Real-time PCR, a method fit for detection and quantification of Erwinia amylovora

Trees - Structure and Function

Volumn 26, Issue 1, 2012, Pages 165-178

  Dreo, Tanja ^a   Pirc, Manca ^a   Ravnikar, Maja ^a  

^a NATIONAL INSTITUTE OF BIOLOGY   (Slovenia)

Author keywords

Analytical sensitivity; Erwinia amylovora; Fire blight; Real time PCR

Indexed keywords

AGRICULTURAL PRODUCTIONS; ANALYTICAL SENSITIVITY; CAUSATIVE AGENTS; DETECTION AND DIAGNOSIS; ERWINIA AMYLOVORA; FIRE BLIGHT; FRUIT TREES; GENE EXPRESSION ANALYSIS; LOW CONCENTRATIONS; NUMBER OF SAMPLES; ON-SITE DETECTION; REAL-TIME PCR; REAL-TIME PCR ASSAY;

AGRICULTURE; ASSAYS; BACTERIA; DIAGNOSIS; GENE EXPRESSION; ORCHARDS;

POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); ERWINIA AMYLOVORA;

EID: 84856227570     PISSN: 09311890     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00468-011-0654-7     Document Type: Article

References (64)

1. Bentley HA, Belloni DR, Tsongalis GJ (2005) Parameters involved in the conversion of real-time PCR assays from the ABI prism 7700 to the Cepheid SmartCycler II. Clin Biochem 38(2): 183-186.
2. Bereswill S, Bugert P, Bruchmüller I, Geider K (1995) Identification of the fire blight pathogen, Erwinia amylovora, by PCR assays with chromosomal DNA. Appl Environ Microb 61(7): 2636-2642.
3. Bonn WG, van der Zwet T (2000) Distribution and economic importance of fire blight. In: Vanneste JL (ed) Fire blight the disease and its causative agent, Erwinia amylovora. UK CAB International, Wallingford, pp 37-53.
4. Braun-Kiewnick A, Lehmann A, Duffy B, Dreo T, Ravnikar M, Stockwell VO (2011) Detection of Erwinia amylovora in orchards using quantitative PCR and lateral-flow immunography. Acta Hortic 896: 73-76.
5. Bugert P, Geider K (1995) Molecular analysis of the ams operon required for exopolysaccharide synthesis of Erwinia amylovora. Mol Microbiol 15: 917-933.
6. Burns M, Valdivia H (2007) Modelling the limit of detection in real-time quantitative PCR. Eur Food Res Technol 226(6): 1513-1524.
7. Burrill TJ (1882) The Bacteria: an account of their nature and effects, together with a systematic description of the species. Illinois Industrial University 11th Report, 1882, pp 93-157.
8. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Reinhold M, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4): 611-622.
9. Cankar K, Štebih D, Dreo T, Žel J, Gruden K (2006) Critical points of DNA quantification by real-time PCR-effects of DNA extraction method and sample matrix on quantification of genetically modified organisms. BMC Biotechnol 6(1): 37.
10. Chandelier A, Planchon V, Oger R (2010) Determination of cycle cut off in real-time PCR for the detection of regulated plant pathogens. EPPO Bull 40(1): 52-58.
11. De Bellis P, Schena L, Cariddi C (2007) Real-time Scorpion-PCR detection and quantification of Erwinia amylovora on pear leaves and flowers. Eur J Plant Pathol 118(1): 11-22.
12. de Kok JB, Hendriks JCM, van Solinge WW, Willems HL, Mensink EJ, Swinkels DW (1998) Use of real-time quantitative PCR to compare DNA isolation methods. Clin Chem 44(10): 2201-2204.
13. Dreo T (2009) Is there a need and a place for Real-Time PCR in detection of Erwinia amylovora? Zaštita bilja 60(270): 209-226.
14. Duffy B, Schärer H, Bünter M, Klay A, Holliger E (2005) Regulatory measures against Erwinia amylovora in Switzerland. EPPO Bull 35: 239-244.
15. European Patent Application EP1770172, Determination of the cycle threshold (Ct) value in a PCR amplification curve by cluster analysis with variable cluster endpoint, http://www. freepatentsonline. com/EP1770172. html.
16. Geider K, Auling G, Jakovljević V, Völksch B (2009) A polyphasic approach assigns the pathogenic Erwinia strains from diseased pear trees in Japan to Erwinia pyrifoliae. Lett Appl Microbiol 48(3): 324-330.
17. Gianetti G, Garofalo MC, Morone C, Scortichini M (2004) First report of Erwinia amylovora in Piedmont. Informatore Agrario 60(5): 62-63.
