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

Completed

Phases

Unknown

Study type

Observational

Source

ClinicalTrials.gov

Registry ID

NCT07256405

Acronym

METADIAG 2

Enrollment

100

Registered

2025-12-01

Start date

2024-03-11

Completion date

2025-12-31

Last updated

2026-07-07

For informational purposes only — not medical advice. Sourced from public registries and may not reflect the latest updates. Terms

Conditions

Bone, Fracture, Infection

Keywords

Nanopore, Fracture, Metagenomic, Trauma, Infection, High throughput sequencing

Brief 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.

Interventions

DIAGNOSTIC_TESTMetagenomic sequencing

Samples shall be submitted to high throughput sequencing using both illumine MiSeq and Oxford Nanopore Technologies.

Study design

Observational model

COHORT

Time perspective

PROSPECTIVE

Eligibility

Sex/Gender

ALL

Age

18 Years to No maximum

Healthy volunteers

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.

Design outcomes

Primary

Measure	Time frame	Description
Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)	1 month	Metagenomic sequencing will be used to determine the microbiome of fracture-related infections. Data will be compared with those of reference microbiological identification techniques (culture).

Secondary

Measure	Time frame	Description
Time to obtain final microbiological results by sequencing compared with the reference technique (culture)	1 month	Duration (in days) for definitive microbiological diagnosis using both culture and NGS-based protocols.
Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.	1 month	Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.
Microbial abundance defined by the number of reads (sequence reads) obtained per phylotype	1 month	To describe the microbiome of fracture related infection in terms of microbial diversity and abundance in order to discuss both raw reads number and relative abundance roles when considering NGS results in this context.

Countries

France

Contacts

STUDY_DIRECTORLACÔTE-DELARBRE David, MD

Military Teaching Hospital Sainte Anne

Outcome results

None listed

Source: ClinicalTrials.gov · Data processed: Jul 8, 2026