MicroGenDX Testing For Urinary Tract Infections

Can MicroGenDX help if you experience ongoing urinary tract symptoms? 

If there’s one thing we’ve learned from our community, it’s that many more people who experience recurrent and chronic UTIs feel they are not getting the healthcare they need. One of the reasons this appears to be the case is that standard urine testing is highly inaccurate. 

Advanced testing methods, like those offered by MicroGenDX, have helped many people obtain deeper insights about the cause of their infection and seek more effective treatment.

If you’re looking for where to order a MicroGenDX urine test kit, use the link for your region:

1. United States
2. United Kingdom via Regenerus Laboratories
3. European Union (EU)
4. Other locations

How Can Advanced UTI Testing Methods Help You?

As mentioned above, standard urine testing methods are highly inaccurate. More sensitive types of testing are available, and for some people, this has meant the difference between chronic illness and complete recovery, often after years of unresolved symptoms.

One such test is provided by MicroGenDX. This test uses two molecular testing technologies to identify bacteria and fungi in a urine sample (or a sample from any part of the body) against a database of 60,000+ microorganisms. The vast majority of these microorganisms cannot be detected by urine culture, as culture testing is able to grow only ~2% of known bacteria. Results are delivered in as little as 24 hours after their lab receives your sample.

“A year ago I had a UTI that was mistreated for several weeks that ended up turning into a terribly painful kidney infection. I spent 3 days in the hospital where their culture test reported E. coli and I was yet again put on the wrong antibiotics. Fortunately, I had sent in a urine sample to MicroGenDX the day I went into the hospital (on my own). Within a couple days back home from the hospital I began feeling kidney pain again. I brought the hospital and MicroGenDX reports back to the hospital so the doctor could see them side by side. I was in a great deal of back pain, very frustrated, and scared that the infection was getting worse and causing damage to my kidneys! My MicroGenDX report said 3% was E. coli and 82% was Enterobacter hormaechei! This is a bug they would have never found using standard culture tests. Within 24hrs of being put on the correct antibiotic to treat that bug I was feeling better, and within a few days the nightmare was completely over.”

Lori – Chicago, IL, Patient

When Can MicroGenDX Help?

For many, urine culture and antibiotic treatment are enough to prevent further UTI episodes. More advanced testing may be helpful in these scenarios: 

• Multiple rounds of antibiotics, with UTI symptoms always returning
• Negative urine test results despite symptoms of a UTI
• Urine culture results that identify one or more pathogens and antibiotic sensitivity, yet the recommended treatment is ineffective
• A diagnosis of Interstitial Cystitis despite believing a bladder infection is present
• Urinary tract infections caused by antibiotic-resistant bacteria
• Identified UTI that does not improve with, treatment, lifestyle and/or hygiene changes

There are many reasons people end up in this position, and inaccurate testing is one of them. 

If any of the experiences above are familiar to you, and you’re looking for answers, MicroGenDX may be able to help.

What Type Of Testing Does MicroGenDX Offer?

MicroGenDX uses both qPCR and NGS technologies to test your urine sample, providing comprehensive results. They offer single or combined test kits to collect multiple sample types:

1. UroKEY – a urine-sample-only test 
2. VaginalKEY – a vaginal-swab-only test
3. WomensKEY Complete – urine sample and vaginal swab
4. MensKey Complete – urine sample and semen sample
5. CouplesKEY – test bundles for partner testing (US only – see more below)

(Use these links for United Kingdom orders and European Union orders).

Watch our interview with Dr. Nicholas Sanford, Vice President of Medical Affairs at MicroGenDX, to learn more:

MicroGenDX Partner Testing Options

New research shows that partners can transfer infection-related microbes during sexual activity. To test for this possibility, MicroGenDX offers CouplesKEY test bundles for heterosexual and same-sex couples. Test pairings include urine + vaginal swab AND urine + semen, or two of the same kits for same-sex couples. Results are delivered side-by-side at the same time, making it easier for a doctor to uncover a shared infection and treat both partners together, with the goal of preventing reinfection. 

Please note that the CouplesKEY test bundle is currently only available in the U.S.

Urine Culturing vs. MicroGenDX Testing

Urine culture has been the standard UTI test since the 1950s, but it was never intended to help diagnose lower urinary tract infections, and it has never been completely accurate. 

In fact, studies show that standard urine culture may miss up to 50% of infections and is only able to grow 2% of known bacteria, leaving many people with negative culture results despite experiencing UTI symptoms. 

“For years, we’ve been trusting urine cultures and trusting it when it says that there’s no bacteria there but the patients still were sick, the patients were still having symptoms. We were left without anything to do. Now, we have a tool that we can go back and say, ‘Look, there is a bacterial or a fungal etiology to your symptoms”.

Roscoe Nelson, Urologist

Bladder Biofilms And The Urinary Microbiome

One of the biggest discoveries that has helped put the inaccuracy of culture testing in context is that the urinary tract has a complex microbiome of its own. The second important step has been an increased understanding of how biofilms and intracellular pathogens can cause chronic infection in the bladder. 

Bacteria that have been living in a biofilm are less likely to grow in a culture than free-floating bacteria. Free-floating bacteria have been shown to make up less than 1% of the bacterial cells in natural pathogenic ecosystems, meaning very little of such an ecosystem can be cultured.

Fortunately, DNA sequencing methods can detect the DNA of pathogens within a biofilm, which means the tests offered by MicroGenDX are not subject to this limitation of a urine culture. 

Having said that, if your sample does not contain pieces of any biofilms present, or infected bladder lining cells, no test will be able to detect the pathogens contained within them. And at this stage, it is not possible for a DNA sequencing test to tell you if any identified microorganisms were part of a biofilm or intracellular community or not.

We’ve outlined more of the issues with standard urine culture (SUC) and why it’s not as reliable as it needs to be. 

“There were certainly a lot of times that we were pretty convinced somebody had some type of infection in their bladder, and the tests were coming out negative. What we found is through working with some of these tests [from MicroGenDX] that sometimes some of those patients truly do have some bacteria in their urine that’s not being picked up on the regular cultures.”

Ginger Isom-Batz, Urologist

How To Read MicroGenDX Test Results

MicroGenDX provides results from two different testing technologies in one report:

1. qPCR with biomarker results

2. Next Generation Sequencing (NGS) comprehensive identification

Both qPCR and NGS results are delivered together in a single report within about 24 hours of the lab receiving your sample.

MicroGenDX results do not look like typical urine culture results, and it helps to have assistance in reading them. This short video helps explain the results, and we’ve shared more detail in the next section.

MicroGenDX Biomarkers & qPCR Technology

The first section in your report will include results from a rapid, DNA-based screening of your sample using quantitative Polymerase Chain Reaction (qPCR) to identify specific pathogens and antibiotic resistance genes. 

The biomarker portion of the test is an optional add-on and it helps test for leukocyte esterase and the pH level of your urine sample. Leukocytes are white blood cells that, when present in urine, indicate the immune system is likely responding to an infection in the urinary tract.

Some types of bacteria can change the pH level of your urine because of how they behave and what they release. In this way, pH levels can also be used as an indicator of a UTI. Similarly, certain pH levels can also encourage or discourage bacterial growth. 

Biomarkers allow clinicians to better evaluate whether organisms that are identified are indicative of an infection or likely represent a healthy balance of organisms within the urinary microbiome. Please note that the add-on service of biomarker testing is currently only available in US states, excluding New York.

MicroGenDX qPCR Test

The qPCR test with MicroGenDX looks for the following pathogens in a urine sample:

1. Prevotella bivia
2. Klebsiella pneumoniae
3. Gardnerella vaginalis
4. Pneumocystis jirovecii
5. Escherichia coli (E. coli)
6. Bacterial load
7. Fungal load
8. Chlamydia trachomatis (STI add-on)
9. Neisseria gonorrhoeae (STI add-on)
10. Mycoplasma genitalium (STI add-on)
11. Trichomonas vaginalis (STI add-on)

In addition to the pathogens listed above, the test also looks for 17 drug resistance genes (see more below) that can be shared between the pathogens in an infection..

Approximately 80% of MicroGenDX qPCR samples are positive for at least one pathogenic microbe. But it’s important to understand the following:

1. qPCR testing only detects the specific microorganisms it is made to look for (for example, those in the qPCR panel list above). 
2. If the microorganism causing your infection is not listed on the qPCR panel, the test cannot tell you if it was present or not.
3. Because qPCR testing looks for specific microorganisms only, it is unable to provide a picture of how these microorganisms are represented within the total urinary microbiome – maybe they are significant, maybe they aren’t – to learn this, you need a more comprehensive test.

MicroGenDX NGS Testing: Comprehensive Genetic Identification

The second testing technology MicroGenDX provides is called Next Generation Sequencing (NGS) and it uses urine from the same sample as the qPCR test. NGS looks for a specific gene that is common to all bacteria, called the 16s ribosomal RNA, and a gene common to all fungi, the 18s ribosomal RNA. 

NGS testing is more comprehensive than qPCR as it looks at all the genetic material contained within a sample, and compares it against a database of 60,000+ microorganisms (bacteria, fungi, mycobacteria), rather than only detecting the species listed on the qPCR panel above. MicroGenDX’s NGS testing is 99.2% accurate, as independently verified by the College of American Pathology each year.

Why Are The qPCR and NGS Results Different?

MicroGenDX will likely list more organisms in the NGS results section than in the qPCR section. When the more comprehensive NGS testing is done, it can detect vastly more organisms.

