Skip to main content
SpringerLink
Log in

Molecular Typing Tools: From Pattern Recognition to Genome-Based Algorithms

  • Protocol
  • First Online:
Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1247))

  • 3268 Accesses

Abstract

In the present chapter, we discuss DNA-based typing methods for microbial pathogens that were frequently used in the past two decades and their essential features, as well as virtues and downsides. We conclude with an outlook on the fundamental changes that can be expected in the era of high-throughput genomics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. de Beer JL, van Ingen J, de Vries G et al (2013) Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey. J Clin Microbiol 51:1193–1198

    PubMed Central  PubMed  Google Scholar 

  2. Pitondo-Silva A, Santos AC, Jolley KA, Leite CQ, Darini AL (2013) Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis. J Microbiol Methods 93:42–48

    CAS  PubMed  Google Scholar 

  3. Fritsch I, Luyven G, Kohler H, Lutz W, Mobius P (2012) Suspicion of Mycobacterium avium subsp. paratuberculosis transmission between cattle and wild-living red deer (Cervus elaphus) by multitarget genotyping. Appl Environ Microbiol 78:1132–1139

    CAS  PubMed Central  PubMed  Google Scholar 

  4. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218

    CAS  PubMed Central  PubMed  Google Scholar 

  5. McAuliffe L, Kokotovic B, Ayling RD, Nicholas RA (2004) Molecular epidemiological analysis of Mycoplasma bovis isolates from the United Kingdom shows two genetically distinct clusters. J Clin Microbiol 42: 4556–4565

    CAS  PubMed Central  PubMed  Google Scholar 

  6. Hotzel H, Schneider B, Sachse K (1998) Investigation of Mycoplasma bovis field isolates using PCR fingerprinting. In: Leori G, Santini F, Scanziani E, Frey J (eds) Mycoplasmas of ruminants: pathogenicity, diagnostics, epidemiology and molecular genetics, vol 2. European Commission, Brussels, Belgium, pp 17–19

    Google Scholar 

  7. Butler JA, Pinnow CC, Thomson JU, Levisohn S, Rosenbusch RF (2001) Use of arbitrarily primed polymerase chain reaction to investigate Mycoplasma bovis outbreaks. Vet Microbiol 78:175–181

    CAS  PubMed  Google Scholar 

  8. Schrenzel M, Nicolas M, Witte C et al (2008) Molecular epidemiology of Mycobacterium avium subsp. avium and Mycobacterium intracellulare in captive birds. Vet Microbiol 126:122–131

    CAS  PubMed  Google Scholar 

  9. Kauppinen J, Hintikka E, Iivanainen E, Katila M (2001) PCR-based typing of Mycobacterium avium isolates in an epidemic among farmed lesser white-fronted geese (Anser erythropus). Vet Microbiol 81:41–50

    CAS  PubMed  Google Scholar 

  10. Scheibl P, Gerlach GF (1997) Differentiation of Mycobacterium paratuberculosis isolates by rDNA-spacer analysis and random amplified polymorphic DNA patterns. Vet Microbiol 57:151–158

    CAS  PubMed  Google Scholar 

  11. Petersen L, Newell DG (2001) The ability of Fla-typing schemes to discriminate between strains of Campylobacter jejuni. J Appl Microbiol 91:217–224

    CAS  PubMed  Google Scholar 

  12. Sayada C, Andersen AA, Storey C et al (1995) Usefulness of omp1 restriction mapping for avian Chlamydia psittaci isolate differentiation. Res Microbiol 146:155–165

    CAS  PubMed  Google Scholar 

  13. van Embden JD, Cave MD, Crawford JT et al (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31:406–409

    PubMed Central  PubMed  Google Scholar 

  14. Erler W, Martin G, Sachse K et al (2004) Molecular fingerprinting of Mycobacterium bovis subsp. caprae isolates from central Europe. J Clin Microbiol 42:2234–2238

    CAS  PubMed Central  PubMed  Google Scholar 

  15. Michel AL, Hlokwe TM, Coetzee ML et al (2008) High Mycobacterium bovis genetic diversity in a low prevalence setting. Vet Microbiol 126:151–159

    CAS  PubMed  Google Scholar 

  16. Pavlik I, Horvathova A, Dvorska L et al (1999) Standardisation of restriction fragment length polymorphism analysis for Mycobacterium avium subspecies paratuberculosis. J Microbiol Methods 38:155–167

    CAS  PubMed  Google Scholar 

  17. Mobius P, Luyven G, Hotzel H, Kohler H (2008) High genetic diversity among Mycobacterium avium subsp. paratuberculosis strains from German cattle herds shown by combination of IS900 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing. J Clin Microbiol 46: 972–981

    PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  19. Bouchet V, Huot H, Goldstein R (2008) Molecular genetic basis of ribotyping. Clin Microbiol Rev 21:262–273

    CAS  PubMed Central  PubMed  Google Scholar 

  20. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    CAS  PubMed Central  PubMed  Google Scholar 

  21. Wagenaar JA, van Bergen MA, Newell DG, Grogono-Thomas R, Duim B (2001) Comparative study using amplified fragment length polymorphism fingerprinting, PCR genotyping, and phenotyping to differentiate Campylobacter fetus strains isolated from animals. J Clin Microbiol 39:2283–2286

    CAS  PubMed Central  PubMed  Google Scholar 

  22. Hu H, Lan R, Reeves PR (2002) Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type-specific markers and potential for microarray typing. J Clin Microbiol 40:3406–3415

    CAS  PubMed Central  PubMed  Google Scholar 

  23. Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37: 67–75

    CAS  PubMed  Google Scholar 

  24. Herschleb J, Ananiev G, Schwartz DC (2007) Pulsed-field gel electrophoresis. Nat Protoc 2:677–684

    CAS  PubMed  Google Scholar 

  25. On SL, Harrington CS (2001) Evaluation of numerical analysis of PFGE-DNA profiles for differentiating Campylobacter fetus subspecies by comparison with phenotypic, PCR and 16S rDNA sequencing methods. J Appl Microbiol 90:285–293

