Comparative genomics of Brucella suis discriminates different biovars

Abstract

Brucella suis TANUVAS_1 was isolated from a case of porcine abortion and whole genome sequenced. In the present study, comparative genomics of B. suis strains (n=33), including the newly sequenced strain TANUVAS_1 was carried out for accurate discrimination of the biovars. To alleviate the problems associated with conventional biovar identification techniques, a whole genome-based approach was used in the present study. The whole genome phylogeny of B. suis clearly differentiated strains on the basis of biovars. A total of 43 virulence genes were predicted, of which the btpA gene was present in only 14 strains, whereas the wbkA gene was absent in 19 strains. Multi locus sequence typing (MLST) analysis showed 5 different sequence types (14, 15, 16, 17 and 19) and the maximum number of strains belonged to ST14. There were 6 different STs assigned on the basis of core genome MLST, and the maximum number of strains belonged to ST50. Pangenome analysis of the strains showed that a total of 1948 genes (30.47%) were core genes and 4445 genes (69.53%) were accessory genes, suggesting that the B. suis genome has an open pan genomic structure. SNP analysis revealed 17 biovar 1 specific SNPs, 2142 biovar 2 specific SNPs, 673 biovar 3 specific SNPs, 714 biovar 4 specific SNPs and 2308 biovar 5 specific SNPs. The results show that cgMLST can be used for accurate discrimination of strains on the basis of biovars. Similarly, biovar specific SNPs can be employed for developing molecular assays that can discriminate biovars.