Tag Archives: fungal

Rapid Pathogen Detection for the 21st Century: A Look at PathogenDx

By Aaron G. Biros
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In 1887, Julius Petri invented a couple of glass dishes, designed to grow bacteria in a reproducible, consistent environment. The Petri dish, as it came to be known, birthed the scientific practice of agar cultures, allowing scientists to study bacteria and viruses. The field of microbiology was able to flourish with this handy new tool. The Petri dish, along with advancements in our understanding of microbiology, later developed into the modern field of microbial testing, allowing scientists to understand and measure microbial colonies to detect harmful pathogens in our food and water, like E. coli and Salmonella, for example.

The global food supply chain moves much faster today than it did in the late 19th century. According to Milan Patel, CEO of PathogenDx, this calls for something a little quicker. “Traditional microbial testing is tedious and lengthy,” says Patel. “We need 21st century pathogen detection solutions.”

Milan Patel first joined the parent company of PathogenDx back in 2012, when they were more focused on clinical diagnostics. “The company was predominantly built on grant funding [a $12 million grant from the National Institute of Health] and focused on a niche market that was very specialized and small in terms of market size and opportunity,” says Patel. “I realized that the technology had a much greater opportunity in a larger market.”

Milan Patel, CEO of PathogenDx
Photo: Michael Chansley

He thought that other markets could benefit from that technology greatly, so the parent company licensed the technology and that is how PathogenDx was formed. Him and his team wanted to bring the product to market without having to obtain FDA regulatory approval, so they looked to the cannabis market. “What we realized was we were solving a ‘massive’ bottleneck issue where the microbial test was the ‘longest test’ out of all the tests required in that industry, taking 3-6 days,” says Patel. “We ultimately realized that this challenge was endemic in every market – food, agriculture, water, etc. – and that the world was using a 140-year-old solution in the form of petri dish testing for microbial organisms to address challenges of industries and markets demanding faster turnaround of results, better accuracy, and lower cost- and that is the technology PathogenDx has invented and developed.”

While originally a spinoff technology designed for clinical diagnostics, they deployed the technology in cannabis testing labs early on. The purpose was to simplify the process of testing in an easy approach, with an ultra-low cost and higher throughput. Their technology delivers microbial results in less than 6 hours compared to 24-36 hours for next best option.

The PathogenDx Microarray

Out of all the tests performed in a licensed cannabis testing laboratory, microbial tests are the longest, sometimes taking up to a few days. “Other tests in the laboratory can usually be done in 2-4 hours, so growers would never get their microbial testing results on time,” says Patel. “We developed this technology that gets results in 6 hours. The FDA has never seen something like this. It is a very disruptive technology.”

When it comes to microbial contamination, timing is everything. “By the time Petri dish results are in, the supply chain is already in motion and products are moving downstream to distributors and retailers,” Patel says. “With a 6-hour turnaround time, we can identify where exactly in the supply chain contaminant is occurring and spreading.”

The technology is easy to use for a lab technician, which allows for a standard process on one platform that is accurate, consistent and reproduceable. The technology can deliver results with essentially just 12 steps:

  1. Take 1 gram of cannabis flower or non-flower sample. Or take environmental swab
  2. Drop sample in solution. Swab should already be in solution
  3. Vortex
  4. Transfer 1ml of solution into 1.5ml tube

    A look at how the sample is added to the microarray
  5. Conduct two 3-minute centrifugation steps to separate leaf material, free-floating DNA and create a small pellet with live cells
  6. Conduct cell lysis by adding digestion buffer to sample on heat blocks for 1 hour
  7. Conduct Loci enhancement PCR of sample for 1 hour
  8. Conduct Labelling PCR which essentially attaches a fluorescent tag on the analyte DNA for 1 hour
  9. Pipette into the Multiplex microarray well where hybridization of sample to probes for 30 minutes
  10. Conduct wash cycle for 15 minutes
  11. Dry and image the slide in imager
  12. The imager will create a TIFF file where software will analyze and deliver results and a report

Their DetectX product can test for a number of pathogens in parallel in the same sample at the same time down to 1 colony forming unit (CFU) per gram. For bacteria, the bacterial kit can detect E. coli, E. coli/Shigella spp., Salmonella enterica, Listeria and Staph aureus, Stec 1 and Stec 2 E.coli. For yeast and mold, the fungal kit can test for Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus.

