I recently had an interview with a new lab called Aperiomics that can identify all known pathogens using next-generation sequencing of DNA and RNA. This test can create a complete genetic fingerprint of all microorganisms, allowing them to test for EVERYTHING at once instead of a few things at a time.
What is even more interesting is that they are using the test to identify pathogens in the IC bladder, and are finding some very interesting trends that they will be publishing in a paper this year.
Here is the website of the lab. https://aperiomics.com/
I wanted to summarize the interview I had with Dr. Icenhour to help people understand how this lab is different than many of the ones we have encountered in the conventional medicine world. I will be working with one of my medical directors to give me access to run this lab for my patients so that they can take the results to their doctor to get treated. Hopefully we will see this test become standard among the medical community so that we can get closer to improving the outcome of IC treatments worldwide!
How are you different than Microgen DX? Microgen uses 16s sequencing, which looks for 200 – 400 base pair gene fragments. Basically, by looking at 1 small gene fragment you can differentiate between some bacteria. A drawback to this is that you can’t really get a species level or strain level since you are looking at a very small gene fragment. In this method, they use PCR to amplify copies of gene fragments. This often can create great bias and really skew the abundance numbers in the specimen. The reason for this is that running PCR preferentially amplifies bacteria that have DNA base pairs with adenine and thymine, but it also underreports bacteria that are high in guanine and cytosine. That is because it is more difficult to amplify the latter with PCR technology. So in essence, they can only identify bacteria to a certain degree. Often times their abundance reports are totally wrong. For example, Aperiomics will report the same species but in much different abundances. E coli, for example, is rich in AT base pairs and is often times reported at high levels in Microgen specimen reports.
My thoughts- This is a pretty significant difference that can lead to a snipe hunt of the wrong bacteria and administration of the wrong antibiotics. As a person who has taken way too much antibiotics in my lifetime, I know that nobody wants to take the wrong antibiotics. It can be destructive to your gut and immune system
What is your experience with IC? Icenhour’s mother had IC and they discovered there was a viral component involved in it. After treating the virus and getting the numbers down, she was able to heal from the condition. She is not cured, but she has the condition under control. Since then, they have tested over 80 patients with IC and are publishing a paper this year on their findings. There are some trends they have identified, which will be helpful in diagnosing and treating some of the root causes of IC.
My thoughts-I believe Aperiomics will be the standard test moving forward in IC diagnosis! This is exciting!
What does it cost to run this test? Right now, it is $1000 cash price per sample to run the test. However, they are working with some insurance companies and they have CPT codes. If insurance covers the cost, then it’s a $200 co-insurance per sample.
Can biofilm busters help identify more species that may be hidden in biofilm communities?
The use of biofilm busters is still up for debate. Theoretically, the biofilm should shed in the urine. The collection procedure is to urinate in a standard urine cup and add a preservative to stabilize the sample for 30 days. That breaks apart the biofilm—if the biofilm is shed into sample, it will be picked up.
So far, biofilm busters have not made huge difference. However, they will continue to monitor it. Best thing for patients to do is to make a note on the lab form to indicate they have taken a biofilm buster so that they can continue to identify trends.
How do you differentiate pathogens vs. normal inhabitants of the bladder?
They calculate the overall microbial burden-if the burden is high, it indicates infection. They need to compare to healthy controls to get a baseline of what healthy is. For example, the presence of a virus combined with symptoms would associate the virus with the pathology of the disease. Just because there is bacteria present there does not mean there is an infection. There has to be symptoms and other factors should be evaluated. They send report out to the doctor and they can schedule a consult with them to discuss. It’s not uncommon for cultures to report something different than their test.
Do you report antibiotic susceptibility or drug resistant genes identified?
They don’t at the moment. Doctors don’t need as much as they think they do when they give a report. Much of what they find are not the usual suspects….by in large, they get the chronic and complicated UTI’s and the offending agents are not really antibiotic resistant. What she thinks is happening is the infections are very complicated….most of the time it’s a dozen or more bacteria. Therefore, it is not as simple as a single bacteria developing resistance to drug.
How often should someone expect to run this test? This is a case by case situation. Often times the test may need to be run several times to see if the initial infection has cleared. Isenhour’s mother had to run the test three times until her pathogenic microbial load declined enough to allow the bladder to heal.
How long should someone wait after a course of antibiotics to run this test?
Absolute minimum of 3 days off of antibiotics and 2 weeks off of probiotics.
Any other special preparation instructions?
It is recommended to be off of all herbal supplements for 2 weeks. Many herbs are contaminated with fungus, and it can give a false positive. One herbal supplement company was reported to FDA-turned out dozens of pathogenic fungi that was consumed is milk thistle extract. There is a body of literature of mycotoxins and herbal supplements. Herbs that elicit a herximeier reaction are a red flag. Mycotoxins are part of a plant mycobiome.
The medical director I am working with to gain access to this lab for my patients is Dr. Marcus Ettinger. Dr. Ettinger is a southern California Licensed Doctor of Chiropractic with more than 29 years of experience. Since struggling with chronic migraine headaches as a child, he’s been obsessed with natural and Functional Medicine solutions like diet, exercise, supplements, sleep, gratitude, and positive thinking that serve to handle the underlying problem rather than just treat symptoms.
Marcus is passionate about gut health and those who consider themselves as “tough cases” like those with H. pylori, Klebsiella, Pseudomonas, chronic vaginosis, and conditions where biofilm may be present. If you’re struggling with a chronic gut or chronic health challenge, Dr. Ettinger is ready to coach you on your healing journey. He is a truly a good person and a friend whom I trust very much. He has been an amazing mentor for me. I give him 5 stars!