Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis

BMC Microbiology

Volumn 12, Issue , 2012, Pages

  Richards, Vincent P ^a   Zadoks, Ruth N ^a,c   Pavinski Bitar, Paulina D ^a   Lefébure, Tristan ^a,d   Lang, Ping ^e   Werner, Brenda ^a   Tikofsky, Linda ^a,f   Moroni, Paolo ^a,b   Stanhope, Michael J ^a  

^a Cornell University ^*  (United States)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

^d UNIVERSITÉ DE LYON   (France)

^e Department of Obstetrics Gynecology   (United States)

^f NONE   (United States)

Author keywords

Bovine; Canine; Comparative genomics; Host adaptation; Lateral gene transfer; Mastitis; Pathogen; Streptococcus canis; Zoonotic

Indexed keywords

DNA METHYLTRANSFERASE; GUANOSINE TRIPHOSPHATASE; RIBOSOME RNA; TRANSFER RNA; VIRULENCE FACTOR;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM CULTURE; BACTERIUM ISOLATE; BOVINE MASTITIS; CONTROLLED STUDY; COW; FEMALE; GENE SEQUENCE; GENOME ANALYSIS; GENOTYPE; HORIZONTAL GENE TRANSFER; LISTERIA MONOCYTOGENES; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHYLOGENY; POPULATION GENETIC STRUCTURE; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PYROSEQUENCING; RIBOTYPING; SEQUENCE ANALYSIS; STREPTOCOCCUS; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS CANIS; STREPTOCOCCUS DYSGALACTIAE;

BOVINAE; CANIS FAMILIARIS; FELIDAE; LANGAT VIRUS; MAMMALIA; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS CANIS; STREPTOCOCCUS DYSGALACTIAE SUBSP. DYSGALACTIAE; STREPTOCOCCUS URINALIS;

EID: 84871152470     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-12-293     Document Type: Article

References (98)

