Researchers at the Stanford University School of Medicine have made a breakthrough in their ongoing efforts to develop a diagnostic test that can tell health care providers whether a patient has a bacterial infection and will benefit from antibiotics, according to a study published in Science Translational Medicine.

Antibiotics have saved millions of lives and created a world in which complex and lifesaving surgeries are possible. But the overuse of antibiotics threatens to create a global scourge of antibiotic-resistant bacterial pathogens. Because of this problem, public health experts regularly remind physicians to prescribe antibiotics only for bacterial infections––but too often there is no easy way for doctors to tell whether a patient’s illness is bacterial or viral or, sometimes, whether there is even any infection at all.

“A lot of times you can’t really tell what kind of infection someone has,” said lead author Timothy Sweeney, MD, PhD. “If someone comes into the clinic, a bacterial or a viral infection often look exactly the same.”

The team used publicly available gene-expression data to identify seven human genes whose activity changes during an infection; the genes’ pattern of activity can distinguish whether an infection is bacterial or viral.

The seven-gene test is a major improvement over earlier tests that looked at the activity of hundreds of genes, the researchers said. Because so few genes are involved, the new test will be cheaper and faster while remaining accurate, they said.

The assay, however, faces two hurdles before it can be made available to doctors in a few years. First, it must be thoroughly tested in a clinical setting. Until now, the data and test results for this ongoing work have all come from pre-existing, online digital data sets of gene expression from patients with different kinds of infections—not from current patients.

The new study tested the seven-gene test on blood samples from 96 critically ill children using an assay called NanoString and found that the test was accurate, but the assay needs to be further validated in larger numbers of patient blood samples, the researchers said.

Second, the test needs to be incorporated into a device that can give a result within one hour or less. The preliminary NanoString version of the blood test takes four to six hours—too long for people who are seriously ill. In patients who have sepsis, for example, the risk of death increases by 6% to 8% for every hour that antibiotics are delayed, so it is critically important for clinicians to act quickly.

In a patient who is obviously severely ill, Sweeney said, prescribing antibiotics would be the default. But often patients have early bacterial infections and doctors don’t realize the patient is in danger. The gene-expression test could remove doubt in a matter of minutes, allowing doctors to prescribe antibiotics sooner and save lives.

For that reason, the Stanford team is working with other researchers on a way to engineer the gene-expression test to provide results in less than an hour. The plan is to combine an 11-gene test the researchers created a few months ago with the more-recent seven-gene test. The 11-gene test reveals whether a patient has an infection at all. If he or she does have an infection, the seven-gene test reveals whether it is bacterial or viral. Both tests would be run at the same time.

The researchers envision the two tests as a decision tree. “When you put the new seven-gene set together with the 11-gene set, we can make a decision tree that matches how a physician might think about a patient,” Sweeney said. “First we ask, ‘Is an infection present?’ Because some people present with an inflammation, a fever, a high heart rate, but it’s not due to an infection. Then we ask, ‘If so, what kind?’”

The 18-gene combination test would first be used in hospitals, Sweeney said. It’s possible, he added, that an even cheaper test just using the seven genes could be used in outpatient clinics.

Source: Stanford Medicine; July 6, 2016.

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