This page explains in detail why dipsticks and standard cultures are unreliable in diagnosing UTIs. Despite researchers having disproved the accuracy and effectiveness of dipsticks and cultures to diagnose UTI, do not be surprised if your busy practitioner is unaware of the facts we explain here. We also look at new information about DNA-based molecular tests available in the United States and whether this is proving to be a reliable alternative to traditional tests for UTI.
There is a lot of information to cover in this important topic, so we have broken it down to help make it easier to digest. If you’re only reading this page to learn more about DNA tests, go ahead and scroll towards the bottom of the page.
Today in Australia, dipsticks are often the first diagnostic tool GPs use to confirm an infection. These tests look for signs of infection, such as white blood cells (leucocytes or pus cells), blood, pH levels and nitrites. Although they are useful in confirming a clearly positive diagnosis, studies in the early 1990s concluded they are highly insensitive and unreliable at excluding infection in most clinical settings4. About a decade later, another team of researchers comprehensively studied the reliability of urinary dipsticks and determined that these first-line screening tests were not up to the job of excluding significant UTI. It found dipsticks identified white blood cells just 55 percent of the time and nitrites (another positive indicator of infection) only 10 percent of the time. A negative result offers no useful information in ruling out a UTI3. Given the proven shortcomings of urinary dipsticks, GPs should be extremely cautious when relying on this test to rule out a UTI.
After your GP listens to your symptoms and dipsticks your sample, she or he will probably send your urine sample to the lab to see what bacteria is causing your UTI. The lab will use a quantitative microbial culture from a mid-stream urine (MSU) sample to grow the bugs. The lab (either a real life technician or an automated machine) will also conduct a urinalysis and look at a small amount of your urine under a microscope to check for other signs of infection, such as white blood cells, red blood cells, epithelial cells and any other signs. These readings will be used alongside the MSU culture results to determine if there is a genuine infection. There is a more detailed explanation of culture testing further down the page.
Although MSU cultures are considered the gold standard for diagnosing UTI, and have been used since the late 1950s (originally to diagnose kidney infections), for over 30 years researchers have warned of serious deficiencies with these tests. Research shows that MSU culture tests miss at least 50 percent of infections1,5. Studies have been repeated and calls for the abandonment of MSU culturing have been echoed, but these warnings have gone ignored and MSU culturing remains the main diagnostic tool for UTI around the world.
This 2019 study by Sathiananthamoorthy and colleagues confirms previous research raising doubts about the accuracy of ‘gold standard’ tests used to diagnose UTI. The researchers used DNA analysis to detect urinary pathogens and compared the results with those of the traditional MSU culture test. This demonstrated that MSU cultures miss a significant proportion of bacteria, including recognised uropathogens.
While patients harbour up to 500 microbes in their bladder and controls harbour up to 400, MSU cultures grow only a small proportion of these microbes due to limitations of selective culture media. The authors conclude that the bladder biome is more complex than commonly understood, and that MSU cultures cannot distinguish between patients with confirmed UTI and asymptomatic controls.
“We make our clinical decisions in infectious disease in urology based on technology that’s over 100-years-old. We’re still taking urine samples, plating it on an AGAR, and putting it in 24 hours in an incubator and then making a decision. We now know that we grow less than one percent of potential uropathogens by this technique; we don’t culture biofilm bacteria; and we miss 99.9 precent of possible microorganisms that are in the environment that might be related to infectious disease.” Dr Curtis Nickel, Professor of Urology, Queen’s University, Canada. Click to hear to listen to the full 2017 Australian interview.
“That’s another myth, the fact that infections are present only when the bacteria are present at 10^5 or greater. And that was never the intent of Kass’ original report. The amount of bacteria in people that have UTI varies. When you get up the urine has been concentrated during the night, sure it can be 10^5. But when you’ve had coffee and urinated it can be 10^2 and that’s also significant. But labs aren’t culturing at 10^2. We miss a lot of true UTIs by setting cut-off limits based on dogma that we think needs to be trashed.” Dr Paul Schreckenberger, Loyola University, Chicago, USA. Watch the full 2014 interview here.
