR025024
M036BI-7ERR025025
M037BI-7ERR025035
M038BI-7ERR025039
M039BI-7ERR025040
M040BI-7ERR025041
M041BI-7ERR025042
M042BI-7ERR025043
M043BI-7ERR025044
M044BI-7ERR025045
M045BI-7ERR025046
M046BI-7ERR025036
M047BI-7ERR025037
M048BI-7ERR025038
M049BI-7ERR025048
M050BI-7ERR025052
M051BI-7ERR025053
M052BI-7ERR025054
M053BI-7ERR025055
M054BI-7ERR025056
M055BI-7ERR025057
M056BI-7ERR025058
M057BI-7ERR025059
M058BI-7ERR025049
M059BI-7ERR025050
M060BI-7ERR025051
M061BI-7ERR025061
M062BI-7ERR025065
M063BI-7ERR025066
M064BI-7ERR025067
M065BI-7ERR025068
M066BI-7ERR025069
M067BI-7ERR025070
M068BI-7ERR025071
M069BI-7ERR025072
M070BI-7ERR025062
M071BI-7ERR025063
M072BI-7ERR025064
M073BI-7ERR025330
M074BI-7ERR025334
M075BI-7ERR025335
M076BI-7ERR025336
M077BI-7ERR025337
M078BI-7ERR025338
M079BI-7ERR025339
M080BI-7ERR025340
M081BI-7ERR025341
M082BI-7ERR025331
M083BI-7ERR025332
M084BI-7ERR025333

Clostridium difficile ribotype 027 resequencing

Sample

Strain

Run Accession

CD196b027ERR026352
Liv38027ERR026356
Liv39027ERR026357
Liv40027ERR026358
Liv41027ERR026359
Liv42027ERR026360
Liv43027ERR026361
Liv48027ERR026362
Liv49027ERR026363
Liv050027ERR026353
Liv051027ERR026354
Liv052027ERR026355
Liv053027ERR026365
Liv054027ERR026369
Liv055027ERR026370
Liv056027ERR026371
Liv057027ERR026372
Liv058027ERR026373
Liv059027ERR026374
Liv060027ERR026375
Liv061027ERR026376
Liv062027ERR026366
Liv063027ERR026367
Liv064027ERR026368
Liv065027ERR028721
Liv066027ERR028725
Liv067027ERR028726
Liv068027ERR028727
Liv069027ERR028728
Liv070027ERR028729
Liv071027ERR028730
Liv072027ERR028731
Liv073027ERR028732
Liv074027ERR028722
CD196c027ERR028723
Liv075027ERR028724
Liv076027ERR026378
Liv077027ERR026382
Liv078027ERR026383
Liv079027ERR026384
Liv080027ERR026385
Liv081027ERR026386
Liv082027ERR026387
Liv083027ERR026388
Liv084027ERR026389
Liv085027ERR026379
Liv086027ERR026380
Liv087027ERR026381
Liv088027ERR026391
Liv089027ERR026395
Liv090027ERR026396
Liv091027ERR026397
Liv092027ERR026398
Liv093027ERR026399
Liv094027ERR026400
Liv095027ERR026401
CD196d027ERR026402
Liv096027ERR026392
Liv097027ERR026393
Liv098027ERR026394
Liv099027ERR026404
Liv100027ERR026408
Liv101027ERR026409
Liv102027ERR026410
Liv103027ERR026411
Liv104027ERR026412
Liv127027ERR026413
Liv131027ERR026414
Liv132027ERR026415
Liv136027ERR026405
Sin001027ERR026406
Sin002027ERR026407
Sin003027ERR025343
Bel023027ERR025347
Bel024027ERR025348
Bel025027ERR025349
R20291d027ERR025350
Bel026027ERR025351
Bel027027ERR025352
Bel028027ERR025353
Bel029027ERR025354
Bel030027ERR025344
Bel031027ERR025345
Bel032027ERR025346
Bel033027ERR026417
ham001027ERR026421
ham002027ERR026422
ham003027ERR026423
ham006027ERR026426
ham007027ERR026427
ham008027ERR026428
ham009027ERR026418
ham010027ERR026419
ham011027ERR026420
Cam001027ERR026830
Cam002027ERR026834
Cam003027ERR026835
Cam004027ERR026836
Cam005027ERR026837
Cam006027ERR026838
Cam007027ERR026839
Cam008027ERR026840
Cam009027ERR026841
Cam010027ERR026831
Cam011027ERR026832
Cam012027ERR026833
Cam013027ERR026869
Cam014027ERR026873
Cam015027ERR026874
Cam016027ERR026875
R20291e027ERR026876
Cam017027ERR026877
Cam018027ERR026878
Cam019027ERR026879
Cam020027ERR026880
Cam021027ERR026870
Cam022027ERR026871
Cam023027ERR026872
Cam024027ERR026856
Cam025027ERR026860
Cam026027ERR026861
Cam027027ERR026862
Cam028027ERR026863
Cam029027ERR026864
Cam030027ERR026865
Cam031027ERR026866
Cam032027ERR026867
Cam033027ERR026857
Cam034027ERR026858
Cam035027ERR026859
Cam036027ERR026843
Cam037027ERR026847
Cam038027ERR026848
Cam039027ERR026849
lon001027ERR026850
lon002027ERR026851
R20291f027ERR026852
lon003027ERR026853
lon004027ERR026854
lon005027ERR026844
lon006027ERR026845
lon007027ERR026846
ham004027ERR026424
ham005027ERR026425

Clostridium difficile ribotype 027 resequencing II

Sample

Strain

Run Accession

R20291_1027ERR031674
Exe001027ERR031678
Exe002027ERR031679
Exe003027ERR031680
Exe004027ERR031681
Exe005027ERR031682
Exe006027ERR031683
Exe009027ERR031684
Exe010027ERR031685
Exe011027ERR031675
Exe012027ERR031676
Exe013027ERR031677
Exe014027ERR029481
Exe015027ERR029485
R20291_2027ERR029486
ham003a027ERR029487
Aus001027ERR029488
Aus002027ERR029489
Aus003027ERR029490
Aus004027ERR029491
Aus005027ERR029492
Aus006027ERR029482
wal001027ERR029483
Wal002027ERR029484
Bir001027ERR030283
Bir002027ERR030287
Bir003027ERR030288
R20291_3027ERR030289
Bir004027ERR030290
Bir005027ERR030291
Bir006027ERR030292
Bir007027ERR030293
Bir008027ERR030294
Bir009027ERR030284
Bir010027ERR030285
Bir011027ERR030286
Bir012027ERR030296
Bir013027ERR030300
Bir014027ERR030301
Bir015027ERR030302
R20291_4027ERR030303
Bir016027ERR030304
Bir017027ERR030305
Bir018027ERR030306
Bir019027ERR030307
Bir020027ERR030297
Bir021027ERR030298
Bir022027ERR030299
Bir023027ERR029494
Bir024027ERR029498
Bir025027ERR029499
Bir026027ERR029500
Bir027027ERR029501
R20291_5027ERR029502
Bir028027ERR029503
Bir029027ERR029504
Bir030027ERR029505
Bir031027ERR029495
Bir032027ERR029496
Bir033027ERR029497
Bir034027ERR030322
Bir035027ERR030326
Bir036027ERR030327
Bir037027ERR030328
Bir038027ERR030329
Bir039027ERR030330
R20291_6027ERR030331
HK034027ERR030332
BI-2027ERR030333
BI-3027ERR030323
BI-10027ERR030324
Can001027ERR030325
Can002027ERR030335
Can003027ERR030339
Can004027ERR030340
Can005027ERR030341
Can006027ERR030342
Can007027ERR030343
Can007027ERR034221
Can008027ERR030344
CD196e027ERR030345
Can009027ERR030346
Can010027ERR030336
Can011027ERR030337
Can012027ERR030338
Can012027ERR034222
Liv145027ERR030348
Liv145027ERR034223
Liv146027ERR030352
Liv147027ERR030353
Liv148027ERR030354
Liv149027ERR030355
Liv150027ERR030356
Liv150027ERR034224
Liv151027ERR030357
Liv152027ERR030358
CD196f027ERR030359
Liv153027ERR030349
Liv154027ERR030350
Liv155027ERR030351
Liv155027ERR034225
Liv156027ERR030361
Liv157027ERR030365
Liv158027ERR030366
Liv159027ERR030367
CD196g027ERR030368
Liv160027ERR030369
Liv160027ERR034226
Liv161027ERR030370
Liv162027ERR030371
Liv163027ERR030372
Liv164027ERR030362
Liv165027ERR030363
Liv166027ERR030364
Liv166027ERR034227
Liv167027ERR030309
Liv168027ERR030313
Liv169027ERR030314
Liv170027ERR030315
Liv171027ERR030316
Liv172027ERR030317
Liv172027ERR034228
Liv173027ERR030318
CD196h027ERR030319
Liv174027ERR030320
Liv175027ERR030310
Liv176027ERR030311
Liv177027ERR030312
Liv178027ERR030387
Liv179027ERR030391
Liv180027ERR030392
Liv181027ERR030393
Liv182027ERR030394
Liv183027ERR030395
Liv184027ERR030396
CD196i027ERR030397
Liv185027ERR030398
Liv186027ERR030388
Liv187027ERR030389
Liv188027ERR030390
Liv189027ERR030374
Liv190027ERR030378
Ham004027ERR030379
Ham005027ERR030380
Cam018a027ERR030381
Cam038a027ERR030382
Liv039027ERR030383
Liv050a027ERR030384
CD196j027ERR030385
Liv016027ERR030375
Liv017027ERR030376
Liv018027ERR030377
Liv019027ERR031687
Liv020027ERR031691
Liv021027ERR031692
M7404027ERR031693
ham010a027ERR031694
Liv005027ERR031695
CD196k027ERR031696
Liv008027ERR031697
Liv009027ERR031698
kor001027ERR031688
kor002027ERR031689
kor003027ERR031690
kor004027ERR029507
kor005027ERR029511
kor006027ERR029512
LSTM001027ERR029513
LSTM002027ERR029514
LSTM003027ERR029515
LSTM004027ERR029516
LSTM005027ERR029517
LSTM006027ERR029518
CD196l027ERR029508
LSTM007027ERR029509
LSTM008027ERR029510
LSTM009027ERR029520
LSTM010027ERR029524
LSTM011027ERR029525
LSTM012027ERR029526
LSTM013027ERR029527
LSTM014027ERR029528
CD196m027ERR029529
LSTM015027ERR029530
LSTM016027ERR029531
LSTM017027ERR029521
LSTM018027ERR029522
LSTM019027ERR029523
LSTM020027ERR029533
LSTM021027ERR029537
LSTM022027ERR029538
LSTM023027ERR029539
LSTM024027ERR029540
CD196n027ERR029541
LSTM025027ERR029542
LSTM026027ERR029543
LSTM027027ERR029544
LSTM028027ERR029534
LSTM029027ERR029535
LSTM030027ERR029536
LSTM031027ERR031700
LSTM032027ERR031704
LSTM33027ERR031705
LSTM34027ERR031706
LSTM35027ERR031707
LSTM36027ERR031708
LSTM37027ERR031709
LSTM38027ERR031710
CD196o027ERR031711
Liv3a027ERR031701
Liv6a027ERR031702
Liv10a027ERR031703
Lei001027ERR044825
Lei002027ERR044826
Lei003027ERR044827
Lei004027ERR044828
Lei006027ERR044829
Lei007027ERR044830
Lei008027ERR044831
Lei009027ERR044832
Lei010027ERR044833
Lei011027ERR044834
Lei012027ERR044835
R20291_7027ERR044836
Lei013027ERR044837
Lei014027ERR044838
Lei015027ERR044839
Lei016027ERR044840
Lei017027ERR044841
Lei018027ERR044842
Lei019027ERR044843
Lei020027ERR044844
Lei021027ERR044845
Lei022027ERR044846
Lei023027ERR044847
Lei024027ERR044848
Lei025027ERR044801
Lei026027ERR044802
Lei027027ERR044803
Lei028027ERR044804
Lei029027ERR044805
Lei030027ERR044806
Lei031027ERR044807
Lei032027ERR044808
Lei033027ERR044809
Lei034027ERR044810
Lei035027ERR044811
Lei036027ERR044812
R20291_8027ERR044813
Jap001027ERR044814
Jap002027ERR044815
Jap003027ERR044816
Jap004027ERR044817
Jap005027ERR044818
M7404-1027ERR044819
M7404-2027ERR044820
M7404-3027ERR044821
M7404-4027ERR044822
M7404-5027ERR044823
M7404-6027ERR044824
LD01UnknownERR658291
LD02UnknownERR658292
LD03UnknownERR658293
LD04UnknownERR658294
LD05UnknownERR658295
LD06UnknownERR658296
LD07UnknownERR658297
LD08UnknownERR658298
LD09UnknownERR658299
LD10UnknownERR658300
MM01UnknownERR658301
MM02UnknownERR658302
MM03UnknownERR658303
MM04UnknownERR658304
MM05UnknownERR658305
MM06UnknownERR658306
MM07UnknownERR658307
TA01UnknownERR658308
TA02UnknownERR658309
TA03UnknownERR658310
TA04UnknownERR658311
TA05UnknownERR658312
TA06UnknownERR658313
TA07UnknownERR658314

