Rapid detection of phytophthora ramorum and P. kernoviae by two-minute DNA extraction followed by isothermal amplification and amplicon detection by generic lateral flow device

Phytopathology

Volumn 100, Issue 2, 2010, Pages 143-149

  Tomlinson, J A ^a   Dickinson, M J ^b   Boonham, N ^a  

^a FOOD AND ENVIRONMENT RESEARCH AGENCY   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAL DNA; CYTOCHROME C OXIDASE;

ARTICLE; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; NUCLEIC ACID AMPLIFICATION; OAK; PHYTOPHTHORA; PLANT DISEASE; RHODODENDRON;

DNA, ALGAL; ELECTRON TRANSPORT COMPLEX IV; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYTOPHTHORA; PLANT DISEASES; QUERCUS; RHODODENDRON;

PHYTOPHTHORA; PHYTOPHTHORA KERNOVIAE; PHYTOPHTHORA RAMORUM;

EID: 75949094540     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-100-2-0143     Document Type: Article

References (38)

1. Brasier, C. M., Beales, P. A., Kirk, S. A., Denman, S., and Rose, J. 2005. Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in the UK. Mycol. Res. 109:853-859.
2. Carter, D. J., and Cary, R. B. 2007. Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography. Nucleic Acids Res. 35:e74
3. Danks, C., and Barker, I. 2000. On-site detection of plant pathogens using lateral-flow devices. OEPP/EPPO Bull. 30:421-426.
4. Danks, C., and Boonham, N. September 2007. Purification method and kits. Patent WO/2007/104962.
5. Deborggraeve, S., Claes, F., Laurent, T., Mertens, P., Leclipteux, T., Dujardin, J. C., Herdewijn, P., and Büscher, P. 2006. Molecular dipstick test for diagnosis of sleeping sickness. J. Clin. Microbiol. 44:2884-2889.
6. Fukuta, S., Iida, T., Mizumkami, Y., Ishida, A., Ueda, J., Kanbe, M., and Ishimoto, Y. 2003. Detection of Japanese yam mosaic virus by RT-LAMP. Arch. Virol. 148:1713-1720.
7. Fukuta, S., Kato, S., Yoshida, K., Mizukami, Y., Ishida, A., Ueda, J., Kanbe, M., and Ishimoto, Y. 2003. Detection of Tomato yellow leaf curl virus by loop-mediated isothermal amplification reaction. J. Virol. Methods 112:35-40.
8. Fukuta, S., Ohishi, K., Yoshida, K., Mizukami, Y., Ishida, A., and Kanbe, M. 2004. Development of immunocapture reverse transcription loopmediated isothermal amplification for the detection of Tomato spotted wilt virus from chrysanthemum. J. Virol. Methods 121:49-55.
9. Gill, P., and Ghaemi, A. 2008. Nucleic acid isothermal amplification technologies-a review. Nucleosides Nucleotides Nucleic Acids 27:224-243.
10. Goldmeyer, J., Li, H., McCormac, M., Cook, S., Stratton, C., Lemieux, B., Kong, H., Tang, W., and Tang, Y. W. 2008. Identification of Staphylococcus aureus and determination of methicillin resistance directly from positive blood cultures by isothermal amplification and a disposable detection device. J. Clin. Microbiol. 46:1534-1536.
11. Hughes, K. J. D., Giltrap, P. M., Barton, V. C., Hobden, E., Tomlinson, J. A., and Barber, P. 2006. On-site real-time PCR detection of Phytophthora ramorum causing dieback of Parrotia persica in the UK. Plant Pathol. 55:813.
12. Hughes, K. J. D., Tomlinson, J. A., Griffin, R. L., Boonham, N., Inman, A. J., and Lane, C. R. 2006. Development of a one-step real-time polymerase chain reaction assay for diagnosis of Phytophthora ramorum. Phytopathology 96:975-981.
13. Iwamoto, T., Sonobe, T., and Hayashi, K. 2003. Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J. Clin. Microbiol. 41:2616-2622.
14. Jeffers, S. N., and Martin, S. B. 1986. Comparison of two media selective for Phytophthora and Pythium species. Plant Dis. 70:1038-1043.
15. Kiatpathomchai, W., Jaroenram, W., Arunrut, N., Jitrapakdee, S., and Flegel, T. W. 2008. Shrimp Taura syndrome virus detection by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick. J. Virol. Methods 153:214-217.
16. Lane, C. R., Hobden, E., Walker, L., Barton, V. C., Inman, A. J., Hughes, K. J. D., Swan, H., Colyer, A., and Barker, I. 2007. Evaluation of a rapid diagnostic field test kit for identification of Phytophthora species, including P. ramorum and P. kernoviae at the point of inspection. Plant Pathol. 56:828-835.
