Doctors mark diagnostic milestone, use DNA test in race to crack bacteria mystery


A team of doctors pressed for time used DNA testing to diagnose a rare bacterial infection in a 14-year-old boy with encephalitis.  The case, written up in the New England Journal of Medicine and widely covered in media reports this week, represents what could one day become commonplace as medical innovations make it easier to do these tests in a shorter timeframe.

Researchers at University of California at San Francisco collaborated with doctors at American Family Children’s Hospital in Madison Wisconsin to do the test after securing permission from Joshua Osborn’s parents. Using samples of Osborn’s cerebrospinal fluid, they were able to come up with the cause of his condition within 48 hours of doing the DNA testing.

In an interview with The New York Times, Dr. Joseph DeRisi, a biochemist at UCSF, said, “It’s a demonstration that this technology has arrived…It can make a difference in real time.”


Dr. Charles Chiu, a professor of laboratory medicine at UC San Francisco, is a senior author of the case study. In a description of the medical breakthrough, a UCSF article said it was:

“a convergence of faster DNA sequencing, ever-growing genome databases for identifying pathogens and other organisms, and more sophisticated computational analysis tools to quickly analyze millions of data points. The protocol enabled rapid sequencing and simultaneous identification of all DNA in the patient samples without culturing.”

Next generation sequencing has generally been too slow to be of much use to diagnose infectious disease. But some clinical labs have used it to identify cancer mutations in clinical trials.

Dr. Michael Wilson, an assistant professor of neurology at UCSF and the lead author of the study, worked with Chiu’s lab team to generate a library of millions of DNA sequences from samples of the patient’s cerebrospinal fluid and blood, and from a control sample, according to the article.  The medical researchers used a MiSeq DNA sequencer made by Illumina, which was approved for use in clinical diagnostic labs by the U.S. Food and Drug Administration. The  sequencing was done overnight.

A DNA analysis tool developed by Chiu was critical in narrowing down the bacteria to Leptospira. The bacteria is transmitted through the urine of certain animals. Osborn is believed to have contracted the rare bacteria on a visit to Puerto Rico.

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