Monthly Archives: April 2015

“The chicken and the egg”

I am currently at the ECCMID conference in Copenhagen. So far, and in my humble opinion it has been better than last year’s ECCMID in Barcelona; better conference facilities, more seating, nicer food, better use of Information Technology etc.. Even though the conference is only in its second day it has already provoked several ideas and concepts for me to work on when I get back to New Zealand.

One continuing issue I have though is the difficulty in differentiating between the sessions sponsored by industry and the independent sessions. It is an important distinction to make, for obvious reasons.

During a couple of the industry sponsored sessions, both involving the promotion of new automated platforms, I have heard the following quote: “The shortage of skilled scientists has prompted the need for automation”or something to that effect.

Hmmm.., I am not buying that one.

Automation in the world of microbiology has several benefits (see this article for more), relating mainly to standardisation of processes and reduction of errors. You can also be sure that automation is cost effective compared to the traditional methods, otherwise it would not happen.

These, along with the technological advances that have made automation feasible, are the principle drivers in this direction.

The lack of skilled staff I suspect is not one of the main drivers, but is however still used as an “excuse” for automation, particularly by the companies manufacturing and promoting these systems. 

What automation certainly does do is reduce the number of skilled staff required to process the samples. It also changes the skill sets needed by both incumbent and trainee scientists. 

So for me, in this conundrum, the automation comes first, and the effects on scientists are the consequence, not the other way round…..



“Let’s get candid:a discussion on yeast infection.”


Here are three concepts regarding yeasts which challenge the dogma and traditional practice of most clinical microbiology labs.

  • Vaginal candidiasis is best diagnosed by microscopy as opposed to culture. I daren’t think how many vaginal swabs have been cultured for yeasts by microbiology labs over the years. Millions probably. Yet we know that yeasts in small numbers colonise the female genital tract in about 10% of the (asymptomatic) population. Thus there is a very poor correlation between the culture of yeasts and symptoms caused by vaginal candidiasis. A better approach is to just look for the presence of yeasts/candida on microscopy. This will miss very small numbers of yeasts but will pick up the patients with larger numbers, i.e. the patients in whom the yeasts are more likely to be causing symptoms. In essence one is decreasing sensitivity in order to improve specificity. This may be a bit unpopular with some people, “We are missing them“, but that is the whole point….


  • For the vast majority of swabs all we need to know about the yeast is that it is a yeast. When we do culture a yeast, then sure it is nice to show exactly what type of yeast it is, but is it really necessary? Identification of yeasts, although usually straightforward, is not labour or consumable free, and it may delay a report going out to the clinicians. In the vast majority of cases, who actually cares if the yeast is a Candida albicans, parapsilosis or a glabrata? For non-critical swabs a better approach might be to put out a report such as “Yeast isolated. Identification +/- susceptibilities on request if clinically indicated.” 99 times out a 100, they won’t be needed.


  • Candida infection of the mouth is best diagnosed without the help of the microbiology laboratory. Oral candidiasis is very much a clinical diagnosis and usually very easily treated with either topical applications or a stat dose of oral anti-fungals. In all but the most exceptional cases, the lab should not be getting involved in the diagnosis of this condition. The sensitivity and specificity of the clinical diagnosis should more than match anything that the laboratory can offer here.

Have a think about what is done with regards to yeast processing at your lab or institution. You may not follow any of the processes above, or you might do all of them, but query and discuss what you have been doing nevertheless. Is it the best way?

Always question dogma. Just because something has been done at your lab for decades, it doesn’t mean it is right. Don’t be scared to be the person to suggest a change, and don’t be afraid to be the first lab to make the change.


“Ticking the boxes”

No one gives a second thought to the microbiology (or laboratory) request form when we are reviewing all our processes, and looking for efficiency and quality improvements.

However the humble request form and how it is structured is an extremely important factor with regards to influencing both the quality and quantity of test ordering.

If you have a request form with dozens of tick boxes present, each one representing a different test, you are making it very easy for the laboratory user to request a  lot of tests, many of which may be either unnecessary or inappropriate.

On the other hand, if your request form is essentially a blank sheet of paper on which microbiological tests need to be pro-actively documented, it encourages test requesting only where a clear rationale exists. The downside of this approach is that the requestor may forget to include a test that should really have been done because it wasn’t visible on the form to trigger his/her memory.

There is no correct answer of course to what is the best way to structure a request form. However my personal preference is for the blank page approach, because it encourages the requestor to think carefully about what they are requesting, and to focus on the problem at hand.

However I suspect that as electronic requesting becomes more common so too will tick box request forms, as this style very much suits electronic requesting and the necessity to “code” the test requests (Thus the importance of making clinical details a pre-requisite for completing an electronic request).

Next time you see a microbiology/laboratory request form in your area, look at it carefully to see how it is structured. Is it a “Tick box” form or a “Blank Page”?

It matters, and more than you think….