Metagenomic Next-Generation Sequencing for the Diagnosis of Fracture-related Infection (METADIAG 2)

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.

Study Overview

• Status: Active, not recruiting
• Conditions: Infection; Bone; Fracture
• Intervention / Treatment: Diagnostic test: Metagenomic sequencing

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.

• Study Type: Observational
• Enrollment (Actual): 100

Contacts and Locations

Study Locations

• France
  • Bouches-du-Rhône
    • Marseille, Bouches-du-Rhône, France, 13005
      • IHU, service des maladies infectieuses chroniques
  • VAR
    • Toulon, VAR, France, 83000
      • Military Teaching Hospital Sainte Anne

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Patients admitted to hospital following trauma for whom a fracture-related infection was diagnosed.

Description

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.

Study Plan

How is the study designed?

Number of groups / cohorts

1

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Fracture-related infection; Patients suspected of having acute or chronic post-traumatic osteoarticular infection according to the criteria of the FRI (Fracture-Related Infection) consensus group and scheduled to undergo a bone and/or soft tissue biopsy as part of routine care	Diagnostic test: Metagenomic sequencing; Samples shall be submitted to high throughput sequencing using both illumine MiSeq and Oxford Nanopore Technologies.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)	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).	1 month

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Time to obtain final microbiological results by sequencing compared with the reference technique (culture)	Duration (in days) for definitive microbiological diagnosis using both culture and NGS-based protocols.	1 month
Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.	Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.	1 month
Microbial abundance defined by the number of reads (sequence reads) obtained per phylotype	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.	1 month

Collaborators and Investigators

• Sponsor: Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
• Collaborators: Institut Hospitalo-Universitaire Méditerranée Infection; Military Teaching Hospital Sainte Anne, Toulon
• Investigators: Study Director: LACÔTE-DELARBRE David, MD, Military Teaching Hospital Sainte Anne

Publications and helpful links

General Publications

• Tarabichi M, Shohat N, Goswami K, Alvand A, Silibovsky R, Belden K, Parvizi J. Diagnosis of Periprosthetic Joint Infection: The Potential of Next-Generation Sequencing. J Bone Joint Surg Am. 2018 Jan 17;100(2):147-154. doi: 10.2106/JBJS.17.00434.
• Goswami K, Shope AJ, Tokarev V, Wright JR, Unverdorben LV, Ly T, Chen See J, McLimans CJ, Wong HT, Lock L, Clarkson S, Parvizi J, Lamendella R. Comparative meta-omics for identifying pathogens associated with prosthetic joint infection. Sci Rep. 2021 Dec 9;11(1):23749. doi: 10.1038/s41598-021-02505-7.
• Sanderson ND, Street TL, Foster D, Swann J, Atkins BL, Brent AJ, McNally MA, Oakley S, Taylor A, Peto TEA, Crook DW, Eyre DW. Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices. BMC Genomics. 2018 Sep 27;19(1):714. doi: 10.1186/s12864-018-5094-y.
• Ivy MI, Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Hanssen AD, Abdel MP, Chia N, Yao JZ, Tande AJ, Mandrekar JN, Patel R. Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing. J Clin Microbiol. 2018 Aug 27;56(9):e00402-18. doi: 10.1128/JCM.00402-18. Print 2018 Sep.
• Walter N, Orbenes N, Rupp M, Alt V. The State of Research in Fracture-Related Infection-A Bibliometric Analysis. Medicina (Kaunas). 2022 Aug 29;58(9):1170. doi: 10.3390/medicina58091170.

Study record dates

Study Major Dates

• Study Start (Actual): March 11, 2024
• Primary Completion (Estimated): December 31, 2025
• Study Completion (Estimated): December 31, 2025

Study Registration Dates

• First Submitted: November 20, 2025
• First Submitted That Met QC Criteria: November 20, 2025
• First Posted (Estimated): December 1, 2025

Study Record Updates

• Last Update Posted (Actual): December 5, 2025
• Last Update Submitted That Met QC Criteria: December 1, 2025
• Last Verified: November 1, 2025

More Information

Terms related to this study

• Keywords: Infection; Trauma; Fracture; Metagenomic; High throughput sequencing; Nanopore
• Additional Relevant MeSH Terms: Fractures, Bone; Wounds and Injuries; Infections
• Other Study ID Numbers: 2023-CHITS-017

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No