Phytoparasitica 25:1, 1997 3 Molecular Detection Tools in Integrated Disease Management: Overcoming Current Limitations Taxonomy continues to be the cornerstone of any pest management research or applications. It is imperative that pest organisms be identified properly so that judicious use of the literature can be made and management strategies can be designed as quickly as possible. Numerous pathogens are difficult to identify by morphological characteristics and require extensive, time-consuming work with pure cultures and/or pathogenicity tests. It is challenging for most plant pathologists to identify isolates routinely from fungal genera such as Fusarium and Pythium because each includes a range of plant pathogenic and saprophytic species. In entomology, great improvements in Integrated Pest Management practices have been achieved by the use of pheromone traps which attract only individuals from a single pest species. Mechanical trapping devices which capture fungal spores are available to plant pathologists; however, the usefulness of these tools is limited by the painstaking microscopic sorting and identification required after trapping. Selective media can help but in most cases they go only as far as genus selectivity. Baiting methods used for trapping motile stages of certain water moulds can reduce the range of isolates to be sorted out but the selectivity of the baits used for the water moulds is poor and the taxonomy of these fungi is so complex that identifying what colonized a given bait still remains difficult. Technologies that would enable pathologists to identify pathogens from plants, traps, baits or in soil samples rapidly and accurately would be very useful in epidemiological and ecological studies as well as for detecting initial inoculum in disease forecasting systems. Although numerous publications describe novel molecular techniques for faster, more accurate and reliable detection of pathogens, there are a few instances where these new tools are being used in disease management. Applications and limitations of molecular techniques for diagnosis of bacterial diseases were discussed recently (6). Are there recent advances that might accelerate the adoption of molecular technologies into integrated disease management programs? What are the challenges that these new technologies will have to address to become more widely used? The number of molecular detection techniques has increased to such an extent in the recent past that some journals now refuse to publish incremental additions to these technologies unless there is also some novelty in the techniques (2). Many of the published reports described species-specific applications of the polymerase chain reaction (PCR), a revolutionary technique by which specific regions of DNA are copied or amplified over a million-fold (9). If the DNA of the pathogen is present, the species-specific primers (short chains of nucleotides that determine the region of DNA to be copied) will bind to the DNA and will be amplified during the PCR reaction. One can use multiple pairs of primers in a single reaction and use the size difference of the PCR products for each different pair to test for several pathogens in a single PCR reaction (16). An interesting variation on this technology was developed recently. This technology, called TaqMan , uses different fluorescent labels attached to nested primers and can detect as well as quantify in a single reaction up to three pathogens at a time without having to run an agarose gel (1). The hardware with this technology also allows dynamic monitoring of the PCR reaction, facilitating quantitation, one of the most difficult issues with molecular detection systems. A potential limitation of most current, antibody or DNA-based, detection technologies is that only a single (or a few) species is detected per assay. Although convenient when a large number of samples must be assessed for the presence of one pathogen, they are inefficient when samples must be assessed for several different pathogens. Quarantine testing, the first line of defense in pest management, is only one area that would benefit greatly from the availability of multi-pathogen assays. As free-trade agreements between countries become the norm, rapid testing for possible food contamination from a wide range of quarantined organisms (nematodes, fungi, viruses, bacteria and even human TM pathogens such as amoebae) will be in high demand. For a wide range of disease management applications, there is a need for comprehensive diagnostic kits that can detect the presence of numerous pathogens in a single test. One could have a kit that could identify all the pathogenic Fusarium species and formae speciales present in a given sample. Kits could also be host-based by having the capability of concurrently testing for all the key pathogens of a given host. Medical laboratories working on cystic fibrosis have designed a method that can detect several disease-related mutations in a single assay 4 C.A. L´evesque (7). This technique, called the reverse dot-blot, involves the use of multiplex PCR to amplify and label simultaneously the regions of the DNA that contain the mutations. The PCR products are then used as probes for hybridization with a membrane that contains an array of oligonucleotides representing several different mutations and their corresponding normal sequences. The hybridization results are read like a checklist, where the mutations and normal alleles in a patient are determined from the positive reactions in the test. A similar approach was designed to monitor bacteria from environmental samples (15). Such approaches bring us closer to the kind of comprehensive pathogen testing that could lead to new practical applications in integrated disease management. Although computers have been used in molecular biology since its inception and