You are here

İnfeksiyon Hastalıklarının Tanısında Kullanılan DNA Probları ve Nükleik Asid Çoğaltma (Amplifikasyon) Yöntemleri

DNA probes and nucleic acid amplification techniques to diagnose infectious diseases

Journal Name:

Publication Year:

Author NameUniversity of AuthorFaculty of Author
Abstract (2. Language): 
At present, DNA probes and nucleic acid amplification techniques are most useful for the characterization of microorganisms for which culture and serological methods are difficult, extremely expensive, or unavailable. DNA-probe based assays are particularly well suited for in situ hibridization in tissue in which the localization and distribition of the microorganisms must be ascertained. Nucleic acid amplification procedures are complex methods that determine whether DNA or RNA from a particular organism is present in the clinical specimen. Because of this complexity, it is useful to assign such methods to one of three general categories; 1) target amplification systems such as polymerase chain reaction (PCR), self-sustaining sequence amplification (3SR), or strand displacement amplification (SDA); 2) probe amplification systems, which include Qb replicase or ligase chain reaction (LCR); and 3) signal amplification, in which the signal generated from each probe molecule is increased by using compound probes or branched-probe technology (bDNA). Recent advances in molecular technology may revolutionize the clinical microbiology laboratory. These new techniques, their advantages and disadvantages, and some of the recent applications have been discussed in this review. [Journal of Turgut Özal Medical Center 1997;4(3):329-344
Abstract (Original Language): 
Günümüzde, DNA probları ve nükleik asit amplifikasyon (NAÇ) yöntemleri, özellikle kültür ve serolojik testleri zor, pahalı veya bulunmayan mikroorganizmaların özelliklerini tanımlamada çok yararlıdır. Bu testlerden DNA prob temelli olanlar, özellikle dokuda mikroorganizmanın lokalizasyon ve dağılımını tespit etmek için uygundur. NAÇ yöntemleri ise klinik örnekte, belirli bir mikroorganizmanın DNA veya RNA 'sının bulunup bulunmadığını tesbit için kullanılır. NAÇ yöntemleri oldukça komplekstir. Bu komplekslikten dolayı, bu yöntemler 3 grupta incelenir; 1) hedef amplifikasyon yöntemleri: polimeraz zincir reaksiyonu (PCR), kendinden devamlı sekans amplifikasyon (3SR) veya iplikçik uzaklaştırarak amplifikasyon (SDA); 2) prob amplifikasyon yöntemleri: Qb replikaz ve ligaz zincir reaksiyonu (LCR); 3) bileşik prob veya dallanmış prob (bDNA) yöntemleri. Moleküler yöntemlerdeki bu ilerlemeler, klinik mikrobiyoloji laboratuvarında devrim niteliğindedir. Bu derlemede; yeni yöntemler ile bunların avantaj, dezavantaj ve uygulama alanları tartışılmıştır. [Turgut Özal Tıp Merkezi Dergisi 1997;4(3):329-344]
329-344

REFERENCES

References: 

