STP Specialisms | Clinical Microbiology

First things first, if you are going to take on the wonderful world of clinical microbiology as an STP, you need to be okay with things that smell. Sometimes they smell nice, certain species of Streptococcus smell like caramel; sometimes not so nice, I dread opening the fridge at work where we store all our C. difficile culture plates. If you can get past the smell, you’ve jumped the first hurdle of microbiology! Well done!

So other than invest in a lot of clothes pegs and Vicks vapour rub, what do I do as a Clinical Microbiology trainee?

Year 1

The first year laboratory rotations are Virology, Molecular and Bacteriology. These are mostly spent at each bench learning the basics with the laboratory assistants and then learning to record and report results accurately with the biomedical scientists. Key skills are reading culture plates, disc diffusion sensitivities and good molecular laboratory practice. You also learn what organisms are significant for different sample sites and which patient groups might need more than routine testing; similarly when results should be escalated to the clinical teams.

Epidemiology is much less laboratory-based. In my case, I visited the Field Epidemiology Services and Health Protection teams for the South-West. This rotation is all about surveillance of infection and public health action. You look at outbreak response, routine surveillance, prevention, monitoring and the implications of different pathogens in the context of public health.

The purpose of the first year rotations is to understand how patient results are achieved so that when you are looking to give clinical advice, you are familiar with the process, relevance of results and how they apply to a specific disease.

Year 2 & 3

Your knowledge is extended into clinical practice looking at high-risk patient groups, healthcare-acquired infections, and further laboratory work in parasitology and mycology. These are designed to lead to wider understanding of the role and burden of infection in healthcare, in a local and global context. Antimicrobial resistance is always a hot topic, but is also covered within our rotations, through infection control and laboratory monitoring.  As a second year you’ll see more clinical practice; attending MDTs and contacting hospitals, health protection teams, and other microbiology laboratories with results and advice. We tend to be much less patient facing than some other disciplines, but there is still the opportunity to sit in on patient clinics relating to our specialism.

There’s a lot to remember, with better techniques for identifying pathogens, the list of significant organisms gets longer every year. However, now is an exciting time, as infection sciences is following the personalised medicine trend with more emphasis on host factors and microbiomes. We’ll all be working closely alongside immunologists, geneticists and bioinformaticians in the future to improve patient outcomes.

When you emerge as a fully qualified clinical scientist at the end of your third year, there are a few options open to you career –wise. Remaining in microbiology as one of the clinical team, or working as a health protection practitioner are both great options. You can also go into research or development; we have several clinical scientists responsible for the development of new in-house assays.

I hope that this has given you a short insight into Clinical Microbiology, it’s a fascinating specialism. Just don’t try and talk about it over dinner….

Author: H Pymont

STP in Infection Sciences

4 thoughts on “STP Specialisms | Clinical Microbiology”

  1. Hello,
    I just want to say thanks so much for this post, it has been very helpful to me! Do you think I could email you to pick your brain a little more? I am very eager to get on this specialism!!
    Many thanks


  2. Hello!
    Thank you for the post. My friend is interested in this specialism and has tried to leave a comment that won’t work! Would you mind her asking you a few questions over email please?
    Many thanks


  3. Hi Megan,
    Yes I’d be happy to answer her questions.
    I think my email should appear to you in the reply in your inbox, if not I have your email address from your post and will send it directly to you.


  4. Hi 🙂
    I am looking to apply to clinical microbiology STP this year and was wondering if I could ask you a couple of questions?


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