RAPD typing in microbiology - A technical review

Journal of Hospital Infection

Volumn 34, Issue 4, 1996, Pages 247-265

  Power, E G M ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

RAPD typing

Indexed keywords

BACTERIAL DNA;

BACTERIUM IDENTIFICATION; DNA FINGERPRINTING; DNA TEMPLATE; GENE AMPLIFICATION; MICROBIOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; RANDOM AMPLIFIED POLYMORPHIC DNA; REVIEW; SEROTYPING;

EID: 0030443332     PISSN: 01956701     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0195-6701(96)90106-1     Document Type: Review

References (55)

1. Anderson ES, Williams REO. Bacteriophage typing of enteric pathogens and staphylococci and its use in epidemiology. J Clin Path 1956; 9: 94-127.
2. Pitt TL. Bacterial typing systems: the way ahead. J Med Microbiol 1994; 40: 1-2.
3. Arbeit RD. Laboratory procedures for epidemiologic analysis. In: Murray PR, Barn EJ, Pfaller MA, Tenover FC, Yolher RH, Eds. Manual of Clinical Microbiology, 6th edn. Washington DC: ASM Press.
4. Wachsmuth K. Genotypic approaches to the diagnosis of bacterial infections: plasmid analyses and gene probes. Infect Control 1985; 6: 100-109.
5. Mekalanos JJ. Environmental signals controlling expression of virulence determinants in bacteria. J Bacteriol 1992; 174: 1-7.
6. Gaston MA, Duff PS, Naidoo J et al. Evaluation of electrophoretic methods for typing methicillin-resistant Staphylococcus aureus. J Med Microbiol 1988; 26: 189-197.
7. Mulligan ME, Kwok RYY, Citron DM, John Jr JF, Smith PB. Immunoblots, antimicrobial resistance and bacteriophage typing of oxacillin-resistant Staphylococcus aureus. J Clin Microbiol 1988; 26: 2395-2401.
8. Selander RK, Cangant DA, Ochman H, Muser JM, Gilmour MN, Whittam TS. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol 1986; 51: 873-884.
9. 35S-methionine. J Clin Pathol 1987; 40: 1070-1087.
10. Dryden MS, Talsania HG, Martin S et al. Evaluation of methods for typing coagulase-negative staphylococci. J Med Microbiol 1992; 37: 109-117.
11. Archer GL, Karchmer AW, Vishniarsky N, Johnston JL. Plasmid pattern analysis for the differentiation of infecting from non-infecting Staphylococcus epidermidis. J Infect Dis 1984; 149: 913-920.
12. Shlaes DM, Curie-McCumber CA. Plasmid analysis in molecular epidemiology: a summary and future directions. Rev Infect Dis 1986; 8: 738-746.
13. Marco F, Jimenez de Anta MT. Typing methods: plasmid analysis. Advantages and disadvantages. Enfermedades Infec Microbiol Clin 1993; 11: 97-101.
14. Branchini ML, Morthland VH, Tresoldi AT, Von Nowakovsky A, Dias MB, Pfaller MA. Application of genomic DNA subtyping by pulsed field gel electrophoresis and restriction enzyme analysis of plasmid DNA to characterize the methicillin-resistant Staphylococcus aureus from two nosocomial outbreaks. Diagn Microbiol Infect Dis 1993; 17: 275-281.
15. Fry NK, Warwick S, Saunders NA, Embley TM. The use of 16S ribosomal RNA analysis to investigate the phylogeny of the family Legionellaceae. J Gen Microbiol 1991; 137: 1215-1222.
16. Peterson CR, Petzel RA, Clabots CR, Fasching CE, Gerding DW. Medical technologists using molecular epidemiology as part of the infection control team. Diagn Microbiol Infect Dis 1993; 16: 303-311.
17. John JF. Molecular analysis of nosocomial epidemics. Infect Dis Clin N Am 1989; 3: 683-700.
18. Bingen EH, Desamur E, Elion J. Use of ribotyping in epidemiological surveillance of nosocomial outbreaks. Clin Microbiol Rev 1994; 7: 311-327.
19. Mullis KB. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 1987; 155: 335-350.
20. Gaydos CA, Bobo L, Welsh L, Hook EW 3rd, Viscidi R, Quinn TC. Gene typing of Chlamydia trachomatis by polymerase chain reaction and restriction endonuclease digestion. Sex Trans Dis 1992; 19: 303-308.
21. Navarrow E, Simonet P, Normand P, Bardin R. Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol 1992; 157: 107-115.
22. Kostman JR, Edlind TD, LiPuma JJ, Stull TL. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol 1992; 30: 2084-2087.
23. Kostman JR, Alden MB, Mair M et al. A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J Infect Dis 1995; 171: 205-208.
24. Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 1990; 18: 7213-7218.
25. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990; 18: 6531-6535.
26. Woods CR Jr, Versalovic J, Koeuth T, Lupski JR. Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J Clin Microbiol 1992; 30: 2921-2929.
27. van Belkum A, De Jonckheere J, Quint WGV. Genotyping Naeglaria spp. and Naeglaria fowleri isolates by interrepeat polymerase chain reaction. J Clin Microbiol 1992; 30: 2595-2598.