1. Tompkins LS. The use of molecular methods in infectious diseases. N Engl J Med 1992;327:1290-7.
2. Eisenstein BI. New molecular techniques for microbial epidemiology and the diagnosis of infectious diseases. J Infect Dis 1990; 161:595-602.
3. Persing DH. ln vitro nucleic acid amplification techniques. "Persing DH, Smith TF, Tenover FC, White TJ. (ed): Diagnostic Molecular Microbiology". American Society for Microbiology, Washington 1993:51.
4. Goto MS, Oka S, Okuzumi K, et al: Evaluation of acridinium-ester labeled DNA probes for identification of Mycobacterium tuberculosis and Mycobacterium avium-Mycobacterium intracellulare complex in culture. J Clin Microbiol
1991;29:2473-6.
5. Huffnagle KE, Gander RM. Evaluation of Gen-Probe's Histoplasma capsulatum and Cryptococcus neoformans
AccuProbes. J Clin Microbiol 1993;31:419-21.
6. Padhye AA, Smith G, McLaughlin D, et al. Comparative evaluation of a chemiluminescent DNA probe and an exoantigen test for rapid identification of Histoplasma capsulatum. J Clin Microbiol 1992;30:3108-11.
7. Hosein IK, Kaunitz AM, Craft SJ. Detection of cervical Chlamydia trachomatis and Neisseria gonorrhoeae with deoxyribonucleic acid probe assays in obstetric patients. Am J Obstet Gynecol 1992;167:588-91.
8. Limberger RJ, Biega R, Evancoe A, et al. Evaluation of culture and the Gen-Probe PACE 2 assay for detection of Neisseria gonorrhoeae and Chlamydia trachomatis in endocervical specimens transported to a state health laboratory. J Clin
Microbiol 1992;30:1162-6.
9. Blanding J, Hirsch L, Stratton N, et al: Comparison of the clearview chlamydia, the PACE 2 assay and culture for detection of Chlamydia trachomatis from cervical specimens in a low-prevalence population. J Clin Microbiol
1993;31:1622-5.
10. Warren R, Dwyer B, Plackett M, et al: Comparative evaluation of detection assays for Chlamydia trachomatis. J Clin
Microbiol 1993;31:1663-6.
11. Tenover FC. Diagnostic deoxyribonucleic acid probes for infectious diseases. Clin Microbiol Rev 1988;1:82-101.
12. Eisenstein BI. The polymerase chain reaction. N Engl J Med
1990;322:178-83.
13. Peter JB. The polymerase chain reaction: Amplifying our
options. Rev Infect Dis 1991;13:166-71.
14. Persing DH. Polymerase chain reaction: Trenches to benches. J
Clin Microbiol 1991;29:1281-5.
15. Erlich HA, Gelfand D, Sninsky JJ. Recent advances in the polymerase chain reaction. Science 1991;252:1643-51.
16. Woolford AJ, Dale JW. Simplified procedures for detection of amplified DNA using fluorescent label incorporation and
reverse probing. FEMS Microbiol Lett 1992;99:311-6.
17. Nickerson DA, Kaiser R, Lappin S, et al. Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci USA 1990;87:8923-7.
18. Cimino GD, Metchette KC, Tessman JW, et al: Post-PCR
sterilization: A method to control carryover contamination for the polymerase chain reaction. Nucleic Acids Res 1991;19:99-
107.
19. Longo MC, Berninger MS, Hartley JL. Use of uracil DNA
glycosylase to control carry-over contamination in polymerase chain reaction. Gene 1990;93:125-8.
20. Reischl U, Kochanowski B. Quantitative PCR. A Survey of the Present Technology. Mol Biotechnol 1995;3: 55-71.
21. Lau JY. Davis GL, Kniffen J, et al. Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet 1993;341: 1501-4.
22. Mulder J, McKinney N, Christopherson C, et al. Rapid and simple PCR assay for quantitation of human immunodeficiency virus type I RNA in plasma: application to acute retroviral infection. J Clin Microbiol 1994;32 : 292-300.
