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New genetic tests for germs quickly reveal the source of infection

Brian Jetter was life-sustaining, a healthy 40-year-old suddenly struggling against pneumonia and sepsis, and a number of tests had failed to find the cause.

Such mysterious diseases kill thousands of people each year when germs can not be identified quickly enough to reveal the right treatment. Now, genetic tests are helping to solve these cases.

One was finally used to search Jitter's blood for non-human genetic pieces of viruses, fungi and the like. It discovered unusual bacteria that were likely to enter the man's lungs in Connecticut when, weeks before, he swallowed the remains of a burger and inadvertently inhaled.

With the right medicine, he recovered and went home to his 5-year-old son.

"I realized how fragile life is," said Jetter. "No matter how healthy you are, the smallest microbe can destroy you."

Physicians routinely use genetic testing to detect hereditary diseases and to control cancer treatment. However, their use for detecting infectious diseases is so new that few doctors and even fewer patients know they are available. A trial trial will be published Thursday in the New England Journal of Medicine.

They are modernizing a field that is long overdue for overhaul.

To identify bacteria, laboratories still rely on centuries-old techniques by Louis Pasteur Place a few drops of blood or another sample in a lab dish and wait days or sometimes weeks to see which germs are growing. To test for a virus, a doctor usually has to guess what the patient is suffering from. Testing for a fungus or other things can take a long time.

Several companies and university labs now offer gene-based tests for blood or spinal fluid. Once fragments of foreign DNA or other genetic material have been found, their code is analyzed or sequenced to identify bacteria, viruses, fungi, and parasites that cause sepsis, meningitis, encephalitis, and other fatal diseases.

"The main benefit of sequencing is that it can search for everything at once," Dr. Charles Chiu, microbiologist at the University of California in San Francisco.

He led the study of the New England Journal attempting a spinal cord test on 204 children and adults with meningitis or encephalitis, dangerous diseases that are not always caused by infection.

The genetic test was not perfect. Some cases were overlooked, as well as others that lacked standard tests.

A total of 58 infections were diagnosed. The genetic test was consistent with the results of the standard laboratory in 1

9 cases, 13 others indicated that the standard tests were missing, and 26 that the standard tests ultimately resulted.

Doctors say the gene-based tests could be a quick, non-invasive first step for serious or unusual cases.

"For infectious diseases, you need to know the answer today," Dr. Asim Ahmed, Medical Director of Karius Inc.

California-based Redwood City sells a blood test developed by scientists at Stanford University, which simultaneously examines 1,200 bacteria, fungi, viruses, and parasites, and delivers results within two days. In a study in the journal Nature Microbiology, the test was largely consistent with the standard laboratory tests.

"The biggest problem is the cost" – about $ 2,000 for the Karius test, said Ali Torkamani, a San Diego scientist who directs a genetics conference. These tests were conducted in March. More competition could lower prices and lead to wider use, he said.

Karius has his own test laboratory. Other companies offer software and tools that enable hospitals to develop their own genetic tests. One of them, California-based Massachusetts-based Arc Bio, offers blood virus testing and answers in less than two days.

San Francisco-based IDbyDNA uses a lab in Utah that works with 3,000 US hospitals. There will be an answer in about 48 hours, as soon as a sample arrives, said his chief physician, dr. Robert Schlaberg, a pathologist from the University of Utah.

So far, hospitals use these tests for the worst cases – long unexplained illnesses or very vulnerable patients, such as children and people with cancer or weak immune systems.

Dr. Asha Shah tried it for the first time last year when Jetter was visibly deteriorating at Stamford Hospital in Connecticut.

"He had several blood tests, chest X-ray, CAT scan, as you call it," she said. "I thought that does not make sense, why do not we get answers?"

The Karius test revealed unusual oral bacteria in his lungs, suggesting that he had inhaled some while swallowing the burger.

An even more unusual story came to mind when Dr. Amir Khan, an infectious disease specialist at the Carle Foundation Hospital in Urbana, Illinois, ordered a karius test for 47-year-old Ryan Springer, whose doctors first suspected cancer.

Breathing made my lungs feel like they were on fire, "said Springer, a program director for a radio station in Champaign, Illinois.

It turned out that he was suffering from a tularemia, sometimes referred to as "rabbit fever", when rodents or feces were run over by a lawn mower. With the right treatment he recovered.

"This is the future of medicine," Khan said. When patients are very ill, "every minute and hour counts."


Marilynn Marchione can be traced at http://twitter.com/MMarchioneAP .


The Department of Press Health and Science is supported by the Department of Science Education, Howard Hughes Medical Institute. The content is the sole responsibility of the AP.

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