Whole genome characterization of Shiga toxin-producing Escherichia coli in Free-ranging Red Deer from Italian Central Alps

Free-ranging red deer (Cervus elaphus) in Stelvio National Park (Italian Alps) have been suggested as potential carriers for LEE-negative, subAB positive Shiga toxin-producing Escherichia coli (STEC), which have been reported in human diseases. This work describes the genomic characterization of such isolates in order to define the zoonotic potential of wildlife-associated STEC. Whole genome analysis of 9 STEC isolates collected in the Stelvio National Park during the winter season 2016-2017 from feces of culled free-ranging red deer was performed. One STEC isolate harbored stx1 and stx2 genes, whereas 5 and 3 possessed stx2 and stx1 only, respectively. Subtype stx1a was carried by three strains and stx1c was observed in one isolate. Only subytpe stx2b was observed in the six stx2 positive strains. No STEC isolate possessed the eaeA gene. The serogroups identified included O146, O91, O113 and O174. Seven isolates of serogroups O146, O91 or O113 possessed the subAB locus. The core genome MLST analysis of the four O146:H28 showed that the strains’ genomes fell within the 37-95 alleles differences. Our results strengthen the hypothesis that red deer may represent carriers for LEE-negative, subAB positive STEC strains. Such strains display features similar to those causing illness to humans. The similarity in the genome of O146 STEC strains suggests that a population of these STEC isolates is circulating in the area. Our findings underline the zoonotic potential of STEC strains isolated from wild ruminants, including free-ranging deer.