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Abstract Background Insertion Sequence (IS) elements are mobile genetic elements widely distributed among bacteria. Their activities cause mutations, promoting genetic diversity and sometimes adaptation. Previous studies have examined their copy number and distribution in <it>Escherichia coli</it> K-12 and natural isolates. Here, we map most of the IS elements in <it>E. coli</it> B and compare their locations with the published genomes of K-12 and O157:H7. Results The genomic locations of IS elements reveal numerous differences between B, K-12, and O157:H7. IS elements occur in <it>hok-sok</it> loci (homologous to plasmid stabilization systems) in both B and K-12, whereas these same loci lack IS elements in O157:H7. IS elements in B and K-12 are often found in locations corresponding to O157:H7-specific sequences, which suggests IS involvement in chromosomal rearrangements including the incorporation of foreign DNA. Some sequences specific to B are identified, as reported previously for O157:H7. The extent of nucleotide sequence divergence between B and K-12 is <2% for most sequences adjacent to IS elements. By contrast, B and K-12 share only a few IS locations besides those in <it>hok-sok</it> loci. Several phenotypic features of B are explained by IS elements, including differential porin expression from K-12. Conclusions These data reveal a high level of IS activity since <it>E. coli</it> B, K-12, and O157:H7 diverged from a common ancestor, including IS association with deletions and incorporation of horizontally acquired genes as well as transpositions. These findings indicate the important role of IS elements in genome plasticity and divergence.</p

Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers.