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Hop Latent Viroid (HLVd) & Pathogen Diagnostics: A Comprehensive Overview

By Tassa Saldi, Ph.D.
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Hop latent viroid (HLVd) has gained attention as the molecular cause of “dudding disease” and is causing significant economic losses in the cannabis industry.1,2 Estimates indicate that upwards of 4 billion dollars of market value are lost each year to this pathogen alone.3 The impact of HLVd on cannabis plants necessitates the development and implementation of effective pathogen diagnostics to mitigate its spread and minimize crop damage. With collaborative research efforts, we can gain valuable insights into the characteristics, spread, symptoms and preventive measures associated with HLVd in the cannabis industry.

Viroids: A Brief Overview

Figure 1: Virus vs Viroid

Viroids are unique infectious agents composed solely of genetic material, distinct from viruses. Unlike viruses, viroids lack a protective protein layer and solely rely on the host plant for replication and spread. Their stability and ability to persist in various environments make viroids a formidable threat to plant health.

Hop Latent Viroid: Origin and Global Spread

Hop latent viroid was initially identified in hop plants in 19884 and was found to be largely asymptomatic in this crop. Consequently, HLVd has spread worldwide, mostly unchecked by the hops industry. This pathogen has been identified on most continents and in some fields more than 90% of hops plants are infected.5 Hop latent viroid very likely jumped from hops into cannabis, due to similar genetics. The timing and mechanism of cross-species transmission to cannabis remains unknown, but the prevalence of HLVd suggests this viroid has been circulating within cannabis for an extended period. Data collected at TUMI Genomics indicates that HLVd is present in all states in the United States where cannabis is legal as well internationally including; Canada, the United Kingdom, France, the Netherlands, Thailand, Austria and Switzerland.

Symptoms and Impacts on Cannabis Plants 

Figure 2: HLVd Symptoms

HLVd exhibits a wide range of symptoms, which can vary from severe to subtle, affecting the growth, leaf development, flower quality and overall vitality of cannabis plants. Understanding these symptoms is crucial for timely diagnosis and appropriate disease management strategies.  However, HLVd can also present asymptomatically, especially in vegetative plants. The only way to determine if your plants are infected is by routine molecular testing.

Modes of Transmission

Mechanical Transmission: HLVd primarily spreads mechanically through contact with infected sap during activities like trimming and handling. Additionally, transmission through contaminated water and the potential role of insects, fungal pathogens and seeds in spreading HLVd have also been observed.

Seed Transmission: Although no published studies exist in cannabis describing the frequency of seed transmission, HLVd does transmit through seeds in hop plants at a rate of around 8%.7 Preliminary studies performed by TUMI Genomics in collaboration with EZ-genetics suggest cannabis seed transmission does occur at variable rates depending on strain and level of infection of the parent plants.

Water Transmission: It has also been observed that viroids are in high concentration in the roots8 and can move from the root into runoff water.9 Plants sharing a common water source with infected plants, such as recirculating water systems or flood and drain procedures, are at risk for transmission of the viroid.

Insect and Other Vector Transmission: The jury is still out as to whether or not insects can transmit HLVd. However, multiple viroids are transmitted via insects, so it is likely that HLVd insect transmission occurs. Recent studies also indicate that fungal pathogens, like Fusarium, can transmit viroid infections.6 While pathogenic fungus is a major concern for cannabis growers in its own right, limiting the prevalence and spread of fungal pathogens in your facility could help limit hop latent viroid transmission as well.

Therefore, implementing proper sanitation practices and limiting pest access can help minimize transmission risks.

Preventive Measures

Prevention plays a vital role in safeguarding cannabis crops against HLVd. The STOP program, developed by TUMI Genomics, offers a comprehensive approach that includes maintaining a Sterile environment, Testing mother plants regularly, Organizing the facility to minimize pathogen spread, and Protecting the facility’s borders from introduction of infected plant material, insects and contaminated water. More details on these preventative measures can be found here.

Pathogen Diagnostics

Protecting your plants from hop latent viroid requires accurate identification and removal of infected plants before the infection spreads to other plants. To accomplish this, several critical factors should be considered:

Type of test: HLVd and all viroids can only be detected by a molecular test (a test that detects the presence of DNA/RNA). Among common molecular tests, PCR is generally the most sensitive and accurate method. PCR can provide both a diagnosis and an approximate viroid level, allowing informed management decisions. Other types of molecular tests, such as LAMP and RPA, can formally be as sensitive as PCR, but the classic versions of these assays often suffer from false positive/negative results, reducing accuracy.

Figure 3: HLVd Levels and Distribution

Tissue type: An important consideration for HLVd detection is the plant tissue selected for testing, especially when identifying low-level or early infections when HLVd is not yet systemic. Studies completed by TUMI Genomics and others show root tissue contains the highest levels of HLVd and is the most reliable tissue for detection of viroid infection. While upper root tissue appears to contain the highest levels of viroid, roots from anywhere in the root ball are predictive of infection. Samples taken from the leaves/foliage tend to have lower levels of viroid and may produce false negative results.

Figure 4: Testing Schedule

Testing frequency: Routine pathogen testing is standard practice in general agriculture and is critical to maintain a healthy cannabis crop. Testing of mother plants every 4-6 weeks for economically critical pathogens (such as HLVd) will help ensure a successful run and a high-quality product.

Disinfection Methods

Studies have shown that viroids can remain infectious for longer than 24 hours on most common surfaces11 and 7 weeks in water.10 Making effective disinfection methods essential to limit the spread of HLVd. While common disinfectants like alcohol and hydrogen peroxide are ineffective against viroids, a 10% bleach solution has shown efficacy in destroying HLVd. Proper tool sterilization practices, such as soaking tools in bleach for 60 seconds, are crucial to prevent transmission during plant handling.

Figure 5: Bleach Dilution

Hop latent viroid poses a significant threat to the cannabis industry, leading to substantial economic losses. Timely and accurate pathogen diagnostics, along with stringent preventive measures, are essential for minimizing the impact of HLVd. Regular testing, proper disinfection protocols and adherence to pathogen prevention programs can help ensure the health and vitality of cannabis crops in the face of this global pandemic.


References

  1. Bektas, A., et al. “Occurrence of Hop Latent Viroid in Cannabis Sativa with Symptoms of Cannabis Stunting Disease in California.” APS Journals, 21 Aug. 2019, doi.org/10.1094/PDIS-03-19-0459-PDN.
  2. Warren, J.G., et al. “Occurrence of Hop Latent Viroid Causing Disease in Cannabis Sativa in California.” APS Journals, 21 Aug. 2019, doi.org/10.1094/PDIS-03-19-0530-PDN.
  3. Cooper, Benjie. “Hop Latent Viroid Causes $4 Billion Cannabis Industry Loss – Candid Chronicle.” Candid Chronicle – Truthful, Straightforward, Blunt Cannabis News, 16 Aug. 2021, candidchronicle.com/hop-latent-viroid-causes-4-billion-cannabis-industry-loss/.
  4. Puchta H, Ramm K, Sänger HL. The molecular structure of hop latent viroid (HLV), a new viroid occurring worldwide in hops. Nucleic Acids Res. 1988 May 25;16(10):4197-216. doi: 10.1093/nar/16.10.4197. PMID: 2454454; PMCID: PMC336624.
  5. Faggioli, Franceso, et al. “Geographical Distribution of Viroids in Europe.” Viroids and Satellites, 31 July 2017, www.sciencedirect.com/science/article/abs/pii/B9780128014981000449#bib47.
  6. Wei S, Bian R, Andika IB, Niu E, Liu Q, Kondo H, Yang L, Zhou H, Pang T, Lian Z, Liu X, Wu Y, Sun L. Symptomatic plant viroid infections in phytopathogenic fungi. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):13042-13050. doi: 10.1073/pnas.1900762116. Epub 2019 Jun 10. PMID: 31182602; PMCID: PMC6600922.
  7. Singh RP. The discovery and eradication of potato spindle tuber viroid in Canada. Virus disease. 2014 Dec;25(4):415-24. doi: 10.1007/s13337-014-0225-9. Epub 2014 Dec 2. PMID: 25674616; PMCID: PMC4262315.
  8. Jama, Aisha, et al. TUMI Genomics, Fort Collins, CO, 2022, Hop Latent Viroid Levels and Distribution in Cannabis Plant Tissue.
  9. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.
  10. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.
  11. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.

Building An Integrated Pest Management Plan – Part 4

By Phil Gibson
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This is the fourth in a series of articles designed to introduce an integrated pest management framework for cannabis cultivation facilities. To see Part One, an overview of the plan and pest identification, click here. For Part Two, on pest monitoring and record keeping, click here. For Part Three, on preventative measures, click here. Part Five comes out next week on how to build a framework for control actions and how to monitor them. More to come!

This is Part 4: Direct Control Options

Even when the best methods are implemented and precautions are taken to protect your infrastructure, determined pests can penetrate your perimeter. Before you see crawling, hopping or flying insects, or sickly-looking plants, be sure to implement your physical protection (positive pressure airflow sealed facilities) and personal hygiene methods (shoe baths, sticky mats, & air shower entrances) to protect your crops. Equip your employees with personal protection equipment (PPE) proper gloves, masks and clothing as discussed in our last chapter, preventative measures.

Figure 1: Fungus Gnats Unleashed In A Grow Room

When things do break-out beyond your acceptable thresholds, Direct Control Options include non-chemical microbial biofungicides, microbial bioinsecticides and direct chemical control options. Lots of big scary words there, all of which are toxic even under safe application methods and when used at recommended concentrations levels. This means training in their use and protective clothing is required. Careful application of these control options is necessary so you exterminate your pests and not your people! This seems obvious, but do not just “wing it.”

These chemical elements can be applied in diluted concentration levels, manual wipe-down application, concentrated flush frequencies, or root drench applications, foliar spray mist applications, HVAC aerial diffusions and aerial knock-down sprays. You may even choose to remove badly infected plants and destroy them completely.

Use experts when you are planning for these tools. All of these methods require handling and safety precautions. Proper breathing filters, eye & skin protection, as well as disposable gowns/hazmat suits should be used when applications are performed and until the applications have dissipated to safe levels. Be careful not to co-mingle removed plant materials. Gloves become transport and infection spreaders after use.

Please also be sure to review your harvest testing requirements and what treatments are safe for your consumers and within legal limits. No one wants to have their harvest rejected due to pesticide contamination.

Figure 2: Municipal Water Treatment, RAIR Cannabis, Michigan

Clean-up after application may be required depending on the bioinsecticide or chemical that is used. Again, always ensure the safety of your employees and take precautions.

Start the application of your control options with your site map, room assignments and scout monitoring teams. Where does air flow into and within the facility? When your scouting team count logs go beyond your acceptable thresholds, here are some options for you.

Let’s begin with cleaning your irrigation and nutrient water sources. For a walk-through tutorial for incoming water treatment, humidity recovery and nutrient water recycling, please review the video tour of Water Treatment at RAIR Cannabis to see how an expert has done it.

From the IPM Planning Guide standpoint, peroxide and acid sterilizers can be used to clear irrigation water, for surface wipe-downs or as direct plant applications. We will cover those first. Caustic sterilizers require PPE for cleaning. Forgive my image here, we were just using water.

Concentrated Cleaners for Surfaces & Irrigation Sources (Hydrogen Peroxide & Sanitizers)

Plant interacting interfaces, i.e. surfaces, benches, walls, floors, trays, utensils, clippers, etc. should be sterilized with every use. Methods can include direct wipe-down or scrub, concentrated or diluted sprays or room vaporizers. A good example of hydrogen peroxide (H2O2) liquid would be a food grade sanitizer with 3-35% H2O2 content. Use acceptable diluted versions of these cleaners as appropriate.

Figure 3: Cleaning & Scrubbing, Where’s the PPE?

A commercial example would be Zerotol 2.0 with 27% H2O2 & their proprietary acid mix. Alternatively, you can use direct hydrogen peroxide generators from commercial sources to generate your H2O2 at various concentrations. More detailed examples are included in the complete Integrated Pest Management Guide (link at the end of this article). Establish your procedures for sterilizing your rooms and tools before you introduce plants, and describe what is to be done after every harvest and room turn. Track the cleaning materials used for your operational records. You will find this useful to track operational cost over time.

Sanitizing Acids for Surfaces & Irrigation Sources

Similar to hydrogen peroxide, hypochlorous acid (HOCl) comes in many commercial forms and can also be generated onsite using purchased generators. Commercial mix examples are UC Roots, Watermax and Athena Cleanse. They come in 0.028% to 15% concentrations. Self-generators range in output from highly precise 0.01% to 1% concentrations with more examples in the guide.

Treatment Tools

OK, so enough on cleaning preparation. Here are some tools that can be used to fight back against a pest intrusion:

Non-Chemical Microbial Biofungicide for Pathogens in Soil or Fertigation Water

Microbial fungicides are available to clear nutrient irrigation systems by minimizing pathogens and improving plant resistance to infections. Some fungicide versions target root pathogens by attacking the diseases directly. Others control or suppress common water carried challenges like pythium, rhizoctonia, phytophthora, fusarium and others. Brand names include Botanicare, Bonide, BioWorks, Actinovate, Mycostop and many more. Details covered in the guide.

Non-Chemical Microbial Bioinsecticides for Larval Stages

These biological tools attack the organisms or insects at a physical or mechanical way by breaking down the pest’s nervous system, biochemistry, or structural integrity (exoskeletons, etc.). These are engineered or living organisms (bugs to attack bugs) that are developed as targeted attacks for specific pests. Brand names are BioCeres, Botanigard, Venerate, Bio Solutions and others.

Minimal Risk Chemical Pesticides for Airborne Critters

Figure 3: Example Fungus Gnat Infestation – Royal Queen Seeds blog

Regularly approved for used in most locales, essential oils, natural acids (like citric acid) and insecticidal soap are commonly available in every hydroponic store. These work very well as safe spray “knock-down” insecticides for crawling or flying pests. Commercial examples use a proprietary mix of various oils, citric acids or isopropyl alcohol to do their task (examples in guide). Insecticidal soaps and fungicides for surface cleaning perform a similar purpose and typically use potassium salts or fatty acid mixtures.

Biochemical Pesticides

These tools are used to inhibit insect or fungal growth to acceptable levels. The multifaceted and commonly used neem oil comes in many commercial versions and is a naturally occurring pesticide extracted from the leaves and seeds of the neem tree. Example brand names are Bonide, Monterey, Triact and others. They range in concentrations from 0.9% to 70% concentrations. These oils suffocate living organisms or eliminate moisture to kill insects, spores or fungus at their initiation and throughout their lifespan.

Another option here are Azadirachtins. These act as insect growth regulators and disrupt the bugs natural evolution. Brand names are AzaGuard, AzaMax and others in the guide.

In summary, this week

We summarized some of the many pest control options available for water treatment, soil borne, intermediate or flying pests. We also covered various concentrations for these pesticide and sterilizer options. If you are not familiar with dilution ratios, %, PPM terms and how to apply the correct level of pesticide, you may find our plant science test kitchen blog on this topic of use here.

