Identification of bacterial plant pathogens using multilocus polymerase chain reaction/electrospray ionization-mass spectrometry

Phytopathology

Volumn 98, Issue 11, 2008, Pages 1156-1164

  Postnikova, E ^a   Baldwin, C ^b   Whitehouse, C A ^b   Sechler, A ^a   Schaad, N W ^a   Sampath, R ^c   Harpin, V ^c   Li, F ^c   Melton, R ^c   Blyn, L ^c   Drader, J ^c   Hofstadler, S ^c   Schneider, W L ^a,d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^c Ibis Biosciences Inc   (United States)

^d U S DEPARTMENT OF AGRICULTURE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIUM; ELECTROSPRAY MASS SPECTROMETRY; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; PLANT; POLYMERASE CHAIN REACTION; REPRODUCIBILITY;

BACTERIA; DNA, BACTERIAL; PLANTS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

BACTERIA (MICROORGANISMS);

EID: 56049097958     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-98-11-1156     Document Type: Article

References (25)

1. Bystricka, D., Lenz, O., Mraz, I., Dedic, P., and Sip, M. 2003. DNA microarray: Parallel detection of potato viruses. Acta Virol. 47:41-44.
2. Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Bandela, A. M., Cardenas, E., Garrity, G. M., and Tiedje, J. M. 2007. The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35(Database issue):D169-D172.
3. Ecker, D. J., Sampath, R., Blyn, L. B., Eshoo, M. W., Samant, V., Russell, K., Freed, N., Barrozo, C. Wu, J., Rudnick, K., Desai, A., Moradi, E., Hannis, J. C., Harrell, P. M., Massire, C. Hall, T. A., Jiang, Y., Ranken, R., Drader, J. J., White, N., McNeil, J. A., Crooke, S. T., Hofstadler, S. A. 2005. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc. Natl. Acad. Sci. USA 102:8012-8017.
4. Freitag, J. H., and Frazier, N. W. 1954. Natural infectivity of leafhopper vectors of Pierce's disease virus of grape in California. Phytopathology 44:7-11.
5. Hampton, R. O., Ball, E. M., De Boer, S. H., eds. 1990. Serological Methods for Detection and Identification of Viral and Bacterial Plant Pathogens. American Phytopathological Society, St. Paul, MN.
6. Henson, J. M., and French, R. 1993. The polymerase chain reaction and plant disease diagnosis. Annu. Rev. Phytopathol. 31:81-109.
7. Hofstadler, S. A., Sampath, R., Blyn, L. B., Eshoo, M. W., Hall, T. A., Jiang, Y., Drader, J. J., Hannis, J. C., Sannes-Lowery, K. A., Cummins, L. L., Libby, B., Walcott, D. J., Schink, A., Massire, C., Ranken, R., Gutierrez, J., Manalili, S., Ivy, C., Melton, R., Levene, H., Barrett-Wilt, G., Li, F., Zapp, V., White, N., Samant, V., McNeil, J. A., Knize, D., Robbins, D., Rudnick, K., Desai, A., Moradi, E., and Ecker, D. J. 2005. TIGER: The Universal Biosensor. Int. J. Mass Spectrom. 242:23-41.
8. Honisch, C., Chen, Y., Mortimer, C., Arnold, C., Schmidt, O., van den Boom, D., Cantor, C., Shah, H., and Gharbia, S. 2007. Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing. Proc. Natl. Acad. Sci. USA 104:10649-10654.
9. Jackson, G. W., McNichols, R. J., Fox, G. E., and Wilson, R. C. 2006. Universal bacterial identification by mass spectrometry of 16S ribosomal cleavage products. Int. J. Mass Spectrom. 261:218-226.
10. Jiang, Y., and Hofstadler, S. A. 2003. A highly efficient and automated method of purifying and desalting PCR products for analysis by electrospray ionization mass spectrometry. Anal. Biochem. 316:50-57.