“Many women with the appropriate symptoms are dismissed as not suffering from an infection when they do in fact have one. This controversial view is supported by much published literature. I am sorry to record this, because in doing so I identify a worrying deficiency in our diagnostic protocols, but the evidence is out there for everyone to read.” Professor James Malone-Lee, Emeritus Professor of Nephrology, UCL, and chronic UTI specialist, London, UK. Here more from Professor Malone-Lee in this 2018 Canadian radio interview.
The following information is for those who like detail. For the rest of you, all you need to remember is researchers have known for over 30 years that MSU cultures miss at least half of the infections they test for, yet they are still considered the gold standard method for diagnosing UTI around the world. This is not good enough!
The MSU culture was first introduced by Edward Kass 60 years ago. He was looking for a method to determine a dividing line between ‘infection’ and ‘contamination’ in pregnant women with acute pyelonephritis (a kidney infection)—a much more severe and serious form of urinary infection.
Kass applied a quantitative culture method to urine which became widely known as the Kass Criteria. The Kass Criteria requires a pure growth of a known urinary pathogen that reaches a colony count of 10^5, or greater. These methods were soon adopted by labs for diagnosing acute UTI. Kass’ report was never intended or validated for this purpose, yet this has become the gold standard around the world for diagnosing acute UTI6.
To understand why MSU cultures miss at least 50 percent of urinary infections, it will help to break it down further.
Kass held the belief, common at the time, that the urinary tract was sterile—so any single urinary pathogen that grew from an uncontaminated sample must be the offending pathogen. But we now know urine is not sterile. The recently published discovery that the urinary tract houses its very own microbiome, containing many hundreds of different species7, completely undermines the traditional significance of what ‘grows’ and whether it is a pathogen, a harmless commensal (part of the normal bladder flora) or a contaminant.
Kass also followed a set of principles developed in the late 1880s referred to as Koch’s Postulates. This rule stipulates only a single organism is responsible for an infection (pure growth). The requirement of a pure growth ignores the possibility of polymicrobial infections, which have recently become accepted by researchers as commonplace with UTI6. Polymicrobial infections can either involve more than one bacterial species, a combination of two non-pathogenic bacteria that come together to become pathogenic, or it can be a mix of a bacteria, fungus, virus or mould that give each other the pathogenic edge8. As the science world moves past the limitations of Koch’s Postulates, the understanding of polymicrobial infections is increasing rapidly and the list of known polymicrobial diseases is growing. From 2010 to 2012, publications of polymicrobial infections increased by 300 percent9.
This TED talk by a molecular biologist, Bonnie Bassler, gives a fascinating insight into how bacteria in polymicrobial communities cooperate and communicate, both within their own species and between different species.
Despite the rapid understanding of polymicrobial infections, as it stands today in clinical labs, MSU cultures that grow more than one species will most likely be reported as (depending on the lab), ‘no significant growth’, ‘mixed growth of no/doubtful significance’ or ‘contamination’. This could mean countless genuine polymicrobial urinary infections are being routinely discarded and these patients are not receiving treatment for their infections.
To identify the pathogen responsible for a UTI, what grows must be a ‘known urinary pathogen’. Traditionally, known urinary pathogens are: Escherichia coli (80 percent), Staphylococcus saprophyticus (10–15 percent), Klebsiella, Enterobacter, Proteus species and enterococci10.
The criterion of a ‘known uropathogen’ has lost integrity since the discovery of the female urinary microbiome (FUM). Recent researcher has even found that microbial species in the bladder and the vagina are interconnected. The urinary tract contains a community of hundreds upon hundreds of microbes. Some of these are pathogenic—others possibly play a protective role. Some of these microbes culture easily—others will not culture at all using existing lab methods7. Knowledge of the FUM now suggests that because one species grows easily under existing culturing methods (i.e. Escherichia coli), it does not necessarily mean it is the pathogen causing symptoms. Likewise, it is also very possible that the offending pathogen is unculturable and never identified. This creates a dilemma for clinical microbiology that can no longer be ignored.
