Amplified-fragment length polymorphism analysis: The State of an Art

Journal of Clinical Microbiology

Volumn 37, Issue 10, 1999, Pages 3083-3091

  Savelkoul, P H M ^a   Aarts, H J M ^b   De Haas, J ^c   Dijkshoorn, L ^d   Duim, B ^b   Otsen, M ^e   Rademaker, J L W ^e   Schouls, L ^f   Lenstra, J A ^e  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c Section Biotechnology   (Netherlands)

^d LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^e UTRECHT UNIVERSITY   (Netherlands)

^f NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL GENETICS; DNA FINGERPRINTING; GENOTYPE; MICROBIOLOGY; MOLECULAR GENETICS; PRIORITY JOURNAL; REPRODUCIBILITY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SHORT SURVEY;

ANIMALIA;

EID: 0032878117     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.37.10.3083-3091.1999     Document Type: Short Survey

References (123)

1. Aarts, H. J. M., L. A. J. T. van Lith, and J. Keijer. 1998. High-resolution genotyping of Salmonella strains by AFLP-fingerprinting. Lett. Appl. Microbiol. 26:131-135.
2. Ajmone-Marsan, P., A. Valentini, M. Cassandro, G. Vecchiotti-Antaldi, G. Bertoni, and M. Kuiper. 1997. AFLP markers for DNA fingerprinting in cattle. Anim. Genet. 28:418-426.
3. Akerman, S., J. Tammisola, M. Regina, and V. Kauppinen. 1996. Segregation of AFLP markers in Betula pendula (Roth). Forest Gen. 3:117-123.
4. Arnold, C., L. Metherell, J. P. Clewley, and J. Stanley. 1999. Predictive modelling of fluorescent AFLP: a new approach to the molecular epidemiology of E. coli. Res. Microbiol. 150:33-44.
5. Bachem, C. W., R. S. van der Hoeven, S. M. de Bruijn, D. Vreugdenhil, M. Zabeau, and R. G. Visser. 1996. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 9:745-753.
6. Ballvora, A., J. Hesselbach, J. Niewohner, D. Leister, F. Salamini, and C. Gebhardt. 1995. Marker enrichment and high-resolution map of the segment of potato chromosome VII harbouring the nematode resistance gene Grol. Mol. Gen. Genet. 249:82-90.
7. Becker, J., P. Vos, M. Kuiper, F. Salamini, and M. Heun. 1995. Combined mapping of AFLP and RFLP markers in barley. Mol. Gen. Genet. 249:65-73.
8. Beismann, H., J. H. Barker, A. Karp, and T. Speck. 1997. AFLP analysis sheds light on distribution of two Salix species and their hybrid along a natural gradient. Mol. Ecol. 6:989-993.
9. Beltran, P., J. M. Musser, R. Helmuth, J. J. Farmer, III, W. M. Frerichs, et al. 1988. Toward a population genetic analysis of Salmonella. Genetic diversity and relationship among strains of serotypes S. choleraesuis, S. derby, S. enteritidis, S. heidelberg, S. infantis, S. newport, S. typhimurium. Proc. Natl. Acad. Sci. USA 85:7753-7757.
10. Blanc, D. S., P. M. Hauser, P. Francioli, and J. Bille. 1998. Molecular typing methods and their discriminatory power. Clin. Microbiol. Infect. 4:61-63.
11. Blears, M. J., S. A. De Grandis, H. Lee, and J. T. Trevors. Amplified fragment length polymorphism (AFLP): review of the procedure and its applications. J. Ind. Microbiol. Biotechnol. 21:99-114.
12. Boumedine, K. S., and A. Rodolakis. 1998. AFLP allows the identification of genomic markers of ruminant Chlamydia psittaci strains useful for typing and epidemiological studies. Res. Microbiol. 149:735-744.
13. Breyne, P., W. Boerjan, T. Gerats, M. van Montagu, A. Vangysel. 1997. Applications of AFLP™ in plant breeding, molecular biology and genetics. Belg. J. Bot. 129:107-117.
14. Brigneti, G., J. Garcia-Mas, and D. C. Baulcombe. 1997. Molecular mapping of the potato virus Y resistance gene Rysto in potato. Theor. Appl. Genet. 94:198-203.
15. Bryan, F. L., and M. P. Doyle. 1995. Health risks and consequences of Salmonella and Campylobacter jejuni in raw poultry. J. Food Prot. 58:326-344.
