Abstract
Since the discovery of the doublehelix structure of DNA (1), no single event has had the same impact on the field of molecular biology as the rediscovery by Kary Mullis in the early 1980s of the polymerase chain reaction (PCR) (2-4), which was first published in principle by Keld Kleppe in 1971 (5). This elegant technology with its apparent simple theory has revolutionized almost every aspect of classical molecular biology, and is at the present moment beginning to make a major impact upon many medical—especially diagnostic-specialities. The field of clinical microbiology has been among the first to embrace the polymerase chain reaction technology, and the expectations of the future impact of this technology are high. First and foremost, the diagnostic possibilities of this technology are stunning, but in this era of emerging implementation, it is crucial to focus not only on the possibilities, but also on the pitfalls of the technology. Failure to do so will increase the cost of implementation manifold, and will risk to disrepute the technology in the eyes of the clinicians.
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Watson, J. D. and Crick, F. H. C (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171, 737,738.
Mullis, K. B. (1990) The unusual origin of the polymerase chain reaction. Sci. Am. 262, 36–43.
Saiki, R. K., Scharf, S., Faloona, F., and Mullis, K. B. (1985) Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.
Saiki, R. K., Gelfand, D. H., Stoffel, S., and Scharf, S. J. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.
Kleppe, K., Uhtsuka, E., Kleppe, R., Molineux, I., and Khorana, H. G. (1971) Study on polynucleotides: repair replication of short syntetic DNAs as catalyzed by DNA polymerases. J. Mol. Biol. 56, 341–361.
Chien, A., Edgar, D. B., and Trela, J. M. (1976) Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. J. Bacteriol. 127, 1550–1557.
Higuchi, R., Fockler, C, Dollinger, G., and Watson, R. (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology 11, 1026–1030.
Rychlik, W. (1995) Selection of primers for polymerase chain reaction. Mol. Biotechnol. 3, 129–134.
Lucas, K., Busch, M., Mossinger, S., and Thompson, J. A. (1991) An improved microcomputerprogram for finding gene-or gene family-specific oligonucleotides suitable as primers for polymerase chain reactions or probes. Comput. Appl. Biosci. 7, 525–529.
Osborne, B. I. (1992) HyperPCR: a Macintosh HyperCard program for the determination of optimal PCR annealing temperature. Comput. Appl. Biosci. 8, 83.
Rychlik, W. and Rhoades, R. E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acid Res. 17, 8543–8551.
Rychlik, W., Spencer, W. J., and Rhoads, R. E. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acid. Res. 18, 6409–6412.
Wu, D. Y., Ugozzoli, L., Pal, B. K., Qian, J., and Wallace, R. B. (1991) The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell. Biol. 10, 233–238.
Meinkoth, J. and Wahl, G (1984) Hybridization of nucleic acids immobilized on solid supports. Anal. Biochem. 138, 267–284.
Cheng, S., Fockler, C., Barnes, W. M., and Higuchi, R. (1994) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. USA 91, 5695–5699.
Maga, E. A. and Richardson, T. (1990) Amplification of a 9.0-kb fragment using PCR. BioTechniques 8, 185,186.
Barnes, W. M. (1994) PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc. Natl. Acad. Sci. USA 91, 2216–2220.
Kaufman, D. L. and Evans, G. A. (1990) Restriction endonuclease cleavage at the termini of PCR products. BioTechniques 9, 304–306.
Innis, M. A. and Gelfand, D. H. (1990) Optimization of PCR’s, in PCR Protocols, A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic, San Diego, CA, pp. 3–12.
Carter, I. W. and Cloonan, M. J. (1995) Comparison between three PCR methods for detection of human cytomegalovirus DNA. Pathology 27, 161–164.
Sharkey, D. J., Scalice, E. R., Christy, K. G., Jr., Atwood, S. M., and Daiss, J. L. (1994) Antibodies as thermolabile switches: high temperature triggering for the polymerase chain reaction. Biotechnology 12, 506–509.
Birch, D. E., Kolmodin, L., Laird, W. J., McKinney, N., Wong, J., Young, K. Y., Zangenberg, G. A., and Zoccoli, M. A. (1996) Simplified hot start PCR. Nature 381, 445,446.
Longo, M. C., Berninger, M. S., and Hartley, J. L. (1990) Use of urasil DNA glucosylase to control carry-over contamination in polymerase chain reactions. Gene 93, 125–128.
Lindahl, T., Ljungquist, S., Siegert, W., Nyberg, B., and Sperens, B. (1977) DNA N-glycosidases. J. Biol. Chem. 252, 3286–3294.
Varshney, U., Hutcheon, T., and van de Sande, J. H. (1988) Sequence analysis expression and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung). J. Biol. Chem. 263, 7776–7784.
Ferre, F. (1992) Quantitative or semi-quantitative PCR: reality versus myth. PCR Meth. App. 2, 1–9.
Gilliland, G., Perrin, S., Blanchard, K. A., and Bunn, H. F. (1990) Analysis of cytokine mRNA and DNA: detection and quantitation by competetive polymerase chain reaction. Proc. Natl. Acad. Sci. USA 87, 2725–2729.
Murphy, L. D., Herzog, C. E., Rudick, J. B., Fojo, A. T., and Bates, S. E. (1990) Use of the polymerase chain reaction in the quantitation of mdr-1 gene expression. Biochemistry 29, 10,351–10,356.
Conolly, A. R., Cleland, L. G., and Kirkham, B. W. (1995) Mathematical considerations of competetive polymerase chain reaction. J. Immunol. Methods 187, 201–211.
