The LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagic
Escherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagic E. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics of E. coliO157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of the pchprophage carrying pchA, pchB, pchC, and a newly identified pchgene, pchX. Genomic segments extending from the holin S region to the pchA, pchB, pchC, and pchXgenes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termed pchadjacent genomic regions ( pchAGR). Despite the remarkable degree of variation, the pattern of variation in pchAGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from the LEE1promoter further revealed that variation in the pchAGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in the pchAGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern of pchAGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage.