NCT07256405

Metagenomic Next-Generation Sequencing for the Diagnosis of Fracture-related Infection

Contribution of Metagenomic Sequencing Using Nanopore Technology to the Management of Post-traumatic Bone and Joint Infections

• Status: Active Not Recruiting
• Phase: —
• Study type: Observational
• Enrollment: 100 (actual)
• Sponsor: Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer · Academic / Other
• Sex: All
• Age: 18 Years
• Healthy volunteers: Not accepted

Summary

The value of next-generation sequencing (NGS) using Nanopore technology has been demonstrated in the case of diabetic patients' wounds or in prosthetic joint infections. The aim of this study is to demonstrate its relevance as a new diagnostic approach for fracture-related infections (FRI). Bone samples from patient with FRI will be submitted to shotgun metagenomic Next-generation sequencing using Oxford Nanopore Technology (ONT) in order to establish its diagnostic value in this context in comparison with the reference method.

Detailed description

Tissue samples from patients with FRI used for routine culture and remaining after this step will be retrieved for metagenomic sequencing. Both DNA extraction and host-DNA depletion steps will be performed. The nanopore ligation sequencing protocol along with native barcoding will be used to carry out DNA library preparation. Sequencing will be run using ONT GridION device. The generated reads will be computerized to be assigned at each taxonomic levels. The results will be compared to those of routine diagnosis to determine NGS concordance with culture.

Conditions

• Infection
• Fracture
• Bone

Interventions

Type	Name	Description
DIAGNOSTIC_TEST	Metagenomic sequencing	Samples shall be submitted to high throughput sequencing using both illumine MiSeq and Oxford Nanopore Technologies.

Timeline

• Start date: 2024-03-11
• Primary completion: 2025-12-31
• Completion: 2025-12-31
• First posted: 2025-12-01
• Last updated: 2025-12-05

Locations

2 sites across 1 country: France