Yersinia

The yersiniae are Gram-negative rods belonging to the family Enterobacteriaceae. They consist of 11 species that have been traditionally distinguished by DNA-DNA hybridisation and biochemical analyses. Three of them are pathogenic to humans: Yersinia pestis and the enteropathogenic yersiniae, Yersinia pseudotuberculosis and Yersinia enterocolitica. All three species target the lymph tissues during infection and carry a 70 kb virulence plasmid (pYV), which is essential for infection in these tissues as well as to overcome host defense mechanisms. We have generated reference genomes for two of the human pathogenic Yersinia: Y. pestis and Y. enterocolitica.

Data Downloads

[Genome Research Limited]

The genome of Y. pestis is punctuated with pseudogenes demonstrating that despite its high virulence Y. pestis is in the early stage of genome decay, eliminating genes no longer required outside it mammalian host.

Yersinia enterocolitica is a psychotropic bacterium, which causes acute gastro-enteritis and occasionally more serious disease in humans. In some countries it rivals Salmonella as a food borne pathogen and because it can grow at refrigeration temperature it is an increasing concern in terms of food safety. Y. enterocolitica has evolved into an apparently heterogeneous collection of organisms encompassing six biotypes differentiated by biochemical tests (1A, 1B, 2, 3, 4 and 5). These in vitro biotypes group into three distinct grades of pathogen: a historically defined non-pathogenic group (biogroup 1A); a weakly pathogenic group that are unable to kill mice (biogroups 2 to 5); and a highly pathogenic, mouse-lethal group (biogroup 1B). These biogroups have geographically distinct distributions with biotype 1B being most frequently isolated in North America (termed the ‘New-World’ strains), whereas biogroups 2-5 predominate in Europe and Japan (termed the ‘Old-World’ strains), with biotype 1A strains ubiquitous in the environment.

We have determined the genome sequence of Y. enterocolitica biotype 1B. Our current interests are to determine the genetic differences that define the biotypes and to look at global diversity of the Y. enterocolitica biotypes.

Collaboratrors

Brendan Wren (LSHTM)

Alan McNally (NTU)

Michael Prentice (U of Cork)

Muriel Dufour (ESR NCBID New Zealand)

Thilo M. Fuchs (U of München)

Mark Achtman (U of Cork)

Mikael Skurnik (U of Helsinki)

Elizabeth Carniel (Inst Pasteur)

Published Genome Data

Yersinia pestis

The sequenced strain, CO92, is a recent clinical isolate from the U.S.A. The chromosome sequence is 4,653,728 bp in length with a G+C content of 47.64%, and was generated from 95,000 shotgun reads. The start of the sequence was chosen to correspond with the origin of replication. There are 4,012 protein-coding genes (including 149 pseudogenes). Both the sequence and annotation have been deposited in the public databases with the accession number AL590842. In addition, there are three plasmids: pMT1 (accession number AL117211), pCD1 (accession number AL117189), and pPCP1 (accession number AL109969).

Yersinia enterocolitica

We have sequenced the strain 8081 and the complete sequence consists of a chromosome of 4,615,899 bp, with a G+C content of 47.27%, and a plasmid (pYVe8081) of 67,721 bp, with a G+C content of 43.92%. The complete chromosome sequence and annotation have been deposited in the public databases with the accession number AM286415.