Clostridium difficile 078 diversity

Sample

Strain

Run Accession

078LVP025UnknownERR171245
078LVP023UnknownERR171243
078LVP022UnknownERR171242
078LVP021UnknownERR171241
078LVP020UnknownERR171240
078LVP019UnknownERR171239
078LVP018UnknownERR171238
078LVP017UnknownERR171237
078LVP016UnknownERR171236
078LVP015UnknownERR171235
078LVP014UnknownERR171234
078LVP013UnknownERR171233
078LVP012UnknownERR171232
078LVP011UnknownERR171231
078LVP010UnknownERR171230
078LVP009UnknownERR171229
078LVP008UnknownERR171228
078LVP007UnknownERR171227
078LVP006UnknownERR171226
078LVP005UnknownERR171225
078LVP004UnknownERR171224
078LVP003UnknownERR171223
078LVP002UnknownERR171222
078LVP001UnknownERR171221
078GUE043UnknownERR171220
078GUE042UnknownERR171219
078GUE041UnknownERR171218
078GUE040UnknownERR171217
078GUE039UnknownERR171216
078GUE038UnknownERR171215
078GUE037UnknownERR171214
078GUE036UnknownERR171213
078GUE035UnknownERR171212
078GUE034UnknownERR171211
078GUE033UnknownERR171210
078GUE032UnknownERR171209
078GUE031UnknownERR171208
078GUE030UnknownERR171207
078GUE029UnknownERR171206
078GUE028UnknownERR171205
078GUE027UnknownERR171204
078GUE026UnknownERR171203
078GUE025UnknownERR171202
078GUE024UnknownERR171201
078GUE023UnknownERR171200
078GUE022UnknownERR171199
078GUE020UnknownERR171197
078GUE019UnknownERR171196
078GUE018UnknownERR171195
078GUE017UnknownERR171194
078GUE016UnknownERR171193
078GUE015UnknownERR171192
078GUE014UnknownERR171191
078GUE013UnknownERR171190
078GUE012UnknownERR171381
078GUE011UnknownERR171380
078GUE010UnknownERR171379
078GUE009UnknownERR171378
078GUE008UnknownERR171377
078GUE007UnknownERR171376
078GUE006UnknownERR171375
078GUE005UnknownERR171374
078GUE004UnknownERR171373
078GUE003UnknownERR171372
078GUE002UnknownERR171371
078GUE001UnknownERR171370
078NET085UnknownERR171369
078NET084UnknownERR171368
078NET083UnknownERR171367
078NET082UnknownERR171366
078NET081UnknownERR171365
078NET080UnknownERR171364
078NET079UnknownERR171363
078NET078UnknownERR171362
078NET077UnknownERR171361
078NET076UnknownERR171360
078NET075UnknownERR171359
078NET074UnknownERR171358
078NET073UnknownERR171357
078NET072UnknownERR171356
078NET071UnknownERR171355
078NET070UnknownERR171354
078NET069UnknownERR171353
078NET068UnknownERR171352
078NET067UnknownERR171351
078NET066UnknownERR171350
078NET065UnknownERR171349
078NET064UnknownERR171348
078NET063UnknownERR171347
078NET062UnknownERR171346
078NET061UnknownERR171345
078NET060UnknownERR171344
078NET058UnknownERR171343
078NET057UnknownERR171342
078NET056UnknownERR171341
078NET055UnknownERR171340
078NET054UnknownERR171339
078NET053UnknownERR171338
078NET052UnknownERR171337
078NET051UnknownERR171336
078NET050UnknownERR171335
078NET049UnknownERR171334
078NET047UnknownERR171332
078NET046UnknownERR171331
078NET045UnknownERR171330
078NET044UnknownERR171329
078NET043UnknownERR171328
078NET042UnknownERR171327
078NET041UnknownERR171326
078NET040UnknownERR171325
078NET039UnknownERR171324
078NET038UnknownERR171323
078NET037UnknownERR171322
078NET036UnknownERR171321
078NET035UnknownERR171320
078NET034UnknownERR171319
078NET033UnknownERR171318
078NET032UnknownERR171317
078NET031UnknownERR171316
078NET030UnknownERR171315
078NET029UnknownERR171314
078NET028UnknownERR171313
078NET027UnknownERR171312
078NET026UnknownERR171311
078NET025UnknownERR171310
078NET024UnknownERR171309
078NET023UnknownERR171308
078NET022UnknownERR171307
078NET021UnknownERR171306
078NET020UnknownERR171305
078NET019UnknownERR171304
078NET018UnknownERR171303
078NET017UnknownERR171302
078NET016UnknownERR171301
078NET015UnknownERR171300
078NET014UnknownERR171299
078NET013UnknownERR171298
078NET012UnknownERR171297
078NET011UnknownERR171296
078NET010UnknownERR171295
078NET009UnknownERR171294
078NET008UnknownERR171293
078NET007UnknownERR171292
078NET006UnknownERR171291
078NET005UnknownERR171290
078NET004UnknownERR171289
078NET003UnknownERR171288
078NET002UnknownERR171287
078NET001UnknownERR171286
AgrA_MM_12UnknownERR171284
078GUE021UnknownERR171198
2213STDY5419812UK 127 (AU 011)ERR247091
2213STDY5419811UK 033 (AU 012)ERR247090
2213STDY5419810AU 259ERR247089
2213STDY5419809UK 033 (AU 012)ERR247088
2213STDY5419808AU 169ERR247087
2213STDY5419807UK 063 (AU 003)ERR247086
2213STDY5419806AU 022ERR247085
2213STDY5419805UK 127 (AU 011)ERR247084
2213STDY5419804UK 126 (AU 014)ERR247083
2213STDY5419803UK 237ERR247082
2213STDY5419802AU 137ERR247081
2213STDY5419801RT291ERR247080
2213STDY5419800RT239ERR247079
2213STDY5419799RT127ERR247078
2213STDY5419798RT126ERR247077
2213STDY5419797RT237ERR247076
2213STDY5419796RT078ERR247075
2213STDY5419795NTERR247074
2213STDY5419794RT078ERR247073
2213STDY5419793RT078ERR247072
2213STDY5419792RT126ERR247071
2213STDY5419791RT078ERR247070
2213STDY5419790078ERR247069
2213STDY5419789078ERR247068
2213STDY5419788078ERR247067
2213STDY5419787020ERR247066
2213STDY5419786002ERR247065
2213STDY5419785056ERR247064
2213STDY5419784078ERR247063
2213STDY5419783020ERR247062
2213STDY5419782078ERR247061
2213STDY5419781078ERR247060
2213STDY5419780078ERR247059
2213STDY5419779078ERR247058
2213STDY5419778078ERR247057
2213STDY5419777002ERR247056
2213STDY5419776002ERR247055
2213STDY5419775078ERR247054
2213STDY5419774078ERR247053
2213STDY5419773078ERR247052
2213STDY5419772078ERR247051
2213STDY5419771078ERR247050
2213STDY5419766078ERR247045
2213STDY5419765078ERR247044
2213STDY5419764078ERR247043
2213STDY5419763087ERR247042
2213STDY5419762031ERR247041
2213STDY5419857078ERR247136
2213STDY5419856078ERR247135
2213STDY5419855078ERR247134
2213STDY5419854078ERR247133
2213STDY5419853078ERR247132
2213STDY5419852078ERR247131
2213STDY5419851078ERR247130
2213STDY5419850078ERR247129
2213STDY5419849078ERR247128
2213STDY5419848078ERR247127
2213STDY5419847078ERR247126
2213STDY5419846078ERR247125
2213STDY5419845078ERR247124
2213STDY5419844078ERR247123
2213STDY5419843078ERR247122
2213STDY5419842078ERR247121
2213STDY5419841078ERR247120
2213STDY5419840UK 078 (AU 009)ERR247119
