How Are UTIs Diagnosed? Urinalysis, Urine Culture, PCR, and Advanced Testing Explained

Urinary tract infections (UTIs) are the most common outpatient infection globally. Caused by bacteria or fungi in the urinary tract, which includes the urethra, bladder, ureters, and kidneys, UTIs can manifest in a variety of symptoms that range in severity. Sometimes other conditions can mimic urinary tract infection symptoms, making the clinical diagnosis of UTIs particularly important. But how do doctors actually diagnose UTIs?

The Current Standard of Care

Urinary tract infection is a clinical diagnosis that takes into account a patient's current symptoms, medical history, as well as laboratory findings. It begins with your doctor taking a patient history – that is, asking you questions about what symptoms you are experiencing, when they began, if you have had UTIs previously, and other questions to understand your risk for UTIs. Following this, your doctor will likely order two types of tests to confirm an infection, both of which will require a urine sample. These tests are called a urinalysis and potentially a urine culture [1].

Urinalysis is a test with a quick turnaround time that evaluates your urine across three levels of analysis:

Macroscopic exam -- a visual inspection of your urine sample, assessing color, clarity, and odor for signs of infection or other abnormalities. For example, a UTI can make your urine appear cloudy rather than clear.

Dipstick chemical analysis -- a thin test strip is placed into your urine sample to detect chemical markers. For UTI diagnosis, the most relevant include:

• Leukocyte esterase: an enzyme released by white blood cells; a positive result suggests your immune system may be responding to infection in the urinary tract
• Nitrites: some bacteria convert nitrates naturally present in urine into nitrites; a positive result suggests bacterial infection, though a negative result does not rule one out, since several common UTI-causing bacteria do not produce nitrites
• Blood: can accompany infection when tissues in the urinary tract are damaged by a pathogen, but is not specific to UTI

Microscopic exam -- a laboratory technician examines your urine under a microscope, looking for white blood cells, red blood cells, bacteria, and other cellular material. The presence of elevated white blood cells (called pyuria) is one of the stronger indicators of a urinary tract infection and provides more definitive information than the dipstick alone.

Urine culture is a test that takes one to three days and is often performed in a laboratory outside of the clinic. This test attempts to grow on a petri dish the bacteria or fungi that is present in your urine. The bacteria or fungi that grow are evaluated and counted to estimate the number of live microbes present in the urine. This count is then compared with established clinical thresholds called colony-forming units (CFUs) to determine whether an infection is likely present. Additional testing can be done to help determine which antibiotic to use to treat the infection, which similarly takes one to two more days to complete. Your doctor will evaluate your medical history, urinalysis results, and urine culture findings to determine whether you have a urinary tract infection and guide appropriate treatment.

Limitations to the Standard of Care

Despite continuing to be the standard of care, urinalysis and urine culture often miss the mark in accurately diagnosing urinary tract infections. In fact, as many as 1 in 3 cases are missed by urine culture, making this quite a problem. These cases are called culture-negative UTIs.

Because urine culture attempts to grow the pathogen from a urine sample on a petri dish, it is prone to a variety of issues. Some reasons as to why a urine culture might fail include

• The pathogen causing a UTI does not have the proper conditions or nutrients to grow.
• Some bacteria and fungi may grow too slowly to be reported by the laboratory.
• The amount of bacteria or fungus detected could be below the clinical threshold, and thus not reported, despite it being the cause of UTI symptoms

Sometimes, urine culture is also vulnerable to false positive results, often due to contamination during sample collection or mishandling in the laboratory. When contamination occurs, the laboratory may detect bacteria that are not actually causing the infection, which can lead your clinician to prescribe an antibiotic that is not appropriate for your infection. In fact, this is more common than many patients might expect. One study of 127 accredited laboratories found the national median contamination rate for urine cultures to be approximately 15% [2]. In some cases, when a sample grows multiple organisms, the laboratory may flag it as contaminated and recommend repeat testing, even when more than one pathogen may genuinely be contributing to the infection. This is known as a polymicrobial UTI, and it can be missed or undertreated when contamination is assumed rather than investigated.

Increasingly, doctors are realizing these limitations and the need for new diagnostic tests that are more accurate. These approaches focus on detecting the DNA of the bacteria or fungi causing a UTI rather than trying to grow them from a urine sample.

