FEB 19, 2020 11:00 AM PST

Emerging as the New Gold Standard in Quality & Safety: Parallel DNA Based Cannabis Testing of Multiple Microbes

Sponsored by: PathogenDx
C.E. Credits: P.A.C.E. CE Florida CE
  • Co-Founder and Chief Scientific Officer, PathogenDx
      Dr. Michael Hogan's expertise is in the area of physical chemistry, biosample processing and genetic testing. He is leading multiple programs in technology development at PDx, with special emphasis on building its proprietary DNA microarray technology into the cannabis, food safety and agricultural markets.

      Dr. Hogan has 30 years of experience in translational science, with special emphasis on the application of physical biochemistry to commerce. Hogan has invented, developed & commercialized multiple technologies for medical devices, therapeutics, in vitro diagnostics, genomic testing and biological sample preservation and has been awarded more than 50 patents and has more than 90 peer reviewed publications in those several areas. His team's work in the area of biological sample stabilization was awarded a Frost & Sullivan Award in 2014.

      Dr. Hogan obtained his undergraduate degree in Biology from Dartmouth in 1973; his Ph.D. in Molecular Biophysics from Yale in 1978; and as a post-doc in 1979, was awarded a Damon Runyon Cancer Fellowship at Stanford, where he worked in the Stanford Magnetic Resonance Laboratory.

      In academia, Hogan first served as Assistant Professor of Molecular Biology at Princeton (1979-1988) and then Professor of Biotechnology & Molecular Physiology at Baylor College of Medicine (1989-2001) where he also served as the Founding Director of the Graduate Program in Biotechnology.

      Five companies have been formed from his technology over the past 20 years, all in the area of DNA biotechnology, therapeutics and diagnostics. For each, he served as a Founder and CSO, having worked closely with the equity funding community and directly with multiple academic and commercial partners and customers.
    • Principal Scientist, PathogenDx
        Dr. Katchman leads the research and development of sample preparation and assay development at PathogenDx, a Scottsdale, AZ based company which provides disruptive DNA-based pathogen testing technology and solutions for the cannabis, botanical, food and agricultural industries.

        Previously, Dr. Katchman spent 20 years working with various universities and small companies developing novel nucleic acid and proteomic approaches for biomarker discovery and molecular diagnostics. This includes the development of plate-based and microarray-based diagnostic systems for use in clinical laboratories and point-of-care diagnostics for Arizona State University, FlexBioTech, Inc., and Eccrine Systems, Inc.

        Prior to joining PathogenDx, Dr. Katchman was a Principle Investigator at Eccrine Systems, Inc. where he led all clinical research, regulatory pathway implementation, assay development, and biomarker studies. He was the co-founder of FlexBioTech, Inc., where he led the development of novel OLED-based molecular diagnostic assay platforms.

        Dr. Katchman received a B.S. in Microbiology, from Indiana University in 2005, then carried out graduate research with Prof. Douglas F Lake at Arizona State University where he was the first to identify QSOX1 as a proto-oncogene and novel tumor biomarker resulting in over $2M in funding and multiple patents. He performed his postdoctoral research with Prof. Karen S Anderson and Prof. Joshua LaBaer where he designed novel high-density protein microarrays and novel clinical and point of care diagnostics utilizing flexible OLED based electronics resulting in over $15M in funding, multiple patents and high-impact publications.