Chemical access and use should be restricted to employees familiar with their authorized application. PPE is very important to protect any employee that will come in contact with materials, liquids or vapors for chemical resources (gloves, boots, respirators, Tyvek (or equivalent protective wear) suits and eye protection or goggles.

For more detail on each of these treatments, you can see examples for your integrated pest management procedures in our complete white paper for Integrated Pest Management Recommendations, download the document here.

In our next chapter, Pest Population Control Actions, we will review control thresholds and example plans for a range of problems from biofilm build up to white flies and more. Our final chapter after that will suggest an emergency response framework and how to address pest outbreaks. See you next week.

Building An Integrated Pest Management Plan – Part 1

By Phil Gibson
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This is the first part of a series of articles designed to introduce an integrated pest management framework for cannabis cultivation facilities. Part one details an overview of the plan as well as pest identification. Part two comes out next week and will delve into the world of pest monitoring and record keeping. Stay tuned for more!

Figure 1: Integrated Pest Management Cycle

Background

Integrated Pest Management (IPM) is a philosophy of pest prevention and control that integrates cultural, mechanical, physical and chemical practices to control pest populations within an acceptable degree of economic tolerance.

IPM encourages growers to take a step-wise approach to determine the most appropriate means necessary for avoiding pest-related economic injury through careful consideration of all available pest control practices.

When practicing IPM, less invasive non-chemical practices are given priority, until escalation necessitates otherwise.

This is Part 1: Pest Identification & Monitoring/Communications

Personal experience in a facility is a great place to start. Review your history and identify a list of pests that you have experienced in this or previous grows. Point out which pests currently exist where they were or are currently and possible sources of the contamination/infestation.

Figure 2: Healthy Aeroponic Mother Stock

Map out your facility with clear entry/exits, plumbing & drainage and air flow access to visually see and understand potential access points for crawling, flying or airborne pests.

From your nursery mother room to cloning and vegetation areas, what are the transfer methods as you move from one area to another. Are pests present in these areas? Where could they have come from? Oftentimes, a cultivator may not have the space for their own mother and cuttings/cloning space. In these cases, where did the outsourced clones come from? What are the IPM controls in place for these genetic sources? Are they carriers of the challenges transferred to your own facility? It is important to identify the possible source of pest potentials

Does your flower room have white flies or fungus gnats? Locating these and identifying the likely source is a good place to start if you have an ongoing infestation.

Figure 3: Example Aeroponic Facility Layout For IPM Planning

Powdery mildew is a routine challenge if air into your facility is not filtered and sterilized to eliminate these spores.

What is the Source of Your Irrigation/Fertigation Water?

Water is a crucial element for high-value indoor farms such as those that grow cannabis. However, water can also be a source of disease-causing microorganisms that can negatively impact the growth and yield of crops. Monitoring, filtering and sterilizing the biological contents of water is therefore crucial in ensuring the health and quality of high-value crops.

Unfiltered water can contain a range of pathogens such as bacteria, viruses, fungi and parasites that can cause root, stem and bud rot. These diseases can cause significant losses in crop yield and quality, which can be devastating for indoor farmers growing high-value crops.

Figure 4: Precision Aeroponics at FarmaGrowers GMP Facility, South Africa

Monitoring the quality of water that is brought into the indoor farm is the first step in ensuring that the water is free from harmful pathogens. This involves regular testing of the incoming water for parameters such as pH, dissolved oxygen, TDS, nutrient content and microbial load. This allows cultivators to identify aspects of the incoming water they need to address before the water is provided to their crops to prevent potential problems.

Is your plumbing building biofilm that is feeding into your irrigation lines? Obviously, there are many potential sources when you go through an inventory of the risks for your facility. From that initial step, you will build your management team and label who should be contacted when a pest is found. Do you have an IPM specialist or is this a resource that needs to be contracted to address an infection?

Building this communications tree is your first step to fewer pest issues and higher yields and potency.

For the complete white paper on Integrated Pest Management Recommendations, download the document here. Part two comes out next week and will delve into the world of pest monitoring and record keeping. Stay tuned for more!

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3 Benefits of Conducting Genetic Tests on Your Plants

By Angel Fernandez
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durnagofacility

Many growers may wonder why it’s important to get their plants genetically tested, but the truth is that genetic testing can make growing a lot easier. Genetic analysis in plants can give a wide range of results that can help scientists solve everyday problems in plant cultivation, such as detecting diseases and identifying important traits in plant species.

Currently, three of the most important benefits that genetic testing can give growers are the ability to detect diseases, identify the gender of their plants and control the quality of their crops.

Pathogen detection

Pathogen infections can be difficult to detect and by the time symptoms are obvious, it may be too late and the rest of the crop is already contaminated. This is why DNA tests are a valuable tool for the early detection of diseases in plants. Even though plants reproduce through cloning, it’s crucial to make sure the mother plant is healthy before proceeding, as 100% of the genetic material will be transferred to the clone, including any diseases the mother plant may have, such as a virus.

There are a few ways to detect pathogens in plants, including detection and symptomatology, serological techniques for viruses and microbiological techniques for fungi and bacteria. However, another effective method is detection tests using genetic material, also known as molecular methods. These tests involve screening the plant’s genetic material for any alterations, such as the presence of the pathogen’s genetic material. These tests are particularly useful as they provide accurate results when at least part of the pathogen’s genome sequence is known. This is important as many of these genomes have yet to be fully studied and there may be new unknown variants.

Tobacco Mosaic Virus symptoms can include tip curling, blotching of leaf mosaic patterning, and stunting

The reliability and effectiveness of genetic and molecular tests are due to the use of DNA as the starting material for pathogen detection. DNA is a stable molecule that can withstand adverse conditions, such as high temperatures or low humidity. Additionally, this technique can still be effective even when the samples used are very damaged or necrotic. Due to these qualities, genetic testing is considered one of the best methods for pathogen detection.

In summary, genetic testing is the most effective technique for pathogen detection as it is highly specific, requires a small sample and provides accurate results in a short period of time.

Plant gender detection

In the case of the cannabis plant, it is naturally diploid and dioecious, meaning that it has separate male and female reproductive structures, and each one contributes a chromosome during reproduction. However, there may be mutations that result in hermaphrodite plants, which have both male and female reproductive structures.

Growers who propagate their crops through seeds must wait several weeks to identify the sex of their plants, as their dioecious nature makes it difficult to recognize the plant’s sex in the early stages of growth. This can be time-consuming and resource-intensive. However, thanks to genetic testing, it is possible to determine the sex of a plant long before it reaches the flowering stage.

The sex organs on a Cannabis plant identified.

The determination of the gender of a dioecious plant is influenced by a sex chromosome system. Male plants have an XY sex chromosome system, known as heterogametic, while female plants have the XX sex chromosome system, known as homogametic.

To identify the sex of a plant through genetic studies, DNA or RNA-based molecular markers are used with a tissue sample. These markers typically look for the male trait “Y” in the plant, as the trait “X” is present in both male and female plants. In this way, the presence of the Y chromosome can be used to confirm the plant is male, and its absence can be used to confirm that it is female.

Crop quality control

The same species can often present one or more varieties, and although they may have physical features that distinguish them, it is not always possible to identify them with the naked eye. Beyond physical characteristics, genetic traits can have considerable differences.

Molecular identification is a very accurate tool for identifying varieties

Different varieties of cannabis have been widely cultivated and crossbred, making it possible for plants to have very similar physical traits, making it difficult to identify the variety being cultivated. This is why molecular identification is a very accurate tool for identifying varieties in cases where there is uncertainty about their identity.

Additionally, some plants can produce lower or higher amounts of cannabinoids due to their genetic nature or small mutations that occurred during growth. This is how there are plants with the advantage of having genes that code for high production of THC or CBD. These outstanding traits can be detected through the selection of characteristics using analysis of molecular markers that indicate the presence of these genes in the plant, or that detect the genes responsible for synthesizing these substances and determine their respective quality.

These procedures are performed using a tissue sample from the plant and using DNA as a starting material for testing, which provides information on the genetic traits of interest and validates their function.

The 3-Legged Stool of Successful Grow Operations: Climate, Cultivation & Genetics – Part 4

By Phil Gibson
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This is Part 4 in The 3-Legged Stool of Successful Grow Operations series. Click here to see Part 1, here to see Part 2, and here to see Part 3. Stay tuned for Part 5, coming next week.

Integrated Pest Management (IPM)

Aeroponic & hydroponic systems can operate with little to no soil or media. This eliminates the pest vectors that coco-coir, peat moss/perlite and organic media can harbor as part of their healthy biome approach. Liquid nutrient systems come at the nutrient approach from a different direction. Pure nutrient salts (nitrogen, potassium, magnesium and trace metals) are provided to the plant roots in a liquid carrier form. This sounds ideal for integrated pest management programs, but cultivators have to be aware of water and airborne pathogens that can disrupt operations. I will summarize some aspects to consider in today’s summary.

The elimination of soil media intrinsically helps a pest management program as it reduces the labor required to maintain a grow and the number of times the grow room doors are opened. Join that with effective automation with sensors and software, and you have immediate improvements in pest access. Sounds perfect, but we still have staff to maintain a facility and people become the number one source of contamination in a grow operation.

Figure 1: Example of Pythium Infected & Healthy Roots

Insects do damage directly to plants as they grow and procreate in a grow room. They also carry other pathogens that infect your plants. For example, root aphids, a very common problem, are a known carrier of the root pathogen, Pythium.

Procedures

One of the most common ways for pests to access your sealed, sterile, perfectly managed facilities are in the root stock of outsourced clones. If you must start your grow cycles with externally sourced clones, it is strongly recommended that you quarantine those clones to make sure that they do not import pest production facilities into your operation. Your operation management procedures must be complete. If you take cuttings from an internal nursery of mother plants, any pathogens present in your mother room will migrate through cuttings into your clones, supply lines, and subsequently, flower rooms.

Figure 2: Healthy Mothers & Clones, Onyx Agronomics

Start your gating process with questioning your employees and visitors. Do they grow at home or have they been to another grow operation in the last week? In the last day? You may be surprised by how many people that gain access to your grow will answer these questions in the affirmative.

Developing standard operating procedures (SOPs) that are followed by every employee and every visitor will significantly reduce your pest access and infection rates, and hence, increase your healthy harvests and increase your profitability. Procedures should include clothing, quarantining new genetics and cleaning procedures, such as baking or irradiating rooms to guarantee you begin with a sterile facility. This is covered more in the complete white paper.

Engineering Controls

Figure 3: Access Control: Air Shower, FarmaGrowers

Technology is a wonderful thing but no replacement for regimented procedures. Considered a best practice, professional air showers, that bar access to internal facilities, provide an aggressive barrier for physical pests. These high velocity fan systems and exhaust methods blow off insects, pollen and debris before they proceed into your facility. From that access port into your grow space, positive air flow pressure should increase from the grow rooms, to the hallways, to the outside of your grow spaces. This positive airflow will always be pushing insects and airborne material out of your grow space and away from your plants.

Maintaining Oxidation Reduction Potential (ORP)

ORP is a relative measurement of water health. Perfect water is clear of all material, both inert and with life. Reverse osmosis (RO) is a standard way to clear water but it is not sufficient in removing microscopic biological organisms. UV and chemical methods are needed in addition to RO to clear water completely.

ORP is an electronic measurement in millivolts (mV) that represents the ability of a chemical substance to oxidize another substance. ORP meters are a developing area and when using a meter, it is important to track the change in ORP values rather than the absolute number. This is due to various methods that the different meters use to calculate the ORP values. More on this in the white paper.

Oxidizers

Figure 4: AEssenseGrows Aeroponic Nozzles

There are two significant ways to adjust the ORP of a fertilizer/irrigation (fertigation) solution. The first is by adding oxidizers. Examples are chemical oxidizers like hydrogen peroxide (H2O2), hypochlorous acid (HOCl), ozone (O3) and chlorine dioxide (ClO2). Adding these to a fertigation solution increases the ORP of the fertigation solution by oxidizing materials and organic matter. The key is to kill off the bad things and not affect the growth of plants. Again here, the absolute ORP metric is not the deciding factor in the health of a solution and the methods by which each chemical reaction occurs for each of these chemicals are different. This is compounded by the fact that different ORP meters will show different readings for the same solution.

Another wonderful thing about automation and aeroponic and hydroponic dosing systems is that they can automatically maintain oxidizing rates and our white papers explain the methods executed by today’s automation systems.

Water Chilling

Another way to adjust ORP is to reduce the water temperature of the reservoirs. Maintaining water temperature below the overall temperature of your grow rooms is imperative for minimal biological deposition and nutrient system health. Water chillers use a heat exchanger process to export heat from liquid nutrient dosing reservoirs and maintain desired temperatures.

The benefit of managing ORP in aeroponic and hydroponic grow systems is highly accelerated growth. This is enhanced in aeroponics due to the effectively infinite oxygen exchanging gases at the surface of the plant roots. Nutrient droplets are sprayed or vaporized in parallel and provided to these root surfaces. Maximizing the timing and the best mineral nutrients to the root combustion is the art of grow recipe development. Great recipes drive superior yields and when combined with superior genetics and solid environmental controls, these plants will deliver spectacular profits to a grow operation.

Another Hero Award

Before closing this chapter, we have many cultivators that are producing stellar results with their operational and IPM procedures, so it is hard to choose just one leader. That said, our hats are off to RAIR Systems again and their director of cultivation, Ashley Hubbard. She and her team are determined to be successful and drive pests out of their operations with positive “little critters” and the best water treatment and management that we have seen. You are welcome to view the 7-episode walkthrough of the RAIR facility and their procedures here.

To download the complete guide and get to the beef quickly, please request the complete white paper Top Quality Cultivation Facilities here.

Stay tuned for Part 5 coming next week where we’ll discuss Genetics.

Soapbox

How Do You Know You’re Right? qPCR vs. Plating

By Dr. Sherman Hom
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Cannabis testing to detect microbial contamination is complicated. It may not be rocket science, but it is life science, which means it’s a moving target, or at least, it should be, as we acquire more and more information about how the world we live in works. We are lucky to be able to carry out that examination in ever increasing detail. For instance, the science of genomics1 was born over 80 years ago, and just twenty years ago, genetics was still a black box. We’ve made tremendous progress since those early days, but we still have a long way to go, to be sure.

Much of that progress is due to our ability to build more accurate tools, a technological ladder, if you will, that raises our awareness, expertise, and knowledge to new levels. When a new process or technology appears, we compare it against accepted practice to create a new paradigm and make the necessary adjustments. But people have to be willing to change. In the cannabis industry, rapid change is a constant, first because that is the nature of a nascent industry, and second because in the absence of some universal and unimpeachable standard, it’s difficult to know who’s right. Especially when the old, reliable reference method (i.e. plating, which is basically growing microorganisms on the surface of a nutritional medium) is deeply flawed in its application to cannabis testing vs. molecular methods (i.e., quantitative polymerase chain reaction, or qPCR for short).

