What is genomic testing of urine?
Rick Martin: Molecular diagnostics is done essentially in two types of diagnostic tests. The first is a PCR, polymerase chain reaction, or rapid stream test, and that is followed by a full comprehensive next-generation sequencing. Both tests rely on 16-S, the range on the gene, and NGS also incorporates ITS which is the area for fungal identification.
Why is the older, Agar plate culture, being replaced with genomic testing?
Rick Martin: Agar plate was developed in 1870 by the father of microbiology, Robert Koch. This diagnostic form was developed to identify what Koch identified as professional pathogens. At the time, infections of typhoid, dysentery and so forth, and this technology relied on having to grow the microorganism. We now know that less than 1% of all microorganisms can be grown in any type of medium so it's much more accurate in terms of detecting microorganisms by identifying them by their unique DNA.
Is genomic testing more accurate than cultures?
Rick Martin: Culture technique is still a viable option for diagnosing acute infections. Acute infections are often caused by a single species or pathogen. They are not at all able to detect multiple species which form in biofilm. In chronic infection, we now know based on a lot of research in the last five years, that chronic infections are not caused by a single species but by multiple species living in these collaborative communities and attaching to the bladder wall, and the urinary tract.
They are highly synergistic, they have built a matrix around themselves and they are much more difficult to detect because once the bacteria move into a biofilm phenotype, they express different genes, they behave entirely different, their metabolism is different and they don't easily grow on any type of medium.
In urinary samples alone, we've detected more than 2,000 species of microorganisms, both bacteria and fungus. In many cases, the samples are polymicrobial, multiple species together, again, operating in a biofilm.
When is genomic testing used?
Rick Martin: Most practitioners are going to use it when they've already done a culture, they've already had a patient on antibiotics and the patient is still symptomatic and not responding to therapy. We would argue that it makes more sense to start using DNA sequencing rather than using cultures again.
How specific/accurate is genomic testing?
Rick Martin: We're essentially 99% accurate.
Will the test identify candida and/or other complex fungal infections?
Rick Martin: Yes, we can identify all fungal species. Candida albicans is in our rapid screen PCR panel, but when we do full comprehensive, we will pick up every known mold and yeast in the universe. I believe we've identified more than 500 different fungal species in urine samples.
How does the test identify drug resistances?
Rick Martin: Bacteria develop resistance because they acquire a gene which basically turns off that antibiotic. Those genes now can be detected using PCR technology. We'll build a primer for a specific gene, whether it's the gene that causes beta-lactam resistance, which is basically cephalosporins and penicillin class, or quinolone resistance or aminoglycoside resistance. Each of these antibiotic classes has a known gene which causes resistance. We can detect those genes in the samples and tell the clinician whether you have, within your urine sample of resistance, two specific classes of antibiotics.
Does a doctor have to order the test? Does it require a physician signature?
Rick Martin: We're governed by CAP and CLIA. CLIA does, in certain states, have their own rules for laboratories. Certain states do allow for us to take samples from patients without a physician's signature, other states require a physician signature. We provide a list of those states that do not require a physician's signature on our website. If you are in one of those states that does not require a physician's signature, you can take and follow the directions for a urine sample and send it directly to us.
What do the test results look like? (i.e. quick PCR results vs. 5-day genomic results)
Rick Martin: PCR is delivered overnight, so if you take your urine sample on Sunday and shipped it to us on Monday, by Tuesday afternoon you'll have the rapid screen PCR which is 21 species plus resistant genes. Then two days later, you'll have your full omprehensive next gen sequencing. The delivery time for the full comprehensive NGS is right around 3.4 days.
Do you have any research data showing effectiveness of Microgen’s testing methods?
Rick Martin: We have more published clinical trials than in any lab in the world, when it comes to using molecular as a diagnostic tool for detection of microorganisms. We have published studies in urinary tract infections, where we were statistically significantly superior to culture in relieving patients' symptoms scores and clearing infections from UTIs.
How much does genomic testing cost?
Rick Martin: $259.