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Abstract
BackgroundBrucellosis 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.ResultsSingle 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 IId. 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.ConclusionWe 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 materialThe online version of this article (doi:10.1186/s12864-015-1294-x) contains supplementary material, which is available to authorized users.
Highlights
Brucellosis is an important zoonotic disease that affects both humans and animals
General features The full genome sequences of the Brucella isolates were generated from a single sequencing run using the 316 chips of the Life Technologies Ion Torrent PGM platform
We identified 110 Southeast Asia (SEA) clade-specific single nucleotide polymorphism (SNP) that differentiated the SEA clade from other global B. melitensis strains, suggesting a common ancestor of the SEA B. melitensis strains in this region
Summary
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. Brucella spp. are listed as a category B potential biological warfare agent [1]. A biological warfare attack model built in 1997, based on an aerosol attack using B. melitensis in an urban population, was estimated could cause an economic loss of $477.7 million per 100,000 persons exposed [3]. Owing to the potentially insidious nature of a bioterrorism attack, the intentional release of any biological warfare agent could be difficult to detect. Rapid detection of potential bioterrorism activities that usually starts with few indistinguishable cases from a natural outbreak, is difficult. It relies heavily on precise and sensitive methods, as well as the availability of information about the organism worldwide. Sporadic outbreaks of brucellosis occur worldwide, the probable geographical origin of the source of infection, is difficult to determine
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