Clinical bioinformatics for microbiology

A week or two ago I went to an interesting meeting about the clinical bioinformatics training scheme. This is a clinical scientist training programme, akin to those that train clinical geneticists and microbiologists. The first cohort of 13 students are currently making their way through the scheme.

I had a look through the curriculum after the meeting and thought it might be useful to write a quick post about my thoughts.


Firstly, it is a very thorough and demanding curriculum (the details start about 50 pages into the document). During the three year scheme (which consists of taught modules and ‘experiental’ learning, pedagogues really like their jargon) you learn a broad range of bioinformatics skills, including variant calling and interpretation, web design and image analysis (for medical physics).

For me, the thing which leaps out is the near total absence of anything microbiological. The clinical bioinformatics training scheme has clearly been conceived with human genetics in mind. I don’t have a problem with that, human genetics is going to be a (the?) major use case for NGS in the NHS. It is also closely aligned with the 100000 genomes project and the Prime Minister’s plan for The UK to ‘unlock the power of DNA data‘.

However, I do think that NGS is going to be a major tool in clinical microbiology within the next few years (months? weeks? days? ;-)) and that needs to be acknowledged in the training scheme. Due to the small amount of overlap between human genetics and bacterial genetics, and the already crammed syllabus, I think that there would need to be a subset of people on the training course who were specialising in microbial bioinformatics. Perhaps 10%?

Interestingly, there is a hefty amount of IT in the syllabus. Almost makes you think that the NHS wants clinical scientists who can contribute to technical discussions concerning an area which has been something of a scandal factory for the them.

Bioinformatics is going to get closer and closer to the clinic and we need to be prepared with well trained clinical scientists who really know their assemblies from their alignments. From what I can see, this training programme is a great start for the human biology side. Now, all we need to do is consider the small things.


3 thoughts on “Clinical bioinformatics for microbiology

  1. As one of the trainees I completely agree. I have just spent a month at the PHG foundation on my health informatics rotation. I was working on the infectious diseases project ( trying to map communication flow across clinical microbiology.

    I previously worked in cytogenetics and until last month had no idea that ngs is used elsewhere in the nhs and can see how useful it would be to have some training in microbiology or for microbiology to be a strand on bioinformatics similar to the health informatics and medical physics strands.

    • Thanks Aled! I think that there is a lot in the current syllabus that would be relevant (health informatics for e.g.), but that there should be some optional modules or two different streams within it.

      I would be interested in your thoughts on your future job role when you graduate. Considering it is a completely new qualification, might be a bit daunting!

  2. Pingback: Clinical bioinformatics for microbiology | Viral Bioinformatics Resource Center

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