title: Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
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.
authors.affiliation: Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg–Eppendorf, Hamburg, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Rohde
authors.forename: Junjie
authors.initials: J
authors.lastname: Qin
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.forename: Dongfang
authors.initials: D
authors.lastname: Li
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.forename: Moritz
authors.initials: M
authors.lastname: Hentschke
authors.forename: Wentong
authors.initials: W
authors.lastname: Chen
authors.forename: Fei
authors.initials: F
authors.lastname: Pu
authors.forename: Yangqing
authors.initials: Y
authors.lastname: Peng
authors.forename: Junhua
authors.initials: J
authors.lastname: Li
authors.forename: Feng
authors.initials: F
authors.lastname: Xi
authors.forename: Shenghui
authors.initials: S
authors.lastname: Li
authors.forename: Yin
authors.initials: Y
authors.lastname: Li
authors.forename: Zhaoxi
authors.initials: Z
authors.lastname: Zhang
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.forename: Meiru
authors.initials: M
authors.lastname: Zhao
authors.forename: Peng
authors.initials: P
authors.lastname: Wang
authors.forename: Yuanlin
authors.initials: Y
authors.lastname: Guan
authors.forename: Zhong
authors.initials: Z
authors.lastname: Cen
authors.forename: Xiangna
authors.initials: X
authors.lastname: Zhao
authors.forename: Martin
authors.initials: M
authors.lastname: Christner
authors.forename: Robin
authors.initials: R
authors.lastname: Kobbe
authors.forename: Sebastian
authors.initials: S
authors.lastname: Loos
authors.forename: Jun
authors.initials: J
authors.lastname: Oh
authors.forename: Liang
authors.initials: L
authors.lastname: Yang
authors.forename: Antoine
authors.initials: A
authors.lastname: Danchin
authors.forename: George F
authors.initials: GF
authors.lastname: Gao
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Jianguo
authors.initials: J
authors.lastname: Xu
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Martin
authors.initials: M
authors.lastname: Aepfelbacher
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D000293:Adolescent; D015373:Bacterial Typing Techniques; D002648:Child; D003967:Diarrhea / Q000453:epidemiology / Q000382:microbiology; D004927:Escherichia coli Infections / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D005260:Female; D016680:Genome, Bacterial; D005858:Germany; D006463:Hemolytic-Uremic Syndrome / Q000453:epidemiology / Q000382:microbiology*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D054323:Shiga-Toxigenic Escherichia coli / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification