Development of LAMP and real-time PCR methods for the rapid detection of Xylella fastidiosa for quarantine and field applications

Phytopathology

Volumn 100, Issue 12, 2010, Pages 1282-1288

  Harper, S J ^a   Ward, L I ^a   Clover, G R G ^a  

^a Ministry for Primary Industries   (New Zealand)

Author keywords

Diagnostics

Indexed keywords

PRIMER DNA;

ARTICLE; ECOSYSTEM; GENE AMPLIFICATION; GENETICS; GRAPE; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; OAK; OPEN READING FRAME; PLANT DISEASE; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; XYLELLA;

BASE SEQUENCE; DNA PRIMERS; ECOSYSTEM; GENE AMPLIFICATION; OPEN READING FRAMES; PLANT DISEASES; POLYMERASE CHAIN REACTION; QUERCUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; VITIS; XYLELLA;

BACTERIA (MICROORGANISMS); XYLELLA FASTIDIOSA;

EID: 78650000033     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-06-10-0168     Document Type: Article

References (39)

1. Berisha, B., Chen, Y. D., Zhang, G. Y., Xu, B. Y., and Chen, T. A. 1998. Isolation of Pierce's disease bacteria from grapevines in Europe. Eur. J. Plant Pathol. 104:427-433.
2. Blexine, B., and Child, B. 2007. Xylella fastidiosa genotype differentiation by SYBR green-based qRT-PCR. FEMS Microbiol. Lett.276:48-54.
3. Chen, J., Banks, D., Jarret, R. L., Chang, C. J., and Smith, B. J. 2000. Use of 16S rDNA sequences as signature characters to identify Xylella fastidiosa. Curr. Microbiol. 40:29-33.
4. Chen, J., Civolero, E., Tubajika, K., Livingston, S., and Higbee, B. 2008. Hypervariations of a protease-encoding gene, PD0218 (pspB), in Xylella fastidiosa strains causing Almond leaf scorch and Pierce's disease in California. Appl. Environ. Microbiol. 74:3652-3657.
5. Doddapaneni, H., Yao, J., Lin, H., Walker, M. A., and Civolero, E. L. 2006. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa. BMC Genomics 7:225-240.
6. Dukes, J. P., King, D. P., and Alexandersen, S. 2006. Novel reversetranscription loop-mediated isothermal amplification for rapid detection of foot-and-mouth disease virus. Arch. Virol. 151:1093-1106.
7. Francis, M., Lin H., Cabrera-La Rosa J., Doddapaneni H., and E. L., C. 2006. Genome-based PCR primers for specific and sensitive detection and quantification of Xylella fastidiosa. Eur. J. Plant Pathol. 115:203-213.
8. Fukuta, S., Mizikami, Y., Ishida, A., Ueda, J., Kanabe, M., and Ishimoto, Y. 2003. Detection of Japanese yam mosaic virus by RT-LAMP. Arch. Virol. 148:1713-1720.
9. Goto, M., Honda, E., Ogura, A., Nomoto, A., and Hanaki, K. 2009. Colormetric detection of loop mediated isothermal amplification reaction by using hydroxy napthol blue. Biotechnqiues 46:167-172.
10. Hendson, M., Purcell, A. H., Chen, D., Smart, C., Guilhabert, M., and Kirkpatrick, B. 2001. Genetic diversity of Pierce's disease strain and other pathotypes of Xylella fastidiosa. Appl. Environ. Microbiol. 67:895-903.
11. Hopkins, D. L., and Purcell, A. H. 2002. Xylella fastidiosa: cause of Pierce's disease of grapevine and other emergent diseases. Plant Dis. 86:1056-1066.
12. Huang, Q. 2009. Specific detection and identification of Xylella fastidiosa strains causing oleander leaf scorch using polymerase chain reaction. Curr. Microbiol. 58:393-398.
13. Huang, Q., Bentz, J., and Sherald, J. L. 2006. Fast, easy and efficient DNA extraction and one-step polymerase chain reaction for the detection of Xylella fastidiosa in potential insect vectors. J. Plant Pathol. 88:77-81.
14. 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.
15. Kikuchi, T., Aikawa, T., Oeda, Y., Karim, N., and Kanzaki, N. 2009. A rapid and precise diagnostic method for detecting the pinewood nematode Bursaphelenchus xylophilus by loop-mediated isothermal amplification. Phytopathology 99:1365-1369.
16. Kubota, R., Vine, B. G., Alvarez, A. M., and Jenkins, D. M. 2008. Detection of Ralstonia solanacaerum by loop-mediated isothermal amplification. Phytopathology 98:1045-1051.
17. Kuske, C. R., Banton, K. L., Adorada, D. L., Stark, P. C., Hill, K. K., and Jackson, P. J. 1998. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64:2463-2472.
