Category Archives: The Science of Microbiology

“A taste of my own medicine”

I hadn’t been feeling quite right since Christmas… Upset stomach, loose bowel motions, no appetite, and worst of all I didn’t even feel like a glass of wine in the evenings! The symptoms weren’t that severe, unfortunately not even bad enough to keep me off work, but they just grumbled on and on…

After a few weeks of this, it was time to call in the help of my microbiology laboratory. And sure enough, the enzyme immunoassay for Giardia was positive on my stool sample. I was quite glad it was positive, because at least I had an answer for my symptoms, but also because I hate unnecessary laboratory testing!

I self-prescribed myself some oral metronidazole (“tut, tut…”),  at the high dose that is recommended for Giardiasis. At the higher dosage, it  is not a particularly pleasant medicine to take. It turned my urine so brown, I found myself checking my eyes for jaundice! It also made my morning coffee taste like dishwater.

I now feel much better, back to my normal incorrigible self. Looking back in retrospect, it was a classic textbook case of giardiasis. I have no idea where I got it from, and will probably never know! I don’t envy those who work in the murky waters of Public Health.

There is no better way of learning than experiencing the disease yourself. I would not recommend this however for lots of other infections. Giardiasis is probably one of the “better” ones to catch.


Giardia lamblia trophozoite

Another good way of learning about a particular infection is to get to find out its history. Giardiasis is fascinating in this respect. Giardia trophozoites were first observed in 1681 by Anthony Leeuwenhoek in his very own stool samples, on his funny looking microscopes. Thus it has to be regarded as one of the first infections to be diagnosed by a “laboratory”.

The name Giardia lamblia was in recognition of a French zoologist, Alfred Giard, and a Czech physician, Vilem Lambl,  who each contributed to the description of giardia trophozoites. Initially called Cercomonas intestinalis, it only became known as Giardia lamblia in 1915. It is also still known as Giardia intestinalis.

“Alfred Giard”

However none of these people mentioned actually made the connection between Giardia lamblia and infectious diarrhoea! In fact it wasn’t actually confirmed as a pathogen until the 1970s.

So my awareness of Giardiasis has now increased considerably, and we should all have a low threshold for testing for it in patients with chronic gastrointestinal upset, unexplained weight loss, failure to thrive, etc.

Apparently 200 million people worldwide are infected with Giardia lamblia, so I am not the only one!

Michael

“Cohort Bias”

At my laboratory we only test nasal Staphylococcus aureus susceptibility to mupirocin in the following two circumstances:

  • Prior to joint replacement surgery as part of a Staphylococcal decolonisation bundle
  • In patients where the clinical details state recurrent skin infections

In the patients about to get their joints replaced, our nasal Staph aureus resistance rate to mupirocin is 3%. Not surprising really. This is a generally older cohort, less likely to suffer from impetigo and skin boils etc., and thus less likely to have been exposed recently to mupirocin.

In the patients who have recurrent skin infections, our nasal Staph aureus resistance rate to mupirocin is 15%. This is not surprising either. This cohort is generally young, and due to their clinical history are much more likely to have been exposed to a lot of mupirocin. As a cohort, they potentially have a lot of physical contact with each other (in kindergartens, in the school playground, on the sports field, in cinemas, backs of cars etc..,) facilitating cross-transmission.

This is a good demonstration of how much antibiotic resistance can vary, depending on what population you are looking at. 3% is markedly different from 15% and management of these different rates might be very different from an antibiotic stewardship point of view.

It also reflects the difficulties in measuring antibiotic resistance and then how to report such results in a meaningful manner.

We like to simplify things, and have just one result regardless of what biases might be at play. Measuring resistance rates is complicated enough due to the sheer number of microbe-antimicrobial combinations that can be permutated. To add another level of complexity by calculating different values for any one microbe-antimicrobial combination is too much for most of us to handle! 

But sometimes the difference in values between different population cohorts (as demonstrated above) is just too much to be ignored…

Michael

“The uncertainty of certainty”

There is one thing certain in the microbiology laboratory, that the results will be uncertain. This has nothing to do of course with laboratory systems or the competency of staff members. Just an acceptance that there is no such thing as a certain result…

The other thing to note is that the degree of certainty of results will vary between different tests, not only for separate tests but even for multiple tests contained in the one assay, e.g. any multiplex PCR.

Take for example a multiplex respiratory PCR, containing 24 or so different targets. (Most labs will “demand manage” such expensive assays, allowing them only for immunocompromised patients or the seriously ill. Nevertheless, such assays are becoming increasingly popular.)

In a multiplex respiratory assay, a positive result for rhinovirus is almost certainly going to have a greater chance of being “the genuine article” than a positive result for bocavirus.

This is because each individual target pathogen has a different positive predictive value (PPV), based on both its specificity and its relative prevalence in the tested population. As a result, positive predictive values for individual pathogens within a multiplex can, and do, vary greatly.

But how do we relate such information to the clinicians? Quoting the calculated PPV for each target in a multiplex would make for a long and complex laboratory report. I would not go there… It is probably best to use an appropriate comment for certain results. I.e. “Bocavirus is uncommonly seen in population x, therefore the positive predictive value of this result may be sub-optimal. Close clinical correlation is required.”

Of course, clinicians can increase the degree of certainty by clarifying the “pre-test probability”. I.e. A positive bocavirus result in a 6 month old during the winter season is much more likely to represent a true result than a positive bocavirus result in an adult during the summer season.

With multiplex PCRs, sometimes you are “forced” to perform a test, when it would be better not to know…

Clinicians, in general,  tend to believe that all laboratory results are certain, until we produce one that is very clearly wrong! After that, they will believe all results are uncertain until that trust is rebuilt over time.

To understand certainty of testing, you first of all need to understand the laws of probability. All a laboratory result ever does is convert pre-test probability of disease X into post-test probability. 

It neither confirms nor excludes…

Michael