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How Megan Beat Her Recurring Urinary Tract Infections By Treating Her Gut

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How Megan Beat Her Recurring Urinary Tract Infections By Treating Her Gut

Urinary tract infections (UTIs) are among the most frequent clinical bacterial infections in women. Around 60% of women will experience a UTI, with reinfection rates of 80%.

Although the initial treatment is antimicrobial therapy, a functional medicine approach to chronic UTIs can help you identify underlying factors contributing to the infection allowing the patient to make lifestyle adjustments to reduce reinfections. Below is a case study.


CC: Recurrent UTIs (every 2-3 months), Fatigue, Pain with Urination, Chronic Constipation

Megan* was a 36-year-old female with a history of recurrent UTIs (urinary tract infections) over the past two years (8 total in 2 years).

Additionally, she was experiencing fatigue, particularly as the day went on, no matter how much sleep she got. She had pain with urination about 50% of the time and stated that her constipation was worse than ever with all of the courses of antibiotics she had been taking in the past two years.  

Megan’s health history brought to light that she was sick a lot as a child with chronic ear infections and colds and took many antibiotics courses during her younger years. She had always dealt with constipation, even as a child, and had relied on Miralax in her adult years to have a few bowel movements a week.

She reported having a regular menstrual cycle of 27-28 days since her first period, with minimal PMS-related symptoms. Megan had two children who were 9 and 7 years old at the time of her initial consultation. Her pregnancies and deliveries went well, with no complications, and both babies were delivered vaginally. Megan’s first UTI was two years before our consultation, and they had been recurrent ever since. The only “new” thing in her life that Megan could think of was that around that time, she had switched to using diaphragms for birth control rather than a copper IUD, as she had heavy bleeding with the copper IUD.

Megan was working part-time as a social media manager and loved her job. Her biggest frustration was that she was continually worried about when her next UTI would come on and was concerned that taking so many antibiotics seemed to be worsening her constipation issues.

Her recent urinalysis showed elevated WBC (white blood cells) and bacteria in her urine, even though she had just finished a course of antibiotics (nitrofurantoin). Her doctor had been alternating between ciprofloxacin and nitrofurantoin.

Additional History

Megan’s diet consisted of a lot of grains and carbohydrates. Her morning meal was typically oatmeal with fruit or a bagel with cream cheese; sometimes, she added a pre-made smoothie into the mix if it was a busy day with dropping off the kids and working.

She felt that since she started to have UTIs, fatty food upset her stomach, so she stuck with whole grains and chicken or fish. Her lunch was often a chicken caesar salad or a salad she’d pick up from a local deli, and dinner was often meat or fish with potatoes and green beans or asparagus. She loved having dessert late at night after the kids went to sleep, typically ice cream or a brownie. Megan’s exercise was typically a pilates or barre class 2 or 3 times a week, playing with her kids, and walking the dog.  

Megan was taking the following supplements at the time of her initial consultation:

  • Gummy multivitamin
  • Elderberry syrup
  • Vitamin C
  • Miralax (most nights)

Lab Work

Urinalysis Results

  • Nitrites +
  • Leukocyte esterase +
  • Cloudy
  • Bacteria +
  • Trace RBC +

Comprehensive Stool Test Results

  • Pancreatic elastase LOW
  • Beneficial SCFA’s LOW
  • Fecal Fat HIGH
  • Lactobacillus LOW
  • Bifidobacterium LOW
  • Candida 4+ HIGH
  • E. Coli 4+ HIGH
  • Meat Fibers, Vegetable Fibers MODERATE

NutrEval (Genova Diagnostics) Results

  • Vitamin A LOW
  • Plant-based Antioxidants LOW
  • Glutathione LOW
  • Vitamin C LOW
  • Zinc LOW
  • Magnesium LOW
  • Lipid Peroxides HIGH

Megan’s lab work points to a few core issues that are contributing to her chronic UTIs, fatigue, and constipation.

Microscopic Urinalysis/CBC

Even though she had just finished a course of antibiotics, a recent urinalysis showed Megan still had bacteria and WBC present in her urine, meaning the infection was ongoing. It’s possible she was no longer responding to the nitrofurantoin (resistance infection).

