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Published on: December 23, 2022
Identification of Shiga Toxin-Producing Escherichia coli Outbreaks Using Whole Genome Sequencing
Stefan Bletz1, Alexander Mellmann2, Barbara Middendorf-Bauchart1
1Institute of Hygiene and National Consulting Laboratory for Hemolytic Uremic Syndrome (HUS), University Hospital Münster, Münster, Germany.
Abstract:
Today, whole genome sequencing (WGS)-based typing is the gold standard approach to detect outbreaks of Shiga toxin-producing Escherichia coli (STEC) and to differentiate them from sporadic cases. Here, we describe an optimized protocol to efficiently determine the genome sequences of STEC using short read Illumina technology and provide information on helpful tools for the subsequent bioinformatic analysis.
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