MicroGenDX Testing For Urinary Tract Infections

If you’ve already decided to order a MicroGenDX urine test kit and you are based in the US or internationally outside the UK, you can find the right order page by clicking one of the images below. UK-based tests can be ordered via Regenerus Laboratories.

How Can Advanced UTI Testing Methods Help You?

What Type Of Testing Does MicroGenDX Offer?

MicroGenDX uses three different technologies to test your urine sample, and provides two sets of the results. We’ll explain more about what each report includes soon. They also offer combined test kits to take samples from multiple sites. WomensKEY Complete includes a urine sample and vaginal swab, and MensKEY Complete includes a urine sample and semen sample. (UK order links: WomensKEY and MensKEY)

MicroGenDX First Level Testing: Biomarkers & PCR

The first report will include results from a rapid screening of your sample using Polymerase Chain Reaction (PCR) and urinalysis biomarkers.

MicroGenDX Urinalysis biomarkers

The biomarker portion of this test looks for leukocyte esterase and nitrites and tests the pH level of your urine sample. Leukocytes are white blood cells that, when present in urine, indicate the immune system is responding to an infection in the urinary tract.

Nitrates naturally exist within urine, but when certain bacteria are present (such as E. coli, Klebsiella, and Proteus), they convert nitrates to nitrites. When nitrites are present in urine, a UTI is indicated.

Due to the behaviors and waste products created by bacteria, the presence of some bacteria can influence the pH level of urine. In this way, pH levels can also be used as an indicator of a UTI. Similarly, pH levels can also encourage or discourage bacterial growth. 

With the incorporation of a biomarker test, clinicians can better evaluate whether organisms that are identified using the more sensitive testing methods discussed below are indicative of an infection or likely represent a healthy balance of organisms within the urinary microbiome.

MicroGenDX PCR Test

The PCR level of testing, the MicroGenDX urine panel looks for the following pathogens in a urine sample:

1. Enterococcus faecalis
2. Klebsiella pneumoniae
3. Prevotella bivia
4. Staphylococcus aureus
5. Streptococcus agalactiae
6. Escherichia coli
7. Mobiluncus curtisii
8. Mobiluncus mulieris
9. Gardnerella vaginalis
10. Mycoplasma hominis
11. Ureaplasma urealyticum
12. Ureaplasma parvum
13. Candida albicans (fungus)
14. Chlamydia trachomatis (add-on test)
15. Neisseria gonorrhoeae (add-on test)
16. Mycoplasma genitalium (add-on test)
17. Trichomonas vaginalis (add-on test)

MicroGenDX’s vaginal test uses PCR for a different set of organisms. 

In addition to the 17 pathogens listed above, the test also looks for genes for 10 resistance drug classes, but we’ll go into that more later.

PCR testing is fairly quick – you can get your results within 24 hours of the lab receiving your sample, and approximately 80% of MicroGenDX PCR samples are positive for at least one pathogenic microbe. But it’s important to understand the following:

1. PCR testing only tests for specific microorganisms. The microorganisms tested for may be requested by your doctor, or they may be part of a standard panel (as above) for the type of infection. You can think of a PCR panel as a list of microorganisms the test has been told to look for.
2. If the microorganism causing your infection is not listed on the PCR panel, the test will not tell you whether it was present or not.
3. Because PCR 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.

This is why MicroGenDX provides a second level of testing…

MicroGenDX Second Level Testing: Comprehensive Genetic Identification

Second level testing at MicroGenDX uses urine from the same sample as first level testing. The second level test looks for a specific gene that is common to all bacteria, called 16s ribosomal RNA, and a gene common to all fungi, 18s ribosomal RNA.

This second level test is more comprehensive than PCR testing, in that it looks for the 16s and 18s genes among all the genetic material contained within a sample, against a database of 57,000+ microorganisms, rather than only detecting the 17 species listed on the panel above.

Urine Culturing vs. MicroGenDX Testing

Urine culturing has been the standard UTI test since the 1950s, but this test was never intended to be used to diagnose lower urinary tract infections, and it has never been accurate.

In fact, studies show that standard urine culturing may miss up to 50% of infections, leaving many people with false negative results.