Raeymaekers, L. (1993) Quantitative PCR: theoretical considerations with practical implications. Anal. Biochem. 214, 582–585.
Kwok, S. and Higuchi, R. (1989) Avoiding false positives with PCR. Lancet 339, 237,238.
Persing, D. H. (1990) Polymerase chain reaction: trenches to benches. J. Clin. Microbiol. 29, 1281–1285.
Tokue, Y., Shoji, S., Satoh, K., Watanabe, A., and Motomiya, M. (1991) Detection of methicillin-resistant Staphylococcus aureus (MRSA) using polymerase chain Reaction Amplification. Tohoku J. Exp. Med. 163, 31–37.
Murakami, K., Minamide, W., Wada, K., Nakamura, E., Teraoka, H., and Watanabe, S. (1991) Identification of methicillin-resistant strains of Staphylococci by polymerase chain reaction. J. Clin. Microbiol. 29, 2240–2244.
Zhang, Q. Y., Jones, D. M., Nieto, J. A. S., Trallero, E. P., and Spratt, B. G. (1990) Genetic diversity of penicillin-binding protein 2 genes of penicillin-resistant strains of Neisseria meningitidis revealed by fingerprinting of amplified DNA. Antimicrob. Agents Chemother. 34, 1523–1528.
Arthur, M., Molinas, C., Mabilat, C., and Courvalin, P. (1990) Detection of erythromycin resistance by the polymerase chain reaction using primers in conserved regions of erm rRNA methylase genes. Antimicrob. Agents Chemother. 34, 2024–2026.
Vliegenhart, J. S., Ketelaar-Van Gaalen, P. A. G., and van de Klundert, J. A. M. (1990) Identification of three genes coding for aminoglycoside-modifying enzymes by means of the polymerase chain reaction. J. Antimicrob. Chemother. 25, 759–765.
Levesque, C., Piche, L., Larose, C., and Roy, P. H. (1995) PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob. Agents Chemother. 39, 185–191.
Brisson-Noel, A., Lecossier, D., Nassif, X., Gicquel, B., LevyFrebault, V., and Hance, A. J. (1989) Rapid diagnosis of tuberculosis by amplification of mycobacterial DNA in clinical samples. Lancet ii, 1069–1071.
Vary, P. H., Andersen, P. R., Green, E., Hermon-Taylor, J., and McFadden, J. J. (1990) Use of highly specific DNA probes and the polymerase chain reaction to detect Mycobacterium paratuberculosis in Johne’s disease. J. Clin. Microbiol. 28, 933–937.
Hartskeerl, R. A., De Wit, M. Y. L., and Klatser, P. R. (1989) Polymerase chain reaction for the detection of Mycobacterium leprae. J. Gen. Microbiol. 135, 2357–2364.
Starnback, M. N., Falkow, S., and Tompkins, L. S. (1989) Species-specific detection of Legionella pneumophila in water by DNA amplification and hybridization. J. Clin. Microbiol. 27, 1257–1261.
Mahbubani, M. H., Bej, A. K., Miller, R., Haff, L., DiCesare, J., and Atlas, R. M. (1990) Detection of legionella with polymerase chain reaction and gene probe methods. Mol. Cell. Probes. 4, 175–187.
Lisby, G. and Dessau, R. (1994) Construction of a DNA amplification assay for clinical diagnosis of Legionellae species. Eur. J. Clin. Microbiol. 13, 225–231.
Rosa, P. A. and Schwan, T. G. (1989) A specific and sensitive assay for the Lyme disease spirochete Borrelia burgdorferi using the polymerase chain reaction. J. Infect. Dis. 169, 1018–1029.
Jaulhac, B., Nicolini, P., Piemont, Y., and Monteil, H. (1991) Detection of Borrelia burgdorferi in cerebrospinal fluid of patients with lyme borreliosis. N. Engl. J. Med. 324, 1440.
Bernet, C., Garret, M., De Barbeyrac, B., Bebear, C., and Bonnet, J. (1989) Detection of Mycoplasma pneumoniae by using the polymerase chain reaction. J. Clin. Microbiol. 27, 2492–2496.
Jensen, J. S., Uldum, A. S., Søndergård-Andersen, J., Vuust, J., and Lind, K. (1991) Polymerase chain reaction for detection of Mycoplasma genitalium in clinical samples J. Clin. Microbiol. 29, 46–50.
Dutilh, B., Bebear, C., Rodriguez, P., Vekris, A., Bonnet, J., and Garret, M. (1989) Specific amplification of a DNA sequence common to all chlamydia trachomatis serovars using the polymerase chain reaction. Res. Microbiol. 140, 7–16.
Holland, S. M., Gaydos, C. A., and Quinn, T. C. (1990) Detection and differentiation of Chlamydia trachomatis, Chlamydia psittaci, and Chlamydia pneumoniae by DNA amplification. J. Infect. Dis. 162, 984–987.
Border, P. M., Howard, J. J., Plstow, G. S., and Siggens, K. W. (1990) Detection of Listeria species and Listeria monocytogenes using polymerase chain reaction. Lett. Appl. Microbiol. 11, 158–162.
McDonough, K. A., Schwan, T. G., Thomas, R. E., and Falkow, S. (1988) Identification of a Yersinia pestis-specific DNA probe with potential for use in plague surveillance. J. Clin. Microbiol. 26, 2515–2519.
Wren, B. W. and Tabaqchali, S. (1990) Detection of pathogenic Yersenia enterocolitica by the polymerase chain reaction. Lancet 336, 693.
Lampel, K. A., Jagow, J. A., Truclcsess, M., and Hill, W. E. (1990) Polymerase chain reaction for detection of invasive Shigella flexneri in food. Appl. Envir. Microbiol. 56, 1536–1540.
Olive, D. M., Atta, A. I., and Setti, S. K. (1988) Detection of toxigenic Escherichia coli using biotin-labeled DNA probes following enzymatic amplification of the heat labile toxin gene. Mol. Cell. Probes 2, 47–57.
Victor, T., du Toit, R., van Zyl, J., Bester, A. J., and van Helden, P. D. (1991) Improved method for the routine identification of toxigenic Escherichia coli by DNA amplification of a conserved region of the heat-labile toxin A subunit. J. Clin. Microbiol. 29, 158–161.
Karch, H. and Meyer, T. (1989) Single primer pair for amplifying segments of distinct shiga-like-toxin genes by polymerase chain reaction. J. Clin. Microbiol. 27, 2751–2757.
Pollard, D. R., Johnson, W. M., Lior, H., Tyler, S. D., and Rozee, K. R. (1990) Rapid and specific detection of verotoxin genes in Escherichia coli by the polymerase chain reaction. J. Clin. Microbiol. 28, 540–545.
van Ketel, R. J., de Wever, B., and van Alphen, L. (1990) Detection of Haemophilus influenzae in cerebrospinal fluids by polymerase chain reaction DNA amplification. J. Med. Microbiol. 33, 271–276.
Kristiansen, B. E., Ask, E., Jenkins, A., Fermer, C., Radstrøm, P., and Skød, O. (1991) Rapid diagnosis of meningococcal meningitis by polymerase chain reaction. Lancet 337, 1568,1569.
Houard, S., Hackel, C., Herzog, A., and Bollen, A. (1989) Specific identification of Bordetella pertussis by the polymerase chain reaction. Res. Microbiol. 140, 477–487.
Burstain, J. M., Grimprel, E., Lukehart, S. A., Norgard, M. V., and Radolf, J. D. (1991) Sensitive detection of Treponema pallidum by using the polymerase chain reaction. J. Clin. Microbiol. 29, 62–69.
Grimprel, E., Sanchez, P. J., Wendel, G. D., Burstain, J. M., McCracken, G. H., Radolf, J. D., and Norgard, M. V. (1991) Use of polymerase chain reaction and rabbit infectivity testing to detect Treponema pallidum in amniotic fluid fetal and neonatal sera and cerebrospinal fluid. J. Clin. Microbiol. 29, 1711–1718.
Hoshina, S., Kahn, S. M., Jiang, W., and Green, P. H. R. (1990) Direct detection and amplification of Helicobacter pylori ribosomal 16S gene segments from gastric endoscopi biopsies. Diagn. Microbiol. Infect. Dis. 13, 473–479.
Hill, W. E., Keasler, S. P., Trucksess, M. W., Feng, P., Kaysner, C. A., and Lampel, K. A. (1991) Polymerase chain reaction identification of Vibrio vulnificus in artificially contaminated oysters. Appl. Envir. Microbiol. 57, 707–711.
Pollard, D. R., Johnson, W. M., Lior, H., Tyler, S. D., and Rozee, K. R. (1990) Detection of the aerolysin gene in Aeromonas hydrophila by the polymerase chain reaction. J. Clin. Microbiol. 28, 2477–2481.
Wren, B., Clayton, C., and Tabaqchali, S. (1990) Rapid identification of toxigenic Clostridium difficile by polymerase chain reaction. Lancet 335, 423.
Wilson, I. G., Cooper, J. E., and Gilmour, A. (1991) Detection of enterotoxigenic Staphylococcus aureus in dried skimmed milk: use of the polymerase chain reaction for amplification and detection of Staphylococcal enterotoxin genes entB and entC1 and the thermonuclease gene nuc. Appl. Envir. Microbiol. 57, 1793–1798.
Duggan, D. B., Ehrlich, G. D., Davey, F. P., and Kwok, S. (1988) HTLV-I Induces lymphoma mimicking Hodgkin’s disease. Diagnosis by polymerase chain reaction amplification of specific HTLV-I sequences in tumor DNA. Blood 71, 1027–1032.
Lisby, G. (1993) Search for an HTLV-I-like retrovirus in patients with multiple sclerosis by enzymatic DNA amplification. Acta. Neurol. Scand. 88, 385–387.
Lee, H., Swanson, P., Shorty, V. S., Zack, J. A., Rosenblatt, J. D., and Chen, I. S. Y. (1989) High rate of HTLV-II infection in seropositive IV drug abusers in New Orleans. Science 244, 471–475.
Murakawa, G. J., Zaia, J. A., Spallone, P. A., and Stephens, D. A. (1988) Direct detection of HIV-l RNA from AIDS and ARC patient samples. DNA 7, 287–295.
Holodniy, M., Katzenstein, D. A., Sengupta, S., and Wang, A. M. (1991) Detection and quantification of human immunodeficency virus RNA in patient serum by use of the polymerase chain reaction. J. Infect. Dis. 163, 862–866.
Jackson, J. B., Kwok, S., Sninsky, J., and Hopsicker, J. S. (1990) Human immunodeficiency virus type 1 detected in all seropositive symptomatic and asymptomatic individuals. J. Clin. Microbiol. 28, 16–19.
