Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4

N Engl J Med. 2011 Aug 25;365(8):718-24. doi: 10.1056/NEJMoa1107643. Epub 2011 Jul 27.

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.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Bacterial Typing Techniques
  • Child
  • Diarrhea / epidemiology
  • Diarrhea / microbiology
  • Escherichia coli Infections / microbiology*
  • Feces / microbiology
  • Female
  • Genome, Bacterial*
  • Germany
  • Hemolytic-Uremic Syndrome / epidemiology
  • Hemolytic-Uremic Syndrome / microbiology*
  • Humans
  • Male
  • Molecular Sequence Data
  • Phylogeny
  • Plasmids / genetics
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Shiga-Toxigenic Escherichia coli / classification
  • Shiga-Toxigenic Escherichia coli / genetics*
  • Shiga-Toxigenic Escherichia coli / isolation & purification

Associated data

  • GENBANK/AFOG01000000
  • GENBANK/AFVR00000000
  • GENBANK/AFVS00000000