Comparison of droplet digital PCR and qPCR for the quantification of shiga toxin-producing Escherichia coli in bovine feces

Toxins

Volumn 8, Issue 5, 2016, Pages

  Verhaegen, Bavo ^a,b   De Reu, Koen ^a   De Zutter, Lieven ^b   Verstraete, Karen ^a   Heyndrickx, Marc ^a,b   Van Coillie, Els ^a  

^a INSTITUTE FOR AGRICULTURAL AND FISHERIES RESEARCH ILVO   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Cattle; Droplet digital PCR; PCR inhibition; Real time qualitative PCR; Shiga toxin producing escherichia coli

Indexed keywords

ARTICLE; BACTERIUM CONTAMINATION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA PURIFICATION; DROPLET DIGITAL POLYMERASE CHAIN REACTION; FECES ANALYSIS; GENE DOSAGE; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SHIGA TOXIN PRODUCING ESCHERICHIA COLI; ANIMAL; BACTERIAL GENE; BOVINE; FECES; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; POLYMERASE CHAIN REACTION; PROCEDURES; VIRULENCE;

ANIMALS; CATTLE; FECES; GENES, BACTERIAL; POLYMERASE CHAIN REACTION; SHIGA-TOXIGENIC ESCHERICHIA COLI; VIRULENCE;

EID: 84969285257     PISSN: None     EISSN: 20726651     Source Type: Journal    
DOI: 10.3390/toxins8050157     Document Type: Article

References (27)

