Question: How do you start to go about designing new tests to identify disease causing organisms?

Hannah Tanner answered on 19 Jun 2014:

I’ll try and give you an idea of the process using a recent example but methods will be different for different kinds of test.

Mycoplasma pneumoniae is a bacterium that causes respiratory infections. If someone is infected we know that we’d find the bacterium in their respiratory tract. We’d therefore know we needed a test that could use respiratory samples like sputum, bronchoalveolar lavage or throat swabs as the sample to be tested.

We know Mycoplasma pneumoniae is really slow and difficult to grow on agar plates and by the time we’d grown it, the test result wouldn’t really be useful for a doctor trying to make a decision about how to treat the patient. Because of this we know we need to use a faster technology such as looking for Mycoplasma pneumoniae DNA in the samples by using PCR.
PCR is the polymerase chain reaction. This reaction allows us to detect DNA by amplifying specific small sections of it ’till there is enough for us to detect. You can make PCR amplify any short bit of DNA you want as long as you know the sequence of the DNA you are looking for.
So for Mycoplasma pneumoniae we’d go and look at the published data about it’s whole genome and try and find a gene that is totally unique to Mycoplasma pneumoniae but is still found in all variants of Mycoplasma pneumoniae . Once we have found a gene with think is unique we design the PCR so that it only amplifies this unique bit of DNA.

Next we will try the new PCR on known extracts of Mycoplasma pneumoniae DNA to make sure the unique region of DNA does amplify. We’ll also then test it against extracts of other similar bacteria to make sure it does not unexpectedly amplify DNA from any other kinds of bacteria. We’ll also test it against different amounts of Mycoplasma pneumoniae to see how much or how little we can detect.

Next we will test the new PCR against DNA extracts from respiratory samples from patients who we know do or don’t have the disease to make sure the test is only positive in samples from people with the disease.

Once we are confident the test will be positive in patients with the disease and not in patients who don’t have the disease we can start thinking about getting the test up and running as a service.

Please comment back if that doesn’t answer your question or you want more information.