    CAS  PubMed  Google Scholar 

  26. Nevas M, Lindstrom M, Hielm S et al (2005) Diversity of proteolytic Clostridium botulinum strains, determined by a pulsed-field gel electrophoresis approach. Appl Environ Microbiol 71:1311–1317

    CAS  PubMed Central  PubMed  Google Scholar 

  27. Leclair D, Pagotto F, Farber JM, Cadieux B, Austin JW (2006) Comparison of DNA fingerprinting methods for use in investigation of type E botulism outbreaks in the Canadian Arctic. J Clin Microbiol 44:1635–1644

    CAS  PubMed Central  PubMed  Google Scholar 

  28. Ribot EM, Fair MA, Gautom R et al (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

    CAS  PubMed  Google Scholar 

  29. van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293

    PubMed Central  PubMed  Google Scholar 

  30. Lindstedt BA, Torpdahl M, Vergnaud G et al (2013) Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012. Euro Surveill 18: 20385

    CAS  PubMed  Google Scholar 

  31. Jenkins AO, Venter EH, Hutamo K, Godfroid J (2010) Comparison of the capillary and agarose electrophoresis based multiple locus VNTR (variable number of tandem repeats) analysis (MLVA) on Mycobacterium bovis isolates. Vet Microbiol 145:172–176

    CAS  PubMed  Google Scholar 

  32. Roest HI, Ruuls RC, Tilburg JJ et al (2011) Molecular epidemiology of Coxiella burnetii from ruminants in Q fever outbreak, the Netherlands. Emerg Infect Dis 17:668–675

    PubMed Central  PubMed  Google Scholar 

  33. Thibault VC, Grayon M, Boschiroli ML et al (2007) New variable-number tandem-repeat markers for typing Mycobacterium avium subsp. paratuberculosis and M. avium strains: comparison with IS900 and IS1245 restriction fragment length polymorphism typing. J Clin Microbiol 45:2404–2410

    CAS  PubMed Central  PubMed  Google Scholar 

  34. Supply P, Mazars E, Lesjean S et al (2000) Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 36:762–771

    CAS  PubMed  Google Scholar 

  35. Supply P, Allix C, Lesjean S et al (2006) Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44:4498–4510

    CAS  PubMed Central  PubMed  Google Scholar 

  36. Oelemann MC, Diel R, Vatin V et al (2007) Assessment of an optimized mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis. J Clin Microbiol 45:691–697

    CAS  PubMed Central  PubMed  Google Scholar 

  37. Mazars E, Lesjean S, Banuls AL et al (2001) High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A 98: 1901–1906

    CAS  PubMed Central  PubMed  Google Scholar 

  38. Mandal S, Bradshaw L, Anderson LF et al (2011) Investigating transmission of Mycobacterium bovis in the United Kingdom in 2005 to 2008. J Clin Microbiol 49:1943–1950

    PubMed Central  PubMed  Google Scholar 

  39. Alonso-Rodriguez N, Martinez-Lirola M, Herranz M et al (2008) Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies. BMC Microbiol 8:34

    PubMed Central  PubMed  Google Scholar 

  40. Kasnitz N, Kohler H, Weigoldt M, Gerlach GF, Mobius P (2013) Stability of genotyping target sequences of Mycobacterium avium subsp. paratuberculosis upon cultivation on different media, in vitro- and in vivo passage, and natural infection. Vet Microbiol 167: 573–583

    CAS  PubMed  Google Scholar 

  41. Kamerbeek J, Schouls L, Kolk A et al (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907–914

    CAS  PubMed Central  PubMed  Google Scholar 

  42. Stone MJ, Brown TJ, Drobniewski FA (2012) Human Mycobacterium bovis infections in London and Southeast England. J Clin Microbiol 50:164–165

    CAS  PubMed Central  PubMed  Google Scholar 

  43. Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG (2006) Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat Rev Microbiol 4:670–681

    CAS  PubMed  Google Scholar 

  44. Ruettger A, Nieter J, Skrypnyk A et al (2012) Rapid spoligotyping of Mycobacterium tuberculosis complex bacteria by use of a microarray system with automatic data processing and assignment. J Clin Microbiol 50:2492–2495

    CAS  PubMed Central  PubMed  Google Scholar 

  45. Dale JW, Brittain D, Cataldi AA et al (2001) Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature. Int J Tuberc Lung Dis 5:216–219

    CAS  PubMed  Google Scholar 

  46. Brudey K, Driscoll JR, Rigouts L et al (2006) Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 6:23

    PubMed Central  PubMed  Google Scholar 

  47. Smith NH, Upton P (2012) Naming spoligotype patterns for the RD9-deleted lineage of the Mycobacterium tuberculosis complex; www.Mbovis.org. Infect Genet Evol 12: 873–876

    PubMed  Google Scholar 

  48. Oswald E, Schmidt H, Morabito S et al (2000) Typing of intimin genes in human and animal enterohemorrhagic and enteropathogenic Escherichia coli: characterization of a new intimin variant. Infect Immun 68:64–71

    CAS  PubMed Central  PubMed  Google Scholar 

  49. Blanco M, Schumacher S, Tasara T et al (2005) Serotypes, intimin variants and other virulence factors of eae positive Escherichia coli strains isolated from healthy cattle in Switzerland. Identification of a new intimin variant gene (eae-eta2). BMC Microbiol 5:23

    PubMed Central  PubMed  Google Scholar 

  50. Vanrompay D, Butaye P, Sayada C, Ducatelle R, Haesebrouck F (1997) Characterization of avian Chlamydia psittaci strains using omp1 restriction mapping and serovar-specific monoclonal antibodies. Res Microbiol 148: 327–333

    CAS  PubMed  Google Scholar 

  51. Sachse K, Laroucau K, Hotzel H et al (2008) Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes. BMC Microbiol 8:63

    PubMed Central  PubMed  Google Scholar 

  52. Ruettger A, Feige J, Slickers P et al (2011) Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay. Mol Cell Probes 25:19–27

    CAS  PubMed  Google Scholar 

  53. Geens T, Dewitte A, Boon N, Vanrompay D (2005) Development of a Chlamydophila psittaci species-specific and genotype-specific real-time PCR. Vet Res 36:787–797

    CAS  PubMed  Google Scholar 

  54. Michel H, Wilske B, Hettche G et al (2004) An ospA-polymerase chain reaction/restriction fragment length polymorphism-based method for sensitive detection and reliable differentiation of all European Borrelia burgdorferi sensu lato species and OspA types. Med Microbiol Immunol 193:219–226

    CAS  PubMed  Google Scholar 

  55. Will G, Jauris-Heipke S, Schwab E et al (1995) Sequence analysis of ospA genes shows homogeneity within Borrelia burgdorferi sensu stricto and Borrelia afzelii strains but reveals major subgroups within the Borrelia garinii species. Med Microbiol Immunol 184:73–80

    CAS  PubMed  Google Scholar 

  56. Korczak BM, Zurfluh M, Emler S, Kuhn-Oertli J, Kuhnert P (2009) Multiplex strategy for multilocus sequence typing, fla typing, and genetic determination of antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolates collected in Switzerland. J Clin Microbiol 47:1996–2007

    CAS  PubMed Central  PubMed  Google Scholar 

  57. Maiden MC, Bygraves JA, Feil E et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145

    CAS  PubMed Central  PubMed  Google Scholar 

  58. Perez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA (2013) Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol 16: 38–53

    CAS  PubMed  Google Scholar 

  59. Kidgell C, Reichard U, Wain J et al (2002) Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect Genet Evol 2:39–45

    PubMed  Google Scholar 

  60. Hauser E, Hebner F, Tietze E et al (2011) Diversity of Salmonella enterica serovar Derby isolated from pig, pork and humans in Germany. Int J Food Microbiol 151:141–149

    CAS  PubMed  Google Scholar 

  61. Dean D, Bruno WJ, Wan R et al (2009) Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerg Infect Dis 15:1385–1394

    CAS  PubMed Central  PubMed  Google Scholar 

  62. Pannekoek Y, Dickx V, Beeckman DS et al (2010) Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species. PLoS One 5:e14179

    CAS  PubMed Central  PubMed  Google Scholar 

  63. Klint M, Fuxelius HH, Goldkuhl RR et al (2007) High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis. J Clin Microbiol 45:1410–1414

    CAS  PubMed Central  PubMed  Google Scholar 

  64. Christerson L, Ruettger A, Gravningen K et al (2011) High-resolution genotyping of Chlamydia trachomatis by use of a novel multilocus typing DNA microarray. J Clin Microbiol 49:2838–2843

    PubMed Central  PubMed  Google Scholar 

  65. Tankouo-Sandjong B, Sessitsch A, Liebana E et al (2007) MLST-v, multilocus sequence typing based on virulence genes, for molecular typing of Salmonella enterica subsp. enterica serovars. J Microbiol Methods 69:23–36

    CAS  PubMed  Google Scholar 

  66. Verghese B, Schwalm ND 3rd, Dudley EG, Knabel SJ (2012) A combined multi-virulence-locus sequence typing and Staphylococcal Cassette Chromosome mec typing scheme possesses enhanced discriminatory power for genotyping MRSA. Infect Genet Evol 12:1816–1821

    CAS  PubMed  Google Scholar 

  67. Scholz HC, Vergnaud G (2013) Molecular characterisation of Brucella species. Rev Sci Tech 32:149–162

    CAS  PubMed  Google Scholar 

  68. Glazunova O, Roux V, Freylikman O et al (2005) Coxiella burnetii genotyping. Emerg Infect Dis 11:1211–1217

    CAS  PubMed Central  PubMed  Google Scholar 

  69. Santos AS, Tilburg JJ, Botelho A et al (2012) Genotypic diversity of clinical Coxiella burnetii isolates from Portugal based on MST and MLVA typing. Int J Med Microbiol 302:253–256

    CAS  PubMed  Google Scholar 

  70. Lucchini S, Thompson A, Hinton JC (2001) Microarrays for microbiologists. Microbiology 147:1403–1414

    CAS  PubMed  Google Scholar 

  71. Ballerstedt H, Volkers RJ, Mars AE et al (2007) Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies. Appl Microbiol Biotechnol 75:1133–1142

    CAS  PubMed Central  PubMed  Google Scholar 

  72. Snyder LA, Davies JK, Saunders NJ (2004) Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements. BMC Genomics 5:23

    PubMed Central  PubMed  Google Scholar 

  73. Oh S, Yoder-Himes DR, Tiedje J, Park J, Konstantinidis KT (2010) Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain. Appl Environ Microbiol 76:2980–2988

    CAS  PubMed Central  PubMed  Google Scholar 

  74. Leroy Q, Armougom F, Barbry P, Raoult D (2011) Genomotyping of Coxiella burnetii using microarrays reveals a conserved genomotype for hard tick isolates. PLoS One 6:e25781

    CAS  PubMed Central  PubMed  Google Scholar 

  75. Monecke S, Coombs G, Shore AC et al (2011) A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 6:e17936

    CAS  PubMed Central  PubMed  Google Scholar 

  76. Ballmer K, Korczak BM, Kuhnert P et al (2007) Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray. J Clin Microbiol 45:370–379

    CAS  PubMed Central  PubMed  Google Scholar 

  77. Braun SD, Ziegler A, Methner U et al (2012) Fast DNA serotyping and antimicrobial resistance gene determination of salmonella enterica with an oligonucleotide microarray-based assay. PLoS One 7:e46489

