Revealing what’s not human
Three percent of the DNA in the patient’s cerebral spinal fluid wasn’t human, it was tapeworm!, Joe DeRisi
At the 2017 WCSJ in San Francisco, science writer Carl Zimmer continued his conversation with Joe DeRisi about DeRisi’s collaborative work diagnosing infections through comprehensive, «next-generation» DNA screening. Following up on his widely-read New York Times article from 2014, Zimmer asked about the latest advances with this technique, its future prospects, and about a few of the mysterious diagnoses the method has already made possible.
Joe DeRisi, a professor at the University of California, San Francisco, has been helping to identify infectious agents throughout his career, including discovering the virus behind the SARS outbreak in 2003. Among his more recent pursuits, he’s been collaborating with colleagues such as pathologist Charles Chiu to develop next-generation DNA sequencing tests to diagnose any type of infection—bacterial, viral, fungal, or even parasitic.
Figuring things out when the doctors are stumped
Even under the best circumstances, diagnosing infections can be a challenge. In cases of rare or unknown pathogens, or if a patient is exhibiting atypical symptoms, a patient’s physicians might never reach a correct diagnosis. Furthermore, diagnoses are always dependent on the physicians’ training, as well as their past experiences and biases. But by identifying pathogens by their DNA, this new method helps to bypass such limitations, while simultaneously revealing misleading, improbable, and even previously unknown infectious culprits.
Such was the case of the Californian construction worker who went to his local clinic with headaches and other symptoms, which his physicians initially diagnosed as tuberculosis. After receiving treatment for over a year, the patient continued to steadily decline. Out of options and with a critically ill patient, the physicians reached out to DeRisi’s group to see if they could help. Within 24 hours of receiving the patient’s sample, DeRisi’s group provided the doctors with a critical new piece of information that allowed them to correctly diagnose and treat the patient: «Three percent of the DNA in the patient’s cerebral spinal fluid wasn’t human», explained DeRisi. «It was tapeworm!»
A new age of diagnosing infections
The method has already helped shed light on a range of elusive diagnoses such as the case of a decades-long Rubella infection in a patient’s eye and the case of Balamuthia—a rare and poorly-understood brain-eating amoeba—that inexplicably appeared in an elderly patient in San Francisco’s China Town. DeRisi has even collaborated with local wildlife experts to identify a little-known parasite causing mass shark die-offs in the San Francisco Bay Area.
These new methods, also known as metagenomic sequencing, aren’t yet widespread, but they are becoming available to physicians throughout the U.S. Once prohibitively expensive and time-consuming, such diagnostic DNA tests are getting «cheaper, faster, and better» thanks to ever more powerful computers. «In the past, doctors have had to make diagnoses when they didn’t have all of the data,» explained DeRisi. «That’s all changing now.»