4 Reasons Why Antibiotics Did Not Resolve Your UTI Symptoms

“I took antibiotics for UTI but symptoms are still there”, it’s a common complaint among chronic UTI sufferers but it could mean a lot of different things. I asked Dr. Lisa Hawes a urologist at Chesapeake Urology to help to navigate different case scenarios and discuss what they could potentially mean. However,  do not attempt to self-treat based on this information only.

This post should rather serve you as a guide for a conversation with your doctor. When you know what to mention during your doctor visit, you have higher chances to get better care.

Option #1: Bacterial Antibiotic Resistance

Have you taken all prescribed antibiotics but your symptoms are only getting worse? It could be that your bacteria are resistant to this type of drugs.

You might have heard about superbug bacteria that withstand all available antibiotics. Well, increasingly, bacterial resistance is a real-life problem that physicians facing more often than before. 

Here are the main signs that could signal that your bacteria are resistant to the prescribed medication:

  • You are feeling worse, while you’ve been taking antibiotics diligently for over 48 hours.
  • You are experiencing fever or nausea (must see a physician right away).

“Realistically, you should feel much better by the third day of an antibiotic treatment, bacterial load should be lowered, and therefore symptoms should subside”, says Dr. Lisa Hawes “even if not all symptoms resolved, you definitely should not have cloudiness, odor, or blood in your urine 48 hours after starting antibiotics”.

Signs that UTI is not responding to antibiotics

What if you feel lower back pain? Is this a sure sign that infection is progressing to the kidneys and antibiotics are not working?

“While lower back pain could be an important sign of kidney infection, in many cases low back pain alone is not a sure sign that bacteria ascended to the kidneys, it could be just pain radiating from the bladder due to UTI,” clarifies Dr. Hawes. However, if you are experiencing fever (102 -103 F) and/or nausea, these are very serious symptoms and you should seek immediate medical attention.

This is when the chances are higher to get sick with an infection caused by antibiotic-resistant bacteria:

  • You underwent multiple UTI treatments in your lifetime
  • If you have been using the same antibiotic for previous infections
  • Stopped taking antibiotics and didn’t finish all the pills that your doctor prescribed you
  • If you are guilty of keeping a stash of antibiotics and self-treating UTIs, cold, travel diarrhea, etc.
  • You’ve been recently hospitalized
  • If you are immunosuppressed or have any serious chronic health issues, for example, uncontrolled diabetes.

Dr. Hawes highlights that it is important to request a urine culture test before deciding on a type of antibiotics. If you are taking multiple antibiotics without checking bacterial drug sensitivity, it’s a guessing game that only increases your chances to develop a resistant bacteria.

Read how to revert antibiotic resistance with diet.

Option #2: After antibiotics, UTI symptoms still linger? Maybe it’s not a UTI.

Guess what, UTI is not the only diagnosis responsible for UTI-like symptoms.

Unfortunately, this scenario happens way too often: you have had many well-diagnosed UTIs in the past, so when you complained of UTI-like symptoms, your doctor prescribed you antibiotics right away.

Sometimes, after you take antibiotics you could even feel better but then you notice that some symptoms (urgency or bladder pain) still remained. This could be confusing, especially if antibiotics did bring you a slight relief.

Per Dr. Hawes, if you never had blood in your urine, cloudy urine or funny smelling urine in the first place, if your only symptoms were bladder pain and slight burning with urination, then chances are high that it was not a UTI.

As Dr. Lisa Hawes explains ”After multiple UTIs the bladder lining is damaged and inflamed. When the protective GAG bladder layer is damaged, the acidic urine can easily irritate the bladder and cause pain”.

If you noticed that drinking lots of water help with your condition, it is because you are simply diluting the urine and making it less irritating to your bladder walls.

Medications and supplements that help to coat the lining of the bladder (similar to how Pepto Bismol can protect stomach lining) could greatly reduce these symptoms.

Took antibiotics, some UTI symptoms resolved, other symptoms still linger

So why if it wasn’t a UTI, the prescribed antibiotics worked and you did feel a relief? Well, there could be at least three reasons:

  1. It could be that you are lucky to experience the famous placebo effect. It means that your body healed itself when you are given an irrelevant medication or even a sugar pill. This phenomenon affects up to 75% of patients in controlled groups (depending on a disease) and while it is still not well understood, it’s a real thing.
  2. Another option is a test failure. No tests are 100% accurate. There is always a room for human error, too. So it could be that there was, indeed, an infection in your sample but the lab wasn’t able to culture it. The chances for a mistake are higher when urine is too diluted with water that you were drinking excessively prior to the urine test. It could also be that a certain type of bacteria is more irritating to the bladder even with a lower count.
  3. Moreover, Dr. Hawes encountered many patients in her practice that claim that specifically, Cipro helps them with their UTI-like symptoms even when a lab finds no bacteria in their urine.

