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January 15, 2018.

A new approach to testing for infections may allow healthcare practitioners to quickly determine whether a patient has an infection caused by a bacterium or a virus, and to determine the right treatment in a timely way. New tests have been developed using this approach and studies evaluating them were recently published in journal articles.

Because signs and symptoms, such as fever and inflammation, are not specific, it is often difficult to determine whether a patient has an infection or, if there is an infection, if it is due to a virus or bacteria, and what type of treatment should be prescribed.

"A lot of times you can't really tell what kind of infection someone has," said Timothy Sweeney, MD, PhD, an engineering research associate with the Stanford Institute for Immunity, Transplantation and Infection and lead author of one of the articles. "If someone comes into the clinic, a bacterial or a viral infection often look exactly the same," said Dr. Sweeney in a Stanford Medicine news release.

Currently, healthcare practitioners often use tests, such as Gram stains and cultures, to detect and identify the cause of an infection. These tests usually take days to complete. Meanwhile, a patient may be left waiting for a diagnosis and may receive unnecessary or ineffective treatment.

The new testing approach is based on looking at the activity of genes that are involved in the body's immune system response to infections. When an infection occurs, certain genes become activated and this activation is expressed as a pattern. The pattern of expression depends on whether the immune system is responding to a viral or bacterial infection. By detecting the gene activation and determining the pattern expressed, testing can distinguish between viral and bacterial infections, or no infection. Researchers have used this approach with the goal of developing tests that are low-cost yet accurate and provide results faster than conventional tests.

Quickly identifying the type of infection and timely treatment are especially critical for patients who are seriously ill, such as people with meningitis or encephalitis or blood infections (septicemia) that can lead to sepsis, and for those who are particularly vulnerable, such as newborns or the elderly.

Another advantage of the new testing approach is that it would help healthcare practitioners avoid using antibiotics when an infection is caused by a virus and antibiotics are ineffective. Overuse of antibiotics is known to contribute to the development of antibiotic resistance. Some bacteria have become increasingly resistant to the drugs most commonly used to treat bacterial infections. This problem has been called a global public health threat by organizations such as the Centers for Disease Control and Prevention and the World Health Organization.

To develop a practical test, Dr. Sweeny and colleagues focused on seven genes and their pattern of activation during infections. Their study, published in a July issue of Science Translational Medicine, showed the test to be promising in distinguishing bacterial and viral infections in 96 critically ill children. Now the scientists are looking at combining it with an earlier-developed 11-gene test that may help determine whether or not a patient even has an infection.

Similarly, a preliminary study published in an August issue of the Journal of the American Medical Association found that a test that looked at patterns of gene expression in the blood of 298 newborns was able to distinguish between those with and without bacterial infections. Another study in the same issue evaluated a similar test for distinguishing between bacterial and viral infections in 130 children younger than 5 years old and found the results to be encouraging.

Though these tests show promise, they will need to be evaluated and validated by additional studies that include larger numbers of patients, say the researchers. It will likely take a few years to conduct such studies before these tests are available for use in clinical practice.


(July 6, 2016) Dusheck, Jennie. Cheap blood test can discriminate between bacterial, viral infections. Stanford Medicine News. Available online at Accessed November 7, 2016.

Sweeney T, et al. Robust classification of bacterial and viral infections via integrated host gene expression diagnostics. Science Translational Medicine 06 Jul 2016: Vol. 8, Issue 346. Pg. 346ra91. Available online at Accessed November 7, 2016.

Mahajan P, et al. Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger. JAMA. 2016;316(8):846-857.

Herberg J., et al. Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. JAMA. 2016;316(8):835-845.

(October 24 2016) Schlingman J. Researchers at the Stanford University School of Medicine Develop Cutting-Edge Test to Identify Whether an Infection is Bacterial or Viral. Available online at Accessed November 7, 2016.