Monthly Archives: September 2017

“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…



“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.


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.


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