Tag Archives: microbiology automation

“Reinventing yourself”

In the next generation (20-25 years), the diagnostic microbiology laboratory workforce will be decimated worldwide.

If you are a student, they don’t tell you that at the careers fair…

“You sound like exactly the sort of person we are looking for. Come and “train” for four years in a lecture theatre, and then work in a clinical microbiology laboratory, that is if you are lucky enough to get a job. Unless your Mum and Dad are well off, you will accrue a hefty debt which will likely take you a couple of decades to pay off. However in 20 years time your job will probably not even exist…”

Am I being too harsh?

In terms of general culture based bacteriology, most of it will have gone molecular. Whatever is left of it will be automated, not just partially automated as with the current Kiestra TLA system, but completely automated to include plate interpretation, colony picking, identification, antibiotic susceptibility testing and rule based signout. The whole works…

Most microbiology samples will never touch a laboratory worker’s hands.

Molecular testing will have increased, but on highly automated platforms, processing high volumes of work, with minimum manual input.

Our work will be reduced to oddities and troubleshooting. I would even chance to say that there will be just as many engineers as microbiologists on the laboratory floor.

And then I look at the core components of my own job..

  • Authorising important results:- This will be done automatically using sophisticated rules based computer algorithms. And they will do it much better than I can.
  • Giving antibiotic advice:- Decision support apps downloaded on clinicians’ smartphones will do this more sensibly than me.
  • Laboratory Management:- I fear there will be nobody left in the lab to manage…
  • Demand management:- Although the process of demand management will be performed by software algorithms, there might still be a little work left for me regarding the initiation and governance of such projects.
  • Anti-microbial stewardship:- Anti-microbial resistance is not going away anytime soon so there may be a continuing role in the governance of such programmes. But the nuts and bolts will be highly automated and app-based.

So I am not overly optimistic about my own long term future. No one is immune…

I am fortunate to be attending the ECCMID conference at Vienna in April. It is no accident I will be heavily focusing on presentations in molecular diagnostics and demand management. That should help in the short term at least in securing my usefulness. However it is entirely possible I will need to retrain in something completely different before I am done.

I know my job description as a clinical microbiologist will change out of all recognition before I retire. It is not impossible that clinical microbiology as a career entity will cease to exist altogether.

We need to be constantly looking at what we do today, then imagining what we will potentially be doing tomorrow, and preparing for it as best we can…


“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.


“Bread and Butter”


If you are a microbiology scientist your bread and butter might be reading plates and  identifying Staph aureus etc from wound swabs. In the future, this will be done for you by interpretative software analysing digital images.

If you are a senior scientist, your bread and butter might be validating/authorising microbiology reports. In the future this will be done for you by sophisticated rules engines.

If you are a microbiology technician, your bread and butter might be putting up swabs onto agar plates, setting up Maldi-TOF plates or inoculating susceptibility broths. In the future this will be done for you by automation. (if not already)

If you are a clinical microbiologist your bread and butter might be giving antibiotic or best testing advice to clinicians. In the future this will be done for you by robust apps on the clinicians’ smartphones.


The nature of our jobs are going to change in the future. This might be 2 , 5, 10 or 20 yrs down the line depending on the nature and pace of change. If we expect to continue doing our current job in its current format, then sooner or later your job will be made redundant by advancing technology. Difficult news to swallow, but absolutely the truth.

You might think that the above will lead to a loss of jobs, and it may well lead to a net loss. (This has been debated ad nauseum elsewhere) However on the plus side new jobs (and job descriptions) will almost certainly be created.

For example in the future, new jobs may be available for those who:

  • are expert at maintaining, troubleshooting, configuring and calibrating automated equipment.
  • can develop apps and write rules engines.
  • are comfortable developing testing algorhythms, and composing and formatting online manuals.

We will still need microbiological knowledge, but not in the encyclopaedic way we did a generation ago….

When it comes to this it doesn’t really matter how fast you work or how good you are at your routine work. Advancing technology never pays much attention to these parameters. It just targets bread and butter work and eventually eats it up.

We need to be aware of what our daily bread and butter is in the workplace, what is likely to happen to it in the future, and how we (personally) are going to adapt in order to stay relevant.