    CAS  PubMed Central  PubMed  Google Scholar 

  78. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol 43: 2291–2302

    CAS  PubMed Central  PubMed  Google Scholar 

  79. Schwartz DC, Li X, Hernandez LI et al (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114

    CAS  PubMed  Google Scholar 

  80. Miller JM (2013) Whole-genome mapping: a new paradigm in strain-typing technology. J Clin Microbiol 51:1066–1070

    CAS  PubMed Central  PubMed  Google Scholar 

  81. Sabat AJ, Budimir A, Nashev D et al (2013) Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill 18:20380

    CAS  PubMed  Google Scholar 

  82. Larsen MV, Cosentino S, Rasmussen S et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361

    CAS  PubMed Central  PubMed  Google Scholar 

  83. Mellmann A, Harmsen D, Cummings CA et al (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6:e22751

    CAS  PubMed Central  PubMed  Google Scholar 

  84. Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T et al (2013) Real-time genomic epidemiology of human Campylobacter isolates using whole genome multilocus sequence typing. J Clin Microbiol 51:2526–2534

    CAS  PubMed Central  PubMed  Google Scholar 

  85. Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595

    PubMed Central  PubMed  Google Scholar 

  86. Roetzer A, Diel R, Kohl TA et al (2013) Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10:e1001387

    PubMed Central  PubMed  Google Scholar 

  87. Sherry NL, Porter JL, Seemann T et al (2013) Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol 51: 1396–1401

    PubMed Central  PubMed  Google Scholar 

  88. Poirel L, Bonnin RA, Nordmann P (2011) Analysis of the resistome of a multidrug-resistant NDM-1-producing Escherichia coli strain by high-throughput genome sequencing. Antimicrob Agents Chemother 55: 4224–4229

    CAS  PubMed Central  PubMed  Google Scholar 

  89. Forsberg KJ, Reyes A, Wang B et al (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337:1107–1111

    CAS  PubMed Central  PubMed  Google Scholar 

  90. Koser CU, Holden MT, Ellington MJ et al (2012) Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 366:2267–2275

    CAS  PubMed Central  PubMed  Google Scholar 

  91. Keim P, Price LB, Klevytska AM et al (2000) Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936

    CAS  PubMed Central  PubMed  Google Scholar 

  92. Lista F, Faggioni G, Valjevac S et al (2006) Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis. BMC Microbiol 6:33

    PubMed Central  PubMed  Google Scholar 

  93. Van Ert MN, Easterday WR, Huynh LY et al (2007) Global genetic population structure of Bacillus anthracis. PLoS One 2:e461

    PubMed Central  PubMed  Google Scholar 

  94. Keim P, Van Ert MN, Pearson T et al (2004) Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect Genet Evol 4:205–213

    CAS  PubMed  Google Scholar 

  95. Van Ert MN, Easterday WR, Simonson TS et al (2007) Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. J Clin Microbiol 45:47–53

    PubMed Central  PubMed  Google Scholar 

  96. Fingerle V, Michel H, Hettche G, Hizo-Teufel C, Wilske B (2004) Borrelia burgdorferi s.l. OspA-types are widespread in Bavaria but show distinct local patterns. Int J Med Microbiol 293(suppl 37):165–166

    PubMed  Google Scholar 

  97. Margos G, Gatewood AG, Aanensen DM et al (2008) MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proc Natl Acad Sci U S A 105: 8730–8735

    CAS  PubMed Central  PubMed  Google Scholar 

  98. Foster JT, Price LB, Beckstrom-Sternberg SM et al (2012) Genotyping of Brucella species using clade specific SNPs. BMC Microbiol 12:110

    CAS  PubMed Central  PubMed  Google Scholar 

  99. Bricker BJ, Ewalt DR, Halling SM (2003) Brucella ‘HOOF-Prints’: strain typing by multi-locus analysis of variable number tandem repeats (VNTRs). BMC Microbiol 3:15

    PubMed Central  PubMed  Google Scholar 

  100. Le Fleche P, Jacques I, Grayon M et al (2006) Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC Microbiol 6:9

    PubMed Central  PubMed  Google Scholar 

  101. Whatmore AM, Shankster SJ, Perrett LL et al (2006) Identification and characterization of variable-number tandem-repeat markers for typing of Brucella spp. J Clin Microbiol 44: 1982–1993

    CAS  PubMed Central  PubMed  Google Scholar 

  102. Whatmore AM, Perrett LL, MacMillan AP (2007) Characterisation of the genetic diversity of Brucella by multilocus sequencing. BMC Microbiol 7:34

    PubMed Central  PubMed  Google Scholar 

  103. Wattiau P, Whatmore AM, Van Hessche M, Godfroid J, Fretin D (2011) Nucleotide polymorphism-based single-tube test for robust molecular identification of all currently described Brucella species. Appl Environ Microbiol 77:6674–6679

    CAS  PubMed Central  PubMed  Google Scholar 

  104. Godoy D, Randle G, Simpson AJ et al (2003) Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol 41:2068–2079

    CAS  PubMed Central  PubMed  Google Scholar 

  105. Currie B, Thomas AD, Godoy D, Dance D et al (2007) Australian and Thai isolates of Burkholderia pseudomallei are distinct by multilocus sequence typing: revision of a case of mistaken identity. J Clin Microbiol 45: 3828–3829

    PubMed  Google Scholar 

  106. Vesaratchavest M, Tumapa S, Day NP et al (2006) Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence. J Clin Microbiol 44:2553–2557

    CAS  PubMed Central  PubMed  Google Scholar 

  107. Currie BJ, Haslem A, Pearson T et al (2009) Identification of melioidosis outbreak by multilocus variable number tandem repeat analysis. Emerg Infect Dis 15:169–174