For diagnostic purposes, a bacterium is considered a pathogen only if it grows to a specified level during the culturing process. This is known as a colony forming unit (CFU). The adoption of the CFU criterion came from Kass’ 1950s study of 74 women with acute pyelonephritis (a kidney infection), who had high levels of bacteria rapidly multiplying and thriving in their urine. He then backed up his findings with another study of pregnant women with severe acute pyelonephritis. From these two studies, he determined the (widely criticised) diagnostic measure for pathogenic bacteria should be held at 10^5 CFU.
As well as basing this benchmark on women with severe, acute kidney infections, Kass did not consider variables associated with low bacterial counts—such as difficulties in growing certain bacteria outside the human body, slow growing bacteria, or low concentration of the urine sample. Scientists and researchers have criticised Kass’ threshold as being insensitive and questioned its suitability as a diagnostic measure1,3.
White blood cells
White blood cells (also known as leukocytes, pus cells or pyuria) are also a common UTI indicator used by labs. The threshold was first set by Cuthbert Dukes almost 90 years ago after studying 300 asymptomatic males and females. He concluded a count of 10 or more white blood cells/mm3 as ‘abnormal’. Here are the problems associated with Dukes’ threshold:
The urothelium is a thin tissue that lines the bladder and most of the urinary system*. Elevated epithelial cell counts are considered a normal sign of infection when coupled with bacterial growth that reaches the existing criteria.
You might have experienced a UTI test with elevated epithelial cells but no bacterial growth. This most likely would have been reported as ‘contamination’. When a sample shows elevated epithelial cells without positive bacterial growth, it is usually explained as distal urethra contamination in men and vaginal contamination in women. However, research from the UK12 and the US13 has demonstrated that epithelial cell exfoliation (also known as sloughing or shedding) is a first line defence mechanism/ innate immune response to rid the epithelium of low-grade infection caused by invading pathogens. The amount of cells shed reflects the severity of infection and possibly the strength of the immune response.
It is important to note that UTI researchers no longer accept that elevated epithelial cells, in samples from people with lower urinary tract symptoms (LUTS) and no bacterial growth, is due to sample contamination.
*For more information on the urothelium, please see the following links: www.ncbi.nlm.nih.gov/pubmed/16679827, www.ncbi.nlm.nih.gov/pmc/articles/PMC3309105/, www.sciencedirect.com/topics/medicine-and-dentistry/urothelium.
This is an example of a MSU culture (urine micro/culture) report from someone experiencing fluctuating UTI symptoms for a month. This sample tested positive for leucocytes and nitrites at the GP clinic and was sent to the lab for testing. The lab report showed raised leucocytes (pus cells), erythrocytes (blood), epithelial cells and no significant growth. The clinic informed the patient there was no infection and that treatment was not required. This person continued to have escalating symptoms and further ‘negative’ tests, before being diagnosed with a chronic UTI.
This is an example of a typical positive test result where a single known urinary pathogen has satisfied the testing criteria.
For more information about the shortcomings of gold standard UTI testing tools, please check the PDFs below:
You might still hear people in online patient groups talking about broth culture. There are some international practitioners known to use broth culture as part of their diagnostic tool kit.
Broth culture involves growing bacteria in an enriched liquid environment for an extended period. This technique is different from standard culturing methods and has been found to grow bacteria that standard cultures are unable to replicate. However, many researchers and some chronic UTI specialists warn that broth culture results could wrongly incriminate harmless urinary bacteria that are not involved in causing symptoms.
Broth culture is not available in Australia. It is still used in some labs in the United Kingdom. In the United States, United Medical Laboratories, who once specialised in broth culture for urine, discontinued the test in May 2019.
