Before a doctor can treat a patient, they need to know what's wrong with them, right?
It's not that difficult if chickenpox or a sprained ankle is the problem, but infections can be much more difficult for a diagnostic test to spot. Viral pneumonia and bacterial pneumonia, for example, cause similar symptoms but may require different treatments.
Everyone knows the problem: A diagnostic test is designed to look for only a virus, bacterium, or other specific pathogen in a specific type of sample, such as blood or urine.
Each diagnostic test takes time to analyze, and if the first round of tests is inconclusive, a doctor may need to order another. In summary: patients undergoing the sometimes invasive process of sample collection and delays in treatment
The universal diagnostic test
UC San Francisco scientists they claim to have developed a single diagnostic test that can search for any type of DNA sample for known pathogens and deliver results in just six hours.
We already have tests that look for the genetic code of viruses or bacteria in a sample. An example above all? The most commonly used diagnostic test for COVID-19 (called the RT-PCR test) works by looking for coronavirus RNA.
What UC San Francisco researchers have developed is a diagnostic test that begins by sequencing all the DNA present in a sample (human, viral, bacterial, and fungal) using an existing technique, called next generation metagenomic sequencing (mNGS).
Then, a software program searches all the DNA, looking for matches from a database of every known pathogen - it finds a match and you know which pathogen has infected a patient.
Simple and revolutionary
The versatility of a universal diagnostic test immediately catches the eye. A physician can choose whichever type of sample is most likely to harbor the pathogen (e.g. lung fluid for a patient with signs of pneumonia). However, he no longer has to worry about using a test designed to work with that specific type of sample.
A systematic review
Researchers have previously shown that their technique could be used to detect RNA viruses from different body fluids. For their latest study, published in Nature Medicine, have chosen to focus on a diagnostic test that can identify the DNA of bacteria and fungi.
To begin, the researchers used their diagnostic test to analyze 180 body fluid samples from 160 patients. These samples had already undergone regular diagnostic tests using two traditional methods: culture test (trying to grow microbes in a Petri dish) and PCR tests.
The researchers used two different technologies to generate their sequences: the sequencing of nanopores, which can deliver results in as little as six hours, and the Illumina sequencing, which can handle many samples but takes more than 24 hours.
Both methods matched the diagnoses of traditional methods in approximately 75% of bacterial infections and 91% of fungal infections.
Diagnostic test developer Charles Chiu with a sequencing machine. Credit: Elisabeth Fall
The new test may initially be used after a patient tests negative with other routine methods. Over distance, if it is effective, the universal diagnostic test can supplant most of the current ones.