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  • Writer's pictureNicole Cozean

Can We Blame an "Embedded" Bladder Infection for IC Symptoms?

Updated: Mar 12

Could my IC symptoms possibly be caused by an "embedded" bladder infection my doctors missed?

The symptoms of interstitial cystitis closely resemble those of a UTI, so it's always been tempting to assume IC symptoms are simply an undetected or embedded bladder infection.

For decades, many in the field assumed IC symptoms were really just the result of an undiscovered bladder infection. Patients were treated with long-term antibiotics, even in the absence of a bladder infection or positive culture. This was years before Microgen testing!

Not only did the long-term antibiotics not resolve symptoms, they created new ones. Many antibiotics are harmful to the stomach, and GI issues can exacerbate IC. They can alter the gut microbiome, killing off the 'good' bacteria we need for healthy digestion, as well as create resistant bacteria.

This was so common the American Urological Association (AUA) came out in their IC Guidelines to specifically state antibiotics should not be prescribed in the absence of a proven bladder infection. Multiple clinical studies showed long-term antibiotic use did not 'cure' IC symptoms.

We do a full review of all the most important treatment options, research and ways to find relief in the new IC: Roadmap to Healing online course ($87). but you can read a summary of the research on embedded bladder infections below!

New Microgen Testing for Bacteria and Embedded Infections in the Bladder

Recent (and exciting) advances in the field of urine testing are allowing us to better understand the natural microbiome of the bladder. We are learning that everyone - both those with and without symptoms - have natural bacteria in the bladder. This is similar to how we have a natural microbiome in the gut or vaginal canal.

This doesn't mean there is a 'bladder infection' anymore than the presence of bacteria in the gut means there's a 'gut infection.' The bacteria are just a natural part of the body's biome.

We know that all people have this natural microflora in the bladder, but we have no evidence that it is harmful or the cause of IC symptoms. From early testing, it appears there is no major difference between the bacteria in the bladder of IC patients and asymptomatic people.

The maker of one version of these more accurate tests is called Microgen, and their technology holds a lot of promise for patients!

The Theory of "Embedded" Bladder Infections

Unfortunately, being able to find and identify all the bacteria that have always been in the bladder has led some to re-assert the old notion that IC really is just an undetected bladder infection.

While this is an interesting area of study and more research is absolutely needed, currently there is no evidence that IC is the result of a previously-undetected infection. Long-term antibiotics - the treatment that would be indicated for a bladder infection - have been shown to be ineffective and are specifically not recommended by the American Urological Association.

The term "embedded infection" is also scary, but it's actually really common for bacteria to create "biofilms" as they grow. This is the same thing as calling them "embedded" and is just how bacteria work.

Microgen Testing for IC

Unfortunately, this can be extremely confusing for patients. It's natural to want a 'quick-fix' or easy answer. Even a cure!

If you take a Microgen test, you WILL find bacteria in your urine. Everyone naturally has levels of these bacteria.

The real question is do we see a difference in the bacteria found in patients with IC-like symptoms and people without pain at all? The answer, at least so far, is no. No replicable difference has been shown in the bladder microbiome.

What Do the New Testing Companies Say About Bladder Infection?

Even the CEO of Microgen, the testing company at the forefront of these advances, has specifically stated their testing cannot be used to diagnose an embedded infection.

If It's Not Really an Embedded Bladder Infection, Why Do Some People Report Relief with Antibiotics?

This is actually a really interesting question with a few possible answers, though we don't have enough information to be conclusive yet.

Analgesic and Anti-Inflammatory Properties - We do know that many antibiotics also have - as side effects - analgesic (pain-blocking) and anti-inflammatory properties. It may be some patients respond well to these properties, providing temporary relief with antibiotics. However, there are much safer, healthier ways to harness analgesic and anti-inflammatory properties than antibiotic use. Many natural supplements have similar properties (See Our Article on Supplements for Interstitial Cystitis) with much lower side effects.

The Placebo Effect - We all know the power the mind has over the experience of pain. The Placebo Effect describes the tendency to improve when we believe we will improve, even if the medication or intervention isn't the true cause.

The Placebo Effect can be extremely powerful. It's the reason all medical clinical trials have a control group and an experimental group - even patients given a sugar pill will report improvement in their symptoms. Long Time Horizon - Another reason some patients may report improvement is the long time horizon of long-term antibiotics. They are often administered for months or even years.

We know symptoms of IC naturally fluctuate, and can both flare and resolve. Most patients go into see a doctor or take a Microgren test when their symptoms are at their peak and they're desperate for relief. Natural fluctuations are likely to improve their symptoms over the next few months - even if they hadn't done anything new at all.


Who are We at PelvicSanity?

At PelvicSanity, it's our mission to support patients with pelvic pain and pelvic floor symptoms, regardless of where you live. We can help with:


A Small Subset of Patients May Actually Have a Embedded Bladder Infection - Finally, we want to acknowledge the possibility there may be a small subset of patients who genuinely do have a bladder infection that's been missed. We certainly are open to the idea, and we know everyone with IC is different - there's no one-size-fits-all approach.

However, even if there is a chronic infection in play, it's not just as simple as taking long-term antibiotics. With any chronic pain issue, the brain, the muscles and nerves, and the entire nervous system are involved and need to be brought back to a normal state.

If there is a subset, it must be small - otherwise we would notice it in studies showing long-term antibiotics are not an effective IC treatment.

For more on how to develop a comprehensive action plan, build a medical team, improve your symptoms with self-care and more, check out the IC: Roadmap to Healing Course online now!

Can I Blame an "Embedded" Bladder Infection for my Symptoms?

There is absolutely no evidence that interstitial cystitis symptoms are due to a previously undiscovered bacterial infection. In fact, there’s significant evidence that long-term antibiotic treatment is ineffective, and the American Urological Association specifically states antibiotics should not be used in the absence of a clear, demonstrated bacterial infection.

New testing techniques are now able to detect the natural microflora in the bladder. These bacteria are present in everyone – whether or not you have any symptoms. In fact, in women who have absolutely no pelvic pain, symptoms or problems, an average of 21 different types of bacteria can be found.

For decades doctors treated interstitial cystitis as if it was a bacterial infection they just couldn’t see. They prescribed long-term antibiotics and even IV antibiotic treatment. It was proven to be ineffective. Our new ability to see these bacteria which have always been present – and are present in all people – does not change the way we treat interstitial cystitis.

What is MicroGen Testing for IC?

Traditional urine cultures work by putting bacteria into a place where they can thrive (culturing) and seeing what grows. Unfortunately, it can be difficult to get bacteria to grow using a culture, and the test can be inaccurate and miss a potential infection. It can also be inconclusive, and doesn’t typically identify if a bacteria is drug-resistant.

Microgen testing actually finds and tests the DNA of bacteria in a sample. It doesn’t require the bacteria to be grown, so it can find bacteria that wouldn’t be picked up with a culture. It also has the ability to test for fungal infections. In summary, it’s a more sensitive test which is able to pick up microorganisms in urine (and other areas of the body) that we had previously not been able to detect.

“All urine has microorganisms and that the “micro- biome” within the urinary tract is going to vary by patient. It’s very difficult to say what a quote, “normal microbiome” is.”

-Rick Martin, CEO of MicroGen

What Does Microgen Testing Mean for IC?

First, this is exciting new technology. It should be able to reduce the number of ‘phantom UTIs’, where patients with IC are treated again and again with antibiotics for urinary tract infections that don’t exist. It may also help understand the complex urinary microbiome and what role (if any) it plays in urinary symptoms or pelvic pain.

However, no research at all has been done that changes our underlying understanding of the condition. We have no evidence that IC is due to bacterial infection, and a lot of evidence that it isn’t the case. Long-term treatment with antibiotics has repeatedly proven to be ineffective for interstitial cystitis and is specifically not recommended by the American Urological Association IC guidelines.

“The key point is you have to combine our test with other markers of infection or inflammation. If all other indications, whether it’s patients’ symptoms, burning urgency, whether it’s white blood cells count or leukocyte esterase assessment, whatever said rate CRP, whatever test you’re using, if all markers and symptoms point to infection, we are going to tell you with precision exactly what species are at the site.”

-Rick Martin, CEO of MicroGen

Future Testing

We would love to see additional research in this area. A few studies would tell us a lot more about the role (if any) of normal microflora and bacteria within the urine.

  • Is there any difference between the bacteria in urine of a patient with IC versus people with no symptoms? The first major research question will be to determine if we can detect any pattern at all to the bacteria found in the urine of individuals with and without symptoms. No testing has yet been published in this area, but it would let us know if we should conduct more research into the microbiome of the bladder.

  • ·If there is a difference in microbiomes, does it dictate an effective treatment? After we learn if there is a difference in the bacteria found in the bladder of IC patients, the next step will be to learn if targeted antibiotics or another intervention are able to provide symptom relief.

Until those two main questions are answered, none of our understanding of the condition has changed. While more sensitive testing is always important, it’s equally important to learn how to interpret the findings and not chase after test results that don’t mean anything in terms of practical symptom relief.

For a comprehensive look at IC and how to reduce your symptoms, find the right medical team, and truly understand how to take back control of your health, check out the new online course IC: Roadmap to Healing today!

Not finding a qualified professional in your area or need to create an action plan so you can improve? Schedule a remote consultation with the experts at PelvicSanity today!

Nicole Cozean

Dr. Nicole Cozean is the founder of PelvicSanity Physical Therapy in Orange County, CA. PelvicSanity treats patients from all over the world with remote consultations and the Immersive Out of Town Program. She also runs Pelvic PT Rising, training other pelvic PTs to better serve patients.

Named Physical Therapist of the Year, Dr. Nicole is author of the award-winning book The Interstitial Cystitis Solution and the first PT to serve on the ICA Board of Directors, Her passion is helping those with pelvic health issues - regardless of where they live - find lasting relief.

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