There’s a story playing out over the news channels that is causing me some distress. There is an alpaca on death row who has tested positive for tuberculosis (TB) and therefore been sentenced to be culled as he poses a risk to other animals… He’s called Geronimo and he’s cute!
I have been asked this question a lot recently… maybe people are tired of being on the frontline and they want to escape to a quieter environment or do something else… you are not alone either, quite a few of our friends and colleagues from overseas have also asked. Maybe it’s the impression I give that I have my feet up on my desk, take too many tea breaks or have the time to go and hunt for a box of hospital chocolates to raid!?
It is a common mistake to think that if you pass the right exams you can become a Clinical Microbiologist; it isn’t that simple. Believe it or not, passing the exams is the easy bit!
But before we get into all-of-that let me just tell you what a Clinical Microbiologist does… although if you ask the ECIC she’ll just say “drink coffee and eat cake!”
Bats are getting a hard time at the moment. They seem to be being blamed for all of the infections threatening our species, from Ebola, Marburg, Rabies, Nipah, Hendra and now SARS Cov2. The name for these animal-related human infections is zoonoses. I can just imagine the bats cringing every time the news comes on wondering what they’re going to be blamed for next.
You have to admit, it’s not great PR to be associated with the scariest viruses known to cause deadly human infections. But is this fair? Are bats really MORE likely to be the source of infections in humans? Do bats harbour more nasty viruses than other animals? Or are they just getting a bad press and we should cut them some slack?
As the saying goes, “there ain’t no flies on us, there ain’t no flies on us, there may be flies on some of you guys but there ain’t no flies on us!”
I had a great question last week from Michael Kamdar who asked me “if a healthcare professional who works within a hospital would have the flora of that of a normal person within the community or within a hospital?” Great question! And although I have no specific resources I can comment from experience… Firstly let’s go over the normal flora of non-hospitalised people.
"Why do we give broad spectrum antibiotics like Benzylpeniciilin, Gentamicin and Metronidazole to babies with necrotising enterocolitis [NEC] when their gut is sterile?" asked the Neonatal Unit [NNU] Registrar.
It was the middle of the NNU multidisciplinary ward round.
"Pardon?" said the Microbiologist, caught red-handed reaching for a second chocolate biscuit and suddenly feeling self-conscious as everyone turned to stare at him.
"Babies are born with a sterile gut so when they develop NEC why do they need antibiotics; surely there are no bacteria to cause a problem". The Registrar restated his question again but with more clarity.
The Microbiologist recognised the question was being rephrased; he obviously looked like he did not understand what was being asked! It was actually a very good observation of the Microbiologist! But it was an even better question thought the Microbiologist…so it needed a good answer…
Fortunately the Microbiologist was on the ball, and in fact was armed with the latest research provided by the NNU Pharmacist only a few weeks earlier.
Hopefully everyone knows where babies come from... but do you know where babies gut bacteria come from? Read on...
There are lots of sayings in medicine, often recited by grumpy old doctors like me, to remind more junior staff how medicine “works”, or once worked!! Sayings like “if you hear hooves, think horses”, “common things are common” or “as rare as hen’s teeth”. All of these mean that a patient’s symptoms are usually explained by a common disease rather than a rare one and that treatment and investigations should be targeted at the common diagnoses rather than something more obscure.
Note: those doing exams are often the worst offenders as they are cramming obscure knowledge in order to cover “everything possible” that an exam might test them on, even if it is as rare as hens teeth!
But why do we say this? What is wrong with sending every test you can possibly think of for every possible disease, however rare, that might explain the patient’s symptoms? How do Doctors choose what tests to perform and have you ever considered how reliable the results that come back are!? You might be shocked to know that not all tests are completely accurate.
Okay, bear with me on this. The science is complicated and involves statistics… (stay with me everyone!!!) but it’s a fundamental part of medicine so I’m going to stick with it, come on, come with me… there is a “are you still confused” recap at the end, honest you will get it, Editor-Chief-in-Charge wrote it and she doesn’t do stats!
Once upon a time… a long time ago… in a distant land… and a galaxy far, far away
When I was a Registrar I was lucky enough to do an MSc in Clinical Microbiology at Queen Mary’s University of London. This involved a really early morning once a week to catch a train from Nottingham to London, a two hour journey, a day of practical work and lectures, and then a two hour journey home (it was a gruelling day, gosh I was so lucky!). I learnt a lot doing the MSc and met some great people, but it was during these long train journeys that I came up with an idea about how to pass essay and short note exams. This method became known as the Seven Pillars of Waffledom, but more on why later.
How do you help your examiner mark your essays and short notes?
Now this isn’t about cheating! It’s just a polite observation. During the MSc we had to write essays and short notes on various topics, it was good practice as this was also the standard format of the three hour exam papers in the “olde” FRCPath Part 1 exam; I quickly realised I had to get better at writing essays and short notes. I spoke to my Consultant Supervisors who used to mark these exam papers and they all said the same thing, “make sure your answers are clear and easy to read”. “Is that it?” I replied grouchily. Simply put yes it is, because if you write clearly and legibly your examiner is more likely to look favourably on your essay and may give you the benefit of the doubt with some of your answers. If your answer is illegible and disorganised or if it takes too long to decipher your answer, then they will not be so kind and you won’t get the mark. How long do you think it takes to read an essay and how long extra should they allow to read a badly written one?! This may seem unfair but it is human nature… it’s also a good lesson for clinical work, good communication is really important and that includes your written communication.
A recent conversation got me thinking… a rare occurrence some would say… about the identification of bacteria. The patient I was discussing had two bacteria growing in his blood cultures and we weren’t sure if both were genuine or whether one was a skin contaminant. There was both a Staphylococcus spp. and a Proteus mirabilis growing, but the P. mirabilis was growing all over the Staphylococcus spp. preventing its further identification. I suggested putting up a CLED agar plate (see later in the blog) and a number of people looked at me like I was crazy… and whilst I do occasionally come up with some crazy ideas this really wasn’t one of the them. To understand my logic you have to know a bit about P. mirabilis, especially its laboratory identification. Let me explain further…
Previously I blogged about the use of antibiotics in pancreatitis and I mentioned procalcitonin as an exciting new marker of infection. I have little experience of this laboratory test but have heard many others talk about how useful it is. But what is it? What is it useful for? Can it help in the diagnosis and management of infection?
What is procalcitonin?
Procalcitonin (PCT) is a protein produced by the thyroid, lungs and intestine in response to inflammation, especially when the inflammation is caused by bacterial infection. In contrast, levels of PCT do not increase much when inflammation is caused by viruses or most non-infectious causes. Levels increase quickly (within 2-4 hours) and have a half-life of 24-36 hours. It is suggested (by the manufacturers of the PCT assay machines) that PCT can therefore be used to identify septic patients and predict who is at risk of developing severe sepsis. The amount of PCT is said to be related to the amount of inflammation therefore in theory the level of PCT can also be used to monitor response to treatment; a decrease in PCT corresponding to a favourable response to treatment.
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