1. Streptococcus canis sp. nov.: a species of group G streptococci from animals. Devriese LA, Hommez J, Kilpper-Balz R, Schleifer KH, Int J Syst Bacteriol 1986 36 3 422 425 10.1099/00207713-36-3-422
2. Taxonomic study of Lancefield streptococcal groups C, G, and L (Streptococcus dysgalactiae) and proposal of S. dysgalactiae subsp. equisimilis subsp. nov. Vandamme P, Pot B, Falsen E, Kersters K, Devriese LA, Int J Syst Bacteriol 1996 46 3 774 781 10.1099/00207713-46-3-774 8782689
3. Isolation of Streptococcus canis from a Japanese raccoon dog with fibrinous pleuropneumonia. Murase T, Morita T, Sunagawa Y, Sawada M, Shimada A, Sato K, Hikasa Y, Vet Rec 2003 153 15 471 472 10.1136/vr.153.15.471 14584580
4. Streptococcus canis arthritis in a cat breeding colony. Iglauer F, Kunstyr I, Morstedt R, Farouq H, Wullenweber M, Damsch S, J Exp Anim Sci 1991 34 2 59 65 1883871
5. Fatal Streptococcus canis infections in intensively housed shelter cats. Pesavento PA, Bannasch MJ, Bachmann R, Byrne BA, Hurley KF, Vet Pathol 2007 44 2 218 221 10.1354/vp.44-2-218 17317801
6. Relationship between clinical manifestations and pulsed-field gel profiles of Streptococcus canis isolates from dogs and cats. Kruger EF, Byrne BA, Pesavento P, Hurley KF, Lindsay LL, Sykes JE, Vet Microbiol 2010 146 1-2 167 171 20605376
7. Mitral stenosis with bacterial myocarditis in a cat. Matsuu A, Kanda T, Sugiyama A, Murase T, Hikasa Y, J Vet Med Sci 2007 69 11 1171 1174 10.1292/jvms.69.1171 18057833
8. Fatal necrotising fasciitis and myositis in a cat associated with Streptococcus canis. Sura R, Hinckley LS, Risatti GR, Smyth JA, Vet Rec 2008 162 14 450 453 10.1136/vr.162.14.450 18390855
9. Relatedness of Streptococcus canis from canine streptococcal toxic shock syndrome and necrotizing fasciitis. DeWinter LM, Prescott JF, Can J Vet Res 1999 63 2 90 95 10369564
10. Identification of Streptococcus canis isolated from milk of dairy cows with subclinical mastitis. Hassan AA, Akineden O, Usleber E, J Clin Microbiol 2005 43 3 1234 1238 10.1128/JCM.43.3.1234-1238.2005 15750089
11. An outbreak of Streptococcus canis mastitis in a dairy herd in Israel. Chaffer M, Friedman S, Saran A, Younis A, N Z Vet J 2005 53 4 261 264 10.1080/00480169.2005.36557 16044188
12. Cross-infection between cats and cows: origin and control of Streptococcus canis mastitis in a dairy herd. Tikofsky LL, Zadoks RN, J Dairy Sci 2005 88 8 2707 2713 10.3168/jds.S0022-0302(05)72949-0 16027183
13. Streptococcus canis infections in humans: retrospective study of 54 patients. Galperine T, Cazorla C, Blanchard E, Boineau F, Ragnaud JM, Neau D, J Infect 2007 55 1 23 26 10.1016/j.jinf.2006.12.013 17320186
14. The other group G Streptococcus: increased detection of Streptococcus canis ulcer infections in dog owners. Lam MM, Clarridge JE 3rd, Young EJ, Mizuki S, J Clin Microbiol 2007 45 7 2327 2329 10.1128/JCM.01765-06 17475761
15. Identification of isolates of Streptococcus canis infecting humans. Whatmore AM, Engler KH, Gudmundsdottir G, Efstratiou A, J Clin Microbiol 2001 39 11 4196 4199 10.1128/JCM.39.1.4196-4199.2001 11682560
16. Septicemia caused by Streptococcus canis in a human. Bert F, Lambert-Zechovsky N, J Clin Microbiol 1997 35 3 777 779 9041434
17. Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae. Lefebure T, Richards VP, Lang P, Pavinski-Bitar P, Stanhope MJ, PLoS One 2012 7 5 37607 10.1371/journal.pone.0037607 22666370
18. Delineation of Streptococcus dysgalactiae, its subspecies, and its clinical and phylogenetic relationship to Streptococcus pyogenes. Jensen A, Kilian M, J Clin Microbiol 2012 50 1 113 126 10.1128/JCM.05900-11 22075580
19. Streptococcus ursoris sp. nov., isolated from the oral cavities of bears. Shinozaki-Kuwahara N, Takada K, Hirasawa M, Int J Syst Evol Microbiol 2011 61 Pt 1 40 44 20139281
20. Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB. Tapp J, Thollesson M, Herrmann B, Int J Syst Evol Microbiol 2003 53 Pt 6 1861 1871 14657115
21. Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Suzuki H, Lefebure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ, Genome Biol Evol 2011 3 168 185 10.1093/gbe/evr006 21282711
22. Population-based study of invasive disease due to beta-hemolytic streptococci of groups other than A and B. Broyles LN, Van Beneden C, Beall B, Facklam R, Shewmaker PL, Malpiedi P, Daily P, Reingold A, Farley MM, Clin Infect Dis 2009 48 6 706 712 10.1086/597035 19187026
23. Virulence of Streptococcus canis from canine streptococcal toxic shock syndrome and necrotizing fasciitis. DeWinter LM, Low DE, Prescott JF, Vet Microbiol 1999 70 1-2 95 110 10591501
24. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Kanaya S, Yamada Y, Kudo Y, Ikemura T, Gene 1999 238 1 143 155 10.1016/S0378-1119(99) 00225-5 10570992
25. Variation in the strength of selected codon usage bias among bacteria. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE, Nucleic Acids Res 2005 33 4 1141 1153 10.1093/nar/gki242 15728743
26. Circular genome visualization and exploration using CGView. Stothard P, Wishart DS, Bioinformatics 2005 21 4 537 539 10.1093/bioinformatics/bti054 15479716
27. Mechanism of membrane damage by streptolysin-O. Bhakdi S, Tranum-Jensen J, Sziegoleit A, Infect Immun 1985 47 1 52 60 3880730
28. Characterization of Streptococcus agalactiae CAMP factor as a pore-forming toxin. Lang SH, Palmer M, J Biol Chem 2003 278 40 38167 38173 10.1074/jbc.M303544200 12835325
29. Molecular basis of group A streptococcal virulence. Bisno AL, Brito MO, Collins CM, Lancet Infect Dis 2003 3 4 191 200 10.1016/S1473-3099(03)00576-0 12679262
30. M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island. Panchaud A, Guy L, Collyn F, Haenni M, Nakata M, Podbielski A, Moreillon P, Roten CA, BMC Genomics 2009 10 198 10.1186/1471-2164-10-198 19397826
31. Characterization of a new protective antigen of Streptococcus canis. Yang J, Liu Y, Xu J, Li B, Vet Res Commun 2010 34 5 413 421 10.1007/s11259-010-9414- 1 20490660
32. Genetic locus for streptolysin S production by group A Streptococcus. Nizet V, Beall B, Bast DJ, Datta V, Kilburn L, Low DE, De Azavedo JC, Infect Immun 2000 68 7 4245 4254 10.1128/IAI.68.7.4245-4254.2000 10858242
33. The differentiation of two distinct serologic varieties of streptolysin, streptolysin O and streptolysin S. Todd E, J Pathol Bacteriol 1938 47 423 445 10.1002/path.1700470307
34. Streptolysin S and necrotising infections produced by group G Streptococcus. Humar D, Datta V, Bast DJ, Beall B, De Azavedo JC, Nizet V, Lancet 2002 359 9301 124 129 10.1016/S0140-6736(02)07371-3 11809255
35. Identification of a streptolysin S-associated gene cluster and its role in the pathogenesis of Streptococcus iniae disease. Fuller JD, Camus AC, Duncan CL, Nizet V, Bast DJ, Thune RL, Low DE, De Azavedo JC, Infect Immun 2002 70 10 5730 5739 10.1128/IAI.70.10.5730-5739.2002 12228303
36. Streptolysin S-like virulence factors: the continuing sagA. Molloy EM, Cotter PD, Hill C, Mitchell DA, Ross RP, Nat Rev Microbiol 2011 9 9 670 681 10.1038/nrmicro2624 21822292
37. Streptococcal cellulitis following preparation of fresh raw seafood. Koh TH, Sng LH, Yuen SM, Thomas CK, Tan PL, Tan SH, Wong NS, Zoonoses Public Health 2009 56 4 206 208 10.1111/j.1863-2378.2008.01213.x 19309483
38. Invasive infection with Streptococcus iniae in Taiwan. Sun JR, Yan JC, Yeh CY, Lee SY, Lu JJ, J Med Microbiol 2007 56 Pt 9 1246 1249 17761491
39. Identification and characterization of sporadic isolates of Streptococcus iniae isolated from humans. Facklam R, Elliott J, Shewmaker L, Reingold A, J Clin Microbiol 2005 43 2 933 937 10.1128/JCM.43.2.933-937.2005 15695711