Their QuantX is the world’s first and only multiplex quantification microarray product that can quantify the microbial contamination load for key organisms such as total aerobic bacteria, total yeast & mold, bile tolerant gram negative, total coliform and total Enterobacteriaceae over a dynamic range from 100 CFU/mL up to 1,000,000 CFU/mL.

Not all of the PathogenDx technology is designed for just microbial testing of cannabis or food products. Their EnviroX technology is designed to help growers, processors or producers across any industry identify areas of microbial contamination, being used as a tool for quality assurance and hazard analysis. They conducted industry-wide surveys of the pathogens that are creating problems for cultivators and came up with a list of more than 50 bacterial and fungal pathogens that the EnviroX assay can test for to help growers identify contamination hotspots in their facilities.

Using the EnviroX assay, growers can swab surfaces like vents, fans, racks, workbenches and other potential areas of contamination where plants come in contact. This helps growers identify potential areas of contamination and remediate those locations. Patel says the tool could help growers employ more efficient standard operating procedures with sanitation and sterilization, reducing the facility’s incidence of pathogens winding up on crops, as well as reduction in use of pesticides and fungicides on the product.

Deploying this technology in the cannabis industry allowed Milan Patel and the PathogenDx team to bring something new to the world of microbial testing. Their products are now in more than 90 laboratories throughout the country. The success of this technology provides another shining example of how the cannabis market produces innovative and disruptive ideas that have a major impact on the world, far beyond cannabis itself.

Analytical Instruments You Need to Start a Cannabis Testing Laboratory

By Bob Clifford
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The cannabis industry is growing exponentially, and the use of cannabis for medical purposes is being adopted across the nation. With this boom in cannabis consumers, there has been an increasing need for knowledge about the product.

The role of testing labs has become crucial to the process, which makes owning and operating a lab more lucrative. Scientists testing for potency, heavy metals, pesticides, residual solvents, moisture, terpene profile, microbial and fungal growth, and mycotoxins/aflatoxins are able to make meaningful contributions to the medical industry by making sure products are safe, while simultaneously generating profits and a return on investment.

Here are the key testing instruments you need to conduct these critical analyses. Note that cannabis analytical testing requirements may vary by state, so be sure to check the regulations applicable to the location of your laboratory.

Potency Testing

High-performance liquid chromatograph (HPLC) designed for quantitative determination of cannabinoid content.

The most important component of cannabis testing is the analysis of cannabinoid profiles, also known as potency. Cannabis plants naturally produce cannabinoids that determine the overall effect and strength of the cultivar, which is also referred to as the strain. There are many different cannabinoids that all have distinct medicinal effects. However, most states only require testing and reporting for the dry weight percentages of delta-9-tetrahydrocannabinol (Δ9-THC) and cannabidiol (CBD). It should be noted that delta-9-tetrahydrocannabinolic acid (Δ9-THCA) can be converted to THC through oxidation with heat or light.

For potency testing, traditional high-performance liquid chromatography (HPLC) is recommended and has become the gold standard for analyzing cannabinoid profiles. Look for a turnkey HPLC analyzer that delivers a comprehensive package that integrates instrument hardware, software, consumables and proven HPLC methods.

Heavy Metal Testing

ICP-MS instrument for detecting heavy metals in cannabis.

Different types of metals can be found in soils and fertilizers, and as cannabis plants grow, they tend to draw in these metals from the soil. Heavy metals are a group of metals considered to be toxic, and the most common include lead, cadmium, arsenic and mercury. Most labs are required to test and confirm that samples are under the allowable toxic concentration limits for these four hazardous metals.

