Dr. Linda Brubaker: Why Standard Urine Culture Test Is Not Enough

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If you suffer from recurrent urinary tract infections (rUTI), you’ve probably had your urine cultured for bacteria. This is when your doctor takes a urine sample and sends it to a lab for a day or two to see what kind of bacteria will grow in the specimen. This approach is called the Standard Urine Culture (SUC) and it is currently the diagnostic gold standard for confirming a UTI.
At the same time, urine culture testing is not a very reliable way to confirm an acute infection.

Surprisingly,  the urine culture test as we know it was first documented and entered clinical practice in the 1950s. Those were the times when the clinicians and the researchers did not know much about the human microbiome and believed that healthy urine is sterile, for example. The lack of knowledge about commensal and beneficial bacteria undeniably affected how the results of the test were interpreted.

With the discovery of DNA-based testing we now know that many types of bacteria are present in the bladder at all times, but, the test protocol has not been re-evaluated since the 1950s.

In the article  Urine trouble: should we think differently about UTI? Dr. Linda Brubaker and her team summarize four key points on why the current approach to UTI testing is flawed:

  1. The way we think and talk about UTI does not take into account the bacterial diversity of the bladder’s ecosystem.
  2. Current diagnostic methods are not specific enough to confirm an acute bladder infection.
  3. Escherichia coli (E. coli) has been the most studied UTI microbe. Physicians and researchers are not always attuned to the role of other bacteria in the development of a UTI.
  4. We don’t really know how many bacteria in your urine are enough to cause an infection. Our reliance on the number of colony-forming units (CFU) grown per ml of urine during a culture test is an artificial threshold.

Let’s review in detail why each point is important to consider.

1. Choose your words carefully because they define a treatment strategy

Urine is not sterile. However, most physicians still approach UTI treatment with a mindset of killing the invading bacteria without prioritizing the role of the native bacterial flora normally found in your bladder. This mindset can lead to overuse of antibiotics and the lack of preventive tactics aimed at restoring bacterial balance.

Dr. Brubaker and her team argue: “the goal of UTI treatment should not be to eradicate every microbe in the bladder, especially given the evidence that some members of the urinary microbiota are beneficial and/or protective”.

Instead of imagining invading foreign bacteria in your bladder, we should think about a bacterial dysbiosis—an overgrowth of several types of opportunistic organisms. Most importantly, we should create a treatment plan that helps patients to get their microbial population back in balance.

2. Current methods of UTI testing are not accurate

The dipstick test and urine culture test remain the two most frequently used tests to confirm a UTI diagnosis.

Dipstick test
We wrote extensively about the limitations of OTC UTI tests that are similar to how your doctor’s dipstick test works. For the most part, these tests were designed as screening, not diagnostic tools. The main concern is that the dipstick test is known to miss signs of infection caused by Gram-positive bacteria and is generally less accurate when you are already experiencing UTI symptoms.

Standard urine culture
Would you agree that your bladder environment is different from a Petri dish in a lab?
For example, you do not have much oxygen inside your bladder. However, when placed on a Petri dish in a lab, the microorganisms are exposed to significantly more oxygen. So the bacteria that strongly prefer the environment and nutrients available in the bladder might be too picky to grow on a Petri dish and will be thrown out of your test results.
Even a slightly more robust test approach, called Expanded Quantitative Urine Culture (EQUC)—that basically offers bacteria a large selection of food options for a longer period of time—have repeatedly discovered more bacteria than the Standard Urine Culture (SUC). In fact, in 90% of the cases, the standard culture method failed to grow certain bacteria in the urine specimens when compared to EQUC.

3. Many UTIs are polymicrobial

The Standard Urine Culture test was designed to detect E. coli, and for many years these were the results the medical community was content with. This also means that all other microorganisms that were found were thrown out as a contamination, or there was no attempt at growing them.

However, an extended culture test or a more sophisticated DNA-based test consistently demonstrate that many UTIs are polymicrobial (caused by more than one type of bacteria). And thus, the definition of an acute or chronic infection needs to be reviewed.