2213STDY5419839UK 127 (AU 002)ERR247118
2213STDY5419838UK 127 (AU 011)ERR247117
2213STDY5419837UK 033 (AU 012)ERR247116
2213STDY5419836UK 078 (AU 009)ERR247115
2213STDY5419835UK 127 (AU 011)ERR247114
2213STDY5419834UK 127 (AU 002)ERR247113
2213STDY5419833UK 126 (AU 014)ERR247112
2213STDY5419832UK 126 (AU 014)ERR247111
2213STDY5419831UK 078 (AU 009)ERR247110
2213STDY5419830UK 078 (AU 009)ERR247109
2213STDY5419829UK 033 (AU 012)ERR247108
2213STDY5419828UK 033 (AU 012)ERR247107
2213STDY5419827UK 033 (AU 012)ERR247106
2213STDY5419826UK 033 (AU 012)ERR247105
2213STDY5419825UK 033 (AU 012)ERR247104
2213STDY5419824UK 033 (AU 012)ERR247103
2213STDY5419823UK 033 (AU 012)ERR247102
2213STDY5419822UK 078 (AU 009)ERR247101
2213STDY5419821UK 078 (AU 009)ERR247100
2213STDY5419820UK 078 (AU 009)ERR247099
2213STDY5419819UK 127 (AU 011)ERR247098
2213STDY5419818UK 126 (AU 014)ERR247097
2213STDY5419817UK 126 (AU 014)ERR247096
2213STDY5419816UK 288 (AU 079)ERR247095
2213STDY5419815UK 126 (AU 014)ERR247094
2213STDY5419814UK 127 (AU 002)ERR247093
2213STDY5419813UK 063 (AU 003)ERR247092
2213STDY5419770078ERR247049
2213STDY5419769078ERR247048
2213STDY5419768078ERR247047
2213STDY5419767078ERR247046
2213STDY5419875078ERR256911
2213STDY5419874078ERR256910
2213STDY5419873078ERR256909
2213STDY5419872078ERR256908
2213STDY5419871078ERR256907
2213STDY5419870078ERR256906
2213STDY5419869078ERR256905
2213STDY5419868078ERR256904
2213STDY5419867078ERR256903
2213STDY5419858078ERR256894
2213STDY5419953078ERR256989
2213STDY5419952078ERR256988
2213STDY5419951078ERR256987
2213STDY5419950078ERR256986
2213STDY5419949078ERR256985
2213STDY5419948078ERR256984
2213STDY5419947078ERR256983
2213STDY5419946078ERR256982
2213STDY5419945078ERR256981
2213STDY5419944078ERR256980
2213STDY541994376ERR256979
2213STDY541994276ERR256978
2213STDY541994176ERR256977
2213STDY541994076ERR256976
2213STDY541993976ERR256975
2213STDY541993876ERR256974
2213STDY541993776ERR256973
2213STDY541993676ERR256972
2213STDY5419935UnknownERR256971
2213STDY541993421ERR256970
2213STDY5419933UnknownERR256969
2213STDY5419932220ERR256968
2213STDY54199311ERR256967
2213STDY5419930UnknownERR256966
2213STDY5419929UnknownERR256965
2213STDY54199281ERR256964
2213STDY54199275ERR256963
2213STDY541992678ERR256962
2213STDY54199255ERR256961
2213STDY54199241ERR256960
2213STDY541992310ERR256959
2213STDY5419922UnknownERR256958
2213STDY54199212ERR256957
2213STDY541992010ERR256956
2213STDY5419919220ERR256955
2213STDY5419918UnknownERR256954
2213STDY54199172ERR256953
2213STDY541991610ERR256952
2213STDY541991515ERR256951
2213STDY54199142ERR256950
2213STDY54199132ERR256949
2213STDY5419912220ERR256948
2213STDY5419911UnknownERR256947
2213STDY54199101ERR256946
2213STDY541990910ERR256945
2213STDY5419908UnknownERR256944
2213STDY541990721ERR256943
2213STDY5419906UnknownERR256942
2213STDY5419905UnknownERR256941
2213STDY5419904UnknownERR256940
2213STDY5419903UnknownERR256939
2213STDY5419902UnknownERR256938
2213STDY5419901UnknownERR256937
2213STDY5419900UnknownERR256936
2213STDY5419899UnknownERR256935
2213STDY5419898UnknownERR256934
2213STDY5419897UnknownERR256933
2213STDY5419896UnknownERR256932
2213STDY5419895UnknownERR256931
2213STDY5419894UnknownERR256930
2213STDY5419893UnknownERR256929
2213STDY5419892UnknownERR256928
2213STDY5419891UnknownERR256927
2213STDY5419890UnknownERR256926
2213STDY5419889UnknownERR256925
2213STDY5419888045ERR256924
2213STDY5419887045ERR256923
2213STDY5419886045ERR256922
2213STDY5419885045ERR256921
2213STDY5419884045ERR256920
2213STDY5419883126ERR256919
2213STDY5419882126ERR256918
2213STDY5419881126ERR256917
2213STDY5419880126ERR256916
2213STDY5419879126ERR256915
2213STDY5419878078ERR256914
2213STDY5419877078ERR256913
2213STDY5419876078ERR256912
2213STDY5419866078ERR256902
2213STDY5419865078ERR256901
2213STDY5419864078ERR256900
2213STDY5419863078ERR256899
2213STDY5419862078ERR256898
2213STDY5419861078ERR256897
2213STDY5419860078ERR256896
2213STDY5419859078ERR256895
2213STDY5437181046ERR257033
2213STDY5437180046ERR257032
2213STDY5437179046ERR257031
2213STDY5437178046ERR257030
2213STDY5437177046ERR257029
2213STDY5437176046ERR257028
2213STDY5437175046ERR257027
2213STDY5437174046ERR257026
2213STDY5437173046ERR257025
2213STDY5437172078?ERR257024
2213STDY5437171078ERR257023
2213STDY5437170078ERR257022
2213STDY5437169078ERR257021
2213STDY5437168078ERR257020
2213STDY5437167078ERR257019
2213STDY5437166078ERR257018
2213STDY5437165078ERR257017
2213STDY5437164078ERR257016
2213STDY5437163078ERR257015
2213STDY5437162078ERR257014
2213STDY5437161078ERR257013
2213STDY5437160078ERR257012
2213STDY5437159078ERR257011
2213STDY5437158078ERR257010
2213STDY5437157078ERR257009
2213STDY5437156078ERR257008
2213STDY5437155078ERR257007
2213STDY5437154078ERR257006
2213STDY5437153078ERR257005
2213STDY5437152078ERR257004
2213STDY5437151078ERR257003
2213STDY5437150078ERR257002
2213STDY5437149078ERR257001
2213STDY543713976ERR256991
2213STDY543713876ERR256990
2213STDY5437233081ERR257085
2213STDY5437232080ERR257084
2213STDY5437231079ERR257083
2213STDY5437230078ERR257082
2213STDY5437220078ERR257072
2213STDY5437219078ERR257071
2213STDY5437218078ERR257070
2213STDY5437217078ERR257069
2213STDY5437216078ERR257068
2213STDY5437215078ERR257067
2213STDY5437214078ERR257066
2213STDY5437213078ERR257065
2213STDY5437212078ERR257064
2213STDY5437211078ERR257063
2213STDY5437210078ERR257062
2213STDY5437209078ERR257061
2213STDY5437208078ERR257060
2213STDY5437207078ERR257059
2213STDY5437206078ERR257058
2213STDY5437205078ERR257057
2213STDY5437204078ERR257056
2213STDY5437203078ERR257055
2213STDY5437202078ERR257054
2213STDY5437201078ERR257053
2213STDY5437200078ERR257052
2213STDY5437199078ERR257051
2213STDY5437198078ERR257050
2213STDY5437197078ERR257049
2213STDY5437196078ERR257048
2213STDY5437195078ERR257047
2213STDY5437194078ERR257046
2213STDY5437193078ERR257045
2213STDY5437192078ERR257044
2_39UnknownERR403717
078NET048UnknownERR171333
078LVP024UnknownERR171244

