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Journal article

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

Rohde H, Qin J, Cui Y, Li D, Loman N, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, 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 G, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen M, Wang J, Aepfelbacher M, Yang R, Consortium T ...see all

New England Journal of Medicine, vol. 365, issue 8 (2011) pp. 718-724 Published by Massachusetts Medical Society

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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.

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Authors

  • Holger Rohde

  • Junjie Qin

  • Yujun Cui

  • Dongfang Li

  • Nicholas J. Loman

  • Moritz Hentschke

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