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.