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

Studies

Yersinia enterocolitica Nottingham

Sample

Strain

Run Accession

Ye21402_2Ye214/02ERR024869
Ye22102_2Ye221/02ERR024873
y15_2y15ERR024874
Ye0402_2Ye04/02ERR024875
Ye21802_2Ye218/02ERR024876
Ye0202_2Ye02/02ERR024856
Ye22602_2Ye226/02ERR024860
Ye7703_2Ye77/03ERR024861
Ye4103_2Ye41/03ERR024862
N22232770_2N222 32770ERR024863
N22084574_2N220 84574ERR024864
N2153435_2N21 53435ERR024865
N2982399_2N29 82399ERR024866
21763683_2217 63683ERR024867
Ye15302_2Ye153/02ERR024857
Ye3503_2Ye35/03ERR024858
Ye17702_2Ye177/02ERR024859
Ye17702_2Ye177/02ERR033839
Ye0903_2Ye09/03ERR024540
Ye0902_2Ye09/02ERR024544
Ye2403_2Ye24/03ERR024545
Ye1302_2Ye13/02ERR024546
Ye4602_2Ye46/02ERR024547
Ye11902_2Ye119/02ERR024548
Ye1103_2Ye11/03ERR024549
Ye0803_2Ye08/03ERR024550
Ye22702_2Ye22702ERR024551
Ye23202_2Ye232/02ERR024541
Ye5803_2Ye58/03ERR024542
Ye20302_2Ye203/02ERR024543
Ye20302_2Ye203/02ERR033840
Ye19002_2Ye190/02ERR024553
Ye20402_2Ye204/02ERR024557
Ye11102_2Ye111/02ERR024558
ye0303_2ye03/03ERR024559
Ye23102_2Ye231/02ERR024560
Ye1703_2Ye17/03ERR024561
Ye22802_2Ye228/02ERR024562
Ye1303_2Ye13/03ERR024563
Ye20502_2Ye205/02ERR024564
Ye6903_2Ye69/03ERR024554
Ye21502_2Ye215/02ERR024555
Ye3903_2Ye39/03ERR024556
Ye3903_2Ye39/03ERR033841
Ye21302_2Ye213/02ERR024566
Ye0703_2Ye07/03ERR024570
Ye3403_2Ye34/03ERR024571
N2214757_2N221 4757ERR024572
N22373947_2N223 73947ERR024573
N21282756_2N212 82756ERR024574
N21622789_2N216 22789ERR024575
N21572344_2N215 72344ERR024576
N21383523_2N213 83523ERR024577
N2118599_2N211 8599ERR024567
N2653045_2N26 53045ERR024568
N2453484_2N24 53484ERR024569
N2453484_2N24 53484ERR033842
N21873627N218 73627ERR024579
Ye23702Ye237/02ERR024583
Ye20102Ye201/02ERR024584
Ye20802Ye208/02ERR024585
NZ761915NZ 7-61915ERR024586
NZ1032126NZ 10-32126ERR024587
NZ28081NZ 2-8081ERR024588
NZ832501NZ 8-32501ERR024589
NZ523784NZ 5-23784ERR024590
NZ198109NZ 19-8109ERR024580
NZ1484423NZ 14-84423ERR024581
H3180H31/80ERR024582
H60887H608/87ERR024592
H69294H692/94ERR024595
H32478H324/78ERR024596
H23089H230/89ERR024597
Y127Y127ERR024598
SZ66297SZ 662/97ERR024599
SZ510801SZ 5108/01ERR024600
2093684209-36/84ERR024601
YE5330444YE53/30444ERR024602
YE3688YE36/88ERR024593
SZ16696SZ166/96ERR024594
26012601.0ERR024882
42654265.0ERR024884
25972597.0ERR024885
26032603.0ERR024886
43484348.0ERR024887
25922592.0ERR024888
42634263.0ERR024889
25952595.0ERR024890
25932593.0ERR024891
Ye8850Ye8850ERR024883
ye23802Ye23802ERR024877
Ye042693Ye042693ERR024878
Ye3803v2Ye3803ERR024879
Ye3003v2Ye3003ERR024880
Ye2703v2Ye2703ERR024870
Ye0403v2Ye0403ERR024871
Ye7403v2Ye7403ERR024872
Ye7403v2Ye7403ERR033843