      DATE:  February 19, 2020
      TIME:   11:00am PST, 2:00pm EST
      This WebNR will focus on the key attributes of DNA-based microbial testing, which can be usefully broken into 4 Basic Principles.
      Don’t Ask, Don’t Tell:  Why it is important to test (at high resolution) for individual pathogen species vs the historical practice of (low resolution) testing by plate culture for “Class Indicator Organisms”? For example, most gram negative enterobacteria are harmless (but Salmonella enterica and E coli O157) are not. Similarly, most fungal contamination is harmless including that from most Candidae, but C auris is very pathogenic. Historically, based on plate based culture, such detailed speciation was difficult in many cases. Given that DNA testing can deliver, with very little specialized user expertise, such speciation and sub-speciation among bacteria and fungi, the argument can now be made that testing for such “high resolution” speciation via DNA methods should now be viewed as a “must-have” in cannabis, food, agriculture and environmental screening applications.
      To Enrich or Not Enrich? Historically, a trade-off (devil’s bargain) has been made based on the desire to increase the sensitivity of microbial detection, by the use of non-specific fluid-phase microbial enrichment culture, prior to plate-based or other methods, in the face of the risk of distorting the original microbial population. That well know risk is based on the (inevitable) reality that many microbes in a complex population will grow more poorly than others in any single medium chosen for such “Enrichment”. Given the nearly theoretical (single molecule) sensitivity of PCR-based DNA testing, it can now be shown that, in most cases, fluid phase enrichment is no longer required to detect rare microbes in a population. Based on the nearly perfect sensitivity of PCR and the fact that DNA testing can be performed on very small-volume samples, is it now possible to couple large-volume-to-small-volume sample concentration technology to the intrinsic, single molecule, sensitivity of PCR, thus enabling the faithful detection of all microbes in a population by DNA testing without “Enrichment” of any kind. In the face of that new capacity for un-enriched, DNA based microbial population analysis, the argument can be made that the (distortive) historical practice of “Enrichment” is no longer necessary (at least in small sample volume <25 grams??).
      Live vs Dead? In general, DNA testing detects the presence of all contaminating microbes in a sample: those presently alive, those which used-to-be alive, those which are culturable and those which are hard to culture. In contrast, the historical practice of plate-based culture can only detect a sub-set of the resident microbial contamination in a sample: namely those microbes presently alive and also easy to culture. Having said that, plate based culture has been in existence since the late 19th century and its limited capacity for “live+culturable” microbial detection has, by default, become the “Gold Standard” or “Base Truth” for the whole field of microbial analysis. Given that the residue delivered from dead microbes or “hard to culture” microbes in a sample (i.e. bacterial endotoxins and fungal mycotoxins) present, especially in cannabis and much of environmental testing, much of the pathogenic health risk to man, it is now reasonable to ask if DNA testing can now, at least for cannabis testing, be elevated to the new “Gold Standard” or “Base Truth” for microbial pathogen analysis, with plate culture (which detects only a subset of the resident microbial load) relegated to a confirmatory role. That emerging (primary) role for DNA-based microbial testing is additionally reinforced by new auxiliary technology which can be used to eliminate cell-free DNA from a microbial population, especially that which had arisen from microbial cell death or biofilm formation. That emerging ability, especially in cannabis, to focus DNA-based microbial testing on only the cellular DNA in a sample, additionally reinforces the seminal role that DNA based microbial testing can now play in safety testing for the cannabis supply chain.
      qPCR, PCR+Microarray, PCR+NGS:  In the beginning of the PCR technology era in the late 1970s, it was quickly observed that PCR could change the world of microbiology. A correctly-chosen forward/reverse primer pair could amplify even a single molecule of DNA 10+9 fold, thus delivering enough of its PCR-amplified product to be detected by simple dye staining. Quickly thereafter, it was realized that any DNA with ends complementary to such a primer pair would be amplified by PCR, thus making it impossible, via simple PCR and dye staining, to distinguish closely-related microbial gene variants, especially the gene variation which can be used to distinguish closely-related members of the same microbial family. To enable a more detailed approach to PCR analysis of closely-related gene variants, two new PCR-based technologies were invented at about the same time in the 1990s: TaqMan qPCR and PCR coupled to a microarray. Two decades later (@2010) a third technology was added to the tool set: PCR coupled to Next Generation Sequencing (NGS). All three are based on more less the same sort of initial microbial PCR reaction, which is then coupled to either the interrogation of the PCR product by hybridization to a sequence specific DNA probe (in both qPCR and in microarrays) or coupled to a secondary amplification of individual DNA molecules, followed by sequence analysis of each type of molecule (by NGS). The three technologies are all useful but deliver a continuum of analytical content, which is best catalogued in terms of the number of (microbial) gene variants which can be tested per reaction.
      Practical Analytical Content Limit
      1. qPCR: analysis of less than 5 DNA variants within a gene region;
      2. PCR-Microarray: analysis of less than 50 DNA variants within a gene region;
      3. PCR-NGS: analysis of less than 500 DNA variants within a gene region.
      Each differing significantly in terms of their absolute sensitivity.
      Practical Sensitivity Limit
      1. qPCR: 50 gene copies per reaction
      2. PCR-Microarray: 1 gene copy per reaction
      3. PCR-NGS: 1 gene copy per reaction
      Each differing significantly in terms of sample preparation requirements.
      Practical Sample Purification Requirements
      1. qPCR: requires column or magnetic bead based DNA purification
      2. PCR-Microarray: no purification required for PDx platform
      3. PCR-NGS: requires column or magnetic bead based DNA purification
      Each differening in economics in terms of Total Cost per Sample test (eg Cannabis flower w/ 6 organisms) 
      1. qPCR: >$50 -to-<$80 per sample
      2. 2) PCR: Microarray >$25-to-<$35 per sample
      3. 3) PCR: NGS >$100 per sample
      Learning objectives:
      • Explain the basic principles of widely-used DNA-based microbial testing methods: qPCR, Sequencing, Microarrays.
      • Discuss the origins of intrinsic sensitivity and specificity differences among DNA based microbial testing methods vs culture based testing.
      • Discuss the information content difference obtained from microbial DNA testing methods vs traditional plate culture.
      Webinars will be available for unlimited on-demand viewing after live event.
      LabRoots is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E. ® Program. By attending this webinar, you can earn 1 Continuing Education credit once you have viewed the webinar in its entirety.

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