Open-Source Genomic Analysis of Shiga-Toxin–Producing<i>E. coli</i>O104:H4
Holger Rohde(Universität Hamburg), Junjie Qin(BGI Group (China)), Yujun Cui(BGI Group (China)), Dongfang Li(BGI Group (China)), Nicholas J. Loman, Moritz Hentschke(Universität Hamburg), Wen‐Tong Chen(BGI Group (China)), Fei Pu(BGI Group (China)), Yangqing Peng(BGI Group (China)), Junhua Li(BGI Group (China)), Feng Xi(BGI Group (China)), Shenghui Li(BGI Group (China)), Yin Li, Zhaoxi Zhang(BGI Group (China)), Xianwei Yang(BGI Group (China)), Meiru Zhao(BGI Group (China)), Peng Wang(BGI Group (China)), Yuanlin Guan(BGI Group (China)), Zhong Cen(BGI Group (China)), Xiangna Zhao(Institute of Microbiology), Martin Christner(Universität Hamburg), Robin Kobbe(Universität Hamburg), Sebastian Loos(Universität Hamburg), Jun Oh(Universität Hamburg), Liang Yang(Universität Hamburg), Antoine Danchin, George F. Gao(Czech Academy of Sciences, Institute of Microbiology), Yajun Song(Institute of Microbiology), Yingrui Li, Huanming Yang(BGI Group (China)), Jian Wang, Jianguo Xu(Taiwan Centers for Disease Control), Mark J. Pallen, Jun Wang, Martin Aepfelbacher(Universität Hamburg), Ruifu Yang(BGI Group (China))
Cited by 420Open Access
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.
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