Polymerase-Chain Reaction for UTI

Polymerase-chain reaction, more commonly known as "PCR," is one type of laboratory technique used to detect UTIs. PCR works by identifying small fragments of genetic material, DNA, that are unique to specific bacteria and fungi. Think of it like a photocopier: if a pathogen's DNA is present in a urine sample, PCR copies it millions of times over until it becomes detectable. When enough copies are produced, the pathogen is confirmed to be present, allowing for an accurate and timely diagnosis.

This technique has both benefits and shortcomings in comparison to urine culture. The benefits of using PCR include:

• Faster turnaround time (often within 24 hours)
• Higher sensitivity than urine culture
• Can identify antibiotic resistance genes

Like any diagnostic test, PCR has its limitations. Because it is a "targeted" technique, it can only detect the specific bacteria and fungi it was designed to look for. If an uncommon or atypical pathogen is causing the infection, it may not be included in the test, and could go undetected. On the other hand, PCR is highly sensitive, meaning it can sometimes pick up trace amounts of bacteria or fungi that are present in the urinary tract but are not actually causing the infection. For this reason, your clinician will always interpret the test results alongside your symptoms and medical history to ensure an accurate and personalized diagnosis.

Next-generation sequencing for UTI

The other technique increasingly being used to diagnose urinary tract infections is called next-generation sequencing or NGS. Similar to PCR, it works by analyzing DNA found in a urine sample. However, while PCR acts like a photocopier targeting specific pathogens, NGS casts a much wider net by reading the genetic material of everything present in the sample. Think of it like a fingerprint scanner, each organism has a unique genetic signature, and NGS uses that information to identify which bacteria or fungi are present by comparing the results against a comprehensive database of known microbes.

This broader approach gives NGS several advantages over PCR and urine culture. Because it analyzes all genetic material in a sample rather than looking for specific bacteria or fungi, it is able to detect atypical pathogens or rare organisms that PCR might miss and that may be too difficult to grow in a traditional urine culture. Beyond simply identifying what is present, NGS can also reveal important characteristics of the pathogens detected, such as antibiotic resistance markers, virulence factors, or particularly concerning microbial strains that may require more careful treatment planning. The result is a more comprehensive and actionable diagnosis, delivered with higher sensitivity and a turnaround time comparable to or faster than urine culture. This gives clinicians the information they need to treat infections more precisely and patients greater confidence in their care.

Biotia has developed a next-generation sequencing-based diagnostic test for urinary tract infections that is now directly available to patients suffering from recurrent, complicated, and/or culture-negative urinary tract infections. Called the BIOTIA-ID Urine Test, this test identifies 40+ key urogenital pathogens, including ones often missed by urine culture or excluded from PCR panels. The BIOTIA-ID Urine Test additionally provides doctors with information about antibiotic resistance markers to help guide precision treatment. Additional pathogens, resistance markers, and virulence factors are currently undergoing rigorous clinical validation to add more value to patients and doctors alike. By testing with Biotia, patients experiencing UTI symptoms will also get connected to our partner telehealth providers at Clinova.Solutions, a healthcare practice that focuses on recurrent and complicated urogenital infections and other urinary health issues.

The major drawback to next-generation sequencing tests for UTI, paradoxically, is their novelty. As with any emerging technology, broader adoption depends on accumulating clinical evidence to demonstrate patient benefit, as well as obtaining regulatory clearance and insurance coverage. These processes take time and contribute to the higher costs currently associated with these newer tests. However, as the evidence base grows and the technology becomes more widely used, broader insurance coverage is expected to follow, making next-generation sequencing an increasingly accessible option for patients who need it most.

Is the BIOTIA-ID Urine Test Right For You?

If you are experiencing recurrent UTIs, culture-negative UTI symptoms, or infections that haven't responded to standard antibiotic treatment, the BIOTIA-ID Urine Test may provide the answers your current tests have missed. By identifying 40+ urogenital pathogens and antibiotic resistance markers through next-generation sequencing, the BIOTIA-ID Urine Test can help give you and your doctor a more complete picture — so treatment can be targeted from the start. Learn more about who it is for.