Dr. Sherman Hom, Director of Regulatory Affairs at Medicinal Genomics

Plating systems have been used faithfully for close to 130 years in the food industry, and has performed reasonably well.2 But cannabis isn’t food and can’t be tested as if it were. In fact, plating methods have a host of major disadvantages that only show up when they’re used to detect cannabis pathogens. They are, in no particular order:

  1. A single plating system can’t enumerate a group of microorganisms and/or detect specific bacterial and fungal pathogens. This is further complicated by the fact that better than 98% of the microbes in the world do not form colonies.3 And there is no ONE UNIVERSAL bacterial or fungal SELECTIVE agar plate that will allow the growth of all bacteria or all fungal strains. For example, the 5 genus species of fungal strains implicated in powderly mildew DO NOT plate at all.
  2. Cannabinoids, which can represent 10-30% of a cannabis flower’s weight, have been shown to have antibacterial activity.4 Antibiotics inhibit the growth of bacteria and in some cases kill it altogether. Salmonella species & shiga toxin producing coli (STEC) bacteria, in particular, are very sensitive to antibiotics, which leads to either a false negative result or lower total counts on plates vs. qPCR methods.
  3. Plating methods cannot detect bacterial and fungal endophytes that live a part or all of their life cycle inside a cannabis plant.5,6 Examples of endophytes are the Aspergillus pathogens (A. flavus, A. fumigatus, A. niger, and A. terreus). Methods to break open the plant cells to access these endophytes to prepare them for plating methods also lyse these microbial cells, thereby killing endophytic cells in the process. That’s why these endophytes will never form colonies, which leads to either false negative results or lower total counts on plates vs. qPCR methods.
  4. Selective plating media for molds, such as Dichloran Rose-Bengal Chloramphenicol (DRBC) actually reduces mold growth—especially Aspergillus—by as much as 5-fold.This delivers false negative results for this dangerous human pathogen. In other words, although the DRBC medium is typically used to reduce bacteria; it comes at the cost of missing 5-fold more yeast and molds than Potato Dextrose Agar (PDA) + Chloramphenicol or molecular methods. These observations were derived from study results of the AOAC emergency response validation.7
  5. Finally, we’ve recently identified four bacterial species, which are human pathogens associated with cannabis that do not grow at the plating system incubation temperature typically used.8 They are Aeromonas hydrophila, Pantoea agglomerans, Yersinia enterocolitica, and Rahnella aquatilis. This lowers total counts on plates qPCR methods.

So why is plating still so popular? Better yet, why is it still the recommended method for many state regulators? Beats me. But I can hazard a couple of guesses.

A yeast and mold plate test

First, research on cannabis has been restricted for the better part of the last 70 years, and it’s impossible to construct a body of scientific knowledge by keeping everyone in the dark. Ten years ago, as one of the first government-employed scientists to study cannabis, I was tapped to start the first cannabis testing lab at the New Jersey Dept. of Health and we had to build it from ground zero. Nobody knew anything about cannabis then.

Second, because of a shortage of cannabis-trained experts, members of many regulatory bodies come from the food industry—where they’ve used plating almost exclusively. So, when it comes time to draft cannabis microbial testing regulations, plating is the default method. After all, it worked for them before and they’re comfortable with recommending it for their state’s cannabis regulations.

Finally, there’s a certain amount of discomfort in not being right. Going into this completely new area—remember, the legal cannabis industry didn’t even exist 10 years ago—we human beings like to have a little certainty to fall back on. The trouble is, falling back on what we did before stifles badly needed progress. This is a case where, if you’re comfortable with your old methods and you’re sure of your results, you’re probably wrong.

So let’s accept the fact that we’re all in this uncharted territory together. We don’t yet know everything about cannabis we need to know, but we do know some things, and we already have some pretty good tools, based on real science, that happen to work really well. Let’s use them to help light our way.


References

  1. J. Weissenbach. The rise of genomics. Comptes Rendu Biologies, 339 (7-8), 231-239 (2016).
  2. R. Koch. 1882. Die Aetiologie der Tuberculose.  Berliner Klinische Wochenschrift, 19, 221-230 (1882)
  3. W. Wade. Unculturable bacteria—the uncharacterized organisms that cause oral infections. Journal of the Royal Society of Medicine, 95(2), 91-93 (2002).
  4. J.A. Karas, L.J.M. Wong, O.K.A. Paulin, A. C. Mazeh, M.H. Hussein, J. Li, and T. Vekov. Antibiotics, 9(7), 406 (2020).
  5. M. Taghinasab and S. Jabaji, Cannabis microbiome and the role of endophytes in modulating the production of secondary metabolites: an overview. Microorganisms 2020, 8, 355, 1-16 (2020).
  6. P. Kusari, S. Kusari, M. Spiteller and O. Kayser, Endophytic fungi harbored in Cannabis sativa L.: diversity and potential as biocontrol agents against host plant-specific phytopathogens. Fungal Diversity 60, 137–151 (2013).
  7. K. McKernan, Y. Helbert, L. Kane, N. Houde, L. Zhang, S. McLaughlin, Whole genome sequencing of colonies derived from cannabis flowers & the impact of media selection on benchmarking total yeast & mold detection toolshttps://f1000research.com/articles/10-624 (2021).
  8. K. McKernan, Y. Helbert, L. Kane, L. Zhang, N. Houde, A. Bennett, J. Silva, H. Ebling, and S. McLaughlin, Pathogenic Enterobacteriaceae require multiple culture temperatures for detection in Cannabis sativa L. OSF Preprints, https://osf.io/j3msk/, (2022)
Milan Patel, PathogenDx
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The Need for More Stringent Testing in Cannabis

By Milan Patel
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Milan Patel, PathogenDx

As the demand for legal cannabis continues to rise and more states come online, it is imperative to enact more rigorous and comprehensive testing solutions to protect the health of consumers. People use cannabis products for wellness and to find relief; they should not be susceptible to consuming pathogens and falling ill. Especially for immunocompromised consumers, the consequences of consuming contaminated cannabis or hemp are dire. Of course, there should be federal standards for pathogen testing requirements like we have for the food industry. But right now, as cannabis is not yet federally legal, testing regulations vary between states and in many states, testing requirements are too loose and enforcement is minimal. It is up to state legislators, regulators and cannabis operators to protect the health of consumers through implementing more stringent testing.

From the outset, the environmental elements needed to grow cannabis – heat, light, humidity, soil – make cannabis ripe for pathogens to proliferate. Even when growers follow strict sanitation procedures through the supply chain from seed to sale, contaminations can still occur. Cannabis companies need to be hypervigilant and proactive about testing, not just reactive. The lack of regulations in some states is alarming, and as the cannabis industry is highly competitive and so many companies have emerged in a short time, there are unfortunately unscrupulous actors that have skated by in a loose regulatory landscape, just in the game to make a quick buck, even at the expense of consumer health. And there are notable instances where states do not have enforcement in place to deter harmful manufacturing practices. For instance, there are some states that don’t mandate moisture control and there have been incidents of companies watering down flower so it has more weight and thus can be sold at a higher cost – all the while that added moisture leads to mold, harming the consumer. This vicious circle driven by selfish human behavior needs to be broken by stricter regulations and enforcement.

While in the short term, looser testing regulations may save companies some money, in the long run these regulatory environments carry significant economic repercussions and damage the industry at large, most importantly injury or death to customers and patients. Recalls can tarnish a company’s brand and reputation and cause sales and stock prices to tank, and since cannabis legalization is such a hotly contested issue, the media gloms onto these recalls, which opponents to legalization then leverage to justify their stance. In order to win the hearts and minds of opponents and bring about federal legalization sooner, we need safer products so cannabis won’t be cast in such a dangerous, risky light.