Dr. Hawes hypothesizes that it could be due to some sort of a side-effect from Cipro: perhaps, the medicine does something else to the body besides killing bacteria that could indeed reduce UTI-like symptoms.


Bacteria in my poop could...


Why Your UTI Test May Be Negative Even When You Have Symptoms

How about the study that looked at bacterial DNA in the urine of women with UTI-like symptoms who also had a negative culture test?

To summarize, the researchers looked at urine samples of women without symptoms and a group with UTI-like symptoms. They performed two tests: a culture test and a DNA-sequencing test that allows identifying if there is any bacterial DNA in the urine.

According to the study,  90.5% of symptomatic women with a negative urine culture tested positive for Escherichia coli bacteria with molecular methods compared to about 5.3% of women without symptoms.

This allowed the researchers to conclude that culture tests might not be sufficiently accurate and if a patient complains of urinary tract infection symptoms, she might as well be treated for an acute UTI.

The findings are gaining traction among chronic UTI sufferers who feel that the study finally gives more credibility to their complaints.

“However”, argues Dr. Hawes “the significance of finding bacterial DNA may be different than the significance of finding live growing bacteria. Does the DNA stay around after an infection? If so, for how long? How do you determine antibiotic sensitivity based on DNA findings rather than live growth?”.

If you’ve seen any criminal movies in which the action is taking place after the mid-80s, you expect that police will do a DNA test to confirm who was at the crime scene. However, there is a difference between establishing that a suspect was at the crime scene at some point in time versus finding out where is the suspect now.

As Dr. Hawes concludes, “We don’t yet understand the clinical significance of this data”. In other words, do not dismiss the results of your culture test because of this study.

Discuss with your doctor if some of your UTI symptoms persist after antibiotics

Here are several questions that you should think about prior to  your doctor visit to help your physician with the right information:

  • Are your symptoms stronger when the bladder is full and you feel better after urination?
  • Does a certain position (sitting versus standing) trigger bladder pain?
  • Do you feel that your symptoms stay the same over the course of days and even weeks?
  • Is there blood in your urine, foul smell, or is your urine cloudy?
  • If you’d like more help on how to discuss your UTI with your provider and how to make the most out of your patient-doctor relationships, check out my Actionable Guide here.

Option #3: Persistent UTI Symptoms After Treatment

Here is another option: they sent your urine sample to a lab and later told you that according to the test you have a UTI. However, antibiotics resolved some symptoms (such as blood in urine), but urge to urinate or pain in lower abdomen remained.

As you could imagine, there could be a scenario when not only you have a full-blown UTI, but also an inflamed bladder lining is causing additional symptoms, as discussed above.

In this case, you, most likely, will see a reduction in pain, and your urine will become clear. However, pain in the bladder area and slight irritation after urination might still linger.

Moreover, when patients mention they feel burning in the urethra rather than the bladder, it’s quite normal. In fact, the urethra has more nerve endings that could be easily irritated due to underlying inflammation.

Option #4: UTI Symptoms Return After Antibiotics?

Another story is when your urine test did show a UTI. You then took antibiotics, felt completely fine, but several days later woke up with the same nasty UTI symptoms.

“Here two options are possible: we were unable to eliminate the infection completely or it is reinfection”, says Dr. Hawes “if only 2-3 days elapsed since treatment and symptoms recurred, most likely we were not able to clear the infection. However, if you get an infection 2-3 weeks after your last antibiotic treatment, count it as reinfection”.

Bacteria hide in your bladder lining

One interesting fact from Dr. Hawes: during bladder cystoscopy of chronic UTI patients she frequently sees “pimples” on their bladder surface. The correct medical term is Cystitis cystica, which is a benign lesion of the bladder as a result of chronic inflammation.

These “pimples” are thought to be caused by chronic irritation of the urothelium because of infection, calculi, obstruction, or tumor”.

Per Dr. Hawes, a biopsy of these pimples typically comes back with results of bacterial contamination. Basically, bacteria comfortably reside inside of these “pimples” on a bladder wall. The worst thing, they can reappear from time to time to cause yet another infection. That’s why you notice that UTI symptoms come back after antibiotics.

