Conditions, Cystitis, Interstitial Cystitis

Embedded Infections – The True Cause of Chronic UTIs?

I’ve been meaning to write this post for a long time because it is sooo important. Hopefully by now, many of you will have heard of ‘embedded’ or ‘intracelullar’ bladder infections but if not, please read on.

Recent research suggests, that many cases of chronic UTIs and in fact ‘interstitial cystitis’ may be down to infections having taken hold in the bladder by entering the bladder wall cells and/or hiding under biofilm structures. This allows the pathogens to evade antibiotics and indeed testing.

The great news is that it is treatable!

Could your problems be due to a chronic imbedded infection?

The common scenario seems to be this: a history of urinary tract infections that would occur periodically, perhaps after intercourse but not in every case.

Then at some point, the symptoms would persist and potentially get worse after each course of antibiotics. Some people would then experience frequent flares or constant 24/7 symptoms. Testing would usually come back negative.

Some people may receive a diagnosis of interstitial cystitis. No dietary change or medication would make a real difference.

But what if the inflammation and pain experience in so-called ‘interstitial cystitis’ was actually due to a chronic infection that was evading testing?

What if the flares of chronic UTIs were not new infections, but a chronic infection instead?

We now know, thanks to the great research of one professor Malone-Lee, that this is entirely plausible.

How a chronic UTI develops

  1. If an acute UTI is not completely cleared withing 14 days, pathogens can change their shape and penetrate into the cells of the bladder wall (called ‘urothelium’ and consisting of transitional epithelium), which is around 5 cells deep. This is called ‘intracellular colonisation’.
  2. Once in the cell, microbes go into a dormant state (hibernation) and stop dividing. Only dividing microbes are affected by antibiotics, and thus they can survive short courses. Even just one dormant microbe can, when it wakes up again, divide into a million others.
  3. A cell that has been colonized will now be transmitting distress signals to the immune system, which results in an inflammatory response (the immune response is inflammatory) – blood vessels dilate and the bladder may look red and inflamed (the typical picture of ‘interstitial cystitis’). They may also burst and leak blood into the urine, which may be picked up on testing.
  4. As part of the immune response, white blood cells are sent into the bladder, but detect no problem as the microbes are hiding in the cells. The bladder wall cells disagree, which leads to a ‘standoff’ that causes chronic low-grade inflammation. This is responsible for chronic low-grade symptoms that may persist despite negative test results.
  5. As a protective mechanism for cells, the bladder wall and the wall in the urethra may thicken, causing a degree of obstruction that can cause symptoms such as:
    • Hesitancy
    • reduced stream
    • intermittency
    • terminal dribbling
    • double voiding
    • Reduced bladder capacity
  6. Pro-inflammatory chemicals may also cause the bladder muscles to contract, leading to symptoms such as:
    • Frequency
    • Urgency
    • urge incontinence
    • And generally inflammation causes pain, burning and stinging.
  7. One of the ways the immune system tries to clear the intracellular infection is by shedding cells. This causes the dormant microbes to wake up and start dividing again, causing an acute infection (in which healthy cells can become colonized again). This is responsible for periodic flares.
  8. Another problem can be the formation of biofilms by bacteria (this could be in addition to intracellular bacteria): these are protective structures under which microbes can ‘hide’. Once under a biofilm, microbes cease to divide and become dormant (thus unsusceptible to antibiotics) and can stay attached to cells. They can then break out, divide and cause fresh infections.

Why does my doctor not know about this?

The research around this is fairly new and unfortunately, new research seems to take a while to actually be incorporated into standard healthcare. We’ve only known for a relatively short while that the bladder is not sterile, as previously believed, and that gold standard urine testing is not very accurate as it’s based on outdated science.

But gold standard testing is the main means by which many doctors for assess the bladder and diagnose interstitial cystitis and this is probably the main problem.

How to treat embedded infections

Both long-term antibiotics and more natural approaches can be used to support recovery.

Please stay tuned for my next few blog posts in which I will look at both approaches in detail.

Do you think you might be suffering from chronic embedded infections? Let me know in the comments!

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  • Reply

    Meryl James

    June 11, 2021

    Hello Layla
    I saw a ConsulUrologist December 2020 who put me on antibiotics for t months as I had recurring bouts of uti’s. I am now in month 5 and last week had burning when going too the toilet. I haven’t had any symptoms since taking the tablets so I was devastated I did a sample took to my GP it came back no action didn’t find anything. I rang the Consultant who said he doesn’t know why this happened and because it’s not bacterial it maybe Bladder Pain Syndrome it didn’t give me any advice or help.
    Are you able to offer any advice pleas? What I can take to help stop this happening anything would be helpful?
    Kind regards

  • Reply

    Dena Boggs Baker

    June 21, 2021

    im on my third UTI in 90 days, I’m
    so tired of feeling this way.

  • Reply

    Claude Armstrong

    September 4, 2021

    Having a catheter through my abdomen results in constant pathogen access. After severe bladder hemorrhaging early 2021, I began searching how UTIs can flare when my bladder infection test strips show only moderate infection.

    Embedded biofilms. These combinations of yeasts, virises and bacteria are deadly!

    So, how to attack and destroy?

    Current medicine, which I refuse to allow experimenting on my body, uses deathly lethal antibiotics.

    Yeah, I’m going to kill healthy functions for unhealthy eradication? Talk chemo all day, but nature has far better….

    So, search for natural elements that dissolve and destroy embedded biofilms…

    Do you know that a hidden agenda of cancer chemo uses a natural element to do the actual killing of maverick cells, and the deathly horrible chemo crap is window dressing?

    Yep, good ol baking soda is added to chemo…

    Go figure…

    Cancer cells are embedded pathogens. Period.

    Well, guess what. Baking soda, sodium bicarbonate, has a major cleansing power for embedded anything. Use it to destroy shoe bacteria, shower yeast and bacteria, and dissolve burned carbon in the oven.

    Inside my bladder.. I can irrigate through the catheter, you can use a temporary catheter… BK Penetrates the bladder wall dissolves biofilm, kills pathogens, and gives the bladder needed elements to heal.

    But, I found more.

    Iodine, specifically Povidone. It irritates the bladder, so irrigating is one or two times, and I cut the strength with spring water to 10-20% of the 1% Povidone.

    Then there’s even better…


    I down up to twenty-thirty 225 mcg Icelandic kelp tabs over 24 hour periods. End of infection….

    Get Dr. Sicus’ Iodine book…

  • Reply

    Kate Orton

    September 21, 2021

    Hi Layla, I’ve just found this blog and it’s amazing. I have just recently in the last week starting getting frequency and pressure, lower abdominal pain after a build up of stress and a bit of a panic attack. I have had a history of UTI’s over the years but haven’t had one for 2.5 years so it would seem unusual that these symptoms would be caused by an embedded infection.
    A few questions for you:
    Do you believe that your had an embedded UTI or IC or other?
    Do you think that stress can bring on these symptoms?
    Can you eat / drink whatever you want now without flares?

    • Reply


      October 14, 2021

      To answer your questions:
      1. Yes, I believe it probably was an embedded infections and I believe that often this is ‘IC’.
      2. Stress is very often what brings on symptoms for all kind of things. For me it was a big trigger and when I work with clients it is usally a big stressor that started their symptoms, bladder or other.
      3. I eat and extremely ‘clean’ diet all the time and I do think if I went back to my old ways of eating sooner or later I would run into problems. But I’ve never had any bladder issues again, even if I am less stric about my diet for a while.

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