Streptococci

Molecular Typing in Bacterial Infections

Volumn , Issue , 2013, Pages 109-126

  McGee, Lesley ^a   Beall, Bernard ^a  

^a NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85029354638     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-62703-185-1_8     Document Type: Chapter

References (99)

1. Broyles LN, Van Beneden C, Beall B, Facklam R, Shewmaker PL, Malpiedi P, Daily P, Reingold A, Farley MM (2009) Population-based study of invasive disease due to beta hemolytic streptococci of groups other than A and B. Clin Infect Dis 48:706-712.
2. Hardie JM, Whiley RA (1997) Classification and overview of the genera Streptococcus and Enterococcus. J Appl Microbiol Symp Suppl 83:1S-11S.
3. Wertheim HFL, Nghia HDT, Taylor W et al (2009) Streptococcussuis: An emerging human pathogen. Clin Infect Dis 48:617-625.
4. Baer ET (2000) Iatrogenic Meningitis: The Case for Face Masks. Clin Infect Dis 31:519-521.
5. Schleifer KH, Kilpper-Balz R (1987) Molecular and chemotaxanomic approaches to the classification of streptococci, enterococci and lactococci: a review. Syst Appl Microbiol 10:1-19.
6. Lancefield RC (1933) A serological differentiation of human and other groups of streptococci. J Exp Med 59:141-158.
7. Facklam R (2002) What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613-630.
8. Kilian M, Poulsen K, Blomqvist T, Håvarstein LS, Bek-Thomsen M, Tettelin H, Sørensen UB (2008) Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One 3:e2683.
9. Enright MC, Spratt BG, Kalia A, Cross JH, Bessen DE (2001) Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect Immun 69:2416-2427.
10. Jones N, Bohnsack JF, Takahashi S, Oliver KA, Chan MS, Kunst F, Glaser P, Rusniok C, Crook DW, Harding RM, Bisharat N, Spratt BG (2003) Multilocus sequence typing system for group B streptococcus. J Clin Microbiol 41:2530-2536.
11. Enright MC, Spratt BG (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144:3049-3060.
12. Ahmad Y, Gertz RE Jr, Li Z, Sakota V, Broyles LN, Van Beneden C, Facklam R, Shewmaker PL, Reingold A, Farley MM, Beall BW (2009) Genetic relationships deduced from emm and multilocus sequence typing of invasive Streptococcus dysgalactiae subsp. equisimilis and S. canis recovered from isolates collected in the United States. J Clin Microbiol 47: 2046-2054.
13. McMillan DJ, Bessen DE, Pinho M, Ford C, Hall GS, Melo-Cristino J, Ramirez M (2010) Population genetics of Streptococcus dysgalactiae subspecies equisimilis reveals widely dispersed clones and extensive recombination. PLoS One 5:e11741.
14. Cunningham MW (2000) Pathogenesis of group A streptococcal infections. Clin Microbiol Rev 13:47-511.
15. Johnson DR, Kaplan EL, VanGheem A, Facklam RR, Beall B (2006) Characterization of group A streptococci (Streptococcus pyogenes): correlation of M-protein and emm -type with T-protein agglutination pattern and serum opacity factor. J Med Microbiol 55:157-164.
16. Lancefield RC (1962) Current knowledge of type-specific M antigens of group A streptococci. J Immunol 89:307-313.
17. Sakota V, Fry AM, Lietman TM, Facklam RR, Li Z, Beall B (2006) Genetically diverse group A streptococci from children in far-western Nepal share high genetic relatedness with isolates from other countries. J Clin Microbiol 44:2160-2166.
18. Johnson DR, Kaplan E, Sramek J, Bicova R, Havlicek J, Havlickova H, Motlova J, Kriz P (1996) Laboratory diagnosis of group A streptococcal infections. WHO, Geneva, Switzerland.
19. Mora M, Bensi G, Capo S, Falugi F, Zingaretti C, Manetti AGO, Maggi T, Taddei AR, Grandi G, Telford JL (2005) Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens. Proc Natl Acad Sci USA 102:15641-15646.
20. Falugi F, Zingaretti C, Pinto V, Mariani M, Amodeo L, Manetti AG, Capo S, Musser JM, Orefici G, Margarit I, Telford JL, Grandi G, Mora M (2008) Sequence variation in group A Streptococcus pili and association of pilus backbone types with lancefield T serotypes. J Infect Dis 198:1834-1841.
21. Beall B, Gherardi G, Lovgren M, Facklam R, Forwick B, Tyrell G (2000) emm and sof gene sequence variation in relation to serological typing of opacity-factor-positive group A streptococci. Microbiol 146:1195-1209.
22. Musser JM, Kapur V, Szeto J, Pan X, Swanson DS, Martin DR (1995) Genetic diversity and relationships among Streptococcus pyogenes strain expressing serotype M1 protein: recent intercontinental spread of a subclone causing episodes of invasive disease. Infect Immun 63:994-1003.
23. McGregor KF, Spratt BG, Kalia A, Bennett A, Bilek N, Beall B, Bessen DE (2004) Multilocus sequence typing of Streptococcus pyogenes representing most known emm types and distinctions among subpopulation genetic structures. J Bacteriol 186:4285-4294.
24. Steer AC, Law I, Matatolu L, Beall BW, Carapetis JR (2009) Global emm type distribution of group A streptococci: systematic review and implications for vaccine development. Lancet Infect Dis 9:611-616.
25. Beall B, Facklam R, Thompson T (1996) Sequencing emm -specific PCR products for routine and accurate typing of groupA streptococci. J Clin Microbiol 34:953-958.
26. Facklam R, Beall B, Efstratiou FV, Kaplan E, Kriz P, Lovgren M, Martin D, Schwartz B, Totolian A, Bessen D, Hollingshead S, Rubin F, Scott J, Tyrrell G (1999) Report of an international workshop: demonstration of emm typing and validation of provisional M-types of group A streptococci. Emerg Infect Dis 5:247-253.
27. Centers for Disease Control and Prevention (2011) CDC Streptococcus Laboratory. http:// www.cdc.gov/ncidod/biotech/strep/M-ProteinGene_typing.htm. Accessed 15 May 2011.
28. Collins CM, Kimura A, Bisno AL (1992) Group G streptococcal M protein exhibits structural features analogous to those of class I M protein of group A streptococci. Infect Immun 60:3689-3696.
29. Dale JB, Penfound T, Chiang EY, Long V, Shulman ST, Beall B (2005) Multivalent group A streptococcal vaccine elicits bactericidal antibodies against variant M subtypes. Clin Diagn Lab Immunol 12:833-836.
30. Li Z, Sakota V, Jackson D, Franklin AR, Beall B (2003) The array of M protein gene subtypes in 1061 recent invasive group A streptococcal isolates recovered from the Active Bacterial Core Surveillance. J Infect Dis 188:1587-1592.
31. Lee EH, Ferguson D, Jernigan D, Greenwald M, Coté T, Bos JE, Guarner J, Zaki S, Schuchat A, Beall B, Srinivasan A (2007) Invasive group-A streptococcal infection in an allograft recipient. A case report. J Bone Joint Surg Am 89:2044-2047.
32. Top FH Jr, Wannamaker LW (1968) The serum opacity reaction of Streptococcus pyogenes: frequency of production of streptococcal lipoproteinase by strains of different serological types and the relationship of M protein production. J Hyg (Lond) 66:49-58.
33. Whatmore A, Kapur V, Sullivan D, Musser J, Kehoe M (1994) Non-congruent relationships between variation in emm gene sequences and the population structure of group A streptococci. Mol Microbiol 14:619-631.
34. Rakonjac JA, Robbins JC, Fischetti VA (1995) DNA sequence of the serum opacity factor of group A streptococci: identification of afibronectin-binding repeat domain. Infect Immun 63:622-631.