Heavy metal testing is performed by inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS uses the different masses of each element to determine which elements are present within a sample and at what concentrations. Make sure to include accompanying software that provides assistant functions to simplify analysis by developing analytical methods and automatically diagnosing spectral interference. This will provide easy operation and analytical results with exceptionally high reliability.

To reduce running costs, look for a supporting hardware system that reduces the consumption of argon gas and electricity. For example, use a plasma ignition sequence that is optimized for lower-purity argon gas (i.e., 99.9% argon as opposed to more expensive 99.9999%).

Pesticide Testing

The detection of pesticides in cannabis can be a challenge. There are many pesticides that are used in commercial cannabis grow operations to kill the pests that thrive on the plants and in greenhouses. These chemicals are toxic to humans, so confirming their absence from cannabis products is crucial. The number of pesticides that must be tested for varies from state to state, with Colorado requiring only 13 pesticides, whereas Oregon and California require 59 and 66 respectively. Canada has taken it a step further and must test for 96 pesticides, while AOAC International is developing methods for testing for 104 pesticides. The list of pesticides will continue to evolve as the industry evolves.

Testing for pesticides is one of the more problematic analyses, possibly resulting in the need for two different instruments depending on the state’s requirements. For a majority of pesticides, liquid chromatography mass spectrometry (LCMS) is acceptable and operates much like HPLC but utilizes a different detector and sample preparation.

With excellent sensitivity and ultra-low detection limits, LC-MS/MS is an ideal technique for the analysis of pesticides.

Pesticides that do not ionize well in an LCMS source require the use of a gas chromatography mass spectrometry (GCMS) instrument. The principles of HPLC still apply – you inject a sample, separate it on a column and detect with a detector. However, in this case, a gas (typically helium) is used to carry the sample.

Look for a LC-MS/MS system or HPLC system with a triple quadrupole mass spectrometer that provides ultra-low detection limits, high sensitivity and efficient throughput. Advanced systems can analyze more than 200 pesticides in 12 minutes.

For GCMS analysis, consider an instrument that utilizes a triple quadrupole mass spectrometer to help maximize the capabilities of your laboratory. Select an instrument that is designed with enhanced functionality, analysis software, databases and a sample introduction system. Also include a headspace autosampler, which can also be used for terpene profiles and residual solvent testing.

Residual Solvent Testing

Residual solvents are chemicals left over from the process of extracting cannabinoids and terpenes from the cannabis plant. Common solvents for such extractions include ethanol, butane, propane and hexane. These solvents are evaporated to prepare high-concentration oils and waxes. However, it is sometimes necessary to use large quantities of solvent in order to increase extraction efficiency and to achieve higher levels of purity. Since these solvents are not safe for human consumption, most states require labs to verify that all traces of the substances have been removed.

Testing for residual solvents requires gas chromatography (GC). For this process, a small amount of extract is put into a vial and heated to mimic the natural evaporation process. The amount of solvent that is evaporated from the sample and into the air is referred to as the “headspace.” The headspace is then extracted with a syringe and placed in the injection port of the GC. This technique is called full-evaporated technique (FET) and utilizes the headspace autosampler for the GC.

Look for a GCMS instrument with a headspace autosampler, which can also be used for pesticide and terpene analysis.

Terpene Profile Testing

Terpenes are produced in the trichomes of the cannabis leaves, where THC is created, and are common constituents of the plant’s distinctive flavor and aroma. Terpenes also act as essential medicinal hydrocarbon building blocks, influencing the overall homeopathic and therapeutic effect of the product. The characterization of terpenes and their synergistic effect with cannabinoids are key for identifying the correct cannabis treatment plan for patients with pain, anxiety, epilepsy, depression, cancer and other illnesses. This test is not required by most states, but it is recommended.

