So I do not mean a covid test where it is clear what pathogen to look for. More like:
“Hey lab, here is a sample of a patient that feels bad. Please find out what pathogen is inside of it.”
How does it work? And how does it work so fast that they usually return the results within 1 or 2 days?
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One way you can do it is multiplex PCR where they look for the most common and dangerous types of bacteria or viruses that can cause infections. The alternative is a bacterial or viral culture, but those results usually won’t come back in 1-2 days. They try to grow it on different medium and then look at it under the microscope or use different tests to determine what bacteria it is.
They do not know what looking for, but they know what to do not looking for. ELI5 example, i put in front of you a basket of apples, and ask you. OP theres something wrong inside here, you start digging inside apples, and you find a banana.
Explanation, they know what general or common bacteria and viruses are inside a body (the basket of apple), and not knowing what looking for, they start searching for something different or unusual.
You can put samples on different growth media designed for bacteria, virus and fungi, stick them in suitable climates and see what grows. Cheaper than pcr but takes longer up to two weeks for some fungi if memory serves.
This is why in hospital you may be started on a broad spectrum antibiotic which is changed to targeted once the results come back.
Thats why the doctors tell them a few types that make sense with the symptoms the patient shows.
Once you know it should be one out of x pathogens you make a PCR test against this group and see if you got a hit.
Two ways.
The original method is using a culture medium (usually yummy jelly appropriate for either bacteria or virus or fungi to grow in). Smear the sample of interest onto it, see what grows, you have to dilute the sample sometimes as there can be multiple different bacteria growing. Depending on how much pathogen lives in the sample and what type of pathogen, the sample can grow quickly or slowly.
The other method is to run PCR or antigen tests to against the pathogens you’re interested in looking for and this can be done as a panel where you run tests for pathogen A B C D E as a best guess.
The fastest tests are: Is [specific pathogen] present? Those can be done with a PCR or rapid antigen test. These tests are highly targeted to a specific pathogen (they detect highly specific molecules of the pathogen) and can be done in hours. These tests are useful if a doctor has a good idea of what’s causing the trouble.
The slower tests are: Is there anything growing here that shouldn’t be here? Then you have to grow it in the lab and analyze it. That takes days or weeks to perform. We analyze what the bacteria eat, their Gram stain properties, what they produce/secrete, their shape, and the type of colonies the grow in, and a few other things. This test is useful if the doctor doesn’t have a good idea of what’s causing the trouble.
There are various ways. Until recently, they’d take samples and, in the case of bacteria, mix with a little water and spread it on this nutritious gel in a little dish. After a few days at body temperature, any bacteria in the sample would grow a splotches on the plate. You could stain them with colors and look at them under a microscope. You could feed them different foods and see how they do, and do other things to nail it down.
Viruses were harder because you’d try to grow them in cells and see what kinds of cells they’d infect, then maybe look with a powerful microscope. You would also take purified virus and run tests to see if it would stock to certain proteins. Later, you’d purify a bunch of genetic material from it and sequence it.
Today, things are a bit different. We may still do the standard tests for bacteria because they’re cheap, simple, and don’t require very specialized tools. However, the quick and accurate method is genetic sequencing: you take a sample, wash it with chemicals that remove everting except the genetic material, add enzymes that make copies of the genetic material so you have a bunch, then stick it in a machine that will sequence the genetic material.
As you can imagine, the genetic sequencing gets the sequence of everything in the sample, which includes sequence from the person the sample was taken from. Nearly 20 years back, we worked out the human genetic sequence, so a computer can just identify and ignore that sequence and work with the rest. It takes random genetic sequence fragments and can rebuild the original sequence based on the way random pieces overlap, like putting together a jigsaw puzzle.
The result is that the computer spits out the full genetic sequence of everting in the sample that is not human. We now have very extensive databases of gene sequence from hundreds of thousands of things, and we can almost certainly find it or something related to it in the database. We can also get some understanding of its genes and how it functions. With the genetic sequence, we can produce genetic tests to detect it, and ways to quickly purify it from samples.
COVID-19 was identified using this genetic tools: we took fluid from a patient’s lung and used a kit (a lab can order online) to separate out the genetic material. A machine called a “next generation sequencer” used some crazy elegant chemistry and electronics to get the sequence of billions of ti y bots of genetic material. Software tossed out the bits that were fuzzy and uncertain, then it tossed out bits that were definitely from a human, then it lined up all the other bits that overlapped one another to reconstruct the full genetic sequence of the virus. Then, we used a different computer program to figure out if this sequence matched something we’ve seen before, and we found “yes, the individual genes and their arrangement is very typical of betacononaviruses, and this one is particularly similar to one that caused a disease called SARS in 2004”. With that information, genetic tests to detect it were trivial to make, and we had a jump start on making vaccines and drugs to treat it. The most important part, though, is that we didn’t need to have any idea what we were looking for to start; we didn’t have to figure out how to grow or purify it; we simply used molecular biology and computers to figure it out.
Medical laboratory scientist here the doctors have to place specific orders for the test they need done I.E “covid, stool panel, respiratory culture”. Here in the micro lab we don’t except any order that reqest “test for everything” I think a lot of that is Medicare related, but it helps us to. In the case of bacterial culture we may or may not know what is in it based of site, stain, and experience. Also Doctors have years of education and training to narrow down their diagnosis to a few things that can be tested for. I hope that answers your question.
The easiest to understand way is they promote its growth then look under a microscope. Most of the different types of bacteria look different under a microscope after you stain the samples. Viruses are harder and you need to know what you are looking for then they test for bits of the viral DNA or proteins that are specific to that type of virus.
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