Tag Archives: spike

October 21, 2019

3 Essential Components of Microbial Safety Testing

By Heather Ebling

Microbial contamination on cannabis products represents one of the most significant threats to cannabis consumers, particularly immunocompromised patients who are at risk of developing harmful and potentially fatal infections.

As a result, regulatory bodies in the United States and Canada mandate testing cannabis products for certain microbes. The two most popular methods for microbial safety testing in the cannabis industry are culture-based testing and quantitative polymerase chain reaction (qPCR).

When considering patient safety, labs should choose a method that provides an accurate account of what is living on the sample and can specifically target the most harmful microbes, regardless of the matrix.

1. The Method’s Results Must Accurately Reflect the Microbial Population on the Sample

The main objective of any microbial safety test is to give the operator an indication of the microbial population present on the sample.

Figure 1: MA data collected directly from plant material before and after culture on 3M petrifilm and culture-based platforms.

Culture-based methods measure contamination by observing how many organisms grow in a given medium. However, not all microbial organisms grow at the same rate. In some cases, certain organisms will out-compete others and as a result, the population in a post-culture environment is radically different than what was on the original sample.

One study analyzed fifteen medicinal cannabis samples using two commercially available culture-based methods. To enumerate and differentiate bacteria and fungi present before and after growth on culture-based media, all samples were further subjected to next-generation sequencing (NGS) and metagenomic analyses (MA). Figure 1 illustrates MA data collected directly from plant material before and after culture on 3M petrifilm and culture-based platforms.

The results demonstrate substantial shifts in bacterial and fungal growth after culturing on the 3M petrifilm and culture-based platforms. Thus, the final composition of microbes after culturing is markedly different from the starting sample. Most concerning is the frequent identification of bacterial species in systems designed for the exclusive quantification of yeast and mold, as quantified by elevated total aerobic count (TAC) Cq values after culture in the total yeast and mold (TYM) medium. The presence of bacterial colonies on TYM growth plates or cartridges may falsely increase the rejection rate of cannabis samples for fungal contamination. These observations call into question the specificity claims of these platforms.

The Live Dead Problem

Figure 2: The enzyme is instantaneously inactivated when lysis buffer is added

One of the common objections to using qPCR for microbial safety testing is the fact that the method does not distinguish between live and dead DNA. PCR primers and probes will amplify any DNA in the sample that matches the target sequence, regardless of viability. Critics claim that this can lead to false positives because DNA from non-viable organisms can inflate results. This is often called the Live-Dead problem. However, scientists have developed multiple solutions to this problem. Most recently, Medicinal Genomics developed the Grim Reefer Free DNA Removal Kit, which eliminates free DNA contained in a sample by simply adding an enzyme and buffer and incubating for 10 minutes. The enzyme is instantaneously inactivated when lysis buffer is added, which prevents the Grim Reefer Enzyme from eliminating DNA when the viable cells are lysed (see Figure 2).

2. Method Must Be Able to Detect Specific Harmful Species

Toxic Aspergillus spp., which is responsible for at least one confirmed death of a cannabis patient, grows poorly in culture mediums and is severely underreported by current culture-based platforms. And even when Aspergillus does grow in culture, there is a certain non-pathogenic Aspergillus species that look remarkably similar to their pathogenic cousins, making it difficult to speciate using visual identification alone.

Conversely, qPCR assays, such as the PathoSEEK, are designed to target DNA sequences that are unique to pathogenic Aspergillus species, and they can be run using standard qPCR instruments such as the Agilent AriaMx. The primers are so specific that a single DNA base difference in the sequence can determine whether binding occurs. This specificity reduces the frequency of false positives in pathogen detection, a frequent problem with culture-based cannabis testing methods.

Additionally, Medicinal Genomics has developed a multiplex assay that can detect the four pathogenic species of Aspergillus (A. flavus, A. fumigatus, A. niger, and A. terreus) in a single reaction.

3. The Method Must Work on Multiple Matrices

Figure 4: The team also placed TSB without any E. coli onto a petrifilm to serve as a control.