1. Nataro, J.P.; Kaper, J.B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 1998, 11, 142-201. [PubMed]
2. Jinneman, K.C.; Waite-Cusic, J.G.; Yoshitomi, K.J. Evaluation of shiga toxin-producing Escherichia coli (STEC) method for the detection and identification of STEC O104 strains from sprouts. Food Microbiol. 2012, 30, 321-328. [CrossRef] [PubMed]
3. Lorenz, S.C.; Son, I.; Maounounen-Laasri, A.; Lin, A.; Fischer, M.; Kase, J.A. Prevalence of Hemolysin Genes and Comparison of ehxA Subtype Patterns in Shiga toxin-producing Escherichia coli (STEC) and non-STEC Strains from Clinical, Food, and Animal Sources. Appl. Environ. Microbiol. 2013, 79, 6301-6311. [CrossRef] [PubMed]
4. Thomas, K.M.; McCann, M.S.; Collery, M.M.; Logan, A.; Whyte, P.; McDowell, D.A.; Duffy, G. Tracking verocytotoxigenic Escherichia coli O157, O26, O111, O103 and O145 in Irish cattle. Int. J. Food Microbiol. 2012, 153, 288-296. [CrossRef] [PubMed]
5. EFSA. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2014. EFSA J. 2016, 13, 4329.
6. Munns, K.D.; Selinger, L.B.; Stanford, K.; Guan, L.; Callaway, T.R.; McAllister, T.A. Perspectives on Super-Shedding of Escherichia coli O157:H7 by Cattle. Foodborne Pathog. Dis. 2015, 12, 89-103. [CrossRef] [PubMed]
7. Matthews, L.; McKendrick, I.J.; Ternent, H.; Gunn, G.J.; Synge, B.; Woolhouse, M.E.J. Super-shedding cattle and the transmission dynamics of Escherichia coli O157. Epidemiol. Infect. 2006, 134, 131-142. [CrossRef] [PubMed]
8. Duffy, G.; Burgess, C.M.; Bolton, D.J. A review of factors that affect transmission and survival of verocytotoxigenic Escherichia coli in the European farm to fork beef chain. Meat Sci. 2014, 97, 375-383. [CrossRef] [PubMed]
9. Lawal, D.; Burgess, C.; McCabe, E.; Whyte, P.; Duffy, G. Development of a quantitative real time PCR assay to detect and enumerate Escherichia coli O157 and O26 serogroups in bovine recto-anal swabs. J. Microbiol. Methods 2015, 114, 9-15. [CrossRef] [PubMed]
10. Verhaegen, B.; De Reu, K.; Heyndrickx, M.; De Zutter, L. Comparison of Six Chromogenic Agar Media for the Isolation of a Broad Variety of Non-O157 Shiga toxin-Producing Escherichia coli (STEC) Serogroups. Int. J. Environ. Res. Public Health 2015, 12, 6965-6978. [CrossRef] [PubMed]
11. Verstraete, K.; Van Coillie, E.; Werbrouck, H.; Van Weyenberg, S.; Herman, L.; Del-Favero, J.; De Rijk, P.; De Zutter, L.; Joris, M.-A.; Heyndrickx, M.; et al. A qPCR assay to detect and quantify Shiga toxin-producing E. coli (STEC) in cattle and on farms: A potential predictive tool for STEC culture-positive farms. Toxins (Basel) 2014, 6, 1201-1221. [CrossRef] [PubMed]
12. Luedtke, B.E.; Bono, J.L.; Bosilevac, J.M. Evaluation of real time PCR assays for the detection and enumeration of enterohemorrhagic Escherichia coli directly from cattle feces. J. Microbiol. Methods 2014, 105, 72-79. [CrossRef] [PubMed]
13. Noll, L.W.; Shridhar, P.B.; Shi, X.; An, B.; Cernicchiaro, N.; Renter, D.G.; Nagaraja, T.G.; Bai, J. A Four-Plex Real-Time PCR Assay, Based on rfbE, stx 1, stx 2, and eae Genes, for the Detection and Quantification of Shiga Toxin-Producing Escherichia coli O157 in Cattle Feces. Foodborne Pathog. Dis. 2015, 12, 787-794. [CrossRef] [PubMed]
14. Ahmed, W.; Gyawali, P.; Toze, S. Quantitative PCR measurements of Escherichia coli including shiga toxin-producing E. coli (STEC) in animal feces and environmental waters. Environ. Sci. Technol. 2015, 49, 3084-3090. [CrossRef] [PubMed]
15. Bustin, S.A.; Nolan, T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech. 2004, 15, 155-166. [PubMed]
16. Baker, M. Digital PCR hits its stride. Nat. Methods 2012, 9, 541-544. [CrossRef]
17. Hindson, C.M.; Chevillet, J.R.; Briggs, H.A.; Gallichotte, E.N.; Ruf, I.K.; Hindson, B.J.; Vessella, R.L.; Tewari, M. Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat. Methods 2013, 10, 1003-1005. [CrossRef] [PubMed]
18. Pinheiro, L.B.; Coleman, V.A.; Hindson, C.M.; Herrmann, J.; Hindson, B.J.; Bhat, S.; Emslie, K.R. Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal. Chem. 2012, 84, 1003-1011. [CrossRef] [PubMed]
19. Huggett, J.F.; Novak, T.; Garson, J.A.; Green, C.; Morris-jones, S.D.; Miller, R.F.; Zumla, A. Differential susceptibility of PCR reactions to inhibitors: An important and unrecognised phenomenon. BMC Res. Notes 2008, 1, 1-9. [CrossRef] [PubMed]
20. Doi, H.; Takahara, T.; Minamoto, T.; Matsuhashi, S.; Uchii, K.; Yamanaka, H. Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environ. Sci. Technol. 2015, 49, 5601-5608. [CrossRef] [PubMed]
21. Strain, M.C.; Lada, S.M.; Luong, T.; Rought, S.E.; Gianella, S.; Terry, V.H.; Spina, C.A.; Woelk, C.H.; Richman, D.D. Highly Precise Measurement of HIV DNA by Droplet Digital PCR. PLoS ONE 2013, 8, 1-8. [CrossRef] [PubMed]
22. Sze, M.A.; Abbasi, M.; Hogg, J.C.; Sin, D.D. A comparison between droplet digital and quantitative PCR in the analysis of bacterial 16S load in lung tissue samples from control and COPD GOLD 2. PLoS ONE 2014, 9, 1-6. [CrossRef] [PubMed]
23. Beer, N.R.; Hindson, B.J.; Wheeler, E.K.; Hall, S.B.; Rose, K.A.; Kennedy, I.M.; Colston, B.W. Reaction in Picoliter Droplets. Anal. Chem. 2007, 79, 8471-8475. [CrossRef] [PubMed]
24. Davis, M.A.; Rice, D.H.; Sheng, H.; Hancock, D.D.; Thomas, E.B.; Cobbold, R.; Hovde, C.J.; Besser, T.E. Comparison of cultures from rectoanal-junction mucosal swabs and feces for detection of Escherichia coli O157 in dairy heifers. Appl. Environ. Microbiol. 2006, 72, 3766-3770. [CrossRef] [PubMed]
25. Perna, N.T.; Plunkett, G.; Burland, V.; Mau, B.; Glasner, J.D.; Rose, D.J.; Mayhew, G.F.; Evans, P.S.; Gregor, J.; Kirkpatrick, H.A. Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 2001, 409, 529-533. [CrossRef] [PubMed]
26. Thompson, R.E.; Duncan, G.; McCord, B.R. An Investigation of PCR Inhibition Using Plexor-Based Quantitative PCR and Short Tandem Repeat Amplification. J. Forensic Sci. 2014, 59, 1517-1529. [CrossRef] [PubMed]
27. The R Project for Statistical Computing. Available online: http://www.R-project.org/ (accessed on 7 September 2015).