We’ve covered a number of the reasons these tests are so inaccurate, and it’s a good idea to get an understanding of it, particularly if you’ve received negative culture results despite your UTI symptoms.

One of the biggest discoveries that has helped put the inaccuracy of 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.

Some of the reasons a standard urine culture is inaccurate

• Standard culture time of 24 hours is insufficient – many bacteria take up to 5 days to grow, and some fungi more than 20 days
• Anaerobic bacteria will not grow at all unless an anaerobic culture is requested in addition, and this type of test comes with additional expense
• Results are often biased towards easy to grow microorganisms, while others are completely missed
• Uncommon microorganisms are often considered contamination rather than potential causes of infection
• Bacteria that have been living in a biofilm, are less likely to grow in a culture than free-floating bacteria (see more on this below)
• 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
• As a result, doctors may recommend antibiotic treatment for the bacteria found, but it may not be the cause of infection.

How MicroGenDX testing is different

• Urine samples not easily impacted by time or temperature changes
• DNA sequencing technology does not grow microorganisms, instead, it extracts the microbial DNA in the sample and matches it to a database with 57,000 species sequence codes.
• All microorganisms in their database of 57,000+, including fungi, and all types of bacteria, can be detected in a single test, and do not require different conditions or mediums

“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

To help demonstrate the accuracy of this type of DNA sequencing, when compared to standard urine culturing, MicroGenDX conducted a head-to-head study. Among other findings, one point is clearly relevant to all chronic UTI sufferers, particularly those frustrated by negative culture results:

“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, and hope for chronic UTI sufferers who are yet to find answers.

Can MicroGenDX Test For Biofilms and Intracellular Infection?

First, a quick refresher on biofilms and intracellular infection. We’re hoping you’ve already read our article on chronic infection, and how biofilms are involved.

To put it simply, bacteria and other pathogens can team up to form complex communities that are attached to (or live within) your bladder wall or urinary tract. These communities are very difficult to treat, and your own body can have a very hard time getting rid of them. Biofilms can stick around, causing problems in the bladder indefinitely.

On top of the difficulty of treating biofilms or intracellular communities (IBCs), it’s near impossible to test for them in the first place. At least with standard testing methods.

Even if pieces of the biofilm break off into your urine sample, the pathogens contained within it are very unlikely to grow in a standard urine culture test. So they won’t show up in your results and you’ll be none the wiser.

Fortunately, sequencing methods are able to detect the DNA of pathogens within a biofilm, so this is another area where the tests offered by MicroGenDX are superior to 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 whether any microorganisms identified were part of a biofilm or intracellular community or not.

To increase the chances of collecting a sample that contains pieces of any biofilm, you can take a tip from MicroGenDX and collect a urine sample 4 times in a single day, combining each in the sample container.

All microorganisms naturally form biofilm structures, so if you are experiencing chronic infection, there is a good chance biofilms containing multiple microorganisms are involved.

“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

About MicroGenDX

MicroGenDX was launched as Pathogenius in 2007, and was acquired and rebranded as MicroGenDX. Since 2007 they have delivered over 700,000 qPCR+NGStest results, including around 197,000 urine tests, to more than 23,000 doctors. This amounts to more sequencing tests for microbe identification than any other lab in the world.

“MicroGenDX is facing a massive paradigm shift in medicine, convincing physicians to move from an 1870 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 has worked with some of the top medical centers in the USA, including the Cleveland Clinic and Mayo Clinic and are currently working on a multi-center chronic UTI study with academic centers like Thomas Jefferson in Philadelphia and Wake Forest.

As discussed above, MicroGenDX provides two levels of results:

1. Rapid Screening (PCR Results)
2. Comprehensive Identification (Sequencing Results)

PCR results are available within 24 hours of receipt of your sample, while the sequencing results take 3-5 days.

Although it’s possible to order a MicroGenDX test online, you must have a practitioner’s signature before submitting your sample. It’s always best to work with a practitioner who has experience treating chronic UTI, and preferably, is familiar with DNA sequencing. In the US, for select tests MicroGenDX can provide a signature for your initial testing order as well as a non-treatment prescribing consultation.

