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Specificity and Performance of Diagnostic PCR Assays

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PCR Detection of Microbial Pathogens

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 216))

Abstract

The undisputed success of detection assays based on the polymerase chain reaction (PCR) has been largely due to its rapidity in comparison to many conventional diagnostic methods. For instance, detection and identification of mycobacteria, chlamydiae, mycoplasmas, brucellae, and other slow-growing bacteria can be accelerated from several days to a single working day when clinical samples are directly examined. Other microbial agents that are difficult to propagate outside their natural host often remain undetected by techniques relying on cultural enrichment, thus rendering PCR the only viable alternative to demonstrate their presence. Additionally, there is the enormous potential of DNA amplification assays with regard to sensitivity and specificity.

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References

  1. He, Q., Marjamäki, M., Soini, H., Mertsola, J., and Viljanen, M. K. (1994) Primers are decisive for sensitivity of PCR. BioTechniques 17, 82–87.

    PubMed  CAS  Google Scholar 

  2. Rychlik, W., Spencer, W. J., and Rhoads, R. E. (1990) Optimization of the annealing temperature for DNA amplification in vitro. (Erratum in Nucleic Acids Res 1991; 19:698) Nucleic Acids Res. 18, 6409–6412.

    Article  PubMed  CAS  Google Scholar 

  3. McCulloch, R. K., Choong, C. S., and Hurley, D. M. (1995) An evaluation of competitor type and size for use in the determination of mRNA by competitive PCR. PCR Meth. Appl. 4, 219–226.

    CAS  Google Scholar 

  4. Toouli, C. D., Turner, D., Grist, S. A., and Morley, A. A. (1999) The effect of cycle number and target size on polymerase chain reaction amplification of polymorphic repetitive sequences. Anal. Biochem. 280, 324–326.

    Article  CAS  Google Scholar 

  5. Greisen, K., Loeffelholz, M., Purohit, A., and Leong, D. (1994) PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J. Clin. Microbiol. 32, 335–351.

    PubMed  CAS  Google Scholar 

  6. van Camp, G., Fierens, H., Vandamme, P., Goossens, H., Huyghebaert, A., and de Wachter, R. (1993) Identification of enterpathogenic Campylobacter species by oligonucleotide probes and polymerase chain reaction based on 16S rRNA genes. Syst. Appl. Microbiol. 16, 30–36.

    Google Scholar 

  7. Giesendorf, B.A. J., Quint, W. G. V., Henkens, M. H. C., Stegmann, H., Huf, F. A., and Niesters, H. G. M. (1992) Rapid and sensitive detection of Campylobacter ssp. in chicken products by using the polymerase chain reaction. Appl. Environ. Microbiol. 58, 3804–3808.

    PubMed  CAS  Google Scholar 

  8. Metherell, L. A., Logan, J. M. J., and Stanly, J. (1999) PCR-enzyme-linked immunosorbent assay for detection and identification of Campylobacter species: Application to isolates and stool samples. J. Clin. Microbiol. 37, 433–435.

    PubMed  CAS  Google Scholar 

  9. Cardarelli-Leite, P., Blom, K., Patton, C. M., Nicholson, M. A., Steigerwalt, A. G., Hunter, S. B., Brenner D. J., Barrett T. J., and Swaminathan, B. (1996) Rapid identification of Campylobacter species by restriction fragment length polymorphism analysis of a PCR-amplified fragment of the gene coding for 16S rRNA. J. Clin. Microbiol. 34, 62–67.

    PubMed  CAS  Google Scholar 

  10. Heinemann M. B., Garcia, J. F. Nunes, C. M., et al. (2000) Detection and differentiation of Leptospira spp. serovars in bovine semen by polymerase chain reaction and restriction fragment length polymorphism. Vet. Microbiol. 73, 261–267.

    Article  PubMed  CAS  Google Scholar 

  11. Lammler C. Abdulmawjood, A., and Weiss, R. (1998) Properties of serological group B streptococci of dog, cat and monkey origin. Zentralbl. Veterinärmed. 49, 561–566.

    Google Scholar 

  12. Messmer T. O., Skelton, S. K., Moroney, J. F., Daugharty, H. and Fields, B. S. (1997) Application of a nested, multiplex PCR to psittacosis outbreaks. J. Clin. Microbiol. 35, 2043–2046.

