Category Archives: The Science of Microbiology

“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)

“Dead Certs and Long Shots”

The more uncertain the result will be, the more useful the laboratory test generally is…

Sounds a little paradoxical, but it is absolutely true.

If we are looking to confirm something that is almost certain before the lab test is performed, then we need a “super-sensitive” test to fulfil this task. Otherwise we run the risk of giving false negative results.

For example, if we have a teenager with a sore throat and lymphadenopathy, a lymphocytosis and atypical lymphocytes on blood film, then the probability of this being EBV infection is about 90%. There is little point then in doing a confirmatory Monospot test with a sensitivity of 80-85%. This will only lead to giving negative results on patients who actually have EBV infection.

And if we are looking to diagnose a long shot (aka a very unlikely diagnosis) then we had better be sure our laboratory test is “super-specific”, otherwise we will run the risk of giving false positive results.

For example if we want to diagnose dengue fever in a patient with “flu like” symptoms returning from Mexico (an area of relatively low Dengue endemicity), then we need to think twice about performing Dengue serology testing which has a specificity rate of about 95%. You are just as likely to report a positive test in someone who doesn’t actually have Dengue.

What we are doing in actual practice here is taking our pre-test probability, and using it to give a prevalence rate (by proxy) in our tested population. Once we know this, then we can use our test sensitivity and specificity to calculate positive and negative predictive values, not always with the results we would like…

Laboratory specialists tend to be more aware of testing limitations such as these. Clinicians, in general,  tend to just take the laboratory results as gospel.

But I believe it is ultimately the laboratory’s responsibility to stress the limitations of using laboratory testing for “Dead Certs or Long Shots”, and either prevent such testing taking place, or put big disclaimers on the results.



“Reinventing yourself”

In the next generation (20-25 years), the diagnostic microbiology laboratory workforce will be decimated worldwide.

If you are a student, they don’t tell you that at the careers fair…

“You sound like exactly the sort of person we are looking for. Come and “train” for four years in a lecture theatre, and then work in a clinical microbiology laboratory, that is if you are lucky enough to get a job. Unless your Mum and Dad are well off, you will accrue a hefty debt which will likely take you a couple of decades to pay off. However in 20 years time your job will probably not even exist…”

Am I being too harsh?

In terms of general culture based bacteriology, most of it will have gone molecular. Whatever is left of it will be automated, not just partially automated as with the current Kiestra TLA system, but completely automated to include plate interpretation, colony picking, identification, antibiotic susceptibility testing and rule based signout. The whole works…

Most microbiology samples will never touch a laboratory worker’s hands.

Molecular testing will have increased, but on highly automated platforms, processing high volumes of work, with minimum manual input.

Our work will be reduced to oddities and troubleshooting. I would even chance to say that there will be just as many engineers as microbiologists on the laboratory floor.

And then I look at the core components of my own job..

  • Authorising important results:- This will be done automatically using sophisticated rules based computer algorithms. And they will do it much better than I can.
  • Giving antibiotic advice:- Decision support apps downloaded on clinicians’ smartphones will do this more sensibly than me.
  • Laboratory Management:- I fear there will be nobody left in the lab to manage…
  • Demand management:- Although the process of demand management will be performed by software algorithms, there might still be a little work left for me regarding the initiation and governance of such projects.
  • Anti-microbial stewardship:- Anti-microbial resistance is not going away anytime soon so there may be a continuing role in the governance of such programmes. But the nuts and bolts will be highly automated and app-based.

So I am not overly optimistic about my own long term future. No one is immune…

I am fortunate to be attending the ECCMID conference at Vienna in April. It is no accident I will be heavily focusing on presentations in molecular diagnostics and demand management. That should help in the short term at least in securing my usefulness. However it is entirely possible I will need to retrain in something completely different before I am done.

I know my job description as a clinical microbiologist will change out of all recognition before I retire. It is not impossible that clinical microbiology as a career entity will cease to exist altogether.

We need to be constantly looking at what we do today, then imagining what we will potentially be doing tomorrow, and preparing for it as best we can…