Conditions, Cystitis, Interstitial Cystitis

Can Antibiotics Cause Interstitial Cystitis and Chronic UTIs?

For anyone who has read my own story, you may remember that repeated courses of antibiotics for chronic UTIs kicked off my interstitial cystitis a few years ago. Can antibiotics cause interstitial cystitis and chronic UTIs? For me, they have definitely played a big role.

This question has been at the back of my mind for a while and today I would like to take a look at some of the scientific evidence to answer this question.

Please note that I believe that antibiotics can be life-saving and absolutely necessary in certain situations. If I had another kidney infection, I would take them again. They are probably one of our most important weapons against infectious disease.

But they should not be given out lightly.

We now know about the importance of the human microbiome, which is affected by antibiotics. And because of this, the side effects of antibiotics can be vast.

Overview of Antibiotics

Antibacterials and antibiotics are different groups of drugs used to treat bacterial infections. While antibiotics and antibacterials mainly differ in what source they were developed from, they share common traits of usage and action.

Antibiotics are used to treat bacterial disorders from minor infections such as ear or urinary tract infections to life-threatening infections such as pneumonia or meningitis.

Early antibiotics were derived from natural moulds and fungi but nowadays most of them are synthesized.

Antibiotics were first introduced in the form of penicillin in the 1940s and since then many other classes of antibiotics have been developed.

Each of them have different chemical compositions and can therefore be used against a particular range of bacteria.

Some antibiotics have a broad spectrum of activity against a wide variety of bacteria (‘broad-spectrum antibiotics’) while others only act on a few specific organisms.

Broad-spectrum antibiotics are often used when the disease-causing bacteria strain has not been identified, or to make sure all problematic bacteria are eliminated.

Once a harmful bacteria has been identified in the lab, it can be eradicated with a more targeted antibiotic.

Antibacterials differ from antibiotics in that they are derived from chemicals. They can be classed into quinolones, sulphonamides and some other drugs.

How Antibiotics work

There are seven main classes of antibiotics/antibacterials:

  • Penicillins
  • Cephalosporins
  • Macrolides
  • Tetracyclines
  • Aminoglycosides
  • Lincosamides
  • Quinolones

Antibiotics are either bactericidal or bacteriostatic.

Bactericidal means that these drugs kill growing or dividing bacteria. Some bactericidal drugs work by interfering with chemicals needed by the bacteria to form cell walls, which causes the cell’s outer lining to disintegrate. This causes the bacteria to ‘leak to death’. Other bactericidal drugs kill bacteria by altering the chemical activity inside the bacteria, preventing the production of proteins that the bacteria needs to survive.

Bacteriostatic means that the reproduction of bacteria is prevented. This is also achieved by altering the chemical activity inside the bacteria and disrupting their life and reproduction cycle.

Antibacterials function by preventing growth and multiplication of bacteria. They interfere with the action of enzymes and the production of folic acid, a chemical that is necessary for the growth of bacteria. The bacteria become unable to function and die.

Antibiotics for the Urinary Tract

The following antibiotics/antibacterials are commonly used for urinary tract infections:

  • Penicillins: Amoxicillin, Ampicillin, Co-amoxiclav
  • Cephalosporins: Cefaclor, Cefalexin
  • Tetracyclines: Doxycycline, Tetracycline
  • Aminoglycosides: Amikacin, Gentamicin, Tobramycin
  • Sulphonamide: Co-trimoxazole
  • Other drugs: Ciprofloxacin, Levofloxacin, Nalidixic acid, Nitrofurantoin, Trimethoprim


Most of the drugs used for urinary tract infections, such as tetracyclines, have a broad spectrum action, meaning they kill most bacteria that get in their way.

How Antibiotics can cause bladder problems

Antibiotics were modern medicine’s wonder weapon against infectious disease. But as with everything, the price we pay for this victory may be high.

I said it before and I’ll say it again: there is a time and place for antibiotics and they can probably save many lives. But they have side-effects and they should not be taken lightly.

Although antibiotics were not the cause of my initial problems with chronic cystitis, I kept getting more and more infections after I started using them.

And finally, after several courses of broad spectrum antibiotics in a short period of time, the pain and urgency did not go away again. I was left with interstitial cystitis.

It was clear to me that the antibiotics had something to do with what was happening to me. Now, I understand why and I would do things differently.

Let me start with talking about the microbiome (again).

