The metagenomics technique is suitable for detecting the DNA of microorganisms present in a raw (urine) sample that is taken from a patient. The researchers are now trying to use this technique in daily practice for cystitis diagnosis. It has already been shown that this works better in infectious diseases. Their findings were recently published in the journal the Lancet Microbe.
“You can read the pieces of DNA that are found with a special device. You then enter them into a supercomputer, which compares all the pieces with a library that contains the DNA of all kinds of microorganisms. The DNA is sorted: this is from this bacterium, that is from that bacterium, and so on. Ultimately, you get to see which bacteria DNA has been found from and how they relate to each other,” says PhD student and first author of the study, Victoria Janes.
Detect cystitis
The metagenomics technique is preferred by scientists who study the microbiome in our gut. That is all micro-organisms such as viruses, bacteria and parasites together. Metagenomics is used to create profiles of the microbiome of both sick and healthy people. These are then compared with each other.
“We try to apply the technology for everyday use. This is easier with some infectious diseases than with others. We chose to detect cystitis in urine because it is difficult to detect. You don’t just have to know which bacteria are in it, but also how much,” says Janes.
Metagenomics works better than culture test
The researchers have already shown that the metagenomics technique for detecting a bladder infection works just as well as the culture test that is still the standard. In a culture test, a patient’s urine is cultured. Then it is checked which bacteria are multiplying. It usually takes one to three days before the results of a culture test are known.
It is expected that the new method, through metagenomics, will eventually be able to detect a bladder infection faster and more accurately. With this method, a negative result can even be determined within an hour. A positive result only takes one day.
Pros and cons
The speed with which a bladder infection can be diagnosed is of course a great advantage. This allows a doctor to start treatment earlier. Another advantage is that a culture test sometimes gives a negative result, even though the patient still has complaints. One reason for this may be that the patient was already given antibiotics before the urine was collected. The bacteria have already been killed, so that they no longer grow on the culture plate. With metagenomics, the inflammation can also be demonstrated in those cases, because it also allows the DNA of dead bacteria to be traced.
Another advantage is the fact that the new technique not only looks at the type of bacteria, but also at the properties via the DNA. ” This way you can see how resistant it is: certain antibiotics then have no effect on the bacteria, so you have to prescribe others. As a result, you can also prescribe much more specific antibiotics, so that you do not have to use broad-acting agents too often,” says Janes.
However, there is also a drawback. The costs for applying this technique are relatively high. This can stand in the way of implementation in daily practice as a replacement for the culture test. “But the price of metagenomics is getting lower and lower. The expectation is that this decrease will continue for a while,” concludes Janes.