    PubMed  CAS  Google Scholar 

  13. Madico, G., Quinn, T. C., Bomann, J., and Gaydos, C. A. (2000) Touchdown enzyme release-PCR for detection and identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci using the 16S and 16S-23S spacer rRNA genes. J. Clin. Microbiol. 38, 1085–1093.

    PubMed  CAS  Google Scholar 

  14. Kox, L. F. F., van Leeuwen, J., Knijper, S., Jansen, H. M., and Kolk, A. H. J. (1995) PCR assay based on DNA coding for rRNA for detection and identification of mycobacteria in clinical samples. J. Clin. Microbiol. 33, 3225–3233.

    PubMed  CAS  Google Scholar 

  15. Oggioni, M. R., Fattorini, L., Li, B., et al. (1995) Identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare by selective nested polymerase chain reaction. Mol. Cell. Probes 9, 321–326.

    Article  PubMed  CAS  Google Scholar 

  16. Bascunana, C. R., Mattsson, J. G., Bölske, G., and Johansson, K.-E. (1994) Characterization of the 16S rRNA genes from Mycoplasma sp. strain F38 and development of an identification system based on PCR. J. Bacteriol. 179, 2577–2586.

    Google Scholar 

  17. Giacometti, M., Nicolet, J., Johansson, K.-E., Naglic, T., Degiorgis, M. P., and Frey, J. (1999) Detection and identification of Mycoplasma conjunctivae in infectious keratoconjunctivitis by PCR based on the 16S rRNA gene. Zentralbl. Veterinärmed. 46, 173–180.

    CAS  Google Scholar 

  18. Persson, A., Pettersson, B., Bölske, G., and Johansson, K.-E. (1999) Diagnosis of contagious bovine pleuropneumonia by PCR-laser-induced fluorescence and PCR-restriction endonuclease analysis based on the 16S rRNA genes of My co-plasma mycoides subsp. mycoides SC. J. Clin. Microbiol. 37, 3815–3821.

    PubMed  CAS  Google Scholar 

  19. Wang, R.F., Cao, W.W., Franklin, W., Campbell, W., and Cerniglia, C.E. (1994) A 16S rDNA-based PCR method for rapid and specific detection of Clostridium perfringens in food. Mol. Cell. Probes 8, 131–138.

    Article  PubMed  CAS  Google Scholar 

  20. Lantz, P. G., Knutsson, R., Blixt, Y., Al Soud, W. A., Borch, E., and Radström P. (1998) Detection of pathogenic Yersinia enterocolitica in enrichment media and pork by a multiplex PCR: a study of sample preparation and PCR-inhibitory components. Int. J. Food Microbiol. 45, 93–105.

    Article  PubMed  CAS  Google Scholar 

  21. Subramaniam, S., Chua, K. L., Tan, H. M., Loh, H., Kuhnert, P., and Frey, J. (1997) Phylogenetic position of Riemerella anatipestifer based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 47, 562–565.

    Article  PubMed  CAS  Google Scholar 

  22. Mattsson, J. G., Guss, B., and Johansson, K.-E. (1994) The phylogeny of Myco-plasma bovis as determined by sequence analysis of the 16S rRNA gene. FEMS Microbiol. Lett. 115, 325–328.

    Article  PubMed  CAS  Google Scholar 

  23. Helgason, E., Okstad, O.A., Caugant, D.A., et al. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis- One species on the basis of genetic evidence. Appl. Environm. Microbiol. 66, 2627–2630.

    Article  CAS  Google Scholar 

  24. Fermér, C. and Olsson Engvall, E. (1999) Specific PCR identification and differentiation of the thermophilic campylobacters, Campy lob act er jejuni, C. coli, C. lari, and C. upsaliensis. J. Clin. Microbiol. 37, 3370–3373.

    Google Scholar 

  25. Eyers, M., Chapelle, S., van Camp, G., Goossens, H., and de Wachter, R. (1993) Dis-crimination among thermophilic Campylobacter species by polymerase chain reaction amplification of 23S rRNA gene fragments. J. Clin. Microbiol. 31, 3340–3243.

    PubMed  CAS  Google Scholar 

  26. Everett, K. D. E., and Andersen, A. A. (1999) Identification of nine species of the Chlamydiaceae using RFLP-PCR. Int. J. Syst. Bacteriol. 49, 217–224.

    Article  Google Scholar 

  27. Gürtler, V. and Stanisich, V. A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3–16.

    Article  PubMed  Google Scholar 

  28. Scheinert, P., Krausse, R., Ullmann, U., Soller, R., and Krupp, G. (1996) Molecular differentiation of bacteria by PCR amplification of the 16S-23S rRNA spacer. J. Microbiol. Meth. 26, 103–117.

    Article  CAS  Google Scholar 

  29. O’Sullivan, N. A., Fallon, R., Carroll, C., Smith, T., and Maher, M. (2000) Detection and differentiation of Campylobacter coli in broiler chicken samples using a PCR/DNA probe membrane based colorimetric detection assay. Mol. Cell. Probes 14, 7–16.

    Article  CAS  Google Scholar 

  30. Cartwright, C. P., Stock, F., Beekmann, S. E., Williams, E. C., and Gill, V. J. (1995) PCR amplification of rRNA intergenic spacer regions as a method for epidemiologic typing of Clostridium difficile. J. Clin. Microbiol. 33, 184–187.

    PubMed  CAS  Google Scholar 

  31. Mitchell, T. G., Freedman, E. Z., White, T. J., and Taylor, J. W. (1994) Unique oligonucleotide primers in PCR for identification of Cryptococcus neoformans. J. Clin. Microbiol. 32, 253–255.

    PubMed  CAS  Google Scholar 

  32. Rappelli, P., Are, R., Casu, G., Fiori, P. L., Cappuccinelli, P., and Aceti, A. (1998) Development of a nested PCR for detection of Cryptococcus neoformans in cere-brospinal fluid. J. Clin. Microbiol. 36, 3438–3440.

    PubMed  CAS  Google Scholar 

  33. Drebót, M., Neal, S., Schlech, W., and Rozee, K. (1996) Differentiation of Listeria isolates by PCR amplicon profiling and sequence analysis of 16S-23S rRNA internal transcribed spacer loci. J. Appl. Bact. 80, 174–178.

    Google Scholar 

  34. O’Connor, L., Joy, J., Kane, M., Smith, T. and Maher, M.(2000) Rapid polymerase chain reaction/DNA probe membrane-based assay for the detection of Listeria and Listeria monocytogenes in food. J. Food Prot. 63, 337–342.

    CAS  Google Scholar 

  35. Park, H., Jang, H., Kim, C., Chung, B., Chang, C. L., Park, S. K., and Song, S. (2000) Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus-and species-specific PCR primers. J. Clin. Microbiol. 38, 4080–4085.

    PubMed  CAS  Google Scholar 

  36. Uemori, T., Asada, K., Kato, I., and Harasawa, R. (1992) Amplification of the 16S-23S spacer region in rRNA operons of mycoplasmas by the polymerase chain reaction. System Appl. Microbiol. 15, 181–186.

    CAS  Google Scholar 

  37. Brickell, S. K., Thomas, L. M., Long, K. A., Panaccio, M., and Widders, P. R. (1998) Development of a PCR test based on a gene region associated with the pathogenicity of Pasteurella multocida serotype B:2, the causal agent of haemorrhagic septicaemia in Asia. Vet. Microbiol. 59, 295–307.

    Article  PubMed  CAS  Google Scholar 

  38. Gill, S., Belles-Isles, J., Brown, G., Gagné, S., Lemieux, C., Mercier, J.-P., and Dion, P. (1994) Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates. Can. J. Microbiol. 40, 541–547.

    Article  PubMed  CAS  Google Scholar 

  39. Whiley, R. A., Duke, B., Hardie, J. M., and Hall, L. M. C. (1995) Heterogeneity among 16S-23S rRNA intergenic spacers of species within the Streptococcus milleri group. Microbiology 141, 1461–1467.

    Article  PubMed  CAS  Google Scholar 

  40. Forsman, P., Tilsala-Timisjarvi, A., and Alatossava, T. (1997) Identification of staphylococcal cause of bovine mastitis using 16S-23S rRNA spacer regions. Microbiology 143, 3491–3500.

    Article  PubMed  CAS  Google Scholar 

  41. Fach, P. and Guillou, J.P. (1993) Detection by in vitro amplification of the alpha-toxin (phospholipase C) gene from Clostridium perfingens. J. Appl. Bacteriol. 74, 61–66.

    PubMed  CAS  Google Scholar 

  42. Buogo, C., Capaul, S., Häni, H., Frey, J., and Nicolet, J. (1995) Diagnosis of Clostridium perfringens type C enteritis in pigs using a DNA amplification technique (PCR) Zentralbl. Veterinärmed. 42, 51–58.

    CAS  Google Scholar 

  43. Meer, R. R. and Songer, J. G. (1997) Multiplex polymerase chain reaction assay for genotyping Clostridium perfringens. Am. J. Vet. Res. 58, 702–705.

    PubMed  CAS  Google Scholar 

  44. 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.

    PubMed  CAS  Google Scholar 

  45. Feng, P., and Monday, S. R. (2000) Multiplex PCR for detection of trait and virulence factors in enterohemorrhagic Escherichia coli serotypes. Mol. Cell. Probes 14, 333–337.

    Article  PubMed  CAS  Google Scholar 

  46. Hotzel, H., Erler, W., and Schimmel, D. (1997) Detection of dermonecrotic toxin genes in Pasteurella multocida strains using the polymerase chain reaction (PCR). Berl. Münch. Tierärztl. Wochenschr. 110, 139–142.

    PubMed  CAS  Google Scholar 

  47. Fisher, M. A., Weiser, G. C., Hunter, D. L., and Ward, A. C. (1999) Use of a polymerase chain reaction method to detect the leukotoxin gene lktA in biogroup and biovariant isolates of Pasteurella haemolytica and P. trehalosi. Am. J. Vet. Res. 60, 1402–1406.

    CAS  Google Scholar 

  48. Schaller, A., Djordjevic, S.P., Eamens, G.J., et al. (2001) Identification and detection of Actinobacillus pleuropneumoniae by PCR based on the gene apxIVA. Vet. Microbiol. 79, 47–62.

    Article  CAS  Google Scholar 

  49. Gram, T., Ahrens, P., Andreasen, M., and Nielsen, J.P. (2000) An Actinobacillus pleuropneumoniae PCR typing system based on the apx and omlA genes-evaluation of isolates from lungs and tonsils of pig. Vet. Microbiol. 75, 43–57.

    Article  PubMed  CAS  Google Scholar 

  50. de la Puente-Redondo, V. A., del Blanco, N. G., Gutierrez-Martin, C. B., Mendez, J. N., and Rodriquez Ferri, E. F. (2000) Detection and subtyping of Actinobacillus pleuropneumoniae strains by PCR-RFLP analysis of the tbpA and tbpB genes. Res. Microbiol. 151, 669–681.

    Article  Google Scholar 

  51. Ooyofo, B. A., Thornten, S. A., Burr, D. H., Trust, T. J., Pavlovskis, O. R., and Guerry, P. (1992) Specific detection of Campylobacter jejuni and Campylobacter coli by using polymerase chain reaction. J. Clin. Microbiol. 30, 2613–2619.

    Google Scholar 

  52. Kaltenböck, B., Schmeer, N., and Schneider, R. (1997) Evidence for numerous omp1 alleles of porcine Chlamydia trachomatis and novel chlamydial species obtained by PCR J. Clin. Microbiol. 35, 1835–1841.

    PubMed  Google Scholar 

  53. Caron, J., Ouardani, M., and Dea, S. (2000) Diagnosis and differentiation of Mycoplasma hyopneumoniae and Mycoplasma hyorhinis infection in pigs by PCR amplification of the p36 and p46 genes. J. Clin. Microbiol. 38, 1390–1396.

    PubMed  CAS  Google Scholar 

  54. Kasten, R. W., Carpenter, T. E., Snipes, K. P., and Hirsh, D. C. (1997) Detection of Pasteurella multocida-specific DNA in turkey flocks by use of the polymerase chain reaction. Avian. Dis. 41, 676–682.

    Article  PubMed  CAS  Google Scholar 

  55. Baily, G. G., Krahn, L. B., Drasar, B. S., and Stocker, N. G. (1992) Detection of Brucella melitensis and Brucella abortus by DNA amplification. J. Tropical. Med. Hygiene, 95, 271–275.

    CAS  Google Scholar 

  56. Englen, M. D. and Kelley, L. C. (2000) A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Appl. Microbiol. 31, 421–426.

    Article  CAS  Google Scholar 

  57. van Doorn, L. J., Verschuuren-van Haperen A., Burnens, A., et al. (1999) Rapid identification of thermotolerant Campylobacter lari, and Campylobacter upsaliensis from various geographic locations by a GTPase-based PCR-reverse hybridization assay. J. Clin. Microbiol. 37, 1790–1796.

    PubMed  Google Scholar 

  58. Tanaka, K., Miyazaki, T., Maesaki, S., Mitsutake, K., Kakeya, H., Yamamoto, Y., Yanagihara, K., Hossain, M. A., Tashiro, T., and Kohno, S. (1996) Detection of Cryptococcus neoformans gene in patients with pulmonary cryptococcosis. J. Clin. Microbiol. 34, 2826–2828.

    PubMed  CAS  Google Scholar 

  59. Furrer B., Candrian, U., Hoefelein, Ch., and Luethy, J. (1991) Detection and identification of Listeria monocytogenes in cooked sausage products and in milk by in vitro amplification of haemolysin gene fragments. J. Appl. Bacteriol. 70, 372–379.

    PubMed  CAS  Google Scholar 

  60. Luk, J. M. C., Kongmuang, U., Reeves, P. R., and Lindberg, A. A. (1993) Selective amplification of abequose and paratose synthase genes (rfb) by polymerase chain reaction for identification of Salmonella major serogroups (A, B, C2, and D). J. Clin. Microbiol. 31, 2118–2123.

    PubMed  CAS  Google Scholar 

  61. Hoorfar, J., Baggesen, D. L., and Porting, P. H. (1999) A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates. J. Microbiol. Methods 35, 77–84.

    Article  PubMed  CAS  Google Scholar 

  62. Pinnow, C. C., Butler, J. A., Sachse, K., Hotzel, H., Timms, L. L., and Rosenbusch, R. F. (2001) Detection of Mycoplasma bovis in preservative-treated field milk samples. J. Dairy Sci. 84, 1640–1645.

    Article  PubMed  CAS  Google Scholar 

  63. Hotzel, H., Heller, M., and Sachse, K. (1999) Enhancement of Mycoplasma bovis detection in milk samples by antigen capture prior to PCR. Mol. Cell. Probes 13, 175–178.

    Article  PubMed  CAS  Google Scholar 

  64. Subramaniam, S., Bergonier, D., Poumarat, F., Capaul, S., Schlatter, Y., Nicolet J., and Frey, J. (1998) Species identification of Mycoplasma bovis and Mycoplasma agalactiae based on the uvrC genes by PCR. Mol. Cell. Probes 12, 161–169.

    Article  PubMed  CAS  Google Scholar 

  65. Hance, A. J., Grandshamp, B., Levy-Frebault, V., Lecossier, D., Rauzier, J., Bocart, D., and Gisquel, B. (1989) Detection and identification of mycobacteria by amplification of mycobacterial DNA. Mol. Microbiol. 3, 843–849.

    Article  PubMed  CAS  Google Scholar 

  66. Steingrube, V. A., Gibson, J. L., Brown, B. A., Zhang, Y., Wilson, R. W., Rajagonpalan, M., and Wallace Jr., R. J. (1995) PCR amplification and restriction endonuclease analysis of a 65-kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria. J. Clin. Microbiol. 33, 149–153.

    PubMed  CAS  Google Scholar 

  67. Taylor, T. B., Patterson, C., Hale, Y., and Safranek, W. W. (1997) Routine use of PCR-restriction fragment lenght polymorphism analysis for identification of mycobacteria growing in liquid media. J. Clin. Microbiol. 35, 79–85.

    PubMed  CAS  Google Scholar 

  68. Ericsson, H., and Stalhandske, P. (1997) PCR detection of Listeria monocytogenes in’ gravad’ rainbow trout. Int. J. Food Microbiol. 35, 281–285.

    Article  PubMed  CAS  Google Scholar 

  69. Rahn, K., De Grandis, S. A., Clarke, R. C., et al. (1992) Amplification of an invA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella. Mol. Cell. Probes 6, 271–279.

    Article  PubMed  CAS  Google Scholar 

  70. Wastling J. M., Nicoll, S., and Buxton, D. (1993) Comparison of two gene amplification methods for the detection of Toxoplasma gondii in experimentally infected sheep. J. Med. Microbiol. 38, 360–365.

    Article  PubMed  CAS  Google Scholar 

  71. Manzano, M., Cocolin, L., Cantoni, C., and Comi, G. (1998) A rapid method for the identification and partial serotyping of Listeria monocytogenes in food by PCR and restriction enzyme analysis. Int. J. Food Microbiol. 42, 207–212.

    Article  PubMed  CAS  Google Scholar 

  72. Willems, H., Thiele, D., Frölich-Ritter, R., and Krauss, H. (1994) Detection of Coxiella burnetii in cow’s milk using the polymerase chain reaction (PCR). J. Vet. Med. B. 41, 580–587.

    Article  CAS  Google Scholar 

  73. Schrader, C., Protz, D., and Süss, J. ( 2000) Coxiella burnetii, in Molekular-biologische Nachweismethoden ausgewählter Zoonoseerreger (Sachse K. and Gallien, P., eds.), bgvv-Hefte 02/2000, pp. 63–70.

    Google Scholar 

  74. Roring, S., Hughes, M. S., Skuce, R. A., and Neill, S. D. (2000) Simultaneous detection and strain differentiation of Mycobacterium bovis directly from bovine tissue specimens by spoligotyping. Vet. Microbiol. 74, 227–236.

    Article  PubMed  CAS  Google Scholar 

  75. Thierry, D., Brisson-Noel, A., Vincent-Levy-Frebault, V., Nguyen, S., Guesdon, J. L., and Gicquel, B. (1990) Characterization of a Mycobacterium tuberculosis insertion sequence, IS 6110 and its application in diagnosis. J. Clin. Microbiol. 28, 2668–2673.

    PubMed  CAS  Google Scholar 

  76. de Lassence, A., Lecossier, D., Piere, C., Cadranel, J., Stern, M., and Hance, A. J. (1992) Detection of mycobacterial DNA in pleural fluid from patients with tuberculosis pleurisy by means of the polymerase chain reaction: comparison of two protocols. Thorax 47, 265–269.

    Article  PubMed  Google Scholar 

  77. Mangiapan, G., Vokurka, M., Schouls, L., Cadranel, J., Lecossier, D., van Emb-den, J., and Hance, A. J. (1996) Sequence-capture PCR improves detection of mycobacterial DNA in clinical specimens. J. Clin. Microbiol. 34, 1209–1215.

    PubMed  CAS  Google Scholar 

  78. Redstone, J. S., and Woodward, M. J. (1996) The development of a ligase medi-ated PCR with potential for the differentiation of serovars within Leptospira interrogans. Vet. Microbiol. 51, 351–362.

    Article  CAS  Google Scholar 

  79. Appleyard, G. D., Zarlenga, D., Pozio, E., and Gajadhar, A. A. (1999) Differentiation of Trichinella genotypes by polymerase chain reaction using sequence-specific primers. Int. J. Parasitol. 85, 556–559.

    Article  CAS  Google Scholar 

  80. Innis, M.A. and Gelfand, D.H. ( 1990) Optimization of PCRs, in PCR Protocols: A Guide to Methods and Applications, (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic Press, New York, NY, USA, pp. 3–12.

    Google Scholar 

  81. Sardelli, A. (1993) Plateau effect-understanding PCR limitations. Amplifications 9, 1–5.

    Google Scholar 

  82. Ruano, G., Brash, G. R., and Kidd, K. K. (1991) PCR: The first few cycles. Amplifications 7, 1–4.

    Google Scholar 

  83. Schnell, S. and Mendoza, C. (1997) Theoretical description of the polymerase chain reaction. J. Theor. Biol. 188, 313–318.

    Article  PubMed  CAS  Google Scholar 

  84. Saiki, R. K., Scharf, S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., and Arnheim, N. (1985) Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anaemia. Science 230, 1350–1354.

    Article  PubMed  CAS  Google Scholar 

  85. Schnell, S., and Mendoza, C. (1997) Enzymological considerations for a theoretical description of the quantitative competitive polymerase chain reaction (QC-PCR). J. Theor. Biol. 184, 433–440.

