IMR Press / FBL / Volume 27 / Issue 11 / DOI: 10.31083/j.fbl2711302
Open Access Short Communication
Next Generation Sequencing of Free Microbial DNA for Rapid Identification of Pathogens in Critically Ill Children with Systemic Inflammatory Response Syndrome (SIRS)
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1 Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany
2 West German Centre of Infectious Diseases (WZI), University Hospital Essen, 45147 Essen, Germany
3 Institute of Medical Microbiology, University Medicine Essen, University Duisburg-Essen, 45147 Essen, Germany
4 Institute of Virology, University Medicine Essen, University Duisburg-Essen, 45147 Essen, Germany
5 Noscendo GmbH, Duisburg, 47198 Duisburg, Germany
6 Department of Pediatrics III, Pediatric Hematology and Oncology, Cardiology, Pulmonology, University Hospital Essen, 45147 Essen, Germany
7 Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
*Correspondence: (Sarah C. Goretzki)
Academic Editor: Vijay Kumar
Front. Biosci. (Landmark Ed) 2022, 27(11), 302;
Submitted: 27 July 2022 | Revised: 28 September 2022 | Accepted: 7 October 2022 | Published: 8 November 2022
Copyright: © 2022 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.

Background: Infections, major surgeries, and hyperinflammatory syndromes are known to trigger Systemic Inflammatory Response Syndrome (SIRS). Discrimination between infectious and noninfectious inflammation often poses a challenge in chronically ill patients with multiple comorbidities. These patients are routinely treated with a variety of anti-infective medications before a pathogen is identified. With the goal of improving pathogen detection rates and interventions, we evaluated Next Generation Sequencing (NGS) as a highly sensitive and fast means of detecting free microbial DNA in a small amount of serum samples from children with ongoing SIRS. Methods: We describe seven complex pediatric patients of SIRS or prolonged fever (>38.5 °C) >72 hours in which serum samples analyzed by NGS had a major impact on therapy. One patient was analyzed twice. Results: In eight NGS there were six positive results (two bacterial, three viral, one fungal) which were subsequently confirmed by microbiological culture or polymerase chain reaction (PCR) in five of the six NGS. In five of the eight performed NGS, results led to a change of therapy: antibiotic therapy was discontinued in two, escalated in one, an initiated in another; in one an antiviral was administered. Conclusions: NGS may become a valuable addition to infectious disease diagnostics in cases of pediatric SIRS. However, NGS has not yet been validated as a diagnostic method in pediatric as a diagnostic method in pediatric patients and results should therefore be interpreted with caution. Multi-center NGS evaluation studies are currently being planned.

next generation sequencing
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