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

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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 languageEnglish
Pages (from-to)718-724
Number of pages7
JournalNew England Journal of Medicine
Issue number8
Publication statusPublished - 1 Aug 2011


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