The instrumentation that is used for analyzing terpene profiles is a GCMS with headspace autosampler with an appropriate spectral library. Since residual solvent testing is an analysis required by most states, all of the instrumentation required for terpene profiling will already be in your lab.

As with residual solvent testing, look for a GCMS instrument with a headspace autosampler (see above). 

Microbe, Fungus and Mycotoxin Testing

Most states mandate that cannabis testing labs analyze samples for any fungal or microbial growth resulting from production or handling, as well as for mycotoxins, which are toxins produced by fungi. With the potential to become lethal, continuous exposure to mycotoxins can lead to a buildup of progressively worse allergic reactions.

LCMS should be used to qualify and identify strains of mycotoxins. However, determining the amount of microorganisms present is another challenge. That testing can be done using enzyme linked immunosorbent assay (ELISA), quantitative polymerase chain reaction (qPCR) or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), with each having their advantages and disadvantages.

For mycotoxin analysis, select a high-sensitivity LC-MS/MS instrument. In addition to standard LC, using an MS/MS selective detector enables labs to obtain limits of detection up to 1000 times greater than conventional LC-UV instruments.

For qPCR and its associated needs, look for a real-time PCR amplification system that combines thermal cyclers with optical reaction modules for singleplex and multiplex detection of fluorophores. These real-time PCR detection systems range from economical two-target detection to sophisticated five-target or more detection systems. The real-time detection platform should offer reliable gradient-enabled thermal cyclers for rapid assay optimization. Accompanying software built to work with the system simplifies plate setup, data collection, data analysis and data visualization of real-time PCR results.

Moisture Content and Water Activity Testing

Moisture content testing is required in some states. Moisture can be extremely detrimental to the quality of stored cannabis products. Dried cannabis typically has a moisture content of 5% to 12%. A moisture content above 12% in dried cannabis is prone to fungal growth (mold). As medical users may be immune deficient and vulnerable to the effects of mold, constant monitoring of moisture is needed. Below a 5% moisture content, the cannabis will turn to a dust-like texture.

The best way to analyze the moisture content of any product is using the thermogravimetric method with a moisture balance instrument. This process involves placing the sample of cannabis into the sample chamber and taking an initial reading. Then the moisture balance instrument heats up until all the moisture has been evaporated out of the sample. A final reading is then taken to determine the percent weight of moisture that was contained in the original sample.

A moisture balance can provide accurate determination of moisture content in cannabis.

Look for a moisture balance that offers intuitive operation and quick, accurate determination of moisture content. The pan should be spacious enough to allow large samples to be spread thinly. The halogen heater and reflector plate should combine to enable precise, uniform heating. Advanced features can include preset, modifiable measurement modes like automated ending, timed ending, rapid drying, slow drying and step drying.

Another method for preventing mold is monitoring water activity (aW). Very simply, moisture content is the total amount of water available, while water activity is the “free water” that could produce mold. Water activityranges from 0 to 1. Pure water would have an aW of 1.0. ASTM methods D8196-18 and D8297-18 are methods for monitoring water activity in dry cannabis flower. The aW range recommended for storage is 0.55 to 0.65. Some states recommend moisture content to be monitored, other states monitor water activity, and some states such as California recommend monitoring both.

Final Thoughts

As you can see, cannabis growers benefit tremendously from cannabis testing. Whether meeting state requirements or certifying a product, laboratory testing reduces growers’ risk and ensures delivery of a quality product. As medicinal and recreational cannabis markets continue to grow, analytical testing will ensure that consumers are receiving accurately

labeled products that are free from contamination. That’s why it is important to invest in the future of your cannabis testing lab by selecting the right analytical equipment at the start of your venture.

Fungal Monitoring: An Upstream Approach to Testing Requirements

By Bernie Lorenz, PhD
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Mold is ubiquitous in nature and can be found everywhere.1 Cannabis growers know this all too well – the cannabis plant, by nature, is an extremely mold-susceptible crop, and growers battle it constantly.

