Category Archives: Confessions of a Microbiologist

“Putting your job into perspective”

My baby daughter recently had open heart surgery at just two weeks of age, to repair a serious congenital heart defect (Tetralogy of Fallot). She was desperately sick in the days leading up to the surgery, and required several weeks of convalescence afterwards.

They don’t like doing open heart surgery at such a young age, but decided that this was the lesser of the evils…

On the day of the surgery she was really struggling, despite being in intensive care on maximal therapy. I never thought I would be glad to see my daughter wheeled off to theatre to be put on cardiac bypass.

Fortunately everything went well, and she is now 10 weeks old. She is doing all the things that 10 week old babies should be doing. Except for the scar on her chest, you would not even know what she has been through.

She is, quite literally, a little miracle.

Now things are getting back to normal. I am back at work, and able to think clearly again.

During the long days and nights in the neonatal intensive care unit, my microbiology job was the furthest thing from my mind.

But the whole experience has helped me put my job, and to a large extent my career into perspective.

And I am very aware that my family and I are not the only ones who have been through the emotional wringer. Most people have had major life events at some time or other; bereavements, births, severe illness, redundancy, divorce, etc., etc.

We all have our struggles…

So in future, whenever my workload is starting to feel heavy, I will think to myself “Compared to recent events in life, this is a walk in the park.”

And whenever I am asked to take on extra responsibilities, I will think to myself “I have a young baby to look after and care for. What work responsibilities can possibly be greater than that?”

And if I need to take the odd risk in order to develop and progress the microbiology department that I work in, I will think to myself “This is not a life or death situation. What is the worst that can happen…?”

Sometimes our mind plays tricks with us with regards to the challenges we face at work, to the degree that they start to become stressful and all encompassing.

When work life gets tough, then reflect on your other life, the more important one, and put your job into perspective. 

Michael

“The Introverted Microbiologist”

I am quite far to the left on the introversion/extroversion scale.

And maybe that is why I am a microbiologist…

I have always been a bit of a loner, a dreamer, a wanderer, and most days I need and crave a lot of time by myself. I guess I am a little anti-social, and much prefer talking to people one on one, as opposed to being part of a group conversation.

On occasion my introversion borders on misanthropism, but don’t take it personally. Such feelings never last long.

I hate the idea of networking with strangers at conferences. That is anathema to me! On the contrary I thrive on the amount of time I can get to myself during conference leave. Maybe that is why I am attracted to large “anonymous” conferences such as ECCMID, where I can disappear unknown into the crowd…

You can get away with being an introvert as a microbiologist, regardless of whether you are a scientist, a technician or a clinical microbiologist. Our jobs mean we do not necessarily need to be face to face with other people for large parts of the day. Obviously you need to be able to communicate, but there must be a lot of other professions where a degree of extroversion would be more useful than in microbiology…

I don’t think I am the only microbiologist that is introverted. I look at my colleagues and I can see similar characteristics in many of them, just maybe not to the same extent as myself. It reassures me that I am not the only one!

Sometimes I can override my tendency towards introversion. My desire to have my opinion heard can often conquer my natural reluctance to speak out, particularly when I am in familiar company. I am also not afraid to take risks and try new things out in the microbiology laboratory. My low boredom threshold and innate need for change often overrule the introvert’s need for a “quiet life”. An introvert is not the same thing as a luddite.

However my displays of extroversion are often forced, and short lived in nature. I always end up veering back towards introversion.

So I embrace my introvert personality. I am supremely confident in my ability to be a competent and influential microbiologist in spite of my introvert tendencies.

I might be quiet, but underestimate me at your peril…

Michael

“Nothing is perfect..”

Apologies for the paucity of posts recently. I have had an unwell child.

MALDI-TOF (Matrix Assisted Laser Desorption & Ionisation- Time Of Flight) has revolutionised microrganism identification in the past decade, and in particular bacterial identification in the microbiology laboratory. It will continue to evolve into fields such as filamentous fungi, mycobacteria, antimicrobial resistance etc.

Rarely has such an innovation been so rapidly and comprehensively adopted by the laboratory community. And you can see why. It’s quick, it’s easy, it’s cheap (the consumables are anyway) and it’s reliable.

But it’s not perfect….

Some well known identification limitations are listed below where MALDI-TOF struggles to give the microbe a label, or at least one which fits in with our pre-defined beliefs.

Take the following well known, and not so well known examples…

  • E. coli and Shigella species
  • Streptococcus pneumoniae and Streptococcus mitis
  • Bordetella pertussis and Bordetella bronchiseptica
  • Klebsiella oxytoca and Raoultella ornitholytica
  • Shewanella putrifaciens and Shewanella algae
  • Proteus vulgaris and Proteus penneri
  • Klebsiella pneumoniae and Klebsiella variicola
  • Haemophilus haemolyticus and Haemophilus influenzae
  • Serratia ureilytica and Serratia marcescens

There are many more. Please feel free to suggest others that you have come across. There will be even be differences between different MALDI-TOF platforms, e.g. Bruker and VITEK MS.

Most of the time it does not matter too much from a clinical point of view. Some of the time, it does, and we need to try and clarify with molecular or biochemical means.

It shouldn’t surprise us however that the identification is not perfect. All identification systems are essentially typing systems in disguise, and they all have databases or libraries at the core of their function..

  • “APIs” are a typing system based on biochemical reactions.
  • MALDI-TOF is a typing system based on proteonomics.
  • 16SRNA sequencing is a typing system based on nucleic acid sequences.

Identification systems therefore suffer from the inherent problems of all typing systems. No typing system can be matched exactly against any other typing system.

For all typing systems the ability to group isolates and the ability to discriminate them is a trade-off of sorts. For MALDI-TOF, the bigger the databases get, the more the system can discriminate, and thus the more it can potentially differ from the original (textbook) identification.

So no system is perfect, including MALDI-TOF.

But it’s very, very good….

Michael