16. Buntjer, J. B. 1997. DNA repeats in the vertebrate genome as probes in phytogeny and species identification. Academic thesis, Utrecht University, Utrecht, The Netherlands.
17. Buntjer, J. B. 18 May 1999, revision date. [Online.] http://www.spg.wan .nl/pv/pub/CrossCheck/index.html. [28 July 1999, last date accessed.]
18. Cervera, M. T., J. Gusmao, M. Steenackers, J. Peleman, V. Storme, A. Vanden Broeck, M. van Montagu, and W. Boerjan. 1996. Identification of AFLP molecular markers for resistance against Melampsora larici-populina in Populus. Theor. Appl. Genet. 93:733-737.
19. Chalhoub, B. A., S. Thibault, V. Laucou, C. Rameau, H. Hofte, and R. Cousin. 1997. Silver staining and recovery of AFLP amplification products on large denaturing polyacrylamide gels. BioTechniques 22:216-218.
20. Cho, Y. G., M. W. Blair, O. Panaud, and S. R. McCouch. 1996. Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels. Genome 39:373-378.
21. Cnops, G., B. den Boer, A. Gerarts, M. van Montagu, and M. van Lijsebettens. 1996. Chromosome landing at the Arabidobsis TORNADO1 locus using an AFLP based strategy. Mol. Gen. Genet. 253:32-41.
22. Crosa, J. H., D. J. Brenner, W. H. Ewing, and S. Falkow. 1973. Molecular relationships among the Salmonelleae. J. Bacteriol. 115:307-315.
23. Daly, A. 1998. Evaluation of the AFLP and RAPD molecular marker technologies with regard to the genetic diversity of commercial wheat cultivars. In A. Karp, P. G. Isaac, D. S. Ingram (ed.), Molecular tools for screening biodiversity. Chapman & Hall, London, United Kingdom.
24. Desai, M., A. Tanna, R. Wall, A. Efstratiou, R. George, and J. Stanley. 1998. Fluorescent amplified-fragment length polymorphism analysis of an outbreak of group A streptococcal invasive disease. J. Clin. Microbiol. 36: 3133-3137.
25. Dijkshoom, L., H. Aucken, P. Gerner-Smidt, P. Janssen, M. E. Kaufmann, J. Garaizar, J. Ursing, and T. L. Pitt. 1996. Comparison of outbreak and nonoutbreak Acinetobacter baumannii strains by genotypic and phenotypic methods. J. Clin. Microbiol. 34:1519-1525.
26. Duim, B., E. Kruijt, W. van Leeuwen, F. van Zijderveld, and J. Wagenaar. 1997. Application of the DNA fingerprinting method AFLP to differentiate strains of Salmonella enteritidis and Salmonella dublin, p. 81-86. In Proceedings of the Molecular epidemiology of Campylobacter and Salmonella.
27. Duim, B., T. M. Wassenaar, A. Rigter, and J. A. Wagenaar. 1999. High-resolution genotyping of Campylobacter strains isolated from poultry and humans with AFLP fingerprinting. Appl. Environ. Microbiol. 65:2369-2375.
28. Ellis, T. H. N., S. J. Poyser, M. R. Knox, A. V. Vershinin, and M. J. Ambrose. 1998. Polymorphism of insertion sites of Tyl-copia retrotransposons and its use for linkage and diversity analysis in pea. Mol. Gen. Genet. 260:9-19.
29. Esteve, C. 1997. Is AFLP fingerprinting a true alternative to the DNA-DNA pairing method to assess genospecies in the genus Aeromonas? Int. J. Syst. Bacteriol. 47:245-246.
30. Farmer, J. J., B. R. Davis, F. W. Hickman-Brenner, A. McWorter, G. P. Huntley-Carter, M. A. Asbury, C. Riddle, H. G. Wathen, C. Elias, G. R. Fanning, A. G. Steigerwalt, C. M. O'Hara, G. K. Morris, P. B. Smith, and D. J. Brenner. 1985. Biochemical identification of new species and biogroups of Enterobacteriaceae isolated from clinical specimens. J. Clin. Microbiol. 21:46-76.