Rayfield, M., De Cock, K., Heyvvard, W., and Goldstein, L. (1988) Mixed human immunodeficiency virus (HIV) infection in an individual: demonstration of both HIV type 1 and type 2 proviral sequences by using polymerase chain reaction. J. Infect. Dis. 158, 1170–1176.
Bevan, I. S., Daw, R. A., Day, P. J. R., Ala, F. A., and Walker, M. R. (1991) Polymerase chain reaction for detection of human cytomegalovirus infection in a blood donor population. Br. J. Haemat. 78, 94–99.
Jiwa, N. M., Van Gemert, G., Raap, A. K., and Van de Rijke, F. M. (1989) Rapid detection of human cytomegalovirus DNA in peripheral blood leukocytes of viremic transplant recipients by the polymerase chain reaction. Transplant. 48, 72–76.
Cao, M., Xiao, X., Eghert, B., Darragh, T. M., and Yen, T. S. B. (1989) Rapid detection of cutaneous herpes simplex virus infection with the polymerase chain reaction. J. Invest. Dermatol. 82, 391,392.
Aurelius, E., Johansson, B., Skoldenberg, B., Staland, A., and Forsgren, M. (1991) Rapid diagnosis of herpes simplex encephalitis by nested polymerase chain reaction assay of cerebrospinal fluid. Lancet 337, 189–192.
Koropchak, C. M., Graham, G., Palmer, J., and Winsberg, M. (1991) Investigation of Varicella-Zoster virus infection by polymerase chain reaction in the immunocompetent host with acute varicella. J. Infect. Dis. 163, 1016–1022.
Jilg, W., Sieger, E., Alliger, P., and Wolf, H. (1990) Identification of type A and B isolates of Epstein-Barr virus by polymerase chain reaction. J. Virol. Meth 30, 319–322.
Buchbinder, A., Josephs, S. F., Ablashi, D., Salabuddin, S. Z., and Klotman, M. E. (1988) Polymerase chain reaction amplification and in situ hybridization for the detection of human B-lymphotropiic virus. J. Virol. Meth. 21, 191–197.
Jarrett, R. F., Clark, D. A., Josephs, S. F., and Onions, D. E. (1990) Detection of human herpesvirus-6 DNA in peripheral blood and saliva. J. Med. Virol. 32, 73–76.
Margolis, H. S. and Nainan, O. V. (1990) Identification of virus components in circulating immune complexes isolated during hepatitis A virus infection. Hepatol. 11, 31–37.
Jansen, R. W., Siegl, G., and Lemon, S. M. (1990) Molecular epidemiology of human hepatitis A virus defined by an antigen-capture polymerase chain reaction method. Proc. Natl. Acad. Sci. USA 87, 2867–2871.
Kaneko, S., Miller, R. H., Feinstone, S. M., and Unoura, M. (1989) Detection of serum hepatitis B virus DNA in patients with chronic hepatitis using the polymerase chain reaction assay. Proc. Natl. Acad. Sci. USA 86, 312–316.
Garson, J. A., Tedder, R. S., Briggs, M., and Tuke, P. (1990) Detection of hepatitis C viral sequences in blood donations by “nested” polymerase chain reaction and prediction of infectivity. Lancet 335, 1419–1422.
Weiner, A. J., Kuo, G., Bradley, O. W., and Bonino, F. (1990) Detection of hepatitis C viral sequences in non-A non-B hepatitis. Lancet 335, 1–3.
Zignego, A. L., Deny, P., Feray, C., and Ponzetto, A. (1990) Amplification of hepatitis delta virus RNA sequences by polymerase chain reaction: a tool for viral detection and cloning. Mol. Cell. Probes 4, 43–51.
Reyes, G. R., Purdy, M. A., Kim, J. P., and Luk, K. C. (1990) Isolation of a cDNA from the virus responsible for enterically transmitted non-A non-B hepatitis. Science 247, 1335–1339.
Shibata, D. K., Arnheim, N., and Martin, W. J. (1988) Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction. J. Exp. Med. 167, 225–230.
Anceschi, M. M., Falcinelli, C., Pieretti, M., and Cosmi, E. V. (1990) Multiple primer pairs polymerase chain reaction for the detection of human papillomavirus types. J. Virol. Meth. 28, 59–66.
Ho-Terry, L., Terry, G. M., and Londesborough, P. (1990) Diagnosis of foetal rubella virus infection by polymerase chain reaction. J. Gen. Virol. 71, 1607–1611.
Olive, D. M., Al-Mufti, S., Al-Mulla, W., and Khan, M. A. (1990) Detection and differentiation of picornaviruses in clinical samples following genomic amplification. J. Gen. Virol. 71, 2141–2147.
Rotbart, H. A., Kinsella, J. P., and Wasserman, R. L. (1990) Persistent enterovirus infection in culture-negative meningoencephalitis: demonstration by enzymatic RNA amplification. J. Infect. Dis. 161, 787–791.
Ermine, A., Larzul, D., Ceccaldi, P. E., Guesdon, J. L., and Tsiang, H. (1990) Polymerase chain reaction amplification of rabies virus nucleic acids from total mouse brain RNA. Mol. Cell. Probes 4, 189–191.
Arthur, R. R., Dagostin, S., and Shah, K. V. (1989) Detection of BK virus and JC virus in urine and brain tissue by the polymerase chain reaction. J. Clin. Microbiol. 27, 1174–1179.
Carman, W. F., Williamson, C., Cunliffe, B. A., and Kidd, A. H. (1989) Reverse transcription and subsequent DNA amplification of rubella virus RNA. J. Virol. Methods 25, 21–30.
