RNA-Seq Used to Discriminate between Bacterial and Viral Infections

Genetic Engineering News – The ability of clinicians to discriminate between bacterial and viral infections among their patients is critical, not only to administer the appropriate therapeutic intervention but to help quell the rise in a major global health threat—antibiotic resistance stemming from overuse. Unfortunately, ailments such as lower respiratory tract infections (LRTIs) symptomatically present with similar clinical symptoms, regardless of the root pathogen—making proper diagnosis difficult.

Now, investigators at the University of Rochester Medical Center (URMC) have released findings from a new study that utilized the power of RNA sequencing (RNA-Seq) and transcriptomic analysis to help physicians prescribe antibiotics to patients who need them and avoid giving them to individuals who don’t. Results from the new study were published recently in Scientific Reports in an article entitled “Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness.”

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University of Rochester Medical Center News – Scientists from the University’s National Institutes of Health-funded Respiratory Pathogens Research Center identified 11 genetic markers in blood that accurately distinguished between viral and bacterial infections (antibiotics help us fight bacterial infections, but aren’t effective and shouldn’t be used to treat viruses). The finding, published in the journal Scientific Reports, is important because physicians don’t have a good way to confirm bacterial infections like pneumonia and more-often-than-not default to an antibiotic.

“It’s extremely difficult to interpret what’s causing a respiratory tract infection, especially in very ill patients who come to the hospital with a high fever, cough, shortness of breath and other concerning symptoms,” said Ann R. Falsey, M.D., lead study author, professor and interim chief of the Infectious Diseases Division at UR Medicine’s Strong Memorial Hospital. “My goal is to develop a tool that physicians can use to rule out a bacterial infection with enough certainty that they are comfortable, and their patients are comfortable, foregoing an antibiotic.”

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rna-seq

Shown is a heat map for the 10 predictive genes identified by pathway analysis as predictive of bacterial infection (rows) demonstrating differential expression in the 3 groups, bacterial, mixed viral bacterial and viral alone. Each column represents an individual subject. 

Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR. (2017) Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness. Sci Rep 7(1):6548. [article]

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