Bacteria and fungi that are detected and identified via NGS are listed in order of how much of each was found in the sample. This is called ‘relative abundance’ and is noted as a percentage (%) on your results report.

For instance, if E. coli is reported at 60%, that means 60% of the microbes detected in your sample were E. coli.

In some cases, a pathogen that shows up in the qPCR results will not be present on the NGS results at all. This is because NGS showed that this pathogen was not a prominent part of the overall microbes found in your sample.

If a microbe makes up less than 2% of the total DNA identified, MicroGenDX will not include it in your NGS results. This is to help provide more useful results by screening out potential contaminants and promoting antibiotic stewardship.

If NGS Is More Comprehensive Than qPCR, Why Is qPCR Still Helpful? 

It’s a good question and there are two main reasons MicroGenDX utilizes both qPCR and NGS technologies:

1. MicroGenDX has found that qPCR is currently the best way to detect if there are any genes that indicate the presence of antimicrobial resistance. Identification of resistance genes assists in treatment decisions.
2. qPCR can be more specific than NGS in very rare cases, as some bacterial DNA is so similar when sequenced that NGS can sometimes falsely identify a species. For those species where mutation or similarities with other species are anticipated, the species will be included in the qPCR panel to enhance the ability to differentiate.

MicroGenDX Results: Drug Resistance Genes

Drug resistance refers to an organism’s ability to resist the effects of the drugs used against them, and can occur for both bacteria and fungi.

The good news is that scientists are aware of many common types of drug resistance. By analyzing the DNA of a bacterial or fungal pathogen, antibiotic resistance genes present in a patient’s sample can be identified. MicroGenDX’s qPCR testing detects 17 types of common drug resistance genes.

At the top of the MicroGenDX sample results, there is a list of antimicrobials for consideration.  Each antibiotic class, with its associated resistance genes, is listed in a red box.

If an antibiotic class is detected, this means resistance genes were found in the qPCR results, and this type of antibiotic is likely to be ineffective in treatment. Note that this drug resistance genes testing is generalized and is unable to tie a gene back to a specific pathogen at this time.

The antibiotic classes for which resistance genes are not detected may be more suitable for treatment. A tick cross-referencing a pathogen with an antibiotic means that particular antibiotic is okay to use for that particular microbe.

This antibiotic analysis is based on clinical studies where that antibiotic has been shown to be effective against that bacterial species, not the actual pathogens in your urine. The list of antibiotics is not exhaustive, but it is made up of those commonly prescribed. It is there to provide a starting point for your doctor. 

Of course, any antibiotic should only be prescribed by a doctor who has reviewed the patient’s test results and understands the patient’s medical history. 

How The Urine Pathogenicity Test Can Help

To help your doctor with treatment selection, MicroGenDX results classify the detected microbes as commensal (neutral/helpful), pathogenic (harmful), or unknown based on the latest scientific research.

It’s important to note that the report is meant for your doctor’s use in the context of your full medical history, and is best suited for non-immunocompromised patients. If you have an immune system condition, this item on the report may be inaccurate. 

View this video resource for further explanation of MicroGenDX resistance genes detection and antibiotics for consideration.

Research To Support MicroGenDX Testing

MicroGenDX conducted a head-to-head study between DNA sequencing and standard urine culture to demonstrate the higher accuracy of sequencing:

“In total, 13 of 44 patients had positive urine culture results, whereas 44 of 44 patients had positive DNA NGS results.”

Although the sample size of the study was small, it provides a promising basis for future research into UTI testing methods, and hope for chronic UTI sufferers who are yet to find answers.

A second study demonstrated the effectiveness of NGS testing in preventing UTIs after surgery.

A further study involving multiple institutions compared NGS with culture and found that NGS identified the responsible pathogens in 67 of 69 cases, and detected a median of 3 pathogens, while culture found 1-2 in culture-positive samples. 

NGS also identified bacteria in 16 samples that culture reported as “no growth” and more accurately detected antibiotic resistance in more samples than culture did. The authors concluded that NGS provides better quality insight into the pathogens behind UTIs than culture.

Learn more about interpreting MicroGenDX test results:

How To Order A MicroGenDX UTI Test

1. Talk to your clinician or use the MicroGenDX telehealth option

All US States – Clinician Signature and Insurance: If you have both insurance and a clinician to sign the requisition form, you can order a kit directly via the Patient Test Service (or via the links below), and have it shipped to an address that suits you. This way, you can collect your sample at home, and ask your doctor to sign the form. 

All US States – No Clinician Signature: If you do not have a clinician to sign the requisition form, you can order from the Patient Site with Telehealth to be provided with a telemedicine appointment where a clinician will approve the test on your behalf. The doctor will sign for your test and review your results to help you access the test, but is not able to diagnose and treat.

