capsule locus typing for serovar prediction of.

Abstract

is a causative agent of pleuropneumonia in pigs of all ages..is divided into 19 serovars based on capsular polysaccharides (CPSs) and lipopolysaccharides. The serovars of isolates are commonly determined by serological tests and multiplex PCR. This study aimed to develop a genomic approach fortyping by screening for the presence of the species-specificgene in whole-genome sequencing (WGS) reads and identifying capsule locus (KL) types in genome assemblies. A database of the.KL, including CPS synthesis and CPS export genes, was established and optimized for Kaptive. To test the developed genomic approach, WGS reads of 189.isolates and those of 66 samples from 14 other bacterial species were analysed. ariba analysis showed thatwas detected in all 189.samples. These-positive WGS reads wereassembled into genome assemblies and assessed. A total of 105.genome assemblies that passed the quality assessment were analysed by Kaptive analysis against the.KL database. The results showed that 97 assemblies were classified and predicted as 13 serovars, which matched the serovar information obtained from the literature. The six genome assemblies from previously nontypable isolates were typed and predicted as serovars 17 and 18. Notably, one of the two “” samples waspositive, and its genome assembly was typed as KL03 with high identity and predicted as.serovar 3. Collectively, a genomic approach was established and could accurately determine the KL type of.isolates using WGS reads. This approach can be used with high-quality genome assemblies for predicting.serovars and for retrospective analysis.