Conditions, Cystitis, Interstitial Cystitis, Overactive Bladder, Urinary Incontinence

Fungal Infections in the Urinary Tract

When speaking about urinary tract infections, we usually speak about bacterial infections. Fungi (a.k.a yeasts or mold) are different organisms from bacteria and they can cause infections such as thrush in some parts of the body. Fungal infections in the vagina for example are a well-known condition. But can there also be fungal infections in the urinary tract?

In recent years, new research has established that the urinary bladder is not sterile as it was previously believed.

In fact, it is home to communities of microorganisms that, in the right balance, help to keep the bladder healthy.

Changes in the balance of these microorganisms have been noted to be present in all bladder conditions.

Further, it has been shown that standard testing does not pick up all infections reliably. So if you experience symptoms after a negative test result it does not necessarily mean that no infection is present.

Standard testing also does not test for organisms other than bacteria. But are they even a thing?

Fungal Infections in the Body

Most people will have heard of thrush before. It is an infections caused by the fungus Candida Albicans that can occur in the vagina, on the penis or in the mouth.

Athlete’s foot is another common fungal infection affecting the feet. These fungal infections are well accepted by the medical establishment [1,2] and usually treated with anti-fungal medication.

In the alternative health world, Candida infections have been a buzzword for many years. Candida is what I came across when I first started looking at possible root causes for my bladder pain and IBS.

However, when I unknowingly asked my doctor about Candida infections in the gut, she just told me she ‘doesn’t believe in it’ and sent me home. This was not the only time I heard a doctor say this line.

It is perhaps a bit naïve to blame all infections on Candida, as I frequently came across when I started researching my problems in a more ‘natural health’ context.

But fact is, that the literature contains many papers that talk about gastrointestinal and systemic (whole body) fungal infections [e.g. 3, 4, 5, 6]. Although some of these studies are rather old, they should not be disregarded.

A new study even stated that ‘[Candida] can also become invasive, causing life-threatening systemic and bloodstream infections in immunocompromised hosts, where the mortality rate can be as high as 50 %’ [7].

So much to ‘not believing in it’.

The problem perhaps is, that everything is blamed on Candida when it could well be another fungal strain (such as Saccharomyces or Aspergillus), a different kind of infection or something completely different – symptom are often non-specific and similar.

Luckily we can test the gut now. Stool or antigen tests can show what’s going on. Better even, new metagenomics tests can show us bacteria and fungi (e.g. mapmygut).

Fungal Infections of the Urinary Tract

As you’ve hopefully seen above, systemic fungal infections are a thing – whether your doctor believes in them or not.

Therefore, it makes sense that fungal infections could also affect the urinary tract.

And in fact, recent studies have shown that this is the case.

A study from 2016 used a novel, culture-independent testing method which showed that females with interstitial cystitis/Painful Bladder Syndrome flares showed a greater prevalence of certain fungi, specifically Candida and Saccharomyces species [8].

An even newer study showed that specific microbial patterns correlated with specific urinary tract symptoms. Overall, they actually found a decreased diversity of fungal species in patients with more severe symptoms. Bladder pain patients had altered levels of Malassezia spp while patients with incontinence had changes in Wickerhamomyces spp [9].

The Problem with Testing and Treatment

Current gold standard testing misses a lot of bacterial infections as is but in the case of fungal infections, it doesn’t pick them up at all and other testing methods are needed.

This means that if you have symptoms but no infection has been found it does not guarantee that there isn’t a fungal infection present.

Antibiotic treatment also poses a problem as fungi are not affected by antibiotic treatment. Instead, bacterial species that may keep fungi in check from taking over, may be killed off by antibiotics allowing fungi to proliferate.

Instead, anti-fungal medication is needed but with the lack of adequate testing, doctors are unlikely to prescribe them as there would be no ‘proof’ of an infection.

This shows once again, that the balance of the microbial system is really important.

