PCR or polymerase chain reaction testing

PCR testing (polymerase chain reaction) is a technique used to amplify trace amounts of DNA found in or on almost any liquid or surface.

Every human, animal, plant, parasite, bacteria or virus contains genetic material such as DNA sequences that are unique to their species.

If a urine sample contains segments of DNA, PCR is a method used to amplify (make many more identical copies) of these unique sequences to determine with a very high probability the pathogenic bacteria, fungi or other microbes.

Within urine, PCR testing has detected the DNA of more than 1,200 microbial species.

Benefits of PCR testing

  • PCR tests are not affected by temperature or time delays unlike traditional urine cultures where the urine sample must be delivered to the laboratory within two hours to prevent sample degradation.
  • The results of a PCR test can be available within 24 hours.
  • PCR tests do not grow microbes, they are instead extracting the microbial DNA from a sample and can identify multiple bacteria, anaerobes or fungi.
  • A PRC test needs one sample unlike standard laboratory tests where a separate swab would be required for fungal microbe analysis in addition to a urine sample.  This fungal analysis can take up to 20 days to process.

Limitations of PCR testing

  • Laboratories using this method need to preselect which microorganisms the test looks for.  Urine panels usually comprise of less than a dozen micro-organisms, more often the most common for that type of bacterial infection. Any other organisms not listed in this panel will be excluded from analysis.  It amounts to around 1% of all known microbes.
  • It is currently unknown how the urinary microbiome may differ from the microbiome of the bladder wall and in particular those bacteria embedded into bladder wall cells or those affected by biofilm coverage. To understand the differences further will likely require more invasive sampling procedures such as biopsies.
  • The DNA extraction technique chosen will significantly affect how faithfully the bacterial composition of the original sample is represented by the DNA extracted from it. In some bacteria, such as Gram-positive bacteria and Mycobacteria, it can be more difficult to break down the cell membrane of the bacteria (known as lysis) for study than others in a microbial community and these bacteria may be less represented in a report. On the other hand, if an extraction method is too harsh, the DNA from the easily lysed species may become sheared. Currently, there is no standard technique that works equally well for lysing all bacteria in a given sample.
  • Another limitation of sequencing-based approaches is that they only yield information about the microbial DNA in a sample. While this allows for identification of the types of bacteria present in a biological sample, it does not distinguish between bacteria that are live from those that are dead.
  • In comparison to Next Generation Sequencing testing it is thus limited because it won’t offer a genetic report of everything in the urine sample you provide.
  • PCR reports give percentages on the bacteria or microbes found in your urine. But the understanding of the urinary microbiome is still in development. Are all those identified responsible for your urine infection? Does a higher percentage equate to the causative agent behind your infection?
  • The testing methods are based on individual, unique, patented methods used by each laboratory. They test against a panel of microbes/fungi/anaerobes established by that company. If the infection causing agent is not found against that panel, how are you to be treated
  • There is also the issue of cost. Treatment of a chronic UTI may involve several tests over a period of time and at present, these are extremely expensive. Some patients in the US are able to offset their costs through health insurance but others are unable to do so. International patients cannot offset against health insurance.
  • It can be difficult to find a practitioner who can interpret the laboratory findings and treat accordingly. Treatment guidelines used by GPs and consultants worldwide are based on standard testing protocols. Some patients have found their results have been dismissed or ignored by their doctor or consultant.
  • Finally, as yet, no research studies have been published using PCR testing in a clinical setting to determine successful treatment outcomes for patients using this diagnostic method.
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