title: Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis.
abstract: 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 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. kimkee@um.edu.my.|Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. kimkee@um.edu.my.
authors.forename: Kim-Kee
authors.initials: KK
authors.lastname: Tan
authors.affiliation: Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia. yungchie@codongenomics.com.
authors.forename: Yung-Chie
authors.initials: YC
authors.lastname: Tan
authors.affiliation: Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. changly@um.edu.my.|Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. changly@um.edu.my.
authors.forename: Li-Yen
authors.initials: LY
authors.lastname: Chang
authors.affiliation: Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia. kokwei.lee@codongenomics.com.
authors.forename: Kok Wei
authors.initials: KW
authors.lastname: Lee
authors.affiliation: Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. sitisarahnore@um.edu.my.
authors.forename: Siti Sarah
authors.initials: SS
authors.lastname: Nore
authors.affiliation: Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia. sunny.yee@codongenomics.com.
authors.forename: Wai-Yan
authors.initials: WY
authors.lastname: Yee
authors.affiliation: Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia. emno72@gmail.com.
authors.forename: Mohd Noor
authors.initials: MN
authors.lastname: Mat Isa
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. flela@um.edu.my.
authors.forename: Faizatul Lela
authors.initials: FL
authors.lastname: Jafar
authors.affiliation: Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia. ivan.hoh@codongenomics.com.
authors.forename: Chee-Choong
authors.initials: CC
authors.lastname: Hoh
authors.affiliation: Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. sazaly@um.edu.my.|Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. sazaly@um.edu.my.
authors.forename: Sazaly
authors.initials: S
authors.lastname: AbuBakar
mesh_terms: D017347:Brucella melitensis / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D020451:Contig Mapping; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial