Comparison among the quantification of bacterial pathogens by qPCR, dPCR, and cultural methods

Frontiers in Microbiology

Volumn 8, Issue JUN, 2017, Pages

  Ricchi, Matteo ^a   Bertasio, Cristina ^a   Boniotti, Maria B ^a   Vicari, Nadia ^a   Russo, Simone ^a   Tilola, Michela ^a   Bellotti, Marco A ^a   Bertasi, Barbara ^a  

^a ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLA LOMBARDIA E DELL EMILIA ROMAGNA   (Italy)

Author keywords

Bacteria; dPCR; Pathogens; QPCR; Quantification

Indexed keywords

ARTICLE; BACTERIUM DETECTION; COLONY FORMING UNIT; COMPARATIVE STUDY; CONTROLLED STUDY; DNA EXTRACTION; DROPLET DIGITAL POLYMERASE CHAIN REACTION; FRANCISELLA TULARENSIS; LIMIT OF DETECTION; LIMIT OF QUANTITATION; LISTERIA MONOCYTOGENES; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; NONHUMAN; NUCLEIC ACID AMPLIFICATION; POLYMERASE CHAIN REACTION; QUANTITATIVE POLYMERASE CHAIN REACTION;

EID: 85021430367     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.01174     Document Type: Article

References (42)

1. Anonymous (1998). ISO 11290-2: Microbiology of Food and Animal Feeding Stuffs-Horizontal Method for the Detection and Enumeration of Listeria monocytogenes-Part 2: Enumeration Method. Geneva
2. Anonymous (2005). COMMISSION REGULATION (EC) No 2073/2005 of 15 November 2005 on Microbiological Criteria for Foodstuffs. Rome
3. Anonymous (2009). ISO/TS 19036:2006: Microbiology of Food and Animal Feeding Stuffs-Guidelines for the Estimation of Measurement Uncertainty for Quantitative Determinations. Geneva: AMEDMENT 1
4. Anonymous (2012). ISO/TS 12869: Water quality-Detection and Quantification of Legionella spp. and/or Legionella pneumophila by Concentration and Genic Amplification by Quantitative Polymerase Chain reaction (qPCR). Geneva
5. Anonymous (2014). OIE Validation Guidelines (2014). VALIDATION GUIDELINE 3.6.5. STATISTICAL APPROACHES TO VALIDATION. Paris: World Organisation for Animal Health, 1-12
6. Bland, J. M., and Altman, D. G. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1, 307-310. doi: 10.1016/S0140-6736(86)90837-8
7. Boizeau, L., Laperche, S., Desire, N., Jourdain, C., Thibault, V., and Servant-Delmas, A. (2014). Could droplet digital PCR be used instead of real-time PCR for quantitative detection of the hepatitis B virus genome in plasma? J. Clin. Microbiol. 52, 3497-3498. doi: 10.1128/jcm.01306-14
8. Boulais, C., Wacker, R., Augustin, J. C., Cheikh, M. H., and Peladan, F. (2011). Modeling the occurrence of Mycobacterium avium subsp. paratuberculosis in bulk raw milk and the impact of management options for exposure mitigation. J. Food Prot. 74, 1126-1136. doi: 10.4315/0362-028X.JFP-11-005
9. Burns, M., and Valdivia, H. (2008). Modelling the limit of detection in real-time quantitative PCR. Eur. Food Res. Technol. 226:12. doi: 10.1007/s00217-007-0683-z
10. 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
11. Carvalho, C. L., Lopes de Carvalho, I., Ze-Ze, L., Nuncio, M. S., and Duarte, E. L. (2014). Tularaemia: a challenging zoonosis. Comp. Immunol. Microbiol. Infect. Dis. 37, 85-96. doi: 10.1016/j.cimid.2014.01.002
12. Chiodini, R. J., Chamberlin, W. M., Sarosiek, J., and McCallum, R. W. (2012). Crohn's disease and the mycobacterioses: a quarter century later. Causation or simple association? Crit. Rev. Microbiol. 38, 52-93. doi: 10.3109/1040841X.2011.638273
13. Devonshire, A. S., Honeyborne, I., Gutteridge, A., Whale, A. S., Nixon, G., Wilson, P., et al. (2015). Highly reproducible absolute quantification of Mycobacterium tuberculosis complex by digital PCR. Anal. Chem. 87, 3706-3713. doi: 10.1021/ac5041617
14. Devonshire, A. S., O'Sullivan, D. M., Honeyborne, I., Jones, G., Karczmarczyk, M., Pavšic, J., et al. (2016). The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis. BMC Infect. Dis. 16:366. doi: 10.1186/s12879-016-1696-7
15. Euler, M., Wang, Y., Otto, P., Tomaso, H., Escudero, R., Anda, P., et al. (2012). Recombinase polymerase amplification assay for rapid detection of Francisella tularensis. J. Clin. Microbiol. 50, 2234-2238. doi: 10.1128/JCM.06504-11
16. Gosselin-Theberge, M., Taboada, E., and Guy, R. A. (2016). Evaluation of real-time PCR assays and standard curve optimisation for enhanced accuracy in quantification of Campylobacter environmental water isolates. J. Microbiol. Methods 129, 70-77. doi: 10.1016/j.mimet.2016.07.025
17. Halder, A., Black, D. G., Davidson, P. M., and Datta, A. (2010). Development of associations and kinetic models for microbiological data to be used in comprehensive food safety prediction software. J. Food Sci. 75, R107-R120. doi: 10.1111/j.1750-3841.2010.01687.x
18. Hayden, R. T., Gu, Z., Ingersoll, J., Abdul-Ali, D., Shi, L., Pounds, S., et al. (2013). Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus. J. Clin. Microbiol. 51, 540-546. doi: 10.1128/JCM.02620-12
19. Herthnek, D., Nielsen, S. S., Lindberg, A., and Bölske, G. (2008). A robust method for bacterial lysis and DNA purification to be used with real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in milk. J. Microbiol. Methods 75, 335-340. doi: 10.1016/j.mimet.2008.07.009
20. Hoshino, T., and Inagaki, F. (2012). Molecular quantification of environmental DNA using microfluidics and digital PCR. Syst. Appl. Microbiol. 35, 390-395. doi: 10.1016/j.syapm.2012.06.006
21. Hudecova, I. (2015). Digital PCR analysis of circulating nucleic acids. Clin. Biochem. 48, 948-956. doi: 10.1016/j.clinbiochem.2015.03.015
22. Huggett, J. F., Foy, C. A., Benes, V., Emslie, K., Garson, J. A., Haynes, R., et al. (2013). The digital MIQE guidelines: minimum information for publication of quantitative digital PCR experiments. Clin. Chem. 59, 892-902. doi: 10.1373/clinchem.2013.206375
23. Kralik, P., Beran, V., and Pavlik, I. (2012). Enumeration of Mycobacterium avium subsp. paratuberculosis by quantitative real-time PCR, culture on solid media and optical densitometry. BMC Res. Notes 5:114. doi: 10.1186/1756-0500-5-114
24. Law, J. W., Ab Mutalib, N. S., Chan, K. G., and Lee, L. H. (2014). Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front. Microbiol. 5:770. doi: 10.3389/fmicb.2014.00770
25. Logar, K., Kopinc, R., Bandelj, P., Staric, J., Lapanje, A., and Ocepek, M. (2012). Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA. BMC Vet. Res. 8:49. doi: 10.1186/1746-6148-8-49
26. Nauta, M. J., and van der Giessen, J. W. (1998). Human exposure to Mycobacterium paratuberculosis via pasteurised milk: a modelling approach. Vet. Rec. 143, 293-296. doi: 10.1136/vr.143.11.293
27. Papic, B., Pate, M., Henigman, U., Zajc, U., Gruntar, I., Biasizzo, M., et al. (2017). New approaches on quantification of campylobacter jejuni in poultry samples: the use of digital PCR and real-time PCR against the ISO standard plate count method. Front. Microbiol. 8:331. doi: 10.3389/fmicb.2017.00331
28. 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
29. Pavšic, J., Zel, 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
30. Plain, K. M., Marsh, I. B., Waldron, A. M., Galea, F., Whittington, A. M., Saunders, V. F., et al. (2014). High-throughput direct fecal PCR assay for detection of Mycobacterium avium subsp. paratuberculosis in sheep and cattle. J. Clin. Microbiol. 52, 745-757. doi: 10.1128/JCM.03233-13
31. Ricchi, M., De Cicco, C., Kralik, P., Babak, V., Boniotti, M. B., Savi, R., et al. (2014). Evaluation of viable Mycobacterium avium subsp. paratuberculosis in milk using peptide-mediated separation and Propidium Monoazide qPCR. FEMS Microbiol. Lett. 356, 127-133. doi: 10.1111/1574-6968.12480
32. 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
33. Rothrock, M., Hiett, K. L., Kiepper, B. H., Ingram, K., and Hinton, A. (2013). Quantification of zoonotic bacterial pathogens within commercial poultry processing water samples using droplet digital PCR. Adv. Microbiol. 3:403. doi: 10.4236/aim.2013.35055
34. Seiner, D. R., Colburn, H. A., Baird, C., Bartholomew, R. A., Straub, T., Victry, K., et al. (2013). Evaluation of the FilmArray® system for detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis. J. Appl. Microbiol. 114, 992-1000. doi: 10.1111/jam.12107
35. Sloots, T. P., Nissen, M. D., Ginn, A. N., and Iredell, J. R. (2015). Rapid identification of pathogens using molecular techniques. Pathology 47, 191-198. doi: 10.1097/PAT.0000000000000241
36. Tasara, T., and Stephan, R. (2005). Development of an F57 sequence-based real-time PCR assay for detection of Mycobacterium avium subsp. paratuberculosis in milk. Appl. Environ. Microbiol. 71, 5957-5968. doi: 10.1128/AEM.71.10.5957-5968.2005
37. Traunsek, U., Toplak, N., Jersek, B., Lapanje, A., Majstorovic, T., and Kovac, M. (2011). Novel cost-efficient real-time PCR assays for detection and quantitation of Listeria monocytogenes. J. Microbiol. Methods 85, 40-46. doi: 10.1016/j.mimet.2011.01.018
38. Verhaegen, B., De Reu, K., De Zutter, L., Verstraete, K., Heyndrickx, M., and Van Coillie, E. (2016). Comparison of droplet digital PCR and qPCR for the quantification of shiga toxin-producing Escherichia coli in bovine feces. Toxins (Basel) 8:E157. doi: 10.3390/toxins8050157
39. Versage, J. L., Severin, D. D., Chu, M. C., and Petersen, J. M. (2003). Development of a multitarget real-time TaqMan PCR assay for enhanced detection of Francisella tularensis in complex specimens. J. Clin. Microbiol. 41, 5492-5499. doi: 10.1128/JCM.41.12.5492-5499.2003
40. Wang, D., Yamahara, K. M., Cao, Y., and Boehm, A. B. (2016). Absolute quantification of enterococcal 23S rRNA gene using digital PCR. Environ. Sci. Technol. 50, 3399-3408. doi: 10.1021/acs.est.5b05747
41. Witte, A. K., Fister, S., Mester, P., Schoder, D., and Rossmanith, P. (2016). Evaluation of the performance of quantitative detection of the Listeria monocytogenes prfA locus with droplet digital PCR. Anal. Bioanal. Chem. 408, 7583-7593. doi: 10.1007/s00216-016-9861-9
42. Wood, R. M., Egan, J. R., and Hall, I. M. (2014). A dose and time response Markov model for the in-host dynamics of infection with intracellular bacteria following inhalation: with application to Francisella tularensis. J. R. Soc. Interface 11:20140119. doi: 10.1098/rsif.2014.0119