Godec, M. S., Asher, D. M., Swoveland, P. T., and Eldadah, Z. A. (1990) Detection of measles virus genomic sequences in SSPE brain tissue by the polymerase chain reaction. J. Med. Virol. 30, 237–244.
Yamada, A., Imanishi, J., Nakajima, E., Nakajima, K., and Nakajima, S. (1991) Detection of influenza viruses in throat swab by using polymerase chain reaction. Microbiol. Immunol. 35, 259–265.
Hyypiä, T., Auvinen, P., and Maaronen, M. (1989) Polymerase chain reaction for human picorna-viruses. J. Gen. Virol. 70, 3261–3268.
Torgersen, H., Skern, T., and Blaas, D. (1989) Typing of human rhinoviruses based on sequence variations in the 5′ non-coding region. J. Gen. Virol. 70, 3111–3116.
Gow, J. W., Behan, W. M. H., Clements, G. B., and Woodall, C. (1991) Enteroviral RNA sequences detected by polymerase chain reaction in muscle of patients with post-viral fatigue syndrome. Br. Med. J. 302, 692–696.
Gouvea, V., Glass, R. I., Woods, P., and Taniguchi, K. (1990) Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 28, 276–282.
Allard, A., Girones, R., Juto, P., and Wadell, G. (1990) Polymerase chain reaction for detection of adenoviruses in stool samples. J. Clin. Microbiol. 28, 2659–2667.
Salimans, M. M. M., Van de Rijke, F. M., Raap, A. K., and van Elsacker-Niele, A. M. W. (1989) Detection of parvovirus B19 DNA in fetal tissues by in situ hybridisation and polymerase chain reaction. J. Clin. Pathol. 42, 525–530.
Laille, M., Deubel, V., and Sainte-Marie, F. F. (1991) Demonstration of concurrent dengue 1 and dengue 3 infection in six patients by the polymerase chain reaction. J. Med. Virol. 34, 51–54.
Eldadah, Z. A., Asher, D. M., Godec, M. S., and Pomeroy, K. L. (1991) Detection of Flaviviruses by reverse-transcriptase polymerase chain reaction. J. Med. Virol. 33, 260–267.
Morita, K., Tanaka, M., and Igarashi, A. (1991) Rapid identification of dengue virus serotypes by using polymerase chain reaction. J. Clin. Microbiol. 29, 2107–2110.
Giebel, L. B., Zoller, L., Bautz, I. K. F., and Darai, G. (1990) Rapid detection of genomic variations in different strains of hantaviruses by polymerase chain reaction techniques and nucleotide sequence analysis. Virus Res. 16, 127–136.
Lunkenheimer, K., Hufert, F. T., and Schmitz, H. (1990) Detection of lassa virus RNA in specimens from patients with lassa fever by using the polymerase chain reaction. J. Clin. Microbiol. 28, 2686–2692.
Wakefield, A. E., Pixley, F. J., Banerji, S., and Sinclair, K. (1990) Detection of Pneumocystis carinii with DNA amplification. Lancet 336, 451–453.
Burg, J. L., Grover, C. M., Pouletty, P., and Boothroyd, J. C. (1989) Direct and sensitive detection of a pathogenic protozoan Toxoplasma gondii by polymerase chain reaction. J. Clin. Microbiol. 27, 1787–1792.
Holliman, R. E., Johnson, J. D., and Savva, D. (1990) Diagnosis of cerebral toxoplasmosis in association with AIDS using the polymerase chain reaction. Scand. J. Infect. Dis. 22, 243–244.
Foote, S. J., Kyle, D. E., Martin, R. K., and Oduola, A. M. J. (1990) Several alleles of the multidrug-resistance gene are closely linked to chloroquine resistance in Plasmodium falciparum. Nature 345, 255–258.
Kain, K. C. and Lanar, D. E. (1991) Determination of genetic variation within Plasmodium falciparum by using enzymatically amplified DNA from filter paper disks impregnated with whole blood. J. Clin. Microbiol. 29, 1171–1174.
Tannich, E. and Burchard, G. D. (1991) Differentiation of pathogenic from non-pathogenic Entamoeba histolytica by restriction fragment analysis of a single gene amplified in vitro. J. Clin. Microbiol. 29, 250–255.
Mahbubani, M. H., Bej, A. K., Perlin, M. H., and Schaefer, F. W. III (1992) Differentiation of Giardia duodenalis from other giardia species by using polymerase chain reaction and gene probes. J. Clin. Microbiol. 30, 74–78.
Carl, M., Tibbs, C. W., Dobson, M. E., Paparello, S., and Dasch, G. A. (1990) Diagnosis of acute typhus infection using the polymerase chain reaction. J. Infect. Dis. 161, 791–793.
Kelly, D. J., Marana, D. P., Stover, C. K., Oaks, E. V., and Carl, M. (1990) Detection of Rickettsia tsutsugamushi by gene amplification using polymerase chain reaction techniques. Ann. New York Acad. Sci. 590, 564–571.
Tzianabos, T., Anderson, B. E., and McDade, J. E. (1989) Detection of Rickettsia rickettsii DNA in clinical specimens by using polymerase chain reaction technology. J. Clin. Microbiol. 27, 2866–2868.
Moser, D. R., Kirchhoff, L. V., and Donelson, J. E. (1989) Detection of Trypanosoma cruzi by DNA amplification using the polymerase chain reaction. J. Clin. Microbiol. 27, 1477–1482.