18. Gottsberger RA (2010) Development and evaluation of a real-time PCR assay targeting chromosomal DNA of Erwinia amylovora. Lett Appl Microbiol 51(3): 285-292.
19. Johnson K, Stockwell VO, McLaughlin R, Sugar D, Loper JE, Roberts RG (1993) Effect of antagonistic bacteria on establishment of honey bee-dispersed Erwinia amylovora in pear blossoms and on fire blight control. Phytopathology 83: 995-1002.
20. Kuflik T, Pertot I, Moskovitch R, Zasso R, Pellegrini E, Gessler C (2008) Optimization of fire blight scouting with a decision support system based on infection risk. Comput Electron Agric 62(2): 118-127.
21. Lehman SM, Kim W, Castle AJ, Svircev AM (2008) Duplex real-time polymerase chain reaction reveals competition between Erwinia amylovora and E. pyrifoliae on pear blossoms. Phytopathology 98(6): 673-679.
22. Li X, De Boer SH (1995) Selection of polymerase chain reaction primers from an RNA intergenic spacer region for specific detection of Clavibacter michiganensis subsp. sepedonicus. Phytopathology 85: 837-842.
23. Llop P, Caruso P, Cubero J, Morente C, López MM (1999) A simple extraction procedure for efficient routine detection of pathogenic bacteria in plant material by polymerase chain reaction. J Microbiol Meth 37(1): 23-31.
24. Llop P, Bonaterra A, Peñalver J, López MM (2000) Development of a highly sensitive nested-PCR procedure using a single closed tube for detection of Erwinia amylovora in asymptomatic plant material. App Environ Microb 66(5): 2071-2078.
25. Llop P, Donat V, Rodríguez M, Cabrefiga J, Ruz L, Palomo JL, Montesinos E, López MM (2006) An indigenous virulent strain of Erwinia amylovora lacking the ubiquitous plasmid pEA29. Phytopathology 96(8): 900-907.
26. López MM, Llop P, Olmos A, Marco-Noales E, Cambra M, Bertolini E (2009) Are molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses? Curr Issues Mol Biol 11(1): 13-46.
27. Maes M, Garbeva P, Crepel C (1996) Identification and sensitive endophytic detection of the fire blight pathogen Erwinia amylovora with 23S ribosomal DNA sequences and the polymerase chain reaction. Plant Pathol 45: 1139-1149.
28. Marras SAE, Kramer FR, Tyagi S (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 30(21): e122.
29. Maxson-Stein K, McGhee GC, Smith JJ, Jones AL, Sundin GW (2003) Genetic analysis of a pathogenic Erwinia sp. isolated from pear in Japan. Phytopathology 93: 1393-1399.
30. McGhee GC, Schnabel EL, Maxson-Stein K, Jones B, Stromberg VK, Lacy GH, Jones AL (2002) Relatedness of chromosomal and plasmid DNAs of Erwinia pyrifoliae and Erwinia amylovora. App Environ Microb 68: 6182-6192.
31. Menggad M, Laurent J (1998) Mutations in ams genes of Erwinia amylovora affect the interactions with host plants. Eur J Plant Pathol 104(3): 313-322.
32. Mohammadi M, Moltmann E, Zeller W, Geider K (2009) Characterisation of naturally occurring Erwinia amylovora strains lacking the common plasmid pEA29 and their detection with real-time PCR. Eur J Plant Pathol 124(2): 293-302.
33. Navidi W, Arnheim N, Waterman MS (1992) A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations. Am J Hum Genet 50(2): 347-359.
34. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12): E63.
35. Ordax M, Marco-Noales E, Lopez MM, Biosca EG (2006) Survival strategy of Erwinia amylovora against copper: induction of the viable-but-nonculturable state. App Environ Microb 72(5): 3482-3488.
36. Pastrik KH, Elphinstone JG, Pukall R (2002) Sequence analysis and detection of Ralstonia solanacearum by multiplex PCR amplification of 16S-23S ribosomal intergenic spacer region with internal positive control. Eur J Plant Pathol 108: 831-842.
37. Pester E (2011) Gene expression in the quarantine pest Erwinia amylovora during apple flower-infection. Acta Hortic 896: 173-176.
38. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9): e45.
39. Pirc M, Dreo T, Ravnikar M (2008) Real-time PCR for testing of symptomless fire blight samples. Acta Hortic 793: 533-538.
40. Pirc M, Ravnikar M, Tomlinson J, Dreo T (2009) Improved fireblight diagnostics using quantitative real-time PCR detection of Erwinia amylovora chromosomal DNA. Plant Pathol 58(5): 872-881.