    CAS  PubMed Central  PubMed  Google Scholar 

  108. U'Ren JM, Schupp JM, Pearson T et al (2007) Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiol 7:23

    PubMed Central  PubMed  Google Scholar 

  109. Chantratita N, Vesaratchavest M, Wuthiekanun V et al (2006) Pulsed-field gel electrophoresis as a discriminatory typing technique for the biothreat agent Burkholderia mallei. Am J Trop Med Hyg 74:345–347

    PubMed  Google Scholar 

  110. Ribot EM, Fitzgerald C, Kubota K, Swaminathan B, Barrett TJ (2001) Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni. J Clin Microbiol 39:1889–1894

    CAS  PubMed Central  PubMed  Google Scholar 

  111. Dingle KE, Colles FM, Wareing DR et al (2001) Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 39: 14–23

    CAS  PubMed Central  PubMed  Google Scholar 

  112. Parsons BN, Cody AJ, Porter CJ et al (2009) Typing of Campylobacter jejuni isolates from dogs by use of multilocus sequence typing and pulsed-field gel electrophoresis. J Clin Microbiol 47:3466–3471

    CAS  PubMed Central  PubMed  Google Scholar 

  113. Nachamkin I, Bohachick K, Patton CM (1993) Flagellin gene typing of Campylobacter jejuni by restriction fragment length polymorphism analysis. J Clin Microbiol 31: 1531–1536

    CAS  PubMed Central  PubMed  Google Scholar 

  114. Buchanan CJ, Yoshida C, Kruczkiewicz P et al (2011) High-resolution comparative genomic fingerprinting of Campylobacter jejuni using ArrayTube™ miniaturized diagnostic microarrays. In: Proceedings of 16th international workshop on Campylobacter, Helicobacter and Related Organisms (CHRO 2011). Vancouver, Canada, p 164

    Google Scholar 

  115. El-Adawy H, Hotzel H, Tomaso H et al (2013) Detection of genetic diversity in Campylobacter jejuni isolated from a commercial Turkey flock using flaA typing, MLST analysis and microarray assay. PLoS One 8:e51582

    CAS  PubMed Central  PubMed  Google Scholar 

  116. van Bergen MA, van der Graaf-van BL, Visser IJ, van Putten JP, Wagenaar JA (2006) Molecular epidemiology of Campylobacter fetus subsp. fetus on bovine artificial insemination stations using pulsed field gel electrophoresis. Vet Microbiol 112:65–71

    PubMed  Google Scholar 

  117. van Bergen MA, Simons G, van der Graaf-van BL et al (2005) Amplified fragment length polymorphism based identification of genetic markers and novel PCR assay for differentiation of Campylobacter fetus subspecies. J Med Microbiol 54:1217–1224

    PubMed  Google Scholar 

  118. van Bergen MA, Dingle KE, Maiden MC et al (2005) Clonal nature of Campylobacter fetus as defined by multilocus sequence typing. J Clin Microbiol 43:5888–5898

    PubMed Central  PubMed  Google Scholar 

  119. Miller WG, Chapman MH, Yee E et al (2012) Multilocus sequence typing methods for the emerging Campylobacter species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus. Front Cell Infect Microbiol 2:45

    PubMed Central  PubMed  Google Scholar 

  120. Pannekoek Y, Morelli G, Kusecek B et al (2008) Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis. BMC Microbiol 8:42

    PubMed Central  PubMed  Google Scholar 

  121. Geens T, Desplanques A, Van Loock M, Bönner B et al (2005) Sequencing of the Chlamydophila psittaci ompA gene reveals a new genotype, E/B, and the need for a rapid discriminatory genotyping method. J Clin Microbiol 43:2456–2461

    CAS  PubMed Central  PubMed  Google Scholar 

  122. Laroucau K, Thierry S, Vorimore F et al (2008) High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA). Infect Genet Evol 8:171–181

    CAS  PubMed  Google Scholar 

  123. Laroucau K, Vorimore F, Bertin C et al (2009) Genotyping of Chlamydophila abortus strains by multilocus VNTR analysis. Vet Microbiol 137:335–344

    CAS  PubMed  Google Scholar 

  124. Umeda K, Wada T, Kohda T, Kozaki S (2013) Multi-locus variable number tandem repeat analysis for Clostridium botulinum type B isolates in Japan: comparison with other isolates and genotyping methods. Infect Genet Evol 16:298–304

    CAS  PubMed  Google Scholar 

  125. Maslanka SE, Kerr JG, Williams G et al (1999) Molecular subtyping of Clostridium perfringens by pulsed-field gel electrophoresis to facilitate food-borne-disease outbreak investigations. J Clin Microbiol 37:2209–2214

    CAS  PubMed Central  PubMed  Google Scholar 

  126. Lukinmaa S, Takkunen E, Siitonen A (2002) Molecular epidemiology of Clostridium perfringens related to food-borne outbreaks of disease in Finland from 1984 to 1999. Appl Environ Microbiol 68:3744–3749

    CAS  PubMed Central  PubMed  Google Scholar 

  127. Johansson A, Aspan A, Bagge E et al (2006) Genetic diversity of Clostridium perfringens type A isolates from animals, food poisoning outbreaks and sludge. BMC Microbiol 6:47

    PubMed Central  PubMed  Google Scholar 

  128. Ferreira TSP, Moreno AM, de Almeida RR et al (2012) Molecular typing of Clostridium perfringens isolated from swine in slaughterhouses from Sao Paulo State, Brazil. Cienc Rural 42:1450–1456

    CAS  Google Scholar 

  129. Sawires YS, Songer JG (2005) Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens. Anaerobe 11:262–272

    CAS  PubMed  Google Scholar 

  130. Chalmers G, Martin SW, Prescott JF, Boerlin P (2008) Typing of Clostridium perfringens by multiple-locus variable number of tandem repeats analysis. Vet Microbiol 128:126–135

    CAS  PubMed  Google Scholar 

  131. Knetsch CW, Lawley TD, Hensgens MP et al (2013) Current application and future perspectives of molecular typing methods to study Clostridium difficile infections. Euro Surveill 18:20381

