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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 tools,  https://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)

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.

Medicinal Genomics Salmonella and STEC E. coli Multiplex Assay Certified by AOAC

By Cannabis Industry Journal Staff
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Medicinal Genomics announced today that they have received AOAC International certification for their PathoSEEK® Salmonella and STEC E. coli multiplex assay. In combination with their SenSATIVAx® extraction kits, labs can simultaneously detect Salmonella spp. and STEC E. coli with a single qPCR reaction for flower, concentrates and infused chocolates using the Agilent AriaMx and the BioRad CFx-96 instruments.

The certification came after the multiplex assay was validated according to the AOAC Performance Tested Method Program. According to the press release, the PathoSEEK platform now has more cannabis matrices accredited for Aspergillus, Salmonella, and STEC E. coli than any other product out on the market, according to their press release.

The PathoSEEK microbiological testing platform uses a qPCR assay and internal plant DNA controls for reactions. The two-step protocol verifies performance while detecting microbes, which allegedly helps minimize false negative results from human error or failing conditions.

“AOAC’s validation of our Salmonella/STEC E. coli assay across the various cannabis matrices is further proof of our platform’s robustness and versatility,” says Dr. Sherman Hom, director of regulatory affairs at Medicinal Genomics. “We are excited that our PathoSEEK® platform is moving in concert with the FDA’s new blueprint to improve food safety by modernizing the regulatory framework, while leveraging the use of proven molecular tools to accelerate predictive capabilities, enhance prevention, and enhance our ability to swiftly adapt to pathogen outbreaks that could impact consumer safety.”

Detecting Microbial Contamination in Cannabis

By Mike Clark
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Increasing cannabis use across the US has come with increased scrutiny of its health effects. Regulators and healthcare providers are not just concerned about the direct effects of inhaling or consuming cannabinoids, however, but also about another health risk: microbial contamination in cannabis products. Like any other crop, cannabis is susceptible to contamination by harmful pathogens at several points throughout the supply chain, from cultivation and harvesting to distribution. Many state regulators have set limits for microbial populations in cannabis products. Consequently, testing labs must adopt efficient screening protocols to help companies remain compliant and keep their customers safe.

Some of the pathogens common to cannabis flower include Aspergillus fungus species such as A. flavus, A. fumigatus, A. niger and A. terreus. Cannabis might also harbor harmful E. coli and Salmonella species, including Shiga toxin-producing E. coli (STEC). Regulations vary by state, but most have set specific thresholds for how many colony forming units (CFUs) of particular species can be present in a sellable product.

The gold standard method for detecting microbes is running cultures.

Growers and testing labs need to develop a streamlined approach to remain viable. Current methods, including running cultures on every sample, can be expensive and time-consuming, but by introducing a PCR-based screening step first, which identifies the presence of microbial DNA – and therefore the potential for contamination – laboratories can reduce the number of cultures they need to run, saving money and time.

The Risk of Aspergillus Contamination

Contamination from Aspergillus species can bring harm to cannabis growers and their customers. The state of Michigan is currently undergoing the largest cannabis recall in its history from Aspergillus contamination.

If contamination grows out of control, the pathogen can damage the cannabis plant itself and lead to financial losses. Aspergillus can also cause serious illness in consumers, especially those that are immunocompromised. If an immunocompromised person inhales Aspergillus, they can develop aspergillosis, a lung condition with a poor prognosis.

A Two-Step Screening Process

The gold standard method for detecting microbes is running cultures. This technique takes weeks to deliver results and can yield inaccurate CFU counts, making it difficult for growers to satisfy regulators and create a safe product in a timely manner. The use of polymerase chain reaction (PCR) can greatly shorten the time to results and increase sensitivity by determining whether the sample has target DNA.

Using PCR can be expensive, particularly to screen for multiple species at the same time, but a qPCR-based Aspergillus detection assay could lead to significant cost savings. Since the average presumptive positive rate for Aspergillus contamination is low (between 5-10%), this assay can be used to negatively screen large volumes of cannabis samples. It serves as an optional tool to further speciate only those samples that screened positive to comply with state regulations.

Conclusion

Overall, screening protocols have become a necessary part of cannabis production, and to reduce costs, testing labs must optimize methods to become as efficient as possible. With tools such as PCR technology and a method that allows for initial mass screening followed by speciation only when necessary, laboratories can release more samples faster with fewer unnecessary analyses and more success for cannabis producers in the marketplace.

bioMérieux Gets AOAC Approval for PCR Detection of STEC and Salmonella in Cannabis

By Cannabis Industry Journal Staff
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bioMérieux, a leader in the in vitro diagnostics space and a supporter of the cannabis testing market, announced last month that they have achieved the first ever AOAC International approval for PCR Multiplex Detection of STEC and Salmonella in cannabis flower for their GENE-UP® PRO STEC/Salmonella Assay. The performance tested method approval for their new assay accomodates simultaneous enrichment and detection of STEC (Shiga Toxigenic Escherichia coli) and Salmonella spp. in cannabis samples.