Clostridium difficile toxin A-/B+ ribotype 017 global population structure

Sample

Strain

Run Accession

LSHTM-96017ERR178605
LSHTM-95017ERR178604
LSHTM-94017ERR178603
LSHTM-93017ERR178602
LSHTM-92017ERR178601
LSHTM-91017ERR178600
LSHTM-90017ERR178599
LSHTM-89017ERR178598
LSHTM-88017ERR178597
LSHTM-87017ERR178596
LSHTM-86017ERR178595
LSHTM-85017ERR178594
LSHTM-84017ERR178593
LSHTM-83017ERR178592
LSHTM-82017ERR178591
LSHTM-81017ERR178590
LSHTM-80017ERR178589
LSHTM-79017ERR178588
LSHTM-78017ERR178587
LSHTM-77017ERR178586
LSHTM-76017ERR178585
LSHTM-75017ERR178584
LSHTM-74017ERR178583
LSHTM-73017ERR178582
LSHTM-72017ERR178581
LSHTM-71017ERR178580
LSHTM-70017ERR178579
LSHTM-69017ERR178578
LSHTM-68017ERR178577
LSHTM-67017ERR178576
LSHTM-66017ERR178575
LSHTM-65017ERR178574
LSHTM-64017ERR178573
LSHTM-63017ERR178572
LSHTM-62017ERR178571
LSHTM-61017ERR178570
LSHTM-60017ERR178569
LSHTM-59017ERR178568
LSHTM-58017ERR178567
LSHTM-57017ERR178566
LSHTM-56017ERR178565
LSHTM-55017ERR178564
LSHTM-54017ERR178563
LSHTM-53017ERR178562
LSHTM-52017ERR178561
LSHTM-51017ERR178560
LSHTM-50017ERR178559
LSHTM-49017ERR178558
LSHTM-48017ERR178557
LSHTM-47017ERR178556
LSHTM-46017ERR178555
LSHTM-45017ERR178554
LSHTM-44017ERR178553
LSHTM-43017ERR178552
LSHTM-42017ERR178551
LSHTM-41017ERR178550
LSHTM-40017ERR178549
LSHTM-39017ERR178548
LSHTM-38017ERR178547
LSHTM-37017ERR178546
LSHTM-36017ERR178545
LSHTM-35017ERR178544
LSHTM-34017ERR178543
LSHTM-33017ERR178542
LSHTM-32017ERR178541
LSHTM-31017ERR178540
LSHTM-30017ERR178539
LSHTM-29017ERR178538
LSHTM-28017ERR178537
LSHTM-27017ERR178536
LSHTM-26017ERR178535
LSHTM-25017ERR178534
LSHTM-24017ERR178533
LSHTM-23017ERR178532
LSHTM-22017ERR178531
LSHTM-21017ERR178530
LSHTM-20017ERR178529
LSHTM-19017ERR178528
LSHTM-18017ERR178527
LSHTM-17017ERR178526
LSHTM-16017ERR178525
LSHTM-15017ERR178524
LSHTM-14017ERR178523
LSHTM-13017ERR178522
LSHTM-12017ERR178521
LSHTM-11017ERR178520
LSHTM-10017ERR178519
LSHTM-9017ERR178518
LSHTM-8017ERR178517
LSHTM-7017ERR178516
LSHTM-6017ERR178515
LSHTM-5017ERR178514
LSHTM-4017ERR178513
LSHTM-3017ERR178512
LSHTM-2017ERR178511
LSHTM-1017ERR178510
2220STDY5484081UnknownERR340664
2220STDY5484080CD839 CDRNERR340663
2220STDY5484079CD600 CDRNERR340662
2220STDY5484078CD586 CDRNERR340661
2220STDY5484077CD817 CDRNERR340660
2220STDY5484076CD637 CDRNERR340659
2220STDY5484075CD636 CDRNERR340658
2220STDY5484074CD832 CDRNERR340657
2220STDY5484073CD816 CDRNERR340656
2220STDY5484072SCH6163235ERR340655
2220STDY5484071SCH6148880ERR340654
2220STDY5484070SCH6098043ERR340653
2220STDY5484069SCH5865760ERR340652
2220STDY5484068SCH5864722ERR340651
2220STDY5484067SCH5845567ERR340650
2220STDY5484066SCH5845556ERR340649
2220STDY5484065SCH5842529ERR340648
2220STDY5484064SCH5824693ERR340647
2220STDY5484063SCH5806999ERR340646
2220STDY5484062DS 1383ERR340645
2220STDY5484061Sanger 017.95ERR340644
2220STDY5484060Sanger 017.94ERR340643
2220STDY5484059Sanger 017.93ERR340642
2220STDY5484058Sanger 017.92ERR340641
2220STDY5484055Sanger 017.89ERR340640
2220STDY5484054Sanger 017.88ERR340639
2220STDY5484053Sanger 017.87ERR340638
2220STDY5484052Sanger 017.86ERR340637
2220STDY5484051Sanger 017.85ERR340636
2220STDY5484050Sanger 017.84ERR340635
2220STDY5484047Sanger 017.61ERR340634
2220STDY5484046Sanger 017.59ERR340633
2220STDY5484045Sanger 017.58ERR340632
2220STDY5484044Sanger 017.57ERR340631
2220STDY5484043Sanger 017.56ERR340630
2220STDY5484042Sanger 017.54ERR340629
2220STDY5484039Sanger 017.50ERR340628
2220STDY5484038Sanger 017.48ERR340627
2220STDY5484037Sanger 017.46ERR340626
2220STDY5484036Sanger 017.45ERR340625
2220STDY5484035Sanger 017.42ERR340624
2220STDY5484034Sanger 017.41ERR340623
2220STDY5484033Sanger 017.37ERR340622
2220STDY5484032Sanger 017.36ERR340621
2220STDY5484031Sanger 017.35ERR340620
2220STDY5484030Sanger 017.34ERR340619
2220STDY5484029Sanger 017.33ERR340618
2220STDY5484028Sanger 017.32ERR340617
2220STDY5484027Sanger 017.31ERR340616
2220STDY5484026Sanger 017.30ERR340615
2220STDY5484025Sanger 017.29ERR340614
2220STDY5484024Sanger 017.28ERR340613
2220STDY5484023Sanger 017.27ERR340612
2220STDY5484022Sanger 017.25ERR340611
2220STDY5484021Sanger 017.24ERR340610
2220STDY5484020Sanger 017.23ERR340609
2220STDY5484019Sanger 017.22ERR340608
2220STDY5484018Sanger 017.20ERR340607
2220STDY5484017Sanger 017.18ERR340606
2220STDY5484016Sanger 017.17ERR340605
2220STDY5484015Sanger 017.16ERR340604
2220STDY5484014Sanger 017.15ERR340603
2220STDY5484013Sanger 017.14ERR340602
2220STDY5484012Sanger 017.13ERR340601
2220STDY5484011Sanger 017.12ERR340600
2220STDY5484010Sanger 017.10ERR340599
2220STDY5484009Sanger 017.9ERR340598
2220STDY5484008Sanger 017.8ERR340597
2220STDY5484007Positive Control M68ERR340596
2220STDY5484006Sanger 017.7ERR340595
2220STDY5484005Sanger 017.6ERR340594
2220STDY5484004Sanger 017.5ERR340593
2220STDY5484003Sanger 017.4ERR340592
2220STDY5484002Sanger 017.2ERR340591
2220STDY5484001Sanger 017.1ERR340590
2220STDY5484000DS 21ERR340589
2220STDY54839996084529ERR340588
2220STDY5483998IE 1104ERR340587
2220STDY5483997M05-213ERR340586
2220STDY5483996M04-45ERR340585
2220STDY5483995Enviromental 21ERR340584
2220STDY5483994Enviromental 19ERR340583
2220STDY5483993M04-34ERR340582
2220STDY54839920 8-26ERR340581
2220STDY548399106-378ERR340580
2220STDY548399005-302ERR340579
2220STDY5483989CDP08WTH7ERR340578
2220STDY548398812H00009ERR340577
2220STDY5483987CD1019ERR340576
2220STDY5483986CD404ERR340575
2220STDY5484057Sanger 017.91ERR351990
2220STDY5484056Sanger 017.90ERR351989
2220STDY5484049Sanger 017.83ERR351988
2220STDY5484048Sanger 017.82ERR351987
2220STDY5484041Sanger 017.53ERR351986
2220STDY5484040Sanger 017.52ERR351985
2220STDY5575100SI 006ERR387458
2220STDY5575099MRL-2259ERR387457
2220STDY5575098CD538ERR387456
2220STDY5575097CD345ERR387455
2220STDY5575096Sanger 017.79ERR387454
2220STDY5575095Sanger 017.67ERR387453
2220STDY5575094Sanger 017.40ERR387452
2220STDY5575093WA 1514ERR387451
2220STDY5575092SI 004ERR387450
2220STDY5575091MRL-1230ERR387449
2220STDY5575091MRL-1230ERR485014
2220STDY5575090CD529ERR387448
2220STDY5575089CD334ERR387447
2220STDY5575088Sanger 017.78ERR387446
2220STDY5575087Sanger 017.66ERR387445
2220STDY5575086Sanger 017.38ERR387444
2220STDY5575085WA 1428ERR387443
2220STDY5575084I 6ERR387442
2220STDY5575083MRL-1135ERR387441
2220STDY5575082CD528ERR387440
2220STDY5575081CD257ERR387439
2220STDY5575080Sanger 017.77ERR387438
2220STDY5575079Sanger 017.65ERR387437
2220STDY5575078Sanger 017.26ERR387436
2220STDY5575077WA 1196ERR387435
2220STDY5575076ES-720ERR387434
2220STDY5575075MRL-102ERR387433
2220STDY5575074CD527ERR387432
2220STDY5575073CD210ERR387431
2220STDY5575072Sanger 017.76ERR387430
2220STDY5575071Sanger 017.64ERR387429
2220STDY5575070Sanger 017.21ERR387428
2220STDY5575069WA 0908ERR387427
2220STDY5575068ES 580ERR387426
2220STDY5575067H-219ERR387425
2220STDY5575066CD523ERR387424
2220STDY5575065CD160ERR387423
2220STDY5575064Sanger 017.75ERR387422
2220STDY5575063Sanger 017.62ERR387421
2220STDY5575062Sanger 017.19ERR387420
2220STDY5575061WA 0810ERR387419
2220STDY5575060MRL-991ERR387418
2220STDY55750595992ERR387417
2220STDY5575058CD515ERR387416
2220STDY5575057CD159ERR387415
2220STDY5575056Sanger 017.74ERR387414
2220STDY5575055Sanger 017.60ERR387413
2220STDY5575054Sanger 017.11ERR387412
2220STDY5575053WA 0808ERR387411
2220STDY5575052MRL-985ERR387410
2220STDY55750515733ERR387409
2220STDY5575050CD504ERR387408
2220STDY5575049M0H-849ERR387407
2220STDY5575048Sanger 017.73ERR387406
2220STDY5575047Sanger 017.55ERR387405
2220STDY55750467036732ERR387404
2220STDY5575045SI 099ERR387403
2220STDY5575044MRL-738ERR387402
2220STDY55750435340ERR387401
2220STDY5575042CD493ERR387400
2220STDY5575040Sanger 017.72ERR387398
2220STDY5575039Sanger 017.51ERR387397
2220STDY5575038SI 1101ERR387396
2220STDY5575037SI 064ERR387395
2220STDY5575036MRL-532ERR387394
2220STDY55750355265ERR387393
2220STDY5575034CD479ERR387392
2220STDY5575033M68ERR387391
2220STDY5575032Sanger 017.71ERR387390
2220STDY5575031Sanger 017.49ERR387389
2220STDY5575030PT 1307ERR387388
2220STDY5575029SI 047ERR387387
2220STDY5575028MRL-3836ERR387386
2220STDY55750275264ERR387385
2220STDY5575026CD472ERR387384
2220STDY5575025M0H-82ERR387383
2220STDY5575024Sanger 017.70ERR387382
2220STDY5575023Sanger 017.47ERR387381
2220STDY5575022M04-44ERR387380
2220STDY5575021SI 032ERR387379
2220STDY5575020MRL-2923ERR387378
2220STDY55750194601ERR387377
2220STDY5575018CD425ERR387376
2220STDY5575017Sanger 017.81ERR387375
2220STDY5575016Sanger 017.69ERR387374
2220STDY5575015Sanger 017.44ERR387373
2220STDY5575014M04-43ERR387372
2220STDY5575013SI 010ERR387371
2220STDY5575012MRL-270ERR387370
2220STDY55750114241ERR387369
2220STDY5575010CD409ERR387368
2220STDY5575009Sanger 017.80ERR387367
2220STDY5575008Sanger 017.68ERR387366
2220STDY5575007Sanger 017.43ERR387365
2220STDY5575006M04-38ERR387364
2220STDY5575041M0H-701ERR485013
2220STDY5575041M0H-701ERR387399