35. Courtney HS, Hasty DL, Li Y, Chiang HC, Thacker JL, Dale JB (1999) Serum opacity factor is a majorfibronectin-binding protein and a virulence determinant of M type 2 Streptococcus pyogenes. Mol Microbiol 32:89-98.
36. Beall B, Facklam RR, Elliot JA, Franklin AR, Hoenes T, Jackson D, Laclaire L, Thompson T, Viswanathan R (1998) Streptococcal emm types associated with T-agglutination types and the use of conserved emm gene restriction fragment patterns for subtyping group A streptococci. J Med Microbiol 4:1-5.
37. Espinosa LE, Li Z, Gomez Barreto D, Calderon Jaimes E, Rodriguez RS, Sakota V, Facklam RR, Beall B (2003) M protein gene type distribution among group A streptococcal clinical isolates recovered in Mexico City, Mexico, from 1991 to 2000, and Durango, Mexico, from 1998 to 1999; overlap with type distribution within the United States. J Clin Microbiol 41:373-378.
38. Gardiner D, Harta J, Currie B, Mathews JD, Kemp DJ, Sriprakash KS (1995) Vir typing: a long-PCR typing methods for group A streptococci. PCR Methods App 4:288-293.
39. Shundi L, Surdeanu M, Damian M (2000) Comparison of serotyping, ribotyping and PFGE for distinguishing group A streptococcus strains isolated in Albania. Eur J Epidemiol 16:257-263.
40. Doktor SZ, Beyer JM, Flamm RK, Shortridge VD (2005) Comparison of emm typing and ribotyping with three restriction enzymes to characterize clinical isolates of Streptococcus pyogenes. J Clin Microbiol 43:150-155.
41. Kataja J, Huovinen EA, Perez-Trallero E, Seppala H (2002) Clonal relationships among isolates of erythromycin-resistant Streptococcus pyogenes of different geographical origin. Eur J Clin Microbiol Infect Dis 21:589-595.
42. Nandi S, Ganguly NK, Kumar R, Bakshi DK, Sagar V, Chakraborti A (2008) Genotyping of group A streptococcus by various molecular methods. Indian J Med Res 127:71-77.
43. Gonzalez-Rey C, Belin AM, Jorbeck H, Norman M, Krovacek K, Henriques B et al (2003) PARD-PCR and PFGE as tools in the investigation of an outbreak of beta-hemolytic streptococcus group A in a Swedish hospital. Comp Immunol Microbiol Infect Dis 26:25-35.
44. Verani JR, McGee L, Schrag SJ (2010) Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC) (2010) Prevention of perinatal group B streptococcal disease--revised guidelines from CD. MMWR Recomm Rep 59(RR-10):1-36.
45. Centers for Diseases Control and Prevention (2007) Perinatal group B streptococcal disease after universal screening recommendations-United States, 2003-2005. MMWR Morb Mortal Wkly Rep 56:701-705.
46. Slotved HC, Kong F, Lambertsen L, Sauer S, Gilbert GL (2007) Serotype IX, a Proposed New Streptococcus agalactiae Serotype. J Clin Microbiol 45:2929-2936.
47. Manning SD, Lacher DW, Davies HD, Foxman B, Whittam TS (2005) DNA polymorphism and molecular subtyping of the capsular gene cluster of group B streptococcus. J Clin Microbiol 43:6113-6116.
48. Lancefield RC (1934) Serological differentiation of specific types of bovine haemolytic streptococci (group B). J Exp Med 59:441-458.
49. Johnson DR, Ferrieri P (1984) Group B streptococcal Ibc protein antigen: distribution of two determinants in wild-type strains of common serotypes. J Clin Microbiol 19:506-510.
50. Hakansson S, Burman LG, Henrichsen J, Holm SE (1992) Novel coagglutination method for serotyping group B streptococci. J Clin Microbiol 30:3268-3269.
51. Arakere G, Flores AE, Ferrieri P, Frasch CE (1999) Inhibition enzyme-linked immunosorbent assay for serotyping of group B streptococcal isolates. J Clin Microbiol 37:2564-2567.
52. Park CJ, Vandel NM, Ruprai DK, Martin EA, Gates KM, Coker D (2001) Detection of group B streptococcal colonization in pregnant women using direct latex agglutination testing of selective broth. J Clin Microbiol 39:408-409.
53. Kong F, Gowan S, Martin D, James G, Gilbert GL (2002) Serotype identification of group B streptococci by PCR and sequencing. J Clin Microbiol 40:216-226.
54. Borchardt SM, Foxman B, Chaffin DO, Rubens CE, Tallman PA, Manning SD, Baker CJ, Marrs CF (2004) Comparison of DNA dot blot hybridization and Lancefield capillary precipitin methods for group B streptococcal capsular typing. J Clin Microbiol 42:146-150.
55. Martins ER, Melo-Cristino J, Ramirez M (2007) Reevaluating the serotype II capsular locus of Streptococcus agalactiae. J Clin Microbiol 45:3384-3386.
56. Poyart C, Tazi A, Réglier-Poupet H, Billoët A, Tavares N, Raymond J, Trieu-Cuot P (2007) Multiplex PCR assay for rapid and accurate capsular typing of group B streptococci. J Clin Microbiol 45:1985-1988.
57. Imperi M, Pataracchia M, Alfarone G, Baldassarri L, Orefici G, Creti R (2010) A multiplex PCR assay for the direct identification of the capsular type (Ia to IX) of Streptococcus agalactiae. J Microbiol Methods 80:212-214.
58. Kong F, Ma L, Gilbert GL (2005) Simultaneous detection and serotype identification of Streptococcus agalactiae using multiplex PCR and reverse line blot hybridization. J Med Microbiol 54:1133-1138.
59. Wen L, Wang Q, Li Y, Kong F, Gilbert GL, Cao B, Wang L, Feng L (2006) Use of a serotypespecific DNA microarray for identification of group B streptococcus (Streptococcus agalactiae). J Clin Microbiol 44:1447-1452.
60. Kong F, Gowan S, Martin D, James G, Gilbert GL (2002) Molecular profiles of group B streptococcal surface protein antigen genes: relationship to molecular serotypes. J Clin Microbiol 40:620-626.
61. Elliott JA, Farmer KD, Facklam RR (1998) Sudden increase in isolation of group B streptococci, serotype V, is not due to emergence of a new pulsed-fi eld gel electrophoresis type. J Clin Microbiol 36:2115-2116.
62. Lin FY, Whiting A, Adderson E, Takahashi S, Dunn DM, Weiss R, Azimi PH, Philips JB 3rd, Weisman LE, Regan J, Clark P, Rhoads GG, Frasch CE, Troendle J, Moyer P, Bohnsack JF (2006) Phylogenetic lineages of invasive and colonizing strains of serotype III group B Streptococci from neonates: a multicenter prospective study. J Clin Microbiol 44:1257-1261.
63. Quentin R, Huet H, Wang FS, Geslin P, Goudeau A, Selander RK (1995) Characterization of Streptococcus agalactiae strains by multilocus enzyme genotype and serotype: identification of multiple virulent clone families that cause invasive neonatal disease. J Clin Microbiol 33:2576-2581.
64. Bisharat N, Jones N, Marchaim D, Block C, Harding RM, Yagupsky P, Peto T, Crook DW (2005) Population structure of group B Streptococcus from a low-incidence region for invasive neonatal disease. Microbiology 151:1875-1881.
65. Bohnsack JF, Whiting A, Gottschalk M, Dunn DM, Weiss R, Azimi PH, Philips JB III, Weisman LE, Rhoads GG, Lin FYC (2008) Population structure of invasive and colonizing strains of Streptococcus agalactiae from neonates of six US academic centers from 1995 to 1999. J Clin Microbiol 46:1285-1291.
66. Lund E, Henrichsen J (1978) Laboratory diagnosis, serology and epidemiology of Streptococcus pneumoniae. In: Bergan T, Norris J (eds) Methods in microbiology. Academic, London, pp 241-262.