Yersinia Genus project

Sample

Strain

Run Accession

01102011/02ERR028192
05602056/02ERR028196
05802058/02ERR028197
06102061/02ERR028198
06402064/02ERR028199
06502065/02ERR028200
06802068/02ERR028201
09302093/02ERR028202
09402094/02ERR028203
10702107/02ERR028193
10902109/02ERR028194
11202112/02ERR028195
12002120/02ERR028205
14102141/02ERR028209
14802148/02ERR028210
15902159/02ERR028211
18202182/02ERR028212
IP10066IP10066ERR028213
IP10209IP10209ERR028214
IP23698IP23698ERR028215
IP24139IP24139ERR028216
IP25089IP25089ERR028206
IP25924IP25924ERR028207
IH111554IH 111554ERR028208
IP27925IP27925ERR024919
IP32463IP32463ERR024923
IP32544IP32544ERR024924
IP32670IP32670ERR024925
IP32881IP32881ERR024926
IP32921IP32921ERR024927
IP32938IP32938ERR024928
IP33038IP33038ERR024929
IP33054IP33054ERR024930
IP33177IP33177ERR024920
IP33250IP33250ERR024921
IP33278IP33278ERR024922
IP6945IP6945ERR024906
12311231.0ERR024910
28882888.0ERR024911
OK6311OK6311ERR024912
R148R148ERR024913
260-2260ERR024914
WP931201WP-931201ERR024893
Y25Y25ERR024897
Y228Y228ERR024898
Y233Y233ERR024899
Y252Y252ERR024900
Y428Y428ERR024901
Y716Y716ERR024902
Y718Y718ERR024903
Y719Y719ERR024904
Y722Y722ERR024894
FCF130FCF 130ERR027388
FCF202FCF 202ERR027392
FCF208FCF 208ERR027393
FCF221FCF 221ERR027394
FCF224FCF 224ERR027395
FCF324FCF 324ERR027396
FCF326FCF 326ERR027397
FCF335FCF 335ERR027398
FCF343FCF 343ERR027399
FCF467FCF 467ERR027389
FCF84FCF 84ERR027390
FE80151FE80151ERR024932
FE80200FE80200ERR024936
FE80217FE80217ERR024937
FE80258FE80258ERR024938
FE80982FE80982ERR024939
FE80988FE80988ERR024940
FE82747FE82747ERR024941
9859/85ERR024942
8258982589ERR024943
11984119/84ERR024933
12784127/84ERR024934
127338512733/85ERR024935
14685146/85ERR028179
227148522714/85ERR028183
288528/85ERR028184
3016843016/84ERR028185
3317843317/84ERR028186
3400833400/83ERR028187
388338/83ERR028188
40481404/81ERR028189
49885498/85ERR028190
82184821/84ERR028180
928492/84ERR028181
A125KOH2�125 KOH2ERR028182
BR16597BR165/97ERR027409
BR16697BR166/97ERR027413
IP22404IP22404ERR027414
IP23047IP23047ERR027415
OMBL4OMBL 4ERR027416
RS41RS41ERR027417
542542.0ERR027418
11271127.0ERR027419
33433343.0ERR027401
34303430.0ERR027402
2407024070ERR027403
2693126931.0ERR027404
5873558735.0ERR027405
2C53NMD72/C/53 NM D7ERR027406
RS42RS-42ERR027407
56025602.0ERR027422
940294/02ERR027425
580258/02ERR027426
930293/02ERR027427
650265/02ERR027428
680268/02ERR027429
610261/02ERR027430
640264/02ERR027431
12002-2120/02ERR027432
11202-2112/02ERR027423
10902-2109/02ERR027424
D585D585ERR027420
N916N916ERR027410
OK6088OK6088ERR027411
SP93422SP93422ERR027412
FCF580FCF 580ERR027391
R819R819ERR024895
RD22RD22ERR024896
MW1092MW 109-2ERR024915
N912N912ERR024916
No5No.5ERR024917
OK5586OK5586ERR024907
PT682PT682ERR024908
R1005R1005ERR024909
  • The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

    Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T, Feltwell T, Abdellah Z, Hauser H, Jagels K, Maddison M, Moule S, Sanders M, Whitehead S, Quail MA, Dougan G, Parkhill J and Prentice MB

    PLoS genetics 2006;2;12;e206

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeño-Tárraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PC, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S and Barrell BG

    Nature 2001;413;6855;523-7

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/nlbfr4im