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Volumn 8, Issue FEB, 2017, Pages

A basic guide to real time PCR in microbial diagnostics: Definitions, parameters, and everything

Author keywords

Accuracy; Limit of detection; Limit of quantification; Precision; Quantitative PCR; Trueness

Indexed keywords

FOOD SAFETY; LIMIT OF DETECTION; LIMIT OF QUANTITATION; NOMENCLATURE; QUANTITATIVE STUDY; REAL TIME POLYMERASE CHAIN REACTION; VALIDATION PROCESS;

EID: 85014472755     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.00108     Document Type: Review
Times cited : (666)

References (42)
  • 6
    • 85014422761 scopus 로고    scopus 로고
    • Statistical Approaches To Validation. Paris: World Organisation for Animal Health
    • Anonymous, R. (2014). OIE Validation Guidelines, 3.6.5. Statistical Approaches To Validation. Paris: World Organisation for Animal Health.
    • (2014) OIE Validation Guidelines, 3.6.5
    • Anonymous, R.1
  • 9
    • 67649370543 scopus 로고    scopus 로고
    • Limit of blank, limit of detection and limit of quantitation
    • Armbruster, D. A., and Pry, T. (2008). Limit of blank, limit of detection and limit of quantitation. Clin. Biochem. Rev. 29(Suppl. 1), S49-S52.
    • (2008) Clin. Biochem. Rev , vol.29 , pp. S49-S52
    • Armbruster, D.A.1    Pry, T.2
  • 10
    • 0034792654 scopus 로고    scopus 로고
    • A comparison of nucleic acid amplification techniques for the assessment of bacterial viability
    • Birch, L., Dawson, C. E., Cornett, J. H., and Keer, J. T. (2001). A comparison of nucleic acid amplification techniques for the assessment of bacterial viability. Lett. Appl. Microbiol. 33, 296-301. doi: 10.1046/j.1472-765X.2001.00999.xc.
    • (2001) Lett. Appl. Microbiol , vol.33 , pp. 296-301
    • Birch, L.1    Dawson, C.E.2    Cornett, J.H.3    Keer, J.T.4
  • 12
    • 41549160277 scopus 로고    scopus 로고
    • Modelling the limit of detection in real-time quantitative PCR
    • Burns, M., and Valdivia, H. (2008). Modelling the limit of detection in real-time quantitative PCR. Eur. Food Res. Technol. 226, 1513-1524. doi: 10.1007/s00217-007-0683-z.
    • (2008) Eur. Food Res. Technol , vol.226 , pp. 1513-1524
    • Burns, M.1    Valdivia, H.2
  • 13
    • 0033775615 scopus 로고    scopus 로고
    • Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    • Bustin, S. A. (2000). Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25, 169-193. doi: 10.1677/jme.0.0250169.
    • (2000) J. Mol. Endocrinol , vol.25 , pp. 169-193
    • Bustin, S.A.1
  • 14
    • 64149097786 scopus 로고    scopus 로고
    • The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    • Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., et al. (2009). The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611-622. doi: 10.1373/clinchem.2008.112797.
    • (2009) Clin. Chem , vol.55 , pp. 611-622
    • Bustin, S.A.1    Benes, V.2    Garson, J.A.3    Hellemans, J.4    Huggett, J.5    Kubista, M.6
  • 15
    • 84877768357 scopus 로고    scopus 로고
    • Relative quantification in seed GMO analysis: state of art and bottlenecks
    • Chaouachi, M., Bérard, A., and Saïd, K. (2013). Relative quantification in seed GMO analysis: state of art and bottlenecks. Transgenic Res. 22, 461-476. doi: 10.1007/s11248-012-9684-1.
    • (2013) Transgenic Res , vol.22 , pp. 461-476
    • Chaouachi, M.1    Bérard, A.2    Saïd, K.3
  • 16
    • 84919769709 scopus 로고    scopus 로고
    • Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot
    • Dreo, T., Pirc, M., Ramšak, Ž., Pavšic, J., Milavec, M., Zel, J., et al. (2014). Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot. Anal. Bioanal. Chem. 406, 6513-6528. doi: 10.1007/s00216-014-8084-1.
    • (2014) Anal. Bioanal. Chem , vol.406 , pp. 6513-6528
    • Dreo, T.1    Pirc, M.2    Ramšak, Ž.3    Pavšic, J.4    Milavec, M.5    Zel, J.6
  • 17
    • 24144470799 scopus 로고    scopus 로고
    • Estimation of the Youden Index and its associated cutoffpoint
    • Fluss, R., Faraggi, D., and Reiser, B. (2005). Estimation of the Youden Index and its associated cutoffpoint. Biom. J. 47, 458-472. doi: 10.1002/bimj.200410135.
    • (2005) Biom. J , vol.47 , pp. 458-472
    • Fluss, R.1    Faraggi, D.2    Reiser, B.3
  • 18
    • 14744306436 scopus 로고
    • Simultaneous amplification and detection of specific DNA sequences
    • Higuchi, R., Dollinger, G., Walsh, P. S., and Griffith, R. (1992). Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10, 413-417.
    • (1992) Biotechnology , vol.10 , pp. 413-417
    • Higuchi, R.1    Dollinger, G.2    Walsh, P.S.3    Griffith, R.4
  • 19
    • 70349384628 scopus 로고    scopus 로고
    • A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health
    • Hoffmann, B., Beer, M., Reid, S. M., Mertens, P., Oura, C. A., van Rijn, P. A., et al. (2009). A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health. Vet. Microbiol. 139, 1-23. doi: 10.1016/j.vetmic.2009.04.034.
    • (2009) Vet. Microbiol , vol.139 , pp. 1-23
    • Hoffmann, B.1    Beer, M.2    Reid, S.M.3    Mertens, P.4    Oura, C.A.5    van Rijn, P.A.6
  • 20
    • 0025861818 scopus 로고
    • Detection of specific polymerase chain reaction product by utilizing the 5'-3' exonuclease activity of Thermus aquaticus DNA polymerase
    • Holland, P. M., Abramson, R. D., Watson, R., and Gelfand, D. H. (1991). Detection of specific polymerase chain reaction product by utilizing the 5'-3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 88, 7276-7280.
    • (1991) Proc. Natl. Acad. Sci. U.S.A , vol.88 , pp. 7276-7280
    • Holland, P.M.1    Abramson, R.D.2    Watson, R.3    Gelfand, D.H.4
  • 21
    • 84870531076 scopus 로고    scopus 로고
    • Real-time quantitative PCR, pathogen detection and MIQE
    • Johnson, G., Nolan, T., and Bustin, S. A. (2013). Real-time quantitative PCR, pathogen detection and MIQE. Methods Mol. Biol. 943, 1-16. doi: 10.1007/978-1-60327-353-4_1.
    • (2013) Methods Mol. Biol , vol.943 , pp. 1-16
    • Johnson, G.1    Nolan, T.2    Bustin, S.A.3
  • 22
    • 0035988627 scopus 로고    scopus 로고
    • Quantification using real-time PCR technology: applications and limitations
    • Klein, D. (2002). Quantification using real-time PCR technology: applications and limitations. Trends Mol. Med. 8, 257-260. doi: 10.1016/S1471-4914(02)02355-9.
    • (2002) Trends Mol. Med , vol.8 , pp. 257-260
    • Klein, D.1
  • 23
    • 79952101687 scopus 로고    scopus 로고
    • Development of a predictive model for detection of Mycobacterium avium subsp. paratuberculosis in faeces by quantitative real time PCR
    • Kralik, P., Slana, I., Kralova, A., Babak, V., Whitlock, R. H., and Pavlik, I. (2011). Development of a predictive model for detection of Mycobacterium avium subsp. paratuberculosis in faeces by quantitative real time PCR. Vet. Microbiol. 149, 133-138. doi: 10.1016/j.vetmic.2010.10.009.
    • (2011) Vet. Microbiol , vol.149 , pp. 133-138
    • Kralik, P.1    Slana, I.2    Kralova, A.3    Babak, V.4    Whitlock, R.H.5    Pavlik, I.6
  • 25
    • 84859834394 scopus 로고    scopus 로고
    • PCR detection of aflatoxin producing fungi and its limitations
    • Levin, R. E. (2012). PCR detection of aflatoxin producing fungi and its limitations. Int. J. Food Microbiol. 156, 1-6. doi: 10.1016/j.ijfoodmicro.2012.03.001.
    • (2012) Int. J. Food Microbiol , vol.156 , pp. 1-6
    • Levin, R.E.1
  • 26
    • 84938835518 scopus 로고    scopus 로고
    • Evaluation of different buffered peptone water (BPW) based enrichment broths for detection of Gram-negative foodborne pathogens from various food matrices
    • Margot, H., Zwietering, M. H., Joosten, H., O'Mahony, E., and Stephan, R. (2015). Evaluation of different buffered peptone water (BPW) based enrichment broths for detection of Gram-negative foodborne pathogens from various food matrices. Int. J. Food Microbiol. 214, 109-115. doi: 10.1016/j.ijfoodmicro.2015.07.033.
    • (2015) Int. J. Food Microbiol , vol.214 , pp. 109-115
    • Margot, H.1    Zwietering, M.H.2    Joosten, H.3    O'Mahony, E.4    Stephan, R.5
  • 27
    • 84958893844 scopus 로고    scopus 로고
    • Validation of new real-time polymerase chain reaction assays for detection of hepatitis A virus RNA and parvovirus B19 DNA
    • Molenaar-de Backer, M. W., de Waal, M., Sjerps, M. C., and Koppelman, M. H. (2016). Validation of new real-time polymerase chain reaction assays for detection of hepatitis A virus RNA and parvovirus B19 DNA. Transfusion 56, 440-448. doi: 10.1111/trf.13334.
    • (2016) Transfusion , vol.56 , pp. 440-448
    • Molenaar-de Backer, M.W.1    de Waal, M.2    Sjerps, M.C.3    Koppelman, M.H.4
  • 28
    • 58449118979 scopus 로고    scopus 로고
    • Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques
    • Nocker, A., and Camper, A. K. (2009). Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques. FEMS Microbiol. Lett. 291, 137-142. doi: 10.1111/j.1574-6968.2008.01429.x.
    • (2009) FEMS Microbiol. Lett , vol.291 , pp. 137-142
    • Nocker, A.1    Camper, A.K.2
  • 29
    • 33748746842 scopus 로고    scopus 로고
    • Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells
    • Nocker, A., Cheung, C. Y., and Camper, A. K. (2006). Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67, 310-320. doi: 10.1016/j.mimet.2006.04.015.
    • (2006) J. Microbiol. Methods , vol.67 , pp. 310-320
    • Nocker, A.1    Cheung, C.Y.2    Camper, A.K.3
  • 30
    • 79960555354 scopus 로고    scopus 로고
    • Determination of the LOQ in real-time PCR by receiver operating characteristic curve analysis: application to qPCR assays for Fusarium verticillioides and F. proliferatum
    • Nutz, S., Döll, K., and Karlovsky, P. (2011). Determination of the LOQ in real-time PCR by receiver operating characteristic curve analysis: application to qPCR assays for Fusarium verticillioides and F. proliferatum. Anal. Bioanal. Chem. 401, 717-726. doi: 10.1007/s00216-011-5089-x.
    • (2011) Anal. Bioanal. Chem , vol.401 , pp. 717-726
    • Nutz, S.1    Döll, K.2    Karlovsky, P.3
  • 31
    • 84944676248 scopus 로고    scopus 로고
    • Review of established and innovative detection methods for carbapenemase-producing Gram-negative bacteria
    • Osei Sekyere, J., Govinden, U., and Essack, S. Y. (2015). Review of established and innovative detection methods for carbapenemase-producing Gram-negative bacteria. J. Appl. Microbiol. 119, 1219-1233. doi: 10.1111/jam.12918.
    • (2015) J. Appl. Microbiol , vol.119 , pp. 1219-1233
    • Osei Sekyere, J.1    Govinden, U.2    Essack, S.Y.3
  • 32
    • 84932627774 scopus 로고    scopus 로고
    • Standardization of nucleic acid tests for clinical measurements of bacteria and viruses
    • Pavšic, J., Devonshire, A. S., Parkes, H., Schimmel, H., Foy, C. A., Karczmarczyk, M., et al. (2015). Standardization of nucleic acid tests for clinical measurements of bacteria and viruses. J. Clin. Microbiol. 53, 2008-2014. doi: 10.1128/JCM.02136-14.
    • (2015) J. Clin. Microbiol , vol.53 , pp. 2008-2014
    • Pavšic, J.1    Devonshire, A.S.2    Parkes, H.3    Schimmel, H.4    Foy, C.A.5    Karczmarczyk, M.6
  • 33
    • 84955170622 scopus 로고    scopus 로고
    • Assessment of the real-time PCR and different digital PCR platforms for DNA quantification
    • Pavšic, J., Žel, J., and Milavec, M. (2016). Assessment of the real-time PCR and different digital PCR platforms for DNA quantification. Anal. Bioanal. Chem. 408, 107-121. doi: 10.1007/s00216-015-9107-2.
    • (2016) Anal. Bioanal. Chem , vol.408 , pp. 107-121
    • Pavšic, J.1    Žel, J.2    Milavec, M.3
  • 34
    • 84982176719 scopus 로고    scopus 로고
    • Estimation of Mycobacterium avium subsp. paratuberculosis load in raw bulk tank milk in Emilia-Romagna Region (Italy) by qPCR
    • Ricchi, M., Savi, R., Bolzoni, L., Pongolini, S., Grant, I. R., De Cicco, C., et al. (2016). Estimation of Mycobacterium avium subsp. paratuberculosis load in raw bulk tank milk in Emilia-Romagna Region (Italy) by qPCR. Microbiologyopen 5, 551-559. doi: 10.1002/mbo3.350.
    • (2016) Microbiologyopen , vol.5 , pp. 551-559
    • Ricchi, M.1    Savi, R.2    Bolzoni, L.3    Pongolini, S.4    Grant, I.R.5    De Cicco, C.6
  • 35
    • 84996565838 scopus 로고    scopus 로고
    • Clinical consequences of PCR based diagnosis of intestinal parasitic infections
    • Rijsman, L. H., Monkelbaan, J. F., and Kusters, J. G. (2016). Clinical consequences of PCR based diagnosis of intestinal parasitic infections. J. Gastroenterol. Hepatol. 31, 1808-1815. doi: 10.1111/jgh.13412.
    • (2016) J. Gastroenterol. Hepatol , vol.31 , pp. 1808-1815
    • Rijsman, L.H.1    Monkelbaan, J.F.2    Kusters, J.G.3
  • 37
    • 64549150047 scopus 로고    scopus 로고
    • Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
    • Ruijter, J. M., Ramakers, C., Hoogaars, W. M., Karlen, Y., Bakker, O., van den Hoff, M. J., et al. (2009). Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 37:e45. doi: 10.1093/nar/gkp045.
    • (2009) Nucleic Acids Res , vol.37
    • Ruijter, J.M.1    Ramakers, C.2    Hoogaars, W.M.3    Karlen, Y.4    Bakker, O.5    van den Hoff, M.J.6
  • 38
    • 0023850178 scopus 로고
    • Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
    • Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., et al. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487-491.
    • (1988) Science , vol.239 , pp. 487-491
    • Saiki, R.K.1    Gelfand, D.H.2    Stoffel, S.3    Scharf, S.J.4    Higuchi, R.5    Horn, G.T.6
  • 39
    • 0022372670 scopus 로고
    • Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia
    • Saiki, R. K., Scharf, S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., et al. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350-1354.
    • (1985) Science , vol.230 , pp. 1350-1354
    • Saiki, R.K.1    Scharf, S.2    Faloona, F.3    Mullis, K.B.4    Horn, G.T.5    Erlich, H.A.6
  • 40
    • 55549093064 scopus 로고    scopus 로고
    • On-farm spread of Mycobacterium avium subsp. paratuberculosis in raw milk studied by IS900 and F57 competitive real time quantitative PCR and culture examination
    • Slana, I., Kralik, P., Kralova, A., and Pavlik, I. (2008). On-farm spread of Mycobacterium avium subsp. paratuberculosis in raw milk studied by IS900 and F57 competitive real time quantitative PCR and culture examination. Int. J. Food Microbiol. 128, 250-257. doi: 10.1016/j.ijfoodmicro.2008.08.013.
    • (2008) Int. J. Food Microbiol , vol.128 , pp. 250-257
    • Slana, I.1    Kralik, P.2    Kralova, A.3    Pavlik, I.4
  • 41
    • 33644920393 scopus 로고    scopus 로고
    • Detection and monitoring of virus infections by real-time PCR
    • Watzinger, F., Ebner, K., and Lion, T. (2006). Detection and monitoring of virus infections by real-time PCR. Mol. Aspects Med. 27, 254-298. doi: 10.1016/j.mam.2005.12.001.
    • (2006) Mol. Aspects Med , vol.27 , pp. 254-298
    • Watzinger, F.1    Ebner, K.2    Lion, T.3
  • 42
    • 2542460200 scopus 로고    scopus 로고
    • PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings
    • Yang, S., and Rothman, R. E. (2004). PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect. Dis. 4, 337-348. doi: 10.1016/S1473-3099(04)01044-8.
    • (2004) Lancet Infect. Dis , vol.4 , pp. 337-348
    • Yang, S.1    Rothman, R.E.2


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