Escherichia coli O157:H7 Genome sequencing and assembly

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don't capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.