A patient comes in to hospital with severe central abdominal pain. They are febrile, tachycardic and hypotensive. They are diagnosed with acute pancreatitis based upon a high amylase blood test and admitted under the surgeons. As they are so unwell they are transferred to the surgical high dependency unit. The Surgical Registrar calls the duty Microbiologist to ask whether to start antibiotics in her patient. The Microbiologist does the usual “microbiologist thing” asking a question rather than answering the one posed; “does the patient actually have an infection?” The Surgical Registrar stares at the phone. The Microbiologist continues “perhaps I should ask…why do you want to give antibiotics in pancreatitis”?

​A patient comes in to clinic complaining about a “funny skin rash” on his foot. He has returned from holiday in Indonesia 3 months ago where he saw beggars on the street with missing fingers and toes and he has been reading about the rise of leprosy in the news. You roll your eyes discretely, and it’s only Monday morning! He is worried that he might have caught leprosy. Your initial response is “this is a little far-fetched” but what are you going to do?
 
In the UK we didn’t have an animal vector for leprosy until now… so who’s to blame… well apparently it’s our squirrels. In the UK we have two types of squirrel. The grey squirrel, a non-native introduced in the 1800s from North America, which has rapidly displaced our native species and is considered a bit of a pest. Whereas our native squirrel is the red squirrel. It is much smaller than the grey and in my opinion is considerably cuter! Unfortunately for our native red squirrel they have been found to carry Mycobacterium leprae and the headlines in the national press were “Red squirrels carrying medieval strain of human leprosy as people warned to stay away”. Really?! How many people in the UK have actually seen one of these rare and shy animals let alone got close to one? I’m not sure this really is a major threat to public health…! Ah, rant over…but it did make me realise that I know very little about the disease!

​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.

​A bone marrow transplant patient presented with pneumonia; he was febrile, short of breath and had new changes on his chest X-ray. He was started on IV Piptazobactam and Clarithromycin to give broad spectrum cover including the normal causes of pneumonia plus covering for infections in immunosuppressed patients. All good so far! After three days the patient was no better, so a CT scan was performed to look at the lungs, this showed possible fungal infection (a Radiologist reported this… it all looks the same to me!). The patient was started on empirical Amphotericin B lipid formulation e.g. AmBisome, to cover for possible invasive aspergillosis and blood tests were sent for galactomannan and Beta-D-glucan (blood tests for aspergillosis and other fungi). A few days later the patient continued to deteriorate so a decision was made to do a bronchoscopy to look for the cause of infection. The next day the Beta-D-glucan result was positive and the galactomannan was negative suggesting that there was a fungal infection going on but that it was not aspergillosis!