Today I had a look in the enterics (gut bugs) and in the mycology (fungi) labs. The enterics lab to my surprise was not particularly unpopular among the technicians (who do rotations); the fume hood gets rid of all the smells and the poo might as well be mud (unless a joker colleague switches of the hood of course!) The racks with poo sample tubes are placed in bags, for a good reason I learned. During warm weather, poo starts to ferment and caps screwed loosely are catapulted to the ceiling (I am serious!).
The bugs that cause intestinal problems are very diverse. Microscopy tests are used for the protozoan Giardia and the fungal Microsporidia. A simple strip test is used to check for the presence of roto- and adenoviruses. Noro virus tests are carried out at the virology lab, which also does tests for Clostridium toxins (Clostridium is a bacterium and not a virus, but this test is based on the same cell cultures used for viral screens.) Culture-based tests are used for E. coli O157, Shigella, Salmonella and Campylobacter, and in case the patient has travelled to the tropics or has eaten sea food, also (Vibrio) cholera(e). E. coli O157 is a very nasty enterohaemorrhagic strain which is fortunately uncommon. Salmonella and Campylobacter are both common, although the former is much more notorious as it is associated with outbreaks. This is because if only a small amount of Salmonella find their way into your mouth via your hand via a dirty door knob you can get sick, whereas you need a much heftier dose of Campylobacter to get ill.
Salmonella (top) on XLD agar. Sugar fermentors (below) such as E. coli lower the pH and turn the agar yellow. Shigella doesn’t do this and colonies therefore remain red. Although Salmonella actually DOES ferment sugar, it also decarboxylates lysin, which raises the pH and so the agar stays red as well. Salmonella can be easily told apart from Shigella because of the black hydrogen sulfide it produces. Below Campylobacter on agar containing charcoal. Summers see a spike in Campylobacter infections when people eat rare chicken from the barbeque.
Lastly, I had a look in the mycology lab, where skin scrapings and toe clippings are incubated on selective agar. Microscopy is used too, I saw the ‘spaghetti-and-meatballs’ appearance of the beautifully named Malassezia furfur. Nice name but it gives you a skin rash and dandruff. Fungal infections are usually not easy to treat by the way. In the Tree of Life, fungi are actually quite closely related to us humans and so the chemicals that hurt them tend to hurt us too. If you are not really into flaunting painted toe nails anyway, you might want to choose not to have an infection treated.
Trichophyton rubrum, which causes ‘Malabar itch’.