International Patients: Patients outside continental USA do not need a physician signature to run the test, however, a physician’s signature is required for the antimicrobials for consideration. See the United Kingdom, European Union and other locations links below for more information regarding your region.

2. Order your MicroGenDX testing kit

1. United States (via self-pay or insurance options)
2. United Kingdom via Regenerus Laboratories
3. European Union (EU)
4. Other locations

3. Receive your kit and collect your urine sample

Each test kit ordered from MicroGenDX includes detailed instructions to help you properly collect your urine sample and minimize contamination risks. 

4. Ship your sample

If you follow the instructions correctly, your sample will remain in a suitable condition for testing for up to a week at room temperature. This is plenty of time for express shipping from anywhere in the world to their lab in the US or the EU. If you ordered a kit through your clinician, they may ship it on your behalf. See more information below about shipping. Currently, MicroGenDX is unable to ship to Africa, China, Russia, Ukraine or Bulgaria.

5. Get your results

Both your qPCR and NGS results will be ready in as little as 24 hours after their lab receives your sample. If you placed your order on the patient website, you’ll get an email alert once your results are ready and you’ll be able to access them from your account. If you ordered via your clinician, they will notify you of the results or you can access them by signing up for the MicroGenDX patient portal. 

6. Discuss your treatment options with your clinician

When testing with MicroGenDX, it’s best to work with a practitioner who has experience treating chronic UTI, and preferably, is familiar with molecular testing. If you are in the US and looking for a doctor to diagnose and treat, you can use MicroGenDX’s “Find a Provider” tool or call their Customer Service team at 1-855-208-0019 (M-F, 8 AM – 8 PM EST). Those in the US or elsewhere can also reach out to the Live UTI Free team for information about clinicians in different regions.

For orders placed through the MicroGenDX patient website, you can schedule a consultation with a telemedicine physician to review your results by following the emailed instructions or by contacting MicroGenDX’s Customer Service team. Note they currently cannot provide diagnosis or treatment.

Quick Tips For Collecting A Urine Sample For MicroGenDX Testing

1. Stop taking probiotics and other supplements 2 days prior

Supplements that contain an active metabolite may degrade the DNA within your sample, while it is in shipment.

2. Stop taking antibiotics 2 days prior 

Antibiotics may continue to be active within your sample, and this may impact your results. It’s not always feasible to cease taking medications, and testing may still be possible while on antibiotics, so talk to your doctor about it if you’re worried. Feel free to call MicroGenDX if you have questions.

3. Do not use Lidocaine gel (even if using a catheter)

Lidocaine gel can render a sample invalid or give false negative results due to its DNA degrading properties. Speak with your doctor before changing anything in your current approach.

To increase the chances of collecting a sample that contains pieces of a biofilm present, you can take a tip from MicroGenDX and collect a urine sample the first time you urinate in the morning.

Paying For Your MicroGenDX Urine Test

For US patients seeking to self-pay, MicroGenDX tests can be purchased here. Alternatively, MicroGenDX will bill your insurance company directly, including those that are out-of-network companies. Your insurance company will review the claim and inform you of any additional cost you must cover personally. 

International patients will be required to pay via credit card, at the time of purchasing the test kit.

Most self-pay kits start at $259 and combination kits start at $289. International orders may incur an additional credit card payment fee.

MicroGenDX offers pay-over-time options like Affirm, Klarna, and AfterPay for all orders placed on the patient website.

If your test results are negative, contact MicroGenDX. Their team will review your results and your collection process to determine what may have caused those results. Often, MicroGenDX will offer reruns, but will not cover reruns determined to be caused by improper collection procedures.

It’s extremely important to follow the sample collection instructions provided in order to achieve the most accurate result.

About MicroGenDX

Since 2008, MicroGenDX has delivered over 1,000,000 NGS test results, including over 300,000 urine tests, to more than 30,000 doctors and hundreds of thousands of patients. 

“MicroGenDX is facing a massive paradigm shift in medicine, convincing physicians to move from an 1870’s culture tool to microbial detection by DNA sequencing. We believe that change will occur only with solid medical evidence to prove the clinical utility of NGS. We are investing significantly in clinical research studies to prove the clinical value of our technology. Clinical evidence will be the key to helping more patients gain access to our technology and bring improvement in their lives. We have already delivered more scientific published clinical trials in this space. All of that evidence has clearly shown NGS is superior to culture.“ Rick Martin, MicroGenDX

MicroGenDX is currently working on multi-center studies with academic centers like UCLA and Wake Forest and continues to publish peer-reviewed studies in support of NGS across multiple clinical specialties.

Watch more about MicroGenDx in their feature on Fox 11 News, where they covered a story about how this test helped identify bacteria in individuals with recurrent UTI.

If you have any questions or comments, or you think we’ve missed something, you can comment below or get in touch with the Live UTI Free team.