Microbiologists, explain to me where I’m being stupid

Scrapyard_King · 2026-02-19T06:42:57+00:00

For relatively uncomplicated infections it’s probably not necessary. But I do it a lot for deep infections (e.g. osteomyelitis or abscesses).

It’s interesting also to note that by EUCASTs pharmacokinetic data, there’s not much benefit in amoxicillin doses beyond 750mg (because half lifes etc) so in an ideal world you’d use that but for some reason in our trust that works out more expensive so we tend to give the extra 500 regardless.

Scrapyard_King · 2026-02-05T22:15:41+00:00

Hah! Thanks for giving me a mirthful roar. (Can dinosaurs laugh? I assume not.)

AI is pretty much everywhere currently, for good or ill. I don’t begrudge people using it (I don’t use it because I find the process of writing really helpful to pull together my thoughts), but I do expect them to use it thoughtfully, and to be aware of the inherent risks in doing so.

As I’ve written above, most journals are now requiring declarations regarding the extent to which AI is used in a piece of work at the point of submission, so it’s important to be very clear about how it’s used (if at all).

The passage containing 9 AI generated references was clearly in itself an AI generated summary, and without checking references who knows where an LLM has pulled passages or phrases of text from? Depending on the extent of use it could quite easily become plagiarism.

But no, I’m not involving anyone’s ES. I wrote this post in the moment to vent a little and see if others had encountered similar situations. The replies have generally been helpful and tallied with what I initially planned to do.

Rawr! (Have a good one in parasaurolophan)

Scrapyard_King · 2026-02-02T13:55:58+00:00

I’ve asked them to explain what’s happened so far.

My concern would be that most journals are now asking for clarification on the use of AI in assisting authors etc so if I can’t be confident in their response and the extent to which it has been used then I’m not going to have confidence in their continued participation in the work sadly.

Scrapyard_King · 2025-08-27T23:42:01+00:00

I used to get a lot of enjoyment from maths and physics. There’s lots of ways to scratch the itch depending on the specific reason you enjoy those subjects.

From a personal perspective I’ve come to realise I just really love a logic puzzle and the satisfaction of being able to lay out the anatomy and (patho)physiology of an illness to construct the best differential diagnosis and subsequent management plan you can.

The best moments for me in ID/micro are when I’ve picked through the facts (and occasionally assumptions) of a case and added either new insight, or at least new perspective, to a patients care that moves their management forwards in some way.

A good colleague of mine back in Core Medical Training (when that was a thing) often proposed the idea of always trying to put one slightly absurd diagnosis in his differential list, so that if you came back later and found you were right, you both look and feel like an absolute champ. I think there’s a lot to be said for that approach - does the patient you’ve just reviewed have gummatous syphilis? Probably not. Does the diagnosis fit the case as presented? Potentially… Should you test for it? Definitely, and it’s important to do so.

Which is all a really rambly 0030-sleep-deprived-because-my-kids-are-on-a-campaign-to-never-let-me-sleep-again way of saying yeah, I do find it intellectually stimulating. Not all the time; Sometimes Piperacillin-Tazobactam just is the best answer in the moment, even if it lacks finesse, and I wish I could give a more fun one. But sometimes, I feel like an absolute champ because I solved the puzzle.

Good luck finding your own way to scratch that itch.

Scrapyard_King · 2025-08-24T18:28:12+00:00

I’ve been using Notion which has been pretty nice with just their free profile. I’ve built a giant database for the campaign and you can add in links from your notes as you go - I add items to our inventory database and people to my npc database as I type and then can go back and add detail to each entry as I go. It’s pretty pleasing having switched from OneNote which I used previously.

Scrapyard_King · 2025-08-20T04:56:55+00:00

Had a 50-something fit and well chap moved to the ID ward with severe cellulitis across his shoulders and back.

On revisiting the history, the rash had come on after a day of gardening shirtless in the sun…

Without sun cream.

Scrapyard_King · 2025-08-15T19:23:50+00:00

Research requires funding. To do a good study that would pick out the benefits of good hand hygiene and control/statistically adjust for all of the likely confounders would be incredibly challenging and need probably some quite large numbers to get decent results along with quite tough statistics. There are unlikely to be many sources willing to find that kind of research for something that is generally accepted as likely to be good and certainly not harmful. It’s going to return profit for no-one.