Some practitioners have abandoned traditional MSU cultures and have started using DNA-based molecular testing to identify urinary bacteria. This type of testing is generating interest because of its ability to identify all bacteria in a urine sample.
DNA-based molecular testing is best used by experienced practitioners in conjunction with the patient’s history, symptoms and other tests. Since DNA is not greatly affected by time or temperature, urine samples can be sent by courier without needing to be iced. Current or recent antibiotic use will also not impact the test. Testing technologies between labs vary and tests cost anywhere between $244 and $1,200 AU, depending on the test and the lab.
There is no consensus on the value of DNA-based molecular testing in diagnosing UTIs. Some research experts are critical due to the current lack of understanding of the urinary microbiome and the inability to identify and describe the microbes truly responsible for health and disease. In July 2020 interview, Dr Curtis Nickel said, “Until we know what the normal microbiome looks like in healthy individuals, it will remain difficult to interpret NGS microbiome results from urine specimens submitted by symptomatic patients”.
DNA-based molecular testing is best used by experienced practitioners who can interpret results in conjunction with the patient’s history, symptoms and other tests. In Australia, anecdotal reports so far highlight difficulties for people finding practitioners who understand DNA-based test results and have specialist knowledge in treating chronic UTI.
Although it is still early days, it is hoped that molecular testing will one day allow the identification of a personalised, healthy urinary microbiome and inform future treatment options for UTI.
DNA-based molecular testing is not the straight forward answer we have all been waiting for. DNA tests will identify known microbes in your urine sample (both good and bad) and it will certainly identify microbes where standard cultures are drawing blanks. What we don’t know is if the bacteria identified are causing your symptoms. Let us explain why.
We now know our bladders have a resident bacterial community, therefore it’s expected bacteria will show up in a urine sample from healthy controls and from those with infection. The tests report on the highest bacterial loads, but whether those microbes are responsible for the infection/symptoms is still unknown. If an infection involves intracellular bacteria or bacteria in biofilms, these microbes will only be identified if infected cells have been shed into the urine sample collected and supplied for testing.
At this stage, DNA tests are on offer to willing customers with or without a doctor’s request—but the jury is out when it comes to the accuracy of interpreting these results and prescribing an appropriate treatment for chronic UTI.
Please Note: DNA testing is not cheap and practitioners may require multiple tests throughout treatment. Please do your research to find out more about testing and freight costs. Patients have reported it is important to work with an experienced practitioner who had demonstrated success interpreting the results and who will prescribe treatment for chronic UTI. Please speak to a trusted and knowledgeable practitioner before choosing this option.
Formerly PathoGenius Laboratory, MicroGen DX provides Next-Gen Sequencing for urine testing and is in Texas, USA. This lab accepts samples from international self-requests (i.e. you can order your own test). The website states:
“Recurrent or chronic UTIs are sometimes the result of more than just a single infectious organism. Urine culture is biased towards a single infectious organism based on CFU (colony-forming unit) count, possibly leading to inappropriate therapy. Some problematic organisms are not readily grown in culture which may lead to incorrect treatment or non-treatment. The advantage of NGS is the ability to test and detect multiple organisms simultaneously, including those that may not grow readily in culture. And if the patient is currently on antibiotic therapy or has a recent history of antibiotic therapy, detection of pathogens by NGS is not impacted by the presence of antibiotics.”
It appears the Aperiomics Inc testing lab is no longer operating. Aperiomics Inc did offer Next Generation Sequencing (NGS) with ‘deep shot-gun metagenomic sequencing’. Their technology used 100 percent of the DNA, opposed to NGS 16S that uses .001% of the DNA. The claimed their UTI test was able to identify all known bacteria, viruses, fungi and parasites that have been genetically sequenced. This lab used to accept samples from international self-requests.
There are new DNA testing labs popping up across the United States that offer urine tests. Although we know of DNA testing facilities in Australia, we are unaware of any who offer a urine test at this stage. Please contact us if you have more information on this.