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

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.

Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation

“…Our analysis revealed 109 variants that were similar in all five virulent strains (Supplementary Table S2B). B. melitensis isolates were previously shown to be clustered into five genotypes [26,27]. B. melitensis Ether was denoted as genotype I (Mediterranean strains); B. melitensis M28, ATCC 23457, and NI were denoted as genotype II (Asian strains); and B. melitensis 16M and Rev.1 were denoted as genotype V (American strains).…”

Geographical distribution of Brucella melitensis inferred from rpoB gene variation

“…Two Brucella melitensis strains isolated in Malaysia, namely MY/2009/1483 and BM/Phil/2012/1136, were previously recovered from brucellosis patients who had consumed unpasteurized cow milk in Malaysia and goat milk in the Philippines, respectively [12]. Complete sequences of the rpoB gene were retrieved from draft genomes of previously reported isolates [12].…”

“…Complete sequences of the rpoB gene were retrieved from draft genomes of previously reported isolates [12].…”

Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait

“…Genotyping of B. melitensis isolates is important for contact tracing and epidemiological surveillance in regions endemic for the organism (4). Whole-genome sequencing, by using next-generation sequencing (NGS) technologies, is emerging as a rapid method for the genetic characterization of B. melitensis (5, 6). NGS-based assays are capable of identifying genetic variations in the form of single nucleotide polymorphisms (SNPs) and indels (5, 6).…”

“…Whole-genome sequencing, by using next-generation sequencing (NGS) technologies, is emerging as a rapid method for the genetic characterization of B. melitensis (5, 6). NGS-based assays are capable of identifying genetic variations in the form of single nucleotide polymorphisms (SNPs) and indels (5, 6). In order to identify genetic variations in strains from Kuwait, we did whole-genome sequencing of five B. melitensis strains isolated from patients residing in Kuwait.…”