Marijuana infused products (MIPs) are a very diverse class of matrices that behave very differently than cannabis flowers. Gummy bears, chocolates, oils and tinctures all present different challenges to culture-based techniques as the sugars and carbohydrates can radically alter the carbon sources available for growth. To assess the impact of MIPs on colony-forming units per gram of sample (CFU/g) enumeration, The Medicinal Genomics team spiked a known amount of live E. coli into three different environments: tryptic soy broth (TSB), hemp oil and hard candy. The team then homogenized the samples, pipetted amounts from each onto 3M™ Petrifilm E. coli / Coliform Count (EC) Plates, and incubated for 96 hours. The team also placed TSB without any E. coli onto a petrifilm to serve as a control. Figures 3 and 4 show the results in 24-hour intervals.

Table 1: DNA was spiked into various MIPs

This implies the MIPs are interfering with the reporter assay on the films or that the MIPs are antiseptic in nature.

Many MIPs use citric acid as a flavoring ingredient which may interfere with 3M reporter chemistry. In contrast, the qPCR signal from the Agilent AriaMx was constant, implying there is microbial contamination present on the films, but the colony formation or reporting is inhibited.

Table 3: SenSATIVAx DNA extraction can successfully lyse the cells of the microbes

Table 2: Different numbers of DNA copies spiked into chocolate

This is not an issue with DNA-based methods, so long as the DNA extraction method has been validated on these matrices. For example, the SenSATIVAx DNA extraction method is efficient in different matrices, DNA was spiked into various MIPs as shown in Table 1, and at different numbers of DNA copies into chocolate (Table 2). The SenSATIVAx DNA extraction kit successfully captures the varying levels of DNA, and the PathoSEEK detection assay can successfully detect that range of DNA. Table 3 demonstrates that SenSATIVAx DNA extraction can successfully lyse the cells of the microbes that may be present on cannabis for a variety of organisms spiked onto cannabis flower samples.

August 7, 2018

From The Lab

Quality Plans for Lab Services: Managing Risks as a Grower, Processor or Dispensary, Part 4

By Dr. Edward F. Askew

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In the last three articles, I discussed the laboratory’s responses or defenses used to reply to your questions about laboratory results that place stress on the success of your business. The Quality Control (QC) results can cause this stress if they are not run correctly to answer the following questions:

Are the laboratory results really true?
Can the laboratory accurately analyze sample products like my sample?
Can the laboratory reproduce the sample results for my type of sample?

Now let’s discuss the most important QC test that will protect your crop and business. That QC sample is the Matrix Sample. In the last article in this series, you were introduced to many QC samples. The Matrix Sample and Duplicate were some of them. Take a look back at Part 3 to familiarize yourself with the definitions.

The key factors of these QC sample types are:

Your sample is used to determine if the analysis used by the laboratory can extract the analyte that is being reported back to you. This is performed by the following steps:
1. Your sample is analyzed by the laboratory as received.
2. Then a sub-sample of your sample is spiked with a known concentration of the analyte you are looking for (e.g. pesticides, bacteria, organic chemicals, etc.).
3. The difference between the sample with and without a spike indicates whether the laboratory can even find the analyte of concern and whether the percent recovery is acceptable.
4. Examples of failures are from my experiences:
  1. Laboratory 1 spiked a known amount of a pesticide into a wastewater matrix. (e.g. Silver into final treatment process water). The laboratory failed to recover any of the spiked silver. Therefore the laboratory results for these types of sample were not reporting any silver, but silver may be present. This is where laboratory results would be false negatives and the laboratory method may not work on the matrix (your sample) correctly. .
  2. Laboratory 2 ran an analysis for a toxic compound (e.g. Cyanide in final waste treatment discharge). A known amount of cyanide was spiked into a matrix sample and 4 times the actual concentration of that cyanide spike was recovered. This is where laboratory results would be called false positives and the laboratory method may not work on the matrix (your sample) correctly.
Can the laboratory reproduce the results they reported to you?
1. The laboratory needs to repeat the matrix spike analysis to provide duplicate results. Then a comparison of the results from the first matrix spike with its duplicate results will show if the laboratory can duplicate their test on your sample.
  1. If the original matrix spike result and the duplicate show good agreement (e.g. 20% relative percent difference or lower). Then you can be relatively sure that the result you obtained from the laboratory is true.
  2. But, if the original matrix spike result and the duplicate do not show good agreement (e.g. greater than 20% relative percent difference). Then you can be sure that the result you obtained from the laboratory is not true and you should question the laboratory’s competence.

