Fungicide Resistance Costs Farmers Billions: Conidia Coniphy Maps Threats Before they Spreads
- Marc Violo
- 5 hours ago
- 4 min read
Too long to read? Go for the highlights below.
Fungal diseases destroy 10-23% of cereal crops even with treatment, costing the global agriculture sector an estimated $60 billion annually across rice, wheat, and maize alone, losses equivalent to feeding up to 4 billion people.
French microbiology specialist Conidia Coniphy has developed FungiRESIST, a long-read DNA sequencing platform that maps fungicide resistance across entire pathogen populations in a single test, enabling early detection of resistance hotspots before they spread regionally.
Following deployment across Europe, the company is now targeting India and the United States, where similar resistance patterns are emerging in key agricultural regions.
A Silent Crisis in Global Food Security
Fungal pathogens represent what researchers describe as the greatest biotic challenge to calorie crops worldwide. Despite widespread antifungal use, growers lose between 10 and 23 percent of harvests pre-harvest, with an additional 10-20 percent lost post-harvest. The economic damage to just three staple crops—rice, wheat, and maize—amounts to roughly $60 billion annually. In the United Kingdom alone, a single wheat disease, Septoria tritici, costs the agriculture sector an estimated £132-264 million each year in direct crop losses.
The food lost to fungal diseases globally is equivalent to what could feed between 600 million and 4 billion people annually. Professor Sarah Gurr of the University of Exeter has warned that this threat concerns "global starvation," not science fiction.
The situation is worsening. As global temperatures rise, fungal infections are migrating poleward. Wheat stem rust, a disease historically confined to tropical regions, has now been reported in Ireland and England. Modern farming practices, with vast areas of genetically uniform crops, provide ideal conditions for these fast-evolving organisms, creating what experts describe as a "perfect storm" for pathogen proliferation.
The Resistance Spiral
Compounding the crisis is the very tool designed to solve it. Intensive fungicide application targeting single cellular processes has accelerated the emergence of resistant strains, forcing farmers into a cycle of ever-higher chemical concentrations, which in turn drives further resistance.
Catalina Hernandez, co-founder of French microbiology laboratory Conidia Coniphy, has observed this pattern firsthand. "We are seeing rapid progression of fungicide resistance among phytopathogenic fungi" she explains. "This evolution results from selection pressure due to the use of active substances. The increasing frequency of resistance, combined with varied genetic mechanisms, is making us rethink the strategies employed in chemical control."
"We are seeing rapid progression of fungicide resistance among phytopathogenic fungi" - Catalina Hernandez
What begins as a local problem can become regional within seasons. Resistance spreads through pathogen populations as spores travel by air, vehicles, and equipment. A hotspot in one production basin can, within a few years, become a sector-wide challenge. The total economic impact of pesticide resistance in the United States was calculated at $1.5 billion in 2005—approximately $2.5 billion when adjusted for inflation today. This represents a classic "tragedy of the commons," where the actions of one farmer can affect an entire region.
From Lab to Field: A New Approach to Resistance Mapping
Conidia Coniphy, founded by Catalina Hernandez and Sébastien Vacher in the early 2000s, has spent two decades developing diagnostic tools for industries facing fungal challenges. Now part of the Tentamus Group, the company has turned its expertise toward one of agriculture's most pressing infrastructure gaps: real-time resistance surveillance.
Their solution, FungiRESIST, uses long-read DNA sequencing to analyse entire fungicide target genes in a single test, a significant departure from conventional methods. "Traditional analysis methods are long and laborious," Catalina Hernandez notes. "With FungiRESIST, a single test provides a complete picture of all the resistances present in a phytopathogenic fungus across a given region."
The platform goes beyond detection. Its interactive mapping tools display where resistance mutations are appearing, how they correlate with local agricultural practices, and how they are spreading geographically. This transforms complex genetic data into actionable intelligence for treatment decisions, enabling targeted product selection, limited treatment applications, and adapted concentrations, at scales ranging from individual parcels to entire production basins.
Critically, FungiRESIST can identify not only known resistance markers but also previously unseen genetic modifications, supporting long-term evolutionary monitoring of pathogen populations.
Regulatory Tailwinds and Global Expansion
The European Union has tightened regulations on phytosanitary product use, aiming to slow resistance progression and preserve the efficacy of available treatments. Catalina Hernandez welcomes this shift: "The EU is orienting toward strategies that combine reduced chemical substances, diversified modes of action, and biocontrol solutions."
For Conidia Coniphy, this regulatory environment validates the preventive, surveillance-based approach embedded in FungiRESIST. Early detection of resistance hotspots enables intervention before problems become entrenched, preserving treatment options and reducing overall chemical dependency.
Having deployed the platform across European markets, the company is now preparing expansion into India and the United States, where comparable resistance challenges are emerging in key agricultural sectors. The company's broader diagnostic portfolio including ID-Fungi Plates for rapid fungal identification by Maldi-tof and iDetect kits for early plant disease detection, positions it as an infrastructure provider for precision agriculture systems increasingly reliant on molecular diagnostics.
Article in partnership with Conidia Coniphy a french R&D company developing diagnostic tools for industries facing fungal challenges, from agriculture to the built environment.