Identification of Variable Regions within Genomes of Shiga Toxin Prophage from Escherichia coli O157:H7

Introduction:  Shiga toxin-producing E. coli O157:H7 have been implicated in foodborne outbreaks linked to vehicles including fresh produce and ground beef. They are especially dangerous pathogens due to their low infectious dose. The E. coli O157:H7 Sakai genome encodes genes for Shiga toxin 2 (stx₂) within a prophage designated Sp5. Due to the modular nature of phage genomes, there is a high level of sequence polymorphism between these phage isolated from different strains of E. coliO157:H7 which needs to be better defined.

Purpose:  Identification of genetic differences between stx₂-encoding phage may help improve DNA sequence-based subtyping approaches for identifying transmission routes of E. coli O157:H7 during outbreaks.

Methods: The stx₂-encoding phage from twenty clinical isolates, including the prototypical strains EDL933 and Sakai were isolated after ciprofloxacin induction and sequenced by 454 technology. 

Results:  Comparison of phage sequences identified most sequence variation in genes annotated previously as the encoding cII and cIII protein, exonuclease, recombination protein Bet, host-nuclease inhibition protein Gam, Kil, replication protein O, antirepressor, DNA binding protein, antiterminator Q and C4 Zn-finger protein. Moreover, we observed that the presence and position of an insertion sequence (IS629) element varied. Additionally, the sequenced phages were more similar to Sp5 from strain Sakai than the stx₂-encoding phage from EDL933. We also observed differences in the expression of Stx₂between strains. 

Significance:  The regions identified in this study might be useful as markers to increase the discriminatory power of multilocus sequence typing protocols for E. coli O157:H7 and sequence analysis may provide insights into the responsible mechanism(s).