    CAS  PubMed  Google Scholar 

  132. Neumann AP, Rehberger TG (2009) MLST analysis reveals a highly conserved core genome among poultry isolates of Clostridium septicum. Anaerobe 15:99–106

    CAS  PubMed  Google Scholar 

  133. Arricau-Bouvery N, Hauck Y, Bejaoui A et al (2006) Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing. BMC Microbiol 6:39

    Google Scholar 

  134. Svraka S, Toman R, Skultety L, Slaba K, Homan WL (2006) Establishment of a genotyping scheme for Coxiella burnetii. FEMS Microbiol Lett 254:268–274

    CAS  PubMed  Google Scholar 

  135. Tilburg JJ, Rossen JW, van Hannen EJ et al (2012) Genotypic diversity of Coxiella burnetii in the 2007-2010 Q fever outbreak episodes in The Netherlands. J Clin Microbiol 50:1076–1078

    PubMed Central  PubMed  Google Scholar 

  136. Franck SM, Bosworth BT, Moon HW (1998) Multiplex PCR for enterotoxigenic, attaching and effacing, and Shiga toxin-producing Escherichia coli strains from calves. J Clin Microbiol 36:1795–1797

    CAS  PubMed Central  PubMed  Google Scholar 

  137. Nguyen TV, Le Van P, Le Huy C, Gia KN, Weintraub A (2005) Detection and characterization of diarrheagenic Escherichia coli from young children in Hanoi, Vietnam. J Clin Microbiol 43:755–760

    CAS  PubMed Central  PubMed  Google Scholar 

  138. Muller D, Hagedorn P, Brast S, Heusipp G et al (2006) Rapid identification and differentiation of clinical isolates of enteropathogenic Escherichia coli (EPEC), atypical EPEC, and Shiga toxin-producing Escherichia coli by a one-step multiplex PCR method. J Clin Microbiol 44:2626–2629

    PubMed Central  PubMed  Google Scholar 

  139. Casey TA, Bosworth BT (2009) Design and evaluation of a multiplex polymerase chain reaction assay for the simultaneous identification of genes for nine different virulence factors associated with Escherichia coli that cause diarrhea and edema disease in swine. J Vet Diagn Invest 21:25–30

    PubMed  Google Scholar 

  140. Scheutz F, Teel LD, Beutin L et al (2012) Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature. J Clin Microbiol 50:2951–2963

    CAS  PubMed Central  PubMed  Google Scholar 

  141. Adu-Bobie J, Frankel G, Bain C et al (1998) Detection of intimins alpha, beta, gamma, and delta, four intimin derivatives expressed by attaching and effacing microbial pathogens. J Clin Microbiol 36:662–668

    CAS  PubMed Central  PubMed  Google Scholar 

  142. Jores J, Zehmke K, Eichberg J, Rumer L, Wieler LH (2003) Description of a novel intimin variant (type zeta) in the bovine O84:NM verotoxin-producing Escherichia coli strain 537/89 and the diagnostic value of intimin typing. Exp Biol Med (Maywood) 228: 370–376

    CAS  Google Scholar 

  143. Ramachandran V, Brett K, Hornitzky MA et al (2003) Distribution of intimin subtypes among Escherichia coli isolates from ruminant and human sources. J Clin Microbiol 41: 5022–5032

    PubMed Central  PubMed  Google Scholar 

  144. Barth S, Schwanitz A, Bauerfeind R (2011) Polymerase chain reaction-based method for the typing of F18 fimbriae and distribution of F18 fimbrial subtypes among porcine Shiga toxin-encoding Escherichia coli in Germany. J Vet Diagn Invest 23:454–464

    PubMed  Google Scholar 

  145. Franklin MA, Francis DH, Baker D, Mathew AG (1996) A PCR-based method of detection and differentiation of K88+ adhesive Escherichia coli. J Vet Diagn Invest 8:460–463

    CAS  PubMed  Google Scholar 

  146. Imberechts H, Van Pelt N, De Greve H, Lintermans P (1994) Sequences related to the major subunit gene fedA of F107 fimbriae in porcine Escherichia coli strains that express adhesive fimbriae. FEMS Microbiol Lett 119:309–314

    CAS  PubMed  Google Scholar 

  147. Schilling AK, Hotzel H, Methner U et al (2012) Zoonotic agents in small ruminants kept on city farms in southern Germany. Appl Environ Microbiol 78:3785–3793

    CAS  PubMed Central  PubMed  Google Scholar 

  148. Monecke S, Mariani-Kurkdjian P, Bingen E et al (2011) Presence of enterohemorrhagic Escherichia coli ST678/O104:H4 in France prior to 2011. Appl Environ Microbiol 77:8784–8786

    CAS  PubMed Central  PubMed  Google Scholar 

  149. Geue L, Schares S, Mintel B et al (2010) Rapid microarray-based genotyping of enterohemorrhagic Escherichia coli serotype O156:H25/H-/Hnt isolates from cattle and clonal relationship analysis. Appl Environ Microbiol 76:5510–5519

    CAS  PubMed Central  PubMed  Google Scholar 

  150. Wirth T, Falush D, Lan R et al (2006) Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60:1136–1151

    CAS  PubMed Central  PubMed  Google Scholar 

  151. Garcia Del Blanco N, Dobson ME, Vela AI et al (2002) Genotyping of Francisella tularensis strains by pulsed-field gel electrophoresis, amplified fragment length polymorphism fingerprinting, and 16S rRNA gene sequencing. J Clin Microbiol 40:2964–2972

    CAS  PubMed Central  PubMed  Google Scholar 

  152. Johansson A, Farlow J, Larsson P et al (2004) Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J Bacteriol 186:5808–5818

