Large chromosomal rearrangements associated with recombination between homologous prophage regions are a common feature in E. coli O157 strains and promote phenotypic plasticity in the population

This study characterises large chromosomal rearrangements (LCRs) and their associated phenotypes in E. coli O157 strains. RNA-seq was performed on wildtype strain 9000 and three derivative strains in which LCRs had occurred following experimental bovine colonisation. Gene expression differences between these strains was analysed when each was grown in either LB or M9 media. mRNA and sRNA profiles of strain 9000 and derivative strains Z1615, Z1723 and Z1767 grown in LB medium