31. Felsenstein, J. 1995. PHYLIP (Phylogeny Inference Package), version 3.57c. University of Washington, Seattle.
32. Folkertsma, R. T., J. N. A. M. Rouppe van der Voort, K. E. de Groot, P. M. van Zantvoort, A. Schots, F. J. Gommers, J. Helder, and J. Bakker. 1996. Gene pool similarities of potato cyst nematode populations assessed by AFLP analysis. Mol. Plant-Microbe Interact. 9:47-54.
33. Gibson, J. R., E. Slater, J. Xerry, D. S. Tompkins, and R. J. Owen. 1998. Use of an amplified-fragment length polymorphism technique to fingerprint and differentiate isolates of Helicobacter pylori. J. Clin. Microbiol. 36:2580-2585.
34. Greef, J. M., M. Deuter, C. Jung, and J. Schondelmaier. 1997. Genetic diversity of European Miscanthus species revealed by AFLP fingerprinting. Gen. Res. Crop Evol. 44:185-195.
35. Haas, W. H., W. R. Butler, C. L. Woodley, and J. T. Crawford. 1993. Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex. J. Clin. Microbiol. 31:1293-1298.
36. Habu, Y., S. Fukada-Tanaka, Y. Hisatomi, and S. Lida. 1997. Amplified restriction fragment length polymorphism-based mRNA fingerprinting using a single restriction enzyme that recognizes a 4-bp sequence. Biochem. Biophys. Res. Commun. 234:516-521.
37. Heun, M., R. Schaefer Pregl, D. Klawan, R. Castagna, M. Accerbi, B. Borghi, and F. Salamini. 1997. Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312-1314.
38. Heyndrickx, M., K. Vandemeulebroecke, B. Hoste, P. Janssen, K. Kersters, P. De Vos, N. A. Logan, N. Ali, and R. C. Berkeley. 1996. Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens. Int. J. Syst. Bacteriol. 46:270-279.
39. Hill, M., H. Witsenboer, M. Zabeau, P. Vos, R. Kesseli, and R. Michelmore. 1996. PCR-based fingerprinting using AFLP as a tool for studying genetic relationschips in Lettuca spp. Theor. Appl. Genet. 93:1202-1210.
40. Huys, G., R. Coopman, M. Vancanneyt, I. Kersters, W. Verstraete, K. Kersters, and P. Janssen. 1993. High resolution diferentiation of aeromonads. Med. Microbiol. Lett. 2:248-255.
41. Huys, G., M. Altwegg, M. L. Hanninen, M. Vancanneyt, L. Vauterin, R. Coopman, U. Torck, J. Luthy Hottenstein, P. Janssen, and K. Kersters. 1996. Genotypic and chemotaxonomic description of two subgroups in the species Aeromonas eucrenophila and their affiliation to A. encheleia and Aeromonas DNA hybridization group 11. Syst. Appl. Microbiol. 19:616-623.
42. Huys, G., I. Kersters, R. Coopman, P. Janssen, and K. Kersters. 1996. Genotypic diversity among Aeromonas isolates recovered from drinking water production plants as revealed by AFLP analysis. Syst. Appl. Microbiol. 19:428-435.
43. Huys, G., R. Coopman, P. Janssen, and K. Kersters. 1996. High-resolution genotypic analysis of the genus Aeromonas by AFLP fingerprinting. Int. J. Syst. Bacteriol. 46:572-580.
44. Huys, G., P. Kampfer, M. Altwegg, R. Coopman, P. Janssen, M. Gillis, and K. Kersters. 1997. Inclusion of Aeromonas DNA hybridization group 11 in Aeromonas encheleia and extended descriptions of the species Aeromonas eucrenophila and A. encheleia. Int. J. Syst. Bacteriol. 47:1157-1164.
45. Huys, G., P. Kampfer, M. Altwegg, I. Kersters, A. Lamb, R. Coopman, J. Luthy-Hottenstein, M. Vancanneyt, P. Janssen, and K. Kersters. 1997. Aeromonas popoffii sp. nov., a mesophilic bacterium isolated from drinking water production plants and reservoirs. Int. J. Syst. Bacteriol. 47:1165-1171.
46. Janssen, P., R. Coopman, G. Huys, J. Swings, M. Bleeker, P. Vos, M. Zabeau, and K. Kersters. 1996. Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxomony. Microbiology 142:1881-1893.
47. Janssen, P., and L. Dijkshoorn. 1996. High resolution DNA fingerprinting of Acinetobacter outbreak strains. FEMS Microbiol. Lett. 142:191-194.
