Determination of serogroups and serotypes by WGS
A collection of 56 STEC isolates were subjected to WGS by Illumina Miseq platform, achieving an average coverage of ~36×. Among the 56 isolates, 27 were isolated from cattle and 29 from sheep. The genome sequences identified 21 O serogroups, 17 H types, and a total of 29 O:H serotypes (Fig. 1). Sheep isolates belonged to 15 serotypes, whereas cattle isolates belonged to 14 serotypes, suggesting a high degree of diversity in serotypes. Seven isolates were O-serotype unknown (Ounk), likely because some of the O types are not present in the O-serotype database, or the wzx andwzy genes were not properly assembled. Two isolates were assigned as O153/O178. These two O types cannot be distinguished as these share identical wzx and wzy gene sequences. The predominant serotype was Ounk:H4, which accounted for 7 isolates from cattle; other prevalent serotypes were O8:H25 (5 isolates from cattle), O87:H16 (4 isolates from sheep), O76:H19 (4 isolates from sheep), O5:H19 (4 isolates from sheep), O108:H21 (4 isolates from sheep), and O8:H21 (3 isolates from cattle and sheep). Three serotypes (i.e., O81:H31, O66:H45, and O21:H25) contained two isolates each, whereas 20 serotypes were each represented by only one strain. Notably, no isolate was identified to belong to O157 or the top six O serogroups (i.e., O26, O45, O103, O111, O121, and O145) that are associated with human non-O157 STEC infections.