Digestive Health

Megan’s comprehensive stool test showed us several areas that needed support. She had low growth or beneficial bacteria such as Lactobacillus and Bifidobacterium, with high growth of E. coli and Candida spp, which are potential pathogenic organisms. Additionally, she had several markers indicating decreased digestive enzyme function and the presence of malabsorption. An imbalanced gut microbiome called dysbiosis can contribute to brain-based symptoms such as fatigue and can also contribute to constipation and altered immune function. Without adequately breaking down and absorbing her food, Megan is also at risk of many nutrient deficiencies, some of which we can see in her labs (low zinc, low vitamin D, and low folate, to name a few).  


Megan’s Omega-3 index was quite low, putting her in the high-risk category for inflammation in the body. Paired with the high WBC count, infection present in her urinalysis, and an elevated CRP, it was clear that there was elevated inflammation at her initial consult.

Nutrient Deficiencies

Paired with the results in her stool test of malabsorption, we saw in both her blood draw and Nutreval that several nutrient deficiencies were going on (zinc, vitamin D, folate, vitamin A, glutathione, to name a few), many of which are relevant to the immune system and fighting infections.

Functional Medicine Approach to Chronic UTIs: Interventions

  • Since Megan was able to identify diaphragm use as a significant lifestyle change around the time the infections started, we decided to stop the diaphragm, and she and her husband switched to condom use as their birth control to see if it impacted her symptoms.  
  • We started Megan on daily D-Mannose powder to help clear out her infection; her prescribing doctor switched her to a dose of Cipro while we waited for results to come in, so she had finished an additional round of antibiotics at the time we started our interventions.  
  • We added a few other things to support her gut health, including a probiotic (Metagenics) and Enzymix-Pro digestive enzymes before meals and a targeted elimination diet with the removal of foods that came back in her food sensitivity panel. We also started the product Yeast-Cleanse by SolaRay to address dysbiosis and high Candida spp levels.
  • From a nutritional standpoint, we started to transition Megan to a more balanced macronutrient diet that was lower in sugar and refined carbohydrates due to the chronic infections and high Candida spp. In her stool results. Each meal contained protein, healthy fat, and fiber, primarily in the form of vegetables, low-glycemic fruit, and sweet potatoes rather than white potatoes. We also added more pumpkin seeds and lean red meat at least once per week to help with her zinc levels.
  • Started Vitamin D, 5000 IU per day.
  • Started B Complex once per day.
  • Started omega-3 supplement, Metagenics SPM, 2000 mg per day.
  • Increased water intake.
  • Use of a red light unit for 10-20 minutes per day to support mitochondria and energy production pathways.

3 Month Follow Up


  • Unremarkable

Comprehensive Stool Test Results

  • Not performed

NutrEval (Genova Diagnostics)

  • Not performed

When we re-ran labs and intake at three months, we saw many things trending in the right direction. By this point, Megan felt her energy levels were much better, and she wasn’t experiencing any pain with urination. She had had one episode where she thought she felt a UTI coming on, and she had doubled her dose of D-Mannose and never experienced any full-blown symptoms.

She felt her new nutrition was the most challenging part of the last three months, but we had been supporting her with weekly coaching, which she found very valuable. She still craved something sweet late at night but had switched to more fat-based treat half of the time to help reduce her sugar. She noticed she felt lighter, less bloated, and more inclined to move throughout the day, and she felt she was mentally sharper.

She had had some bowel movement changes while on the Yeast-Cleanse for the first four weeks of her protocol, alternating between constipation and diarrhea, but things had normalized, and she was now having bowel movements without Miralax once per day or every other day.

6 Month Follow Up Labs

Comprehensive Stool Analysis

  • E. Coli 2+
  • Bifidobacterium LOW
  • Candida 1+


This case highlights the interrelatedness of chronic infections, such as UTIs, with other systems in the body. For Megan, switching to a diaphragm likely irritated her urinary tract system. It predisposed her to bacterial tracking into the urinary tract, paired with a lifetime of antibiotic use and likely longstanding gut dysbiosis.  

By supporting her gut health while replenishing nutrients through diet and supplements, we restored balance to her system. We gave her some non-antibiotic tools to help prevent UTIs and prevent further infections.

At her 6-month check-in, she still had not had a UTI recurrence and felt comfortable in her new routine.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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