MicroGenDX results do not look like typical urine culturing results, and it helps to have assistance in deciphering them. This short video helps explain the results:

It should be noted that for patients and clinicians in New York state, a different report will be made available.

MicroGenDX Results: Level 1 & Level 2 Results

If you watched the above video, you would have noticed that more pathogens are listed as being detected in the Level 2 NGS testing than Level 1 PCR testing. 

This can be explained if we go back to the list of pathogens included in the MicroGenDX urine PCR panel. Only pathogens included in the PCR panel can be detected in the Level 1 results.

When the more comprehensive Level 2 testing is done, pathogens from a database of 57,000+ organisms can be detected.

Bacteria and fungi identified via sequencing are listed in order of prominence.

In some cases, a pathogen that shows up in the Level 1 results, will not be present on the Level 2 results at all. This is because comprehensive sequencing showed that this pathogen was not a prominent part of the microbiome.

Any pathogen that makes up less than 2% of the DNA identified will not be included in the sequencing results.

Hopefully you can see why PCR (Level 1) testing alone may not provide enough information.

Differing results in the Level 1 and 2 tests can also mean that treatment may be started based on the first findings, then need to be adjusted based on the second. It will be up to your doctor whether to proceed with treatment immediately, or wait for the level 2 results.

MicroGenDX Results: Drug Resistance Genes

By now, you’re probably familiar with the term antibiotic resistance. This refers to an organism’s ability to resist the effects of an antibiotic they were once sensitive to. The same effect can occur with antifungals and fungi.

Bacteria and fungi can acquire resistance genes in various ways (a complicated topic that deserves an article of its own!).

Resistance genes allow bacteria and fungi to resist specific drugs via particular mechanisms. Many of these mechanisms are known, along with which drugs they are relevant to. These known resistance genes can be identified by looking at the DNA of the bacteria or fungi.

You’ll note that on the top of the MicroGenDX sample results, there is a list of antibiotic recommendations. If a resistance gene is present, that class of antibiotics will not be shown. These antibiotic classes with resistance genes are also listed in a red box above.

If an antibiotic resistance class is detected, as the four shown in the example, this means resistance genes were found in the level 1 results. In this case, these antibiotics should be avoided.

The antibiotic classes that do not have resistance genes may be more suitable. Of course, any antibiotic should only be prescribed by a doctor who has been through a thorough assessment of the patient.

MicroGenDX Results: Complete Antibiotic Analysis

Each of the pathogens in the results is cross-referenced with various drug classes. A tick means that particular antibiotic is okay to use for that microorganism.

This antibiotic analysis is not based on testing antibiotics on the actual pathogens found in your urine, it is based on clinical studies where that antibiotic has been shown to be effective against that bacterial species. The list of antibiotics is not exhaustive, it’s there to provide preliminary guidance to your doctor.

For further explanation of MicroGenDX resistance genes and antibiotic recommendations, you can view this video resource they’ve put together.

Why Have I Never Heard Of The Pathogens On My Results?

This seems important to cover given the number of questions we get about it…

If your results contain pathogens that you or your doctor have never heard of, there’s no reason to panic. Traditional culturing methods have simply been unable to identify the diverse community of microorganisms that live within the urinary tract.

As we now know, the urinary tract is not sterile, but because everyone assumed it was until very recently, we really have very little information about what should and shouldn’t be there.

It’s very unlikely you’re the only person in history to have a particular microorganism in your urine, even if you do happen to be the first person it’s identified in. And if that’s the case, it may take a little more research on your doctor’s part, to decide on a treatment approach.

“I had never heard of most of the bacteria listed on my test results, and they never showed up on any culture tests, so I was kind of freaked out. My doctor talked me through them and came up with a treatment plan and my symptoms started to improve, which was a relief.”

1. Talk to your clinician

Patients who live in continental USA may either obtain their clinician’s signature on their MicroGenDX Lab Requisition Form or order a test directly by requesting a clinician signature via MicroGenDX at checkout. You can order the test kit directly using the link below and have it shipped to an address that suits you. This way you can collect your sample at home.