18. Leu, L. S., and Su, C. C. 1993. Isolation, cultivation, and pathogenicity of Xylella fastidiosa, the causal bacterium of pear leaf scorch disease in Taiwan. Plant Dis. 77:642-646.
19. Mehta, A., and Rosato, Y. 2001. Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences. Int. J. Syst. Evol. Microbiol. 51:311-318.
20. Minsavage, G. V., Thompson, C. M., Hopkins, D. L., Leite, R. M. V. B. C., and Stall, R. E. 1994. Development of a polymerase chain reaction protocol for detection of Xylella fastidiosa in plant tissue. Phytopathology 84:456-461.
21. Mori, Y., Hirano, T., and Notomi, T. 2006. Sequence specific visual detection of LAMP reactions by addition of cationic polymers. BMC Biotechnol. 6:3.
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. Nagamine, K., Hase, T., and Notomi, T. 2002. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell. Probes 16:223-229.
24. 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.
25. Okuda, M., Matsumoto, M., Takana, Y., Subandiah, S., and Iwanami, T. 2005. Characterization of the tufB-secE-nusG-rplKAJL-rpoB gene cluster of the citrus greening organism and detection by loop-mediated isothermal amplification. Plant Dis. 89:705-711.
26. Pooler, M. R., and Hartung, J. S. 1995. Genetic relationships among strains of Xylella fastidiosa from RAPD-PCR data. Curr. Microbiol. 31:134-137.
27. Purcell, A. H. 1997. Xylella fastidiosa, a regional problem or global threat? J. Plant Pathol. 79:99-105.
28. Rodrigues, J. L. M., Silva-Stenico, M. E., Gomes, J. E., Lopes, J. R. S., and Tsai, S. M. 2003. Detection and diversity assessment of Xylella fastidiosa in field-collected plant and insect samples by using 16S rRNA and gyrB sequences. Appl. Environ. Microbiol. 69:4249-4255.
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. Speiss, A. N., Mueller, N., and Ivell, R. 2004. Trehalose is a potent PCR enhancer: Lowering of DNA melting temperature and thermal stabilization of Taq polymerase by the disaccharide trehalose. Clin. Chem. 50:1256-1259.
31. Tomita, N., Mori, Y., Kanda, H., and Notomi, T. 2008. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat. Protocols 3:877-882.
32. Tomlinson, J., Barker, I., and Boonham, N. 2007. Faster, simpler, morespecific methods for improved molecular detection of Phytophthora ramorum in the field. Appl. Environ. Microbiol. 73:4040-4047.
33. Tomlinson, J., and Boonham, N. 2008. Potential of LAMP for detection of plant pathogens. Commonw. Agric. Bur. Rev. Perspect. Agric. Vet. Sci. Nutr. Nat. Resour. 3:1-7.
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. Tomlinson, J. A., Dickinson, M. J., and Boonham, N. 2010. 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 100:143-149.
36. Van Sluys, M. A., de Oliveira, M. C., Monteiro-Vitorello, C. B., Miyaki, C. Y., Furlan, I. R., Camargo, L. E. A., da Silva, A. C. R., Moon, D. H., Takita, M. A., Lemos, E. G. M., Machado, M. A., Ferro, M. I. T., da Silva, F. R., Goldman, M. H. S., Goldman, G. H., Lemos, M. V. F., El-Dorry, H., Tsai, S. M., Carrer, H., Carraro, D. M., de Oliveira, R. C., Nunes, L. R., Siqueira, W. J., Coutinho, L. L., Kimura, E. T., Ferro, E. S., Harakava, R., Kuramae, E. E., Marino, C. L., Giglioti, E., Aberu, I. L., Alves, L. M. C., do Amaral, A. M., Baia, G. S., Blanco, S. R., Brito, M. S., Cannavan, S., Celestino, A. V., da Cunha, A. F., Fenille, R. C., Ferro, J. A., Formighieri, E. F., Kishi, L. T., Leoni, S. G., Oliveira, A. R., Rosa, V. E., Sassaki, F. T., Sena, J. A. D., de Souza, A. A., Truffi, D., Tsukumo, F., Yanai, G. M., Zaros, L. G., Civolero, E. L., Simpson, A. J. G., Alameida, N. F., Setubal, J. C., and Kitajima, J. P. 2003. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185:1018-1026.
37. 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.
38. 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.
39. Wells, J. M., Raju, B. C., Hung, H. Y., Weisberg, W. G., Mandelco-Paul, L., and Brenner, D. J. 1987. Xylella fastidiosa gen. nov., sp. nov: gramnegative, xylem-limited, fastidious plant bacteria related to Xanthomonas spp. Int. J. Syst. Bacteriol. 37:136-143.