48. Janssen, P., K. Maquelin, R. Coopman, I. Tjernberg, P. Bouvet, K. Kersters, and L. Dijkshoorn. 1997. Discrimination of Acinetobacter genomic species by AFLP fingerprinting. Int. J. Syst. Bacteriol. 47:1179-1187.
49. Jones, C. J., K. J. Edwards, S. Castaglione, M. O. Winfield, F. Sala, C. van de Wiel, G. Bredemeijer, B. Vosman, M. Matthes, A. Daly, R. Brettschneider, P. Bettini, M. Buiatti, E. Maestri, A. Malceschii, N. Marmiroli, R. Aert, G. Volckaert, T. Rueda, R. Linacero, A. Vazques, and A. Karp. 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European Laboratories. Mol. Breed. 3:381-390.
50. Jones, J. T., and B. E. Harrower. 1998. A comparison of differential display and cDNA-AFLPs as tools for the isolation of differentially expressed parasite genes. Fundam. Appl. Nematol. 21:81-88.
51. Kaloshian, I., J. Yaghoobi, T. Liharska, J. Hontelez, D. Hanson, P. Hogan, T. Jesse, J. Wijbrandi, G. Simons, P. Vos, P. Zabel, and V. M. Williamson. 1998. Genetic and physical localization of the root-knot nematode resistance locus mi in tomato. Mol. Gen. Genet. 257:376-385.
52. Kamerbeek, J., L. Schouls, A. Kolk, M. van Achterveld, D. van Soolingen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, M. Goyal, and J. van Embden. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914.
53. Keim, P., A. Kalif, J. Schupp, K. Hill, S. E. Travis, K. Richmond, D. M. Adair, M. Hugh-Jones, C. R. Kuske, and P. Jackson. 1997. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J. Bacteriol. 187:818-824.
54. Koeleman, J. G. M., G. A. Parlevliet, L. Dijkshoorn, P. H. M. Savelkoul, and C. M. J. E. Vandenbroucke-Grauls. 1997. Nosocomial outbreak of multi-resistant Acinetobacter baumannii on a surgical ward: epidemiology and risk factors for acquisition. J. Hosp. Infect. 37:113-123.
55. Koeleman, J. G. M., J. Stoof, D. J. Biesmans, P. H. M. Savelkoul, and C. M. J. E. Vandenbroucke-Grauls. 1998. Comparison of ARDRA, RAPD and AFLP fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J. Clin. Microbiol. 36:2522-2529.
56. Kühn, I., M. J. Albert, M. Ansaruzzaman, N. A. Bhuiyan, S. A. Alabi, M. S. Islam, P. K. Neogi, G. Huys, P. Janssen, K. Kersters, and R. Mollby. 1997. Characterization of Aeromonas spp. isolated from humans with diarrhea, from healthy controls, and from surface water in Bangladesh. J. Clin. Microbiol. 35:369-373.
57. Kühn, I., G. Huys, R. Coopman, K. Kersters, and P. Janssen. 1997. A 4-year study of the diversity and persistence of coliforms and Aeromonas in the water of a Swedish drinking water well. Can. J. Microbiol. 43:9-16.
58. Kuipers, E. J., N. Dawn, A. Israel, J. G. Kusters, M. M. Gerrits, J. Weel, A. van der Ende, R. W. M. van der Hulst, S. A. Thompson, H. P. Wirth, J. Höök-Nikanne, and M. J. Blaser. Evidence for quasispecies development of H. pylori by study of paired isolates obtained years apart in the same host. Submitted for publication.
59. Leissner, C. E. W., M. L. Niessen, and R. F. Vogel. 1997. Use of the AFLP technique for the identification and discrimination of Fusarium graminearum. Cereal Res. Commun. 25:555-556.
60. Lin, J. J., J. Kuo, and J. Ma. 1996. A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria. Nucleic Acids Res. 24:3649-3650.
61. Lu, J., M. R. Knox, M. J. Ambrose, J. K. M. Brown, and T. H. N. Ellis. 1996. Comparative analysis of genetic diversity in pea assessed by RFLP- and PCR-based methods. Theor. Appl. Genet. 93:1103-1111.
62. Mackill, D. J., Z. Zhang, E. D. Redona, and P. M. Colowit. 1996. Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969-977.