    Article  PubMed  CAS  Google Scholar 

  86. Morrison, C., and Gannon, F. (1994) The impact of the PCR plateau phase on quantitative PCR. Biochim. Biophys. Acta 1219, 493–498.

    PubMed  CAS  Google Scholar 

  87. Bloch, W. (1991) A biochemical perspective of the polymerase chain reaction. Biochem. 30, 2735–2747.

    Article  CAS  Google Scholar 

  88. Chester, N., and Marshak, D. R. (1993) Dimethyl sulfoxide-mediated primer Tm reduction: A method for analyzing the role of renaturation temperature in the polymerase chain reaction. Anal. Biochem. 209, 284–290.

    Article  PubMed  CAS  Google Scholar 

  89. Compton, T. ( 1990) Degenerate primers for DNA amplification, in PCR Protocols: A Guide to Methods and Applications, (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic Press, New York, pp. 39–45.

    Google Scholar 

  90. Viswanathan, V. K., Krcmarik, K., and Cianciotto, N. P. (1999) Template secondary structure promotes polymerase jumping during PCR amplification. BioTechniques 27, 508–511.

    PubMed  CAS  Google Scholar 

  91. Loewen, P. C. and Switala, J. (1995) Template secondary structure can increase the error frequency of the DNA polymerase from Thermus aquaticus. Gene 164, 56–63.

    Article  Google Scholar 

  92. Don, R. H., Cox, P. T., Wainwright, B. J., Baker, K., and Mattick, J. S. (1991) Touchdown PCR to circumvent spurious priming during gene amplification. Nucl. Acids Res. 19, 4008.

    Article  PubMed  CAS  Google Scholar 

  93. Watson, R. (1989) The formation of primer artifacts in polymerase chain reactions. Amplifications 2, 5–6.

    Google Scholar 

  94. Gelfand, D. H. and White, T. J. ( 1990) Thermostable DNA polymerases, in PCR Protocols: A Guide to Methods and Applications, (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic Press, New York, NY, pp. 129–141.

    Google Scholar 

  95. Erlich, A. H., Gelfand, D., and Sninsky, J. J. (1991) Recent advances in the polymerase chain reaction. Science 252, 1643–1651.

    Article  PubMed  CAS  Google Scholar 

  96. Chou, Q., Russell, M., Birch, D. E., Raymond, J., and Bloch, W. (1992) Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucl. Acids Res. 20, 1717–1723.

    Article  PubMed  CAS  Google Scholar 

  97. Wages, J. M. and Fowler, A. K. (1993) Amplification of low copy number sequences. Amplifications 11, 1–3.

    Google Scholar 

  98. Birch, D. E., Kolmodin, J., Wong, J., et al. (1996) The use of a thermally activated DNA polymerase PCR gives improved specificity, sensitivity and product yield without additives or extra process steps. Nature 381, 445–446.

    Article  PubMed  CAS  Google Scholar 

  99. Kellogg, D. E., Rabalkin, I., Chen, S., et al. (1994) TaqStart antibody: &quote;hot start&quote; PCR facilitated by neutralizing monoclonal antibody directed against Taq DNA polymerase. BioTechniques 16, 1134–1137.

    PubMed  CAS  Google Scholar 

  100. Ailenberg, M., and Silverman, M. (2000) Controlled hot start and improved specificity in carrying out PCR utilizing touch-up and loop incorporated primers (TULIPS). BioTechniques 29, 1018–1024.

    PubMed  CAS  Google Scholar 

  101. Kainz, P., Schmiedlechner, A., and Strack, H. B. (2000) Specificity-enhanced hot-start PCR: Addition of double-standed DNA fragments adapted to the annealing temperature. BioTechniques 28, 278–282.

    PubMed  CAS  Google Scholar 

  102. Albert J., and Fenyö, E. M. (1990) Simple, sensitive, and specific detection of human immunodeficiency virus type 1 clinical specimens by polymerase chain reaction with nested Primer. J. Clin. Microbiol. 28, 1560–1564.

