Hey so I was just playing Plague Inc when it got a question to pop into my head as I the game we can tell a virus from a bacteria or fungus because we are the one’s in control but can someone please how we can do that IRL or if we even can?
In: Biology
Loads of different ways.
You can identify their genetic material through PCR. You can grow them under culture conditions that some survive and others don’t. You can look at them under a microscope. Etc etc.
Not everything is viable for every pathogen, and many techniques require that you know what you’re looking for to some degree. Signs/symptoms in the patient as well as their history (clinical but also certain risk behaviours) can point you in the right direction.
Answer: Testing
Longer explanation: There are different parts that make up each organism. A bacteria will have an outer surface made of specific proteins and sugars that are put together in a certain way, while fungus and viruses will have a different specific set of proteins/sugars/fats put together in a different way. Not only that, but different branches of the “tree of life” have certain compounds or markers (IE ribosomes), and within branches, the set of genes that each organism has will be generally unique. Bacteria 1 might have genes A, B, C, and D, while Bacteria 2 has genes A, D, H, and L, and Bacteria 3 has genes L, P, S, Y. By looking at the products of those genes, like enzymes, we can tell if an organism has a certain set of genes.
As a real life example for the lab I work in, when testing for Salmonella, we first use an enrichment broth based on the substance that may be contaminated. We then transfer some of that enrichment to a second type of broth that will inhibit most bacteria besides Salmonella, because there are certain compounds that Salmonella can tolerate, while other bacteria cannot. From there, we put the second broth onto agar plates that also inhibit non-Salmonella species, and since there is some variation even within Salmonella, these plates will change color based on the species of Salmonella that may be present. To confirm that yes indeed, this is Salmonella X vs Salmonella Y, we can then move on to another agar that tests for several things at once, giving us a better profile of what type of Salmonella it is (and isn’t). Then, we can do further testing with a larger number of tests – what sugars can be used, what proteins are produced, etc.
All of that will allow us to know this is Salmonella typhi, or Salmonella gaminara, or Salmonella mbandanka, etc.
So yes, we can tell the difference (in most cases), and we do so frequently.
Microscopes.
It really can be that simple. A big enough, powerful enough microscope can show you what you’re dealing with. You don’t even need to have something super-powerful and super cool to see to that depth.
Yes we can, up to the point of general sequencing them entirely, but it’s a very broad question so I’ll pick an example to narrow it down.
Let’s say that you come in with fever and a cough. The first thing I do is take your symptoms and a medical history – how long have you had the cough? Is it getting worse or better? Do you have any other symptoms like headaches, diarrhoea, pain anywhere? Have you travelled anywhere recently? Is anyone else sick? What do you do for work? Do you have any other conditions? Etc. etc
I then look at signs – these are things I can test. I might listen to your lungs with a stethoscope, take your temperature, tap on your chest to listen to see if the sound changes, take your pulse and blood pressure and blood oxygen etc.
You have a fever, a crackly chest, and a productive cough.
OK, so now I think that you have pneumonia. That’s an inflammation of the lungs, normally caused by infection. Infectious pneumonia is normally bacterial or viral – it can also be caused by fungi and parasites, but unless you have risk factors for these (like you’ve got AIDS or you’re a chicken farmer), we’ll focus on the first two.
I now might use imaging to help, so I send you off to radiology and you get a chest X-ray. I can see that one of the lobes of your lungs is all consolidated because it’s whiter than the rest, which are full of air. That’s normally associated with bacterial pneumonia, acquired in the community as you haven’t been in hospital recently, so that’ll be my running diagnosis.
If it isn’t that bad, I’ll use my medical knowledge and guidelines to pick a broad-spectrum antibiotic that targets the most common causes of pneumonia and send you off. However, you finish the course and it’s no better and you come back. Evidently my antibiotics didn’t work, so I need to find out what bacteria might be infecting you. I ask for a sputum sample (get you to hack up some phlegm into a pot) and send it off to the lab for testing. I also take blood samples, to get lots of different measurements including measures of immune function, infection, inflammation and also the type of white blood cells you have a lot of. Viral infections are targets by different types of white blood cells than bacterial infections, so this is useful to double-check.
In the lab, they take your sputum sample and then grow cultures from it on agar plates to multiply up the bacteria. Some of it is stained and looked at under a microscope – different types of bacteria take on different stains, and the shape of the bacteria can also help with diagnosis. Some bacteria are grown on different growth media – they’re fed different foods and given different chemical challenges to see if they grow, as this helps with diagnosis too.
If we think it’s antibiotic resistant, we might try growing it with different concentrations of different antibiotics to find one that works.
After all of this, we’ve found out that it’s *Haemophilia influenzae* resistant to our normal antibiotics, so we follow guidelines and give you levofloxacin. You survive, hooray!
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