RNA transcriptional biosignature analysis for identifying febrile infants with serious bacterial infections in the emergency department: A feasibility study

Prashant Mahajan*, Nathan Kuppermann, Nicolas Suarez, Asuncion Mejias, Charlie Casper, J. Michael Dean, Octavio Ramilo, E. Powell, D. Levine, M. Tunik, L. Nigrovic, G. Roosevelt, L. Bjaj, E. Alpern, L. Browne, S. Atabaki, R. Ruddy, J. Hoyle, D. Borgialli, E. CrainS. Blumberg, J. Anders, B. Bonsu, D. Cohen, P. Dayan, R. Greenberg, D. Jaffe, J. Muenzar, A. Cruz, L. Tzimenatos, R. Gattu, A. Rodgers, A. Brayer, K. Lillis, Febrile Infant Working Group for the Pediatric Emergency Care Applied Research Network (PECARN)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Objectives: To develop the infrastructure and demonstrate the feasibility of conducting microarray-based RNA transcriptional profile analyses for the diagnosis of serious bacterial infections in febrile infants 60 days and younger in a multicenter pediatric emergency research network. Methods: We designed a prospective multicenter cohort study with the aim of enrolling more than 4000 febrile infants 60 days and younger. To ensure success of conducting complex genomic studies in emergency department (ED) settings, we established an infrastructure within the Pediatric Emergency Care Applied Research Network, including 21 sites, to evaluate RNA transcriptional profiles in young febrile infants. We developed a comprehensive manual of operations and trained site investigators to obtain and process blood samples for RNA extraction and genomic analyses. We created standard operating procedures for blood sample collection, processing, storage, shipping, and analyses. We planned to prospectively identify, enroll, and collect 1 mL blood samples for genomic analyses from eligible patients to identify logistical issues with study procedures. Finally, we planned to batch blood samples and determined RNA quantity and quality at the central microarray laboratory and organized data analysis with the Pediatric Emergency Care Applied Research Network data coordinating center. Below we report on establishment of the infrastructure and the feasibility success in the first year based on the enrollment of a limited number of patients. Results: We successfully established the infrastructure at 21 EDs. Over the first 5 months we enrolled 79% (74 of 94) of eligible febrile infants. We were able to obtain and ship 1 mL of blood from 74% (55 of 74) of enrolled participants, with at least 1 sample per participating ED. The 55 samples were shipped and evaluated at the microarray laboratory, and 95% (52 of 55) of blood samples were of adequate quality and contained sufficient RNA for expression analysis. Conclusions: It is possible to create a robust infrastructure to conduct genomic studies in young febrile infants in the context of a multicenter pediatric ED research setting. The sufficient quantity and high quality of RNA obtained suggests that whole blood transcriptional profile analysis for the diagnostic evaluation of young febrile infants can be successfully performed in this setting.

Original languageEnglish (US)
Pages (from-to)1-5
Number of pages5
JournalPediatric emergency care
Issue number1
StatePublished - Jan 21 2015


  • RNA transcriptional profiles
  • febrile infant
  • microarray
  • serious bacterial infection

ASJC Scopus subject areas

  • Pediatrics, Perinatology, and Child Health
  • Emergency Medicine


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