What to Do When You Have an Active Pathogen Outbreak

A pathogen outbreak in your cannabis operation can shut down production fast and cost a lot of money. Acting quickly is the difference between containing the issue and facing widespread crop loss. When this happens, accurate testing helps you know the right steps to take to ensure recovery and minimize crop loss. From the cannabis pathogen experts at TUMI Genomics, here are steps to immediately take once an outbreak has been discovered.

Recognize the Signs of a Pathogen Outbreak

The first step in handling an outbreak is knowing what to look for. Experienced growers already know to watch out for common symptoms, including discoloration, wilting, mold growth, and stunted or uneven growth. Catching these signs early can make a huge difference, but spotting symptoms isn’t enough; accurate testing is essential to identify the specific pathogen and determine the best course of action.

Unfortunately, pathogens such as Hop Latent Viroid (HLV) and Fusarium are often asymptomatic, especially in veg plants or in early infections. It can spread silently and only manifest during the flowering cycle, where it devastates yields, cannabinoid content, and your profit margin. This is why routine pathogen management in cannabis cultivation must include proactive testing, not just symptom recognition.

Testing and Identifying the Pathogen

Proper testing is critical because mitigating the wrong pathogen can waste time, money, and crops. Lab testing provides thorough results, but can often take days, which can allow the outbreak to spread. On-site testing is a faster option and can give you actionable information in hours, helping you respond before the problem escalates.

Currently, onsite testing is available for Hop Latent Viroid (HLVd), and fast turnaround is critical for timely pathogen management in cannabis cultivation. The best methods can process up to high throughput (48+) plants in one hour with high sensitivity and specificity, minimizing false positives and negatives. This type of testing is essential to identify infected plants, even those with low levels, so they can be removed before infection spreads, allowing growers to make informed and timely management decisions before disease spreads to the entire crop. 

For fungal pathogens, testing of inputs such as water, soil, and other materials is important, as these are common sources of infection. It is also critical to work with a lab that can identify the correct species of Fusarium and Pythium, as some species are pathogenic to cannabis while others are not. 

Immediate Containment Measures

When you notice an outbreak, immediate action is crucial. Disposing of infected plants is always the safest choice but if you cannot due to production demands for example, isolate infected plants or sections of your grow area, move them to a separate, clearly marked space to prevent the pathogen from spreading.

Implement quarantine procedures for cannabis plants by designating “clean zones” and “dirty zones” within your facility. Restrict worker movement and enforce strict entry/exit protocols in the affected areas.

Thoroughly sanitize all tools, trays, and equipment that have come into contact with affected plants using a disinfectant that is effective against the pathogen of concern. For fungal pathogens, quaternary ammonium products are among the most effective sanitizers when used according to label instructions. 

For HLVd, however, the most studied and effective option is a 10% bleach solution with a contact time of at least one minute. Tools must remain wet with disinfectant for the full contact period to ensure efficacy. Wash or change gloves and sanitize hands before handling anything else.

For fungal pathogens, maintain proper humidity and airflow  in the affected area and avoid over watering. Be especially cautious about shared runoff water between containers or trays, as this is a common way root pathogens like Fusarium and Pythium spread.

Finally, document everything you do so you have a clear record. All details of your production process and plant symptoms should be documented to help identify points of pathogen introduction/spread, environmental factors influencing plant health and areas where following up testing might be needed. 

Remediation and Mitigation Strategies

Steps for treating infected cannabis plants include:

• Remove Infected Plants or Materials: Pull out any plants showing severe symptoms and safely dispose of them. This prevents the pathogen from spreading to healthy plants and reduces overall contamination.

• Testing: Use strategic testing techniques (e.g., environmental swabbing, input testing, and mother plant testing) to locate the source of the infection. This will help your team evaluate the scope of the problem and how much remediation will be required.

• Use Safe and Effective Treatment Options: Depending on the pathogen, treatments can include biological controls, effective sanitizers, or cultural practices. For example, incorporating input testing can help prevent Fusarium and Pythium infections, while focused mother plant testing protocols are essential for stopping a systemic HLVd infection. Targeted approaches help control the outbreak without spreading the infection to your remaining plants.

• Document and Monitor: Once again, keep a detailed record of what actions you’ve taken, including which areas were treated and which plants were removed. Regularly monitor your grow space for signs of recurring infections, and adjust your management practices as needed to prevent future outbreaks.

Preventing Future Outbreaks with TUMI Genomics

Stopping one outbreak is just the start—pathogen prevention is key to keeping your operation healthy. Implement regular pathogen testing and monitoring protocols so you catch problems before they escalate. This means keeping strict sanitation and hygiene practices across your grow space, from tools and trays to hands and footwear.

Effective pathogen management in cannabis cultivation requires routine surveillance, consistent sanitation, and staff training. By creating a culture of vigilance, you reduce the risk of the next cannabis disease outbreak.

For growers looking for a complete solution, TUMI Genomics offers the TUMI360 Cannabis Pathogen Control Program. It provides 360-degree coverage of your grow, with regular environmental assessments, actionable insights, and expert guidance customized to your operation. With a detailed plan in place, you can safeguard your crop, optimize performance, and reduce the risk of costly future outbreaks.

Need more information on active pathogen testing, containment, and prevention? Contact TUMI today to learn how to stop a pathogen outbreak in a cannabis grow room with proven strategies and tools.