Narrative review evaluates Oxford Nanopore sequencing for pediatric infectious disease diagnostics

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Frontiers in Medicine Published May 8, 2026 Medically reviewed May 8, 2026 DOI ↗ By Dr. Amelia Tan, PhD · Internal Medicine & Chronic Disease

Key Takeaway

Note bioinformatics complexity and analytical standardization limits for ONT sequencing in pediatric infections.

This narrative review focuses on the application of Oxford Nanopore Technologies (ONT) sequencing within the setting of pediatric emergency infectious diseases. The scope covers acute respiratory infections, bloodstream infections, and central nervous system infections in pediatric patients. The authors explore how this technology might support pathogen identification, antimicrobial resistance profiling, strain typing, and host-pathogen interactions compared to conventional diagnostic approaches.

The review highlights that specific primary outcomes were not reported in the source material. Secondary outcomes discussed include the ability to perform detailed pathogen identification, antimicrobial resistance profiling, strain typing, and analysis of host-pathogen interactions. The authors note that the sample size was not reported for this synthesis.

Significant limitations identified by the authors include bioinformatics complexity and a lack of analytical standardization. Safety data, including adverse events and tolerability, were not reported. The review does not establish causality and maintains a cautious stance regarding practice relevance due to these gaps.

Study Details

Study typeSystematic review

EvidenceLevel 1

PublishedMay 2026

View Original Abstract ↓

Pediatric emergency infectious diseases necessitate rapid and accurate etiologic diagnosis to inform timely, life-saving interventions. However, conventional diagnostic approaches are often hindered by prolonged turnaround times and limited capability in detecting diverse pathogens. Oxford Nanopore Technologies (ONT) sequencing, a fourth-generation, real-time genomic platform, offers a transformative solution. With unique features such as ultra-long read lengths, real-time data streaming, and portability, ONT enables comprehensive microbial characterization directly at the point of care, even from low-biomass clinical specimens. This review outlines the fundamental principles of ONT sequencing and recent advances in protocol optimization for challenging pediatric samples. We highlight its groundbreaking applications in acute respiratory, bloodstream, and central nervous system infections, demonstrating its capacity to simultaneously deliver pathogen identification, antimicrobial resistance profiling, and strain typing. Moreover, ONT facilitates novel insights into host-pathogen interactions through integrated genomic and transcriptomic analyzes. We also address current challenges, including bioinformatics complexity and analytical standardization, and propose pathways toward integration within a precision infectious disease framework. Beyond diagnostics, ONT is emerging as a powerful tool to advance infection biology and improve clinical outcomes in children.