In silico Multilocus Sequence Typing (MLST) and core-genome SNP analysis
The 56 STEC isolates were typed into 20 sequence types (STs). STs of four isolates were not matched in the MLST database, which suggests that they may belong to novel STs. ST10 is the most prevalent ST, which is represented by 11 strains. Other frequent STs include ST3249, ST40, ST447, and ST675, each containing over 4 strains. Eight STs were represented only once. ST40, ST447, and ST675 are represented by sheep isolates from Korla; and ST3249 from cattle isolates were obtained in 2016-2018. For the STs that contain more than two isolates, a great majority of these (75%) contain strains of the same O serotype.
Two isolates SG18-D13 and CG17-d36-2 assigned O153/O178 are phylogenetically distantly related, suggesting that these are very likely different serotypes. Two ST43 isolates (CD15-213 and SG17-J10) and 11 ST10 isolates belonging to various serotypes were clustered together and assigned to CC10. SD18-A3 and the clade of SG18-D1, SG18-D27, and SG18-D26 are almost identical in terms of ST, O:H serotype, and virulence profile, except for SD18-A3 that lacks thestx 2b gene. Nonetheless, our tree based on core-genome SNP analysis can clearly separate SD18-A3 from the other three, whereas a classical MLST could not (Supplemental Fig. 1).
Some isolates are identical with respect to the characteristics tested, suggesting that these likely originated from the same clone, e.g., the ST675 group. Similarly, SG18-2-2, SG18-2-1, and SG18-2-7 are nearly identical with respect to serotype, ST (the same novel ST type), and virulence factors. Despite the fact that these three strains and SG18-2-15 were isolated from the same location at the same time and clustered together, SG18-2-15 apparently gained a few virulence genes, including HPI-encoded irp2 and fyuA and plasmid-borneehxA and subA . SG18-6-2 stands out as it belongs to the unique ST25 and unique O128:H2 serotype. Although CG17-d36-3 and CG16-B21 both belonging to ST58 are in the same clade, these were assigned different serotypes and have distinct virulence gene profiles (Fig. 1).