Celebrating National Pathology Week: What is a clinical microbiologist?

To celebrate this week being National Pathology Week , I thought I should take some time to post about what a clinical microbiologist is. I do this because, when I was at university, I really didn’t know that this career path existed. So here is a shout out to all those students who are trying to decide their next steps. You too will find your way.

When I googled microbiologist this is the first item that comes up

Microbiologists study microorganisms (microbes) in order to understand how they affect our lives and how we can exploit them

Prospects.ac.uk

This seems like a pretty good cover-all description. It goes on to discuss that there are microbiologists in many different areas:

  • medicine.
  • healthcare (I’m not sure how they differentiate this from medicine or visa versa).
  • research.
  • agriculture and food safety.
  • environment and climate change.

I must admit that when I was at university most of the options I encountered were linked to the food and drink industry or pure research. I think that their list missed things like Pharmaceuticals (although they may count that as medicine) and other forms of production, i.e. cosmetics.

At university I only did one module of microbiology (I was reading Zoology) and that module was about environmental bacteria and plating out bacteria onto agar plates to see what grew.

How did I go from Zoology to Microbiology?

I really wanted to work in an area of science where I could work to make a difference. I wanted to work somewhere that I could see that difference being made. Working in research felt too abstract to me. When I discovered, through a friend, that I could become a scientist in healthcare I knew it was what I wanted to be.

The National Careers service says you need to have two to three A-levels to become a microbiologist, plus a post-graduate degree. That is mostly true. However, in a world of apprenticeships and T-Levels, that is no longer the only route.

When I became a Healthcare Scientist I became a Clinical Microbiology trainee. So, what was the difference between that and what I’d done at University? The main difference with clinical microbiology is that I focus on organisms that cause infection: parasites, viruses, fungi and bacteria.

I also discovered that there was so much more to microbiology than agar plates. Although – don’t get me wrong – agar plates are still a mainstay of life within the bacteriology laboratory.

One of the techniques I learnt to love was polymerase chain reaction (PCR), which enables us to look for the DNA or RNA of a microorganism instead of growing it. Viruses and parasites don’t grow on agar plates and bacteria and fungi may not grow well if exposed to antibiotics or if present in low levels. PCR allows us to diagnose patients with infections that would not be diagnosed otherwise, or to speed up the process so patients get put on the right treatment faster.

Variable number tandem repeat typing of Klebsiella pneumoniae

PCR also enables us to do things that are harder to do using traditional bacterial techniques such as culture. The picture is of patterns that are like bacterial fingerprints so that they can be clustered into similar groups. This enables me, as a clinical microbiologist, to tell whether bacteria within the same species are the same or not. This is important when deciding whether a bacteria has spread from one patient to another. It helps in acting like a hospital detective, which is a lot of my work in Infection Prevention and Control.

As a trainee I spent four years rotating within laboratory settings. I spent one year in a molecular laboratory, diagnosing patients using PCR. I then spent six months rotating between benches (each sample type has its own laboratory bench) in bacteriology: wounds, respiratory samples, faecal samples, blood cultures, urines, fluids (cerebral spinal fluid etc.) and the primary bench where samples were put onto agar plates. Six months in virology, a year in research and time in food and water, parasitology and mycology (fungal) labs.

The diagnostic process is pretty similar in principle between the specialisms:

  • collect specimen from possible site of infection.
  • select the most appropriate test to detect any organisms (agar plate for bacteria, PCR primers for viruses, etc.)
  • evaluate whether the result (positive or negative) is accurate and whether there are other tests that should be done, i.e. further characterisation of positives such as antimicrobial sensitivity.
  • decide on treatment or management of the infectious cause, i.e. antimicrobials or non-antibiotic management such as surgery.
  • advise on infection control if actions are needed to investigate where the infection came from or to protect others from risk.

During my first four years I spent most of my time in the laboratory doing the first three bullet points.

Time goes on. I’ve been in the NHS for 17 years. Most of my time is spent at my desk in the on-call bathroom. Since 2010, most of my time has been spent either in Infection Prevention and Control undertaking the final bullet point or increasing my skills by gaining Fellowship of the Royal College of Pathologists to do bullet point four.

I still support the lab and, occasionally, get my lab coat on – but not as much as I’d like. It is, therefore, possible to be a clinical microbiologist and be anywhere on the spectrum. You can go as far as you’d like and do the type of work that makes you happy. It’s why being a clinical microbiologist is a great career!

Modernising Scientific Careers Framework

All opinions on this blog are my own

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