Frequently Asked Questions

MicroGen DX is an innovative, CAP accredited, CLIA licensed, molecular diagnostic laboratory utilizing proprietary PCR (Polymerase Chain Reaction) technology. But what sets us apart in delivering truly superior molecular diagnostics is our Proprietary Bioinformatics System and our process in using NGS (Next Generation Sequencing) for precise detection of infectious diseases at high levels of sensitivity and specificity.

MicroGen Vet is the exclusive reseller of NGS services from MicroGen DX to the global veterinary markets, including equine, small animal, livestock and exotic/zoo segments.  MicroGen Vet is responsible for building comprehensive sales and delivery channels from distributors and online resellers in the target markets and for establishing a broad network of leading clinicians to assist with market education and translation from human to animal markets.

MicroGen Vet and MicroGen DX are separate business entities and do not have any common ownership.  MicroGen Vet was established in 2017 to bring the NGS services offered by MicroGen DX to the human healthcare markets to veterinarians in order to improve animal health outcomes.

MicroGen DX is an innovative, CAP accredited, CLIA licensed, molecular diagnostic laboratory utilizing proprietary PCR (Polymerase Chain Reaction) technology. But what sets us apart in delivering truly superior molecular diagnostics is our Proprietary Bioinformatics System and our process in using NGS (Next Generation Sequencing) for precise detection of infectious diseases at high levels of sensitivity and specificity.

MicroGen DX We are CAP and CLIA certified. College of American Pathologists (CAP) is a laboratory accreditation program that is widely recognized as the ‘gold standard’ and has served as a model for various federal, state, and private laboratory accreditation programs throughout the world. The Clinical Laboratory Improvement Amendments (CLIA) establish quality standards for all laboratory testing to ensure the accuracy, reliability, and timeliness of patient test results regardless of where the test was performed.

MicroGen DX was founded in 2008 under the DBA Pathogenius by Randy Wolcott, MD of Southwest Regional PCR. In 2017 the company was acquired and rebranded as MicroGen DX Laboratory. Collectively this laboratory has been used by more than 8,000 doctors and delivered over 300,000 NGS lab results.

1. 1. 24 hour turn-around for PCR Lab results (from sample receipt) for PCR reports
   2. Detection of Resistance Genes
   3. Overall treatment cost reduction and avoidance
   4. Reduced antibiotic utilization and better antibiotic stewardship
   5. Increased heal rates
   6. Increased patient satisfaction

Polymerase chain reaction (PCR) is a molecular biology technique that amplifies a DNA base pair sequence up to several orders of magnitude (billions and trillions of copies). PCR (Polymerase Chain Reaction) is a proprietary technology that accomplishes the task of DNA amplification in a multiplex format; e.g. amplifying the DNA of multiple organisms in a single reaction.

Next Generation Sequencing (NGS), also known as high-throughput sequencing, Next Generation Sequencing refers to non-Sanger-based high-throughput DNA sequencing technologies. Millions or billions of DNA strands can be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragment-cloning methods that are often used in Sanger sequencing of genomes.

1. Superior specificity of 99.9% microbes within an infection site
2. Fast results in 3-5 business days (from sample receipt)
3. Simultaneous identification of bacteria fungi, viruses, parasites, Candida and antibiotic resistance
4. Detection of bacteria in the presence of antibiotics
5. Increased sensitivity and specificity
6. Simplicity of sample collection

We do not need to follow the same guidelines for transportation as culture samples, as DNA is not easily affected by time and temperature.

1. Rapid PCR Level 1 delivers detection of microbes on the chosen panel within 24 hours. Also, bacterial load and 8 gene resistances for immediate antibiotic therapy are delivered.
2. NGS Level 2 is delivered within 3-5 business days of receipt typically. The complex processing and verification associated with Next-Gen Sequencing typically takes 3-5 days. The superior data delivered in the Comprehensive report provides all the detected microbes within the sample and their relative abundances. With this next level of data, physicians can target therapy to over 25,000 major contributors of the disease state in great depth regardless of aerobic or anaerobic state.

No, however we do test for the following resistance genes:

• Vancomycin
• Methicillin
• Beta-lactam
• Carbapenem
• Macrolide
• Aminoglycoside
• Tetracycline

We also provide the antimicrobial recommendation for each species detected. These recommendations are research based, similar to an antimicrobial guide reference. When a more typical bacteria is detected that is easily grown in the micro lab, like e-coli, your local antibiogram which tracks local resistance patterns should be referenced. This will only apply to 20-25 microbial species that are easily grown in culture.

No. MicroGen DX does molecular testing, not microbiological testing. However, we deliver the class of antibiotics per species found from the National Library of Microbiology.

A single sample bag and order form for each box.

Call FedEx at 1-800-GOFEDEX (1-800-463-3339) and give them the tracking number (12 digit number under the barcode). When calling say “agent” twice to speak to agent. Let them know it’s biohazard prepaid pick-up.

Drop off at any FedEx/Kinkos location and drop inside at front of the store.

Our packages are accepted at FedEx® main facility locations and FedEx® Drop Boxes. FedEx® Office locations WILL NOT accept this type of package. Visit FedEx.com  to find a location near you.

Always retain the *Keep for your records* shipping label copy from your FedEx Express® shipping label. Go to FedEx.com and type in the tracking number of your package to check the delivery status.

FedEx® routes may vary from location to location. Call 1-800-GO-FEDEX (1-800-463-3339) to obtain a pickup schedule for your area. Only request a FedEx Express® pickup schedule, as other FedEx® methods do not apply.

Only FedEx Express® drivers will accept UN3373 Clinical Paks. FedEx Ground® drivers will not accept packages classified as such.

Diagnostic tests such as PCR and NGS are tools used in conjunction with patient symptoms, history, and other appropriate companion diagnostic tests (complete blood count, inflammatory markers, etc) that the provider deems appropriate to properly diagnose and treat.

Multiplex and comprehensive molecular technology is more sensitive than culture and can reliably detect multiple organisms in the specimen in the presence of antimicrobial therapy. NGS removes the human bias and variation of culture from microbiology laboratories, and does not require organism viability. Results may not always correlate due to the fact that NGS can detect organisms that are not readily grown in culture.

Both sensitivity (or the limit of detection – LoD) and specificity of NGS testing is determined as a part of our validation protocol. The steps outlined by the Clinical Laboratory Standards Institute are summarized in a document prepared by MicroGen DX and is available for circulation to our clients and their staff. Additional information about the sensitivity and specificity of a particular target on any one of the panels is also available upon request.

1. 1. Recurrent or chronic UTIs are sometimes the result of more than just a single infectious organism. Urine culture is biased towards a single infectious organism based on CFU (colony-forming unit) count, possibly leading to inappropriate therapy. Some problematic organisms are not readily grown in culture which may lead to incorrect treatment or non-treatment. The advantage of NGS is the ability to test and detect multiple organisms simultaneously, including those that may not grow readily in culture. And if the patient is currently on antibiotic therapy or has a recent history of antibiotic therapy, detection of pathogens by NGS is not impacted by the presence of antibiotics.

2 ways to retrieve your lab reports:

1. MDX Secure Email
2. Secure FAX

We provide an antimicrobial recommendation for each species detected. These recommendations are research based, similar to an antimicrobial guide reference. When a more typical bacteria is detected that is easily grown in the micro lab, like e-coli, your local antibiogram which tracks local resistance patterns should be referenced. This will only apply to 20-25 microbial species that are easily grown in culture. Click Here to View Example

This sometimes happens when a strain of E coli or Kleb has a mutation at our primer binding site for our Level 1 assay. The mutation will cause it to not be detected by the Level 1. However, since Level 2, using a completely different site and technology, will be able to detected those strains.

In general: Level 1 will be able to detect panel organisms at a lower concentration than level 2 (level 1 is more sensitive) However, Level 2 will detect numerous more organisms than Level 1.

Value of NGS over PCR is that we can still identify that’s had a strain mutation when the narrow range of PCR will not identify them.

Recurrent or chronic UTIs are sometimes the result of more than just a single infectious organism. Urine culture is biased towards a single infectious organism based on CFU (colony-forming unit) count, possibly leading to inappropriate therapy. Some problematic organisms are not readily grown in culture which may lead to incorrect treatment or non-treatment. The advantage of NGS is the ability to test and detect multiple organisms simultaneously, including those that may not grow readily in culture. And if the patient is currently on antibiotic therapy or has a recent history of antibiotic therapy, detection of pathogens by NGS is not impacted by the presence of antibiotics.

