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

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Tan, Kim Kee ^a   Tan, Yung Chie ^b   Chang, Li Yen ^a   Lee, Kok Wei ^b   Nore, Siti Sarah ^a   Yee, Wai Yan ^b   Mat Isa, Mohd Noor ^c   Jafar, Faizatul Lela ^a   Hoh, Chee Choong ^b   AbuBakar, Sazaly ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

^b Faculty of Medicine ^*  (Malaysia)

^c Kemeneterian Sains Teknologi dan Inovasi   (Malaysia)

Author keywords

Bioterrorism; Brucella; Genome; Phylogenetic; SNPs; Zoonotic

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL TRANSMISSION; BACTERIUM ISOLATION; BRUCELLA MELITENSIS; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; GENOTYPE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; CONTIG MAPPING; DNA SEQUENCE; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION;

ANIMALIA; BRUCELLA; BRUCELLA MELITENSIS; BRUCELLA MELITENSIS BIOVAR ABORTUS;

BACTERIAL DNA;

BRUCELLA MELITENSIS; CLUSTER ANALYSIS; CONTIG MAPPING; DNA, BACTERIAL; GENETIC VARIATION; GENOME, BACTERIAL; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84949130712     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1294-x     Document Type: Article

References (56)

1. Song L, Ahn S, Walt DR. Detecting biological warfare agents. Emerg Infect Dis. 2005;11(10):1629-32.
2. Franz DR, Parrott CD, Takafuji ET. The US biological warfare and biological defense programs. In: Sidell FR, Takafuji ET, Franz DR, editors. Medical Aspects of Chemical and Biological Warfare. United of States: Office of The Surgeon General (Army; 1997. p. 425-36.
3. Kaufmann AF, Meltzer MI, Schmid GP. The economic impact of a bioterrorist attack: are prevention and postattack intervention programs justifiable? Emerg Infect Dis. 1997;3(2):83-94.
4. Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, et al. Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol. 2009;191(8):2864-70.
5. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003;423(6935):81-6.
6. Foster JT, Price LB, Beckstrom-Sternberg SM, Pearson T, Brown WD, Kiesling DM, et al. Genotyping of Brucella species using clade specific SNPs. BMC Microbiol. 2012;12:110.
7. Liu W, Jing Z, Ou Q, Cui B, He Y, Wu Q. Complete genome sequence of Brucella melitensis biovar 3 strain NI, isolated from an aborted bovine fetus. J Bacteriol. 2012;194(22):6321.
8. Wang F, Hu S, Gao Y, Qiao Z, Liu W, Bu Z. Complete genome sequences of Brucella melitensis strains M28 and M5-90, with different virulence backgrounds. J Bacteriol. 2011;193(11):2904-5.
9. Ke Y, Yuan X, Wang Y, Bai Y, Xu J, Song H, et al. Genome sequences of Brucella melitensis 16 M and its two derivatives 16M1w and 16M13w, which evolved in vivo. J Bacteriol. 2012;194(19):5489.
10. Ding J, Pan Y, Jiang H, Cheng J, Liu T, Qin N, et al. Whole genome sequences of four Brucella strains. J Bacteriol. 2011;193(14):3674-5.
11. Wattam AR, Williams KP, Snyder EE, Almeida Jr NF, Shukla M, Dickerman AW, et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191(11):3569-79.
12. Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, et al. Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence. J Bacteriol. 2014;196(5):920-30.
13. Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, et al. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. mBio. 2012;3(5):e00246-00211.
14. Girault G, Blouin Y, Vergnaud G, Derzelle S. High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. BMC Genomics. 2014;15(1):288.
15. Chen PE, Willner KM, Butani A, Dorsey S, George M, Stewart A, et al. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS One. 2010;5(8):e12397.
16. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2014;42(Database issue):D581-91.
17. Song J, Xu Y, White S, Miller KW, Wolinsky M. SNPsFinder-a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes. Bioinformatics. 2005;21(9):2083-4.
18. Elberg SS, Faunce K. Immunization Against Brucella Infection VI. Brucella melitensis immunity conferred on goats by a nondependent mutant from a streptomycin-dependent mutant strain of Brucella melitensis. J Bacteriol. 1957;73(2):211-7.
19. Cloeckaert A, Grayon M, Grépinet O. Identification of Brucella melitensis vaccine strain Rev. 1 by PCR-RFLP based on a mutation in the rpsL gene. Vaccine. 2002;20(19):2546-50.
20. Moreno E. Genome evolution within the alpha proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? FEMS Microbiol Rev. 1998;22(4):255-75.
21. Capasso L. Bacteria in two-millennia-old cheese, and related epizoonoses in Roman populations. J Infect. 2002;45(2):122-7.
22. Capasso L. Brucellosis at Herculaneum (79 AD). Int J Osteoarchaeol. 1999;9(5):277-88.
23. Valdezate S, Navarro A, Villalon P, Carrasco G, Saez-Nieto JA. Epidemiological and phylogenetic analysis of Spanish human Brucella melitensis strains by multiple-locus variable-number tandem-repeat typing, hypervariable octameric oligonucleotide fingerprinting, and rpoB typing. J Clin Microbiol. 2010;48(8):2734-40.
