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Enterobacteriaceae

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Molecular Typing in Bacterial Infections

Part of the book series: Infectious Disease ((ID))

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Abstract

A number of the members of the family Enterobacteriaceae can serve as human and animal pathogens, causing a wide range of nosocomial, zoonotic, and foodborne illnesses. The ability to characterize these microorganisms to determine the relationship between members of a particular species is important to develop strategies to limit bacterial disease. There are multiple molecular typing methods that are available to characterize different microorganisms; in general these typing methods can be delineated into three general categories: those based on the comparison of profiles generated following restriction digestion of the bacterial DNA, those based on the differential amplification profiles generated following amplification of particular genetic target using polymerase chain reactions (PCR), and those based on the direct detection of sequence differences in the bacterial genome. This chapter explores these various typing approaches and the specific methods that are available to differentiate bacterial pathogens, focusing on the strengths and weaknesses of the molecular typing methods to distinguish among members of the different Enterobacteriaceae species, which should provide insights on the best technique(s) for particular typing applications.

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References

  1. Busch U, Nitschko H (1999) Methods for the differentiation of microorganisms. J Chromatogr B Biomed Sci Appl 722:263–278

    Article  PubMed  CAS  Google Scholar 

  2. Foley SL, White DG, McDermott PF, Walker RD, Rhodes B, Fedorka-Cray PJ, Simjee S, Zhao S (2006) Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. J Clin Microbiol 44:3569–3577

    Article  PubMed  CAS  Google Scholar 

  3. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669

    PubMed  CAS  Google Scholar 

  4. Schaberg DR, Tompkins LS, Falkow S (1981) Use of agarose gel electrophoresis of plasmid deoxyribonucleic acid to fingerprint Gram-negative bacilli. J Clin Microbiol 13:1105–1108

    PubMed  CAS  Google Scholar 

  5. Mayer LW (1988) Use of plasmid profiles in epidemiologic surveillance of disease outbreaks and in tracing the transmission of antibiotic resistance. Clin Microbiol Rev 1:228–243

    PubMed  CAS  Google Scholar 

  6. Kado CI, Liu ST (1981) Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145:1365–1373

    PubMed  CAS  Google Scholar 

  7. Olsen JE, Brown DJ, Skov MN, Christensen JP (1993) Bacterial typing methods suitable for epidemiological analysis. Applications in investigations of salmonellosis among livestock. Vet Q 15:125–135

    Article  PubMed  CAS  Google Scholar 

  8. Nauerby B, Pedersen K, Dietz HH, Madsen M (2000) Comparison of Danish isolates of Salmonella enterica serovar enteritidis PT9a and PT11 from hedgehogs (Erinaceus europaeus) and humans by plasmid profiling and pulsed-field gel electrophoresis. J Clin Microbiol 38:3631–3635

    PubMed  CAS  Google Scholar 

  9. Aktas Z, Day M, Kayacan CB, Diren S, Threlfall EJ (2007) Molecular characterization of Salmonella Typhimurium and Salmonella Enteritidis by plasmid analysis and pulsed-field gel electrophoresis. Int J Antimicrob Agents 30:541–545

    Article  PubMed  CAS  Google Scholar 

  10. Olsen JE (2000) Molecular typing of Salmonella. In: Wray C, Wray A (eds) Salmonella in Domestic Animals. CAB International, U.K., pp 429–443

    Google Scholar 

  11. Foley SL, Zhao S, Walker RD (2007) Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens. Foodborne Pathog Dis 4:253–276

    Article  PubMed  CAS  Google Scholar 

  12. Nayak R, Stewart T, Wang RF, Lin J, Cerniglia CE, Kenney PB (2004) Genetic diversity and virulence gene determinants of antibiotic-resistant Salmonella isolated from preharvest turkey production sources. Int J Food Microbiol 91:51–62

    Article  PubMed  CAS  Google Scholar 

  13. Johnson JR, Sannes MR, Croy C, Johnston B, Clabots C, Kuskowski MA, Bender J, Smith KE, Winokur PL, Belongia EA (2007) Antimicrobial drug-resistant Escherichia coli from humans and poultry products, Minnesota and Wisconsin, 2002–2004. Emerg Infect Dis 13:838–846

    Article  PubMed  CAS  Google Scholar 

  14. Capilla S, Goni P, Rubio MC, Castillo J, Millan L, Cerda P, Sahagun J, Pitart C, Beltran A, Gomez-Lus R (2003) Epidemiological study of resistance to nalidixic acid and other antibiotics in clinical Yersinia enterocolitica O:3 isolates. J Clin Microbiol 41:4876–4878

    Article  PubMed  CAS  Google Scholar 

  15. Liu PY, Lau YJ, Hu BS, Shyr JM, Shi ZY, Tsai WS, Lin YH, Tseng CY (1995) Analysis of clonal relationships among isolates of Shigella sonnei by different molecular typing methods. J Clin Microbiol 33:1779–1783

    PubMed  CAS  Google Scholar 

  16. Kumao T, Ba-Thein W, Hayashi H (2002) Molecular subtyping methods for detection of Salmonella enterica serovar Oranienburg outbreaks. J Clin Microbiol 40:2057–2061

    Article  PubMed  CAS  Google Scholar 

  17. Nayak R, Stewart T, Nawaz M, Cerniglia C (2006) In vitro antimicrobial susceptibility, genetic diversity and prevalence of UDP-glucose 4-epimerase (galE) gene in Campylobacter coli and Campylobacter jejuni from turkey production facilities. Food Microbiol 23:379–392

    Article  PubMed  CAS  Google Scholar 

  18. Kwon HJ, Park KY, Yoo HS, Park JY, Park YH, Kim SJ (2000) Differentiation of Salmonella enterica serotype gallinarum biotype pullorum from biotype gallinarum by analysis of phase 1 flagellin C gene (fliC). J Microbiol Methods 40:33–38

    Article  PubMed  CAS  Google Scholar 

  19. Shima K, Kawamura N, Hinenoya A, Sugimoto N, Wu Y, Asakura M, Nishimura K, Nair GB, Yamasaki S (2008) Rapid culture-free identification and molecular typing of Shiga toxin-producing Escherichia coli by PCR-RFLP. Microbiol Immunol 52:310–313

    Article  PubMed  CAS  Google Scholar 

  20. Saken E, Roggenkamp A, Aleksic S, Heesemann J (1994) Characterisation of pathogenic Yersinia enterocolitica serogroups by pulsed-field gel electrophoresis of genomic NotI restriction fragments. J Med Microbiol 41:329–338

    Article  PubMed  CAS  Google Scholar 

  21. Bailey JS, Fedorka-Cray PJ, Stern NJ, Craven SE, Cox NA, Cosby DE (2002) Serotyping and ribotyping of Salmonella using restriction enzyme PvuII. J Food Prot 65:1005–1007

    PubMed  CAS  Google Scholar 

  22. Landeras E, Mendoza MC (1998) Evaluation of PCR-based methods and ribotyping performed with a mixture of PstI and SphI to differentiate strains of Salmonella serotype Enteritidis. J Med Microbiol 47:427–434

    Article  PubMed  CAS  Google Scholar 

  23. Grimont F, Grimont PA (1986) Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur Microbiol 137B:165–175

    Article  PubMed  CAS  Google Scholar 

  24. Bischoff KM, White DG, McDermott PF, Zhao S, Gaines S, Maurer JJ, Nisbet DJ (2002) Characterization of chloramphenicol resistance in beta-hemolytic Escherichia coli associated with diarrhea in neonatal swine. J Clin Microbiol 40:389–394

    Article  PubMed  CAS  Google Scholar 

  25. Ling JM, Lo NW, Ho YM, Kam KM, Hoa NT, Phi LT, Cheng AF (2000) Molecular methods for the epidemiological typing of Salmonella enterica serotype Typhi from Hong Kong and Vietnam. J Clin Microbiol 38:292–300

    PubMed  CAS  Google Scholar 

  26. Hahm BK, Maldonado Y, Schreiber E, Bhunia AK, Nakatsu CH (2003) Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP. J Microbiol Methods 53:387–399

    Article  PubMed  CAS  Google Scholar 

  27. Clermont O, Cordevant C, Bonacorsi S, Marecat A, Lange M, Bingen E (2001) Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains. J Clin Microbiol 39:4549–4553

    Article  PubMed  CAS  Google Scholar 

  28. Lobato MJ, Landeras E, Gonzalez-Hevia MA, Mendoza MC (1998) Genetic heterogeneity of clinical strains of Yersinia enterocolitica traced by ribotyping and relationships between ribotypes, serotypes, and biotypes. J Clin Microbiol 36:3297–3302

    PubMed  CAS  Google Scholar 

  29. Mendoza MC, Alzugaray R, Landeras E, Gonzalez-Hevia MA (1996) Discriminatory power and application of ribotyping of Yersinia enterocolitica O:3 in an epidemiological study. Eur J Clin Microbiol Infect Dis 15:220–226

    Article  PubMed  CAS  Google Scholar 

  30. Cabrera R, Echeita A, Herrera S, Usera MA, Ramirez M, Bravo L, Fernandez A (2006) Antibiotic resistance, plasmid profile and ribotyping in Cuban Shigella sonnei strains. Rev Esp Quimioter 19:76–78

    PubMed  CAS  Google Scholar 

  31. Foley SL, Walker R (2005) Methods of differentiation among bacterial foodborne pathogens. Iowa State University, Ames, IA

    Google Scholar 

  32. Swaminathan B, Barrett TJ (1995) Amplification methods for epidemiologic investigations of infectious diesease. J Microbiol Methods 2:129–139

    Article  Google Scholar 

  33. Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB, Swaminathan B, Barrett TJ (2006) Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 3:59–67

    Article  PubMed  CAS  Google Scholar 

  34. Thisted Lambertz S, Danielsson-Tham ML (2005) Identification and characterization of pathogenic Yersinia enterocolitica isolates by PCR and pulsed-field gel electrophoresis. Appl Environ Microbiol 71:3674–3681

    Article  PubMed  CAS  Google Scholar 

  35. Lukinmaa S, Nakari U-M, Eklund M, Siitonen A (2004) Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens. APMIS 112:908–929

    Article  PubMed  CAS  Google Scholar 

  36. Kam KM, Luey KY, Chiu AW, Law CP, Leung SF (2007) Molecular characterization of Salmonella enterica Serotype Typhi isolates by pulsed-field gel electrophoresis in Hong Kong, 2000–2004. Foodborne Pathog Dis 4:41–49

    Article  PubMed  CAS  Google Scholar 

  37. Gerner-Smidt P, Kincaid J, Kubota K, Hise K, Hunter SB, Fair MA, Norton D, Woo-Ming A, Kurzynski T, Sotir MJ, Head M, Holt K, Swaminathan B (2005) Molecular surveillance of shiga toxigenic Escherichia coli O157 by PulseNet USA. J Food Prot 68:1926–1931

    PubMed  Google Scholar 

  38. Gerner-Smidt P, Scheutz F (2006) Standardized pulsed-field gel electrophoresis of Shiga toxin-producing Escherichia coli: the PulseNet Europe Feasibility Study. Foodborne Pathog Dis 3:74–80

    Article  PubMed  CAS  Google Scholar 

  39. Proctor ME, Kurzynski T, Koschmann C, Archer JR, Davis JP (2002) Four strains of Escherichia coli O157:H7 isolated from patients during an outbreak of disease associated with ground beef: importance of evaluating multiple colonies from an outbreak-associated product. J Clin Microbiol 40:1530–1533

    Article  PubMed  Google Scholar 

  40. Yokoyama E, Uchimura M (2007) Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains. J Food Prot 70:2583–2588

    PubMed  Google Scholar 

  41. Foley SL, Simjee S, Meng J, White DG, McDermott PF, Zhao S (2004) Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans. J Food Prot 67:651–657

    PubMed  CAS  Google Scholar 

  42. Hyytia-Trees E, Smole SC, Fields PA, Swaminathan B, Ribot EM (2006) Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157). Foodborne Pathog Dis 3:118–131

    Article  PubMed  CAS  Google Scholar 

  43. Talukder KA, Dutta DK, Albert MJ (1999) Evaluation of pulsed-field gel electrophoresis for typing of Shigella dysenteriae type 1. J Med Microbiol 48:781–784

    Article  PubMed  CAS  Google Scholar 

  44. Kariuki S, Muthotho N, Kimari J, Waiyaki P, Hart CA, Gilks CF (1996) Molecular typing of multi-drug resistant Shigella dysenteriae type 1 by plasmid analysis and pulsed-field gel electrophoresis. Trans R Soc Trop Med Hyg 90:712–714

    Article  PubMed  CAS  Google Scholar 

  45. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  46. Scott F, Threlfall J, Stanley J, Arnold C (2001) Fluorescent amplified fragment length polymorphism genotyping of Salmonella Enteritidis: a method suitable for rapid outbreak recognition. Clin Microbiol Infect 7:479–485

    Article  PubMed  CAS  Google Scholar 

  47. Lindstedt BA, Heir E, Vardund T, Kapperud G (2000) Fluorescent amplified-fragment length polymorphism genotyping of Salmonella enterica subsp. enterica serovars and comparison with pulsed-field gel electrophoresis typing. J Clin Microbiol 38:1623–1627

    PubMed  CAS  Google Scholar 

  48. Nair S, Schreiber E, Thong KL, Pang T, Altwegg M (2000) Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping. J Microbiol Methods 41:35–43

    Article  PubMed  CAS  Google Scholar 

  49. Tamada Y, Nakaoka Y, Nishimori K, Doi A, Kumaki T, Uemura N, Tanaka K, Makino SI, Sameshima T, Akiba M, Nakazawa M, Uchida I (2001) Molecular typing and epidemiological study of Salmonella enterica serotype Typhimurium isolates from cattle by fluorescent amplified-fragment length polymorphism fingerprinting and pulsed-field gel electrophoresis. J Clin Microbiol 39:1057–1066

    Article  PubMed  CAS  Google Scholar 

  50. Jonas D, Spitzmuller B, Weist K, Ruden H, Daschner FD (2003) Comparison of PCR-based methods for typing Escherichia coli. Clin Microbiol Infect 9:823–831

    Article  PubMed  CAS  Google Scholar 

  51. Tsai TY, Luo WC, Wu FT, Pan TM (2005) Molecular subtyping for Escherichia coli O157: H7 isolated in Taiwan. Microbiol Immunol 49:579–588

    PubMed  CAS  Google Scholar 

  52. Sirisriro T, Sethabutr O, Mason C, Talukder KA, Venkatesan MM (2006) An AFLP-based database of Shigella flexneri and Shigella sonnei isolates and its use for the identification of untypable Shigella strains. J Microbiol Methods 67:487–495

    Article  PubMed  CAS  Google Scholar 

  53. Boghenbor KK, On SL, Kokotovic B, Baumgartner A, Wassenaar TM, Wittwer M, Bissig-Choisat B, Frey J (2006) Genotyping of human and porcine Yersinia enterocolitica, Yersinia intermedia, and Yersinia bercovieri strains from Switzerland by amplified fragment length polymorphism analysis. Appl Environ Microbiol 72:4061–4066

    Article  PubMed  CAS  Google Scholar 

  54. Fearnley C, On SL, Kokotovic B, Manning G, Cheasty T, Newell DG (2005) Application of fluorescent amplified fragment length polymorphism for comparison of human and animal isolates of Yersinia enterocolitica. Appl Environ Microbiol 71:4960–4965

    Article  PubMed  CAS  Google Scholar 

  55. Fontana C, Favaro M, Pistoia ES, Minelli S, Bossa MC, Altieri A, Testore GP, Leonardis F, Natoli S, Favalli C (2007) The combined use of VIGI@ct (bioMerieux) and fluorescent amplified length fragment polymorphisms in the investigation of potential outbreaks. J Hosp Infect 66:262–268

    Article  PubMed  CAS  Google Scholar 

  56. Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV (2001) PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7:382–389

    PubMed  CAS  Google Scholar 

  57. Micheli MR, Bova R, Pascale E, D’Ambrosio E (1994) Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method. Nucleic Acids Res 22:1921–1922

    Article  PubMed  CAS  Google Scholar 

  58. Meunier JR, Grimont PA (1993) Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. Res Microbiol 144:373–379

    Article  PubMed  CAS  Google Scholar 

  59. Franklin RB, Taylor DR, Mills AL (1999) Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD). J Microbiol Methods 35:225–235

    Article  PubMed  CAS  Google Scholar 

  60. Chansiripornchai N, Ramasoota P, Bangtrakulnonth A, Sasipreeyajan J, Svenson SB (2000) Application of randomly amplified polymorphic DNA (RAPD) analysis for typing avian Salmonella enterica subsp. enterica. FEMS Immunol Med Microbiol 29:221–225

    Article  PubMed  CAS  Google Scholar 

  61. Guerra B, Laconcha I, Soto SM, Gonzalez-Hevia MA, Mendoza MC (2000) Molecular characterisation of emergent multiresistant Salmonella enterica serotype [4,5,12:i:-] organisms causing human salmonellosis. FEMS Microbiol Lett 190:341–347

    PubMed  CAS  Google Scholar 

  62. Mare L, Dick LM, Van Der Walt ML (2001) Characterization of South African isolates of Salmonella enteritidis by phage typing, numerical analysis of RAPD-PCR banding patterns and plasmid profiles. Int J Food Microbiol 64:237–245

    Article  PubMed  CAS  Google Scholar 

  63. Kruger A, Padola NL, Parma AE, Lucchesi PM (2006) Intraserotype diversity among Argentinian verocytotoxigenic Escherichia coli detected by random amplified polymorphic DNA analysis. J Med Microbiol 55:545–549

    Article  PubMed  CAS  Google Scholar 

  64. Johnson JR, Kuskowski MA, Menard M, Gajewski A, Xercavins M, Garau J (2006) Similarity between human and chicken Escherichia coli isolates in relation to ciprofloxacin resistance status. J Infect Dis 194:71–78

    Article  PubMed  CAS  Google Scholar 

  65. Blixt Y, Knutsson R, Borch E, Radstrom P (2003) Interlaboratory random amplified polymorphic DNA typing of Yersinia enterocolitica and Y. enterocolitica-like bacteria. Int J Food Microbiol 83:15–26

    Article  PubMed  CAS  Google Scholar 

  66. Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831

    Article  PubMed  CAS  Google Scholar 

  67. Poh CL, Ramachandran V, Tapsall JW (1996) Genetic diversity of Neisseria gonorrhoeae IB-2 and IB-6 isolates revealed by whole-cell repetitive element sequence-based PCR. J Clin Microbiol 34:292–295

    PubMed  CAS  Google Scholar 

  68. Snelling AM, Gerner-Smidt P, Hawkey PM, Heritage J, Parnell P, Porter C, Bodenham AR, Inglis T (1996) Validation of use of whole-cell repetitive extragenic palindromic sequence-based PCR (REP-PCR) for typing strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and application of the method to the investigation of a hospital outbreak. J Clin Microbiol 34:1193–1202

    PubMed  CAS  Google Scholar 

  69. Dombek PE, Johnson LK, Zimmerley ST, Sadowsky MJ (2000) Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl Environ Microbiol 66:2572–2577

    Article  PubMed  CAS  Google Scholar 

  70. Mohapatra BR, Broersma K, Nordin R, Mazumder A (2007) Evaluation of repetitive extragenic palindromic-PCR for discrimination of fecal Escherichia coli from humans, and different domestic- and wild-animals. Microbiol Immunol 51:733–740

    PubMed  CAS  Google Scholar 

  71. Rajashekara G, Haverly E, Halvorson DA, Ferris KE, Lauer DC, Nagaraja KV (2000) Multidrug-resistant Salmonella Typhimurium DT104 in poultry. J Food Prot 63:155–161