23. Boivin G. Edelman CK, Pedneault L, et al. Phenotypic and genotypic characterization of acyclovir-resistant varicella-zoster virus isolated from patients with AIDS. J Infect Dis 1994;170 : 68-75.
24. Bagnarelli P, Menzo S, Vlenza A, et al. Quantitative molecular monitoring of human immunodeficiency virus type I activity during therapy with specific antiretroviral compounds. J Clin Microbiol 1995;33: 16-23.
342
Turgut Özal Tıp Merkezi Dergisi 4(3): 1997
Özerol İH.
DNA
probe
s and nucleic acid amlification techniques to diagnose infectious diseases
25. Louwagie J, McCutchan E, Peeters M, et al. Phylogenetic analysis of gag genus from 70 international HIV-I isolates provides evidence for multipl genotypes. AIDS 1993;7:.769-80.
26. Novati R, Thiers V, d'Arminio-Monforte A, et al. Mother-to-child transmission of hepatitis C virus detected by nested polymerase chain reaction. J Infect Dis 1992;165: 720-3.
27. Pyra H, Böni J, Schüpbach J. Ultrasensitive retrovirus detection by a revers transcriptase assay based on product enhancement. Proc Natl Acad Sci USA 1994;91 : 1544-8.
28. Heneine W, Yamamoto S, Switzer WM, et al. Detection of reverse transcriptase by a highly sensitive assay in sera from persons infected with human immunodeficiency virus type I. J Infect Dis 1995;171: 1210-6.
29. Eisenbach KD, Sifford MD, Cave D, et al. Detection of
Mycobacterium tuberculosis in sputum samples using a polymerase chain reaction. Am Rev Respir Dis
1991;144:1160-3.
30. Abbott M, Poiesz B, Byrne S, et al. Enzymatic gene amplification: Qualitative and quantitative methods for detecting proviral DNA amplified in-vitro. J Infect Dis
1988;158:1158-69.
31. Butcher A, Spadoro J. Using PCR for detection of HIV-1 infection. Clin Immunol Rev 1992;12:73-6.
32. Piatak M, Saag MS, Yang LC, et al. High levels of HIV-1 in
plasma during all stages of infection determined by competitive PCR. Science 1993;259:1749-53.
33. Young KKY, Resnick RM, Myers TW. Detection of hepatitis
C virus RNA by a combined reverse transcription-polymerase chain reaction assay. J Clin Microbiol 1993;31:882-6.
34. Shibata D, Martin WJ, Appleman MD, et al. Detection of
cytomegalovirus DNA in peripheral blood of patients infected with the human immunodeficiency virus. J Infect Dis
1988;158:1185-92.
35. Kuypers JM, Critchlow CW, Gravitt PE, et al. Comparison of dot filter hybridization, Southern transfer hybridization, and polymerase chain reaction for diagnosis of anal human papillomavirus infection. J Clin Microbiol 1992;31:1003-6.
36. Loeffelholz MJ, Lewinski CA, Silver SR, et al. Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction. J Clin Microbiol 1992;30:2847-51.
37. Relman DA, Loutit JS, Schmidt TM, et al. The agent of
bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med 1990;323:1573-80.
38. Relman DA, Falkow S. Identification of uncultured microoganisms: Expanding the spectrum of characterized microbial pathogens. Infect Agents Dis 1992:1:245-53.
39. Relman DA, Schmidt TM, MacDermott RP, et al.
Identification of the uncultured bacillus of Whipple's disease. N Engl J Med 1992;327:293-301.
40. Kwoh DY, Davis GR, Whitfield KM, et al. Transcription-
based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc Natl Acad Sci USA 1989;86:1173-
7.
41. Froussard P. rPCR: a powerful tool for random amplification of whole RNA sequences, PCR Meth Applic 1993; 2: 185.
42. Compton J. Nucleic acid sequence amplification. Nature 1991;350: 91.
43. Gingeras TR, Prodanovich P, Latimer T. Use of self sustained sequence replication reaction to analyze and detect mutations in zidovudine-resistant Human immunodeficiency virus. J