are now an integral component in data analysis and automation of complex tasks such as automated sequencing, only recently have applications resulted from the direct merging of microchip fabrication and DNA-based technologies (5). The goal of this merger is the integration of all the steps of a diagnostic test (from DNA extraction and amplification to hybridization and/or electrophoresis) into a microchip. Over 10 oligonucleotides/cm can be attached to a solid support in arrays that can be used like the reverse dot-blot assay discussed above (8). The microfabricated lab or ‘mini-lab on a microchip’ is only a few years away. Recent developments are primarily targeting the medical field; however, several applications could be adapted to plant pathology. The single most important limitation in applying medical technology to plants occurs with DNA extraction. Plant pathologists must extract DNA from substrates which vary greatly in composition: from the soft, easily lysed tissue of ripe fruits to the hard, lignified tissue of trees. It is unlikely that the automated DNA extraction devices being developed for human samples will be easily adapted to plant tissues unless this technology expands in handling capacity to all types of human tissue including bone. However, even if DNA extraction does not become miniaturized, improvements to existing protocols to make them faster and cheaper are being made regularly (13). Many of the technologies discussed above are expensive to develop and to use. This issue is particularly critical for developing countries that would probably benefit the most from the new technologies because of the diversity of their pathosystems. The majority of new applications in DNA-based technologies comes from medical research. Several of these new technologies, including PCR, have been patented with human applications in mind. Use of these technologies in the agricultural sector will necessitate the consideration of market differences between human and agriculture diagnostics by the companies granting licenses. However, one of the possible benefits from microfabrication technology might be a reduction in costs. The replacement of expensive pieces of equipment with disposable microchips, along with the drastically lowered (ca 10 ) requirements of reagents, will aid in the implementation of these molecular diagnostic technologies to a wider range of laboratories. The development of new tests will still depend largely on DNA sequencing and oligonucleotide design: technologies that will likely be available only in well funded laboratories. Molecular diagnostic and detection techniques do what the name says: they detect molecules. What is the significance of finding in a given sample some DNA known to belong to a pathogen? The condition of these molecules is a function of the condition of the organism from which they were isolated. Degradation of DNA varies depending on soil type (10) and moisture. Slower rates of DNA degradation were observed in desiccated soil than in control soil (4). Therefore, population studies of soil-dwelling pathogens sampled from drier or cooler soils may be more biased towards detection of 6 _6 2 dead organisms than samples conducted in humid soils, where the DNA is more readily degraded. Further data on DNA or RNA degradation in natural systems will be required to improve correlation of molecular detection with populations of living organisms. Proper controls will have to be incorporated to detect the PCR inhibition often observed with processing of environmental samples. Protocols such as the BIO-PCR (12) can be used to minimize this problem. Complex extrapolations will have to be performed with most molecular technologies to make them quantitative, increasing the risk for error. The factors used for these extrapolations can also have their own large variation, unlike traditional techniques such as dilution plating, where the error of the dilution is negligible compared with the biological variation in the propagule counts. In order to make proper use of quantitative data from new detection technologies, it will be imperative to incorporate proper error terms along with the quantitative estimates. Replication will always be required for any population study no matter how sophisticated the technology. GenBank, a widely used database of molecular sequences, has more than doubled its entries in the past year alone (3). The new on-line phylogenetic taxonomy of the fungi, one of the different ways to access GenBank through the World Wide Web, is a very exciting recent innovation (14). As the database increases and as insightful interpretations of the data allow updates of the on-line classification, integration of more organisms into detection systems and identification of the causal agents of new diseases are likely to become simpler tasks. The decline of financial support for taxonomic work will undoubtedly have an impact on the analysis of the increasing body of molecular data and ultimately on disease management. Some of these issues were recently reviewed (11). However, one hopes that the negative impact of the worldwide decline in funding for taxonomy and its related services will be somewhat mitigated by new technologies that will facilitate routine detection and identification for disease management. C. Andr´e L´evesque Pacific Agri-Food Research Centre Agriculture and Agri-Food Canada Summerland, B.C., Canada, V0H 1Z0 [Fax: +1-250-494-0755; e-mail: levesqueca@em.agr.ca] REFERENCES 1. Anon. (1995) TaqMan LS-50B PCR Detection System, Perkin-Elmer, Foster City, CA, USA. 2. Anon. (1996) Phytopathology 96:7-11. 6 C.A. L´evesque 3. Benson, D.A., Boguski, M., Lipman, D.J. and Ostell, J. (1996) Nucleic Acids Res. 24:1-5. 4. Brim, H., Dijkmans, R. and Mergeay, M. (1994) FEMS Microbiol. Ecol. 15:169-176. 5. 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