Understanding PCR Testing: What It Really Reveals About UTIs (and What It Doesn’t)

By Dr. Tamra Lewis, MD, UroGynecologist & Women’s Health Specialist, Comprehensive Urologic Care (In partnership with Uqora & MyUTI)

Why “Knowing What’s Really Causing Your UTI” Is So Hard

For many women struggling with recurrent urinary tract infections, the most frustrating part isn’t always the symptoms — it’s the lack of answers. One week, you’re told your urine culture is negative. The next, you’re prescribed another round of antibiotics “just in case.”

If you’ve ever felt stuck in that cycle, you’re not alone. The truth is, the type of test used to look for infection can dramatically influence what’s found  and what’s missed.

“Many women are told their urine is ‘clear,’ but they still feel all the symptoms,” says Dr. Lewis. “That disconnect often comes from how testing is done and interpreted, not that nothing’s wrong.”

In this article, we’ll unpack how different UTI tests work — from dipsticks to urine cultures to PCR — and what these results really mean.

Dipsticks: A Quick but Limited Tool

Most people are first tested for a UTI with a urine dipstick, a small strip that changes color when dipped into a urine sample. Dipsticks detect leukocyte esterase (a marker of white blood cells) and nitrites (a byproduct of certain bacteria like E. coli).

The problem? Not all bacteria produce nitrites. Common UTI organisms such as Enterococcus faecalis and Staphylococcus saprophyticus don’t, meaning the dipstick can easily miss them.

“Dipsticks are a starting point, not an answer,” explains Dr. Lewis. “They can miss infections that don’t produce enough of those markers to trigger a positive result or patients can overhydrate which makes this less sensitive. They can also look ‘dirty’ if the sample is not collected using good technique”

Dipsticks are useful for quick screening but should never be the final word on whether you have an infection especially if your symptoms are clear.

Urine Cultures: The Traditional ‘Gold Standard’

If you’ve had a “formal” UTI test, it was likely a urine culture. This method dates back to the 1950s and involves spreading a small portion of urine onto a petri dish and waiting to see what grows.

If bacteria multiply beyond a certain threshold — typically 100,000 colony-forming units per milliliter (10⁵ CFU/mL) — the culture is called positive. Then, the lab tests which antibiotics stop that growth, creating a sensitivity report your clinician can use to guide treatment.

That sounds straightforward, but there’s a catch.

Cultures can miss what’s really there

• They only detect organisms that grow well in oxygen-rich environments (aerobes). Many anaerobic bacteria, such as Gardnerella vaginalis, Prevotella, and Atopobium vaginae, can’t survive those conditions.
• Fastidious or slow-growing pathogens like Ureaplasma urealyticum, Mycoplasma hominis, Corynebacterium, and Actinotignum schaalii may never appear on a culture plate, even when they’re causing symptoms.
• When multiple bacteria are present, called polymicrobial infections, one may outgrow the others, hiding co-infections that contribute to symptoms.

“Culture technology dates back to the 1950s and was designed for use in the hospital not necessarily the community setting,” says Dr. Lewis. “It’s still useful, but it’s like trying to judge an ecosystem by what grows on one kind of soil.”

The result? Many women get told their urine culture is “negative” even when the infection just didn’t meet the lab’s growth threshold or involved organisms that don’t grow well in standard culture conditions.

PCR Testing: Detecting the Genetic Fingerprints of Bacteria

PCR, short for Polymerase Chain Reaction, is a modern testing method that detects bacteria based on their genetic code (DNA) rather than waiting for them to grow.

Instead of asking, “Can we grow it?”, PCR asks, “Can we find it?”

This technology has revolutionized diagnostics in infectious disease, including urinary tract infections. By amplifying tiny fragments of bacterial DNA, PCR can detect organisms at much lower levels and even identify multiple bacteria at once.

“PCR helps us see what’s really there — even when traditional cultures can’t grow it,” explains Dr. Lewis. “It gives a molecular snapshot of your urinary microbiome.”

What PCR can detect

PCR panels (like the one used by MyUTI) can identify dozens of organisms commonly associated with urinary and vaginal infections, including:

• E. coli
• Klebsiella pneumoniae
  
• Enterococcus faecalis
• Ureaplasma and Mycoplasma species
  
• Gardnerella vaginalis
• Proteus mirabilis, Citrobacter, and others

Because PCR looks for gene markers unique to each species, it can find infections that would otherwise go undetected. It also reveals polymicrobial infections, where multiple pathogens are contributing to symptoms, something cultures often miss.

Understanding “Load”: When Detection Becomes Diagnosis

PCR is highly sensitive which is both its power and its challenge. It can detect bacterial DNA at extremely low levels, even when that bacteria isn’t necessarily causing symptoms.

That’s where the idea of “load” comes in. Load represents how much bacterial DNA is found, a kind of molecular “count.”

“Finding DNA doesn’t always mean an active infection,” Dr. Lewis explains. “The amount and context matter just as much as the detection itself.”

For example:

• Low levels of Staphylococcus epidermidis or Lactobacillus — both common skin or vaginal flora — may simply reflect normal contamination.
• High levels of E. coli, Klebsiella pneumoniae, or Enterococcus faecalis are more likely to represent an active urinary infection.

In PCR reports, these quantitative findings are often expressed in categories such as low, moderate, or high load, which helps clinicians interpret what’s meaningful.

Still, symptoms matter most. A skilled clinician will always interpret results alongside what the patient is experiencing and not just in isolation.

NGS (Next-Generation Sequencing): Beyond PCR

You may also see people in online communities mention NGS, or Next-Generation Sequencing. This technology scans all the genetic material in a sample, identifying every organism present  not just those on a targeted list.

That can sound appealing, but it comes with caveats.

NGS can detect hundreds of different microbes, including those with uncertain clinical roles for example, Cutibacterium acnes, Finegoldia magna, or obscure environmental bacteria. These may be part of the background microbiome, not the cause of symptoms.

“NGS can show you every microbe in the mix but the challenge is knowing which ones actually matter,” says Dr. Lewis. “PCR is more focused on organisms we know are associated with urinary symptoms.”

NGS is powerful for research and discovery, but in most clinical contexts, PCR remains the preferred diagnostic tool because its results are clearer, validated, and easier to interpret.

Limitations and Practical Realities

Advanced testing for UTIs (like PCR or NGS) has made it possible to identify infections with far more precision than ever before. But getting access to these tests can still be confusing, especially if you’re not already seeing a specialist.

Traditionally, molecular testing required a physician’s prescription, meaning patients had to schedule an office or virtual visit, pay for the consultation, and then wait for a lab referral. Some testing platforms, such as Pathnostics, still operate through that clinician-directed model. Others, including MicroGenDX and MyUTI, now offer direct-access options that simplify the process for consumers.

“The biggest barrier isn’t the science it’s the system,” says Dr. Lewis. “Accessing advanced testing shouldn’t require multiple appointments or waiting weeks for answers.”

Where these services differ is in how streamlined and supportive the process feels. MyUTI offers both insurance-covered and cash-pay pathways, with physician authorization built into the process through a CLIA-certified lab. That means patients can initiate testing online, without having to wait weeks and failed treatment to gain access to testing. 

Whether you pursue testing through your healthcare provider, a specialty lab, or a direct-access service like MyUTI or MicroGenDX, the goal is the same: to empower patients with clearer data and help clinicians make more targeted, evidence-based treatment decisions.

How to Bring Your PCR (or Any Test) Results to Your Doctor

Bringing advanced test results to your doctor can feel intimidating, but it shouldn’t. The goal isn’t to replace your clinician’s judgment — it’s to give them clearer data to work with.

Here’s how to approach that conversation:

1. Bring your report and your symptom timeline.
   Having both helps your provider see the full picture.
2. Highlight key findings.
   Point out any organisms reported at moderate or high load, especially those known to cause UTIs like E. coli, Enterococcus, or Klebsiella.
3. Ask for interpretation, not confirmation.
   A clinicians concern is that a patient will come in with results and demand antibiotics. You might say something like:
   

   ‘I noticed that some bacteria — like Enterococcus and E. coli — were detected in my test results. Do you think these findings are related to my symptoms, or could something else be causing them?’

   Or, if your results don’t show high levels of bacteria:
   ‘If the test didn’t show significant bacterial growth, are there other possible explanations for my symptoms?’
   
4. Compare results over time.
   If you’ve had both cultures and PCR tests, bring both. Seeing patterns (like recurring detection of the same organism) helps guide more targeted treatment or help unearth underlying causes.
   

The more collaborative your approach, the more your clinician can integrate these insights into your care plan.

The Bottom Line: Precision Brings Clarity

For decades, women with urinary symptoms have been caught between vague tests and incomplete answers. Modern molecular diagnostics, like PCR, finally offer a clearer view.

PCR can identify bacteria that traditional methods miss, detect infections earlier, and help explain why some women keep experiencing symptoms even when cultures are “negative.”

But even with these advances, testing is only part of the story. Clinical judgment, symptom context, and patient history still matter most.  A test alone cannot determine treatment, but a better test combined with proper patient evaluation can help guide effective management, and better understanding for prevention in the future.

“No single test defines your infection,” says Dr. Lewis. “But advanced diagnostics like PCR give us data that finally fits the patient, not the other way around.”

When you understand your results, you can have more informed conversations, avoid unnecessary antibiotics, and work toward a lasting solution — not just another short-term fix.

This article was developed in collaboration between Uqora and MyUTI to help women better understand their diagnostic options for recurrent urinary tract infections. Clinical insights provided by Dr. Tamra Lewis, MD.

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