11. Lapa, S., Mikheev, M., Shchelkunov, S., Mikhailovich, V., Sobolev, A., Blinov, V., Babkin, I., Guskov, A., Sokunova, E., Zasedatelev, A., Sandakhchiev, L., and Mirzabekov, A. 2002. Species-level identification of orthopoxviruses with an oligonucleotide microchip. Clin. Microbiol. 40:753-757.
12. Liu, W. J., Chang, Y. S., Wang, C. H., Kou, G. H., and Lo, C. F. 2005. Microarray and RT-PCR screening for white spot syndrome virus immediate-early genes in cycloheximide-treated shrimp. Virology 334:327-341.
13. Louws, F. J., and Cuppels, D. 2001. Molecular Techniques. Pages 321-333 in: Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd ed. N. W. Schaad, J. B. Jones, and W. Chun, eds. American Phytopathological Society, St. Paul, MN.
14. McCoy, W. F., and Olson, B. H. 1985. Fluorometric determination of the DNA concentration in municipal drinking water. Appl. Environ. Microbiol. 49:811-817.
15. Muddiman, D. C., Anderson, G. A., Hofstadler, S. A., and Smith, R. D. 1997. Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry. Anal. Chem. 69:1543-1549.
16. Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., and Frey, J. 2005. Microarray-based detection of 90 antibiotic resistance genes of Gram-positive bacteria. J. Clin. Microbiol. 43:2291-2302.
17. Sampath, R., Hofstadler, S. A., Blyn, L. B., Eshoo, M. W., Hannis, J. C., Harrell, P. M., Massire, C., Hall, T. A., Levene, H. M., Samant, V., Neuman, B., Buchmeier, M. J., Jiang, Y., Ranken, R., Drader, J. J., Griffey, R. H., McNeil, J. A., Crooke, S. T., and Ecker, D. J. 2005. Rapid identification of emerging infectious diseases: A coronavirus. Emerg. Infect. Dis. 11:373-379.
18. Schaad, N. W., Frederick, R. D., Shaw, J., Schneider, W. L., Hickson, R., Petrillo, M. D., and Luster, D. G. 2003. Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annu. Rev. Phytopathol. 41:305-324.
19. Schaad, N. W., Jones, J. B., and Chun, W. (eds.) 2001. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. American Phytopathological Society, St. Paul, MN.
20. Schaad, N. W., Postnikova, E., Lacy, G., Fatmi, M., and Chang, C. J. 2004. Xylella fastidiosa subspecies: X. fastidiosa subsp. piercei, subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov. Syst. Appl. Microbiol. 27:290-300. (Erratum 27:763).
21. Thammakijjawat, P., Thaveechai, N., Kositratana, W., Chunwongse, C., Frederick, R. D., and Schaad, N. W. 2001. Genetic analysis of Ralstonia solanacearum strains from different hosts in Thailand using PCRrestriction fragment length polymorphism. Kasetsart J. Nat. Sci. 35:397-408.
22. Tranvik, L. J. 1997. Rapid fluorometric assay of bacterial density in lake water and seawater. Limnol. Oceanogr. 42:1629-1634.
23. Wang, D., Coscoy, L., Zylberberg, M., Avila, P. C, Boushey, H. A., Ganem, D., and DeRisi, J. L. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99:15687-15692.
24. Wang, D., Urisman, A., Liu, Y.-T., Springer, M., Ksiazek, T. G., Erdman, D. D., Mardis, E. R., Hickenbotham, M., Magrini, V., Eldred, J., Latreille, J. P., Wilson, R. K., Ganem, D., and DeRisi, J. L. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1:257-260.
25. Van Vuurde, J. W. L. 1990. Immunofluorescence colony staining. Pages 295-305 in: Serological Methods for Detection and Identification of Viral and Bacterial Plant Pathogens. R. Hampton, E. Ball, and S. De Boer, eds. American Phytopathological Society, St. Paul, MN.