    PubMed  CAS  Google Scholar 

  72. Chadfield M, Skov M, Christensen J, Madsen M, Bisgaard M (2001) An epidemiological study of Salmonella enterica serovar 4, 12:b:- in broiler chickens in Denmark. Vet Microbiol 82:233–247

    Article  PubMed  CAS  Google Scholar 

  73. Millemann Y, Gaubert S, Remy D, Colmin C (2000) Evaluation of IS200-PCR and comparison with other molecular markers to trace Salmonella enterica subsp. enterica serotype typhimurium bovine isolates from farm to meat. J Clin Microbiol 38:2204–2209

    PubMed  CAS  Google Scholar 

  74. Amavisit P, Markham PF, Lightfoot D, Whithear KG, Browning GF (2001) Molecular epidemiology of Salmonella Heidelberg in an equine hospital. Vet Microbiol 80:85–98

    Article  PubMed  CAS  Google Scholar 

  75. Johnson LK, Brown MB, Carruthers EA, Ferguson JA, Dombek PE, Sadowsky MJ (2004) Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl Environ Microbiol 70:4478–4485

    Article  PubMed  CAS  Google Scholar 

  76. Falcao JP, Falcao DP, Pitondo-Silva A, Malaspina AC, Brocchi M (2006) Molecular typing and virulence markers of Yersinia enterocolitica strains from human, animal and food origins isolated between 1968 and 2000 in Brazil. J Med Microbiol 55:1539–1548

    Article  PubMed  CAS  Google Scholar 

  77. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  PubMed  CAS  Google Scholar 

  78. Lindstedt BA, Vardund T, Aas L, Kapperud G (2004) Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis. J Microbiol Methods 59:163–172

    Article  PubMed  CAS  Google Scholar 

  79. Denoeud F, Vergnaud G (2004) Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a web-based resource. BMC Bioinformatics 5:4

    Article  PubMed  Google Scholar 

  80. Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME (2000) Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936

    Article  PubMed  CAS  Google Scholar 

  81. Lindstedt BA, Vardund T, Aas L, Kapperud G (2005) Multiple-locus variable-number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26:2567–2582

    Article  PubMed  CAS  Google Scholar 

  82. Lindstedt BA, Heir E, Gjernes E, Kapperud G (2003) DNA fingerprinting of Salmonella enterica subsp. enterica serovar Typhimurium with emphasis on phage type DT104 based on variable number of tandem repeat loci. J Clin Microbiol 41:1469–1479

    Article  PubMed  CAS  Google Scholar 

  83. Keys C, Kemper S, Keim P (2005) Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing. J Appl Microbiol 98:928–940

    Article  PubMed  CAS  Google Scholar 

  84. Noller AC, McEllistrem MC, Pacheco AG, Boxrud DJ, Harrison LH (2003) Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J Clin Microbiol 41:5389–5397

    Article  PubMed  CAS  Google Scholar 

  85. Ramisse V, Houssu P, Hernandez E, Denoeud F, Hilaire V, Lisanti O, Ramisse F, Cavallo JD, Vergnaud G (2004) Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes. J Clin Microbiol 42:5722–5730

    Article  PubMed  CAS  Google Scholar 

  86. Torpdahl M, Sorensen G, Lindstedt BA, Nielsen EM (2007) Tandem repeat analysis for surveillance of human Salmonella Typhimurium infections. Emerg Infect Dis 13:388–395

    Article  PubMed  CAS  Google Scholar 

  87. Liang SY, Watanabe H, Terajima J, Li CC, Liao JC, Tung SK, Chiou CS (2007) Multilocus variable-number tandem-repeat analysis for molecular typing of Shigella sonnei. J Clin Microbiol 45:3574–3580

    Article  PubMed  Google Scholar 

  88. Klevytska AM, Price LB, Schupp JM, Worsham PL, Wong J, Keim P (2001) Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. J Clin Microbiol 39:3179–3185

    Article  PubMed  CAS  Google Scholar 

  89. Pourcel C, Andre-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G (2004) Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol 4:22