40. Streptococcus pseudoporcinus sp. nov., a novel species isolated from the genitourinary tract of women. Bekal S, Gaudreau C, Laurence RA, Simoneau E, Raynal L, J Clin Microbiol 2006 44 7 2584 2586 10.1128/JCM.02707-05 16825387
41. Invasive infections due to a fish pathogen, Streptococcus iniae. S. iniae Study Group. Weinstein MR, Litt M, Kertesz DA, Wyper P, Rose D, Coulter M, McGeer A, Facklam R, Ostach C, Willey BM, et al. N Engl J Med 1997 337 9 589 594 10.1056/NEJM199708283370902 9271480
42. Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T, Int J Syst Bacteriol 1995 45 2 406 408 10.1099/00207713-45-2-406 7537076
43. Pneumococcal virulence factors: structure and function. Jedrzejas MJ, Microbiol Mol Biol Rev 2001 65 2 187 207 first page, table of contents 10.1128/MMBR.65.2.187-207.2001 11381099
44. Multiple roles for Bordetella lipopolysaccharide molecules during respiratory tract infection. Harvill ET, Preston A, Cotter PA, Allen AG, Maskell DJ, Miller JF, Infect Immun 2000 68 12 6720 6728 10.1128/IAI.68.12.6720-6728. 2000 11083787
45. Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Glaser P, Rusniok C, Buchrieser C, Chevalier F, Frangeul L, Msadek T, Zouine M, Couve E, Lalioui L, Poyart C, et al. Mol Microbiol 2002 45 6 1499 1513 10.1046/j.1365-2958.2002.03126.x 12354221
46. Regulation of Streptococcus pneumoniae clp genes and their role in competence development and stress survival. Chastanet A, Prudhomme M, Claverys JP, Msadek T, J Bacteriol 2001 183 24 7295 7307 10.1128/JB.183.24.7295-7307.2001 11717289
47. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Blum G, Ott M, Lischewski A, Ritter A, Imrich H, Tschape H, Hacker J, Infect Immun 1994 62 2 606 614 7507897
48. Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536. Dobrindt U, Blum-Oehler G, Nagy G, Schneider G, Johann A, Gottschalk G, Hacker J, Infect Immun 2002 70 11 6365 6372 10.1128/IAI.70.11.6365-6372.2002 12379716
49. Identification of a DNA cytosine methyltransferase gene in conjugative transposon Tn5252. Sampath J, Vijayakumar MN, Plasmid 1998 39 1 63 76 10.1006/plas.1997.1316 9473447
50. Bacterial transformation with plasmid DNA. Saunders J, Saunders V, Methods in Microbiology Volume 21 London: Academic Press, Grinsted J, Bennett P, 1988
51. Extracellular deoxyribonuclease made by group A Streptococcus assists pathogenesis by enhancing evasion of the innate immune response. Sumby P, Barbian KD, Gardner DJ, Whitney AR, Welty DM, Long RD, Bailey JR, Parnell MJ, Hoe NP, Adams GG, et al. Proc Natl Acad Sci U S A 2005 102 5 1679 1684 10.1073/pnas.0406641102 15668390
52. Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Richards VP, Lang P, Bitar PD, Lefebure T, Schukken YH, Zadoks RN, Stanhope MJ, Infect Genet Evol 2011 11 6 1263 1275 10.1016/j.meegid.2011.04.019 21536150
53. Emergence and Global Dissemination of Host-Specific Streptococcus agalactiae Clones. Sørensen UB, Poulsen K, Ghezzo C, Margarit I, Kilian M, MBio 2010 1 3
54. Genomic diversity and evolution within the species Streptococcus agalactiae. Brochet M, Couve E, Zouine M, Vallaeys T, Rusniok C, Lamy MC, Buchrieser C, Trieu-Cuot P, Kunst F, Poyart C, et al. Microbes Infect 2006 8 5 1227 1243 10.1016/j.micinf.2005.11.010 16529966
55. Hyperinvasive neonatal group B Streptococcus has arisen from a bovine ancestor. Bisharat N, Crook DW, Leigh J, Harding RM, Ward PN, Coffey TJ, Maiden MC, Peto T, Jones N, J Clin Microbiol 2004 42 5 2161 2167 10.1128/JCM.42.5.2161- 2167.2004 15131184
56. Prophage genomics. Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H, Microbiol Mol Biol Rev 2003 67 2 238 276 10.1128/MMBR.67.2.238-276.2003 12794192
57. Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria. Lucchini S, Desiere F, Brussow H, Virology 1999 263 2 427 435 10.1006/viro.1999.9959 10544115
58. Inactivation of the alpha C protein antigen gene, bca, by a novel shuttle/suicide vector results in attenuation of virulence and immunity in group B Streptococcus. Li J, Kasper DL, Ausubel FM, Rosner B, Michel JL, Proc Natl Acad Sci U S A 1997 94 24 13251 13256 10.1073/pnas.94.24.13251 9371832
59. Isolation of Streptococcus urinalis from a human blood culture. Peltroche-Llacsahuanga H, Frye B, Haase G, J Med Microbiol 2012 61 Pt 5 740 742 22245791
60. An unusual Streptococcus from human urine, Streptococcus urinalis sp. nov. Collins MD, Hutson RA, Falsen E, Nikolaitchouk N, LaClaire L, Facklam RR, Int J Syst Evol Microbiol 2000 50 Pt 3 1173 1178 10843060
61. The VirB4 family of proposed traffic nucleoside triphosphatases: common motifs in plasmid RP4 TrbE are essential for conjugation and phage adsorption. Rabel C, Grahn AM, Lurz R, Lanka E, J Bacteriol 2003 185 3 1045 1058 10.1128/JB.185.3.1045-1058.2003 12533481
62. Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae,S. dysgalactiae subsp. dysgalactiae, and S. uberis. Haenni M, Saras E, Bertin S, Leblond P, Madec JY, Payot S, Appl Environ Microbiol 2010 76 24 7957 7965 10.1128/AEM.00805-10 20952646
63. Co-transfer of vanA and aggregation substance genes from Enterococcus faecalis isolates in intra- and interspecies matings. Paoletti C, Foglia G, Princivalli MS, Magi G, Guaglianone E, Donelli G, Pruzzo C, Biavasco F, Facinelli B, J Antimicrob Chemother 2007 59 5 1005 1009 10.1093/jac/dkm057 17350988
64. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, et al. Proc Natl Acad Sci U S A 2001 98 8 4658 4663 10.1073/pnas.071559398 11296296
65. Experimentally induced intramammary infection with multiple strains of Streptococcus uberis. Pryor SM, Cursons RT, Williamson JH, Lacy-Hulbert SJ, J Dairy Sci 2009 92 11 5467 5475 10.3168/jds.2009-2223 19841209
66. Use of molecular epidemiology in veterinary practice. Zadoks RN, Schukken YH, Vet Clin North Am Food Anim Pract 2006 22 1 229 261 10.1016/j.cvfa.2005.11. 005 16517304
67. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Excoffier L, Smouse PE, Quattro JM, Genetics 1992 131 479 491 1644282
68. Inference of bacterial microevolution using multilocus sequence data. Didelot X, Falush D, Genetics 2007 175 3 1251 1266 17151252
69. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Guttman DS, Dykhuizen DE, Science 1994 266 5189 1380 1383 10.1126/science.7973728 7973728
70. A comparison of homologous recombination rates in bacteria and archaea. Vos M, Didelot X, ISME J 2009 3 2 199 208 10.1038/ismej.2008.93 18830278
71. Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray comparative genomic hybridization. Lang P, Lefebure T, Wang W, Zadoks RN, Schukken Y, Stanhope MJ, Infect Genet Evol 2009 9 2 179 188 10.1016/j.meegid.2008.10.015 19056519
72. Neutral microepidemic evolution of bacterial pathogens. Fraser C, Hanage WP, Spratt BG, Proc Natl Acad Sci U S A 2005 102 6 1968 1973 10.1073/pnas.0406993102 15684071
73. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG, J Bacteriol 2004 186 5 1518 1530 10.1128/JB.186.5.1518-1530.2004 14973027
74. Inference of population structure using multilocus genotype data. Pritchard JK, Stephens M, Donnelly P, Genetics 2000 155 2 945 959 10835412
75. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Falush D, Stephens M, Pritchard JK, Genetics 2003 164 4 1567 1587 12930761
76. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Evanno G, Regnaut S, Goudet J, Mol Ecol 2005 14 8 2611 2620 10.1111/j.1365-294X.2005.02553.x 15969739
