Tag Archives: molecular platforms

“The Swedish Variant: Selection Pressure by Diagnosis”

When we think about selection pressure the first thing that comes to mind are antibiotics that selectively kill susceptible bacteria and thus allow more resistant bacteria to fill the ecological niche.

But fewer people realise that selection pressure can also be caused (indirectly) by laboratory diagnosis. Microbes which are diagnosed in the laboratory often end up getting treated and eradicated. However a microbe which mutates sufficiently to avoid diagnosis will have a selection advantage over its diagnosable counterpart. This concept is particularly applicable to microbes which are diagnosed by molecular techniques such as PCR where only a minor mutation or deletion can potentially create sufficient change in the base sequence to make the microbe undetectable by the original molecular test.

The most classic example of this is the “Swedish Variant”.

In 2006, a drop in Chlamydia trachomatis diagnoses was noticed on a particular molecular platform X, but not on others in use within Sweden. Further analysis revealed that a mutant strain of Chlamydia trachomatis (nvCT) containing a 377 base pair deletion was circulating. This was undetectable on platform X, but detectable on other molecular platforms.

Interestingly the nvCT strain had a much higher prevalence in geographical areas where platform X was used. In areas where other platforms were utilised, it wasn’t so successful as it didn’t have any selection advantage. But this makes perfect sense when you realise that a strain that avoids laboratory detection and consequently destruction is bound to do better than a strain that is easily diagnosed.

So what implications does all this have for laboratory practice?

Centralisation, tendering, and “packaged” contracts means that we are increasingly relying on just the one molecular assay to diagnose a particular pathogen within a large geographical area.

Laboratories or regions, or even countries which just rely on just one molecular test to diagnose a pathogen are always vulnerable to “escape mutants” such as nvCT emerging which escape detection and thus thrive in the population.

Testing a cohort of samples on alternative molecular platforms to validate the results and to look for these escape mutants is an important quality assurance measure.

The story of the Swedish variant also demonstrates the importance of using the percentage positivity rate of a molecular test over time as a Quality Control measure.

Even though the Swedish variant was diagnosed over 10 years ago, the lessons that can be learned from this episode are probably even more important in the large volume, centralised laboratory landscape that we have today.

In summary, one must be careful not to put all their eggs in one basket…


Check out this article for a more detailed overview of the Swedish variant. (about a 10 minute read)

“Something for the weekend?”

I know it is difficult to believe, but patients tend to be just as sick on Saturday and Sunday as they are from Monday to Friday.

I am not sure if the concept of the “weekend” is secondary to religion or the industrial revolution. Regardless of its origins, in healthcare facilities throughout the world, the clinical service that is provided at the end of the week is reduced somewhat. Weekends are good for society, but not so good for patients…

And the weekend is not always just two days. Add on a Public Holiday Monday and the weekend can stretch to three days. Over Christmas, New Year and Easter, the “weekend” is often four days. Four days is a long time if you are sick.

In clinical microbiology laboratories everywhere, molecular testing traditionally never happened at the weekend. The molecular department happily shut up shop on Friday afternoon, and re-opened again on Monday morning. In times gone by, this was due to the rather specialised nature of the testing, and also the relatively slow turnaround times.

Take the following hypothetical scenario, which you may be familiar with…

It is the evening before the Christmas break. A cerebrospinal fluid (CSF) sample comes in to the microbiology laboratory from a patient in ICU with meningoencephalitis. A viral PCR panel is requested to try and ascertain the cause of the patient’s symptoms. However because it is the weekend coming up, followed by two public holidays, it will be 5 (long) days before the PCR is performed.

A viral CSF PCR result can have the following positive effects on patient management:

  • A negative (HSV) result can allow empirical therapies such as acyclovir to be discontinued, or in the case of a positive result, the dose to be optimised.
  • A positive result can prevent further investigations, such as MRI scanning, and  other “exotic” laboratory tests being carried out on the CSF.
  • Can expedite discharge, when diagnosis is known.

The long weekend progresses, and the microbiology department continues to analyse significant volumes of relatively low value specimens. e.g. ear swabs, peri-anal abscess swabs, vaginal swabs, swabs from leg ulcers etc, etc. Yet sitting there patiently in the fridge is that CSF, probably the most important sample in the laboratory, and the one which could have the most immediate and profound effect on patient management. It looks on enviously at all the attention the other samples in the laboratory are getting!

This model doesn’t really cut the mustard anymore… We need to utilise the new (user friendly and rapid turnaround) molecular platforms (Cepheid Genexpert, BD Max as examples), so that we can offer a laboratory service at the weekend which has a genuine clinical impact.

Things are changing however. Molecular testing is slowly being introduced at the weekend in many microbiology laboratories. C. difficile testing and Influenza/RSV PCR are a couple of examples. But this progress takes time, and sometimes it takes more time than it should do.

We need to “disrupt” traditional weekend work at the clinical microbiology laboratory… On the weekend, put those ear and vaginal swabs back in the fridge, and find a way (somehow) to take the CSF out!


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