Moser, D. R., Cook, G. A., Ochs, D. E., and Bailey, C. P. (1989) Detection of Trypanosoma congolense and Trypanosoma brucei subspecies by DNA amplification using the polymerase chain reaction. Parasitology 99, 57–66.
Gottstein, B. and Mowatt, M. R. (1991) Sequencing and characterization of an Echinococcus multilocularis DNA probe and its use in the polymerase chain reaction. Mol. Biochem. Parasitol. 44, 183–194.
McLaughlin, G. L., Vodkin, M. H., and Huizinga, H. W. (1991) Amplification of repetitive DNA for the specific detection of Naegleria fowleri. J. Clin. Microbiol. 29, 227–230.
Gasser, R. B., Morahan, G., and Mitchell, G. F. (1991) Sexing single larval stages of Schistosoma mansoni by polymerase chain reaction. Mol. Biochem. Parasitol. 47, 255–258.
Gottstein, B., Deplazes, P., Tanner, I., and Skaggs, J. S. (1991) Diagnostic identification of Taenia saginata with the polymerase chain reaction. Trans. Roy. Soc. Trop. Med. Hyg. 85, 248,249.
Zarlenga, D. S., McManus, D. P., Fan, P. C., and Cross, J. H. (1991) Characterization and detection of a newly described Asian Taeniid using cloned ribosomal DNA fragments and sequence amplification by the polymerase chain reaction. Exp. Parasitol. 72, 174–183.
Lopez-Berestein, G., Bodey, G. P., Fainstein, V., and Keating, M. (1989) Treatment of systemic fungal infections with liposomal amphotericin B. Arch. Intern. Med. 149, 2533–2536.
Buchman, T. G., Rossier, M., Merz, W. G., and Charache, P. (1990) Detection of surgical pathogens by in vitro DNA amplification. Part I rapid identification of Candida albicans by in vitro amplification of a fungus-specific gene. Surgery 108, 338–347.
Vilgalys, R. and Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172, 4238–4246.
Kemker, B. J., Lehmann, P. F., Lee, J. W., and Walsh, T. J. (1991) Distinction of deep versus superficial clinical and nonclinical isolates of Trichosporon beigelii by isoenzymes and restriction fragment length polymorphisms of rDNA generated by polymerase chain reaction. J. Clin. Microbiol. 29, 1677–1683.
Woese, C. R. (1987) Bacterial evolution. Microbiol. Rev. 51, 221–271.
Chen, K., Neimark, H., Rumore, P., and Steinman, C. R. (1989) Broad range DNA probes for detection and amplifying eubacterial nucleic acids. FEMS Microbiol. Lett. 57, 19–24.
Böddinghaus, B., Rogall, T., Flohr, T., Blöcker, H., and Böttger, E. C. (1990) Detection and identification of mycobacteria by amplification of rRNA. J. Clin. Microbiol. 28, 1751–1759.
Kirschner, P., Rosenau, J., Springer, B., Teschner, K., Feldmann, K., and Böttger, E. (1996) Diagnosis of mycobacterial infections by nucleic acid amplification: 18 month prospective study. J. Clin. Microbiol. 34, 304–312.
Relman, D. A., Schmidt, T. M., MacDermott, R. P., and Falkow, S. (1992) Identification of the uncultured bacillus of Whipple’s disease. N. Engl. J. Med. 327, 293–301.
Relman, D. A., Loutit, J. S., Schmiidt, T. M., Falkow, S., and Tompkins, L. S. (1990) The agent of bacillary angiomatosis. N. Engl. J. Med. 323, 1573–1580.
Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., and Tingey, S. V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res. 18, 6531–6535.
Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acid Res. 18, 7213–7218.
Williams, J. G. K., Hanafey, M. K., Rafalski, J. A., and Tingey, S. V. (1993) Genetic analysis using random amplified polymorphic DNA markers. Methods Enzymol. 218, 704–740.
Akopyanz, N., Bukanov, N. O., Westhlum, T. U., Kresovich, S., and Berg, D. E. (1992) DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 20, 5137–5142.
Kersulyte, D., Woods, J. P., Keath, E. J., Goldman, W. E., and Berg, D. E. (1992) Diversity among clinical isolates of Histoplasma capsulatum detected by polymerase chain reaction with arbitrary primers. J. Bacteriol. 174, 7075–7079.
Wang, G., Whittam, T. S., Berg, C. M., and Berg, D. E. (1993) RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains. Nucleic Acid Res. 21, 5930–5933.
Berg, D. E., Akopyants, N. S., and Kersulyte, D. (1994) Fingerprinting microbial genomes using the RAPD or AP-PCR method. Methods Mol. Cell. Biol. 5, 13–24.
Thanos, M., Schonian, G., Meyer, W., Schweynoch, C., Graser, Y., Mitchell, T. G., Presber, W., and Tietz, H. J. (1996) Rapid identification of Candida species by DNA fingerprinting with PCR. J. Clin. Microbiol. 34, 615–621.
Mahenthiralingam, E., Campbell, M. E., Foster, J., Lam, J. S., and Speert, D. P. (1996) Random amplified polymorphic DNA typing of Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis. J. Clin. Microbiol. 34, 1129–1135.
Lin, A. W., Usera, M. A., Barret, T. J., and Goldsby, R. A. (1996) Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis. J. Clin. Microbiol. 34, 870–876.
Weyant, R. S., Edmonds, P., and Swaminathan, B. (1990) Effect of ionic and nonionic detergents on the taq polymerase. BioTechniques 9, 308,309.
