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

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.

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.

Inclusion Criteria:

• Age ≥ 18 years
• Diagnosis of fracture-related infection (FRI consensus group)
• Patient scheduled to undergo a bone and/or soft-tissue biopsy as part of routine care

Exclusion Criteria:

• Patient opposition
• Patient under a legal protection measure.