Cell-free DNA detects pathogens and quantifies damage

Cell-free DNA detects pathogens and quantifies damage

A common problem in diagnosing infectious disease is that the presence of a potential pathogen in the body does not necessarily mean the patient is sick. This can be particularly challenging for the treatment of organ transplant recipients, who often grapple with infection as well as complications related to immunosuppression.

A new study, published in Proceedings of the National Academy of Sciences, presents a technique to identify viruses and bacteria in the human body and quantify injuries to organs by using dead fragments of DNA, called cell-free DNA, that roam throughout the bloodstream and urine. The resulting test is simple, fast, low cost and generalizable enough to identify thousands of bacteria and viruses.

"This really came about through collaboration with clinicians who explained to us this common problem in infectious disease diagnosis," said co-senior author. "So we developed an assay that would simultaneously inform us about the presence or absence of a wide range of pathogens, but at the same time would also tell us about the injury of different host tissues. The combined information enables us to more definitively say whether a person is dealing with disease or not."

Lead author used high-throughput DNA sequencing to identify any microorganisms that were present in clinical samples and distinguish them from the host DNA via bisulfite sequencing, a process in which the cell-free DNA is treated with salt to reveal methylation marks. These marks helped the researchers trace the cell-free DNA's tissues of origin and measure the degree of injury to different host tissues.

"In the field, doctors who try to diagnose infectious diseases and people who run microbiology labs are getting more and more excited about the use of genomic medicine approaches for diagnosis," the co-senior author said. "But there was still a big gap to assess whether that organism is actually causing disease.

"That's really a critical question," the author said. "Because some organisms are just commensals, they live side by side with the host. Our guts are filled with microbes, but those microbes may not be the reason you're suffering from disease. In a way, you're infected. You're colonized, but that's just part of normal biology."

The test is so generalizable that virtually any organism that has a DNA genome can be identified.

"Infectious diseases are a leading cause of disease burden worldwide," the lead author said. "They affect almost every single demographic, and they are not very easy to understand. So to have a test that can potentially help this large amount and wide range of people is exciting."

For co-senior author the test is especially helpful in diagnosing damage due to BK polyomavirus (BKV) infection. While 25% to 30% of kidney transplant recipients have the virus in their blood or urine, only 5% experience nephropathy, or kidney disease, from the virus, the author said.

"In this investigation, we were able to demonstrate that the kidney-specific urine cell-free DNA is higher in individuals with BKV nephropathy as compared to those with BKV replication alone and those with no BKV replication, suggesting a role for this assay to monitor kidney damage in the face of active viral replication and infection," the author said. "This is particularly important because there is no specific therapy for active BKV replication."