Chronic UTIs & Interstitial Cystitis: Beyond the Standard Approach
Urinary tract infections (UTIs) are among the most common bacterial infections, affecting millions each year—particularly women. Most people are familiar with the acute, short-lived UTI that responds to a 3–7 day course of antibiotics. But for some, symptoms become persistent, returning again and again despite multiple rounds of treatment. These are the chronic UTIs—and they require a very different approach.

Acute vs Chronic UTIs
Lower UTIs (cystitis) affect the bladder and typically present with burning during urination, urgency, frequency, lower abdominal discomfort, and cloudy or strong-smelling urine.
Upper UTIs (pyelonephritis) involve the kidneys and may present with fever, flank pain, vomiting, and sometimes sepsis—requiring urgent medical attention and usually intravenous antibiotics.

In standard medicine, acute infections are treated with short courses of antibiotics, often bringing fast relief. However, up to 60% of women with a UTI will experience recurrence—and in chronic cases, bacteria can embed deep into the bladder wall or form biofilms, making them invisible to standard urine culture and resistant to typical antibiotics.

Why Standard Testing Often Misses Chronic Infection
The common “midstream urine culture” (MSU) used by most doctors only detects bacteria at concentrations above 100,000 CFU/mL and only those that grow under standard lab conditions. Chronic, embedded infections often fall below this threshold or involve organisms that are difficult to culture.

Alternatives include:

-Fresh unspun microscopy (pioneered by Prof. James Malone-Lee, (founder of Harley St clinic, now Artemis Clinic in the UK) – assesses white and epithelial cells within 15 minutes of urine collection, offering clues to chronic infection.

-PCR and Next Generation Sequencing (NGS) – advanced DNA-based testing that detects bacteria, fungi, and antibiotic resistance genes missed by culture.

-Vaginal microbiome testing – identifies vaginal flora imbalances that can fuel UTIs.

Ruth Kriz’s Approach: Precision Testing with MicroGenX.
Ruth Kriz, NP, (see:https://ruthkriz.com/our-approach/ )has dedicated decades to treating chronic UTIs, interstitial cystitis, prostatitis, and urethritis. Her philosophy: test smarter, treat longer, and target biofilms. She bases her treatment around MicroGenX Testing that uses PCR + NGS to detect over 50,000 potential pathogens. It also identifies antibiotic resistance genes so treatment is targeted and effective. Testing is recommended for urine, and vaginal swabs (women), or semen (men). The test helps uncover polymicrobial infections (more than one bacteria or fungus at a time).

This testing can reveal why previous antibiotics failed—either the wrong drug was used, or only part of the infection was treated.

Treatment Strategies

Treatment involves one or a combination of:

Longer-term, targeted antibiotics (when appropriate, based on sensitivity results)

Anti-biofilm agents (to break down the protective matrix bacteria hide in)

Immune support (e.g., vitamin D, zinc, probiotics)

Vaginal and urinary probiotics to restore protective Lactobacillus species

Dietary changes to reduce inflammation and bladder irritation

Listen to her podcast discuss her approach to chronic UTIs and Interstitial Cystitis* https://www.betterhealthguy.com/episode158

The Harley Street (UK) Long-Term Antibiotic Protocol

Professor Malone-Lee’s team on Harley Street in London has treated thousands of chronic UTI patients with continuous, low-dose antibiotics for 6–12 months (sometimes longer). Their rationale: chronic infections often require persistent pressure on bacteria to prevent regrowth while the bladder heals. Treatment decisions are guided by symptom tracking and fresh unspun urine microscopy, rather than relying solely on culture results. Critics warn of antibiotic resistance risks, but Malone-Lee’s published work suggests that targeted, continuous therapy can be effective and well-tolerated when carefully monitored. Gut support is essential to compensate for the impact of chronic antibiotic use.

Natural & Supportive Therapies
Even with advanced testing and medical treatment, supporting the urinary tract environment can improve outcomes:

D-mannose – Prevents bacterial adhesion (especially E. coli).

Cranberry extract – May help prevent recurrence, though results vary in chronic cases.

Targeted probiotics – Lactobacillus crispatus shows particular promise in reducing recurrence.

Anti-inflammatory diet – Rich in antioxidants, omega-3 fatty acids, and free of processed sugars.

Hydration – Enough water to urinate every 3 hours, but avoid overhydration during antibiotic therapy.

Stress management – Chronic stress can suppress immune function.

Addressing gut health – Reducing intestinal inflammation and restoring healthy microbiota can improve immune defenses against UTIs.

When to Seek Specialist Care
If you have: 3 or more UTIs per year, Symptoms that persist despite antibiotics, Blood in your urine or UTI symptoms as a male patient…it’s time to seek a practitioner with expertise in chronic urinary infections.

Key Takeaway
Chronic UTIs and interstitial cystitis are often under-diagnosed and under treated due to the limitations of standard urine cultures. Approaches like Ruth Kriz’s MicroGenX precision testing are helping patients find answers after years of frustration. Combining targeted medical treatment with natural bladder and immune support offers the best chance for long-term relief.

Author Doreen Schwegler is a Medical Scientist and Naturopath who offers MicrogenX testing information, online consults for treating cUTI and IC and fresh urine microscopy in Mosman (Sydney).

Contact doreen@holistichealth.com.au for more information

Tania Delahoy also provides fresh urine microscopy in Wonga Park, Melbourne, Victoria: http://haemanalysis.com.au/contact/

*Note Ruth Kriz is no longer taking on clients, but has trained practitioners around the world, including Doreen Schwegler in Australia

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