Infect Dis 1991;164: 1066.
44. Gingeras TR, Kwoh DY. In vitro nucleic acid amplitication techniques: issues and benefits. Praxis Biotechnol 1992;4:
403.
45. Guatelli JC, Whitfield KM, Kwoh DY, et al. Isothermal, in
vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci USA
1990;87:1874-8.
46. Davis GR, Blumeyer K, DiMichele LJ, et al. Detection of human immunodeficiency virus type 1 in AIDS patients using amplification-mediated hybridization analyses: Reproducibiltiy and quantitative limitations. J Infect Dis 1990;162:13-20.
47. Bush CE, Donovan RM, Rich Peterson W, et al. Detection of
human immunodeficiency virus type 1 RNA in plasma samples from high-risk pediatric patients using the self-sustained sequence replication reaction. J Clin Microbiol
1992;30:281-6.
48. Walker GT, Little MC, Nadeau JG, Shank DD. Isothermal in
vitro amplification of DNA by a restriction enzyme/DNA
polymerase system. Proc Natl Acad Sci USA 1992;89: 392.
49. Walker GT, Fraiser ML, Schram JL, et al. Strand displacement amplification-an isothermal, in oitro DNA amplification
technique. Nucleic Acids Res 1992; 20:1691-6.
50. Dey MJ, Down A,.Howard D, et al. Strand displacement amplification (SDA) of M. tuberculosis DNA from clinical isolates, abstr. U-41, Abstr. 93d Gen. Meet. Am Soc Microbiol 1993. American Society for Microbiology, Washington DC
1993:176.
51. Landegren U, Kaiser R. Sanders J, Hood L. A ligase mediated gene detection technique. Science 1988;241: 1077.
52. Backman K. Ligase chain reaction: Diagnostic technology for the 1990s and beyond. Clin Chem 1992;38:457-8.
53. Wolcott MJ. Advances in nucleic acid-based detection
methods. Clin Microbiol Rev 1992;5:370-86.
54. Barany F. Genetic disease detection and DNA amplification using thermostable DNA ligase. Proc Natl Acad Sci USA
1991;88: 189.
55. Wiedmann M, Wilson WJ, Czajka J, et al. Ligase chain reaction (LCR)-overview and applications PCR Meth Applic
1994;3: 51.
56. Birkenmeyer L, Armstrong AS. Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J Clin Microbiol 1992;30:3089-94.
57. Dille BJ, Butzen CC, Birkenmeyer LG. Amplification of Chlamydia trachomatis DNA by ligase chain reaction. J Clin Microbiol 1993;31:729-31.
58. Iovannisci DM, Winn-Deen ES. Ligation amplification and fluorescence detection of Mycobacterium tuberculosis DNA.
Mol Cell Probes 1993;7:35-43.
59. Lizardi P, Guerra C, Lomeli H, et al. Exponential amplification of recombinantRNA hybridization probes. Biotechnology
1988;6:1197-202.
Journal of Turgut Özal Medical Center 4(3):1997
343
İnfeksiyon hastalıklarının tanısında DNA probları ve nükleik asid çoğaltma yöntemleri
İH. Özerol
60. Prichard CG., Stefano JE. Amplified detection of viral nucleic acid at subattomole levels using Q beta replicase. Ann Biol
Chem (Paris) 1990;48:492-7.
61. Eoyang L, August.J. Q beta RNA polymerase from phage Q beta infected E. coli, In Cantoni GL, Davis DR (eds), P ocedu es in Nucleic Acid Research, vol. 2. Harper & Row,
Publishers, Inc., New York. 1971; 829-39.
62. Kacian D, Mills D, Kramer F, et al. A replicating RNA molecule suitable for detailed analysis of extracellular evolution and recombination. Proc Natl Acad Sci USA
1972;69:3038-42.
63. Miele EA, Mills DR, Kramer FR. Autocatalytic replication of a
recombinant RNA. J Mol Biol 1983;171:281-95.
64. Levisohn R, Spiegelman S. The cloning of a self replicating
RNA molecule. Proc Natl Acad Sci USA 1968;60: 866.
65. Lomell H, Tyagi S, Prichard CG, et al. Quantitative assays based on the usc of replicatable hybridization probes. Clin
Chem 1989;35: 1826.
