Many recent headlines regarding DNA and genetic science have been complex and hard for the average person to relate to. When the technology saves a young person's life, such as what happened recently at the University of California, San Francisco, the science takes on human qualities, and as a public, we can truly grasp just how important and revolutionary this combination of biology and technology really is.
Dr. James Gern, a professor of pediatrics and medicine at the University of Wisconsin School of Medicine and Public Health in Madison, contacted Joseph DeRisi for help after his patient, a 14-year-old boy, was hospitalized with encephalitis. The prognosis was so severe that the young man had been hospitalized for six weeks and put into a medically induced coma, according to a press release. None of the tests and procedures run so far had managed to point out the cause of the boy’s illness. Gern contacted DeRisi, chair of biochemistry and biophysics at UCSF, due to his expertise in new genomic techniques. These techniques involved identifying pathogens that were previously unknown, such as that which caused the young man's illness. According to DeRisi, with this new technology, essentially any pathogen can now be detected with a single test. Once the cause was found, correct treatment could be administered.
The case study can be found published online in the New England Journal of Medicine. Using SURPI, a tool used in “next generation-sequencing,” a team of researchers quickly and efficiently found the cause of the young man’s illness. With the help of the technology, the team compared samples of the boy’s DNA to the GenBank databases maintained by the National Center for Biotechnology Information with awe-inspiring speed, doing in 96 minutes what before took at least a day. Researchers determined that 475 distinct DNA sequences among the three million DNA sequences obtained in the patient’s cereospinal fluid came from a type of bacteria called Leptospira.
The team was even able to pinpoint the exact strain of Leptospira that they boy had been contaminated with: one native to the Caribbean and warmer climates. Based on these findings, researchers decided to treat the boy using penicillin without having the diagnosis validated with a clinically approved test. The antibiotics treatment was successful in ridding the boy’s body of infection, and he was discharged and sent home shortly afterward. Validation by a clinically approved test could have taken upward of five months to confirm, and by this time the boy may not have survived. "From the perspective of cost and turnaround time, this is a very powerful technology that has become practical to implement routinely in clinical laboratories," Charles Chiu, a senior author of the case study, explained in the press release.
Encephalitis is inflammation, or swelling, of the brain tissue. It can be caused by a virus or a bacterial infection. Encephalitis occurs in one of every two million people, most of whom are young children or those over the age of 65. In nearly half the cases of encephalitis, no cause can be identified. Not being able to distinguish the cause of the disease can be serious.
Researchers at UCSF hope to create a meningitis and encephalitis center at their school’s medical center and UCSF Benioff Children’s Hospital San Francisco. These facilities would, in part, use the NGS technique, such as the one previously mentioned, to more quickly and accurately diagnosis the cause of not only encephalitis, but also meningitis and other neuroinflammatory conditions.
"This case was a test run for how you would validate and deploy a clinically-approved test," Chiu explained, in reference to UCSF’s goal. Unfortunately, no NGS test for infectious disease has been validated for use in commercial clinical labs or approved for routine diagnosis by a regulatory agency. Chui hopes that within months the HGS diagnostic tests will gain approval and he will be able to offer than at the UCSF clinical microbiology laboratories.