Tag Archives: coliform

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.

emerald test retail

Analyzing The Emerald Test Results: Cannabis Labs Making Progress

By Aaron G. Biros
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emerald test retail

The Emerald Test advisory panel recently convened to review the results from the Fall 2016 round of the semi-annual Inter-Laboratory Comparison and Proficiency Test (ILC/PT), ahead of the third annual Emerald Conference just a few weeks away. After reviewing and analyzing the results, the panel noticed a significant improvement across the board over their Spring 2016 round of proficiency testing.rsz_emerald-scientific_letterhead-1

Emerald Scientific’s ILC/PT program is a tool laboratories use to check how accurate their testing capabilities are compared to other labs. A lab receiving The Emerald Test badge indicates their testing meets the criteria established by the panel to demonstrate competency. This means that they were within two standard deviations of the consensus mean for all analytes tested, according to Wes Burk, vice president of Emerald Scientific. He says the labs performed better than expected on both the microbial and pesticide tests.

Wes Burk, vice president of Emerald Scientific.
Wes Burk, vice president of Emerald Scientific.

emerald test retailEach lab has access to raw, anonymized data including a consensus mean, z-scores and kernel density plots. This round measured how well 35 cannabis labs perform in testing for potency, pesticides, residual solvents and microbial contaminants such as E. coli, Salmonella, Coliform, yeast and mold.

The advisory panel includes: Robert Martin, Ph.D., founder of CW Analytical, Cynthia Ludwig, director of technical services at AOCS, Rodger Voelker, Ph.D., lab director, OG Analytical, Tammie Mussitsch, QA manager at RJ Lee Group, Shawn Kassner, senior scientist at Neptune & Company, Inc., Jim Roe, scientific director at Steep Hill Labs, Chris Hudalla, Ph.D., founder and chief scientific officer at ProVerde Labs, Sytze Elzinga, The Werc Shop and Amanda Rigdon, Chief Technical Officer at Emerald Scientific.

amandarigdon
Amanda Rigdon, chief technical officer at Emerald Scientific

According to Amanda Rigdon, chief technical officer at Emerald Scientific, the labs performed very well in potency, residual solvents and microbial testing PTs. This is the first year the proficiency testing includes pesticides. “All of the labs did a great job identifying every pesticide in our hemp-based PT, but some more work will most likely have to be done to bring quantitative results in line,” says Rigdon. “Since this was the first pesticide PT we had offered, we were pretty conservative when choosing analytes and their levels. For the most part, analytes and levels were taken from the Oregon pesticide list, which is widely recognized to be the most reasonable and applicable pesticide list out there to date.” They covered pesticides of high concern, like abamectin and Myclobutanil, but also included a wide range of other pesticides that labs are expected to encounter.

Shawn Kassner, senior scientist at Neptune
Shawn Kassner, senior scientist at Neptune & Company, Inc.

Shawn Kassner, senior scientist at Neptune & Company, Inc., believes microbial contamination proficiency testing should be a priority for improving public health and safety going forward. Although five participating labs did not receive badges for the microbial contamination PTs, panel members say the overall performance was really quite good. “Microbiology testing are essential analyses for all cannabis products and it’s just slower in regulatory implementation than potency testing,” says Kassner. “The risk of Salmonella and E. coli to an individual using a medical cannabis product could be very life threatening. Microbiology contamination is a huge concern for any public health agency, which is why we have seen that microbiology testing is usually the first analytical test required after potency.” Kassner notes that there were few outliers and with each Emerald PT program, he is seeing an improvement in overall laboratory performance.

For The Emerald Test’s next round, the panel hopes to make some improvements in the test’s robustness and consistency, like obtaining assigned values for all samples and comparing to a consensus mean. “We want to develop permanent badge criteria, streamline the appeals process and possibly implement a qualitative performance review in the pesticide PT,” says Burk. For the next round of pesticide PTs, they want to build a better list of pesticides to cover more states, allowing labs to pick a set based on their state’s regulations. Burk says they also want to collect data on whether or not matrix-matched curves were used for pesticides.

Rodger Voelker, Cynthia Ludwig and Shawn Kassner, all members of the advisory panel, will be speaking at the Emerald Conference, discussing some of their findings from this round of proficiency testing. The Emerald Conference will take place February 2nd and 3rd in San Diego, CA.