Tissue can be accepted as a specimen source but it is recommended that the tissue be no larger than the size of a pea.

Yes.

Yes.

Orange.

Red.

Be Thorough swabbing the entire area of suspected infection site. Detailed instructions are in the how-to video and PDF found on the Wound Care specialty page.

Yes. Sluff will carry DNA of microbes.

Red.

No, urine must be transferred to the yellow capped 60ml Vial.

Yes.

Add approximately 10mls of urine.

No.

The next day, or week is just fine. DNA is not easily affected by time and temperature. If you weren’t able to ship out the same day or even missed last time of Friday ship the sample the next business day.

MGV Pack and Ship Instructions

MGV How To Collect Lower Respiratory Sample

MGV How To Collect Ortho Sample

MGV How To Collect Urine Sample

5 reasons your sample may have been compromised

1. Sample was collected from a site where there was no microbial species.
2. Biocides or Lidocaine at 4% or higher was on the sample.
3. Sample contained an overabundance of host DNA.
4. Sample contained only non-viable material – ie, pus, mucus.
5. In the case of urine an antibiotic active metabolite was in the sample vial and degraded the DNA. This can occur if the patient is on antibiotics.

Culture sensitivities can only be performed if you can “grow” the microbe.

Being able to culture “grow” a microbe is not the determining factor to verify if the species is a problem for the host.

Only 1% of all known microorganisms can be grown in culture. Most physicians have only seen 30-50 species on C&S reports their entire medical career.

We currently know the sequence codes for more than 25,000 species.

We do provide antibiotic resistance by detection of the resistant gene for the antibiotic classes.

ECSMID guidelines make the point that antibiotic sensitivities have no clinical value when treating a biofilm infection.

Breakpoints to determine S-I-R have been established for planktonic bacteria however, breakpoints haven’t been established for the biofilm or community of microorganisms.

Dead or Non Viable bacteria DNA degrades within 24 hours within the host environment.

Viable or Live bacteria once removed from the host environment it will take about 5 days for the DNA to die or degrade and become non-viable.

• If you refrigerate the sample it will be good for weeks. If you freeze the sample, the DNA will not degrade, and will be good forever.
• Due to the rapid degradation of DNA in dead bacterial cells it becomes extremely challenging for the technology to reach the threshold of DNA reads. If we don’t achieve enough DNA reads we can not detect the species.
• If the bacterial species is listed in our report it has met our criteria for DNA reads.

Detecting multiple species in a sample may be overwhelming, especially seeing species that you do not recognize. We are providing a complete picture of the microorganisms at the site the sample was taken from.  If the sample was taken from an area of the host which has an established microbiome, (sinus cavity, mouth) interpretation can be more of a challenge. The following are points you should consider when reviewing our report.

• When treating a chronic infection you are dealing with biofilm phenotype.
• CDC and NIH “have estimated that biofilm infections now constitute 65% to 80% (respectively) of bacterial infections treated by physicians in the developed world.
• All bacteria / microorganisms will move to a biofilm phenotype.
• If we detect multiple species from a host site that is normally sterile, there is a high probability you are dealing with a Biofilm.

What do I treat?

1. Answer: Treatment decisions are based on multiple diagnostic criteria. Our report is not to be used in isolation. A common approach is to treat the dominant species when there is a concern for using multiple antimicrobials.

Is there a cut off of which species to treat?

1. Answer: No. Multiple species identified could be interpreted as a biofilm. In the case of biofilm infections the microorganisms are a “collaborative community” and are highly synergistic. When the sample is taken from a site other than the mouth, sinus cavity, gut, or areas in the body where we have an established microbiome, there are no commensal bacteria (Good Bacteria). Commensals need specific host related mechanisms and those host dependent processes are not possible in wounds, RTI, UTI, or joint infections.

You will find microorganism DNA in healthy people BUT you are going to have other diagnostic information to indicate infection. We give you precise information on what was detected at the site.

We only report species that make up greater than 2% of the DNA detected.