Monthly Archives: August 2016

“The Art of Interpretation”


At the moment I would estimate that 5% of agar plates worldwide are read by the examination of a digital image, as opposed to someone holding the plate in their hand.

In 10-15 years I predict this percentage will be closer to 50%…

And currently, the vast majority of agar plates are still analysed manually, by a scientist examining the colonies present on the cultured agar plate. 

This also is going to change dramatically over the next 10-15 years…

The process of automated plate interpretation has started. Some automated systems have software in place which can already do the following:

  • Interpret negative/no growth plates, by comparing with a negative template.
  • Interpret chromogenic plates, looking for colonies with a specific colour.
  • Measure and interpret susceptibility zone sizes to antimicrobials.

But this is a science just in its infancy, and I suspect the software will soon be able to do the following:

  • Triage and quantify different colony types on a plate, based on size, colour, edge contour, level of haemolysis. This will then allow Maldi-tof analysis on different colony types.
  • Will be able to assess if the plate growth is sufficient for reading, as opposed to waiting for a pre-programmed time period.

I find it interesting, and somewhat surprising, that a lot of microbiology laboratories are concentrating on “front end” automation ( inoculation and plate spreading) at the moment.

For me, it’s the “back end” which is really going to progress and change over the next decade. Automated colony pickers, combined with plate interpretation software as described above is going to absolutely revolutionise traditional plate reading as we know it…

It is a very exciting area, and plate interpretation software will undoubtedly become very powerful. The great unknown however, is how long culture based microbiology can survive the ever increasing sophistication of molecular diagnosis.

So in summary, by 2030 I think we will be using a lot less agar plates than we do today. But I do think we will still be setting up at least some. However, of those agar plates that are set up, I think at least 50% of them will never be seen by a scientist…


“Why you should not buy a microbiology textbook…”


If you are doing under or postgraduate exams in microbiology, I would advise you not to buy a microbiology textbook, even if you have been given a reading list full of them!

I attended the ASM conference in Boston recently and was blown away by how many book stands there were dotted around the industry hall.

I didn’t realise there were so many microbiology textbooks out there.

So someone must be buying them…

But not me… I haven’t bought a textbook of any description whatsoever in almost 20 years. That doesn’t mean however I don’t study. Far from it.

Here are the reasons why I don’t buy microbiology textbooks, in no particular order:

  • They are too expensive. I am a self-confessed academic skinflint, who prefers spending his disposable income on nice wine and travel.
  • They are too heavy. I have too many bad memories of lugging around a large satchel full of books at school.
  • They teach you a very standardised set of microbiology facts. i.e. they stick to the syllabus. I think syllabuses are much over used, over detailed, and over-rated.
  • They teach you stuff that everyone else knows/is supposed to know. There is a finite resource of information in a textbook, so it leaves little room for exploring an area in more detail, or one that is of particular interest to you.
  • They become out of date very quickly. My own laboratory contains a whole shelf of historical textbooks, none less than 10 years old.

I use the Internet instead. I stay away from patient websites, commercial websites, and chat forums, but most of the rest is reasonably reliable.

By using the internet I can (metaphorically speaking) wander around, get second opinions, and look for stuff on a particular topic that other people are not likely to know. I ask myself a few specific questions, then search for the answers. To learn stuff in more detail, I occasionally source out a journal article or two. I know it sounds stupid, but I make a point of never learning stuff that I know already. I know lots of people that do. I am much more of a gap filler.

Some people might argue that there is stuff in the textbook that is not online. I don’t buy that. Everything is online.

Don’t feel compelled to read a microbiology textbook, just because someone from the establishment has told you to read it. Set your own learning agenda…


“Four more years…”


Four years is the time period between Olympic Games. It is the time period of an American presidency.

It is also the time required to train as a microbiology scientist in New Zealand.

Four years is a long, long time…

Four years sitting in a lecture theatre or mock laboratory, amassing debt, and learning (increasingly irrelevant) microbiology facts.

Would you recommend it to your children..?

This is an outdated model of training. If there was ever a profession that lent itself to an online, problem based learning course, combined with laboratory attachments from day 1, it is medical laboratory science, and especially microbiology.

Medical laboratory scientists in NZ (in all disciplines) do not get into a “real laboratory” until Year 4 of their training. What about if you enter the laboratory in year 4 and decide that spending day after day in a laboratory environment is just not for you.

Wasted years…

Microbiology laboratories are changing fast. The technology is changing, the skill requirements are changing, the manpower requirements are changing.

The training (and the exams) needs to change as well in order to keep up…