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Background  Strains of  Escherichia coli  that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd + ) is mediated by the  dnd  operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the  dnd  operon in Dnd +  E. coli  strains and to improve their typeability. Investigations into the genetic environments of the  dnd  operon in various  E. coli  strains led to the discovery that the  dnd  operon is harboured in various diverse genomic islands.    Results  The  dndBCDE  genes ( dnd  operon) were detected in all Dnd +  E. coli  strains by PCR. The addition of thiourea improved the typeability of Dnd +  E. coli  strains to 100% using PFGE and the Dnd +  phenotype can be observed in both clonal and genetically diverse  E. coli  strains.  Genomic analysis of 101  dnd  operons from genome sequences of  Enterobacteriaceae  revealed that the  dnd  operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of  dnd  operons of 52  E. coli  genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated  dnd -encoding GIs. The  dnd -encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two  dnd  operons were found within a strain although the biological implication is unknown. Surprisingly,  dnd  operons were frequently found in pathogenic  E. coli  although their link with virulence has not been explored.    Conclusion  Genomic islands likely play an important role in facilitating the horizontal gene transfer of the  dnd  operons in  E. coli  with 7 different types of islands discovered so far.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1421-8) contains supplementary material, which is available to authorized users.

The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands