Category Archives: Confessions of a Microbiologist

“The Ageing Microbiologist”

“Predicted self-portrait in 2050.”

At the age of 44, I like to think I am not old. But I am not young either…

In my last year at primary school, the first school computer arrived, a “BBC Micro”, and it was trundled from classroom to classroom on a trolley.

Whilst at medical school in the early 1990s, email was very much a novelty, and we used to email jokes to each other in the university library. There was even a few people that had (very large) mobile phones.

I gave my first powerpoint presentation in the year 2000. Sadly it wasn’t the last…

Whilst training in clinical microbiology in the early 2000s, all the culture work-up was written on the back of the request form. The average turnaround time for a sample was still about 3 days. “APIs” were all the rage. MALDI-TOF for organism identifcation didn’t even exist. Molecular diagnostics was highly specialised and painstakingly slow. And if you had mentioned bacteriology automation, you would have been laughed out of the laboratory!

Change in the practice of microbiology is difficult to perceive from month to month, even year on year. But over a generation, and particularly the last one, it has changed out of all recognition.

Even though I am ageing, I still feel quite young. I try to observe younger microbiology scientists and clinical microbiologists and then think to myself. What do they know that I don’t? How can I upgrade my skills to match someone half my age!

The knowledge and skills that were essential for me 20 years ago are only partially useful to me today. I have had to “re-invent myself” and acquire lots of new skills; Real-time PCR, pivot tables, middleware, website development, just for starters. I have had to learn about new assays that didn’t even exist when I first qualified as a microbiologist… And I have also forgotten a lot of the old stuff.

That’s ok.

But age does have one big advantage.

Experience.

The ability to spot the unusual, to recognise patterns, to (sub-conciously) know when to follow up on a result and when it can be left alone. All these things are painstakingly learnt over time, and by learning from your previous mistakes and failures.

The combination of experience and re-invention can be a potent one.

It is easy for the ageing microbiologist to look back at how things used to be. But it is even more important to look forward and try to predict how things are going to be in the future.

Michael

Are you an ageing microbiologist? Feel free to share your experiences in the comments!

“The Knee Aspirate….Telling stories”

We receive a lot of knee joint aspirates into our laboratory. But often we don’t know the story as to why the sample has been taken and sent to us…

  • …It might be a elderly patient with a knee replacement who has gradually decreasing mobility over the past 6 weeks.
  • …It might be a young sex worker who has an acutely swollen hot knee with associated fevers.
  • …It might be a middle aged male with a history of recurrent gout.
  • …It might be a patient who got a prosthetic joint inserted a couple of weeks ago and now presents with a discharging wound and fevers.
  • …It might be a patient with osteoarthritis who got a steroid injection into their knee joint a couple of weeks ago and it is now red and painful.
  • …It might be an aid worker who has just returned from working in Sub-Saharan Africa for two years.

or it might be something else altogether.

Who knows? Unfortunately not always the microbiology laboratory.

There are so many ways in which the “story” that comes with the sample can affect the microbiological processing:

  • Whether additional tests in addition to standard culture are indicated?
  • Whether a Gram stain and/or crystal microscopy is performed?
  • What incubation conditions are used (aerobic/CO2/anaerobic) for the culture plates?
  • Which culture media are set up on the sample?
  •  Whether the culture isolates are deemed to be significant or not.
  • Whether susceptibility testing should be performed, and what antimicrobials to test against?
  • Which culture isolates should be reported to the requestor?
  • Which antimicrobial susceptibilities are released to the requestor?
  • Whether an interpretative comment is added to the report, and what the comment should entail?

If we recieve a sample into the microbiology laboratory which has no clinical details on it, then we return the following comment to the requestor:

“No clinical details have been received with this specimen. The lack of clinical information provided to the laboratory represents a potential clinical risk. In the absence of clinical details, optimal test and media selection, susceptibility testing, and result reporting cannot be guaranteed by the laboratory.”

By the end of this year we hope to have introduced a policy of mandatory clinical details in order for laboratory testing to proceed. However, “critical” or “difficult to get” samples such as knee aspirates are always going to have to be exceptions to such a policy. We cannot reject a knee joint aspirate, just because we don’t know the story behind it…

This is a bit of a shame really because ironically it is these types of samples where the clinical details can potentially have the biggest impact on microbiological processing.

And there will always be a small minority of clinicians that will grumble at having to put clinical details on the request form.

Such grumbles are for me however, simply water off a duck’s back…

Michael

“Are you doing what you should be doing?”

If you are a microbiology scientist and spend a good chunk of your day setting up samples and aliquoting urines, you should be worried. I am sure you didn’t go and spend 4 years in university in order to do this.

If you are a clinical microbiologist and spend a good chunk of your day signing out/authorising routine urine and wound swab results, you should be worried. You didn’t achieve multiple degrees and other qualifications to do this day in day out…

If you are a microbiology technician, and spending a good chunk of your day unpacking boxes and carrying stuff around the lab, you should be worried. Someone off the street could easily come and do this…

And if you are a microbiology lab manager and find yourself spending a good chunk of your day on the bench, you should be worried. Old habits die hard, and who then is managing the lab?

Of course we all need to do things occasionally that we are over-qualified for, or that is not specifically in our job description. But when such tasks are taking up a large proportion of our jobs, we need to take a close look at ourselves, and what we are actually doing from day to day.

We need to make absolutely sure that we are performing tasks that justifies both our position and our qualifications. If we are not, then we need to do something about it.

If you spend most of your day doing something that is likely to be automated a few years down the track you should be concerned. But if you are doing lots of  things daily that could be getting carried out by someone else less qualified, you should be even more worried.

It is easy to get very comfortable when you fall into one of the categories above “This is easy money, I can do this with my eyes closed, there is no need to change anything.” It’s a dangerous mindset to get into however, because in my experience, such scenarios as described above are never left hanging indefinitely in the long term…

Diagnostic medical laboratories are businesses nowadays, and employers are always on the lookout for ways they can get the same job done for less money.

And they are very good at it…

Michael