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.
One of the most common mistakes I come across in my daily practice is doctors giving antibiotics to treat bacteria that are not actually causing infection. It might surprise you that there are in fact three main reasons why a microorganism might be present in a microbiology sample, only one of which is infection; the others are contamination and colonisation. In order to understand how colonisation differs from infection and contamination it is first necessary to know what infection and contamination are.
What is infection?
Infection is the presence of microorganisms causing damage to body tissues, usually in the presence of acute inflammation (pain, swelling, redness, heat and loss of function). For example Staphylococcus aureus on intact skin does not cause a problem; it is the normal flora for skin. However, if you cut your skin, Staphylococcus aureus can cause infection in the cut.
Microorganisms can also cause damage in the absence of inflammation but it is unusual, e.g. in neutropaenic patients with angio-invasive fungal infections causing tissue infarction.
Okay I sound a bit like a two-year old (and probably sometimes behave like one as well!) but the question “why?” is often a much more important question than “what?” in microbiology and medicine. Let me explain…
Once in the Lab...
The blood culture bottles have arrived safely (see earlier blog) and are loaded on an automated incubator, which uses that barcode you now know not to peel off! How long it takes to signal positive depends on the type of organism, some take longer than others. Routinely negative blood cultures are destroyed after 5 days. That is really unhelpful if your patient has a slow growing microorganism or possible infective endocarditis. Did you write those details on the request form? If you did then the blood cultures will be incubated for up to 14 days.
The clinical details also help the laboratory decide how to safety process the blood cultures after they have signalled positive. So if you forgot to add the possibility of a high risk specimen e.g. typhoid or paratyphoid, you risk exposing the biomedical scientist handling the positive culture to a potential pathogen...blood-borne viruses, tuberculosis, shigellosis, salmonellosis, E.coli O157, Neisseria meningitidis, brucellosis, etc. Surely, being too busy to add these clinical details is negligent to your colleagues in the laboratory?
As I dust off my vampire outfit for our Halloween party it seems fitting that I talk about the blood sciences for this spooky edition of the blog.
I have been asked on many occasions “why do microbiology laboratories not highlight on their reports what of this result is normal and what is abnormal?” Essentially microbiology laboratories report the presence or absence of microorganisms or the immune response to those microorganisms. In order to decide if the result is normal or abnormal requires an understanding of what is going on in that specific patient. Most of the time microbiology laboratories don’t have that information available, partly because request forms are not completed and partly the forms don’t actually allow for a detailed clinical history.
I am often asked “why should I bother learning about normal flora, what I need to know is what bacteria cause infections”. This is an understandable approach however it doesn't allow for the fact that the presence of bacteria can be entirely normal and even healthy. The Microbiologist’s secret is that they know where these normal bacteria should be and recognise when they are in the wrong place. Treating normal flora is a very common mistake in medicine. Some doctors think that if bacteria are identified in a laboratory report these bacteria must be causing an infection and therefore prescribe an antibiotic. But this is not always the case. Microbiology laboratories report the presence or absence of bacteria. Depending on the clinical scenario the presence could be highly significant or alternatively just normal flora. As a student said last week “so what you’re saying is that a lot of antibiotics are given to try and treat normal flora not infection”. Yes, the presence of bacteria does not necessarily mean the presence of infection.
Bacteria like to colonise warm moist sites with poor blood supply and hence a poor immune response. They especially like broken areas of skin such as ulcers and lacerations.
Broken areas of skin are not sterile. Wounds should be colonised with relatively harmless bacteria like the Coagulase-negative Staphylococci, Coryneform bacteria (Diptheroids) and Propionibacterium spp. This normal process prevents more dangerous bacteria from getting in and causing infections such as Staphylococcus aureus and the Beta-haemolytic Streptococci. It is therefore really important that we only treat breaks in the skin when infections have occurred, rather than trying to prevent them occurring.