International patients do not need a physician signature to run the test, however, a physician’s signature IS required for the antimicrobial recommendations. As for US-based patients, you can order the test kit directly using the link below. However, without a signature from a clinician, your results will contain information about any organisms identified, but no treatment recommendations.

2. Order your MicroGenDX testing kit

Both US and international patients based outside the UK can order a testing kit directly from MicroGenDX. UK-based patients can order directly via Regenerus Laboratories. This option gives you the opportunity to request the results be sent directly to you, as well as your clinician. Some patients prefer this option, particularly if they have multiple practitioners or wish to be notified of results immediately. You can also ask your clinician to order a testing kit on your behalf. 

3. Receive your kit

If you ordered a kit directly, you’ll receive it by post. If your clinician ordered on your behalf, you can collect it from them. Remember, for continental USA patients, you’ll need to get a clinician to sign the included requisition form. International patients don’t need to worry about this.

4. Collect your urine sample

You can find more detailed information below on how to collect a urine sample for a MicroGenDX test. 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.

5. Ship your sample

The testing kit includes instructions on how to ship your sample – for both US based and international patients. If you ordered a kit through your clinician, they may ship it on your behalf. See more information below about shipping.

6. Testing of your sample

Once MicroGenDX receives your sample, it will be processed and tested, as described above.

7. Get your results

Your first level PCR results will be ready within 24 hours of your sample being received. The comprehensive sequencing results take 3-5 days. You’ll receive both via email if you ordered on the MicroGenDX website and provided your email address. If you ordered via your clinician, they will notify you of the results.

8. Discuss your treatment options with your clinician

Your results will be unique to you. You’ll need to chat with your clinician about how to best treat what is found in your urine sample.

Shipping For US And International Testing

MicroGenDX has conducted testing on urine samples to evaluate any changes that occur when the sample is kept both at room temperature and refrigerated for up to week. In both cases, no changes to the bacterial load or species identified was observed. This indicates that samples will remain viable for testing throughout shipment.

Currently, MicroGenDX is unable to ship to Africa, China, Russia, Ukraine or Bulgaria. Please note that the add-on service of biomarker testing is currently only available in US states, excluding New York.

Paying For Your MicroGenDX Urine Test

For US patients, 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.

The maximum out-of-pocket amount any patient will pay is USD335 plus shipping for a UTI only kit, or USD370 for a combination kit, regardless of where they are based. This amount may be reduced by insurance coverage.

International orders may incur an additional credit card payment fee.

MicroGenDX offers a Patient Assistance Program for US patients that allows payments in monthly installments for any out of pocket expenses.

If the results of your test are negative, MicroGenDX will reprocess your sample a further 2 times. This applies to both US based and international patients.

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

We probably don’t need to say it, but for a test to be accurate, your sample must contain the pathogens it is trying to look for. To help with this, there are a few things you can do to get the best sample possible:

1. Read the MicroGenDX instructions

A full set of instructions on how to collect a viable sample and use the collection kit are provided in the kit and online. It’s best to read and understand these before you’re perched over a toilet!

2. Stop taking probiotics and other supplements 2 days prior

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

3. 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.

4. Do not use Lidocaine gel (even if cathing)

Lidocaine gel can render a sample invalid or give false negative results.

5. Do a ‘prep’ urination, then cease fluid intake

About 2 hours before collecting your sample, empty your bladder. Then in the 2 hours leading up to your sample collection, don’t drink any fluids. If this isn’t possible, minimize your fluid intake.

6. Clean the area, pee in the sample cup and follow the instructions

First, clean the genital area with soap and water. Next, get in to a position you’re comfortable with. Separate the labia with your free hand and fill the sample cup to the red line. Then follow the rest of the kit instructions.

We know it’s a lot of information to consider, but it’s best to be well informed when it comes to your health!

Ultimately, we want to provide you with as many avenues as possible to find answers, and to find the right treatment for you.

US-based patients and international patients based outside the UK, click on the images below to place an order. UK-based patients and clinicians can order directly from Regenerus Laboratories for faster shipping.

To get answers to other commonly asked questions about chronic and recurrent UTI, visit our FAQ page. If you have any questions or comments, or you think we’ve missed something, you can comment below, or get in touch with our team.