If that’s the case, Dr. Hawes’ identifies the type of bacteria via a culture test and which antibiotic bacteria are susceptive to. After that, she combines a short-term intensive antibiotic therapy with a long-term (1-3 month) low dose antibiotics. This normally kills bacteria that keep reappearing out of the cysts into your bladder.

Many thanks to Dr. Lisa Hawes who took the time off her weekend to share these insights. We hope this information will help you when discussing a treatment plan with your urologist. And if you are happened to be in Maryland, here is contact information for Dr. Hawes’ practice.

What Else Can You Do When Antibiotics Fail?

When it comes to the best treatment for recurrent chronic UTIs there are two main camps.

Some physicians prefer a long-term antibiotic treatment protocol, frequently prescribing a variety of antibiotics over the course of several months (or even years).

Others advocate for the mindful use of antibiotics and focus on correcting underlying dysbiosis as the main reason for recurrent UTIs. In fact, we are still learning about the human microbiome and the effect bacteria have on our health and it seems less and less probable that antibiotics alone could solve chronic issues.

Moreover, antibiotics were developed when we thought that a healthy bladder is sterile which we now know is far from the truth.

What is the best approach to cure a chronic UTI? Here is a selection of posts that can help you to get up to speed:

  1. A holistic approach to UTI treatment
  2. Best UTI treatment is systemic
  3. And don’t waste your money on re-packaged D-Mannose or attempt to prevent UTI with Vitamin C.

38 thoughts on “4 Reasons Why Antibiotics Did Not Resolve Your UTI Symptoms”

  1. Hi I’ve had uti’s in the past so when I got the symptoms I went to the doctor immediately I happened to be sick at the time so they prescribed me amoxicillin and pyridum for the symptoms. I ended up having an allergic reaction to the amoxicillin, and they put me on Bactrim for a week and I asked for another dosage of pyridium cause it seemed to be the only thing helping. I finished my Bactrim yesterday, and have one pill left for pyridium and I just don’t feel better. It’s been about a week and a half and the pyridum was the only thing helping, now nothing is, and I feel like that week of antibiotics just didn’t work. I’m conflicted on what to do. My culture results came back positive for a uti. I don’t want to pay for another doctor appointment if not necessary, that and even more medication, but none of my other uti’s have been like this. Any advice is appreciated. I developed pyleonphritis 2 years ago from a uti that the medication didn’t work for, so I want to avoid that from happening again.

    1. Anastasia Visotsky

      Liz, especially with your medical history of previous complications, I’d suggest you go back to see a doctor. You can discuss an alternative path with them but it’s unlikely they support any other route than antibiotics since you developed kidney infection in the past. It’s hard to say any more than that in your case based on your message but you clearly should not delay calling your doctor. Sorry, I can’t be more helpful! Best wishes,

  2. Hi,
    Looking for advise and completely freaking out. This started about 3 weeks ago. My wife and I used a different condom and the next morning I woke up and his this frequent urination. I did go to a doctor since I also had an eye infection and told him. He prescribed an antibiotic that he said would help with both issues. As it turns out I had a cyst on the eyelid which I had removed and after that procedure I was again put on further antibiotics. The frequency to urinate then came back. I finished the antibiotics and went to a see a urologist randomly. A urine test showed trace of blood in the urine as the only flag.

    I went back to the GP and he put me on a course of doxycycline and prednisone for 5 days. The frequency to urinate decreased. I did however increase my water intake. At no point does my urine look cloudy or red etc. Looks clear to me or pale clearish. I went back to do another urine test and again theres a trace. I am freaking out that I have something sinister. The urge to go is comes from my penis ,sometimes I feel theres spasms (no pain) and I noticed that I do have 2 streams coming out….
    I am so scared…I have another urogolist appointment next week Tuesday.
    Colour Yellow
    Clarity Clear >
    Protein Not detected
    Glucose Not detected
    Ketones Not detected
    Blood/Haemoglobin Trace
    Leucocyte esterase Not detected
    Nitrite Negative
    Urobilinogen Not detected
    Bilirubin Not detected
    pH (4.8-7.4) 6.5
    S.G. (1.016-1.022) MICROSCOPY
    RED CELLS None observed per HPF
    Casts Not observed
    Squamous epithelium Not observed
    > Viable count No growth
    > Routine culture (urine) No growth

    1. Anastasia Visotsky

      Hi there Marcus 🙂 I’m happy you are seeing a doctor and surprised your first physician didn’t do a thorough physical exam and just gave you antibiotics (maybe they did, but it’s not clear from your comment). I’m sure it’s nothing disastrous, perhaps an enlarged prostate. Your symptoms and urine culture seem to indicate no bacterial growth in the bladder, so while it’s crazy for me (I’m not a medical professional) to even try to diagnose you, I don’t think it’s a UTI. Just make sure your doc does a prostate check and an imaging study, if needed, and you’ll be on your way to recovery.

  3. I have had UTIs many times before and always take Macrobid. This time I have been taking it and my bladder symptoms went away but I started to have a dull back ache. No fever or nausea. I’m scared the Macrobid did not work and now I have a kidney infection. Should I wait for more symptoms before seeing a doctor? I don’t want to take more antibiotics if it’s not necessary.

    1. Anastasia Visotsky

      Hi there, I wish I could reassure you, but I’m not a medical professional and doctors wouldn’t normally provide feedback online either. You can discuss antibiotic prescription with your doctor as well as your desire to limit the exposure to antibiotics. You can ask them to perform a urine culture test before agreeing to more antibiotics. Best wishes,

  4. I’m not sure what my bladder problem is…last year I had a urinary tract infection and the doctor gave me Cipro. It went away but 10 days later my urine had a foul odor and was “milky”. Again I took Cipro, but the culture came back “not significant” and the doctor said to quit the Cipro. I had two more cultures after that and each one came back “not significant”. It has been 8 months but…when I get up in the morning my urine is normal. It is after I eat that it gets cloudy and has an odor. I plan to ask for another culture just to keep an eye on it, but I’m wondering what this can be. The doctor thought it might be cystitis and has left it at that.

  5. I have seen 4 different doctors over the 10 months for a UTI that just won’t go. I was diagnosed last November with a UTI, after suffering for a month with them on and off until I had had enough, and the antibiotics worked for a while, it then returned around a month later and since it just won’t go. I have burning in the morning, then as I drink more it goes. It burns after sex (not straight after but the next morning or the next time I pee) even though I ALWAYS go straight after, and also if I drink coffee or am dehydrated/ don’t go straight away I get the same symptoms. Also, I drink lots of water but I am constantly peeing, and after a while my bladder actually starts to hurt, and I constantly feel like I have to pee desperately. It’s either a burning sensation or feeling like I desperately need to go. Every time my urine cultures come back negative, but I am given antibiotics that just seem to aggravate my bladder and make my symptoms worse. I am in dispair, after my second round of antibiotics I started taking d mannose, then that seemed to stop working as well and all my symptoms came back. I am sick of being told by doctors that there isn’t anything wrong and to go to a GUM clinic, even though I am in a long term relationship and both me and my partner are clear, and just not being listened to. I read on here the symptoms of bladder inflammation, and I thought maybe that might be the issue here? I understand your not a medical professional, but I am in dispair and wondered if you had any adivce that you could give me? I am 23 and am afraid to leave the house in case I am not near a toilet, drink coffee and have sex because I am scared of these symptoms flaring up! And sorry for the essay, and if it is to much information!

    1. Anastasia Visotsky

      Hi there, I’m sorry for you feeling that way 🙁 You know, I’d suggest consulting with a homeopathic doctor or a naturopath. Unfortunately, Western medicine practitioners focus on one organ at a time and this approach just seems not to work well for chronic issues. I’d also consider an IC diet and see how your bladder feels then. Best wishes,

    2. Hi there, I’ve had many similar experiences. I had recurrent UTIs for a few years of my life, and eventually had to have a cystoscopy to remove scar tissue from my urethra. Since then, I’ve found that I’ll frequently feel like I have a UTI, go to the doctor and all the tests come back as negative. They’ve told me I have something called “sensitive bladder syndrome”. I don’t really know if I believe it but I’ve had to find ways to cope, unfortunately. I now take cranberry supplements daily, Azo when I really need it, avoid eating anything super acidic (ex. pineapple), avoid wearing tight underwear like thongs, and I’ve starting drinking 100 oz of water everyday, which seems to help quite a bit. I completely understand your frustration, I’ve been there also. I hope you feel better soon!

    3. Hi there- I’m curious if you have discussed interstitial cystitis with your doctor? Your recurring UTI symptoms and flare ups related to caffeine sound like symptoms of IC or ‘painful bladder syndrome’… Alcohol, Citrus, and spicy foods can also cause it to flare up. I only suggest this because I am going through a similar dilemma and am being tested next week for Interstitial cystitis. I hope you find some relief soon!

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