24. Sayan M, Yumuk Z, Bilenoglu O, Erdenlig S, Willke A. Genotyping of Brucella melitensis by rpoB gene analysis and re-evaluation of conventional serotyping method. Jpn J Infect Dis. 2009;62(2):160-3.
25. Marianelli C, Ciuchini F, Tarantino M, Pasquali P, Adone R. Molecular characterization of the rpoB gene in Brucella species: new potential molecular markers for genotyping. Microb Infect/Institut Pasteur. 2006;8(3):860-5.
26. Kay GL, Sergeant MJ, Giuffra V, Bandiera P, Milanese M, Bramanti B, et al. Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio. 2014;5(4):e01337-01314.
27. Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet. 2010;42(12):1140-3.
28. Godfroid J, Kasbohrer A. Brucellosis in the European Union and Norway at the turn of the twenty-first century. Vet Microbiol. 2002;90(1-4):135-45.
29. Kampen AH, Bakken EH, Jore S, Klevar S. The surveillance programme for Brucella melitensis in small ruminants in Norway 2013. In: Surveillance programmes for terrestrial and aquatic animals in Norway Annual report 2013. Oslo: Norwegian Veterinary Institute; 2014.
30. Meyer ME, Morgan W. Designation of neotype strains and of biotype reference strains for species of the genus Brucella Meyer and Shaw. Int J Syst Bacteriol. 1973;23(2):135-41.
31. Verger J-M, Grimont F, Grimont PA, Grayon M. Brucella, a monospecific genus as shown by deoxyribonucleic acid hybridization. Int J Syst Bacteriol. 1985;35(3):292-5.
32. Herzberg M, Elberg S. Immunization against Brucella infection I.: Isolation and Characterization of a Streptomycin-Dependent Mutant1. J Bacteriol. 1953;66(5):585.
33. Lucero NE, Ayala SM, Escobar GI, Jacob NR. Brucella isolated in humans and animals in Latin America from 1968 to 2006. Epidemiol Infect. 2008;136(4):496-503.
34. Olsen S, Bellaire B. Brucella. In McVey DS, Kennedy M, Chengappa MM, editors. Veterinary Microbiology, 3 edn. United of States: Wiley; 2013. P. 127-133
35. Robinson A. Guidelines for coordinated human and animal brucellosis surveillance. 2003.
36. Wongphruksasoong V, Santayakorn S, Sitthi W, Chuxnum T, Pipatjaturong N, Kunthu A, et al. An Outbreaks of Brucella melitensis among goat farmers in Thailand, December 2009. Outbreak, Surveillance and Investigation Reports. 2012;5(1):14-21.
37. Sam IC, Karunakaran R, Kamarulzaman A, Ponnampalavanar S, Syed Omar SF, Ng KP, et al. A large exposure to Brucella melitensis in a diagnostic laboratory. J Hosp Infect. 2012;80(4):321-5.
38. Manosuthi W, Thummakul T, Vibhagool A, Vorachit M, Malathum K. Case report: Brucellosis: a re-emerging disease in Thailand. Southeast Asian J Trop Med Public Health. 2004;35(1):109-12.
39. Jama'ayah MZ, Heu JY, Norazah A. Seroprevalance of brucellosis among suspected cases in Malaysia. Malays J Pathol. 2011;33(1):31-4.
40. Bamaiyi PH, Hassan L, Khairani-Bejo S, Zainal Abidin M, Ramlan M, Krishnan N, et al. Isolation and molecular characterization of Brucella melitensis from seropositive goats in Peninsula Malaysia. Trop Biomed. 2012;29(4):513-8.
41. Al-Garadi MA, Khairani-Bejo S, Zunita Z, Omar A. Isolation and identification of Brucella melitensis in goats. J Anim Vet Adv. 2011;10(8):972-9.
42. Mick V, Le Carrou G, Corde Y, Game Y, Jay M, Garin-Bastuji B. Brucella melitensis in France: persistence in wildlife and probable spillover from Alpine ibex to domestic animals. PLoS One. 2014;9(4):e94168.
43. Corner LA, Alton GG. Persistence of Brucella abortus strain 19 infection in adult cattle vaccinated with reduced doses. Res Vet Sci. 1981;31(3):342-4.
44. Meyer ME, Nelson CJ. Persistence of Brucella abortus, strain 19 infection in immunized cattle. Proc Annu Meet US Anim Health Assoc. 1969;73:159-65.
45. Ke Y, Yuan X, Zhen Q, Wang Y, Li T, Sun Y, et al. Genome sequence of Brucella melitensis S66, an isolate of sequence type 8, prevalent in China. J Bacteriol. 2012;194(19):5451.
46. Corbel MJ, Stuart FA, Brewer RA. Observations on serological cross-reactions between smooth Brucella species and organisms of other genera. Dev Biol Stand. 1984;56:341-8.
47. Francis E, Evans AC: Agglutination, cross-agglutination and agglutinin absorption in tularaemia. Public Health Rep. 1896-1970. 1926;1273-1295
48. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394-403.
49. Bonfield JK, Whitwham A. Gap5-editing the billion fragment sequence assembly. Bioinformatics. 2010;26(14):1699-703.
50. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33(Web Server issue):W686-9.
51. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-8.
52. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29(12):2607-18.
53. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10.
54. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000;28(1):45-8.
55. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999;27(1):29-34.
56. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17(8):754-5.