67. Park IH, Pritchard DG, Cartee R, Brandao A, Brandileone MC, Nahm MH (2007) Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. J Clin Microbiol 45:1225-1233.
68. Bratcher PE, Kim KH, Kang JH, Hong JY, Nahm MH (2010) Identification of natural pneumococcal isolates expressing serotype 6D by genetic, biochemical, and serological characterization. Microbiology 156(Pt 2):555-560.
69. Slotved HC, Kaltoft M, Skovsted IC, Kerrn MB, Espersen F (2004) Simple, rapid latex agglutination test for serotyping of pneumococci (Pneumotest-Latex). J Clin Microbiol 42:2518-2522.
70. Park MK, Briles DE, Nahm MH (2000) A latex bead-based fl ow cytometric immunoassay capable of simultaneous typing of multiple pneumococcal serotypes (Multibead assay). Clin Diagn Lab Immunol 7:486-489.
71. Findlow H, Laher G, Balmer P, Broughton C, Carrol ED, Borrow R (2009) Competitive inhibition fl ow analysis assay for the non-culture-based detection and serotyping of pneumococcal capsular polysaccharide. Clin Vaccine Immunol 16:222-229.
72. Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, Collins M, Donohoe K, Harris D, Murphy L, Quail MA, Samuel G, Skovsted IC, Kaltoft MS, Barrell B, Reeves PR, Parkhill J, Spratt BG (2006) Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet 2:262-269.
73. Pai R, Gertz RE, Beall B (2006) Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae. J Clin Microbiol 44:124-131.
74. Dias CA, Teixeira LM, Carvalho Mda G, Beall B (2007) Sequential multiplex PCR for determining capsular serotypes of pneumococci recovered from Brazilian children. J Med Microbiol 56:1185-1188.
75. Morais L, Carvalho Mda G, Roca A, Flannery B, Mandomando I, Soriano-Gabarró M, Sigauque B, Alonso P, Beall B (2007) Sequential multiplex PCR for identifying pneumococcal capsular serotypes from South-Saharan African clinical isolates. J Med Microbiol 56:1181-1184.
76. Antonio M, Hakeem I, Sankareh K, Cheung YB, Adegbola RA (2009) Evaluation of sequential multiplex PCR for direct detection of multiple serotypes of Streptococcus pneumoniae from nasopharyngeal secretions. J Med Microbiol 58:296-302.
77. da Gloria CM, Pimenta FC, Jackson D, Roundtree A, Ahmad Y, Millar EV, O'Brien KL, Whitney CG, Cohen AL, Beall BW (2010) Revisiting pneumococcal carriage by use of broth enrichment and PCR techniques for enhanced detection of carriage and serotypes. J Clin Microbiol 48:1611-1618.
78. Saha SK, Darmstadt GL, Baqui AH, Hossain B, Islam M, Foster D, Al-Emran H, Naheed A, Arifeen SE, Luby SP, Santosham M, Crook D (2008) Identification of serotype in culture negative pneumococcal meningitis using sequential multiplex PCR: implication for surveillance and vaccine design. PLoS One 3:e3576.
79. Azzari C, Moriondo M, IndolfiG, Massai C, Becciolini L, de Martino M, Resti M (2008) Molecular detection methods and serotyping performed directly on clinical samples improve diagnostic sensitivity and reveal increased incidence of invasive disease by Streptococcus pneumoniae in Italian children. J Med Microbiol 57:1205-1212.
80. Yu J, Carvalho Mda G, Beall B, Nahm MH (2008) A rapid pneumococcal serotyping system based on monoclonal antibodies and PCR. J Med Microbiol 57:171-178.
81. Tarragó D, Fenoll A, Sánchez-Tatay D, Arroyo LA, Muñoz-Almagro C, Esteva C, Hausdorff WP, Casal J, Obando I (2008) Identification of pneumococcal serotypes from culture-negative clinical specimens by novel real-time PCR. Clin Microbiol Infect 14:828-834.
