Infection- 3 basic principles most of us fail to understand

Apologies for not writing on here for a while. Those that follow me on Instagram will know I’ve been working 6 day weeks at the moment, trying to catch up with my research now that I’m back on full time clinical.

I’m really enjoying my clinical job at the moment and I’m certainly learning a lot. I take calls for microbiology from medical staff in and out of the hospital. Usually these questions relate to choosing antibiotic therapy for patients. In my short time as a registrar so far it has occurred to me that most of us leave medical school with a very fuzzy understanding of treating infection (myself included). So, I’m going to teach you guys the 3 key things to understand when you’re dealing with infection cases and trying to learn microbiology…

  1. It’s usually the right organism in the wrong place

This is one of the most important things to realise early on.  As humans, we are literally teeming with microbes, many of which actually help us to function. So long as they stay where they should do that is. With the exceptions of human to human spread and infections such as anthrax and tetanus (infections that come from the environment), most infections in patients are caused by their normal microbes (‘flora’) getting into a different part of body. 

The simplest example, and the one I think most people grasp, is urinary tract infections (UTIs). Most of these infections are bowel flora that make their way into the urinary tract and thrive. It’s why they are common in women- our anatomy doesn’t leave much of a….divide, shall we say? But even when they get there, they don’t always cause infection, sometimes they just live there happily and don’t bother you. (It’s why we Infection doctors get so irritated when people treat off a dipstick in an asymptomatic patient. It CAN be normal; we call this “colonisation”.)

Like I said, most medics understand this principle with UTIs. They seem to forget to apply the principle to other infections. If you have a ‘bowel’ bug swimming around your bloodstream, that’s either going to have got there from a nasty UTI or from the abdomen (often gallbladder). If you have a Staph aureus in your blood stream, you should be looking at skin sources.

Once you grasp this principle and apply it, you are already in a much better position to be caring for your patient.

2. Choosing your antibiotics- think of your “Grams”

When you ring microbiology for advice, they are usually asking a million questions to try to work out point 1- where is this infection coming from? Point 2 is about then choosing appropriate antibiotics. The way to think of this broadly is, ‘Are you trying to cover Gram positive organisms (live on skin and some in bowel); Gram negative organisms (mostly bowel/urine) or anaerobes (this is an arbitrary distinction but explains the thought pattern- we tend to cover these in bowel issues and bad skin infections)?’

A great example for this is a regimin that most hospitals in the UK use for intra-abdominal infections first line:

  • Amoxicillin (has very broad cover but I think of this as being there to cover my gram positives like enterocci that are sensitive; if they aren’t then you’ll find that we often substitute this for another Gram positive-hitting antibiotic eg Vancomycin).
  • Gentamicin- has very good gram negative cover.
  • Metronidazole- is pretty much THE anaerobic cover.

It’s why we’re flabberghasted when doctors leave people on metronidazole monotherapy too by the way… except for C diff and some parasitic infections, metronidazole monotherapy is usually not the answer to your patients’ problems.

So, we choose antibiotics based on 1. their spectrum of activity for what we’re trying to treat and 2. how well that antibiotic gets into that part of the body.

3. There’s no such thing as “strong” antibiotics

My approach to most colleagues calling that ask ‘silly questions’ is that they’re not silly. After all, I’m very much still learning and they often ask things that I can learn from. However, I have been frustrated by early morning calls from people essentially asking for piperacillin/tazobactam (pip/taz or ‘Tazocin’) when the antibiotics they need to give are in the drug chart- they just think the antibiotics are not ‘strong enough.’

This way of thinking is the poorest and part of the reason that we are concerned about the Antibiotic Armageddon.

Think about Pneumonia for example. A patient comes in unwell with a low blood pressure and a high lactate. CXR and bloods confirm a Community Acquired Pneumonia with a CURB score of 4. This is a scoring system that shows that this patient is severely unwell. Many UK hospitals use Coamoxiclav and Clarithromycin for CURBs of 3 and above. But this patient was “really sick” when they came in- maybe they should get pip/taz instead?

WRONG!! ****tears hair out and sobs at being called for this***** 😀

The antibiotic guidelines in hospitals are written partly according to the senior’s preference and partly due to the spectrum of microbes that cause infections in that hospital’s population. Coamox and clari are brilliant for most CAPs because they appropriately target the microbes causing the infections. Pip/taz is not ‘stronger’ it is broader- it covers more organism but that’s not necessarily what’s needed here (it usually isn’t).

So why do we use pip/taz when patients have Hospital-Acquired Pneumoniae? This brings us full circle to point 1- after 48hrs to 5 days of being in a hospital, patients’ normal flora in their mouths/throats often change. Which means they require an antibiotic with a different spectrum of cover because the microbes causing the infection are not the usual ones in the community.

We are working to reserve antibiotics with the broadest cover as a last resort. We’re not been miserly by controlling who gets pip/taz or meropenem. We are protecting the broadest-covering antibiotics that we have, for the sickest patients. Get rid of the notion of the antibiotics not being “strong” enough from your heads. You are looking for antibiotics that cover the organisms causing the infection. So if your patient isn’t getting better on a regimin of antibiotics then yes, talk to us- between us we can work out what will give your patient the best (and hopefully most targeted) cover.


Hope this helps. I think these principles really are the key to understanding the treatment of infection. Students get really bogged down with mechanisms and pathology but they often come away not realising these 3 principles above. Once you’ve understood this, you will be much better at treating your patient and be able to have much clearer conversations with your infection team!!


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