41. PO EP (1992) EPPO Standards PM 3/40 Erwinia amylovora. Sampling and test methods. EPPO Bull 22: 225-231.
42. PO EP (2004) Diagnostic protocols for regulated pests PM 7/20, Erwinia amylovora. EPPO Bull 34: 159-171.
43. PO EP (2007) Basic requirements for quality management in plant pest diagnosis laboratories. EPPO Bull 37(3): 580-588.
44. PO EP (2010a) PM 7/76 (2): Use of EPPO diagnostic protocols. EPPO Bull 40: 350-352.
45. PO EP (2010b) PM 7/98 (1): specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. EPPO Bull 40(1): 5-22.
46. Powney R, Smits THM, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B (2011) Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to rubus plants. J Bacteriol 193(3): 785-786.
47. R Development Core Team (2010) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www. R-project. org/.
48. Reisenzein H, López MM, Duffy B, Dreo T, Paulin JP, Poliakoff F (2010) Development and validation of innovative diagnostics tools for the detection of fire blight (Erwinia amylovora) (ERWINDECT): EUPHRESCO final report, 2010. 65 f.
49. Ritz C, Streibig JC (2005) Bioassay Analysis using R. J Stat Softw 12(5): 22.
50. Roselló M, Garcia Vidal S, Tarin A, Llop P, Gorris MT, Donat V, Chartier R, Paulin JP, Gardan L, Peñalver J, López MM (2002) Characterization of an Erwinia sp. isolated from necrotic pear blossoms in Valencia, Spain. Acta Hortic 590: 139-142.
51. Salm H, Geider K (2004) Real-time PCR for detection and quantification of Erwinia amylovora, the causal agent of fireblight. Plant Pathol 53(5): 602-610.
52. Sebaihia M, Bocsanczy AM, Biehl BS, Quail MA, Perna NT, Glasner JD, DeClerck GA, Cartinhour S, Schneider DJ, Bentley SD, Parkhill J, Beer SV (2010) Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946. J Bacteriol 192(7): 2020-2021.
53. Smits THM, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B (2010a) Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity. BMC Genomics 11(1): 2.
54. Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B (2010b) Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Mol Plant Microbe In 23(4): 384-393.
55. Steinberger EM, Beer SV (1988) Creation and complementation of pathogenicity mutants of Erwinia amylovora. Mol Plant Microbe In 1: 135-144.
56. Stöger A, Schaffer J, Ruppitsch W (2006) A rapid and sensitive method for direct detection of Erwinia amylovora in symptomatic and asymptomatic plant tissues by polymerase chain reaction. J Phytopathol 154(7-8): 469-473.
57. Svircev AM, Kim W, Lehman SM, Castle AJ (2009) Erwinia amylovora: modern methods for detection and differentiation. Methods Mol Biol 508: 115-129.
58. Temple TN, Johnson KB (2010) Evaluation of loop-mediated isothermal amplification for rapid detection of Erwinia amylovora on pear and apple fruit flowers. Plant Dis 12: 423-430.
59. Thomson S (2000) Epidemiology of fire blight. In: Vanneste JL (ed) Fire blight the disease and its causative agent, Erwinia amylovora. UK CAB International, Wallingford, pp 9-36.
60. Thomson S, Schroth M, Moller W, Reil W (1975) Occurrence of fire blight of pears in relation to weather and epiphytic populations of Erwinia amylovora. Phytopathology 65: 353-358.
61. van der Zwet T (2006) Present worldwide distribution of fire blight and closely related diseases. Acta Hortic 704: 35-36.
62. van der Zwet T, Beer SV (1995) Fire blight: its nature, prevention, and control: a practical guide to integrated disease management, vol 631. United States Department of Agriculture (Washington, DC), 91pp.
63. Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede JRC, Rogers LA, Smith GH (1920) The families and the genera of the bacteria. Final report of the Committee of the Society of American Bacteriologists on characterization and classification of bacterial types. J Bacteriol 5(S): 191-229.
64. Won-Sik K, Jock S, Paulin JP, Rhim SL, Geider K (2001) Molecular detection and differentiation of Erwinia pyrifoliae and host range analysis of the Asian pear pathogen. Plant Dis 85: 1183-1188.