It took UCSF physicians just 48 hours to identify the bacteria in cerebrospinal fluid that was causing fourteen-year-old Joshua Osborn’s hydrocephalus and status epilepticus
There’s rich irony in the FDA’s recent announcement that it would move forward with plans to regulate “laboratory-developed tests ” (LDTs) just weeks after the national media published stories about how innovative use of an LDT helped physicians make an accurate diagnosis that saved the life of seriously-ill 14-year old boy.
Pathologists and clinical laboratory managers may be aware of the case of Joshua Osborn. It was a laboratory-developed test that used next-generation gene sequencing in a unique approach that gave his care team the diagnostic information they needed to select the right therapies for his condition.
In its story about the case, The New York Times described how unbiased next-generation sequencing was used to identify illness-causing pathogens that typically elude other methods of diagnosis. For Osborn, who was developing hydrocephalus, lab scientists used a technique that extracted every scrap of DNA in a sample of his cerebrospinal fluid, then sifted out the pathogen’s genetic fragments before sequencing all of them.
Test for Pathogen’s DNA Identifies Bacteria Affecting Teen
Osborn, age 14, had presented at American Family Children’s Hospital in Madison, Wisconsin, three times over four months with fever and a headache that progressed to hydrocephalus and status epilepticus. His condition necessitated a medically-induced coma.
Suffering from an immune disorder from the age of two months, Joshua had been a long-time patient of James Gern, M.D, a Pediatrician at the University of Wisconsin School of Medicine and Public Health (UWSMPH). Gern sent samples of Joshua’s cerebrospinal fluid and blood to scientists at the University of California, San Francisco (UCSF) for testing after Joshua had undergone an exhaustive list of tests at UWSMPH.
Next-Gen Gene Sequencing Helped Identify a Lethal Pathogen
Researchers at the UCSF were able to identify the existence of a lethal pathogen in Joshua’s cerebrospinal fluid. It was Leptospira, an obscure species of bacteria. It took just 48 hours for the UCSF medical laboratory team to identify the pathogen using the unbiased next-generation sequencing technique. While Leptospira is a dangerous bacteria, it is quite treatable with penicillin. “It was a very exciting phone call to make to Wisconsin,” said Michael R. Wilson, M.D., a UCSF Neurologist. “Not only was there an answer, but there was something they could potentially do about it.”
Once diagnosed, Joshua began receiving large doses of penicillin, and the swelling in brain began subsiding almost immediately. Within two weeks, he was walking, noted the New York Times story.
Stressing the significance of this diagnostic technique, Wilson, who authored the academic paper on this case, noted that the some causes of encephalitis are elusive and often go undiagnosed. “About 60% of the time, we never make a diagnosis [in encephalitis],” he said. “It’s frustrating whenever someone is doing poorly, but it’s especially frustrating when we can’t even tell the parents what the hell is going on.”
Wilson’s paper was published by The New England Medical Journal in the June 4, 2014 issue.
UCSF Scientists Continue to Investigate Promise of DNA Microarray Chip
Researchers at UCSF have been exploring methods to identify pathogens based on their DNA since 2003, when Joseph DeRisi, Ph.D., a UCSF Professor of Biochemistry and Biophysics and Howard Hughes Medical Institute, investigator in Genomics and Infectious Diseases, developed a microarray chip that was able to identify the newly emerging SARS (severe acute respiratory syndrome) virus within minutes.
Two years later, DeRisi created a DNA microarray chip that contains a huge library of genetic sequences of all known human and animal viruses that have ever been sequenced. It also has the capability of detecting previously unknown viruses, noted a report published April 14, 2003, by The Dark Report . His partner, David Wang, at the time a postdoctoral student at Massachusetts Institute of Technology, but now an Assistant Professor at Washington University in St. Louis, created a software program to evaluate the microarray’s success.
The microarray’s success was verified by using a laser microscope to compare SARS genetic samples from the Center for Disease Control and Prevention (CDC) with his microarray, which contained genetic sequence of 1,000 viruses. Within a few minutes, DeRisi was able to establish the relationship between SARS and other viruses in the coronavirus family, The Dark Report explained.
DeRisi DNA Test May Offer Quick Answers for Toughest Cases
A number of scientists now hope to adapt this technique to diagnosing the infections of individual patients, noted the New York Times, by simply running a next-generation DNA sequencing test to identify the bug. This would eliminate the existing guessing game that has physicians running clinical laboratory test after test to determine if suspected viruses, bacteria, fungi, or parasites are present. “It could be one test to rule them all,” DeRisi told the Times reporter, pointing out that such a test would be useful only if it were fast. He noted that sorting through millions of DNA fragments has been an intensive technological challenge, as efforts to identify a match with an infectious agent can take weeks.
“The problem is that your critically ill patient will be dead by the time you make a diagnosis,” said Charles Chiu, M.D., a UCSF Pathologist who collaborates with DeRisi on diagnostic technologies. Chiu and his colleagues have developed software that rapidly compares DNA fragments with genetic sequences stored in online databases. This was described in a paper, also published June 4, 2014, in the journal Genome Research. Last July DeRisi and Chiu got the opportunity to test their methods when Gern contacted them to ask for help in figuring out what was wrong with Osburn.
How Quickly Will Genomic Knowledge Revolutionize Laboratory Medicine?
DeRisi’s DNA-based diagnostic technique demonstrates how quickly genetic knowledge is revolutionizing laboratory medicine and healthcare. While it may take years of research before this diagnostic approach is approved for universal use by clinical laboratories, its potential to improve accuracy by returning a result in a timely manner is obvious.
Moreover, the publication of the Osburn’s case within weeks of the FDA’s notice to Congress (on July 31) of its intention to issue rules for regulation of laboratory-developed tests is symbolic. It demonstrates how clinical applications in molecular diagnostics, genetic testing, and next-generation gene sequencing are advancing at such a pace that even most pathologists and Ph.D.s are challenged to stay current with the state of this research. Osborn’s case raises a legitimate question: can the FDA establish a scheme to regulate LDTs without inhibiting the swift adoption of innovative medical laboratory tests used in appropriate clinical applications that benefit patients?
—By Patricia Kirk