The major serotype present in each sample was determined by batch screening of the de novo assemblies in Ridom SeqSphere+ v 7.0.6 (Ridom, Münster, Germany) using the genes deposited in the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/) for E. coli as part of their web-based tool, SerotypeFinder 2.0 (https://cge.cbs.dtu.dk/services/SerotypeFinder/).

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