“Back to the Coalface”


I have just returned from a 5 week road trip across the USA with my wife and 5 children. What a trip! Lots of adventures were had. Sure, it was tiring and stressful on occasion (we got lost several times), but never dull. We saw a lot of places, experienced many different landscapes, and encountered lots of different people, the whole spectrum of American society. 

And at the end there was a nice sense of achievement in getting everybody across the country in one piece!

It was great to experience all the different cultures, the small towns (mostly pro-Trump!), the big cities, and the native Indian settlements, all interesting in their own way.

But the biggest culture shock of all has been coming back to work!

Back to my cubicle, back to signing out wound swabs, back to phone calls about multi-resistant urines, back to laboratory politics, back to emails and meetings….

It all seems a bit mundane after the US. Hopefully the motivation will come back in due course.

And who knows, I might even write about microbiology in my next post!



“Leading from the Middle”


It is now over 6 months since we installed the Kiestra TLA platform into our laboratory. The initial teething problems have been surmounted, and the sytem is now running beautifully (touch wood!).

The engineering and lean processing support from BD has been outstanding. Our initial fears about installing such a system in the relative isolation of provincial New Zealand have very much been allayed.

We can now start to dream about the future potential that such a system offers us.

But aside from all that, what has impressed me most is how well the scientific and technical staff have embraced the new system.

Not only are they comfortable with the operation and troubleshooting of the Kiestra TLA system, but they are more than willing to come up with suggestions as to how to improve it further…

Staff members of all grades and ages have not been shy at volunteering their ideas and opinions, much more freely than I have ever witnessed before. This is just fantastic. Bring it on. We have a short meeting at 8.30am every morning and this works very well as a platform for starting discussions and building team spirit.

The “Kiwiestras” (as we call our department Pub Quiz team!), are now a confident and self-assured bunch of people. They know they are working in a progressive and high quality microbiology laboratory, a lab which aspires to be one of the best in the world…

And the team are responding to the challenge…


p.s. No more microbiology posts from me until mid-October as I am off on a road trip across the US. I will however post occasional updates from the trip onto “The Wandering Microbiologist” page of this website.


“Time Out”


We have been implementing some quite big processing changes in the microbiology laboratory recently with significant effects on users. Examples include making clinical details pre-requisite for selected sample types, and restrictions on the use of faecal occult blood (FOB) testing for symptomatic patients. The changes closely follow best practice guidelines, but  have proved unpopular with some people. Sometimes politics plays a part, for others it is the inconvenience of having to justify laboratory requests. Occasionally it is just a general reluctance to embrace change…

This confirms to me what I already knew, that you just cannot please everyone all of the time…

And nobody likes to be told what to do. I should understand that. I hate it more than most!

Sometimes in the past few weeks it has felt like that the world is against me. At these points it is definitely worthwhile taking a step back, reminding yourself of why the changes were implemented in the first place, and trying to gain as much peer support as possible.

I have also improved somewhat at convincing others of my point of view. This is something I have always been notoriously weak at. I have learnt that “face to face” meetings are undoubtedly best for this, emails are the worst, with telephone calls somewhere in between…

In short, you need to show people that you are human.

In trying to get things done and make progress, I have also been learning that there is a very delicate balance between “unilateralism” and trying to get consensus from everyone by collaboration. You will never get agreement from everyone, but there does need to be a “critical mass” of believers in order to carry and enforce policies.

There is little doubt that a couple of years ago, I would have buckled under the pressure, reversed the changes and gone back to my lab cubicle with my tail between my legs.

My skin has become a little thicker…

I have definitely learnt to see past the initial pain, and to visualise the long-term quality gains that have been made within the department, and for the clinical microbiology service as a whole.

These things take their toll however over the weeks and months… When working on such issues without a break, both the stress and exhaustion levels build slowly over time. The two terrible twins form a synergistic relationship.

But there is light at the end of the tunnel!

Next weekend I am going on a 5 week road trip with the family across the USA, from LA to NY.

It couldn’t have come at a better time… I can forget all about the microbiology laboratory for a while, the incessant phone calls and emails, the complaints, the politics, and the bureaucracy. I can concentrate on my life outside of the microbiology lab and recharge the batteries.

And hopefully when I get back I will still want to be here!



“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…