Certainly, there’s a bit of irony at play here – the lack of federal regulations heightens the risk of contaminated cannabis reaching consumers, and on the flip side recalls are used by opponents to justify stigmatizing the plant and keeping it illegal. Nevertheless, someday in the not-too-distant future, cannabis will be legalized at the federal level. And when that day happens, federal agents will aggressively test and regulate cannabis; they’ll swab every area in facilities and demand thorough records of testing up and down the supply chain; current good manufacturing practices (cGMP) will be mandated. No longer will violations result just in a slap on the wrist – businesses will be shut down. To avoid a massive shock to the system, it makes sense for cannabis companies to pivot and adopt rigorous and wide-sweeping testing procedures today. Wait for federal legalization, and you’ll sink.

Frankly, the current landscape of cannabis regulation is scary and the consequences are largely yet to be seen. Just a few months ago, a Michigan state judge reversed part of a recall issued by the state’s Marijuana Regulatory Agency (MRA) on cannabis that exceeded legal limits of yeast, mold and aspergillus, bringing contaminated cannabis back to shelves without even slapping a warning label on the packaging to inform consumers of the potential contamination. This is a classic case of the power of the dollar prevailing over consumer safety and health. Even in well-established markets, the lack of regulations is jarring. For example, before this year in Colorado, testing for aspergillus wasn’t even required. (Aspergillus inhalation, which can cause Aspergillosis, can be deadly, especially for people who are immunocompromised). Many states still allow trace amounts of aspergillus and other pathogens to be present in cannabis samples. While traces may seem inconsequential in the short term, what will happen to frequent consumers who have been pinging their lungs with traces of pathogens for 30 years? Consistently inhaling trace amounts of pathogens can lead to lung issues and pulmonary disease down the road. Look what happened to people with breathing and lung issues during the last two years with COVID. What’s going to happen to these people when the next pandemic hits?

We need state regulators and MSOs to step up and implement more aggressive testing procedures. These regulators and companies can create a sea of change in the industry to better protect the health and well-being of consumers. Just complying with loose regulations isn’t good enough. We need to bring shortcomings around testing into the limelight and demand better and more efficient regulatory frameworks. And we should adopt the same standards for medical and adult use markets. Right now, several states follow cGMP for medical but not adult use – that’s ridiculous. Potentially harming consumers goes against what activists seeking legalization have been fighting for. Cannabis, untainted, provides therapeutic and clinical value not just to medical patients but to all consumers; cannabis companies should promote consumer health through their products, not jeopardize it.

For best practices, companies should conduct tests at every step in the supply chain, not just test end products. And testing solutions should be comprehensive. Most of the common tests used today are based on petri dishes, an archaic and inefficient technology dating back over a century, which require a separate dish to test for each pathogen of interest. If you’re waiting three to five days to see testing results against fifteen pathogens and a pathogen happens to be present, by the time you see results, the pathogen could have spread and destroyed half of your crops. So, not only do petri dishes overburden state-run labs, but due to their inherent inefficiencies, relying on these tests can significantly eat into cannabis companies’ revenues. At PathogenDx, we’ve created multiplexing solutions that can identify and detect up to 50 pathogens in a single test and yield accurate results in six hours. To save cannabis companies money in the long run and to make sure pathogens don’t slip through the cracks, more multiplexing tests like the ones we’ve created should be implemented in state labs.

Right now, while the regulatory landscape is falling short in terms of protecting consumer health, better solutions already exist. I urge state regulators and cannabis companies to take testing very seriously, be proactive and invest in creating better testing infrastructure today. Together, we can protect the health of consumers and create a stronger, more trustworthy and prosperous cannabis industry.

Beyond Compliance: Understanding and Combating Contamination

By Jill Ellsworth MS, RDN, Tess Eidem, Ph.D.
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As an emerging field in cannabis, contaminant testing remains a gray area for many businesses. The vast differences in state-by-state regulations, along with the frequent changes of previously established rules make testing a difficult, time-consuming process. But at its core, the science and reasoning behind why we test cannabis is very clear – consumer safety and quality assurance are key factors in any legal, consumer market. The implications of federal legalization make cannabis testing even more important to the future of the cannabis supply chain. Understanding the types of contaminants, their sources and how to prevent them is essential to avoiding failures, recalls and risking consumer safety.

When talking about cannabis contaminant testing there are four groups of contaminants: pesticides, heavy metals, foreign materials and microbes. The microbes found on cannabis include plant pathogens, post-harvest spoiling microbes, allergens, toxin release and human pathogens. While all of these can be lurking on the surface of cannabis, the specific types that are tested for in each state vary widely. Understanding the full scope of contaminants and looking beyond state-specific compliance requirements, cultivators will be able to prevent these detrimental risks and prepare their business for the future.

Environmental controls are essential to monitor and regulate temperature and humidity

Beyond just the health of the plant, both medical patients and adult use consumers can be adversely affected by microbial contaminants. To immunocompromised patients, Aspergillus can be life-threatening and both adult use and medical consumers are susceptible to allergic reactions to moldy flower. But Aspergillus is just one of the many contaminants that are invisible to the human eye and can live on the plant’s surface. Several states have intensive testing regulations when it comes to the full breadth of possible harmful contaminants. Nevada, for example, has strict microbial testing requirements and, in addition to Aspergillus, the state tests for Salmonella, STEC, Enterobacteriaceae, coliforms and total yeast and mold. Over 15 states test for total yeast and mold and the thresholds vary from allowing less than 100,000 colony forming units to allowing less than 1,000 colony forming units. These microbes are not uncommon appearances on cannabis – in fact, they are ever-present – so understanding them as a whole, beyond regulatory standards is a certain way to future-proof a business. With such vast differences in accepted levels of contamination per state, the best preparation for the future and regulations coming down the pipeline is understanding contamination, addressing it at its source and harvesting disease-free cannabis.

The risk of contamination is present at every stage of the cultivation process and encompasses agricultural practices, manufacturing processes and their intersection. From cultivation to manufacturing, there are factors that can introduce contamination throughout the supply chain. A quality control infrastructure should be employed in a facility and checkpoints within the process to ensure aseptic operations.

Microbial monitoring methods can include frequent/consistent testing

Cultivators should test their raw materials, including growing substrates and nutrient water to ensure it is free of microbial contamination. Air quality plays an important role in the cultivation and post-harvest processes, especially with mold contamination. Environmental controls are essential to monitor and regulate temperature and humidity and ensure unwanted microbes cannot thrive and decrease the value of the product or make it unsafe for worker handling or consumers. Developing SOPs to validate contact surfaces are clean, using proper PPE and optimizing worker flow can all help to prevent cross-contamination and are part of larger quality assurance measures to prevent microbes from spreading across cultivars and harvests.

Methods of microbial examination include air quality surveillance, ATP surface and water monitoring, raw materials testing, and species identification. Keeping control of the environment that product is coming into contact with and employing best practices throughout will minimize the amount of contamination that is present before testing. The solution to avoiding worst case scenarios following an aseptic, quality controlled process is utilizing a safe, post-harvest kill-step, much like the methods used in the food and beverage industries with the oversight of the FDA.

The goal of the grower should be to grow clean and stay clean throughout the shelf life of the product. In order to do this, it is essential to understand the critical control points within the cultivation and post-harvest processes and implement proper kill-steps. However, if a product is heavily bio-burdened, there are methods to recover contaminated product including decontamination, remediation and destroying the product. These measures come with their own strengths and weaknesses and cannot replace the quality assurance programs developed by the manufacturer.

Leaders in Cannabis Testing – Part 1: A Q&A with Milan Patel, CEO and Co-Founder of PathogenDx

By Aaron Green
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In this “Leaders in Cannabis Testing” series of articles, Green interviews cannabis testing laboratories and technology providers that are bringing unique perspectives to the industry. Particular attention is focused on how these businesses integrate innovative practices and technologies to navigate a rapidly changing landscape of regulatory constraints and B2B demand.