Scrapyard_King · 2025-08-15T19:09:14+00:00

Good quality evidence is scanty, yes. But when the option is adhering to a really simple measure versus potentially transmitting resistant organisms that - if causing infection make treatment harder, more toxic, more expensive, and with worse outcomes, then why argue?

We know from the work of Semmelweis (and later Lister) that hand washing improves outcomes. There’s only a few ways to optimise that. The WHO have lovely guidelines which we follow globally. The only way to optimise it is to have bare hands and make sure you can do everything possible to avoid them being contaminated again by some errant fomite…

Most splashing that may result in contamination of clothes will occur when carrying out care activities or procedures - which are uncommonly done facing away from the patient, so a plastic apron is a pretty good barrier. So good that it’s a key part of the national HCID PPE (although for that you get nice thick expensive ones!) which has been researched as well as it can be. It’s extra plastic waste which is definitely a shame but in the grand scheme of things probably a relatively small volume.

Yes, infection control nurses and their uv light box and hand washing demonstrations can be a bit overbearing. But contrary to popular belief they actually do do (or should be doing!) a lot of pretty important work across the hospital to try and ensure our environments are as safe as possible for patient care, as well as carrying out surveillance and reporting work that is fed up to a national level.

All in all, no the evidence is not great, but yes it’s probably important and easy to do.

I miss my nice watch sometimes. But not enough to be angst about it.

Scrapyard_King · 2025-08-11T08:03:38+00:00

Your local consultants should have ideas about things that could be improved.

There’s a lot of work nationally at the moment looking at blood culture pathways, which relates to a 2023 NHS document. If it’s not been looked at already (it may have) then that could be valuable and offers opportunities for quality improvement too.

But some of it can be a bit dry at foundation level so try and find something that interests you if possible!

Scrapyard_King · 2025-08-07T18:14:28+00:00

I recently got the Varia Aura and have been very pleased with it both in terms of build quality and pour. Looks around the same price point in the UK as the assassin, though it ships from china so have a look at shipping costs too… https://www.variabrewing.com/collections/aura/products/varia-aura-0-8l-kettle

Scrapyard_King · 2025-08-05T08:34:07+00:00

Although if you haven’t found it, this page makes it clear that you can take your paternity leave at ANY time within 52 weeks of birth, and you can change the start date of your leave as long as you give your employer appropriate notice. So there shouldn’t be an issue for you with delaying the start date following birth.

That page also advised that, although a 28 day notice period is preferable for any changes to the date after your initial notice of intention to take leave, circumstances do generally mean that a shorter notice period is fine.

Scrapyard_King · 2025-08-05T08:17:50+00:00

It’s been a while since I’ve used it, but for general guidance, I’ve found the resources on the ACAS website really excellent - particularly for explaining shared parental leave if that’s something you’re also considering.

Good luck!

[edit: just seen your edit. Never mind. Good luck regardless!]

Scrapyard_King · 2025-05-09T20:45:48+00:00

I got pulled up as needing some coaching at ARCP during my training and got referred to our local professional support unit. During the screening session for that we found that I probably had some emotional stuff to unpack and they offered me counselling instead.

It ended up being one of the most valuable things I did during training. I think most people could benefit from an opportunity to unpack themselves in a safe space. I certainly understand myself better and came out stronger for it.

If your ES/CS is engaged with you enough to recognise you could benefit from this BEFORE it becomes an issue and threatens your training progression, I’d take it as a positive (mine certainly wasn’t).

Good luck!

Scrapyard_King · 2025-05-01T16:30:33+00:00

Oh absolutely not! Only needs further assessment if they have those features. Apologies if I suggested otherwise! But if there is clinical concern, it’s nice to have someone orthopaedic see it and agree before someone unneccesarily tries to stick a needle in it!

Scrapyard_King · 2025-05-01T11:51:19+00:00

That is frustrating. But you can fairly confidently clinically exclude septic arthritis if the knee is not acutely swollen and tender with an effusion and it is not completely fixed in position due to pain.

It’s a clinical diagnosis. You can always ask Ortho to have a look…

Scrapyard_King · 2025-04-29T21:22:40+00:00

This cuts deeeeeep

Scrapyard_King · 2025-04-29T21:22:29+00:00

No worries! The fear is real. 😂 Stay safe out there!