Of course, managing mold doesn’t mean eradicating mold entirely – that’s impossible. Instead, cultivation professionals must work to minimize the amount of mold to the point where plants can thrive, and finished products are safe for consumption.

Let’s begin with that end in mind – a healthy plant, grown, cured and packaged for sale. In a growing number of states, there’s a hurdle to clear before the product can be sold to consumers – state-mandated testing.

So how do you ensure that the product clears the testing process within guidelines for mold? And what tools can be employed in biological warfare?

Mold: At Home in Cannabis Plants

It helps to first understand how the cannabis plant becomes an optimal environment.

The cannabis flower was designed to capture pollen floating in the air or brought by a pollinating insect.

Photo credit: Steep Hill- a petri dish of mold growth from tested cannabis

Once a mold spore has landed in a flower, the spore will begin to grow. The flower will continue to grow as well, and eventually, encapsulate the mold. Once the mold is growing in the middle of the flower, there is no way to get rid of it without damaging the flower.

A Name with Many Varieties

The types of spores found in or around a plant can make or break whether mold will end with bad product.

Aspergillus for example, is a mold that can produce mycotoxins, which are toxic to humans2. For this reason, California has mandatory testing3for certain aspergillus molds.

Another example, Basidiospores, are found outside, in the air. These are spores released from mushrooms and have no adverse effects on cannabis or a cannabis cultivation facility.

Fungi like powdery mildew and botrytis (PM and Bud Rot) typically release spores in the air before they are physically noticed on plants. Mold spores like these can survive from one harvest to the next – they can be suspended in the air for hours and be viable for years.

How Mold Travels

Different types of spores – the reproductive parts of mold – get released from different types of mold. Similar to plants and animals, mold reproduces when resources are deemed sufficient.

The opposite is also true that if the mold is under enough stress, such as a depleting nutrient source, it can be forced into reproduction to save itself.4

In the end, mold spores are released naturally into the air for many reasons, including physical manipulation of a plant, which, of course, is an unavoidable task in a cultivation facility.5

Trimming Areas: A Grow’s Highest Risk for Mold

Because of the almost-constant physical manipulation of plants that happen inside its walls, a grow’s trimming areas typically have the highest spore counts. Even the cleanest of plants will release spores during trimming.

Best practices include quality control protocols while trimming

These rooms also have the highest risk for cross contamination, since frequently, growers dry flower in the same room as they trim. Plus, because trimming can be labor intensive, with a large number of people entering and leaving the space regularly, spores are brought in and pushed out and into another space.

The Battle Against Mold

The prevalence and ubiquitous nature of mold in a cannabis facility means that the fight against it must be smart, and it must be thorough.

By incorporating an upstream approach to facility biosecurity, cultivators can protect themselves against testing failures and profit losses.

Biosecurity must be all encompassing, including everything from standard operating procedures and proper environmental controls, to fresh air exchange and surface sanitation/disinfection.

One of the most effective tactics in an upstream biosecurity effort is fungal monitoring.

Ways to Monitor Mold

Determining the load or amount of mold that is in a facility is and always will be common practice. This occurs in a few ways.

Post-harvest testing is in place to ensure the safety of consumers, but during the growing process, is typically done using “scouting reports.” A scouting report is a human report: when personnel physically inspect all or a portion of the crop. A human report, unfortunately, can lead to human error, and this often doesn’t give a robust view of the facility mold picture.

Another tool is agar plates. These petri dishes can be opened and set in areas suspected to have mold. Air moves past the plate and the mold spores that are viable land on the dishes. However, this process is time intensive, and still doesn’t give a complete picture.

Alternatively, growers can use spore traps to monitor for mold.

Spore traps draw a known volume of air through a cassette.The inside of the cassette is designed to force the air toward a sticky surface, which is capable of capturing spores and other materials. The cassette is sent to a laboratory for analysis, where they will physically count and identify what was captured using a microscope.

Spore trap results can show the entire picture of a facility’s mold concerns. This tool is also fast, able to be read on your own or sent to a third party for quick and unbiased review. The information yielded is a useful indicator for mold load and which types are prevalent in the facility.

Spore Trap Results: A Story Told

What’s going on inside of a facility has a direct correlation to what’s happening outside, since facility air comes infromthe outside. Thus, spore traps are most effective when you compare a trap inside with one set outside.

When comparing the two, you can see what the plants are doing, view propagating mold, and understand which of the spore types are only found inside.

Similar to its use in homes and businesses for human health purposes, monitoring can indicate the location of mold growth in a particular area within a facility.

These counts can be used to determine the efficacy of cleaning and disinfecting a space, or to find water leaks or areas that are consistently wet (mold will grow quickly and produce spores in these areas).

Using Spore Traps to See Seasonality Changes, Learn CCPs

Utilizing spore traps for regular, facility-wide mold monitoring is advantageous for many reasons.

One example: Traps can help determine critical control points (CCP) for mold.

What does this look like? If the spore count is two times higher than usual, mitigating action needs to take place. Integrated Pest Management (IPM) strategies like cleaning and disinfecting the space, or spraying a fungicide, are needed to bring the spore count down to its baseline.

For example, most facilities will see a spike in spore counts during the times of initial flower production/formation (weeks two to three of the flower cycle).

Seasonal trends can be determined, as well, since summer heat and rain will increase the mold load while winter cold may minimize it.

Using Fungal Monitoring in an IPM Strategy

Fungal monitoring – especially using a spore trap – is a critical upstream step in a successful IPM strategy. But it’s not the only step. In fact, there are five:

  • Identify/Monitor… Using a spore trap.
  • Evaluate…Spore trap results will indicate if an action is needed. Elevated spore counts will be the action threshold, but it can also depend on the type of spores found.
  • Prevention…Avoiding mold on plants using quality disinfection protocols as often as possible.
  • Action…What will be done to remedy the presence of mold? Examples include adding disinfection protocols, applying a fungicide, increasing air exchanges, and adding a HEPA filter.
  • Monitor…Constant monitoring is key. More eyes monitoring is better, and will help find Critical Control Points.

Each step must be followed to succeed in the battle against mold.

Of course, in the battle, there may be losses. If you experience a failed mandatory product testing result, use the data from the failure to fix your facility and improve for the future.

The data can be used to determine efficacy of standard operating procedures, action thresholds, and other appropriate actions. Plus, you can add a spore trap analysis for pre- and post- disinfection protocols, showing whether the space was really cleaned and disinfected after application. This will also tell you whether your products are working.

Leveraging all of the tools available will ensure a safe, clean cannabis product for consumers.


References

  1. ASTM D8219-2019: Standard Guide for Cleaning and Disinfection at a Cannabis Cultivation Center (B. Lorenz): http://www.astm.org/cgi-bin/resolver.cgi?D8219-19
  2. Mycotoxin, Aspergillus: https://www.who.int/news-room/fact-sheets/detail/mycotoxins
  3. State of California Cannabis Regulations: https://cannabis.ca.gov/cannabis-regulations/
  4. Asexual Sporulation in Aspergillus nidulans (Thomas H. Adams,* Jenny K. Wieser, and Jae-Hyuk Yu):  https://pdfs.semanticscholar.org/7eb1/05e73d77ef251f44a2ae91d0595e85c3445e.pdf?_ga=2.38699363.1960083875.1568395121-721294556.1562683339
  5. ASTM standard “Assessment of fungal growth in buildings” Miller, J. D., et al., “Air Sampling Results in Relation to Extent of Fungal Colonization of Building Materials in Some Water Damaged Buildings,” Indoor Air, Vol 10, 2000, pp. 146–151.
  6. Zefon Air O Cell Cassettes: https://www.zefon.com/iaq-sampling-cassettes