The method is aimed at increasing efficiency in cannabis testing labs by reducing sample preparation time for microbiological testing. With the single enrichment and real-time multiplex PCR detection, bioMérieux says their new assay can provide reliable detection of STEC and Salmonella in 24 hours using just a single test.

PCR technology is one of the most widely utilized testing methods for detecting pathogens in a variety of matrices. bioMérieux claims it is easy to use, scientifically robust and reduces costs, time spent testing and errors.

Maria McIntyre, cannabis strategic operations business manager at bioMérieux, says that AOAC performance tested method approval is setting the bar for cannabis testing laboratories and furthering cannabis science. “AOAC International impacts cannabis science by setting analytical method standards that act as the benchmark for method validation,” says McIntyre. “This simplifies the validations needed by cannabis laboratories and assures the utmost confidence in product safety and human health.”

AOAC Approves New Microbial Testing Validations

By Cannabis Industry Journal Staff
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In a press release sent out this month, bioMérieux announced they have received the very first approvals in cannabis and hemp for AOAC Research Institute Performance Testing Methods (PTM). AOAC approved method validation for the detection of Salmonella and STEC (Shiga toxin-producing E. coli) in cannabis flower utilizing bioMérieux GENE- UP® SLM2 (PTM 121802) and EHEC (PTM 121806) assays.

According to the press release, these validations are the first of their kind in the cannabis and hemp industries. The AOAC-validated testing methods are approved for 1-gram and 10-gram samples.

Dr. Stan Bailey, senior director of scientific affairs at bioMérieux, says these approvals demonstrate the company’s commitment to innovative and validated science in the cannabis and hemp industries. “We are especially proud that the GENE-UP SLM2 and EHEC are the first two AOAC approvals in the United States for cannabis and hemp,” says Dr. Bailey. “This is increasingly important with now over half the population of the US living in states that have approved cannabis for recreational use and most states approving cannabis for medical use.”

The AOAC PTM designations are recognized by the US Department of Agriculture, the Food and Drug Administration, and global regulatory agencies. The validation guidance builds on AOAC’s Cannabis Analytical Science Program (CASP).

bioMérieux is a French in vitro diagnostics company that serves the global testing market. They provide diagnostic solutions such as systems, reagents, software and services.

emerald test retail

The Emerald Test Gets Record Lab Participation

By Aaron G. Biros
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emerald test retail

According to a press release released by Emerald Scientific, their spring Emerald Test had a 25% increase in participation over the fall 2017 test.

77 laboratories from 18 states and two foreign countries participated in the bi-annual Emerald Test, an inter-laboratory comparison and proficiency testing (PT) program. The program is a tool for labs to demonstrate their competence to existing clients, potential customers, regulatory agencies and accreditation bodies.

Overall, the company shipped 314 PT samples, with the majority in a hemp or hemp oil matrix. According to the press release, the new PTs including potency in hemp oil, STEC, Aspergillus Mold and Mycotoxins attracted a good deal of labs. “Many laboratories have been regular participants which speaks volumes about their commitment to quality assurance, regulatory compliance, and consumer safety,” says Ken Groggel, director of Emerald Scientific’s proficiency testing program. “The collegial attitude of open communication and shared experience increases our knowledge and ensures continued success for all involved. Our goal is to establish an industry benchmark for cannabis testing while providing valuable feedback to each laboratory’s quality assurance system.”

This marks the first time the Emerald Test used two potency PTs- the original in solution and a new hemp oil matrix. “Of the 62 labs that participated in the Potency PT, 48 took the PT in solution with 47 receiving an Emerald Badge,” reads the press release. “Another 23 labs took the PT in hemp oil, with 22 awarded an Emerald Badge. Nine labs took both PTs.”

39 labs took PTs in APC, Total Coliform, E. coli, Enterobacteriaceae and Yeast/Mold and 38 of those received the badge. 45 reported results for Salmonella and 42 of them were able to correctly identify the contaminated sample. 12 labs took the Aspergillus Mold PT and 11 of them were awarded the badge. 24 participated in the pesticides PT and 19 of them met criteria for the badge, while four of them did not report results.

The press release noted that the pesticides and residual solvents in hemp oil PTs were some of the more challenging tests in the spring program. 43 labs reported results for the residual solvents in hemp oil PT and only 31 received badges. The terpenes in hemp oil PT was also a challenging test where 21 labs participated and only 11 received the badge, marking the lowest passing rate of all the PTs.

The advisory panel for The Emerald Test consists of chemists, accreditation providers, laboratory owners, and other industry experts to keep it representative of industry needs. “The Emerald Test is the most comprehensive testing program in the world for the cannabis industry, but as the market grows more testing will be needed,” says Groggel. “We intend to continue introducing new proficiency tests while expanding the menu of matrix choices in response to laboratory requests and regulatory requirements.”

According to the press release, their fall program is open for enrollment until today. Testing begins in mid-October.