Project
Development of an easy, field-ready rapid test for Arsenophonus phytopathogenicus by leveraging CRISPR-Cas12a technology
Problem
Emerging Crop Disease: Candidatus Arsenophonus phytopathogenicus (hereafter A. phytopathogenicus) is an emerging bacterial threat endangering European agriculture. It was first identified in the 1990s causing a sugar beet disease known as Syndrome “Basses Richesses” (SBR), French for “low sugar syndrome” [1]. In sugar beets, SBR infections significantly reduce both yield and sugar content, root yield losses up to 25% and sugar content drops of about 5 percentage points due to Arsenophonus (in association with a co-infecting phytoplasma) were reported [2]. Such losses have severe economic impacts on growers and the sugar industry, as seen in 2020 when an unprecedented decline in sugar yields was recorded in parts of Switzerland amid SBR outbreaks [3].

Sugar beet is a cornerstone of Europe’s sugar supply, so a disease that shrinks yields and sugar concentration poses a serious food security concern. Farmers not only harvest fewer beets, but those beets also produce less sugar, undermining both profits and sugar production volumes [2].
Beets to Potatoes and Beyond: For decades Arsenophonus was limited to sugar beet fields, spread by the sap-sucking planthopper Pentastiridius leporinus that thrives on beet crops [1], [4]. Recently, however, this hidden pathogen jumped to new hosts, raising alarms across the agricultural sector. In 2023, Swiss plant health surveys detected Arsenophonus infecting potato crops in regions that had SBR in sugar beets. Molecular tests confirmed Arsenophonus as the culprit, indicating the bacterium had spread via the planthopper from nearby sick beet fields into potato fields [5]. Around the same time, German researchers also observed the planthopper transmitting Arsenophonus into potato, with infected plants displaying yellowing foliage and low-quality tubers [4].

This host expansion is alarming – it suggests other crops could potentially be at risk if they grow in proximity to the insect vector or infected fields. Potatoes are a staple food and a key European crop, so the emergence of Arsenophonus in potato threatens not only farmers’ yields but also downstream industries. In fact, certain potato varieties infected by Arsenophonus have tubers that develop brown discoloration when fried, rendering them unusable for making chips or fries [5]. This has raised serious concerns in the food processing industry, which fears significant losses if “brown fries” and rubbery potatoes become widespread [5]. In switzerland experts estimate the A. phytopathogenicus related crop losses to around 30% [6]. The specter of Arsenophonus moving from sugar beets into potatoes – and possibly other crops – represents a multi-front threat to food security and supply chains in Europe.
Today's Solution
Stealthy, Hard-to-Detect Invader: One of the biggest challenges with A. phytopathogenicus is that it is practically invisible to conventional detection methods. The bacterium lives deep within the plant’s phloem (sap vessels) and often causes only subtle, nonspecific symptoms. In sugar beets, SBR can resemble nutrient deficiencies or viral yellows, plants may develop mild leaf yellowing or slightly deformed new leaves, changes easily overlooked until the damage (like sugar loss) is already done [2], [4]. In potatoes, early infection might not be obvious until tubers are harvested and found to be of poor quality.
This pathogen’s “stealth mode” means that fields can be infected without farmers realizing, silently undermining crop productivity. Worse, A. phytopathogenicus cannot be cultured on lab media like many common bacteria [7]. It is a “Candidatus” organism, a microbe known only by its DNA signature. Since scientists cannot grow it in Petri dishes, traditional diagnostic tests fail [7]. Instead, specialized molecular tools like PCR or DNA amplification are required to detect its presence. Techniques that are expensive, time-consuming, or not readily available in the field [8].

This combination of hidden infection and non-cultivability makes A. phytopathogenicus extremely hard to monitor and contain. By the time a problem is recognized (for example, when sugar content is inexplicably low at harvest, or a batch of potatoes fries poorly), the bacterium may have already spread extensively. These factors create a diagnostic blind spot for farmers and agronomists, allowing ARSEPH to slip through standard crop health inspections undetected.
Challenges in Control and Plant Protection: Managing the A. phytopathogenicus threat has proven very difficult, and currently there is no cure for infected plants. Once inside the phloem, the bacteria cannot be targeted with any chemical treatment available to farmers. Thus, efforts focus on prevention and slowing the spread, but even these measures are limited in effectiveness:
- Vector Control (Insecticides): The only direct way to prevent A. phytopathogenicus from spreading is to control its insect vector, P. leporinus. Unfortunately, insecticide treatments against this planthopper are often less than 50% effective [9]. The insect’s life cycle, involving nymphs hiding on roots and adults flying in from surrounding crops, makes it hard to reach with pesticides, and overuse of insecticides raises environmental concerns. This means chemical control alone cannot stop SBR transmission in the field [9].
- Crop Rotation Strategies: Adjusting farming practices offers some relief. P. leporinus typically lays eggs on sugar beet and overwinters in fields with winter wheat. Researchers found that replacing winter wheat with alternative crops (like winter rye) in the rotation can disrupt the pest’s life cycle and reduce planthopper infestations by roughly 30% [9]. This strategy can slow the spread of A. phytopathogenicus to new sugar beet fields. However, rotation changes are not always feasible for every farm, and they only partially mitigate the risk (a 30% reduction still leaves significant vector presence) [9].
- Breeding for Resistance/Tolerance: In the long term, developing sugar beet varieties that can withstand infection is a promising approach. Trials have identified certain beet genotypes that show tolerance to SBR. Infected plants of those varieties exhibit less yellowing and suffer less sugar loss [10]. Seed companies are now working to introduce such tolerant cultivars, which could help maintain yields even in the presence of A. phytopathogenicus. However, breeding and deploying resistant crops takes time, and current commercial varieties still remain largely vulnerable [9].
Each of these measures only partially address the problem. Insect control is imperfect, crop rotation can only slow the pathogen’s advance, and resistant varieties are still in development. Consequently, European farmers have been left struggling to contain an outbreak that they often cannot easily see or confirm until it’s too late.
This high-risk scenario highlights the urgent need for better diagnostic tools and rapid field tests to catch A. phytopathogenicus infections early and enable prompt action [10]. Without innovative solutions, this silent bacterial invader will continue to spread under the radar, endangering crop yields, food processing industries, and ultimately the food security of millions.
Our Idea
As SwissCas, our goal is to develop a rapid, easy-to-use testing device based on CRISPR-Cas12a technology. With this tool, we aim to give farmers an accessible alternative to the current qPCR-based diagnostic methods, which require specialized equipment and laboratories. Instead of relying on centralized testing, farmers would be able to screen their own crops directly in the field and obtain quick results.
This is especially important because, at present, there is no treatment for crops already infected with Arsenophonus phytopathogenicus. The only available strategies are preventive: adjusting crop rotations to avoid host plants that sustain the bacterium, or attempting to control the insect vector (Pentastiridius leporinus) with insecticides. Both approaches offer only partial protection and require timely information on whether and where the pathogen is present.
By enabling farmers to monitor their fields in real time, our Cas12a-based test can provide the epidemiological insights needed for informed decisions. With accurate, on-site detection, farmers can better plan crop rotations, implement targeted pest management, and ultimately reduce the risk of unnoticed pathogen spread. We see our test not only as a diagnostic tool, but also as a strategic instrument to strengthen plant protection, safeguard yields, and protect European food security against this emerging threat.