MicroGenDX Testing For Urinary Tract Infections

By Melissa Kramer

15 mins

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 suffer from recurrent and chronic UTI than the statistics let on. 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 piece together enough information about the cause of their infection, to seek more effective treatment.

Article Quick Links

  • How can advanced UTI testing methods help chronic UTI sufferers? >>>>
  • What type of testing does MicroGenDX offer? >>>>
  • How to read MicroGenDX test results. >>>>
  • How to order a MicroGenDX UTI test. >>>>
  • Collecting a urine sample for testing. >>>>

If you’ve already decided to order a MicroGenDX urine test kit, you can find the right order page by clicking here for patients, and here for practitioners. If you want to learn more about it first, read on below.

How Can Advanced UTI Testing Methods Help You?

As mentioned above, standard urine testing methods are highly inaccurate. So much so, that millions of people have been told they do not have an infection, despite their UTI symptoms, and have been given no further advice on how to pursue better health.

In recent years, more accurate types of testing have become 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 different technologies to identify bacteria, fungi and parasites in a urine sample (or a sample from any part of the body) against a database of 30,000+ microorganisms.

The vast majority of these microorganisms cannot be cultured, and this means MicroGenDX has a dramatically improved ability to find the cause of infection, over standard urine testing.

MicroGenDX Testing For Patients

Every day, we hear from people who suffer from recurrent and chronic UTI – after all – that’s the purpose of our site.

Experiences range from weeks to decades, and symptoms vary from person to person, but there are few things that come up over and over again among chronic UTI sufferers:

  • Multiple rounds of antibiotics, with UTI symptoms always returning
  • Negative urine test results despite symptoms of a UTI
  • UTIs as frequently as every month, regardless of home remedies or medication
  • A diagnosis of Interstitial Cystitis despite believing they have a bladder infection
  • An escalation of symptoms over time, and a fear that there is no solution
  • Constant pain in their urinary tract, with little or no relief

There are many reasons people end up in this position, and inaccurate testing is one of them. Without accurate testing it’s not possible to pinpoint what is causing the issue, and without knowing the cause, it’s impossible to confidently prescribe a treatment.

If any of the experiences above are familiar to you, and you want to take another shot at finding answers, MicroGenDX may be able help.

A Quote On Live UTI Free About Recurrent UTIs“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 as the problem 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. After reviewing both the hospital culture report and the MicroGenDX report I brought these reports back to the hospital so the doctor could see them both side by side. I was in a great deal of back pain, very frustrated, and scared that this infection is getting worse causing damage to my kidneys! My MicroGenDX report said 3% was E. coli and the actual cause of my infection was 82% Enterobacter hormaechei, 82%! This is a bug they would have never found using standard culture tests. My story ends well ONLY because of MicroGenDX! 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

MicroGenDX Testing For Doctors

Just as chronic UTI sufferers can wind up in a place where their options appear to be exhausted, so can doctors trying to help their patients.

Primary care physicians and specialists have told us of patients who:

  • Continue to experience recurrent UTI despite treatment
  • Have taken multiple rounds of antibiotics with little or no improvement, and have experienced other health issues due to overuse of antibiotics
  • Receive test results that identify one or more pathogens and antibiotic sensitivity, yet the recommended treatment is ineffective
  • Receive negative urine culture results despite obvious symptoms of a urinary tract infection
  • Have urinary tract infections caused by antibiotic resistant bacteria
  • Do not improve with lifestyle and/or hygiene changes
A Doctor Quote About Recurrent UTIs On Live UTI Free “The patient’s frustrated because sometimes they think they’re crazy because they have the symptoms and nothing is coming back [on standard culture tests]. I’m frustrated because I have this patient that thinks she has a urinary tract infection. I have no answers for her. Then the [MicroGenDX] test actually detected multiple bacteria. It was really nice. You can actually then really give the patient the correct antibiotic.”

Margarita Johnston, Urologist

If you’re a practitioner with a patient who has not responded to previous approaches, the testing options MicroGenDX offers may help guide future treatment.

What Type Of Testing Does MicroGenDX Offer?

MicroGenDX uses two different technologies to test your urine sample, and provides two sets of the results.

MicroGenDX First Level Testing: PCR

The first is a rapid screening of your sample using Polymerase Chain Reaction (PCR). In this first level of testing, MicroGenDX looks for the following pathogens in a urine sample:

  1. Enterococcus faecalis
  2. Klebsiella pneumoniae
  3. Serratia marcescens
  4. Enterococcus faecium
  5. Pseudomonas aeruginosa
  6. Staphylococcus aureus
  7. Streptococcus agalactiae
  8. Streptococcus pyogenes
  9. Proteus mirabilis
  10. Escherichia coli
  11. Mobiluncus curtisii
  12. Mobiluncus mulieris
  13. Gardnerella vaginalis
  14. Staphylococcus saprophyticus
  15. Ureaplasma urealyticum
  16. Ureaplasma parvum
  17. Candida albicans (fungus)
  18. Chlamydia trachomatis
  19. Neisseria gonorrhoeae
  20. Mycoplasma genitalium
  21. Trichomonas vaginalis

In addition to the 21 pathogens listed above, the test also looks for 8 drug resistance genes, 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 30,000+ microorganisms, rather than only detecting the 21 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 here, 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 30,000 species sequence codes.
  • All microorganisms in their database of 30,000+, including fungi, parasites and all types of bacteria, can be detected in a single test, and do not require different conditions or mediums
A Doctor Quote About Recurrent UTIs On Live UTI Free “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.

Chronic Urinary Tract Infection - Simplified UTI Pathway

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.

Testing for biofilms in urine

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.

An Expert Tip About Recurrent UTIs on Live UTI FreeTo 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.

A Doctor Quote About Recurrent UTIs On Live UTI Free “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 recently acquired and rebranded as MicroGenDX. Since 2007 they have delivered over 300,000 test results, including around 30,000 urine tests, to more than 10,000 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.

How To Read MicroGenDX Test Results

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 of receipt of your sample, while the sequencing results take 3-5 days.

Although it’s possible to order a MicroGenDX test privately, it’s always best to work with a practitioner who has experience treating chronic UTI, and preferably, is familiar with DNA sequencing.

MicroGenDX results do not look like typical urine culturing results, and it helps to have assistance in deciphering them:

MicroGenDX urine test results - how to read them

MicroGenDX Results: Level 1 & Level 2 Results

If you click on the sample results above and take a look at the full report, you’ll notice a few things:

  • First level PCR results are on the left, and second level sequencing results on the right
  • More pathogens are listed as detected on the right, than the left

This second point can be explained if we go back to the list of pathogens included in the MicroGenDX urine PCR panel. In this example, Enterococcus faecalis was the only pathogen on the panel that was identified in the sample.

When the more comprehensive sequencing test was done, additional pathogens were detected in the sample, including fungi which are listed beneath the bacteria found, in the level 2 results (right side).

Bacteria and fungi identified via sequencing are listed in order of prominence. In some cases, a pathogen that shows up on the left side, will not be present on the right side 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% off 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 left side of the MicroGenDX sample results, there is a list of antibiotic classes. Each is confirmed as either detected or not detected.

If an antibiotic class is listed as ‘Detected,’ as Methicillin is in the example, this means resistance genes were found in the level 1 results. In this case, Methicillin antibiotics should not be used.

The antibiotic classes listed as ‘Not Detected’ 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

On the last page of MicroGenDX results, an antibiotic analysis for each of the prominent pathogens will be provided. 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 results, 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.

A Quote On Live UTI Free About Recurrent UTIs“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.”

How To Order A MicroGenDX UTI Test

1. Talk to your doctor

Patients who live in continental USA require a physician signature on their MicroGenDX Lab Requisition Form. This is not a requirement for international patients. Regardless, it will be a smoother process if you have a doctor on board to help you interpret your test results and guide you on treatment options. Your own doctor may not be open to this type of testing. If that’s the case, you may have to seek help elsewhere.

2. Order your MicroGenDX testing kit

Both US and international patients can order a testing kit directly here. This option gives you the opportunity to request the results be sent directly to you, as well as your doctor. Some patients prefer this option, particularly if they have multiple practitioners or wish to be notified of results immediately. You can also ask your doctor to order a testing kit on your behalf, here.

3. Receive your kit

If you ordered a kit directly, you’ll receive it by post. If your doctor ordered on your behalf, you can collect it from them. Remember, for continental USA patients, you’ll need to get your doctor to sign the included requisition form either way. 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 doctor, 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 doctor, they will notify you of the results.

8. Discuss your treatment options with your doctor

Your results will be unique to you. You’ll need to chat with your doctor 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.

Paying For Your MicroGenDX Urine Test

For US patients, MicroGenDX will bill most insurance companies directly, after providing your test results to your doctor. 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 USD199 plus shipping, regardless of where they are based. This amount may be reduced by insurance coverage.

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

If the results of your test are negative, MicroGenDX will reprocess your sample a further 2 times. Should the results still be negative after these 3 runs, you will be invited to submit a new sample for testing at no additional charge.

This applies to both US based and international patients. Note that although the retest is free, shipping costs are the responsibility of the patient. It’s extremely important to follow the sample collection instructions provided in order to achieve the most accurate result.

Collecting A Urine Sample For MicroGenDX Testing

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 here. 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 between ¼ and ½. 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.

Order a MicroGenDX test           MicroGenDX test order

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.

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Shelley Caskanette says:

Do you have any labs in Ontario Canada?

Hi Shelley, I saw you also sent us an email, so I’ve replied to that with more info. Melissa

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