17. Maeda, H., Kokeguchi, S., Fujimoto, C., Tanimoto, I., Yoshizumi, W., Nishimura, F., and Takashiba, S. 2005. Detection of periodontal pathogen Porphyromonas gingivalis by loop-mediated isothermal amplification method. FEMS Immunol. Med. Microbiol. 43:233-239.
18. Mavrodieva, V., Levy, L., and Gabriel, D. W. 2004. Improved sampling methods for real-time polymerase chain reaction diagnosis of citrus canker from field samples. Phytopathology 94:61-68.
19. Mens, P. F., van Amerongen, A., Sawa, P., Kager, P. A., and Schallig, H. D. F. H. 2008. Molecular diagnosis of malaria in the field: development of a novel 1-step nucleic acid lateral flow immunoassay for the detection of all 4 human Plasmodium spp. and its evaluation in Mbita, Kenya. Diagn. Microbiol. Infect. Dis. 61:421-427.
20. Mori, Y., Hirano, T., and Notomi, T. 2006. Sequence specific visual detection of LAMP reactions by addition of cationic polymers. BMC Biotechnol. 6:3.
21. Mori, Y., Kitao, M., Tomita, N., and Notomi, T. 2004. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J. Biochem. Biophys. Methods 59:145-157.
22. Mori, Y., Nagamine, K., Tomita, N., and Notomi, T. 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem. Biophys. Res. Commun. 289:150-154.
23. Mumford R., Boonham, N., Tomlinson, J., and Barker, I. 2006. Advances in molecular phytodiagnostics-new solutions for old problems. Eur. J. Plant Pathol. 116:1-19.
24. Nagamine, K., Hase, T., and Notomi, T. 2002. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell. Probes 16:223-229.
25. Nagamine, K., Watanabe, K., Ohtsuka, K., Hase, T., and Notomi, T. 2001. Loop-mediated isothermal amplification reaction using a nondenatured template. Clin. Chem. 47:1742-1743.
26. Nie, X. 2005. Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y. Plant Dis. 89:605-610.
27. Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., and Hase, T. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28:e63.
28. Rizzo, D. M., Garbelotto, M., Davidson, M., Slaughter, J. M., and Koike, G. W. 2002. Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California. Plant Dis. 86:205-214.
29. Schaad, N. W., Opgenorth, D., and Gaush, P. 2002. Real-time polymerase chain reaction for one-hour on-site diagnosis of Pierce's disease of grape in early season asymptomatic vines. Phytopathology 92:721-728.
30. Srisala, J., Tacon, P., Flegel, T. W., and Sritunyalucksana, K. 2008. Comparison of white spot syndrome virus PCR-detection methods that use electrophoresis or antibody-mediated lateral flow chromatographic strips to visualize PCR amplicons. J. Virol. Methods 153:129-133.
31. Suarez, M. B., Walsh, K., Boonham, N., O'Neill, T., Pearson, S., and Barker, I. 2005. Development of real-time PCR (TaqMan) assays for the detection and quantification of Botrytis cinerea in planta. Plant Physiol. Biochem. 43:890-899.
32. Tomlinson, J., and Boonham, N. 2008. Potential of LAMP for detection of plant pathogens. In: CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 3: article 066.
33. Tomlinson, J. A., Barker, I., and Boonham, N. 2007. Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field. Appl. Environ. Microbiol. 73:4040-4047.
34. Tomlinson, J. A., Boonham, N., Hughes, K. J. D., Griffin, R. L., and Barker, I. 2005. On-site DNA extraction and real-time PCR for detection of Phytophthora ramorum in the field. Appl. Environ. Microbiol. 71:6702-6710.
35. Varga, A., and James, D. 2006. Use of reverse transcription loop-mediated isothermal amplification for the detection of Plum pox virus. J. Virol. Methods 138:184-190.
36. Ward, E., Foster, S. J., Fraaije, B. A., and McCartney, H. A. 2004. Plant pathogen diagnostics: immunological and nucleic acid-based approaches. Ann. Appl. Biol. 145:1-16.
37. Weller, S. A., Elphinstone, J. G., Smith, N. C., Boonham, N., and Stead, D. E. 2000. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl. Environ. Microbiol. 66:2853-2858.
38. Werres, S., Marwitz, R., Manin't Veld, W. A., De Cock, W. A. M., Bonants, P. J. M., De Weerdt, M., Themann, K., Ilieva, E., and Baayen, R. P. 2001. Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and Viburnum. Mycol. Res. 105:1155-1165.