Non-Oncology Applications: 2 of 14

Infectious Disease

When someone has a serious infection and doctors do not know what is causing it, one of the standard tools is culture. A blood sample is placed in a bottle with nutrients and kept warm. If bacteria are present and able to grow, they multiply until there are enough to identify. This method has been central to infection diagnosis for more than a century and still works very well for many common organisms.

It can also be slow. A seriously ill person may need treatment long before a culture has had time to grow. Some organisms will not grow in the bottle at all, including most viruses, many fungi, and certain difficult bacteria. Antibiotics can make the problem worse by damaging the organisms before the sample is collected, even if the infection is still causing harm.

Instead of growing the organism, researchers can look for its genetic material directly. Microbes in the bloodstream release fragments of DNA alongside the patient's own DNA. A laboratory can read the DNA fragments in the sample and sort them by which species they came from. Reading the chemical letters of DNA in order is called sequencing. When a laboratory sequences everything in the sample rather than looking only for one organism it already suspects, the approach is called metagenomic sequencing.

That opens the door to bacteria, viruses, fungi, and parasites in the same test. It can also find an unexpected organism because the laboratory does not have to choose the target in advance. Previous antibiotic treatment tends to interfere less with DNA detection than with culture, and results may come back faster.

The awkward part is that the test can find too much. Blood may contain DNA from harmless microbes that normally live on or in the body, microbes that entered the bloodstream briefly after something as ordinary as brushing your teeth, or contamination from laboratory equipment and reagents. The sequencing system reports those signals too. A clinician still has to decide which finding, if any, explains the illness. Detecting microbial DNA also does not prove that the organism is alive, since fragments can remain after an infection has been treated.