Cerebrospinal fluid metagenomic next-generation sequencing (mNGS) is currently revolutionizing how clinicians manage pediatric central nervous system disorders. In cases of suspected neonatal intracranial infections, early and accurate pathogen identification remains vital for survival. Traditional methods like culture often fall short because of low pathogen loads or prior antibiotic use. Consequently, researchers are turning to advanced molecular tools like mNGS for neonatal intracranial infections to improve diagnostic yields and precision. Recent data suggests that this technology offers a much more comprehensive view of the microbial landscape than conventional testing alone.

Furthermore, researchers at the Children's Hospital, Zhejiang University School of Medicine, conducted a retrospective study analyzing 61 neonates with suspected infections. The results showed that mNGS successfully identified pathogens in half of the etiologically confirmed cases. Interestingly, 50% of these specific pathogens were detected exclusively by mNGS. While the sensitivity of mNGS reached 31.3%, it outperformed culture and PCR, which collectively reached only 18.8%. Although this difference did not achieve statistical significance, the clinical utility remained substantial. Moreover, multivariate analysis identified a positive mNGS result as an independent factor associated with a positive clinical impact.

Clinical Impact of mNGS for Neonatal Intracranial Infections

In addition to its diagnostic superiority, mNGS significantly influences bedside clinical decisions. In the evaluated cohort, 37.7% of patients experienced a direct change in management based on their mNGS results. For 12 infants, positive findings guided specific treatment adjustments and targeted therapies. Conversely, 11 infants with negative results benefited from antibiotic de-escalation or complete discontinuation. This dual role highlights how mNGS helps both in confirming difficult infections and in supporting robust antibiotic stewardship. Therefore, incorporating this advanced tool into neonatal care could potentially reduce unnecessary drug exposure and improve long-term outcomes.

Frequently Asked Questions

How does mNGS compare to traditional CSF culture in neonates?

mNGS offers higher sensitivity than traditional culture, especially when pathogens are difficult to grow or when patients have already received antibiotics. In this study, mNGS provided unique etiological diagnoses in 50% of confirmed cases where culture failed.

Can mNGS results support antibiotic stewardship in the NICU?

Yes. Negative mNGS results can provide clinicians with the confidence to de-escalate or discontinue broad-spectrum antibiotics, thereby reducing the risk of drug toxicity and the development of antibiotic resistance in neonates.

Disclaimer: This content is for informational and educational purposes only and does not constitute medical advice, diagnosis, or treatment. Always seek the advice of a qualified healthcare provider with any questions regarding a medical condition. Refer to the latest local and national guidelines for clinical practice.

References

Li L et al. [Clinical value of cerebrospinal fluid metagenomic next genera-tion sequencing in diagnosing neonatal intracranial infections]. Zhejiang Da Xue Xue Bao Yi Xue Ban. 2026 Jun 08. doi: 10.3724/zdxbyxb-2025-0965. PMID: 42260308.

Zhang Y et al. Metagenomic Next-Generation Sequencing for the Diagnosis of Neonatal Infectious Diseases. Microbiol Spectr. 2022;10(6):e0121322. doi: 10.1128/spectrum.01213-22.

Wang S et al. Diagnostic Performance of Clinical Metagenomic Next-Generation Sequencing for Suspected Central Nervous System Infections. Front Cell Infect Microbiol. 2023;13:1138217. doi: 10.3389/fcimb.2023.1138217.