    Article  PubMed  CAS  Google Scholar 

  90. Ciammaruconi A, Grassi S, De Santis R, Faggioni G, Pittiglio V, D’Amelio R, Carattoli A, Cassone A, Vergnaud G, Lista F (2008) Fieldable genotyping of Bacillus anthracis and Yersinia pestis based on 25-loci Multi Locus VNTR Analysis. BMC Microbiol 8:21

    Article  PubMed  CAS  Google Scholar 

  91. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145

    Article  PubMed  CAS  Google Scholar 

  92. Spratt BG (1999) Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr Opin Microbiol 2:312–316

    Article  PubMed  CAS  Google Scholar 

  93. Tartof SY, Solberg OD, Manges AR, Riley LW (2005) Analysis of a uropathogenic Escherichia coli clonal group by multilocus sequence typing. J Clin Microbiol 43:5860–5864

    Article  PubMed  CAS  Google Scholar 

  94. Fakhr MK, Nolan LK, Logue CM (2005) Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J Clin Microbiol 43:2215–2219

    Article  PubMed  CAS  Google Scholar 

  95. Kotetishvili M, Stine OC, Kreger A, Morris JG Jr, Sulakvelidze A (2002) Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J Clin Microbiol 40:1626–1635

    Article  PubMed  CAS  Google Scholar 

  96. Choi SY, Jeon YS, Lee JH, Choi B, Moon SH, von Seidlein L, Clemens JD, Dougan G, Wain J, Yu J, Lee JC, Seol SY, Lee BK, Song JH, Song M, Czerkinsky C, Chun J, Kim DW (2007) Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries. J Med Microbiol 56:1460–1466

    Article  PubMed  CAS  Google Scholar 

  97. Kotetishvili M, Kreger A, Wauters G, Morris JG Jr, Sulakvelidze A, Stine OC (2005) Multilocus sequence typing for studying genetic relationships among Yersinia species. J Clin Microbiol 43:2674–2684

    Article  PubMed  CAS  Google Scholar 

  98. Esaki H, Noda K, Otsuki N, Kojima A, Asai T, Tamura Y, Takahashi T (2004) Rapid detection of quinolone-resistant Salmonella by real time SNP genotyping. J Microbiol Methods 58:131–134

    Article  PubMed  CAS  Google Scholar 

  99. Levy DD, Sharma B, Cebula TA (2004) Single-nucleotide polymorphism mutation spectra and resistance to quinolones in Salmonella enterica serovar Enteritidis with a mutator phenotype. Antimicrob Agents Chemother 48:2355–2363

    Article  PubMed  CAS  Google Scholar 

  100. Mortimer CK, Peters TM, Gharbia SE, Logan JM, Arnold C (2004) Towards the development of a DNA-sequence based approach to serotyping of Salmonella enterica. BMC Microbiol 4:31

    Article  PubMed  CAS  Google Scholar 

  101. Zhang W, Qi W, Albert TJ, Motiwala AS, Alland D, Hyytia-Trees EK, Ribot EM, Fields PI, Whittam TS, Swaminathan B (2006) Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Res 16:757–767

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA

    Steven L. Foley Ph.D. & Rajesh Nayak

  2. Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77341, USA

    Aaron M. Lynne

Authors
  1. Steven L. Foley Ph.D.
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  2. Aaron M. Lynne
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  3. Rajesh Nayak
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Correspondence to Steven L. Foley Ph.D. .

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  1. Instituto Nacional de Controle de, Qualidade em Saúde, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil 4365, Rio de Janeiro, 21045-900, Rio de Janeiro, Brazil

    Ivano de Filippis

  2. Microbiology, BioReliance Corporation, Broschart Road 14920, Rockville, 20850, Maryland, USA

    Marian L. McKee

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Foley, S.L., Lynne, A.M., Nayak, R. (2013). Enterobacteriaceae. In: de Filippis, I., McKee, M. (eds) Molecular Typing in Bacterial Infections. Infectious Disease. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-185-1_4

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  • DOI: https://doi.org/10.1007/978-1-62703-185-1_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-184-4

  • Online ISBN: 978-1-62703-185-1

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