Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4

Nicholas Loman; Mark Pallen; Holger Rohde; Junjie  Qin; Yujun  Cui; Dongfang  Li; Moritz  Hentschke; Wentong Chen; Fei  Pu; Yangqing  Peng; Junhua  Li; Feng  Xi; Shenghui  Li; Yin Li Li; Zhaoxi  Zhang; Xianwei  Yang; Meiru  Zhao; Peng  Wang; Yuanlin  Guan; Zhong  Cen; Xiangna  Zhao; Martin  Christner; Robin  Kobbe; Sebastian  Loos; Jun  Oh; Liang  Yang; Antoine  Danchin; George F.  Gao; Yajun  Song; Yingrui  Li; Huanming  Yang; Jian  Wang; Jianguo  Xu; Jun  Wang; Martin  Aepfelbacher; Ruifu  Yang

doi:10.1056/NEJMoa1107643

Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4

Nicholas Loman, Mark Pallen, Holger Rohde, Junjie Qin, Yujun Cui, Dongfang Li, Moritz Hentschke, Wentong Chen, Fei Pu, Yangqing Peng, Junhua Li, Feng Xi, Shenghui Li, Yin Li Li, Zhaoxi Zhang, Xianwei Yang, Meiru Zhao, Peng Wang, Yuanlin Guan, Zhong CenXiangna Zhao, Martin Christner, Robin Kobbe, Sebastian Loos, Jun Oh, Liang Yang, Antoine Danchin, George F. Gao, Yajun Song, Yingrui Li, Huanming Yang, Jian Wang, Jianguo Xu, Jun Wang, Martin Aepfelbacher, Ruifu Yang

Biosciences

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Abstract

An outbreak caused by Shiga-toxin-producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.

Original language	English
Pages (from-to)	718-724
Number of pages	7
Journal	New England Journal of Medicine
Volume	365
Issue number	8
DOIs	https://doi.org/10.1056/NEJMoa1107643
Publication status	Published - 1 Aug 2011

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Loman2011New EnglandJournalMedicineAccepted author manuscript, 743 KB

xBASE: A bioinformatics resource for the AgriFood Bacteriology Community
Pallen, M. & Stekel, D.
Biotechnology & Biological Sciences Research Council
1/02/07 → 31/01/12
Project: Research Councils

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Loman, N., Pallen, M., Rohde, H., Qin, J., Cui, Y., Li, D., Hentschke, M., Chen, W., Pu, F., Peng, Y., Li, J., Xi, F., Li, S., Li, Y. L., Zhang, Z., Yang, X., Zhao, M., Wang, P., Guan, Y., ... Yang, R. (2011). Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4. New England Journal of Medicine, 365(8), 718-724. https://doi.org/10.1056/NEJMoa1107643

@article{dc2f84f769894d10bfd329e56db1c70a,

title = "Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4",

abstract = "An outbreak caused by Shiga-toxin-producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.",

author = "Nicholas Loman and Mark Pallen and Holger Rohde and Junjie Qin and Yujun Cui and Dongfang Li and Moritz Hentschke and Wentong Chen and Fei Pu and Yangqing Peng and Junhua Li and Feng Xi and Shenghui Li and Li, {Yin Li} and Zhaoxi Zhang and Xianwei Yang and Meiru Zhao and Peng Wang and Yuanlin Guan and Zhong Cen and Xiangna Zhao and Martin Christner and Robin Kobbe and Sebastian Loos and Jun Oh and Liang Yang and Antoine Danchin and Gao, {George F.} and Yajun Song and Yingrui Li and Huanming Yang and Jian Wang and Jianguo Xu and Jun Wang and Martin Aepfelbacher and Ruifu Yang",

year = "2011",

month = aug,

day = "1",

doi = "10.1056/NEJMoa1107643",

language = "English",

volume = "365",

pages = "718--724",

journal = "New England Journal of Medicine",

issn = "1533-4406",

publisher = "Massachusetts Medical Society",

number = "8",

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Loman, N, Pallen, M, Rohde, H, Qin, J, Cui, Y, Li, D, Hentschke, M, Chen, W, Pu, F, Peng, Y, Li, J, Xi, F, Li, S, Li, YL, Zhang, Z, Yang, X, Zhao, M, Wang, P, Guan, Y, Cen, Z, Zhao, X, Christner, M, Kobbe, R, Loos, S, Oh, J, Yang, L, Danchin, A, Gao, GF, Song, Y, Li, Y, Yang, H, Wang, J, Xu, J, Wang, J, Aepfelbacher, M & Yang, R 2011, 'Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4', New England Journal of Medicine, vol. 365, no. 8, pp. 718-724. https://doi.org/10.1056/NEJMoa1107643

TY - JOUR

T1 - Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4

AU - Loman, Nicholas

AU - Pallen, Mark

AU - Rohde, Holger

AU - Qin, Junjie

AU - Cui, Yujun

AU - Li, Dongfang

AU - Hentschke, Moritz

AU - Chen, Wentong

AU - Pu, Fei

AU - Peng, Yangqing

AU - Li, Junhua

AU - Xi, Feng

AU - Li, Shenghui

AU - Li, Yin Li

AU - Zhang, Zhaoxi

AU - Yang, Xianwei

AU - Zhao, Meiru

AU - Wang, Peng

AU - Guan, Yuanlin

AU - Cen, Zhong

AU - Zhao, Xiangna

AU - Christner, Martin

AU - Kobbe, Robin

AU - Loos, Sebastian

AU - Oh, Jun

AU - Yang, Liang

AU - Danchin, Antoine

AU - Gao, George F.

AU - Song, Yajun

AU - Li, Yingrui

AU - Yang, Huanming

AU - Wang, Jian

AU - Xu, Jianguo

AU - Wang, Jun

AU - Aepfelbacher, Martin

AU - Yang, Ruifu

PY - 2011/8/1

Y1 - 2011/8/1

N2 - An outbreak caused by Shiga-toxin-producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.

AB - An outbreak caused by Shiga-toxin-producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.

U2 - 10.1056/NEJMoa1107643

DO - 10.1056/NEJMoa1107643

M3 - Article

C2 - 21793736

SN - 1533-4406

VL - 365

SP - 718

EP - 724

JO - New England Journal of Medicine

JF - New England Journal of Medicine

IS - 8

ER -

Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4

Abstract

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