PathogenDx is an Arizona-based provider of microbial testing technologies. Since their inception in 2014, they have broadened their reach to 26 states in the US. In addition to cannabis product testing, PathogenDx also provides technologies for food safety testing, environmental testing and recently started offering human diagnostics testing to support COVID-19 response efforts.

We interviewed Milan Patel, CEO and co-founder of PathogenDx. Milan founded PathogenDx as a spin-off from one of his investments in a clinical diagnostics company testing for genetic markers in transplant organs. Prior to PathogenDx, Milan worked in finance and marketing at Intel and later served as CFO at Acentia (now Maximus Federal).

Aaron Green: What’s the history of PathogenDx?

Milan Patel: PathogenDx was effectively a spin-off of a clinical diagnostics company that my partner Dr. Mike Hogan, the inventor of the technology, had founded when he was a professor at the University of Arizona, but previously at Baylor Medical College back in 2002. I had invested in the company back then and I had realized that his technology had a broad and wide sweeping impact for testing – not just for pathogens in cannabis specifically, but also for pathogens in food, agriculture, water and even human diagnostics. In the last 14 months, this became very personal for every single person on the planet having been impacted by SARS-CoV-2, the viral pathogen causing Covid-19. The genesis of the company was just this, that human health, food and agricultural supply, and the environment has and will continue to be targeted by bacterial, fungal and viral pathogens impacting the safety and health of each human on the planet.

We founded PathogenDx and we pivoted the company from its original human organ transplant genetics market scope into the bigger markets; we felt the original focus was too niche for a technology with this much potential. We licensed the technology, and we repurposed it into primarily cannabis. We felt that achieving commercial success and use in the hands of cannabis testing labs at the state level where cannabis was first regulated was the most logical next step. Ultimately, our goal was and is to move into markets that are approved at the federal regulatory side of the spectrum, and that is where we are now.

Green: What year was that?

Milan Patel, CEO and Co-Founder of PathogenDx
Photo credit: Michael Chansley

Patel: 2014.

Green: So, PathogenDx started in cannabis testing?

Patel: Yes, we started in cannabis testing. We now have over 100 labs that are using the technology. There is a specific need in cannabis when you’re looking at contamination or infection.

In the case of contamination on cannabis, you must look for bacterial and fungal organisms that make it unsafe, such as E. coli, or Salmonella or Aspergillus pathogens. We’re familiar with recent issues like the romaine lettuce foodborne illness outbreaks at Chipotle. In the case of fungal organisms such as Aspergillus, if you smoke or consume contaminated cannabis, it could have a huge impact on your health. Cannabis regulators realized that to ensure public health and safety there was more than just one pathogen – there were half a dozen of these bugs, at a minimum, that could be harmful to you.

The beauty of our technology, using a Microarray is that we can do what is called a multiplex test, which means you’re able to test for all bacterial and fungal pathogens in a single test, as opposed to the old “Adam Smith” model, which tests each pathogen on a one-by-one basis. The traditional approach is costly, time consuming and cumbersome. Cannabis is such a high value crop and producers need to get the answer quickly. Our tests can give a result in six hours on the same day, as opposed to the two or three days that it takes for these other approved methods on the market.

Green: What is your business model? Is there equipment in addition to consumables?

Patel: Our business model is the classic razor blade model. What that means is we sell equipment as well as the consumables – the testing kits themselves.

The PathogenDx technology uses standard, off-the-shelf lab equipment that you can find anywhere. We didn’t want to make the equipment proprietary so that a lab has to buy a specific OEM branded product. They can use almost any equipment that’s available commercially. We wanted to make sure that labs are only paying a fraction of the cost to get our equipment, as opposed to using other vendors. Secondly, the platform is open-ended, meaning it’s highly flexible to work with the volumes that different cannabis labs see daily, from high to low.

One equipment set can process many different types of testing kits. There are kits for regulated testing required by states, as well as required environmental contamination.

Green: Do you provide any in-house or reference lab testing?

Patel: We do. We have a CLIA lab for clinical testing. We did this about a year ago when we started doing COVID testing.

We don’t do any kind of in-house reference testing for cannabis, though we do use specific reference materials or standards from Emerald Scientific, for example, or from NCI. Our platform is all externally third-party reference lab tested whether it’s validated by our external cannabis lab customers or an independent lab. We want our customers to make sure that the actual test works in their own hands, in their own facility by their own people, as opposed to just shrugging our shoulders and saying, “hey, we’ve done it ourselves, believe us.” That’s the difference.

Green: Can you explain the difference between qPCR and endpoint PCR?

Patel: The difference between PathogenDx’s Microarray is it uses endpoint PCR versus qPCR (quantitative real time PCR). Effectively, our test doesn’t need to be enriched. Endpoint PCR delivers a higher level of accuracy, because when it goes to amplify that target DNA, whether it’s E. coli, Salmonella or Aspergillus pieces, it uses all the primer reagent to its endpoint. So, it amplifies every single piece of an E. Coli (for example) in that sample until the primer is fully consumed. In the case of qPCR, it basically reaches a threshold and then the reaction stops. That’s the difference which results in a much greater level of accuracy. This provides almost 10 times greater sensitivity to identify the pathogen in that sample.

The second thing is that we have separated out how the amplified sample hybridizes to the probe. In the case of our assay, we have a microarray with a well in it and we printed the actual probe that has the sequence of E. coli in there, now driving 100% specificity. Whereas in the qPCR, the reaction is not only amplifying, but it’s also basically working with the probe. So, in that way, we have a higher level of efficiency in terms of specificity. You get a definite answer exactly in terms of the organism you’re looking for.

In terms of an analogy, let’s take a zip code for example which has the extra four digits at the end of it.  In the case of endpoint PCR, we have nine digits. We have our primer probes which represent the standard five digits of a zip code, and the physical location of the probe itself in the well which serves as the extra four digits of that zip code. The analyte must match both primary and secondary parts of the nine-digit zip code for it to lock in, like a key and a lock. And that’s the way our technology works in a nutshell.

Endpoint PCR is completely different. It drives higher levels of accuracy and specificity while reducing the turnaround time compared to qPCR – down to six hours from sample to result. In qPCR, you must enrich the sample for 24 to 48 hours, depending on bacteria or fungus, and then amplification and PCR analysis can be done in one to three hours. The accuracies and the turnaround times are the major differences between the endpoint PCR and qPCR.

Green: If I understand correctly, it’s a printed microarray in the well plate?

Patel: That’s correct. It’s a 96-well plate, and in each well, you’ve now printed all the probes for all targets in a single well. So, you’re not running more than one well per target, or per organism like you are for qPCR. You’re running just one well for all organisms. With our well plates, you’re consuming fewer wells and our patented foil-cover, you only use the wells you need. The unused wells in the well plate can be used in future tests, saving on costs and labor.

Green: Do you have any other differentiating IP?

The PathogenDx Microarray

Patel: The multiplex is the core IP. The way we process the raw sample, whether it’s flower or non-flower, without the need for enrichment is another part of the core IP. We do triplicate probes in each well for E. Coli, triplicate probes for Salmonella, etc., so there are three probes per targeted organism in each of the wells. We’re triple checking that you’re definitively identifying that bug at the end of the day. This is the cornerstone of our technology.

We were just approved by the State of New York, and the New York Department of Health has 13 different organisms for testing on cannabis. Think about it: one of the most rigorous testing requirements at a state level – maybe even at a federal level – and we just got approved for that. If you had to do 13 organisms separately, whether it’s plate culture or qPCR, it would become super expensive and very difficult. It would break the very backs of every testing lab to do that. That’s where the multiplexing becomes tremendously valuable because what you’re doing is leveraging the ability to do everything as a single test and single reaction.

Green: You mentioned New York. What other geographies are you active in?

Patel: We’re active in 26 different states including the major cannabis players: Florida, Nevada, California, Arizona, Michigan, New York, Oklahoma, Colorado and Washington – and we’re also in Canada. We’re currently working to enter other markets, but it all comes down to navigating the regulatory process and getting approval.

We’re not active currently in other international markets yet. We’re currently going through the AOAC approval process for our technology and I’m happy to say that we’re close to getting that in the next couple of months. Beyond that, I think we’ll scale more internationally.

I am delighted to say that we also got FDA EUA federal level authorization of our technology which drives significant credibility and confidence for the use of the technology. About a year ago, we made a conscious choice to make this technology federally acceptable by going into the COVID testing market. We got the FDA EUA back on April 20, ironically. That vote of confidence by the FDA means that our technology is capable of human testing. That has helped to create some runway in terms of getting federalized with both the FDA and the USDA, and certification by AOAC for our different tests.

Green: Was that COVID-19 EUA for clinical diagnostics or surveillance?

Patel: It was for clinical diagnostics, so it’s an actual human diagnostic test.

Green: Last couple of questions here. Once you find something as a cannabis operator, whether its bacteria or fungus, what can you do?

Patel: There are many services that are tied into our ecosystem. For example, we work with Willow Industries, who does remediation.

There’s been a lot of criticism around DNA based technology. It doesn’t matter if it’s qPCR or endpoint PCR. They say, “well, you’re also including dead organisms, dead DNA.” We do have a component of separating live versus dead DNA with a biomechanical process, using an enzyme that we’ve created, and it’s available commercially. Labs can test for whether a pathogen is living or dead and, in many cases, when they find it, they can partner with remediation companies to help address the issue at the grower level.

Another product we offer is an EnviroX test, which is an environmental test of air and surfaces. These have 50 pathogens in a single well. Think about this: these are all the bad actors that typically grow where soil is – the human pathogens, plant pathogens, powdery mildew, Botrytis, Fusarium – these are very problematic for the thousands of growers out there. The idea is to help them with screening technology before samples are pulled off the canopy and go to a regulated lab. We can help the growers isolate where that contamination is in that facility, then the remediation companies can come in, and help them save their crop and avoid economic losses.

Green: What are you most interested in learning about?

Patel: I would prefer that the cannabis industry not go through the same mistakes other industries have gone through. Cannabis started as a cottage industry. It’s obviously doubled every year, and as it gets scaled, the big corporations come in. Sophistication, standards, maturity all help in legitimacy of a business and image of an industry. At the end of the day, we have an opportunity to learn from other industries to really leapfrog and not have to go through the same mistakes. That’s one of the things that’s important to me. I’m very passionate about it.

One thing that I’ll leave you with is this: we’re dealing with more bugs in cannabis than the food industry. The food industry is only dealing with two to four bugs and look at the number of recalls they are navigating – and this is a multi-billion-dollar industry. Cannabis is still a fraction of that and we’re dealing with more bugs. We want to look ahead and avoid these recalls. How do you avoid some of the challenges around antimicrobial resistance and antibiotic resistance? We don’t want to be going down that road if we can avoid it and that’s sort of a personal mission for myself and the company.

Cannabis itself is so powerful, both medicinally as well as recreationally, and it can be beneficial for both consumers and industry image if we do the right things, and avoid future disasters, like the vaping crisis we went through 18 months ago because of bad GMPs. We must learn from those industries. We’re trying to make it better for the right reasons and that’s what’s important to me.

Green: Okay, great. That concludes the interview. Thank you, Milan.

Patel: Thank you for allowing me to share my thoughts and your time, Aaron.

The Power of Prevention: Pathogen Monitoring in Cannabis Cultivation and Processing Facilities

By Nathan Libbey
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As the cannabis market matures and the value chain becomes modernized, it’s important to address product safety in a comprehensive way. In other areas of manufacturing, Hazard Analysis & Critical Control Points (HACCP) has been the standard for reducing hazards both for employees and for the products themselves. A Critical Control Point (CCP) is any spot from conception to consumption where a loss of control can potentially result in risk (Unnevehr, 1996). In the food realm, HACCP has been used to drive quality enhancements since the 1980s (Cichy, 1982).

In a nutshell, HACCP seeks to help identify where a problem may enter a product or environment and how that problem may be addressed before it escalates. In cannabis, these hazards include many of the same problems that food products have: specifically molds, yeasts, and pathogenic bacteria (Listeria, E. coli, etc.). While the current industry standard is to test products at the end stage for these contaminants, this late-stage pass/fail regimen leads to huge lots of destroyed product and a risk for consumer distrust (Yamashiro, 2019). HACCP, therefore, should be applied at every stage of the production process.

Pathogen Environmental Monitoring (PEM) is a tool that can be used to identify CCPs in a cannabis cultivation or processing facility. The main goal of a PEM program is to find a contaminant before it reaches a surface that touches the product or the product itself. PEM is conducted using a pre-moistened swab or a sponge to collect a sample from the cannabis environment. The swab can then be sent to a lab for microbial testing. Keys to an effective PEM are:

1. Start with a broad stroke – When the FDA comes to a facility suspected of producing pathogen-laced food products, they conduct what is known as a Swab-a-thon. A Swab-a-thon is a top to bottom collection of samples, usually totaling 100 or more. Similarly, preemptively swabbing should be the first step in any PEM—swab everything to see what exists as a baseline.

2. Map your scene – identify on a map of your facility the following:

  • Cannabis contact surfaces (CCS) (belts, clippers, tables, etc)
  • Non-cannabis contact surfaces (Non-CCS) (floors, lighting, drains, etc)
  • Flow of air and people (where do air and people enter and where do they go?

Identifying the above zones will help deepen your understanding of where contaminants may come into contact with cannabis and how they may migrate from a Non-CCS to a CCS. 

3. Plan and execute:

  • Based on the results of mapping, and Swab-a-thon, identify where and when you will be collecting samples on a consistent and repeatable basis. Emphasis should be placed on areas that are deemed a risk based on 1) and 2). Samples should be collected at random in all zones to ensure comprehensive screening.

4. Remediate and modify:

  • If you get a positive result during PEM, don’t panic—pathogens are ubiquitous.
  • Remediate any trouble spots with deep cleaning, remediation devices or other protocols.
  • Re-test areas that were positive for pathogens to ensure remediation is successful.
  • Revisit and modify the plan at least once a year and each time a new piece of equipment is added or production flow is otherwise changed.

The steps above are a good starting point for a grower or processor to begin a PEM. Remember that this is not a one-size-fits-all approach to safety; each facility has its own unique set of hazards and control points.

Comprehensive guides for PEM can be found at the links below, many of the concepts can be applied to cannabis production.


https://affifoodsafety.org/lcp/advanced-search/

http://www.centerforproducesafety.org/amass/documents/document/263/Listeria%20Guidance%20UFPA%202013.pdf

Cichy, R. (1982). HACCP as a quality assurance tool in a commissary food-service system. International Journal of Hospitality Management, 1(2), 103-106.

Unnevehr, L., & Jensen, H. (1996). HACCP as a Regulatory Innovation to Improve Food Safety in the Meat Industry. American Journal of Agricultural Economics, 78(3), 764-769.

Yamashiro, C, & Baca, Y. (2019).  Prevent high-value cannabis crop loss with innovative environmental monitoring tool.