Beutler, E., Gelbart, T., and Kuhl, W. (1990) Interference of heparin with the polymerase chain reaction. BioTechniques 9, 166.
Holodnly, M., Kim, S., Katzenstein, D., Konrad, M., Groves, E., and Merigan, T. C. (1991) Inhibition of human immunodeficiency virus gene amplification by heparin. J. Clin. Microbiol. 29, 676–679.
Thin, N. and Stafford, D. W. (1976) Isolation of high-molecular-weight DNA. Nucleic Acid Res. 3, 2303–2308.
Millar, D. S., Withey, S. J., Tizard, M. L. V., Ford, J. G., and Hermon-Taylor, J. (1995) Solid phase hybridisation-capture of low abundance target DNA sequences: application to the PCR detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum. Analyt. Biochem. 226, 325–330.
Mangiapan, G., Vokurka, M., Schouls, L., Cadranel, J., Lecossier, D., van Emb-den, J., and Hance, A. (1996) Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens. J. Clin. Microbiol. 34, 1209–1215.
Loeffelholz, M. J., Lewinski, C. A., Silver, S. R., Purohit, A. P., Herman, S. A., Buonagurio, D. A., and Dragon, E. A. (1992) Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction. J. Clin. Microbiol. 30, 2847–2851.
Ishizawa, M. Y., Kobayashi, T., and Matsuuva, S. (1991) Simple procedure of DNA isolation from human serum. Nucleic Acid Res. 19, 5792.
Lanciotti, R. S., Calisher, C. H., Ciubler, D. J., Chang, G. J., and Vornadam, A. V. (1992) Rapid detection and typing of Dengue viruses from clinical samples by using reverse transcription-polymerase chain reaction. J. Clin. Microbiol. 30, 545–551.
Shankar, P., Manjunath, N., Mohan, K. K., Prasad, K., Behari, M., Shriniwas, P., and Ahuja, G. K. (1991) Rapid diagnosis of tuberculous meningitis by polymerase chain reaction. Lancet 337, 5–7.
Lisby, G., Dessau, R., Andersen, C. B., and Ladefoged, S. (1994) Polymerase chain reaction as a rapid diagnostic assay for cytomegalovirus infection in renal transplant recipients. APMIS 102, 690–694.
Higuchi R. (1989) Simple and rapid preparation of samples for PCR, in PCR Technology: Principles and Applications for DNA Amplification (Erlich, H. A., ed.), Stockton, New York, pp. 31–38.
Cousins, D. V., Wilton, S. D., Francis, B. R., and Gow, B. L. (1992) Use of polymerase chain reaction for rapid diagnosis of tuberculosis. J. Clin. Microbiol. 30, 255–258.
Frankel, G., Riley, L., Giron, J. A., Valmassoi, J., Freidmann, A., Stokbine, N., Falkow, S., and Schoolnik, G. K. (1990) Detection of Shigella in feces using DNA amplification. J. Infect. Dis. 161, 1252–1256.
Kwok, S. (1990) Procedures to minimize PCR-carry over, in PCR Protocols: A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J., White, T. J., eds.), Academic, San Diego, pp. 142–145.
Dragon, E. A., Spadoro, J. P., and Madej, R. (1993) Quality control of polymerase chain reaction, in Diagnostic Molecular Microbiology—Principles and Applications (Persing, D. H., Smith, T. F., Tenover, F. C., and White, T. J., eds.), American Society for Microbiology, Washington, DC, pp. 160–168.
Sheppard, H. W., Ascher, M. S., Busch, P. R., and Sohmer, P. R. (1991) A multicenter proficiency trial of gene amplification (PCR) for the detection of HIV-1. J. Acquir. Immun. Defic. Syndr. 4, 277–283.
Zaaijer, H. L., Cuypers, H. T. M., Reesink, H. W., and Winkel, I. N. (1993) Reliability of polymerase chain reaction for detection of hepatitis C virus. Lancet 341, 722–724.
Jackson, J. B., Drew, J., Lin, H. J., and Otto, P. (1993) Establishment of a quality assurance program for Human Immunodeficiency Virus type 1 DNA polymerase chain reaction assays by the AIDS clinical trials group. J. Clin. Microbiol. 31, 3123–3128.
Mahony, J. B., Luinstra, K. E., Waner, J., and McNab, G. (1994) Interlaboratory agreement study of a double set of PCR plasmid primers for detection of Chlamydia trachomatis in a variety of genitourinary specimens. J. Clin. Microbiol. 32, 87–91.
Barany, F. (1991) The ligase chain reaction in a PCR world. PCR Methods Applic. 1, 5–16.
Barany, F. (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88, 189–193.
Abravaya, K., Carrino, J. J., Muldoon, J., and Lee, H. H. (1995) Detection of point mutations with a modified ligase chiain reaction (Gap-LCR). Nucleic Acids Res. 23, 675–682.
Dille, B. J., Butzen, C. C., and Birkenmeyer, L. G. (1993) Amplification of Chlamydia trachomatis DNA by ligase chain reaction. J. Clin. Microbiol. 31, 729–731.
Birkenmeyer, L. G. and Armstrong, A. S. (1992) Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J. Clin. Microbiol. 30, 3089–3094.
van Doornum, G. J. J., Buimer, M., Prins, M., Henquet, C. J. M., Coutinho, R. A., Plier, P. K., Tomazic-Allen, S., Hu, H., and Lee, H. (1995) Detection of Chlamydia trachomatis infection in urine samples from men and women by ligase chain reaction. J. Clin. Microbiol. 33, 2042–2047.
Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., and Barringer, K. J. (1990) Isothermal in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA 87, 1874–1878.
Gingeras, T. R., Whitfield, K. M., and Kwoh, D. Y. (1990) Unique features of the self-sustained sequence replication (3SR) reaction in the in vitro amplification of nucleic acids. Ann. Biol. Clin. 48, 498–501.
Fahy, E., Kwoh, D. Y., and Gingeras, T. R. (1991) Self-sustained sequence replication (3SR): An isothermal transcription-based amplification system alternative to PCR. PCR Methods Appl. 1, 25–33.
Compton, J. (1991) Nucleic acid sequence-based amplification. Nature 350, 91,92.
Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., and Gingeras, T. R. (1989) Transcription-based amplification system and detection of amplified human deficiency virus type 1 with a bead-based sandwich hybridization format. Proc. Natl. Acad. Sci. USA 86, 1173–1177.
Gingeras, T. R. and Kwoh, D. Y. (1992) In vitro nucleic acid target amplification techniques: issues and benefits. Praxis Biotechnol. 4, 403–429.
Zaaijer, H. L., Kok, W., ten-Veer, J. H., Reesink, H. W., Foolen, H., Winkel, I. N., Huisman, J. G., Cuypers, H. T., Kievits, T., and Lelie, P. N. (1995) Detection of HIV-1 RNA in plasma by isothermal amplification (NASBA) irrespective of the stage of HIV-1 infection. J. Virol. Methods. 52, 175–181.
Vandamme, A. M., Van-Dooren, S., Kok, W., Goubau, P., Fransen, K., Kievits, T., Schmit, J. C., De-Clercq, E., and Desmyter, J. (1995) Detection of HIV-1 RNA in plasma and serum samples using the NASBA amplification system compared to RNA-PCR. J. Virol. Methods. 52, 121–132.
Abe, C., Hirano, K., Wada, M., and Kazumi, Y. (1993) Detection of Mycobacterium tuberculosis in clinical specimens by polymerase chain reaction and Gen-Probe amplified Mycobacterium tuberculosis direct test. J. Clin. Microbiol. 31, 3270–3274.
Miller, N., Hernandez, S. G., and Cleary, T. J. (1994) Evaluation of Gen-Probe amplified Mycobacterium tuberculosis direct test and PCR for direct detection of Mycobacterium tuberculosis in clinical specimens. J. Clin. Microbiol. 32, 393–397.
Kern, D. G., Sheridan, P. J., Stempien, M. S. III, and Yeghiazarian, Y. (1992) Quantitation of HIV-1 RNA in plasma using branched DNA technology. 15th AIDS Clinical Trial Group Meeting, Washington, DC, November 3-6.
Todd, J., Stempien, M., Kojima, E., and Shirasaka, T. (1993) Quantitation of HIV plasma RNA using the branched DNA (bDNA) and reverse transcription coupled polymerase chain reaction (RT-PCR) assays. IXth International Conference on AIDS, Berlin, Germany, June 7-11.
Cao, Y., Ho, D. D., Todd, J., Kokka, R., Urdea, M., Lifson, J. D., Piatak, M., Jr., Chen, S., Hahn, B. H., and Saag, M. S. (1995) Clinical evaluation of branched DNA signal amplification for quantifying HIV type l in human plasma. AIDS Res. Hum. Retrovir. 11, 353–361.
Mellors, J. W., Kingsley, L. A., Rinaldo, C. R., Todd, J. A., Hoo, B. S., Kokka, R. P., and Gupta, P. (1995) Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann. Intern. Med. 122, 573–579.
Martell, M., Esteban, J. I., Quer, J., and Genesca, J. (1992) Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J. Virol. 66, 3225–3229.
Sherman, K. E., O’Brien, J., Gutierrez, A. G., and Harrison, S. (1993) Quantitative evaluation of hepatitis C virus RNA in patients with concurrent human immunodeficiency virus infections. J. Clin. Microbiol. 31, 2679–2682.
Lau, J. Y., Davis, G. L., Kniffen, J., and Qian, K. P. (1993) Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet 341, 1501–1504.
Yamada, G., Takatani, M., Kishi, F., Takahashi, M., Doi, T., Tsuji, T., Shin, S., Tanno, M., Urdea, M. S., and Kolberg, J. A. (1995) Efficiacy of interferon alpha therapy in chronic hepatitis C patients depend primarily on hepatitis C virus RNA level. Hepatology 22, 1351–1354.
Watabe, Y., Hino, K., Iino, S., and Suzuki H. (1993) Detection of HBV DNA by DNA probe method and its clinical usefulness. International Symposium on Viral Hepatitis and Liver Disease, Tokyo, Japan, May 10-14.
Hendricks, D. A., Stowe, B. J., Hoo, B. S., Kolberg, J., Irvine, B. D., Neuwald, P. D., Urdea, M. S., and Perrillo, R. P. (1995) Quantitation of HBV DNA in human serum using a branched DNA (bDNA) signal amplification assay. Am. J. Clin. Pathol. 104, 537–546.
Urdea, M. (1993) Synthesis and characterization of branched DNA (bDNA) for the direct and quantitative detection of CMV, HBV, HCV, and HIV. Clin. Chem. 39, 725,726.
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Lisby, G. (1998). Application of Nucleic Acid Amplification in Clinical Microbiology. In: Meltzer, S.J. (eds) PCR in Bioanalysis. Methods In Molecular Medicine™, vol 92. Humana Press. https://doi.org/10.1385/0-89603-497-6:1
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