TraDIS study on Clostridium difficile

Sample

Strain

Run Accession

Cdiff_027_4_2027ERR377415
Cdiff_027_4_2027ERR377423
Cdiff_027_4_1027ERR377414
Cdiff_027_4_1027ERR377422
Cdiff_027_3_2027ERR377413
Cdiff_027_3_2027ERR377421
Cdiff_027_3_1027ERR377420
Cdiff_027_3_1027ERR377412
Cdiff_027_2_2027ERR377411
Cdiff_027_2_2027ERR377419
Cdiff_027_2_1027ERR377418
Cdiff_027_2_1027ERR377410
Cdiff_027_1_2027ERR377409
Cdiff_027_1_2027ERR377417
Cdiff_027_1_1027ERR377408
Cdiff_027_1_1027ERR377416
C1bClostridium difficile R20291ERR417557
C1bClostridium difficile R20291ERR417619
C1aClostridium difficile R20291ERR417556
C1aClostridium difficile R20291ERR417618
5_2_5_2Clostridium difficile R20291ERR417555
5_2_5_2Clostridium difficile R20291ERR417617
5_2_4_2Clostridium difficile R20291ERR417554
5_2_4_2Clostridium difficile R20291ERR417616
5_2_3_2Clostridium difficile R20291ERR417553
5_2_3_2Clostridium difficile R20291ERR417615
5_2_2_2Clostridium difficile R20291ERR417552
5_2_2_2Clostridium difficile R20291ERR417614
5_2_1_2Clostridium difficile R20291ERR417613
5_2_1_2Clostridium difficile R20291ERR417551
5_1_5_2Clostridium difficile R20291ERR417550
5_1_5_2Clostridium difficile R20291ERR417612
5_1_4_2Clostridium difficile R20291ERR417549
5_1_4_2Clostridium difficile R20291ERR417611
5_1_3_2Clostridium difficile R20291ERR417548
5_1_3_2Clostridium difficile R20291ERR417610
5_1_2_2Clostridium difficile R20291ERR417609
5_1_2_2Clostridium difficile R20291ERR417547
5_1_1_2Clostridium difficile R20291ERR417546
5_1_1_2Clostridium difficile R20291ERR417608
3_2_5_2Clostridium difficile R20291ERR417607
3_2_5_2Clostridium difficile R20291ERR417545
3_2_4_2Clostridium difficile R20291ERR417544
3_2_4_2Clostridium difficile R20291ERR417606
3_2_3_2Clostridium difficile R20291ERR417605
3_2_3_2Clostridium difficile R20291ERR417543
3_2_2_2Clostridium difficile R20291ERR417604
3_2_2_2Clostridium difficile R20291ERR417542
3_2_1_2Clostridium difficile R20291ERR417541
3_2_1_2Clostridium difficile R20291ERR417603
3_1_5_2Clostridium difficile R20291ERR417540
3_1_5_2Clostridium difficile R20291ERR417602
3_1_4_2Clostridium difficile R20291ERR417601
3_1_4_2Clostridium difficile R20291ERR417539
3_1_3_2Clostridium difficile R20291ERR417538
3_1_3_2Clostridium difficile R20291ERR417600
3_1_2_2Clostridium difficile R20291ERR417537
3_1_2_2Clostridium difficile R20291ERR417599
3_1_1_2Clostridium difficile R20291ERR417536
3_1_1_2Clostridium difficile R20291ERR417598
1_2_5_2Clostridium difficile R20291ERR417597
1_2_5_2Clostridium difficile R20291ERR417535
1_2_4_2Clostridium difficile R20291ERR417534
1_2_4_2Clostridium difficile R20291ERR417596
1_2_3_2Clostridium difficile R20291ERR417533
1_2_3_2Clostridium difficile R20291ERR417595
1_2_2_2Clostridium difficile R20291ERR417532
1_2_2_2Clostridium difficile R20291ERR417594
1_2_1_2Clostridium difficile R20291ERR417531
1_2_1_2Clostridium difficile R20291ERR417593
1_1_5_2Clostridium difficile R20291ERR417592
1_1_5_2Clostridium difficile R20291ERR417530
1_1_4_2Clostridium difficile R20291ERR417529
1_1_4_2Clostridium difficile R20291ERR417591
1_1_3_2Clostridium difficile R20291ERR417590
1_1_3_2Clostridium difficile R20291ERR417528
1_1_2_2Clostridium difficile R20291ERR417527
1_1_2_2Clostridium difficile R20291ERR417589
1_1_1_2Clostridium difficile R20291ERR417588
1_1_1_2Clostridium difficile R20291ERR417526
5_2_5_1Clostridium difficile R20291ERR417525
5_2_5_1Clostridium difficile R20291ERR417587
5_2_4_1Clostridium difficile R20291ERR417524
5_2_4_1Clostridium difficile R20291ERR417586
5_2_3_1Clostridium difficile R20291ERR417523
5_2_3_1Clostridium difficile R20291ERR417585
5_2_2_1Clostridium difficile R20291ERR417584
5_2_2_1Clostridium difficile R20291ERR417522
5_2_1_1Clostridium difficile R20291ERR417521
5_2_1_1Clostridium difficile R20291ERR417583
5_1_5_1Clostridium difficile R20291ERR417520
5_1_5_1Clostridium difficile R20291ERR417582
5_1_4_1Clostridium difficile R20291ERR417519
5_1_4_1Clostridium difficile R20291ERR417581
5_1_3_1Clostridium difficile R20291ERR417518
5_1_3_1Clostridium difficile R20291ERR417580
5_1_2_1Clostridium difficile R20291ERR417517
5_1_2_1Clostridium difficile R20291ERR417579
5_1_1_1Clostridium difficile R20291ERR417516
5_1_1_1Clostridium difficile R20291ERR417578
3_2_5_1Clostridium difficile R20291ERR417515
3_2_5_1Clostridium difficile R20291ERR417577
3_2_4_1Clostridium difficile R20291ERR417514
3_2_4_1Clostridium difficile R20291ERR417576
3_2_3_1Clostridium difficile R20291ERR417513
3_2_3_1Clostridium difficile R20291ERR417575
3_2_2_1Clostridium difficile R20291ERR417512
3_2_2_1Clostridium difficile R20291ERR417574
3_2_1_1Clostridium difficile R20291ERR417511
3_2_1_1Clostridium difficile R20291ERR417573
3_1_5_1Clostridium difficile R20291ERR417510
3_1_5_1Clostridium difficile R20291ERR417572
3_1_4_1Clostridium difficile R20291ERR417509
3_1_4_1Clostridium difficile R20291ERR417571
3_1_3_1Clostridium difficile R20291ERR417508
3_1_3_1Clostridium difficile R20291ERR417570
3_1_2_1Clostridium difficile R20291ERR417507
3_1_2_1Clostridium difficile R20291ERR417569
3_1_1_1Clostridium difficile R20291ERR417506
3_1_1_1Clostridium difficile R20291ERR417568
1_2_5_1Clostridium difficile R20291ERR417505
1_2_5_1Clostridium difficile R20291ERR417567
1_2_4_1Clostridium difficile R20291ERR417504
1_2_4_1Clostridium difficile R20291ERR417566
1_2_3_1Clostridium difficile R20291ERR417565
1_2_3_1Clostridium difficile R20291ERR417503
1_2_2_1Clostridium difficile R20291ERR417502
1_2_2_1Clostridium difficile R20291ERR417564
1_2_1_1Clostridium difficile R20291ERR417563
1_2_1_1Clostridium difficile R20291ERR417501
1_1_5_1Clostridium difficile R20291ERR417562
1_1_5_1Clostridium difficile R20291ERR417500
1_1_4_1Clostridium difficile R20291ERR417499
1_1_4_1Clostridium difficile R20291ERR417561
1_1_3_1Clostridium difficile R20291ERR417498
1_1_3_1Clostridium difficile R20291ERR417560
1_1_2_1Clostridium difficile R20291ERR417559
1_1_2_1Clostridium difficile R20291ERR417497
1_1_1_1Clostridium difficile R20291ERR417496
1_1_1_1Clostridium difficile R20291ERR417558