    CAS  PubMed Central  PubMed  Google Scholar 

  153. Vogler AJ, Birdsell D, Wagner DM, Keim P (2009) An optimized, multiplexed multi-locus variable-number tandem repeat analysis system for genotyping Francisella tularensis. Lett Appl Microbiol 48:140–144

    CAS  PubMed  Google Scholar 

  154. Vogler AJ, Birdsell D, Price LB et al (2009) Phylogeography of Francisella tularensis: global expansion of a highly fit clone. J Bacteriol 191:2474–2484

    CAS  PubMed Central  PubMed  Google Scholar 

  155. Larsson P, Svensson K, Karlsson L et al (2007) Canonical insertion-deletion markers for rapid DNA typing of Francisella tularensis. Emerg Infect Dis 13:1725–1732

    CAS  PubMed Central  PubMed  Google Scholar 

  156. Svensson K, Back E, Eliasson H et al (2009) Landscape epidemiology of tularemia outbreaks in Sweden. Emerg Infect Dis 15: 1937–1947

    CAS  PubMed Central  PubMed  Google Scholar 

  157. Castellanos E, de Juan L, Dominguez L, Aranaz A (2012) Progress in molecular typing of Mycobacterium avium subspecies paratuberculosis. Res Vet Sci 92:169–179

    CAS  PubMed  Google Scholar 

  158. Bannantine JP, Li LL, Sreevatsan S, Kapur V (2013) How does a Mycobacterium change its spots? Applying molecular tools to track diverse strains of Mycobacterium avium subspecies paratuberculosis. Lett Appl Microbiol 57:165–173

    CAS  PubMed  Google Scholar 

  159. Stevenson K, Hughes VM, de Juan L et al (2002) Molecular characterization of pigmented and nonpigmented isolates of Mycobacterium avium subsp. paratuberculosis. J Clin Microbiol 40:1798–1804

    CAS  PubMed Central  PubMed  Google Scholar 

  160. de Juan L, Mateos A, Dominguez L, Sharp JM, Stevenson K (2005) Genetic diversity of Mycobacterium avium subspecies paratuberculosis isolates from goats detected by pulsed-field gel electrophoresis. Vet Microbiol 106: 249–257

    PubMed  Google Scholar 

  161. Sevilla I, Li LL, Amonsin A et al (2008) Comparative analysis of Mycobacterium avium subsp paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing. BMC Microbiol 8:204

    PubMed Central  PubMed  Google Scholar 

  162. Amonsin A, Li LL, Zhang Q et al (2004) Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp. paratuberculosis strains. J Clin Microbiol 42:1694–1702

    CAS  PubMed Central  PubMed  Google Scholar 

  163. Thibault VC, Grayon M, Boschiroli ML et al (2008) Combined multilocus short-sequence-repeat and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing of Mycobacterium avium subsp paratuberculosis isolates. J Clin Microbiol 46:4091–4094

    PubMed Central  PubMed  Google Scholar 

  164. Kasnitz N, Kohler H, Weigoldt M, Gerlach GF, Mobius P (2013) Stability of genotyping target sequences of Mycobacterium avium subsp. paratuberculosis upon cultivation on different media, in vitro- and in vivo passage, and natural infection. Vet Microbiol 167: 573–583

    CAS  PubMed  Google Scholar 

  165. Dvorska L, Bull TJ, Bartos M et al (2003) A standardised restriction fragment length polymorphism (RFLP) method for typing Mycobacterium avium isolates links IS901 with virulence for birds. J Microbiol Methods 55:11–27

    CAS  PubMed  Google Scholar 

  166. van Soolingen D, Bauer J, Ritacco V et al (1998) IS1245 restriction fragment length polymorphism typing of Mycobacterium avium isolates: proposal for standardization. J Clin Microbiol 36:3051–3054

    PubMed Central  PubMed  Google Scholar 

  167. Johansen TB, Olsen I, Jensen MR et al (2007) New probes used for IS1245 and IS1311 restriction fragment length polymorphism of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. hominissuis isolates of human and animal origin in Norway. BMC Microbiol 7:14

    PubMed Central  PubMed  Google Scholar 

  168. Johansen TB, Djonne B, Jensen MR, Olsen I (2005) Distribution of IS1311 and IS1245 in Mycobacterium avium subspecies revisited. J Clin Microbiol 43:2500–2502

    CAS  PubMed Central  PubMed  Google Scholar 

  169. McLernon J, Costello E, Flynn O, Madigan G, Ryan F (2010) Evaluation of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat analysis and spoligotyping for genotyping of Mycobacterium bovis isolates and a comparison with restriction fragment length polymorphism typing. J Clin Microbiol 48:4541–4545

    CAS  PubMed Central  PubMed  Google Scholar 

  170. McAuliffe L, Ayling RD, Nicholas RA (2007) Identification and characterization of variable-number tandem-repeat markers for the molecular epidemiological analysis of Mycoplasma mycoides subspecies mycoides SC. FEMS Microbiol Lett 276:181–188

    CAS  PubMed  Google Scholar 

  171. Yaya A, Manso-Silvan L, Blanchard A, Thiaucourt F (2008) Genotyping of Mycoplasma mycoides subsp. mycoides SC by multilocus sequence analysis allows molecular epidemiology of contagious bovine pleuropneumonia. Vet Res 39:14

    PubMed  Google Scholar 

  172. Lorenzon S, Arzul I, Peyraud A, Hendrikx P, Thiaucourt F (2003) Molecular epidemiology of contagious bovine pleuropneumonia by multilocus sequence analysis of Mycoplasma mycoides subspecies mycoides biotype SC strains. Vet Microbiol 93:319–333

    CAS  PubMed  Google Scholar 

  173. Churchward CP, Hlusek M, Nicholas RA, Ayling RD, McAuliffe L (2012) A simplified PCR method for genotyping Mycoplasma mycoides subspecies mycoides small colony: the aetiologic agent of contagious bovine pleuropneumonia. Vet Microbiol 159:257–259

