Microbial cell-free DNA-sequencing as an addition to conventional diagnostics in neonatal sepsis

Julian Balks; Silke Grumaz; Sonia Mazzitelli; Ulrike Neder; Lotte Lemloh; Tamene Melaku; Kirsten Glaser; Andreas Mueller; Florian Kipfmueller

doi:10.1038/s41390-024-03448-1

Microbial cell-free DNA-sequencing as an addition to conventional diagnostics in neonatal sepsis

Pediatr Res. 2024 Aug 14. doi: 10.1038/s41390-024-03448-1. Online ahead of print.

Authors

Julian Balks^{1

2}, Silke Grumaz³, Sonia Mazzitelli³, Ulrike Neder³, Lotte Lemloh¹, Tamene Melaku¹, Kirsten Glaser⁴, Andreas Mueller¹, Florian Kipfmueller⁵

Affiliations

¹ Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany.
² Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany.
³ Noscendo, Duisburg, Germany.
⁴ Division of Neonatology, Department of Women's and Children's Health, University Medical Center Leipzig, Leipzig, Germany.
⁵ Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany. florian.kipfmueller@ukbonn.de.

PMID: 39143203
DOI: 10.1038/s41390-024-03448-1

Abstract

Background: Bloodstream infections remain a challenge for neonatologists, as traditional culture-based methods are time-consuming and rely on adequate blood volume. Next-generation sequencing (NGS) offers an alternative, as it can identify microbial cell-free DNA (mcfDNA) in a small blood sample, providing rapid pathogen detection. This study aimed to assess the diagnostic performance of DISQVER®-NGS compared to blood cultures in neonatal patients with suspected sepsis.

Methods: In neonates with suspected sepsis, blood cultures and samples for NGS were prospectively collected. Patients were divided into four categories: 1) sepsis, blood culture positive, 2) clinical sepsis, culture negative, 3) suspected sepsis, 4) validation cohort.

Results: NGS detected bacterial, viral or fungal mcfDNA in 24 of 82 samples. Blood cultures were collected in 46 of 84 patients (15/46 positive). DISQVER® correctly identified pathogens in 9/15 patients with a positive blood culture, two with intrinsic resistance to their antibiotic regimen. In seven samples NGS reported the mcfDNA of bacteria that could have theoretically grown in culture but did not.

Conclusions: NGS may enhance sensitivity in sepsis diagnostics by detecting mcfDNA in neonates with suspected sepsis. Interpreting NGS results requires correlation with clinical data, laboratory values, and routine microbiological tests for a comprehensive understanding of the patient's condition.

Impact: Conventional blood culture methods have limitations in accuracy and turnaround time. The study aimed to investigate the diagnostic performance of the Next-Generation Sequencing method DISQVER® compared to traditional blood cultures in neonatal patients with suspected sepsis. Our findings suggest that NGS has the potential to augment the precision of conventional diagnostic techniques, can lead to improved detection of pathogens and targeted treatment approaches in neonatal sepsis. It is emphasized that further validation and integration with clinical and microbiological data are required to ensure optimal clinical utility.