Clostridium difficile clinical samples

Sample

Strain

Run Accession

2703STDY5570851CD70ERR425927
2703STDY5570851CD70ERR425997
2703STDY5570850CD69ERR425996
2703STDY5570850CD69ERR425926
2703STDY5570849CD68ERR425925
2703STDY5570849CD68ERR425995
2703STDY5570848CD67ERR425994
2703STDY5570848CD67ERR425924
2703STDY5570847CD66ERR425923
2703STDY5570847CD66ERR425993
2703STDY5570846CD65ERR425922
2703STDY5570846CD65ERR425992
2703STDY5570845CD64ERR425921
2703STDY5570845CD64ERR425991
2703STDY5570844CD63ERR425990
2703STDY5570844CD63ERR425920
2703STDY5570843CD62ERR425919
2703STDY5570843CD62ERR425989
2703STDY5570842CD61ERR425988
2703STDY5570842CD61ERR425918
2703STDY5570841CD60ERR425917
2703STDY5570841CD60ERR425987
2703STDY5570840CD59ERR425986
2703STDY5570840CD59ERR425916
2703STDY5570839CD58ERR425985
2703STDY5570839CD58ERR425915
2703STDY5570838CD57ERR425914
2703STDY5570838CD57ERR425984
2703STDY5570837CD56ERR425913
2703STDY5570837CD56ERR425983
2703STDY5570836CD55ERR425982
2703STDY5570836CD55ERR425912
2703STDY5570835CD54ERR425981
2703STDY5570835CD54ERR425911
2703STDY5570834CD53ERR425980
2703STDY5570834CD53ERR425910
2703STDY5570833CD52ERR425909
2703STDY5570833CD52ERR425979
2703STDY5570832CD51ERR425908
2703STDY5570832CD51ERR425978
2703STDY5570831CD50ERR425907
2703STDY5570831CD50ERR425977
2703STDY5570830CD49ERR425906
2703STDY5570830CD49ERR425976
2703STDY5570829CD48ERR425975
2703STDY5570829CD48ERR425905
2703STDY5570828CD47ERR425974
2703STDY5570828CD47ERR425904
2703STDY5570827CD46ERR425903
2703STDY5570827CD46ERR425973
2703STDY5570826CD45ERR425972
2703STDY5570826CD45ERR425902
2703STDY5570825CD44ERR425971
2703STDY5570825CD44ERR425901
2703STDY5570824CD43ERR425970
2703STDY5570824CD43ERR425900
2703STDY5570823CD42ERR425899
2703STDY5570823CD42ERR425969
2703STDY5570822CD41ERR425968
2703STDY5570822CD41ERR425898
2703STDY5570821CD40ERR425897
2703STDY5570821CD40ERR425967
2703STDY5570820CD39ERR425896
2703STDY5570820CD39ERR425966
2703STDY5570819CD38ERR425965
2703STDY5570819CD38ERR425895
2703STDY5570818CD37ERR425894
2703STDY5570818CD37ERR425964
2703STDY5570817CD36ERR425893
2703STDY5570817CD36ERR425963
2703STDY5570816CD35ERR425892
2703STDY5570816CD35ERR425962
2703STDY5570815CD34ERR425891
2703STDY5570815CD34ERR425961
2703STDY5570814CD33ERR425960
2703STDY5570814CD33ERR425890
2703STDY5570813CD32ERR425889
2703STDY5570813CD32ERR425959
2703STDY5570812CD31ERR425888
2703STDY5570812CD31ERR425958
2703STDY5570811CD30ERR425887
2703STDY5570811CD30ERR425957
2703STDY5570810CD29ERR425956
2703STDY5570810CD29ERR425886
2703STDY5570809CD28ERR425885
2703STDY5570809CD28ERR425955
2703STDY5570808CD27ERR425954
2703STDY5570808CD27ERR425884
2703STDY5570807CD26ERR425883
2703STDY5570807CD26ERR425953
2703STDY5570806CD25ERR425882
2703STDY5570806CD25ERR425952
2703STDY5570805CD24ERR425951
2703STDY5570805CD24ERR425881
2703STDY5570804CD23ERR425950
2703STDY5570804CD23ERR425880
2703STDY5570803CD22ERR425879
2703STDY5570803CD22ERR425949
2703STDY5570802CD21ERR425878
2703STDY5570802CD21ERR425948
2703STDY5570801CD20ERR425947
2703STDY5570801CD20ERR425877
2703STDY5570800CD19ERR425946
2703STDY5570800CD19ERR425876
2703STDY5570799CD18ERR425875
2703STDY5570799CD18ERR425945
2703STDY5570798CD17ERR425874
2703STDY5570798CD17ERR425944
2703STDY5570797CD16ERR425943
2703STDY5570797CD16ERR425873
2703STDY5570796CD15ERR425872
2703STDY5570796CD15ERR425942
2703STDY5570795CD14ERR425941
2703STDY5570795CD14ERR425871
2703STDY5570794CD13ERR425940
2703STDY5570794CD13ERR425870
2703STDY5570793CD12ERR425939
2703STDY5570793CD12ERR425869
2703STDY5570792CD11ERR425868
2703STDY5570792CD11ERR425938
2703STDY5570791CD10ERR425867
2703STDY5570791CD10ERR425937
2703STDY5570790CD09ERR425936
2703STDY5570790CD09ERR425866
2703STDY5570789CD08ERR425935
2703STDY5570789CD08ERR425865
2703STDY5570788CD07ERR425864
2703STDY5570788CD07ERR425934
2703STDY5570787CD06ERR425933
2703STDY5570787CD06ERR425863
2703STDY5570786CD05ERR425862
2703STDY5570786CD05ERR425932
2703STDY5570785CD04ERR425861
2703STDY5570785CD04ERR425931
2703STDY5570784CD03ERR425860
2703STDY5570784CD03ERR425930
2703STDY5570783CD02ERR425859
2703STDY5570783CD02ERR425929
2703STDY5570782CD01ERR425858
2703STDY5570782CD01ERR425928
CD65CD65ERR496934
CD59CD59ERR496933
CD16CD16ERR496932
CD3CD3ERR496931

