A genome-wide SNP-based phylogenetic analysis distinguishes different biovars of Brucella suis

• Published in: Infection, genetics and evolution Vol. 41; pp. 213 - 217
• Main Authors: Sankarasubramanian, Jagadesan, Vishnu, Udayakumar S., Gunasekaran, Paramasamy, Rajendhran, Jeyaprakash
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2016
• Subjects: Alignment-free; Animals; B. suis; Bacterial Proteins - genetics; Bacterial Vaccines - genetics; Base Sequence; Biovar; Brucella; Brucella suis - classification; Brucella suis - genetics; Brucella suis - pathogenicity; Brucellosis - epidemiology; Brucellosis - microbiology; China - epidemiology; Chromosome Mapping; Genome, Bacterial; Mutation; Phosphotransferases (Phosphomutases) - genetics; Phylogeny; Polymorphism, Single Nucleotide; Sequence Alignment; SNP; Swine; Type IV Secretion Systems - genetics; Virulence Factors - genetics; B. suis; Phylogeny; SNP; Biovar; Alignment-free; Brucella
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2016.04.012

Brucellosis is an important zoonotic disease caused by Brucella spp. Brucella suis is the etiological agent of porcine brucellosis. B. suis is the most genetically diverged species within the genus Brucella. We present the first large-scale B. suis phylogenetic analysis based on an alignment-free k-mer approach of gathering polymorphic sites from whole genome sequences. Genome-wide core-SNP based phylogenetic tree clearly differentiated and discriminated the B. suis biovars and the vaccine strain into different clades. A total of 16,756 SNPs were identified from the genome sequences of 54 B. suis strains. Also, biovar-specific SNPs were identified. The vaccine strain B. suis S2–30 is extensively used in China, which was discriminated from all biovars with the accumulation of the highest number of SNPs. We have also identified the SNPs between B. suis vaccine strain S2–30 and its closest homolog, B. suis biovar 513UK. The highest number of mutations (22) was observed in the phosphomannomutase (pmm) gene essential for the synthesis of O-antigen. Also, mutations were identified in several virulent genes including genes coding for type IV secretion system and the effector proteins, which could be responsible for the attenuated virulence of B. suis S2–30. [Display omitted] •B. suis biovars distinguished by the genome-wide SNPs•Core SNPs and biovar specific SNPs of B. suis were identified.•SNP based phylogeny gave better resolution than MLST- and whole genome-based tree.•Divergence of B. suis biovars was identified.•SNPs associated with the attenuated virulence of B. suis S2–30 were identified.