Testing for Chronic Infections and Biofilms

Next Generation Sequencing (NGS)

Advanced testing for chronic urogenital infections, interstitial cystitis, prostatitis, chronic sinus infections, and recurring infections that do not resolve with standard care.

Some infections are easy to diagnose. Others are not. Many people with chronic or recurring symptoms are told their culture is “negative,” “contaminated,” or “normal,” even though their symptoms continue. This can happen with recurrent urinary tract symptoms, bladder pain, interstitial cystitis, chronic prostatitis, chronic sinus infections, vaginal or urogenital symptoms, and other persistent infections.

At Jade Medicine, I use MicroGenDX Next Generation Sequencing (NGS) testing when appropriate to look more deeply for bacterial and fungal organisms that may be missed by standard culture. MicroGenDX uses qPCR plus NGS microbial DNA diagnostics, designed to provide answers in cases where culture or PCR alone may fail.

Why standard cultures can miss chronic infections

Traditional culture testing is useful, but it has limits.

A standard culture is designed to grow certain organisms under specific lab conditions. But not all organisms grow well in culture. Some infections involve multiple microbes living together in a community. Others may be partially suppressed by antibiotics, herbs, immune factors, or biofilm formation.

This is especially important in chronic infections, where microbes may not behave like a simple, free-floating infection.

Biofilms are organized microbial communities that can make infections harder to detect and harder to treat. MicroGenDX NGS testing can identify multiple bacteria and fungi that may make up a biofilm, along with their relative distribution in a sample. The test can detect 60,000 referenced microbes.

What is NGS testing?

Next Generation Sequencing is a form of molecular testing that looks for microbial DNA in a sample. Instead of only asking, “What grows in culture?” NGS asks a broader question:

What microbial DNA is present here?

This can help identify bacteria and fungi that may be contributing to chronic symptoms, especially when routine testing has been unrevealing.

Depending on the clinical situation, testing may include urine, vaginal, semen/prostate-related, sinus, wound, or other appropriate samples.

Conditions where this may be helpful

NGS testing may be considered for people with:

  • Recurrent urinary tract infections

  • Persistent urinary burning, urgency, or frequency

  • Interstitial cystitis/bladder pain syndrome

  • Chronic prostatitis or chronic pelvic pain

  • Chronic or recurrent sinus infections

  • Chronic vaginal, urethral, or urogenital symptoms

  • Recurrent infections that return after treatment

  • Symptoms with repeatedly negative or unclear cultures

  • Suspected biofilm-associated infections

  • Complex infections involving more than one organism

This does not mean every chronic symptom is caused by infection. The goal is to use testing thoughtfully, in context, and avoid guessing whenever possible.

Looking beyond the pathogen: biofilms and coagulation markers

In chronic infections, identifying the organism is only part of the picture.

Some patients appear more prone to biofilm formation or difficulty breaking down biofilm structures. Biofilms may contain fibrin and other protective materials that help microbes persist. Ruth Kriz’s chronic UTI and interstitial cystitis model emphasizes not only DNA testing for urinary pathogens, but also looking at factors that may contribute to immune dysfunction, bladder wall damage, embedded infection, and biofilm persistence.

When clinically appropriate, I may also evaluate coagulation and fibrin-related markers that can be involved in biofilm formation and persistence, such as:

  • Fibrinogen activity

  • Thrombin-antithrombin complexes

  • Prothrombin fragment 1+2

  • PAI-1 activity

  • Protein S activity

  • Activated protein C resistance

  • Factor II/prothrombin mutation

  • Factor V Leiden

  • Homocysteine

  • Lipoprotein(a)

These markers do not directly “diagnose biofilm,” but they can provide important clues about the type of biofilm environment a person may be producing. Coagulation and fibrin-related markers can help identify whether biofilms may be more fibrin-dominant, clotting-driven, inflammatory, or associated with impaired breakdown of fibrin and other protective matrices. This information can help guide treatment more precisely, including the selection of biofilm-disrupting therapies, fibrinolytic support, antimicrobial strategy, and sequencing of care.

A more complete approach to chronic infection care

When I evaluate chronic or recurring infections, I am not just looking for a positive lab result. I am looking for the pattern.

That may include:

  • Your symptom history

  • Prior cultures and antibiotic responses

  • Past imaging or specialist evaluations

  • NGS or molecular testing results

  • Coagulation and fibrin-related markers

  • Immune function

  • Hormonal and mucosal health

  • Microbiome balance

  • Inflammation

  • Biofilm-related risk factors

  • Medication tolerance and safety

  • Antibiotic resistance concerns

Treatment is individualized. Depending on the findings, care may include prescription antimicrobials, herbal antimicrobials, biofilm-directed therapies, mucosal support, immune support, microbiome restoration, anti-inflammatory strategies, and collaboration with urology, gynecology, ENT, or other specialists when needed.

Chronic urinary symptoms and interstitial cystitis

Many patients with bladder pain, urinary urgency, frequency, burning, or pelvic discomfort are eventually told they have interstitial cystitis, which is usually seen as an inflammatory condition devoid of microbial origin and treated as a bladder pain condition, but in some patients, chronic or embedded infection, dysbiosis, biofilms, vaginal or urinary microbiome disruption, immune factors, and tissue irritation may all contribute to symptoms.

This is where advanced testing can be useful. It may help clarify whether bacteria, fungi, or mixed microbial communities are present and whether treatment should be directed at infection, inflammation, tissue repair, biofilm support, or all of the above.

Chronic prostatitis and pelvic pain

Chronic prostatitis can be frustrating because symptoms may persist even when routine testing is negative.

Symptoms may include pelvic pain, urinary frequency, burning, painful ejaculation, testicular discomfort, low back or rectal pressure, and recurrent flares. In some cases, chronic prostatitis may involve difficult-to-detect organisms, biofilm communities, or mixed infections.

NGS testing may provide additional information when standard urine or semen cultures have not explained the clinical picture.

Chronic sinus infections

Chronic sinus symptoms can also involve biofilms and mixed microbial communities.

For patients with recurrent sinus infections, chronic congestion, postnasal drip, facial pressure, or repeated antibiotic use, NGS testing may help identify organisms that are not found on routine culture. This can be especially helpful when symptoms keep returning or when treatment only provides temporary relief.

What to expect

A visit usually begins with a detailed review of your history, prior testing, treatments, and symptom pattern. If NGS testing is appropriate, we will discuss the best sample type, how to collect it, timing around antibiotics or supplements, and what the results can and cannot tell us.

Once results are available, we review them in the context of your symptoms. The goal is not to treat every organism blindly. The goal is to identify clinically meaningful patterns and build a treatment plan that is targeted, safe, and realistic.

Important note about specialty testing

Some specialty labs may not be covered by insurance. Payment may be made directly to the laboratory, and reimbursement depends on your insurance plan. Jade Medicine’s financial policy notes that many functional and specialty labs do not bill insurance, and patients are responsible for confirming laboratory benefits, coverage, deductibles, coinsurance, and restrictions with their insurance plan.

Is this right for you?

This type of evaluation may be a good fit if you have chronic or recurring infection symptoms and feel like standard testing has not explained what is happening.

It may be especially helpful if you have been told:

  • “Your culture is negative.”

  • “It’s probably just inflammation.”

  • “There is nothing to treat.”

  • “Your test was contaminated.”

  • “You have symptoms, but the labs are normal.”

  • “You keep getting infections, but we don’t know why.”

Chronic infections are rarely solved by guessing. A better plan starts with better information.

Schedule a consultation to discuss whether NGS testing and biofilm-focused evaluation are appropriate for your case.