63. Maslow, J. N., M. E. Mulligan, and R. D. Arbeit. 1993. Molecular epidemiology: application of contemporary techniques to the typing of microorganisms. Clin. Infect. Dis. 17:153-164.
64. Meijer, A., S. A. Morré, A. J. C. van den Brule, P. H. M. Savelkoul, and J. M. Ossewaarde. 1999. Genomic relatedness of Chlamydia isolates determined by amplified fragment length polymorphism analysis. Submitted for publication. J. Bacteriol. 181:4469-4475.
65. Michelmore, R. W., I. Paran, and R. V. Kesseli. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis; a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88:9828-9832.
66. Milbourne, D., R. Meyer, J. E. Bradshaw, N. Bonar, J. Provan, W. Powell, and R. Waught. 1997. Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol. Breed. 3:127-136.
67. Money, T., S. Reader, L. J. Qu, R. P. Dunford, and G. Moore. 1996. AFLP-based mRNA fingerprinting. Nucleic Acids Res. 24:2616-2617.
68. Morel, V. 1997. Bacteria diversify through warfare. Science 278:575.
69. Morré, S. A., T. M. Ossewaarde, P. H. M. Savelkoul, J. Stoof, C. J. L. M. Meijer, and A. J. C. van den Brule. Analysis of genetic heterogeneity in Chlamydia trachomatis biovars and clinical isolates of the serovars D, E and F by amplified fragment length polymorphism. Submitted for publication.
70. Mueller, U. G., S. E. Lipari, and M. G. Milgroom. 1996. Amplified fragment length polymorphism (AFLP) fingerprinting of symbiotic fungi cultured by the fungus-growing ant Cyphomyrmex minutus. Mol. Ecol. 5:119-122.
71. Nandi, S., P. K. Subudhi, D. Senadhira, N. L. Manigbas, S. Sen-Mandi, and N. Huang. 1997. Mapping OTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol. Gen. Genet. 255:1-8.
72. Olsen, J. E., D. J. Brown, M. N. Skov, and J. P. Christensen. 1993. Bacterial typing methods suitable for epidemiological studies. Applications in investigations of salmonellosis among livestock. Vet. Q. 15:125-135.
73. Olsen, J. E., M. N. Skov, E. J. Threlfall, and D. J. Brown. 1994. Clonal lines of Salmonella enterica serotype Enteritidis documented by IS-200, ribo-, pulsed-field gelelectrophoresis and RFLP typing. J. Med. Microbiol. 40:15-22.
74. Otsen, M., M. den Bieman, M. T. Kuiper, M. Pravenec, V. Kren, T. W. Kurtz, H. J. Jacob, A. Lankhorst, and B. F. van Zutphen. 1996. Use of AFLP markers for gene mapping and OTL detection in the rat. Genomics 37:289-294.
75. Otsen, M., et al. Unpublished data.
76. Pakniyat, H., W. Powell, E. Baird, L. L. Handley, D. Robinson, C. M. Scrimgeour, E. Nevo, C. Hacket, and P. D. Caligari. 1997. AFLP variation in wild barley (Hordeum spontaeum C. Koch) with reference to salt tolerance and associated ecogeography. Genome 40:332-341.
77. Palittapongarnpim, P., S. Chomyc, A. Fanning, and D. Kunimoto. 1993. DNA fingerprinting of Mycobacterium tuberculosis isolates by ligation-mediated polymerase chain reaction. Nucleic Acids Res. 21:761-762.
78. Paul, S., F. N. Wachira, W. Powell, and R. Waugh. 1997. Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers. Theort. Appl. Genetics 94:255-263.
79. Pearson, K. 1926. On the coefficient of racial likeness. Biometrika 18:105-117.
80. Picardeau, M., G. Prod'Hom, L. Raskine, M. P. LePennec, and V. Vincent. 1997. Genotypic characterization of five subspecies of Mycobacterium kansasii. J. Clin. Microbiol. 35:25-32.
81. Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey, and A. Rafalski. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breeding 2:225-238.
82. Qi, X., and P. Lindhout. 1997. Development of AFLP markers in barley. Mol. Gen. Genet. 254:330-336.
83. Rademaker, J. L. W., F. J. Louws, U. Rossbach, P. Vinuesa, and F. J. de Bruijn. 1999. Computer-assisted pattern analysis of electrophoretic fingerprints and database construction, p. 1-33. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, Suppl. 4. Kluwer Academic Publishers, Dordrecht, The Netherlands.
