Category Archives: Confessions of a Microbiologist

“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…


“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….


“A paradigm shift…”

At the moment most antibiotics are initiated without waiting for the microbiological result, if they are thought to be clinically necessary.

Quite right too.

This is so called “empirical therapy”.

There is a good reason for this. Traditionally, microbiology tests have neither been good enough nor fast enough to make the antibiotic prescription dependent on the result.

Take for example the patient who sees his GP with a productive cough and fevers. The GP is not going to say to the patient “Let’s just wait a few days until we get the sputum culture result back. By the way there is a good chance it will be negative even if you do happen to have a pneumonia. And on the flipside, if it does grow something it might just represent the bacteria in your throat.”

No chance…, the GP will simply prescribe an antibiotic based on the most likely pathogens, and also the local antibiotic susceptibility patterns.

Along the same lines, the GP is not going to say to the patient a couple of days later. “Your sputum sample has come back negative, so let’s stop your antibiotic.” Sputum cultures are nowhere near sensitive enough to allow this approach.

On the very odd occasion, the treatment will actually change as a consequence of the microbiology result, if there happens to be an unusual or resistant organism.

And sputa are only one sample type. Ear swabs, peri-anal swabs, & ulcer swabs probably have even less impact on patient management…

In fact for the vast majority of  samples (probably > 95%) that get processed by the microbiology laboratory, the impact on patient management is rather small indeed.

However change is coming on to the horizon. The newer microbiological tests, and in particular the polymerase chain reaction (PCR) assays, are both fast enough and sensitive enough to start genuinely impacting on patient management right at the time of prescribing.

Take the following potential examples:

  • Macrolide antibiotics could be witheld in a patient with suspected whooping cough until the Bordetella pertussis PCR is back.
  • Patients with urethral discharge and suspected gonorrhoea would only be treated if the Neisseria gonorrhoeae PCR result comes back positive.
  • Patients with meningo-encephalitis could have acyclovir to cover HSV, dependent on the CSF viral panel result.
  • Legionella cover in a patient with moderate to severe community acquired pneumonia could be dependent on the result of the Legionella PCR in a sputum sample.

These are all tests which, if performed quickly enough, can significantly reduce the amount of antibiotics given to the tested cohort, so they all have potential to play a big part in any antimicrobial stewardship program.

So we need to get such assays into our microbiology laboratories, whatever it takes.

Microbiology matters, but we need to ensure that we utilise new tests and technology to make it matter even more…