Clustering of the distribution of ExPEC-associated genes in close relatives of MS499. The distribution of ExPEC-associated genes from MS499 are clustered according to the row dendrogram. Three broad groups of genes can be resolved from this analysis: (1) chromosomal genes which appear to be ancestral to the MS499 lineage, (2) chromosomal genes which are present in a subset of 7 genomes in the group, including MS499 and its six closest relatives, and, (3) plasmid genes present in MS499 and its three most proximal phylogenetic relatives. The column dendrogram has been ordered according to the phylogenetic relatedness between the strains as show in Additional file 5. From these relationships, a model can be proposed where the MS499 acquired some chromosomally encoded ExPEC genes in two stages, with the acquisition of the plasmid occurring subsequently (red arrows). This model suggests that the plasmid has been lost in the lineage leading to MS 182–1 and the two HVH strains (blue arrow).