82. Wang Y, Kong F, Yang Y, Gilbert GL (2008) A multiplex PCR-based reverse line blot hybridization (mPCR/RLB) assay for detection of bacterial respiratory pathogens in children with pneumonia. Pediatr Pulmonol 43:150-159.
83. Hermans PW, Sluijter M, Hoogenboezem T, Heersma H, van Belkum A, de Groot R (1995) Comparative study offive different DNAfingerprint techniques for molecular typing of Streptococcus pneumoniae strains. J Clin Microbiol 33:1606-1612.
84. Coffey TJ, Enright MC, Daniels M, Morona JK, Morona R, Hryniewicz W, Paton JC, Spratt BG (1998) Recombinational exchanges at the capsular polysaccharide biosynthetic locus lead to frequent serotype changes among natural isolates of Streptococcus pneumoniae. Mol Microbiol 27:73-83.
85. Muñoz R, Coffey TJ, Daniels M, Dowson CG, Laible G, Casal J, Hakenbeck R, Jacobs M, Musser JM, Spratt BG et al (1991) Intercontinental spread of a multiresistant clone of serotype 23F Streptococcus pneumoniae. J Infect Dis 164:302-306.
86. Brueggemann AB, Pai R, Crook DW, Beall B (2007) Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog 3:e168.
87. Beall BW, Gertz RE, Hulkower RL, Whitney CG, Moore MR, Brueggemann AB (2011) Shifting genetic structure of invasive serotype 19A pneumococci in the United States. J Infect Dis 203:1360-1368.
88. McGee L, McDougal L, Zhou J, Spratt BG, Tenover FC, George R, Hakenbeck R, Hryniewicz W, Lefévre JC, Tomasz A, Klugman KP (2001) Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol 39:2565-2571.
89. Do T, Jolley KA, Maiden MC, Gilbert SC, Clark D, Wade WG, Beighton D (2009) Population structure of Streptococcus oralis. Microbiology 155:2593-2602.
90. Alam S, Brailsford SR, Whiley RA, Beighton D (1999) PCR-Based methods for genotyping viridans group streptococci. J Clin Microbiol 37:2772-2776.
91. Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG (2009) Assigning strains to bacterial species via the internet. BMC Biol 7:3.
92. Delorme C, Poyart C, Ehrlich SD, Renault P (2007) Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group. J Bacteriol 189:1330-1341.
93. Shewmaker PL, Gertz RE Jr, Kim CY, de Fijter S, DiOrio M, Moore MR, Beall BW (2010) Streptococcus salivarius meningitis case strain traced to oral fl ora of anesthesiologist. J Clin Microbiol 48:2589-2591.
94. Srinivasan V, Chitnis AS, Gertz Jr RE, Shewmaker PL, McGee L, Patrick S, Guh AY, Van Beneden C, Turabelidze G and Beall BW (2011) Streptococcus salivarius meningitis case strain traced to oral fl ora of healthcare provider. In: 111th General Meeting of the American Society for Microbiology. New Orleans, LA, USA.
95. Chatellier S, Gottschalk M, Higgins R, Brousseau R, Harel J (1999) Relatedness of Streptococcus suis serotype 2 isolates from different geographic origins as evaluated by molecularfingerprinting and phenotyping. J Clin Microbiol 37:362-366.
96. King SJ, Leigh JA, Heath PJ, Luque I, Tarradas C, Dowson CG, Whatmore AM (2002) Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis: identification of virulent clones and potential capsular serotype exchange. J Clin Microbiol 40:3671-3680.
97. Coffey TJ, Pullinger GD, Urwin R, Jolley KA, Wilson SM, Maiden MC, Leigh JA (2006) First insights into the evolution of Streptococcus uberis: a multilocus sequence typing scheme that enables investigation of its population biology. Appl Environ Microbiol 72:1420-1428.
98. Webb K, Jolley KA, Mitchell Z, Robinson C, Newton JR, Maiden MC, Waller A (2008) Development of an unambiguous and discriminatory multilocus sequence typing scheme for the Streptococcus zooepidemicus group. Microbiology 154:3016-3024.
99. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG (2004) eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186:1518-1530.