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Brian Jetter was in the resuscitation phase, a healthy 40-year-old man battling pneumonia and sepsis, and many tests failed to determine the cause.
Mysterious diseases such as this one kill thousands of people every year when germs can not be identified quickly enough to reveal the proper treatment. Now, genetic testing is helping to solve these cases.
One of them was eventually used to search the bloodstream for fragments of nonhuman genetic material from viruses, fungi, etc. He detected an unusual bacterium that likely entered the lungs of Connecticut man after choking and accidental inhalation of hamburger pieces a few weeks earlier.
With the right drugs, he recovered and returned home with his 5-year-old son.
"I realized how fragile life is," said Jetter. "No matter what your condition is, the smallest microbe can destroy you."
Doctors regularly use genetic tests to detect hereditary diseases and guide cancer treatment. But their use to detect infectious diseases is so new that few doctors and even fewer patients know they are available. A study of a test is published Thursday in the New England Journal of Medicine.
They are modernizing an area long awaited for a redesign.
To identify the bacteria, the laboratories still use the centuries-old techniques of Louis Pasteur: put a few drops of blood or other samples in a laboratory dish and wait for days, even weeks, to see what germs develop. To look for a virus, the doctor usually has to guess what the patient is sick. Screening for a fungus or some other things can be time consuming.
Several companies and university laboratories now offer genetic tests on blood or cerebrospinal fluid. Once fragments of DNA or other genetic material have been discovered, their code is analyzed or sequenced to identify the bacteria, viruses, fungi, and parasites that cause sepsis, meningitis, and encephalitis and other life-threatening diseases.
"The main benefit of sequencing is that it can search all at the same time" rather than doing separate tests for each virus or other suspected microbe, said Dr. Charles Chiu, a microbiologist at the University of California at San Francisco.
He led the New England Journal study that tested 204 adult patients and children with meningitis or encephalitis, a dangerous disease that is not always caused by infection.
The genetic test was not perfect. He missed some cases, but also found others that lacked standard tests.
In all, 58 infections were diagnosed. The genetic test matched the standard lab results in 19 cases, found 13 more than the missing standard tests and 26 missing that the standard tests eventually found.
Physicians believe that genetic testing could be a quick and non-invasive first step for serious or unusual cases.
"For infectious diseases, you need to know the answer today," because the risk of a patient's death increases as the cause goes away, said Dr. Asim Ahmed, Medical Director of Karius Inc.
The Redwood City, Calif., Company sells a blood test developed by Stanford University scientists that looks for 1,200 bacteria, fungi, viruses, and parasites at once and gives a result within two days. The test showed strong agreement with standard laboratory tests in a study of Nature Microbiology.
"The biggest problem is the cost" – about US $ 2,000 for the Karius test, said Ali Torkamani, a San Diego scientist who runs a genetics conference presenting these tests in March. Increased competition could lower the price and lead to wider use, he said.
Karius has his own laboratory for his test. Other companies offer software and tools that hospitals can use to develop their own genetic tests. One of them, Arc Bio, based in California and Massachusetts, offers tests for screening the virus from blood and gives an answer in less than two days.
IDbyDNA, based in San Francisco, uses a Utah lab that operates with 3,000 US hospitals. It gives an answer in about 48 hours once a sample has arrived, said its medical officer, Dr. Robert Schlaberg, a pathologist at the University of Utah.
Until now, hospitals are using these tests for the most severe cases – long and unexplained illnesses or highly vulnerable patients such as children and people with cancer or weakened immune systems. .
Dr. Asha Shah tried one for the first time last year, while Jetter was rapidly worsening at Stamford Hospital in Connecticut.
"He has had several blood tests, chest X-rays, CT scans, for example," she said. "I thought it made no sense, why did not we have answers?"
Karius's test revealed the presence of unusual mouth bacteria in his lungs, suggesting that he had inhaled it while he was choking on the burger.
An even more unusual story came when Dr. Amir Khan, an infectious disease specialist at the Carle Foundation Hospital in Urbana, Illinois, commissioned a 47-year-old Ryan Springer Karius test, whose doctors were suspected to have cancer.
"Breathing gave me the impression that my lungs were on fire," said Springer, program director of a radio station in Champaign, Illinois.
It has been found to have tularemia, sometimes called "rabbit fever," which can come from inhaling bacteria from infected rodents or their excrement with a lawn mower. With the right treatment, he recovered.
"It's the future of medicine," Khan said. When patients are very sick, "every minute and every hour counts."
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Marilynn Marchione can be followed at http://twitter.com/MMarchioneAP .
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The Associated Press Health and Science Department is supported by the Howard Hughes Medical Institute's Department of Science Education. The AP is solely responsible for all content.
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