Diagrammatic representation of the similarity between the MS499 genome and its close relatives in reference to the ExPEC-associated DNA found within its genome. We compared the MS499 genome sequence to its close relatives to investigate the structure and variation in the ExPEC-associated regions in the MS499 genome (a). Regions of the non-ExPEC associated DNA in the MS499 genome which are also found in the isolate are coloured white, regions of this DNA which are not found in the isolate are coloured yellow. ExPEC-associated DNA which is found in the isolate are coloured grey, and ExPEC-associated DNA which is not found in the isolate are red. Several regions of clear variation between the MS499 genome and the related isolates are evident (listed i – iv), within which the ExPEC-associated DNA appears to be concentrated. We then investigated the proportion of the MS499 ExPEC-associated DNA which could be found in the genomes of these relatives (b), which showed that closer phylogenetic relatives of MS499 tend to encode more of the ExPEC-associated DNA in common with MS499 than do other, more distantly related isolates. The dendrograms presented alongside each panel are linear representations of the phylogeny in Additional file 7: Figure S4 with bootstrap values removed.