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Gene Expression Test Aims to Reduce Antibiotic Overuse

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Doctor with ER patient

Caption: Duke physician-scientist Ephraim Tsalik assesses a patient for a respiratory infection.
Credit: Shawn Rocco/Duke Health

Without doubt, antibiotic drugs have saved hundreds of millions of lives from bacterial infections that would have otherwise been fatal. But their inappropriate use has led to the rise of antibiotic-resistant superbugs, which now infect at least 2 million Americans every year and are responsible for thousands of deaths [1]. I’ve just come from the World Economic Forum in Davos, Switzerland, where concerns about antibiotic resistance and overuse was a topic of conversation. In fact, some of the world’s biggest pharmaceutical companies issued a joint declaration at the forum, calling on governments and industry to work together to combat this growing public health threat [2].

Many people who go to the doctor suffering from respiratory symptoms expect to be given a prescription for antibiotics. Not only do such antibiotics often fail to help, they serve to fuel the development of antibiotic-resistant superbugs [3]. That’s because antibiotics are only useful in treating respiratory illnesses caused by bacteria, and have no impact on those caused by viruses (which are frequent in the wintertime). So, I’m pleased to report that a research team, partially supported by NIH, recently made progress toward a simple blood test that analyzes patterns of gene expression to determine if a patient’s respiratory symptoms likely stem from a bacterial infection, viral infection, or no infection at all.

In contrast to standard tests that look for signs of a specific infectious agent—respiratory syncytial virus (RSV) or the influenza virus, for instance—the new strategy casts a wide net that takes into account changes in the patterns of gene expression in the bloodstream, which differ depending on whether a person is fighting off a bacterial or a viral infection. As reported in Science Translational Medicine [4], Geoffrey Ginsburg, Christopher Woods, and Ephraim Tsalik of Duke University’s Center for Applied Genomics and Precision Medicine, Durham, NC, and their colleagues collected blood samples from 273 people who came to the emergency room (ER) with signs of acute respiratory illness. Standard diagnostic tests showed that 70 patients arrived in the ER with bacterial infections and 115 were battling viruses. Another 88 patients had no signs of infection, with symptoms traced instead to other health conditions.


New Strategies in Battle Against Antibiotic Resistance

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Klebsiella pneumoniae Bacteria

Caption: Colorized scanning-electron micrograph showing carbapenem-resistant Klebsiella pneumoniae interacting with a human white blood cell.
Credit: National Institute of Allergy and Infectious Diseases, NIH

Over the past year, the problem of antibiotic resistance has received considerable attention, with concerns being raised by scientists, clinicians, public health officials, and many others around the globe. These bacteria are found not only in hospitals, but in a wide range of community settings. In the United States alone, antibiotic-resistant bacteria cause roughly 2 million infections per year, and 23,000 deaths [1].

In light of such daunting statistics, the need for action at the highest levels is clear, as is demonstrated by an Executive Order issued today by the President. Fighting antibiotic resistance is both a public health and national security priority. The White House has joined together with leaders from government, academia, and public health to create a multi-pronged approach to combat antibiotic resistance. Two high-level reports released today—the White House’s National Strategy for Combating Antibiotic-Resistant Bacteria (CARB) and the complementary President’s Council of Advisors on Science and Technology (PCAST) Report to the President on Combating Antibiotic Resistance—outline a series of bold steps aimed at addressing this growing public health threat.