Genomic analyses of novel pulsotypes and B1/027/NAP1 strains of Clostridium difficile isolated in Costa Rican hospitals during the last decade

Sample

Strain

Run Accession

2871STDY56724456725ERR467625
2871STDY56724446724ERR467624
2871STDY56724436656ERR467623
2871STDY56724426655ERR467622
2871STDY56724416654ERR467621
2871STDY56724406653ERR467620
2871STDY56724396518ERR467619
2871STDY56724386511ERR467618
2871STDY56724376510ERR467617
2871STDY56724366507ERR467616
2871STDY56724356293ERR467615
2871STDY56724346292ERR467614
2871STDY56724336291ERR467613
2871STDY56724326290ERR467612
2871STDY56724316289ERR467611
2871STDY56724306285ERR467610
2871STDY56724296284ERR467609
2871STDY56724286283ERR467608
2871STDY56724276281ERR467607
2871STDY56724266280ERR467606
2871STDY56724256279ERR467605
2871STDY56724246278ERR467604
2871STDY56724236277ERR467603
2871STDY56724226276ERR467602
2871STDY56724216275ERR467601
2871STDY56724205809ERR467600
2871STDY56724195785ERR467599
2871STDY56724185784ERR467598
2871STDY56724175778ERR467597
2871STDY56724165774ERR467596
2871STDY56724155772ERR467595
2871STDY56724145771ERR467594
2871STDY56724135768ERR467593
2871STDY56724125767ERR467592
2871STDY56724115766ERR467591
2871STDY56724105765ERR467590
2871STDY56724095764ERR467589
2871STDY56724085763ERR467588
2871STDY56724075762ERR467587
2871STDY56724065761ERR467586
2871STDY56724055760ERR467585
2871STDY56724045759ERR467584
2871STDY56724035758ERR467583
2871STDY56724025757ERR467582
2871STDY56724015755ERR467581
2871STDY56724005754ERR467580
2871STDY56723995753ERR467579
2871STDY56723985751ERR467578
2871STDY56723975750ERR467577
2871STDY56723965749ERR467576
2871STDY56723955745ERR467575
2871STDY56723945744ERR467574
2871STDY56723935742ERR467573
2871STDY56723925740ERR467572
2871STDY56723915738ERR467571
2871STDY56723905737ERR467570
2871STDY56723895734ERR467569
2871STDY56723885733ERR467568
2871STDY56723875730ERR467567
2871STDY56723865720ERR467566
2871STDY56723855719ERR467565
2871STDY56723845718ERR467564
2871STDY56723835717ERR467563
2871STDY56723825714ERR467562
2871STDY56723815713ERR467561
2871STDY56723805712ERR467560
2871STDY56723795711ERR467559
2871STDY56723785710ERR467558
2871STDY56723775709ERR467557
2871STDY56723765708ERR467556
2871STDY56723755707ERR467555
2871STDY56723745706ERR467554
2871STDY56723735705ERR467553
2871STDY56723725704ERR467552
2871STDY56723715703ERR467551
2871STDY56723705701ERR467550
2871STDY56723695700ERR467549
2871STDY56723685437ERR467548
2871STDY56723675436ERR467547
2871STDY56723665434ERR467546
2871STDY56723653150ERR467545
2871STDY56723643147ERR467544
2871STDY56723633145ERR467543
2871STDY56723623144ERR467542
2871STDY56723613137ERR467541
2871STDY56723603135ERR467540
2871STDY56723593129ERR467539
2871STDY56723583125ERR467538
2871STDY56723573124ERR467537
2871STDY56723562992ERR467536
2871STDY56723552955ERR467535
2871STDY56723542945ERR467534
2871STDY56723532812ERR467533
2871STDY56723522811ERR467532
2871STDY56723512809ERR467531
2871STDY56723502784ERR467530

NCTC 3000

Sample

Strain

Run Accession

3012STDY5802526NCTC13307ERR581143
3012STDY5802526NCTC13307ERR550480
3012STDY5802526NCTC13307ERR550486
  • Murine models to study Clostridium difficile infection and transmission.

    Lawley TD and Young VB

    Anaerobe 2013;24;94-7

  • Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection.

    Adamu BO and Lawley TD

    Current opinion in microbiology 2013;16;5;596-601

  • The agr locus regulates virulence and colonization genes in Clostridium difficile 027.

    Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne HP, Pettit L, Dougan G, Lawley TD and Wren BW

    Journal of bacteriology 2013;195;16;3672-81

  • Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains.

    Chen JW, Scaria J, Mao C, Sobral B, Zhang S, Lawley T and Chang YF

    Journal of proteome research 2013;12;3;1151-61

  • SpoIVA and SipL are Clostridium difficile spore morphogenetic proteins.

    Putnam EE, Nock AM, Lawley TD and Shen A

    Journal of bacteriology 2013;195;6;1214-25

  • Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

    He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D'Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J and Lawley TD

    Nature genetics 2013;45;1;109-13

  • Current application and future perspectives of molecular typing methods to study Clostridium difficile infections.

    Knetsch CW, Lawley TD, Hensgens MP, Corver J, Wilcox MW and Kuijper EJ

    Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin 2013;18;4;20381

  • Global analysis of the sporulation pathway of Clostridium difficile.

    Fimlaid KA, Bond JP, Schutz KC, Putnam EE, Leung JM, Lawley TD and Shen A

    PLoS genetics 2013;9;8;e1003660

  • The Clostridium difficile spo0A gene is a persistence and transmission factor.

    Deakin LJ, Clare S, Fagan RP, Dawson LF, Pickard DJ, West MR, Wren BW, Fairweather NF, Dougan G and Lawley TD

    Infection and immunity 2012;80;8;2704-11

  • Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile.

    Mullany P, Williams R, Langridge GC, Turner DJ, Whalan R, Clayton C, Lawley T, Hussain H, McCurrie K, Morden N, Allan E and Roberts AP

    Applied and environmental microbiology 2012;78;7;2147-53

  • Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.

    Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J and Dougan G

    PLoS pathogens 2012;8;10;e1002995

  • Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens.

    Lawley TD, Clare S, Deakin LJ, Goulding D, Yen JL, Raisen C, Brandt C, Lovell J, Cooke F, Clark TG and Dougan G

    Applied and environmental microbiology 2010;76;20;6895-900

  • Evolutionary dynamics of Clostridium difficile over short and long time scales.

    He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G and Parkhill J

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;16;7527-32

  • Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts.

    Lawley TD, Clare S, Walker AW, Goulding D, Stabler RA, Croucher N, Mastroeni P, Scott P, Raisen C, Mottram L, Fairweather NF, Wren BW, Parkhill J and Dougan G

    Infection and immunity 2009;77;9;3661-9

  • Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores.

    Lawley TD, Croucher NJ, Yu L, Clare S, Sebaihia M, Goulding D, Pickard DJ, Parkhill J, Choudhary J and Dougan G

    Journal of bacteriology 2009;191;17;5377-86

  • Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

    Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G and Wren BW

    Genome biology 2009;10;9;R102

  • The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.

    Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeño-Tárraga AM, Wang H, Holden MT, Wright A, Churcher C, Quail MA, Baker S, Bason N, Brooks K, Chillingworth T, Cronin A, Davis P, Dowd L, Fraser A, Feltwell T, Hance Z, Holroyd S, Jagels K, Moule S, Mungall K, Price C, Rabbinowitsch E, Sharp S, Simmonds M, Stevens K, Unwin L, Whithead S, Dupuy B, Dougan G, Barrell B and Parkhill J

    Nature genetics 2006;38;7;779-86

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/5vj3bq4y