Now, the question is why a laboratory would not perform these matrix spike and duplicate QC samples? Well, the following may apply:

These matrix samples take too much time.
These matrix samples add a cost that the laboratory cannot recover.
These matrix samples are too difficult for the laboratory staff to perform.
Most importantly: Matrix samples show the laboratory cannot perform the analyses correctly on the matrix.

So, what types of cannabis matrices are out there? Some examples include bud, leaf, oils, extracts and edibles. Those are some of the matrices and each one has their own testing requirements. So, what should you require from your laboratory?

The laboratory must use your sample for both a matrix spike and a duplicate QC sample.
The percent recovery of both the matrix spike and the duplicate will be between 80% and 120%. If either of the QC samples fail, then you should be notified immediately and the samples reanalyzed.
If the relative percent difference between the matrix spike and the duplicate will be 20% or less. If the QC samples fail, then you should be notified immediately and the samples should be reanalyzed.

The impact of questionable laboratory results on your business with failing or absent matrix spike and the duplicate QC samples can be prevented. It is paramount that you hold the laboratory responsible to produce results that are representative of your sample matrix and that are true.

The next article will focus on how your business will develop a quality plan for your laboratory service provider with a specific focus on the California Code Of Regulations, Title 16, Division 42. Bureau Of Cannabis Control requirements.

May 9, 2018

IoT & Environmental Controls: urban-gro Launches Soleil Technologies Portfolio

By Aaron G. Biros

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Back in November of 2017, urban-gro announced the development of their Soleil Technologies platform, the first technology line for cannabis growers utilizing Internet-of-Things (IoT). Today, urban-gro is announcing that line is now officially available.

The technology portfolio, aimed at larger, commercial-scale growers, is essentially a network of monitors, sensors and controls that give cultivators real-time data on things like temperature, humidity, light, barometric pressure and other key factors. The idea of using IoT and hypersensitive monitoring is not new to horticulture, food or agriculture, but this is certainly a very new development for the cannabis growing space.

According to Brad Nattrass, chief executive officer and co-founder of urban-gro, it’s technology like this that’ll help growers control microclimates, helping them make the minor adjustments needed to ultimately improve yield and quality. “As ROI and optimized yields become increasingly important for commercial cultivators, the need for technologies that deliver rich granular data and real-time insights becomes critical,” says Nattrass. “With the ability to comprehensively sense, monitor, and control the microclimates throughout your facility in real-time, cultivators will be able to make proactive decisions to maximize yields.”

The heat map allows you to find problem microclimates throughout the grow space.

One of the more exciting aspects of this platform is the integration of sensors, and controls with automation. With the system monitoring and controlling fertigation, lighting and climate, it can detect when conditions are not ideal, which gives a cultivator valuable insights for directing pest management or HVAC decisions, according to Dan Droller, vice president of corporate development with urban-gro. “As we add more data, for example, adding alerts for when temperatures falls or humidity spikes can tell a grower to be on the lookout for powdery mildew,” says Droller. “We saw a corner of a bench get hot in the system’s monitoring, based on predefined alerts, which told us a bench fan was broken.” Hooking up a lot of these nodes and sensors with IoT and their platform allows the grower to get real-time monitoring on the entire operation, from anywhere with an Internet connection.

soleil visuals — Figures in the system, showing temperature/time, humidity/time and light voltage

Droller says using more and more sensors creates super high-density data, which translates to being able to see a problem quickly and regroup on the fly. “Cannabis growers need to maintain ideal conditions, usually they do that with a handful of sensors right now,” says Droller. “They get peace of mind based on two or three sensors sending data points back. Our technology scales to the plant and bench level, connecting all of the aggregate data in one automated system.”

In the future, urban-gro is anticipating this will lay the groundwork for using artificial intelligence to learn when controls need to be adjusted based on the monitoring. Droller hopes to see the data from environmental conditions mapped with yield and by strain type, which could allow for ultra-precise breeding based on environmental conditions. “As we add more and more data and develop the platform further, we can deliver some elements of AI in the future, with increased controls and more scientific data,” says Droller.