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Updated: May 30, 2026
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
Published on: December 23, 2022
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4
Holger Rohde1, Junjie Qin, Yujun Cui
1Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg–Eppendorf, Hamburg, Germany.
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.
