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Completed

NCT Number: NCT07256405

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

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.

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Key information

Conditions

Infection Bone Fracture Fractures, Bone Infections Wounds and Injuries

Age range

18 year and older

Sex eligibility

All sexes

Study type

Observational

Primary location

IHU, service des maladies infectieuses chroniques, Marseille, Bouches-du-Rhône, France

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About this study

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.

Who can participate

Healthy volunteers accepted: No

Only the study team can determine whether someone qualifies for participation.

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.

Treatment and study plan

Metagenomic sequencing

Diagnostic Test

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

Primary outcomes

  1. Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)

    Time frame: 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 outcomes

  1. Time to obtain final microbiological results by sequencing compared with the reference technique (culture)

    Time frame: 1 month

    Duration (in days) for definitive microbiological diagnosis using both culture and NGS-based protocols.

  2. Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.

    Time frame: 1 month

    Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.

  3. Microbial abundance defined by the number of reads (sequence reads) obtained per phylotype

    Time frame: 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.

Sponsors and collaborators

Lead sponsor

Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer

Other

Collaborators

  • Institut Hospitalo-Universitaire Méditerranée Infection
  • Military Teaching Hospital Sainte Anne, Toulon

Registry information

Official study title

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

Acronym: METADIAG 2

Important dates

Study start
2024
Primary completion
2025
Study completion
2025
First posted
Dec 1, 2025
Registry last updated
Jul 7, 2026

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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