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

Research output: Contribution to journalArticle


  • 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

Colleges, School and Institutes


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