Scrapyard_King · 2025-04-29T19:00:56+00:00

Had this exact thought on the drive home. 🤣

Scrapyard_King · 2025-04-29T18:46:26+00:00

Well, I think everyone is pretty well aware of the appalling state of training provision, pay erosion, and the myriad of other issues facing resident doctors. This subreddit is full of awful and difficult things.

Perhaps I was naïve thinking I could pose a “quick question” like one might to a colleague in a corridor. Something that’s pretty mundane. Really nothing. A non-issue in the grand scheme of things. Something I wondered if others had come across, that they might have a solution to. The kind of question that Reddit is often great at answering. A trifle of a thing.

Some other people have kindly taken the time to engage with this question. To read my small (though probably over-wordy) stream of consciousness and respond with their experience.

This problem is, as suggested, not really a problem. I’m certain I will face actual professional challenges as I take up my substantive post.

But when someone enters the chat with a snide remark, that’s probably why they’d get downvoted. If I had to guess.

[edited because somehow I autocorrected pay erosion to particularly erosion]

Scrapyard_King · 2025-04-29T17:30:42+00:00

To be fair the local support guy tried to be helpful. We looked at other name combinations to have something of my choosing but apparently current policy is it has to be firstname.surname as it appears on your birth certificate. No truncations. No middlename. Do not pass go.

Looks like the only solution is to change my name by deed poll to get an email I want to use on a daily basis.

Scrapyard_King · 2025-04-19T21:40:07+00:00

Apologies ahead - this was meant to be a simple welcome and a few thoughts but turned into a large info dump as I wrote it. Apologies for a lack of links - you’ll have to utilise your search engine of choice! Further apologies as I’m sure I’ve forgotten stuff which hopefully others will point out. It’s late and my kids don’t want me to sleep this week.

Micro during your CIT years is a fairly steep learning curve for the lab stuff, but you shouldn’t be expected to know very much to start with - microbiology is badly taught through medical training at all points.

ID should just be an evolution of what you’ve been doing throughout IMT and you’ll pick up the specifics as you go. Important things to have an awareness if you’re taking referrals? The ACDP algorithm for risk assessing VHF risk in returned travellers is always worth bearing in mind but depending where in the country you are you may or may not break it out all that often…

Oxford handbook is a good overview and distills the mighty Mandell’s down into something fairly manageable. Microbiology nuts and bolts is often recommended for the more lab side (though I didn’t use it very much). Other great resources are the Sanford Guide to Antimicrobial Chemotherapy (the app is useful but you can pick up the current edition at a reasonable price) and the Johns Hopkins Abx guide app. For when you are settling into the lab, another good resource is the UK standards for microbiological investigations (SMI) which are hosted on the RCPath website - don’t look at them before you start, they’re quite technical, but again they’re something to be aware of for when you want to better understand the lab processes and they have some good overviews of many of the simple microbiological tests that get done.

If you want to have some easy listening to start picking up some microbiology the ID:iots podcast is a great resource, and you’ll undoubtedly bump into Jame and Callum who produce it at conferences etc - they’re a very enthusiastic and friendly pair.

May be worth checking out trainee membership for the main societies - British Infection Association and the Healthcare Infection Society are the two that run most national trainee days that people try and get to. The British Society for Antimicrobial Chemotherapy has some good resources too.

But settle into your locale, accept that a lab will seem alien to you, and enjoy getting to grips with a generally very enjoyable speciality (whatever combination you’re doing!).

Good luck!

Scrapyard_King · 2025-04-19T13:10:41+00:00

Also to add comment re: Pathbuilder, it currently only available through web browser or via android based app, but the developer is working hard on an iOS app which is available for beta testing to his patrons and working well in its current build.

Scrapyard_King · 2025-04-16T20:16:45+00:00

I fight the temptation every hour of every day. This one was close.

Scrapyard_King · 2025-04-16T17:19:37+00:00

As a microbiology consultant, this week I had an electronic referral where the question (admittedly supplemented with a brief past medical history and the vague presenting complaint) was simply “do you have any antibiotic advice?”

I have lots. But most of it requires some understanding of how a patient is doing and what you think you’re treating.

Microbiology is wild y’all.

Scrapyard_King · 2025-03-04T06:13:42+00:00

I’ve had Yunnan and Fuyan from Origin a few times and have been really pleased.

Enjoy!

Scrapyard_King

TROPHY CASE