28. Hulton CS, Higgins CF, Sharp PM. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 1991; 5: 825-834.
29. Versalovic J, Thearith K, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and applications to fingerprinting of bacterial genomes. Nucleic Acids Res 1991; 19: 6823-6831.
30. Stern MJ, Ames GF, Smith NH, Robinson EC, Higgins CF. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 1984; 37: 1015-1026.
31. Breukel C, Wijnen J, Tops C, van der Klift H, Dauwerse H, Khan PM. Vector-Alu PCR: a rapid step in mapping cosmids and YACs. Nucleic Acids Res 1990; 18: 3097.
32. Raich TJ, Archer JL, Robertson MA, Tabachnik WJ, Beaty BJ. Polymerase chain reaction approaches to Culicoides (Diptera: Ceratopogonidae) identification. J Med Entomol 1993; 30: 228-232.
33. Caetano-Anolles G. Amplifying DNA with arbitrary oligonucleotide primers. PCR Meth Applic 1993; 3: 85-94.
34. Caetano-Anolles G, Bassam BJ, Gresshoff PM. DNA fingerprinting: MAAPing out a RAPD redefinition? BioTechnology 1992; 10: 937.
35. Vos P, Hogers R, Bleeker M et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 1995; 23: 4407-4414.
36. Caetano-Anolles G, Bassam BJ, Gresshoff PM. Primer-template interactions during DNA amplification fingerprinting with single arbitrary oligonucleotides. Mol Gen Genet 1992; 235: 157-165.
37. Bassam BJ, Caetano-Anolles G, Gresshoff PM. DNA amplification fingerprinting of bacteria. Appl Microbiol Biotechnol 1992; 38: 70-76.
38. Young KA, Power EGM, Dryden MS, Phillips I. RAPD typing of Staphylococcus haematolyticus from CAPD patients. Lett Appl Microbiol 1994; 18: 86-89.
39. MacPherson JM, Eckstein PE, Scoles GJ, Gajadhar AA. Variability of the random amplified polymorphic DNA assay among thermal cyclers, and effects of primer and DNA concentration. Mol Cell Probes 1993; 7: 293-299.
40. Saulnier P, Bourneix C, Prevost G, Andremont A. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 1993; 31: 982-985.
41. Rychlik W, Spencer WJ, Rhoads RE. Optimisation of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 1990; 18: 6409-6412.
42. Erlich HA, Gelfand D, Sninsky JJ. Recent advances in polymerase chain reaction. Science 1991; 1643-1651.
43. Mullis KB. The polymerase chain reaction in an anaemic mode: how to avoid cold oligodeoxyribonuclear fusion. PCR Meth Appl 1991; 1: 1-4.
44. van Belkum A, Bax R, Peerbooms P, Goessens W, van Leeuwen N, Quint WGV. Comparison of phage typing and DNA fingerprinting by PCR for discrimination of methicillin-resistant Staphylococcus aureus strains. J Clin Microbiol 193; 31: 798-803.
45. Kwok S, Kellog DE, McKinney N et al. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type I model studies. Nucleic Acids Res 1990; 18: 999-1005.
46. Williams JGK, Kubelik AR, Livak KJ, Rafalshi JA, Tinjey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990; 18: 6531-6535.
47. Fritsch P, Hanson MA, Spore CD, Pack PE, Rieseberg LH. Constancy of RAPD primer amplification strength among distantly related taxa of flowering plants. Plant Mol Biol Res 1993; 11: 10-20.
48. Merz WG. Candida albicans strain delineation. Clin Microbiol Rev 1990; 3: 321-334.
49. Thore M, Kuhn I, Lofdahl S, Burman LG. Drug-resistant coagulase-negative skin staphylococci: evaluation of four marker systems and epidemiology in an orthopaedic ward. Epidemiol Infect 1990; 105: 95-105.
50. Dillon JA, Carballo M. Molecular epidemiology and novel combinations of auxotype, serovar, and plasmid content in tetracycline-resistant Neisseria gonorrhoeae isolated in Canada. Can J Microbiol 1990; 36: 64-67.
51. Vurma-Rapp U, Kayser FH, Hadorn K, Wiederkehr F. Mechanism of imipenem resistance acquired by three Pseudomonas aeruginosa strains during imipenem therapy. Euro J Clin Microbiol Infect Dis 1990; 9: 580-587.
52. Goering RV. Guidelines for evaluating pulsed-field restriction fragment patterns in the epidemiological analysis of nosocomial infection. Third International Meeting on Bacterial Epidemiological Markers. Cambridge, UK 1994; Abstract F19.
53. Persing DH. Target selection and optimization of amplification reactions. In: Persing DH, Smith TF, Tenover FC, White TJ, Eds. Diagnostic Molecular Microbiology: Principles and Applications, Washington D.C.: American Society for Microbiology 1993; 51-87.
54. van Belkum A. DNA fingerprinting of medically important microorganisms by use of PCR. Clin Microbiol Rev 1994; 7: 174-184.52.
55. Tenover FC, Arbeit R, Archer G et Al. Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus. J Clin Microbiol 1994; 32: 407-415.