84. Rademaker, J. L. W., and F. J. de Bruijn. 1997. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis, p. 151-171. In G. Caetoan-Anollés and P. M. Gresshoff (ed.), DNA markers: protocols, applications and overviews. John Wiley & Sons, Inc., New York, N. Y.
85. Rademaker, J. L. W., B. Hoste, K. Kersters, F. J. Louws, J. Swings, L. Vauterin, P. Vauterin, and F. J. de Bruijn. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int. J. Syst. Bacteriol., in press.
86. Ranade, S. A., and P. V. Sane. 1996. Analysis of genetic diversity in plants with molecular techniques. Trop. Ecol. 37:31-37.
87. Reineke, A., P. Karlovsky, and C. P. Zebitz. 1998. Preparation and purification of DNA from insects for AFLP analysis. Insect Mol. Biol. 7:95-99.
88. Replogle, J., W. D. Lord, B. Budowle, T. L. Meinking, and D. Taplin. 1994. Identification of host DNA by amplified fragment length polymorphism analysis: preliminary analysis of human crab louse (Anoplura: Pediculidae) excreta. J. Med. Entomol. 31:686-690.
89. Reyna-Lopez, G. E., J. Simpson, and J. Ruiz-Herrera. 1997. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet. 253:703-710.
90. Rodrigue, D. C., R. V. Tauxe, and B. Rowe. 1990. International increase in Salmonella enteritidis: a new pandemic? Epidemiol. Infect. 105:21-27.
91. Rohlf, F. J. 1993. NTSYS-pc (ver. 1.80). Applied Biostatistics Inc., New York, N.Y.
92. Rosendahl, S., and J. W. Taylor. 1997. Development of multiple genetic markers for studies of genetic variation in arbuscular mycorrhizal fungi using AFLP. Mol. Ecol. 6:821-829.
93. Russell, J. R., Fuller, J. D. Fuller, M. Macaulay, B. G. Hatz, A. Jahoor, W. Powell, and R. Waugh. 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet. 95:714-722.
94. Schouls, L. Unpublished data.
95. Sensi, E., R. Vignani, W. Rohde, and S. Biricolti. 1996. Characterization of genetic biodiversity with Vitis vinifera L, Sangiovese and Colorino genotypes by AFLP and ISTR DNA marker technology. Vitis 35:183-188.
96. Sharma, S. K., M. R. Knox, and T. H. N. Ellis. 1996. AFLP analysis if the diversity and phylogeny of Lens and its comparison with RAPD analysis. Theor. Appl. Genet. 93:751-758.
97. Simoons-Smit, A. M., P. H. M. Savelkoul, T. M. Starink, and C. M. J. E. Vandenbroucke-Grauls. Typing of clinical and domestic animal strains of Staphylococcus aureus by AFLP. Submitted for publication.
98. Sloos, J. H., P. Janssen, C. P. A. van Boven, and L. Dijkshoorn. 1998. AFLP™ typing of Staphylococcus epidermidis in multiple sequential blood cultures. Res. Microbiol. 149:221-228.
99. Sneath, P. H. A., and R. R. Sokal. 1973. Numerical taxonomy. W. H. Freeman & Co., San Francisco, Calif.
100. Speijer, H., P. H. M. Savelkoul, M. J. Bonten, E. E. Stobberingh, and H. T. Tjhie. Application of different genotyping methods for Pseudomonas aeroginosa in an endemic setting on an intensive care. J. Clin Microbiol., in press.
101. Struelens, M. J., et al. 1996. Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. Infect. Dis. 2:2-11.
102. Tenover, F. C., R. Arbeit, G. Archer, J. Biddle, S. Byrne, R. Goering, G. Hancock, G. A. Hébert, B. Hill, R. Hollis, W. R. Jarvis, B. Kreiswirth, W. Eisner, J. Maslow, L. K. McDougal, J. M. Miller, M. Mulligan, and M. A. Pfaller. 1994. Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus. J. Clin. Microbiol. 32:407-415.
103. Tenover, F. C., R. D. Arbeit, R. V. Goering, P. A. Mickelsen, B. E. Murray, D. H. Persing, and B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:2233-2239.
104. Thomas, C. M., P. Vos, M. Zabeau, D. A. Jones, K. A. Norcott, B. P. Chadwick, and J. D. G. Jones. 1995. Identification of amplified restriction fragment polymorphism (AFLP) markers tightly linked to the tomato Cf-9 gene for resistance to Cladosporium fulvum. Plȧnt J. 8:785-794.
