Design and development of a DNA microarray for rapid identification of multiple European quarantine phytopathogenic bacteria
The European and Mediterranean Plant Protection Organization (EPPO) lists for quarantine status 26 phytopathogenic bacteria which pose serious economic threats to agricultural and natural ecosystems. A prototype diagnostic DNA microarray was developed for the rapid and simple identification of 22 of these quarantine bacteria. The microarray has 38 probes targeted to the 16S rDNA and the house-keeping genes rpoB, groEL and ftsZ. The 16S rDNA probes were selected according to a multiple-probe concept taking into account the hierarchical structure of phytobacterial systematics. Hybridisation with Cy3-labelled PCR products of corresponding genes enabled differentiation of the quarantine bacteria down to the species and subspecies level.
KeywordsPlant inspection Bacterial diagnostics Quarantine pathogen Microarray
The authors thank Jörg Samietz for assistance with statistical evaluation and Alicia Timm for critical reading of the manuscript. This work was funded by the Swiss Secretariat for Education and Research (SBF, COST project no. C04.0204), and was conducted within the European research networking frameworks of COST Action 853 (Agricultural Biomarkers for Array Technology) and COST Action 873 (Bacterial diseases of stone fruits and nuts).
- Janse, J. D. (2005). Phytobacteriology: Principles and Practice. Wallingford, Oxfordshire, UK: CABI Publishing.Google Scholar
- Lievens, B., Brouwer, M., Vanachter, A. C. R. C., Lévesque, C. A., Cammue, B. P. A., & Thomma, B. P. H. J. (2003). Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiology Letters, 223, 113–122.PubMedCrossRefGoogle Scholar
- Maiden, M. C., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., et al. (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proceedings of the National Academy of Sciences U.S.A., 17, 3140–3145.CrossRefGoogle Scholar
- Park, D. S., Hyun, J. W., Park, Y. J., Kim, J. S., Kang, H. W., Hahn, J. H., et al. (2005). Sensitive and specific detection of Xanthomonas axonopodis pv. citri by PCR using pathovar-specific primers based on hrpW gene sequences. Microbiology Research, 161, 145–149.Google Scholar
- Pozhitkov, A., Noble, P. A., Domazet-Lošo, T., Nolte, A. W., Sonnenberg, R., Staehler, P., et al. (2006). Tests of rRNA hybridisation to microarrays suggest that hybridisation characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research, 17(66), 2–12.Google Scholar
- Scally, M., Schuenzel, E. L., Stouthamer, R., & Nunney, L. (2005). Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity. Applied and Environmental Microbiology, 71, 8491–8499.PubMedCrossRefGoogle Scholar
- Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kampfer, P., Maiden, M. C., et al. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology, 52, 1043–1047.PubMedCrossRefGoogle Scholar
- Vora, G. J., Meador, C. E., Bird, M. M., Bopp, C. A., Andreadis, J. D., & Stenger, D. A. (2005). Microarray-based detection of genetic heterogeneity, antimicrobial resistance, and the viable but non-culturable state in human pathogenic Vibrio spp. Proceedings of the National Academy of Sciences U.S.A., 102, 19109–19114.CrossRefGoogle Scholar