Genomic structure of stx2i genes and prophages determined in Shiga toxin-producing Escherichia coli isolated from food, animal and human samples in Germany.

Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens and a threat to human health. Their main virulence factor, the Shiga toxin (Stx), is encoded in two subunit genes (stxA and stxB) and occurs in various subtypes. Here, we report the occurrence of strains harbouring the new subtype stx2i. Isolates from food (n=8), animal (n=3) and human (n=2) samples were subjected to whole-genome sequencing for detailed molecular analyses. All strains harboured an identical stx2i variant independent of the genoserotype and differed from the first detected variant in 2016. In five of the strains, inactive stx operons were determined due to a transposon insertion in the stxA2i subunit gene. Stx phages and insertion sites were comparable between the strains of the same genoserotype. As the stx2i variant was also identified in a human clinical sample, we developed a specific PCR, as there are possible cross-reactions with other typing methods currently used in routine diagnostics. In total, our data show that STEC strains of this specific stx2i variant occur in various matrices of food, animals and humans and that there might be an underdetected number of strains due to insufficient typing methods.