What to do if you suspect a Fungal Infection

Unfortunately, adequate testing is not yet widely available. If you’ve had a stool test that indicates fungal infections this may indicate other fungal infections in the body. But we can’t know for sure.

An open-minded doctor may be up for trying anti-fungal medication if other therapies have not worked.

Several natural compounds have both antibacterial and antifungal activity and may be worth trying – however, don’t assume that something is safe only because it is natural. Do your research!


What this shows more than anything is that we need better testing!

Testing is outdated and misses infections with people wrongly being diagnosed with ‘incurable’ IC.

What can we do about it? Speak up, join patient advocate groups such as CUTIC that are campaigning for better testing.

Now I’d like to hear from you: Have you had fungal infections in the past? Do you think your bladder symptoms could be connected to fungi? Let me know in the comments.

Pin it for later:


  1. NHS Choices Vaginal Thrush March 2016
  2. NHS Choices Athlete’s Foot September 2015
  3. William R. Jarvis Epidemiology of Nosocomial Fungal Infections, with Emphasis on Candida Species Clinical Infectious Diseases, Volume 20, Issue 6, 1 June 1995, Pages 1526–1530
  4. Leslie S.Wilson et al The Direct Cost and Incidence of Systemic Fungal Infections Value in Health Volume 5, Issue 1, January–February 2002, Pages 26-34
  5. ERAS, PHILIP et al CANDIDA INFECTION OF THE GASTROINTESTINAL TRACT. Medicine: September 1972 – Volume 51 – Issue 5 – ppg 367-380
  6. R J Prescott et al Fungal infections of the small and large intestine. J Clin Pathology Volume 45, Issue 9
  7. Neil A. R. Gow et al Microbe Profile: Candida albicans: a shape-changing, opportunistic pathogenic fungus of humans 15 August 2017, Microbiology 163: 1145-114
  8. Curtis Nickel et al Assessment of the Lower Urinary Tract Microbiota during Symptom Flare in Women with Urologic Chronic Pelvic Pain Syndrome: A MAPP Network Study J Urol. 2016 Feb; 195(2): 356–362.
  9. Ackerman, A. LenoreResearch Network, MAPP et al. MP29-10 ALTERATIONS IN THE URINARY FUNGAL MYCOBIOME IN PATIENTS WITH BLADDER PAIN AND URINARY URGENCY The Journal of Urology , Volume 197 , Issue 4 , e383 – e384


  • Reply

    Francis Jordan

    August 23, 2017

    I have severe urinary tract infection for over 12 years and no one is interested to deal with them so they just tell me to take these medicines long term. Ciprofloxiacin 500mg One four times a day, I am also taking Fluconazole 50mg One daily, also Flucoxacillin 500mg One four times a daywhich is a fungal medicine, Trimethoprin 200mg take twice a day. There that severe they end me up in hospital if their is a bed free or just remain at home in bed. It would be nice if someone somewhere would be able to deal with these infection that will end up taking my life as last year the infection got into the body system and I was then rushed to hospital and stabilized before moving me to another hospital. I wear pads every day since and it does get a bit embarrassing for me as I am also a diabetic and had to change my pads in front of my eldest sister and my late mother, my wife and you know no one give a rate ass about my health. Doctors would rather give you antibiotic’s instead of finding out a reason why these are always recurring. Even Mr David Ralph, Mr Nan Christopher at University College London Hospital Westmoreland street London who are specialists in Andrology/Urology and they aren’t bothered no one in the medical profession gives a rat ass unless you are a “PRIVATE PATIENT WITH MONEY” if you have no more their not interested. I am under that many doctors not one of them gives a damn about my health and the NHS here in the UK has not got the funding to do new research into anything. In the meantime I have to continue to suffers silently in severe pain or until this infection takes my life. I have done everything I can yet I have still got Severe Urinary Tract Infections and with the amount of antibiotics I am on you would have thought they would have killed the buggers, but no still having infections day in and day out. You tell me who really cares about people who suffers long term with severe urinary tract infections that they do not have a life. I just wish the bloody infection just take my life because it is getting more severe on me. I am under University College London Hospital Westmoreland Street London. Belfast City Hospital Lisburn Road Belfast Northern Ireland, Royal Victorian Hospital Falls Road Belfast Northern Ireland. Out of everyone of these hospital not one has the balls to tackle my Urinary Tract Infections why? I wish someone would tell me honestly why they are not looking into it or why I have suffered these severe bloody urinary tract infections all these years and I am under top specialists in the country and yet they cannot do anything for me why?

    • Reply


      August 24, 2017

      Dear Francis, I’m so sorry you’re going through this, I totally feel for you and agree with you. Have you heard of professor Malone-Lee in London? He is at the Whittington LUTS (lower urinary tract symptom) clinic in London. He has helped many people recover. Unfortunately I think the clinic is closed to new NHS patients atm but you could try getting in touch with – I think they have helped to refer patients there in the past.

  • Reply


    December 4, 2017

    Hi Francis,

    I just read an excellent book by a British naturopath who has an office in London: Philip Weeks, author of Painful Bladder Syndrome: controlling and resolving interstitial cystitis through natural medicine. It would be worthwhile to find his book and get an appointment with him, I think, if you’re near London.

    Best of luck.

  • Reply

    Mary Baugh

    June 4, 2018

    I am from the US. Years ago, I had back surgery. The surgeon cut my sphincter nerve rendering me incontinent both urinary and fecal. I have had many UTIs since then. However, about 6 months ago, I got a finger nail fungus. It was left untreated due to a liver problem. Since March 7, I have had 7 UTIs for which I have received antibiotics. I am now suffering from my next one. I have many of the symptoms listed in another article regarding the correlation between nail fungus and UTIs. My urologist just keeps checking for the regular bacteria. I feel that the nail fungus is a direct cause of the UTIs and the ongoing diarrhea/constipation problems along with many other symptoms. I need help.

    • Reply


      June 4, 2018

      Hi Mary, I have a list of tests on the blog that can pick up fungi as well. I would try and find someone who can help you interpret these and treat accordingly. Some of them you can order yourself but this is only useful if you have someone to treat you accordingly.

  • Reply


    June 28, 2018

    Hi Layla,

    I am switching to a functional medicine doctor that does more thorough testing. Regarding the fungi around possible bladder issues – is this discovered in a stool sample? Are there any specific test I should ask for?

    Also, this may sound like a crazy question but where would the fungi come from to penetrate into the body?

    I am actually going to the podiatrist today to be treated via laser for toenail fungus….interesting….do you think it could be connected in any way?

    Also, I have noticed by bladder issues increase a week prior to my period. What are you thoughts on hormone issues causing some of the issues? I have also been treated for pelvic floor issues – no births.

    • Reply


      June 29, 2018

      Hi, yes you could do a stool or urine organic acids test to look for yeast issues. Fungi are naturally present in the body and have some important biological functions, it is when other microbes are diminished that they can overgrow and cause issues. I think if there’s a fungal issue in the gut then it could become systemic as well, meaning it could affect other parts of the body. If I have a client with yeast issues I would concentrate on the gut more than anything.
      Yes, hormones can have a big influence as they can change the pH of some body sites (e.g. the vagina) which in turn affects the microbes living there. I have an article on this as well. Estrogen, for example, has been shown to be protective against UTIs but in IC sufferers can exacerbate symptoms as it can increase histamine release from mast cells.

  • Reply


    June 28, 2018

    Hi Layla,

    I am switching to a functional medicine doctor after ongoing issues with bladder and pelvic floor. I have not been officially diagnosed with IC but the symptoms definitely align. How would I go about testing for fungi to see if this may have something to do with bladder issues. Now I am just focused on a process of elimination! In 2018 it is baffling to me why no Dr., scientist anywhere in the world can figure out this problem! It is time consuming and very costly!

    What tests do you recommend I do as a process of elimination?

    Also, I was recently diagnosed with a toenail fungus – think this is related in any way or just a coincidence?

    Another thing I would like to mention my bladder “issues” seem to increase a week prior to my menstrual cycle. What is your take that hormones have a role in this issue? I will be 47 this year so I am approaching the “change”.

    • Reply


      June 29, 2018

      Most questions answered in your other comment. With regards to testing there’s a range you can do and it’s up to how much you can afford. If budget is limited I use stool testing first. But there are urine tests you can do – Microgen DX and Aperiomics test for bacteria yeasts (this is a DNA), PCI testing also but this is a culture test and probably not as accurate (but cheaper).

  • Reply


    April 10, 2019

    Twenty years ago, I had what seemed to be a typical bacterial bladder infection. My doctor prescribed Cipra, even though bacterial levels seemed normal when tested. That was followed by 3 years of terrible urgency and pelvic pain. I had to plan any trips out of the house based on the ease of access to public restrooms. Doctor eventually referred me to a urologist. I had already done extensive research by this time, and it was clear that this was interstitial cystitis. Found some on-line discussions of dietary restrictions, and developed a very strict, and initially, extremely limited diet that made a big difference. When I saw the urologist (male), and shared my research–what had worked and what hadn’t–he looked at me, winked, and said, “You don’t want interstitial cystitis. It’s no fun.” … I almost expected him to pat the top of my head, and felt thoroughly dismissed and patronized. Spent the next year convincing my general practitioner to prescribe nystatin, an anti-fungal, based on my research suggesting systemic “candida” infection. Strict adherence to a low-acid diet–no soda, coffee, tea (sun-brewed was okay, limits tannins and acids), artificial sweeteners, acidic fruits or vegetables, fermented products (like soy sauce, saur kraut), or food with yeast (like beer, bread, wine); several months of nystatin; and bladder training to delay urge to go, got me to the point where symptoms were tolerable. Over the years I’ve been able to gradually re-introduce almost everything I ate before (except orange juice and grapes, which still set me off). I experience occasional flare-ups, but I’m generally able to contain these by determining what food might have triggered the flare-up, and using calcium supplements or 1/2 tsp of baking soda in water to soothe urgency and pain.

  • Reply


    July 26, 2019

    I have had kidney stones since I was 18 and I am 53. No one knows why, just happens. UTI’s also have been an issue. About a year ago my dr decided to snatch as many stones as he could so my body could have a rest. I contracted ESBL from a hospital stay and went into sepsis shock a few years ago. Dr said I needed a rest last year and plucked 9 stones out of my kidneys. I started having burning, low grade fever, and extreme fatigue. I went ER and was admitted to hospital with high wbc and large leukocytes in my urine. Dr says you have a UTI. This happened 4 other times over last year. Because I am ESBL positive I am also antibiotic resistant. Reason why I must be admitted when I get a bad infection. This happened in June and I was released. Within 3 days my symptoms came back. The other times it had taken months. I was so exhausted I could hardly function. A urologist saw me and noticed my urine had never grown bacteria. She told me it is medically impossible to have a standard UTI that doesn’t grow bacteria. She had me give a first morning urine 3 days in a row at the lab and tested for fungal. Sure enough my urine grew (c. Albicans) . She prescribed Diflucan to be taken for 14 days and then retest me. She said she suspects I had a fungal UTI all along. Every time I was admitted and given high powered antibiotics, it fed the fungal resulting in me being so sick and eventually knocking me off my feet. I took my first pill yesterday and felt better by last night. Not 100%, but better. There is not a whole lot of info out there on what happened to me. But know this; if there is no bacteria growth in your urine culture, you should not be taking antibiotics for a UTI and they’re misdiagnosing you.

  • Reply


    March 10, 2020

    I’ve had so many utis in last 18 months. I have a bladder that doesn’t empty fully, have had tests and no answers. I have to self catheterise several times daily. Having had many antibiotics over the last year I also have thrush. I am now suspecting that I may have fungal bladder infection especially since I’ve had a few tests that say no infection found.

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