Clinical Metagenomic of Post-traumatic Infections (METADIAG)

Clinical Metagenomic Next-Generation Sequencing for Microbial Infections in Trauma

Treatment of fracture related infection is challenging and often lead to failure in such situation that carry a high health cost burden.

These infections are often polymicrobial, making the identification of all involved microorganisms a major concern to provide tailored antibiotic treatment. Culture-independent methods are needed to better represent the microbial diversity of infected wounds. Metagenomic sequencing might lead to an accurate microbiome characterization in infected trauma-related wound.

Preliminary studies have reported results of metagenomic sequencing in diabetic foot infection but data focusing on non-diabetic infected patients are scarce.

The impact of post-traumatic infected wound microbiome needs to be assessed, with regards to bacterial abundance, diversity including at the strain level and functional genes, along with their longitudinal evolution and association with clinical outcomes.

Study Overview

• Status: Completed
• Conditions: Infections; Fractures, Bone
• Intervention / Treatment: Diagnostic test: Metagenomic sequencing

Detailed Description

DNA will be extracted from samples carried out during surgical procedures. Different extraction protocols will be assessed to determine the best to be used for this type of tissue samples.

Purified DNA will be quantified using the Qubit dsDNA High-Sensitivity Assay Kit (Invitrogen). The quality of the fragment length will be estimated with the DNA high-sensitivity kit in the 2100 Bioanalyzer (Agilent Technologies). DNA sequencing will be performed with Oxford Nanopore Technologie devices: MinIONTM and GridIONTM.

Another sequencing of the same samples will be performed on the MiSeq after libraries preparation using the NexteraXT DNA Library Preparation Kit (Illumina).

Sequenced OTU from both sequencing methods will be confronted at different taxonomic ranks and compared with conventional routine method results (bacterial culture). A functional analysis of sequences will be done to identify potential genes associated with clinical outcome.

• Study Type: Observational
• Enrollment (Actual): 25

Contacts and Locations

Study Locations

• France
  • Var
    • Toulon, Var, France, 83000
      • Military Teaching Hospital Sainte Anne

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years and older (Adult, Older Adult)
• Accepts Healthy Volunteers: N/A

• Sampling Method: Non-Probability Sample

Study Population

Patients admitted to hospital for trauma for which an infection of the traumatic site was diagnosed

Description

Inclusion Criteria:

• Age ≥ 18 years
• Diagnosis of trauma-related infection

Exclusion Criteria:

• Participation in an interventional research during the study
• Patient opposition
• Absence of bone or soft tissue samples stored at -80°C

Study Plan

How is the study designed?

Number of groups / cohorts

1

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Trauma related infection	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
Microbiome of fracture-related and other trauma-related infection	Metagenomic sequencing will be used to determine the microbiome of trauma-related infections using Illumina MiSeq and Oxford Nanopore Technologies. Data will be compared with those from reference microbiological identification techniques (culture).	About 2 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Comparison of high throughput sequencing techniques yield	The FRI-associated microbiomes composition obtained with each sequencing methods will be compared in terms of abundance and variety (K coefficient and frequency)	About 3 months
Number and nature of virulence or resistance factors among identified OTU (operational Taxonomic Unit)	Functional annotation of sequenced bacterial genomes to assess the presence of virulence and/or resistance-associated factors, using Prokka software.	About 6 months
Number of bacteria and their relative abundance according to patients' outcome using the EBJIS (European Bone and Joint Infection) definition	To determine the association of the NGS-based microbiome longtitudinal composition in terms of variety (number of OTU) and abundance (number of reads) with infection persistence according to the EBJIS (European Bone and Joint Infection) definition.	About 6 months

Collaborators and Investigators

• Sponsor: Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
• Collaborators: Military Teaching Hospital Sainte Anne, Toulon; UMR Vitrome, IRD 257
• Investigators: Study Director: David LACÔTE-DELARBRE, MD, Military Teaching Hospital Sainte Anne

Publications and helpful links

General Publications

• 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.
• Jnana A, Muthuraman V, Varghese VK, Chakrabarty S, Murali TS, Ramachandra L, Shenoy KR, Rodrigues GS, Prasad SS, Dendukuri D, Morschhauser A, Nestler J, Peter H, Bier FF, Satyamoorthy K. Microbial Community Distribution and Core Microbiome in Successive Wound Grades of Individuals with Diabetic Foot Ulcers. Appl Environ Microbiol. 2020 Mar 2;86(6):e02608-19. doi: 10.1128/AEM.02608-19. Print 2020 Mar 2.
• Kalan LR, Meisel JS, Loesche MA, Horwinski J, Soaita I, Chen X, Uberoi A, Gardner SE, Grice EA. Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy. Cell Host Microbe. 2019 May 8;25(5):641-655.e5. doi: 10.1016/j.chom.2019.03.006. Epub 2019 Apr 18.
• Mudrik-Zohar H, Carasso S, Gefen T, Zalmanovich A, Katzir M, Cohen Y, Paitan Y, Geva-Zatorsky N, Chowers M. Microbiome Characterization of Infected Diabetic Foot Ulcers in Association With Clinical Outcomes: Traditional Cultures Versus Molecular Sequencing Methods. Front Cell Infect Microbiol. 2022 Mar 24;12:836699. doi: 10.3389/fcimb.2022.836699. eCollection 2022.
• Delarbre D, Lavrard P, Elias A, Bossi V, Kacel I, Janvier F, Fournier PE. Bacterial DNA enrichment for low-inoculum fracture-related infection diagnostic using high-throughput sequencing. Diagn Microbiol Infect Dis. 2024 Jun 22;110(1):116411. doi: 10.1016/j.diagmicrobio.2024.116411. Online ahead of print.

Study record dates

Study Major Dates

• Study Start (Actual): April 27, 2023
• Primary Completion (Actual): July 15, 2023
• Study Completion (Actual): July 15, 2023

Study Registration Dates

• First Submitted: February 7, 2023
• First Submitted That Met QC Criteria: March 14, 2023
• First Posted (Actual): March 16, 2023

Study Record Updates

• Last Update Posted (Actual): July 29, 2024
• Last Update Submitted That Met QC Criteria: July 26, 2024
• Last Verified: July 1, 2024

More Information

Terms related to this study

• Keywords: Infection; Microbiome; Diagnosis; Trauma; High throughput sequencing; Nanopore
• Additional Relevant MeSH Terms: Pathologic Processes; Wounds and Injuries; Disease Attributes; Infections; Communicable Diseases; Fractures, Bone
• Other Study ID Numbers: 2023-CHITS-003

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