77. Etiology and antimicrobial susceptibility of udder pathogens from cases of subclinical mastitis in dairy cows in Sweden. Persson Y, Nyman AK, Gronlund-Andersson U, Acta Vet Scand 2011 53 36 10.1186/1751-0147-53-36 21649936
78. Prevalence and distribution of mastitis pathogens in subclinically infected dairy cows in Flanders, Belgium. Piepers S, De Meulemeester L, de Kruif A, Opsomer G, Barkema HW, De Vliegher S, J Dairy Res 2007 74 4 478 483 17931457
79. Prevalence of intramammary infection in Dutch dairy herds. Sampimon O, Barkema HW, Berends I, Sol J, Lam T, J Dairy Res 2009 76 2 129 136 10.1017/S0022029908003762 19121233
80. The incidence and aetiology of clinical bovine mastitis on 14 farms in Northland, New Zealand. Petrovski KR, Heuer C, Parkinson TJ, Williamson NB, N Z Vet J 2009 57 2 109 115 10.1080/00480169.2009.36887 19471330
81. Cross-sectional study of Streptococcus species in quarter milk samples of dairy cows in the canton of Bern, Switzerland. Guelat-Brechbuehl M, Thomann A, Albini S, Moret-Stalder S, Reist M, Bodmer M, Michel A, Niederberger MD, Kaufmann T, Vet Rec 2010 167 6 211 215 10.1136/vr.167.6.211 20693505
82. Antimicrobial susceptibility of udder pathogens from cases of acute clinical mastitis in dairy cows. Bengtsson B, Unnerstad HE, Ekman T, Artursson K, Nilsson-Ost M, Waller KP, Vet Microbiol 2009 136 1-2 142 149 19058930
83. Avise JC, Phylogeography. The history and formation of species Cambridge, MA: Harvard University Press 2000
84. Templeton AR, Population genetics and microevolutionary theory New Jersey: Wiley 2006
85. Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group. Delorme C, Poyart C, Ehrlich SD, Renault P, J Bacteriol 2007 189 4 1330 1341 10.1128/JB.01058-06 17085557
86. Inter-species genetic movement may blur the epidemiology of streptococcal diseases in endemic regions. Davies MR, Tran TN, McMillan DJ, Gardiner DL, Currie BJ, Sriprakash KS, Microbes Infect 2005 7 9-10 1128 1138 15893492
87. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 5 821 829 10.1101/gr.074492.107 18349386
88. High-throughput functional annotation and data mining with the Blast2GO suite. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A, Nucleic Acids Res 2008 36 10 3420 3435 10.1093/nar/gkn176 18445632
89. van Dongen S, Graph clustering by flow simulation University of Utrecht. 2000
90. Evaluation of clustering algorithms for protein-protein interaction networks. Brohee S, van Helden J, BMC Bioinformatics 2006 7 488 10.1186/1471-2105-7-488 17087821
91. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Enright MC, Spratt BG, Microbiology 1998 144 Pt 11 3049 3060 9846740
92. Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Enright MC, Spratt BG, Kalia A, Cross JH, Bessen DE, Infect Immun 2001 69 4 2416 2427 10.1128/IAI.69.4.2416-2427.2001 11254602
93. Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization. Goh SH, Santucci Z, Kloos WE, Faltyn M, George CG, Driedger D, Hemmingsen SM, J Clin Microbiol 1997 35 12 3116 3121 9399505
94. Development of a PCR assay for rapid detection of enterococci. Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG, J Clin Microbiol 1999 37 11 3497 3503 10523541
95. Multilocus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA. Zadoks RN, Schukken YH, Wiedmann M, J Clin Microbiol 2005 43 5 2407 2417 10.1128/JCM.43.5.2407-2417.2005 15872274
96. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Katoh K, Misawa K, Kuma K, Miyata T, Nucleic Acids Res 2002 30 14 3059 3066 10.1093/nar/gkf436 12136088
97. DNASP, DNA polymorphism analyses by the coalescent and other methods. Rozas J, Sánchez-DelBarrio J, Messegyer X, Rozas R, Bioinformatics 2003 19 2496 2497 10.1093/bioinformatics/btg359 14668244
98. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Excoffier L, Laval G, Schneider S, Evol Bioinform Online 2005 1 47 50