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

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

Holger Rohde, M.D., Junjie Qin, Ph.D., Yujun Cui, Ph.D., Dongfang Li, M.E.,
Nicholas J. Loman, M.B., B.S., Moritz Hentschke, M.D., Wentong Chen, B.S.,
Fei Pu, B.S., Yangqing Peng, B.S., Junhua Li, B.E., Feng Xi, B.E.,
Shenghui Li, B.S., Yin Li, B.S., Zhaoxi Zhang, B.S., Xianwei Yang, B.S.,
Meiru Zhao, M.S., Peng Wang, B.M., Yuanlin Guan, B.E., Zhong Cen, M.E.,
Xiangna Zhao, B.S., Martin Christner, M.D., Robin Kobbe, M.D.,
Sebastian Loos, M.D., Jun Oh, M.D., Liang Yang, Ph.D.,
Antoine Danchin, Ph.D., George F. Gao, Ph.D., Yajun Song, Ph.D.,
Yingrui Li, B.S., Huanming Yang, Ph.D., Jian Wang, Ph.D.,
Jianguo Xu, M.D., Ph.D., Mark J. Pallen, M.D., Ph.D, Jun Wang, Ph.D.,
Martin Aepfelbacher, M.D., Ruifu Yang, M.D., Ph.D.,
and the E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium*</p>

This article (10.1056/NEJMoa1107643) was
published on July 27, 2011, at NEJM.org.
N Engl J Med 2011.

Summary</p>

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.</p>