It is still unclear what role other organisms identified on those tests play and if they are responsible for any particular symptoms or their severity, but we know that UTI is not as simple as we once thought.

4. Outdated test threshold

Many times when discussing urinary culture results we analyze them in respect to the number of colonies forming units (CFU) per ml of urine.

In the1950s the researchers who developed and described the Standard Urine Culture (SUC) used a threshold of ≥10^5 of colony forming units (CFU) to identify an infection. This is how they decided to distinguish the bacteria that originated in the bladder versus bacterial contamination that happened during the collection of the urine sample. Keep in mind, those were the times when the prevailing understanding was that healthy urine is sterile, or totally void of any bacteria in a healthy patient. Moreover, this threshold (10^5 CFU/mL) was originally set to identify women with pyelonephritis (kidney infection) and later applied to diagnose patients with acute cystitis (UTI) instead.

Unfortunately, physicians have relied on a threshold of ≥10^5 CFU/mL of urine to distinguish between significant bacteriuria and bacterial contamination ever since. If bacteria in a urine sample grew less than 10^5 CFU/mL the sample was considered contaminated with bacteria from the outside of the urethra or genitalia.

Not only does the existing standard urine culture test fail to grow bacterial colonies because the environment in the lab is different from the environment in the bladder, but when some bacteria grow, the results are dismissed in comparison to an artificially high threshold that was originally designed to diagnose kidney infection.

“In a population of women seeking urogynecological care we found that a single overall threshold did not distinguish between women who self-reported UTI and those who did not,” suggested the research team in the “Urine trouble: should we think differently about UTI?” paper.

Bottom line: not all patients whose urine sample grows 10^5 CFU/mL have symptoms of a UTI. And “not enough” bacteria grow in the samples of many women who do have UTI symptoms.

What can we do?

The lack of specificity of a Standard Urine Culture (SUC) test is exactly why Dr. Brubaker does not diagnose her patients with a UTI based only on the results of the SUC. When clinically indicated, she prefers to order the Expanded Quantitative Urine Culture (EQUC), along with the urinalysis results which report the presence of white blood cells that could be indicative of inflammation. With EQUC, the laboratory cultures a full spectrum of organisms to guide her treatment protocol.

Unfortunately, it’s not easy for a regular physician to get away from the Standard Urine Culture test as the main diagnostic tool for UTIs.
First of all, we do not have an affordable alternative. The Expanded Quantitative Urine Culture (EQUC) test is not readily available to order for most physicians.

While some patients are ready to pay for the expensive DNA-based test results, most physicians still don’t know how to interpret them. Keep in mind, the results show not only what IS there, but also what is missing.

While the standard urine culture test might remain the only diagnostic tool available for your doctor, there are a couple of things that you could consider to increase the accuracy of your UTI diagnosis if you ask your physician to:
– culture urine longer (5-7 days instead of the standard 24 hours).
– request the lab to report on all bacterial strains found in your urine and do not simply label them as contamination.
– order urinalysis in addition to a urine culture test.

Dr. Brubaker’s treatment strategies

While every UTI patient is unique, there are some common strategies you can consider under the supervision of your physician.

  • Most importantlyl, adopt a whole food, plant-based diet with a variety of fiber and complex carbohydrates. Limit your consumption of sugars, fat, and processed foods. These changes will improve your gut microbiome, which is where most UTI microbes originate.
  • You may wish to limit exposure to opportunistic bacteria, such as E.coli. For example, do not handle or be near raw chicken, a known source of E.coli contamination.
  • Do not contribute to existing dysbiosis by douching or using yogurt vaginally.
  • In her practice, Dr. Brubaker also strives to avoid unnecessary antibiotic use, pending, of course, a thorough review of every patient’s case.

Bottom line: your body is more prone to recurrent UTIs because opportunistic bacteria gained an upper hand in the competition with beneficial and commensal bacteria in your body. A good treatment plan should help identify what contributes to the state of dysbiosis (hormonal changes, contraception methods, digestion issues etc) and address it, along with restoring beneficial flora throughout your body.
First, we need to change how we talk about UTI and how we diagnose the infection, and then we can start treating UTI more holistically.

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