66. Hunsaker WR, Badri H, Lombardo M, et al. Nucleic acid hybridization assays employing dA-tailed capture probes. II. Advanced multiple capture methods. Anal Biochem
1989;181:360-70.
67. Shan JJ, Liu B, Stone W, et al. A novel method for detection of
Mycobacterium tuberculosa directly from sputum, abstr. U-43, Abstr. 93nd Gen Meet. Am Soc Microbiol 1993. American Society for Microbiology, Washington, DC 1993;176.
68. Klinger JD, Pritchard. CG. Amplified probe based assays-possibilities and challenges in clinical microbiology. Clin Microbiol News 1990;12:189-207.
69. Wiedbrauk DL. Molecular methods for virus detection. Lab
Med 1992;23:737-42.
70. Urdea MS, Fultz T, Anderson TJ, et al. Branched amplification multimers for the sensitive, direct detection of human hepatitis viruses. Nucleic Acids Symp Ser 1991;24:197- 200.
71. Feinberg AP, Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific
activity. Anal Biochem 1983;132:6-13.
72. Feinberg AP, Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity (addendum). Anal Biochem 1984;137:266-7.
73. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual, 2nd ed, vol. II, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 1989;10.51-10.70.
74. Diamandis EP, Christopoulos TK. The biotin-(Strept) avidin system: principles and applications in biotechnology. Clin
Chem 1991;37:625-36.
75. Nevinney-Stickel C, Hinzpeter H, Andreas A, et al. Non-radioactive oligotyping for HLA-DR1- DRwlO using
polymerase chain reaction, digoxigenin-labeled oligonucleotides and chemiluminescence detection. Eur J Immunogenet 1991;18:323-32.
76. Pollard-Knight D, Read CA, Downes MJ, et al. Nonradioactive nucleic acid detection by enhanced chemiluminescence using probes directly labeled with horseradish peroxidase. Anal
Biochem 1990;37:84-9.
77. Brahic M, Haase AT. Detection of viral sequences of low reiteration frequency by in situ hybridization. Proc Natl Acad
Sci USA 1978;75:6125-9.
78. Unger ER, Budgeon LR, Myerson D, et al. Viral diagnosis by in situ hybridization: description of a rapid colorimetric
method. Am J Surg Pculwl 1986;10:1-8.
79. Hankin RC. In situ hybridization: principles and applications.
Lab Med 1992;23:764-70.
80. Fahrlander PD, Klausner A. Amplifying DNA probe signals: a "Christmas tree" approach. Bio/Technology 1988;6: 1165.
81. Sanchez-Pescador R. Stempien MS, Urdea MS: Rapid chemiluminescent nucleic acid assays for detection of TEM-I b-lactamase-mediated penicillin resistance in Neisseria gonorrhoea and other bacteria. J Clin Microbiol 1988;26:
1934.
82. Douglas DD, Rakela J, Taswell HF, et al. Correlation of auantitaâve HCV RNA, anti-HCV IgM, and Serum ALT with Histopathological Presentaâon. American Association for the Study of Liver Diseases, Chicago. 1992.
83. Wilber JC, Johnson PJ, Daley PJ, et al. Quantitation of hepatitis C viral RNA in serum or plasma, abstr. S-44, Abstr
92nd Gen Meet. Am Soc Microbiol 1992. American Society for Microbiology, Washington DC. 1992:406.
84. Pachl CA, Kern DG, Sheridan PJ, et al. Quantitative detection of HIV RNA in plasma using a signal amplification probe assay, abstr. Program Abstr. 32nd Intersci Conf Antimicrob Agents Chemother. American Society for Microbiology,
Washington, DC 1992:1247.
85. Shen LP, Kolberg JA, Spaete RR, et al. A quantitative method for detection of human cytomegalovirus DNA using a branched DNA enhanced label amplification assay, abstr.
Abstr. 92nd Gen Meet Am Soc Microbiol 1992. American Society for Microbiology, Washington, DC 1992:S-54, 408.

Thank you for copying data from http://www.arastirmax.com