    PubMed  CAS  Google Scholar 

  103. Chamberlain, J. S., Gibbs, R. A., Rainier, J. L., and Caskey, C. T. ( 1990) Multiplex PCR for the diagnosis of Duchenne muscular dystrophy, in PCR Protocols: A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic Press, New York, pp. 272–281.

    Google Scholar 

  104. Zimmermann, K., and Mannhalter, J. W. (1996) Technical aspects of quantitative competitive PCR. BioTechniques 21, 268–279.

    PubMed  CAS  Google Scholar 

  105. Raeymarkers, L. (1993) Quantitative PCR: Theoretical considerations with practical implications. Anal. Biochem. 214b, 582–585.

    Article  Google Scholar 

  106. Sachse, K., Zagon, J., RĂĽggeberg, H., Kruse, L., and Broll, H. (2001) Detection of genetic modifications in novel foods. Food Rev. Intl. (in press)

    Google Scholar 

  107. Becker-Andró, Hahlbrock, K. (1989) Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res. 17, 9437–9446.

    Article  Google Scholar 

  108. Piatak, M. Jr., Luk K.-C., Williams, B., and Lifson, J. D. (1993) Quantitative competitive polymerase chain reaction for accurate quantitation of HIV DNA and RNA species. BioTechniques 14, 70–81.

    PubMed  Google Scholar 

  109. Bercovich, D., Regev, Z., Ratz, T., Luder, A., Plotsky, Y., and Gruenbaum, Y. (1999) Quantitative ratio of primer pairs and annealing temperature affecting PCR products in duplex amplification. BioTechniques 27, 762–770.

    PubMed  CAS  Google Scholar 

  110. Henegariu, O. Heerema, N. A., Dlouhy, S. R., Vance, G. H., and Vogt, P. H. (1997) Multiplex PCR: Critical parameters and step-by-step protocol. BioTechniques 23, 504–511.

    PubMed  CAS  Google Scholar 

  111. Olcén, P., Lantz, P.-G., Bäckman, A., and Radström, P. (1995) Rapid diagnosis of bacterial meningitis by a seminested PCR strategy. Scand. J. Infect. Dis. 27, 537–539.

    Article  PubMed  Google Scholar 

  112. Radström, P., Bäckman, A., Qian, N., Kragsbjerg, Pahlson, C., and Olcén, P. (1994) Detection of bacterial DNA in cerebrospinal fluid by an assay for simulta neous detection of Neisseria meningitidis, Haemophilus influenzae, and streptococci using a seminested PCR strategy. J. Clin. Microbiol. 32, 2738–2744.

    PubMed  Google Scholar 

  113. Tong, C. Y. W., Donnelly, C., Harvey, G., and Sillis, M. (1999) Multiplex polymerase chain reaction for the simultaneous detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Chlamydia psittaci in respiratory samples. J. Clin. Pathol. 52, 257–263.

    Article  PubMed  CAS  Google Scholar 

  114. Wang, H., Fadl, A. A., and Khan, M. I. (1997) Multiplex PCR for avian pathogenic mycoplasmas. Mol. Cell. Probes 11, 211–216.

    Article  PubMed  CAS  Google Scholar 

  115. Zarlenga, D. S., Chute, M. B., Martin, A., and Kapel, C.M. (1999) A multiplex PCR for unequivocal differentiation of all encapsulated and non-encapsulated genotypes of Trichinella. Int. J. Parasitol. 29, 1859–1867.

    Article  PubMed  CAS  Google Scholar 

  116. Burkardt, H. J. (2000) Standardization and quality control of PCR analyses. Clin. Chem. Lab. Med. 38, 87–91.

    Article  PubMed  CAS  Google Scholar 

  117. Prariyachatigul, C., Chaiprasert, A., Meevootisom, V., and Pattanakitsakul, S. (1996) Assessment of a PCR technique for the detection and identification of Cryptococcus neoformans. J. Med. Vet. Mycol. 34, 251–258.

    Article  PubMed  CAS  Google Scholar 

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Sachse, K. (2003). Specificity and Performance of Diagnostic PCR Assays. In: Sachse, K., Frey, J. (eds) PCR Detection of Microbial Pathogens. Methods in Molecular Biology™, vol 216. Humana Press. https://doi.org/10.1385/1-59259-344-5:03

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  • DOI: https://doi.org/10.1385/1-59259-344-5:03

  • Publisher Name: Humana Press

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