Even a Brain-Eating Amoeba Can’t Hide From This Cutting-Edge DNA Tech

When a middle-aged man who had suffered a seizure was admitted to the University of California San Francisco Medical Center in 2021, doctors seeking the cause for his condition quickly became stumped.

The conventional search for the cause of an infection involves examining patient tissue under a microscope or culturing samples in a petri dish to see if bacteria or other microbes grow. But doctors have to be looking for a particular bug to find it. Such tests are typically ordered after doctors weigh the details of a case and form a hunch about the cause of the infection—a biased approach.

A typical sample might yield 100 million snippets of genetic material, Dr. DeRisi said. Some 99% would be human. Those sequences are computationally stripped away and the remaining 1 million pieces are screened against all the sequences in GenBank in an effort to find a match. In 2014, Dr. DeRisi was among a team of researchers and clinicians at UCSF who reported on one of the first patients to be successfully treated based on metagenomics sequencing—a 14-year-old boy whose treatable, but potentially fatalbacterial brain infection went undiagnosed for several months until the test was performed.

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