    CAS  PubMed  Google Scholar 

  174. Pinho L, Thompson G, Rosenbusch R, Carvalheira J (2012) Genotyping of Mycoplasma bovis isolates using multiple-locus variable-number tandem-repeat analysis. J Microbiol Methods 88:377–385

    CAS  PubMed  Google Scholar 

  175. Amram E, Freed M, Khateb N et al (2013) Multiple locus variable number tandem repeat analysis of Mycoplasma bovis isolated from local and imported cattle. Vet J 197:286–290

    CAS  PubMed  Google Scholar 

  176. Manso-Silvan L, Dupuy V, Lysnyansky I, Ozdemir U, Thiaucourt F (2012) Phylogeny and molecular typing of Mycoplasma agalactiae and Mycoplasma bovis by multilocus sequencing. Vet Microbiol 161:104–112

    CAS  PubMed  Google Scholar 

  177. Malorny B, Hauser E, Diekerman R (2011) New approaches in subspecies-level Salmonella classification. In: Porwollik S (ed) Salmonella, from genome to function. Caister Academic Press, Norfolk, UK, pp 1–24

    Google Scholar 

  178. Wain J, Olsen JE (2013) Current and new approaches to typing of Salmonella. In: Barrow PA, Methner U (eds) Salmonella in domestic animals. CAB International, Oxfordshire, UK, pp 498–517

    Google Scholar 

  179. Wattiau P, Boland C, Bertrand S (2011) Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives. Appl Environ Microbiol 77:7877–7885

    CAS  PubMed Central  PubMed  Google Scholar 

  180. Peters TM, Maguire C, Threlfall EJ et al (2003) The Salm-gene project—a European collaboration for DNA fingerprinting for food-related salmonellosis. Euro Surveill 8:46–50

    CAS  PubMed  Google Scholar 

  181. 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

    CAS  PubMed Central  PubMed  Google Scholar 

  182. Boxrud D, Pederson-Gulrud K, Wotton J et al (2007) Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of Salmonella enterica serotype Enteritidis. J Clin Microbiol 45:536–543

    CAS  PubMed Central  PubMed  Google Scholar 

  183. Malorny B, Junker E, Helmuth R (2008) Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis. BMC Microbiol 8:84

    PubMed Central  PubMed  Google Scholar 

  184. Campioni F, Davis M, Medeiros MI, Falcao JP, Shah DH (2013) MLVA typing reveals higher genetic homogeneity among S. Enteritidis strains isolated from food, humans and chickens in Brazil in comparison to the North American strains. Int J Food Microbiol 162: 174–181

    CAS  PubMed  Google Scholar 

  185. Davis MA, Baker KN, Call DR et al (2009) Multilocus variable-number tandem-repeat method for typing Salmonella enterica serovar Newport. J Clin Microbiol 47:1934–1938

    CAS  PubMed Central  PubMed  Google Scholar 

  186. Foley SL, White DG, McDermott PF et al (2006) Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. J Clin Microbiol 44:3569–3577

    CAS  PubMed Central  PubMed  Google Scholar 

  187. Ross IL, Heuzenroeder MW (2005) Discrimination within phenotypically closely related definitive types of Salmonella enterica serovar typhimurium by the multiple amplification of phage locus typing technique. J Clin Microbiol 43:1604–1611

    CAS  PubMed Central  PubMed  Google Scholar 

  188. Singh P, Foley SL, Nayak R, Kwon YM (2013) Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars. Mol Cell Probes 27:80–85

    CAS  PubMed  Google Scholar 

  189. Scaria J, Palaniappan RU, Chiu D et al (2008) Microarray for molecular typing of Salmonella enterica serovars. Mol Cell Probes 22: 238–243

    CAS  PubMed Central  PubMed  Google Scholar 

  190. Huehn S, Malorny B (2009) DNA microarray for molecular epidemiology of Salmonella. Methods Mol Biol 551:249–285

    CAS  PubMed  Google Scholar 

  191. Matsuda M, Miyazawa T, Moore JE, Buckley TC, Thomas LA (1998) Molecular genotyping by pulsed-field gel electrophoresis of restricted genomic DNA of strains of Taylorella equigenitalis isolated in Ireland and in the United States. Vet Res Commun 22:217–224

    CAS  PubMed  Google Scholar 

  192. Kagawa S, Moore JE, Murayama O, Matsuda M (2001) Comparison of the value of pulsed-field gel electrophoresis, random amplified polymorphic DNA and amplified rDNA restriction analysis for subtyping Taylorella equigenitalis. Vet Res Commun 25:261–269

    CAS  PubMed  Google Scholar 

  193. Kagawa S, Klein F, Corboz L et al (2001) Demonstration of heterogeneous genotypes of Taylorella equigenitalis isolated from horses in six European countries by pulsed-field gel electrophoresis. Vet Res Commun 25: 565–575

    CAS  PubMed  Google Scholar 

  194. Aalsburg AM, Erdman MM (2011) Pulsed-field gel electrophoresis genotyping of Taylorella equigenitalis isolates collected in the United States from 1978 to 2010. J Clin Microbiol 49:829–833

    PubMed Central  PubMed  Google Scholar 

  195. Hunter PR, Gaston MA (1988) Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J Clin Microbiol 26:2465–2466

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743, Jena, Germany

    Konrad Sachse & Petra Moebius

Authors
  1. Konrad Sachse
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Petra Moebius
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Konrad Sachse .

Editor information

Editors and Affiliations

  1. Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal

    Mónica V. Cunha

  2. Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom

    João Inácio

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Sachse, K., Moebius, P. (2015). Molecular Typing Tools: From Pattern Recognition to Genome-Based Algorithms. In: Cunha, M., Inácio, J. (eds) Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies. Methods in Molecular Biology, vol 1247. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2004-4_21

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2004-4_21

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2003-7

  • Online ISBN: 978-1-4939-2004-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation