A Core Genome Multilocus Sequence Typing Scheme for .

Objective: A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in .

Methods: In this work, we propose a publicly available cgMLST scheme for using chewBBACA. In total 72 complete genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.

Results: We identified a total of 205 CGs from 695 strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( , , , , , , , , and ) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.

Conclusion: This research innovatively performs high-resolution molecular typing of using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for .