“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)

“Hand holding and Chinese whispers..”

As part of my job as a clinical microbiologist, I am usually on the telephone 20-30 times per day.

That is a lot of telephone time for a man…

With regards to outgoing calls, a lot of these are simply information gathering. For example, is this patient with Gram negative bacteraemia on appropriate Gram negative cover? Has this patient with Clostridium difficile infection been isolated and treated? Has this patient with Staphylococcus aureus bacteraemia been investigated properly?

Gathering this information by telephone is of course always a little fraught with difficulty. Trying to get hold of the right person to speak to can take up a lot of valuable coffee drinking time. There is also no guarantee that the information you are given is accurate, and has not evolved along a chain of “Chinese whispers”. Sometimes you finish the phone call no more enlightened than when you started…

Many of these calls would not be necessary if the hospital/health network had a live, real time “Electronic Health Record”, along with an electronic/digital drug chart for each patient. These innovations simply cannot come soon enough to my neck of the woods. Objective, readily accessible clinical information is what microbiologists crave.

Incoming calls are generally from clinicians looking for advice on antibiotics, infection control, optimal samples, etc. Much of the information that I give out could easily be accessed from published clinical guidelines. There is often an element of “hand holding” here, of sharing the responsibility for the decision made, and sharing the blame if something goes wrong..

Personally I was never very good at hand-holding…

And then, once or twice a day, an interesting phone call comes along, one which stimulates the mind, and prompts further thought and reading, and reminds me that I do after all work in a microbiology laboratory, and not a call centre…


“Gatecrashing: Neisseria meningitidis as a genital pathogen.”

Neisseria meningitidis is more classically known as the cause of meningococcal sepsis and meningococcal meningitis. However its role as a cause of urethritis/cervicitis has been the subject of ongoing speculation over the years, and several studies have backed such a link up. For example, check this study out, and this one.

A recent study has added more weight to this hypothesis, backing the assertion up with DNA studies of the N. meningitidis isolates showing adaptation to a genital environment. (loss of outer capsules, and acquisition of enzymes facilitating survival in a low oxygen environment)

So what does this all mean for clinical microbiology laboratories?

I guess it shows the inherent weakness of molecular diagnosis. There could be a widespread outbreak of urethritis due Neisseria meningitidis urethritis in your local area, but the laboratory would be completely naïve to it, if it only performs molecular testing for C. trachomatis and N. gonorrhoeae. Particularly in the Sexual Health Clinic setting, adjunctive culture of STI samples is important, and not just to obtain the N. gonorrhoeae susceptibilities.

It is also possible that the selective molecular diagnosis and treatment of N. gonorrhoeae will therefore create a “niche” for organisms like Neisseria meningitidis to adapt physiologically and “gatecrash” the party. (I will talk more about “selective pressure by diagnosis” in the next post.)

And finally on this topic, there is also intriguing data coming out that suggests that some meningococcal vaccines may have a protective effect for N. gonorrhoeae infection. Suspected for some time, this suggestion has been backed up by some observational data in this study. More research is obviously needed. We are still a bit away I suspect from a gonococcal vaccine.

The physiological and evolutionary relationship between Neisseria meningitidis and Neisseria gonorrhoeae is a fascinating one.  We shouldn’t think too much about one without considering the other…