105. Travis, S. E., J. Maschinski, and P. Keim. 1996. An analysis of genetic variation in Astrgalus cremnophylax var. Cremnophylax, a critically endangered plant, using AFLP markers. Mol. Ecol. 6:735-745.
106. Valsangiacomo, C., F. Baggi, V. Gaia, T. Balmelli, R Peduzzi, and J.-C. Piffaretti. 1995. Use of amplified fragment length polymorphism in molecular typing of Legionella pneumophila and application to epidemiological studies. J. Clin. Microbiol. 33:1716-1719.
107. Van Belkum, A. 1994. DNA fingerprinting of medically important microorganisms by use of PCR. Clin. Microbiol. Rev. 7:174-184.
108. Vandenbroucke-Grauls, C. M. J. E., A. M. Simoons-Smit, and P. H. M. Savelkoul. 1997. DNA fingerprinting of Candida spp. by AFLP, abstr. C-238, p. 162. In Abstracts of the 97th General Meeting of the American Society for Microbiology. 1997. American Society for Microbiology, Washington, D.C.
109. Van der Lee, T., I. De Witte, A. Drenth, C. Alfonso, and F. Govers. 1997. AFLP linkage map of the oomycete Phytophthora infestans. Fungal Genet. Biol. 21:278-291.
110. van Eck, H. J., J. R. van der Voort, J. Draaistra, P. van Zandvoort, E. van Enkevort, B. Regers, J. Peleman, E. Jacobsen, and J. Helder. 1995. The inheritance and chromosomal localisation of AFLP markers in a non-inbred potato offspring. Mol. Breed. 4:397-410.
111. Vaneechoutte, M. 1996. DNA fingerprinting techniques for microorganisms. A proposal for classification and nomenclature. Mol. Biotechnol. 6:115-142.
112. Van Embden, J. D. A., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, and P. M. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406-409.
113. van Empel, P. 1998. Omithobacterium rhinotracheale. Academic thesis. Utrecht University, Utrecht, The Netherlands.
114. van Lith, L. A. J. T. Unpublished data.
115. Vantoai, T. T., St. Peng JiQing, S. Martin, and J. Q. Peng. 1996. Using AFLP markers to determine the contribution of parental genomes during selection. Soybean Gen. Newsl. 23:214-216.
116. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:6823-6831.
117. Versalovic, J., C. R. Woods, Jr., P. R. Georghiou, R. J. Hamill, and J. R. Lupski. 1993. DNA-based identification and epidemiologic typing of bacterial pathogens. Arch. Pathol. Lab. Med. 117:1088-1098.
118. Voorrips, R. E., M. C. Jongerius, and H. J. Kanne. 1997. Mapping of two genes for resistances to clubroot (Plasmodiophora brassicae) in a population of doubled haploid lines of Brassica oleracea by means of RFLP and AFLP markers. Theor. Appl. Genet. 94:75-82.
119. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414.
120. Waugh, R., K. McLean, A. J. Flavell, S. R. Pearce, A. Kumar, B. B. Thomas, and W. Powell. 1997. Genetic distribution of Bare-1-liek retrotransposable elements in the barely genome revealed by sequence specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253:687-694.
121. Wayne, L. G., R. C. Good, E. C. Bottger, R. Butler, M. Dorsch, T. Ezaki, W. Gross, V. Jonas, J. Kilburn, P. Kirschner, M. I. Krichevsky, M. Ridell, T. M. Shinnick, B. Springer, E. Stackebrandt, I. Tarnok, Z. Tarnok, H. Tasaka, V. Vincent, N. G. Warren, C. A. Knott, and R. Johnson. 1996. Semantide- and chemotaxonomy-based analyses of some problematic phenotypic clusters of slowly growing mycobacteria, a cooperative study of the International Working Group on Mycobacterial Taxonomy. Int. J. Syst. Bacteriol. 46:280-297.
122. World Health Organization, Centre for Reference and Research on Salmonella. 1980. Antigenic formulae of the Salmonella. World Health Organization International Salmonella Center, Institut Pasteur, Paris, France.
123. Zabeau, M., and P. Vos. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. Publication 0 534 858 A1, bulletin 93/13. European Patent Office, Munich, Germany.