Identification of Shiga Toxin-Producing Escherichia coli Outbreaks Using Whole Genome Sequencing

Bletz S, Mellmann A, Middendorf-Bauchart B

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.