RNA Profiling May Aid in Fever Differentiation in Infants, Children

Treating fevers in young children has been a longstanding challenge for clinicians. Rapid differentiation between viral and bacterial infections can alter the course of clinical care and use of antibiotics. Two new studies published in the Aug. 23/30 issue of the Journal of the American Medical Association (JAMA) show that RNA signatures of host response may represent an important advance in determining the pathogenic source of infection in febrile children.

Currently, seriously ill, febrile children are admitted to the hospital and given antibiotics until culture results can rule out bacterial infection. This poses a major burden on health care resources and a challenge for antibiotic stewardship, but is considered acceptable given the substantial risk of serious bacterial infections (estimated to be approximately eight percent) in febrile infants less than 60 days of age. Researchers are hopeful that a genomic approach, based on analysis of the host response to infection through RNA biosignatures, can more quickly and effectively differentiate bacterial and viral infection sources.

“These two preliminary studies represent promissory notes,” writes Howard Bauchner, M.D., editor in chief of JAMA, in an accompanying editorial. “If the promises of findings reported in the studies … are fulfilled by replication and refinement in other rigorous investigations, it may be possible that such advances will further reduce morbidity, mortality, and costs associated with caring for febrile children. The day when a parent of a febrile child may do a laboratory test at home, call a physician, and mutually decide if that child should be seen for evaluation may soon be here.”

RNA Biosignatures in Febrile Infants
Researchers from the Pediatric Emergency Care Applied Research Network used a convenience sample of 883 febrile infants (median age, 37 days) evaluated for fever (over 38 degrees C) in 22 emergency departments from 2008 to 2010. RNA biosignatures were assessed in 279 infants (89 with bacterial infections—including 32 with bacteremia and 15 with urinary tract infections—and 190 without bacterial infections), along with an additional 19 healthy infants.

The researchers found that 66 classifier genes were identified initially that distinguished infants with and without bacterial infections in the test set with 87 percent sensitivity and 89 percent specificity. A narrowed set of 10 classifier genes could distinguish infants with bacteremia from those without bacterial infections in the test set with 94 percent sensitivity and 95 percent specificity.

“Despite the young age of the febrile infants evaluated, they carried robust RNA biosignatures and demonstrated that regardless of the etiology of the infections, their immune systems are programmed to respond not only with shared elements induced by common microbes but also with specific patterns that allow discrimination by class of pathogen,” writes lead author Prashant Mahajan, M.D.

Genetic Signatures Useful in Older Children, Too Differentiating pathogen source in febrile children is also clinically important in older children.

Researchers from the IRIS Consortium retrospectively assessed samples from febrile children presenting to hospitals internationally between 2009 and 2013. The discovery group included 240 children (median age, 19 months) with 52 cases of definite bacterial infection (of whom 36 required intensive care) and 92 cases of definite viral infection (of whom 32 required intensive care). Ninety-six children had indeterminate infection. RNA expression signatures identified in the discovery group were assessed for diagnostic performance in the validation group. Additional validation occurred in children with meningococcal and inflammatory diseases.

The researchers found that RNA expression data identified a 38-transcript signature that distinguished bacterial from viral infection. A smaller (two-transcript) signature was implemented as a disease risk score in the validation group (130 children, including 23 children with definite bacterial, 28 definite viral, and 79 indeterminate infections; median age, 17 months). The two-transcript signature correctly confirmed definite bacterial infection in all 23 patients with microbiologically confirmed infection (sensitivity, 100 percent) while 27 of 28 patients with definite viral infection were classified correctly (specificity, 96.4 percent). High sensitivity and specificity was seen also in children with meningococcal and inflammatory diseases.

“The DRS signature, distinguishing viral from bacterial infections with only two transcripts, has potential to be translated into a clinically applicable test using current technology such as polymerase chain reaction,” write the authors led by Jethro Herberg, Ph.D. “A major challenge in using transcriptomic signatures for diagnosis is the translation of multitranscript signatures into clinical tests suitable for use in hospital laboratories or at the bedside. … New methods for rapid detection of nucleic acids, including nanoparticles and electrical impedance, have potential for low-cost, rapid analysis of multitranscript signatures.”

Takeaway: RNA-based tests that correctly distinguish febrile infants and children with bacterial infection from those with viral sources are emerging as a viable test that could cut time to diagnosis and reduce inappropriate antibiotic prescription.