Comparative genome analysis of enterohemorrhagic Escherichia coli ATCC 43894 and its pO157-cured strain 277

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 ATCC 43894 (also known as EDL932) has been widely used as a reference strain for studying the pathophysiology of EHEC. To elucidate the role of a large virulence plasmid pO157 and its relationship with acid resistance, for example, both EHEC ATCC 43894 and its pO157-cured derivative strain 277 were well studied. However, it is unclear whether or not these two strains are isogenic and share the same genetic background. To address this question, we analyzed the whole genome sequences of ATCC 43894 and 277. As expected, three and two closed contigs were identified from ATCC 43894 and 277, respectively; two contigs shared in both strains were a chromosome and a small un-identified plasmid, and one contig found only in ATCC 43894 was pO157. Surprisingly, our pan-genome analyses of the two sequences revealed several genetic variations including frameshift, substitution, and deletion mutations. In particular, the deletion mutation of hdeD and gadE in ATCC 43894 was identified, and further PCR analysis also confirmed their deletion of a 2.5-kb fragment harboring hdeD, gadE, and mdtE in ATCC 43894. Taken together, our findings demonstrate that EHEC ATCC 43894 harbors genetic mutations affecting glutamate-dependent acid resistance system and imply that the pO157-cured EHEC 277 may not be isogenic to ATCC 43894. This is the first report that such genetic differences between both reference strains of EHEC should be considered in future studies on pathogenic E. coli.