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Background  Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two  Brucella melitensis  isolates from Malaysia and the Philippines. In addition, we performed a comparative whole-genome single nucleotide polymorphism (SNP) analysis of  B. melitensis  strains collected from around the world, to investigate the potential origin and the history of the global spread of  B. melitensis.Results  Single sequencing runs of each genome resulted in draft genome sequences of MY1483/09 and Phil1136/12, which covered 99.85% and 99.92% of the complete genome sequences, respectively. The  B. melitensis  genome sequences, and two  B. abortus  strains used as the outgroup strains, yielded a total of 13,728 SNP sites. Phylogenetic analysis using whole-genome SNPs and geographical distribution of the isolates revealed spatial clustering of the  B. melitensis  isolates into five genotypes, I, II, III, IV and V. The Mediterranean strains, identified as genotype I, occupied the basal node of the phylogenetic tree, suggesting that  B. melitensis  may have originated from the Mediterranean regions. All of the Asian  B. melitensis  strains clustered into genotype II with the SEA strains, including the two isolates sequenced in this study, forming a distinct clade denoted here as genotype II d . Genotypes III, IV and V of  B. melitensis  demonstrated a restricted geographical distribution, with genotype III representing the African lineage, genotype IV representing the European lineage and genotype V representing the American lineage.    Conclusion  We showed that SNPs retrieved from the  B. melitensis  draft full genomes were sufficient to resolve the interspecies relationships between  B. melitensis  strains and to discriminate between the vaccine and endemic strains .  Phylogeographic reconstruction of the history of  B. melitensis  global spread at a finer scale by using whole-genome SNP analyses supported the origin of all  B. melitensis  strains from the Mediterranean region. The possible global distribution of  B. melitensis  following the ancient trade routes was also consistent with whole-genome SNP phylogeny. The whole genome SNP phylogenetics analysis, hence is a powerful tool for intraspecies discrimination of closely related species .Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1294-x) contains supplementary material, which is available to authorized users.

Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis