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. I am 56 yrs old, female and I have had a reoccurring UTI for at least the last four to five months. Nothing was clearing it up, my dr told me I had taken all of the susceptible oral antibiotics so we tried a week of Rocephin injections right before Christmas. This seemed to have gotten rid of it but this week the all to familiar foul cloudy urine symptoms have returned and the dipstick office test has confirmed that I do I fact have infection. I have a small 3 mm renal stone in my right lower lobe and am developing stress incontinence which is very new for me. I am not having the typical burning sensation when I pee but early on before I knew I had an UTI I was having general pelvic pain. I am not having that since starting on the first rounds of antibiotics thankfully. We are waiting the cultures to come back from the lab but assuming it’s the same bacteria or cause, what might be my next form of treatment? I can not get in to see a urologist for two weeks so my primary doctor is doing his best right now and has me on amoxicillin until we get the cultures. Could this kidney stone be causing the infections?? if so, Would surgery to remove the stone be a reasonable next step? its not obstructing according to the radiologist.

  2. Hi, thank you for your very informative posts.
    Under option 3 you say “pain in the bladder area and slight irritation after urination might still linger”. I think this is what I have after a UTI which has been going on for over two weeks…while the main acute symptoms have gone, I still have moderate pain like a burning sensation around my urethra which is worse after urination. What is the suggested solution to this? Just wait it out or is there something more proactive I can do to get relief quickly and be done with UTI for good? Many thanks

    1. Anastasia Visotsky

      Hi Jessie, glad you found it helpful. Ask your doctor if you could take Ibuprofen or try some herbal remedies with your doc’s permission to decrease the inflammation and speed up recovery. Best wishes,

  3. Hi,

    I was within the last week, diagnosed with my first UTI. I was prescribed antibiotics, a 3 day treatment, 2 pills per day. The only symptoms I had were some burning in and outside of my vagina, and burning while peeing after sex. The antibiotics helped with some of the burning, but it hasn’t seemed to fully have gone away, and today the burning while peeing returned after intercourse, really strongly. I’m not sure what this is or what to do.

    Any thoughts?


    1. Anastasia Visotsky

      Hi Emma, plenty of thoughts, one of them: test for STDs if the symptoms are not going away and at the same time not getting any worse. Also, instead of agreeing to antibiotics ask for urine culture first. And you can check out this post about honeymoon cystitis.. Best wishes!

  4. Hi
    Please I seriously need your help. I was recently diagnosed of UTI, and the doc prescribed some antibiotics and Cipro500. On the first day of taking the medication, I realized some little amount of blood clot in my pants (though initially it wasn’t there), and then later it didn’t appear again. But on the third day of medication I used lemon water to bath and unfortunately I washed my vagina with the same.. and I began having the symptom of the urgency to urinate and some burning as well.. Please I want to know if it is as a result of the lemon water I used to bath that’s why or not.
    Thank you very much.

    1. Anastasia Visotsky

      Hi there, if you are still taking the antibiotic and symptoms are not going away or getting worse, you should call your doctor. While I can imagine lemon water (?!) could be irritating it should not cause persistent problems so if the symptoms are still there the next day, definitely go see your doc.

  5. I’ve had frequent UTIs for almost 6 years now. I just got done taking bactrim, which usually helps me the most, but I still have symptoms. I feel burning and urgency bad enough that I can’t do anything or go anywhere. A year ago I went to see a urologist and I told him my story and symptoms. He checked to make sure I was emptying my bladder, which I was, and then sent me on my way. He didn’t recommend anything that I could take besides cranberry supplements but those dont help me. Any tips for preventing them? I don’t take baths, I don’t wear tight underwear or tight jeans. The doctors thing this happens because of sex but I only sleep and have only slept with my husband and it doesn’t happen every time we have sex. Could it be caused by caffeine? I only drink one pop a day so I doubt that’s it. The utis did start when i started birth control. Could the birth control be causing it?

    1. Anastasia Visotsky

      Hi Emma, lots to unpack 🙂 Basically, the best way for me to weight in on this is to direct you to read my posts or to check out my UTI guide, this will give you some framework to start analyzing your situation. Best wishes,

    2. Hi Emma,

      I hope you don’t mind me reaching out!

      I am a holistic nutrition health coach and I’ve also suffered from recurrent UTIs. It’s usually a dietary issue/gut disbyosis which causes them to recur.

      Do you want some help figuring it out?


      1. Sarah, I too am am suffering residual pain and urgency after500 mg cipro. Redone urine test is negative. I am miserable. Please advise. Thanks Kathy

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