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EC-sponsored Research on Safety of Genetically Modified Organisms - A Review of Results
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image Fungal identification using rapid screening techniques

Background and objectives (1)

Filamentous fungi constitute an economically important group of micro-organisms, primarily due to the wide variety of secondary metabolites they produce. Many species have been identified and are routinely used in fermentation technology and the food industry. Others are known to be agents of disease in animals and plants. Species identified to date constitute a mere 1% of all existing species. With an expansion in the use of genetically modified organisms in the food and medical industries, an improved understanding of fungal diversity is essential. It will enable development of rapid and efficient screening techniques for studying fungal populations, will aid in the identification of new species and will allow for the development of specific probes which can be used to study "problematic" fungi.

To extend and consolidate the current status of fungal identification, we initiated a workshop, inviting international experts on mycology and molecular taxonomy, with the aim of designing recommendations for fungal identification within the European scientific and industrial communities.

(1) This project was a direct follow-on from EC project: “Assessment of methodology for the fast design of fungal DNA probes and PCR tags” (Concerted action BIOT-CT91-0301).



Approach and methodology

The "Fungal Identification Techniques" workshop was held in Barcelona from April 5th-8th, 1995. Forty-three scientists from academia and industry participated, coming from Spain, Italy, Greece, Germany, Holland, England, Ireland, Sweden, Denmark and the USA. A total of 31 talks were given, along with two round-table discussions on "Fungal Identification Techniques – Current Status" and "Fungal Identification Techniques – Application to Complex Samples". All speakers contributed a paper to the proceedings of the meeting, which have been published together with the recommendations of the project group.
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Main findings and outcome

One clear outcome of the workshop was that the requirements for fungal identification are dependent on both the field of application and the use of research (i.e. whether the aim is to improve human health, economise, expand current knowledge of biology, or for financial gain).

In the food and fermentation industries, fungal identification requirements can be separated into two main areas. Firstly, the detection of spoilage and toxic organisms, (which is more often a functional detection than an actual species identification), and secondly, to ensure quality control of fermentation isolates, where identification is more differentiated than simply identifying the species level.

Fungal identification in the pharmaceutical industry is necessary at a level beyond that of species identification. This is to enable correct naming prior to patenting, to ensure quality control of fungal products, and to carry out efficient screening programmes, risk evaluations and process validations.

In the domain of human pathology, rapid fungal detection is more important than precise species identification. Nonetheless, species identification is crucial for the development of specific diagnostic kits. Furthermore, very few relevant species have been identified, however with an increasing number of immuno-compromised patients, a large number of novel species are likely to become relevant.

In plant pathology, detection is substantially more complex than simply identifying a species. This is due to the development by plant pathogens of host range specificity, based on pathogenicity factors. Good identification techniques are essential for the prevention of disease spread, particularly with respect to quarantine regulations.

The overriding problem in the domain of ecology, is the lack of quantitative and qualitative data describing the fungal population. This raises two principal issues: firstly, that some organisms are non-culturable and secondly, that some of the culturable fungi cannot be named using traditional criteria, as they only produce mycelia under laboratory conditions.

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Conclusions

This workshop was particularly informative, showing that a large number of fungi have been, and continue to be incorrectly identified. It also highlighted a clear need to train more classical taxonomists in both classical skills and in the use of molecular techniques. In addition, a multidisciplinary approach is necessary for correct fungal classification and consequent fungal identification. The most promising approach for "fast" nomenclature appears to be the use of ribosomal sequences. Furthermore, some techniques, such as immunological methods and fatty acid profiles, are best suited for detection or identification at a higher (i.e. genus) level. It was also concluded that a concerted effort is required to ensure that DNA sequences are made available through public databases, and that a specific fungal database would be extremely useful. This research is likely to be of benefit where genetically modified filamentous fungi are used in industrial applications, such as when rapid identification of potentially useful fungi is needed for quality control of mixed starter cultures and detection of food pathogens.


Major publication

Rossen L., Frisvad J.C., Dawson M.T. and Rubio V. (eds.), Proceedings from the Workshop on Fungal Identification Techniques, Barcelona, April 1995. Published by the European Commission, ISBN 92-827-5677-7.
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imageConcerted action
 

Contract number
BIO2-CT94-3011

Period
September 1994 - September 1996

Coordinator
L. Rossen
Biotechnological Institute
Hørsholm (DK)

Follow-up of the project
The workshop "Fungal Identification Techniques", Barcelona, April 1995.

 
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Partners


V. Rubio
Universidad Autónoma de Madrid (ES)

J. Frisvad
Technical University of Denmark
Lyngby (DK)

M. Dawson
University College Galway (IE)

 
 
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