METADIAG: Clinical Metagenomic of Post-traumatic Infections
Study Details
Study Description
Brief 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.
| Condition or Disease | Intervention/Treatment | Phase |
|---|---|---|
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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 Design
Arms and Interventions
| Arm | 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.
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Outcome Measures
Primary Outcome Measures
- Microbiome of fracture-related and other trauma-related infection [About 2 months]
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).
Secondary Outcome Measures
- Comparison of high throughput sequencing techniques yield [About 3 months]
The FRI-associated microbiomes composition obtained with each sequencing methods will be compared in terms of abundance and variety (K coefficient and frequency)
- Number and nature of virulence or resistance factors among identified OTU (operational Taxonomic Unit) [About 6 months]
Functional annotation of sequenced bacterial genomes to assess the presence of virulence and/or resistance-associated factors, using Prokka software.
- Number of bacteria and their relative abundance according to patients' outcome using the EBJIS (European Bone and Joint Infection) definition [About 6 months]
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.
Eligibility Criteria
Criteria
Inclusion Criteria:
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Age ≥ 18 years
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Diagnosis of trauma-related infection
Exclusion Criteria:
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Participation in an interventional research during the study
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Patient opposition
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Absence of bone or soft tissue samples stored at -80°C
Contacts and Locations
Locations
| Site | City | State | Country | Postal Code | |
|---|---|---|---|---|---|
| 1 | Military Teaching Hospital Sainte Anne | Toulon | Var | France | 83000 |
Sponsors and Collaborators
- Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
- Military Teaching Hospital Sainte Anne, Toulon
- UMR Vitrome, IRD 257
Investigators
- Study Director: David LACÔTE-DELARBRE, MD, Military Teaching Hospital Sainte Anne
Study Documents (Full-Text)
None provided.More Information
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.
- 2023-CHITS-003