Enterohaemorrhagic Escherichia coli O157:H7 (EHEC O157) is a key zoonotic pathogen responsible for large food-borne outbreaks worldwide. Whole genome sequencing is a relatively novel technology being utilised by Public Health agencies to determine isolate relationship and inform outbreak investigations. However, the main implementation of whole genome sequencing currently utilises “short-read” sequencing which fails to obtain complete information on prophages and genome structure due to the presence of multiple repeat regions in EHEC O157 genomes. In collaboration with Public Health England, this research helped deploy short-read sequencing approaches for routine use at the Scottish Escherichia coli Reference Laboratory (SERL). This has allowed the SERL and affiliated Scottish epidemiologists to better determine whether isolates are related and trace the source of outbreaks. The “long-read” Pacific Biosciences (PacBio) sequencing platform was then used to analyse the complete prophage content (bacteriophage DNA integrated in the chromosome) of a subset of strains. Specifically, the analysis took an in-depth look at prophages encoding the main Shiga toxins (Stx) responsible for the serious pathology associated with EHEC O157 infections. In addition, the sequencing method allowed the observation of large chromosomal rearrangements (LCRs), potentially mediated by areas of homologies present in the prophage population. The significance of such LCRs is still being investigated but the genome plasticity may act to allow the bacterial strain to ‘switch’ phenotypes for niche adaptation. The potential of using “long-read” methods alongside routine “short-read” sequencing of EHEC O157 for public health benefit was investigated and its value demonstrated for outbreaks. For example, by enabling a more accurate prediction of the host/source attribution of an infection strain based on analysis of the Stx-encoding prophage within the isolate. While such approaches show considerable promise, costs and accuracy issues (depending on the platform, PacBio vs Oxford Nanopore MinIon) will need to be surmounted, and the underlying biology studied further, before their use could usurp more high throughput “short-read” methods.