Clinical Metagenomic of Post-traumatic Infections

Infections Clinical Trial

— METADIAG  

Official title:

Clinical Metagenomic Next-Generation Sequencing for Microbial Infections in Trauma

Clinical Trial Details — Status: Completed

Administrative data

• NCT number: NCT05770856
• Other study ID #: 2023-CHITS-003
• Status: Completed
• Start date: April 27, 2023
• Est. completion date: July 15, 2023

Study information

• Verified date: March 2024
• Source: Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
• Contact: n/a
• Is FDA regulated: No
• Study type: Observational

Clinical Trial Summary

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.

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.

Recruitment information / eligibility

• Status: Completed
• Enrollment: 25
• Est. completion date: July 15, 2023
• Est. primary completion date: July 15, 2023
• Gender: All
• Age group: 18 Years and older

Eligibility

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

Related Conditions & MeSH terms

• Communicable Diseases
• Fractures, Bone
• Infections

Intervention

Diagnostic Test:
• Metagenomic sequencing
Samples shall be submitted to high throughput sequencing using both illumine MiSeq and Oxford Nanopore Technologies.

Locations

Country	Name	City	State
France	Military Teaching Hospital Sainte Anne	Toulon	Var

Sponsors (3)

Lead Sponsor	Collaborator
Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer	Military Teaching Hospital Sainte Anne, Toulon, UMR Vitrome, IRD 257

Country where clinical trial is conducted

France, 

References & Publications (4)

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. — View Citation

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. — View Citation

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. — View Citation

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. — View Citation

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	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	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
Secondary	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
Secondary	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