Revolutionising AMR detection in grapevines

Powdery mildew, Botrytis bunch rot and downy mildew are significant fungal diseases affecting Australian grapevines, diminishing both fruit yield and wine quality. Vineyards rely on fungicides to control the pathogens responsible, but this has led to the emergence of fungicide resistance. SAAFE partners Wine Australia, the South Australian Research and Development Institute (SARDI), and Curtin University are working together to address this challenge.

Building on earlier research funded by SARDI and Wine Australia, the SAAFE project is developing advanced laboratory and field-based diagnostic methods, establishing robust sampling protocols, and creating novel tools for monitoring antimicrobial resistance (AMR) in grapevine pathogens.

“This research is crucial for ensuring we meet our vineyard sustainability and production goals,” said Liz Riley, consulting viticulturist and SAAFE Director.

Current methods of detecting resistance are labour-intensive and slow, limiting the number of samples that can be processed and hampering early detection of AMR. Phenotyping involves isolating a pathogen from a diseased plant and testing whether it can survive treatment with different doses, including the recommended dosage, of a particular fungicide in the laboratory.

“If we want to test a sample of powdery mildew or downy mildew from a vineyard using phenotyping, we need to grow the pathogen up again on new plants – that can take two to six weeks,” said project lead Dr Mark Sosnowski from SARDI.

Genotyping – which involves analysing DNA from a swab of the disease – is faster, but it can only be used when the mechanism of fungicide resistance and the associated mutation are known.

One goal of the SAAFE project is to adapt existing methods of high-throughput genotyping, currently used in areas such as medical diagnostics, for use in AMR detection. “Identifying a mutant is much more challenging, because you're looking for just one base pair difference in the DNA,” said Mark. “We need to optimise the technology to detect that level of detail.”

“The other challenge is determining how much of the pathogen is required – how many spores are needed to extract enough DNA to identify the mutant?” said SARDI’s Dr Ismail who leads the powdery/downy mildew research in the project. His team is establishing sampling protocols to define the ideal timing, location, and size of samples for reliable testing in the lab and in the field.

A key innovation within the project is the improvement of a ‘spore trap‘ – a prototype device to capture fungal spores from the air. Based on an air sampler developed by Dr Walt Mahaffee at the US Department of Agriculture, this cost-effective and practical tool allows growers to monitor the presence of resistant pathogens even before they see any infections in their vines.

The researchers have sent spore traps to growers in New South Wales, Victoria, South Australia, Tasmania and Western Australia.

“They send us samples every two weeks so we can compile information about pathogen prevalence and resistance throughout the season in their vineyards,” said Ismail. Coupled with intensive sampling with swabs, the results also reveal the optimal intensity, timing and frequency of sampling, as well as the effect of geographic location, climate, and fungicide spray program.

At the same time, the researchers are building a comprehensive dataset of the AMR status in vine-growing regions around the country. The data is being used to provide guidance and recommendations to growers. “When we detect resistance in a region or to a particular fungicide, it serves as a warning to growers to follow industry guidelines for mitigating fungicide resistance,” said Mark.

With a more comprehensive understanding of fungicide resistance and the potential to process thousands of samples annually, the project is expected to revolutionise disease management in vineyards. Faster turnaround times, greater sensitivity, and better data on AMR prevalence will allow growers to tailor their disease control strategies, ultimately preserving the quality and quantity of grape yields. This approach not only mitigates crop losses but also extends the effective lifespan of fungicides, as well as reducing the costs associated with treatment failures and resistance management.

Industry collaboration is essential to the project’s success. Ismail encourages growers around Australia to submit samples for free and confidential testing. “The more they send us, the more we’ll know about fungicide resistance in the country.”