We now know that we have trillions of microbes living in and on our body that play an extremely important part in our health and well-being.

We also know that in fact the bladder is not sterile but has its very own microbiome.

We also know that when the balance of microbes in our body is disturbed, problems can arise.

And that’s when antibiotics come in. Antibiotics kill bacteria. They can kill ALL bacteria.

This is especially true for broad-spectrum antibiotics such as those often used for UTIs.

Just one course of antibiotics can create a huge shift in the diversity and composition of the microbiome. The gut is affected most, but so are other body sites.

While the microbiome can recover over time, each subsequent course of antibiotics makes recovery less likely and may change the microbiome permanently.

Weakening good bacteria can allow pathogens to ‘overgrow’, the result potentially being chronic infection.

I have looked at this before and there is evidence that an altered urinary microbiota plays a role in most bladder conditions.

Moreover, the microbiome also play a big role in immunity. Therefore, a state of dysbiosis may leave us more prone to catching infections and make it harder to fight them off.

Dysbiosis in the gut could mean increased numbers of pathogens like E. coli. Antibiotics also negatively alter the genital flora, which in the long run would make it easier for pathogens to establish themselves and migrate to the urethra.

Although antibiotics are often helpful for acute infection, they may not be very effective in combating colonization and may exert only a weak or no effect on pathogens that have already adhered to the urothelium and/or have formed biofilms.

Repeated use of antibiotics also often leads to antibiotic resistance amongst urinary pathogens. A recent study found that in children, nearly half of the cases treated for UTIs had developed a resistance to the antibiotic most often used for UTIs in children [1].

One study found that previous antibiotic use increased the risk of catching an UTI in the future. The increased risk was observed both in women that had received antibiotics to treat previous UTIs and for other illnesses unrelated to the urinary tract [2].

And unfortunately quite frequently antibiotics are improperly used due to a misdiagnosis [3].

Another theory is that antibiotics that have a bactericidal mechanisms could potentially damage the GAG layer.

The antibiotics nitrofurantoin, tetracycline and erythromycin (commonly used for UTIs) are bactericidal, meaning they damage the bacterial cell wall. This cell wall is very similar to the GAG layer. In a bladder that already has an altered GAG layer and an unprotected urothelium, this mechanism may theoretically also damage the walls of cells in the bladder lining [4].

Additionally, nitrofurantoin contains ammonium ions. Pathogenic bacteria also produce ammonium ions [5, 6], which bind to the GAG layer and impair its molecules ability to repel charges. One of the GAG layer’s main job is to keep electrically charged chemical in the urine away from the bladder lining. By producing ammonium, bacteria can get through the GAG layer and invade cells of the bladder lining. The presence of ammonium ions in nitrofurantoin may also deactivate the defence mechanism of the GAG layer, perhaps allowing bacteria to get to cells.

No matter if this theory is true or not, nitrofurantoin can have other serious side-effects such as interstitial pneumonitis with fibrosis [7] and neuropathy [8].

But that is not all: Two case reports have linked nitrofurantoin use to the development of lupus erythematosus-like syndrome [9, 10]. Lupus is known to cause bladder problems [11, 12]. The authors of one study also raised the possibility of interstitial cystitis being one of the side-effects of nitrofurantoin therapy [9].

However, a study done on rabbits that exposed the rabbit bladders to a very high amount of nitrofurantoin for 1 minute showed no damage to the urothelium [13]. However, can a rabbit study be translated to humans and is 1 minute long enough to establish long-term use of this antibiotic? Maybe not. But unfortunately there are no further studies (that I know of) that look into this, so we can’t know for sure.

The antibiotic penicillin has also been suggested to cause eosinophilic cystitis [14] in some people.

A special Warning about Fluorquinolones (Cipro)

Fluorquinolones, such as Cipro, are antibiotics used for UTIs and other uncomplicated infections that have serious side effects apart from disruption of the microbiome.

These include tendinitis and tendon rupture that ‘can occur within hours of commencing treatment and months after discontinuing the use of these drugs’ [15]. The evidence for these effects is compelling enough for the FDA to issue a warning [16, 17, 18] against using these antibiotics unless there are no alternatives left. The damage may be debilitating and lasting.

I started looking into Cipro after a reader had told me that she sprained her thumb when she tripped shortly after taking the drug.

I then spoke to my dad who snapped his Achilles heel last year – it turns out he had received Fluorquinolones just before the accident whilst undergoing dental work. He in turn had spoken to a doctor who had experienced the same thing, which is how he made the connection.

If your doctor still prescribes these drugs for UTIs please forward him the studies I have cited.

What to do instead

I personally manage to get rid of my chronic cystitis and IC by using a healthy diet, natural supplements and hygiene hacks to manage cystitis.

Why not download my free guide ‘Goodbye, Cystitis’ for some useful tips and tricks?

If the need for antibiotics arises, there are several natural antibiotics that could be tried before going through courses of antibiotics. However, some of them may also damage the beneficial bacteria.

One that supposedly doesn’t affect any good microbes is Monolaurin.

What if antibiotics are necessary?

If antibiotics are absolutely necessary (for example when the infection has spread to the kidneys):

  • Ideally see a doctor who really know how to use them right (such as Professor Malone-Lee at the Community LUTS Service, Whittington Hospital, London)
  • Seek out targeted antibiotic treatment that is tailored to hidden infections rather than short courses of random broad-spectrum antibiotics
  • Avoid Cipro and nitrofurantoin
  • Take probiotics during and for a while after antibiotic therapy (take them away from the antibiotics themselves though!)


So we can see that there is evidence that some broad-spectrum antibiotics may perpetuate the circle of chronic UTIs and potentially contribute to the development of interstitial cystitis.

Sometimes antibiotics are necessary and I would probably take them again if I had another kidney infection. If used right, they can help people. But unfortunately often they may not be used right.

However, I’d try and avoid infection first –naturally, by strengthening the immune system.

In my experience, uncomplicated UTIs can be managed with a few lifestyle and hygiene adjustments, a good diet and maybe some supplements that boost the immune system and hinder pathogens from adhering to the bladder wall.

We have to be aware of the consequences of antibiotic therapy and how they can potentially perpetuate the very ill we are trying to treat.

So please choose wisely and always weigh the benefits against the risks.

What is your experience with antibiotics? Let me know in the comments.

Pin it for later:



  1. Renal and Urology News Antibiotic Resistance in Children With UTIs a Growing Problem March 21, 2016
  2. Smith, H at al Antecedent antimicrobial use increases the risk of uncomplicated cystitis in young women. Clin Infect Dis. 1997 Jul;25(1):63-8.
  3. Renal and Urology News Improper Antibiotic Use Common Among Misdiagnosed May 25, 2015
  4. Gillespie LM et al Antibiotic-induced interstitial cystitis: a model for cell membrane Proceedings of the International Continence Society, annual meeting (1985), London, p 254
  5. George Mason Hills Ammonia production by pathogenic bacteria Biochem J. 1940 [Jul; 34(7): 1057–1069.] available at:
  6. Robert A Burne, Yi-Ywan M Chen Bacterial ureases in infectious diseases Microbes and Infection April 2000 [Volume 2, Issue 5, Pages 533–542] available at:
  7. Simon J. Simonian et al Chronic Interstitial Pneumonitis with Fibrosis after Long-Term Therapy with Nitrofurantoin The Annals of Thoracic Surgery September 1977 [Volume 24, Issue 3, Pages 284-288] available at:
  8. Tan IL, Polydefkis MJ, Ebenezer GJ, Hauer P, McArthur JC. Peripheral Nerve Toxic Effects of Nitrofurantoin. Arch Neurol. 2012 [69(2):265-268.] available at:
  9. Olof Selroos and Johan Edgren LUPUS-LIKE SYNDROME ASSOCIATED WITH PULMONARY REACTION TO NITROFURANTOIN: Report of Three Cases January 1975 [Volume 197, Issue 1-6: 125–129] available at:
  10. Murie, J. and Agarwa, M. Sub-acute cutaneous lupus erythematosus following nitrofurantoin: causative or coincidental? Scott Med J. 2014 [Nov;59(4):e21-5.] available at:
  11. Min, Jun-Ki et al Urinary Bladder Involvement in Patients with Systemic Lupus Erythematosus: with Review of the Literature Korean J Intern Med. 2000 January [15(1): 42–50.] available at:
  12. ORTH, RUTH W. Lupus Cystitis: Primary Bladder Manifestations of Systemic Lupus Erythematosus Ann Intern Med. 1983 [98(3):323-326.] available at:
  13. Ruggieri, Michael R. et al Current findings and future research avenues in the study of interstitial cystitis Urologic Clinics of North America March 1994 [21(1):163-76] available at:
  14. Tsakiri, A., Balslev, I. & Klarskov, P. Eosinophilic cystitis induced by penicillin Int Urol Nephrol (2004) [36: 159.] available at:
  15. Lewis, Trevor et al Fluoroquinolones and Tendinopathy: A Guide for Athletes and Sports Clinicians and a Systematic Review of the Literature Journal of Athletic Training 2014 [49(3):422–427] Available at:
  16. Renal and Urology News Serious Side Effects With Fluoroquinolones, FDA Warns May 16, 2016
  17. FDA Information for Healthcare Professionals: Fluoroquinolone Antimicrobial Drugs [ciprofloxacin (marketed as Cipro and generic ciprofloxacin), ciprofloxacin extended-release (marketed as Cipro XR and Proquin XR), gemifloxacin (marketed as Factive), levofloxacin (marketed as Levaquin), moxifloxacin (marketed as Avelox), norfloxacin (marketed as Noroxin), and ofloxacin (marketed as Floxin)] July 2016
  18. DEPARTMENT OF HEALTH & HUMAN SERVICES Cipro SUPPLEMENT APPROVAL Reference ID: 2910764 2010,019847s047,019857s054,020780s033,021473s028ltr.pdf




  • Reply


    April 3, 2017

    I disagree, professor malone-lee is proving that they can actually help some people!

    • Reply


      April 4, 2017

      I’m sure they can if used right. Unfortunately there don’t seem to be many people like Professor Malone-Lee who actually know the in and outs of it. I’m going from my own experience here and the research I have found to explain it, that doesn’t mean it’ll be the same for everybody.

  • Reply

    Sheryl Chan

    April 4, 2017

    This was an extremely interesting and concise read. Thanks for sharing this important info! 👍

    • Reply


      April 4, 2017

      Thanks, Sheryl!

  • Reply


    July 22, 2017

    Hi Layla,
    I was given anti-bs for a uti last December which have lead to chronic abdominal pain ever sInce. I have had scans, blood tests for everything and the only thing that came back was in my bladder. I have to go back in Aug to have another cytoscopy (sp?). I have found research on mast cells and ic bit no doc or consultant has suggested this. I’m thinking whatever is causing this pain was triggered by the abs for uti and possibly 2 lots for dental abscess around the same time. So pleased to have read your article, thankyou

    • Reply


      July 22, 2017

      I’m sorry you have to go through this! None of my doctors at the time suggested IC or even referred me to a specialist, I felt at my wits end. I think there’s still not a lot of awareness about these kind of problems. I hope you get better soon!

  • Reply


    November 4, 2017

    I have been on and off doxicycline for months due to small abscesses on an old scar. Now i am experiencing a UTI and I really believe it from taking the same antibiotic. Each time it was prescribed I had a more difficult time tolerating it and this last time I had horrible intestinal issues. I have been taking probiotics but now, one week later, I have developed a UTI. I am not prone to UTIs and have not had one in 16 years. I spiked a fever last night, almosr 103F and took some tylenol. I am feeling better but reading this article confirms to me that it may have been caused by the doxy.

  • Reply

    Johnson Danielle

    November 22, 2017

    I have been suffering from IC (Interstitial Cystitis) symptoms for 8 months. Never had issues before that, but it came all the sudden and it was HORRIBLE! I was left in absolutely excruciating pain after 4 rounds of antibiotics that I was given to treat the “uti” that I had. I was diagnosed with IC 9 months ago. I’ve been on the gaps intro diet for a week now. I’ve been trying to keep my spirits up but I just feel like I’ll never feel normal again, because i have being to several hospital for solution but the doctors could not help me, i was discourage and helpless. not until this faithful day, I saw a testimony on how Dr OGBEFUN, helped people in curing Interstitial Cystiti, Dr OGBEFUN, herbal medicine is a good remedy for Interstitial Cystitis, I contacted him and he guided me. I asked him for solutions and he started the remedies for my health he gave me some comforting words with his herbal medicine for curing Interstitial Cystitis within 3weeks of it, i feel my normal body again Thank God now everything is fine, I’m cured by Dr OGBEFUN Herbal medicine, I’m very Thankful to Dr, for curing my Interstitial Cystitis…, if you are having a similar problem, kindly contact him today and get your problem solved.

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