Clinical trial NCT05770856: Clinical Metagenomic of Post-traumatic Infections
Official title: Clinical Metagenomic Next-Generation Sequencing for Microbial Infections in Trauma
Study type: OBSERVATIONAL
Overall status: COMPLETED
Conditions: Fractures, Bone
Infections
Keywords: High throughput sequencing
Nanopore
Diagnosis
Trauma
Microbiome
Infection
Lead sponsor: Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
Sponsor class: OTHER
Collaborators: name: Military Teaching Hospital Sainte Anne, Toulon
name: UMR Vitrome, IRD 257
First posted: 2023-03-16
Enrollment: 25
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Observational model: COHORT
Time perspective: RETROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Patients admitted to hospital for trauma for which an infection of the traumatic site was diagnosed

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.

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.

Eligibility criteria: 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

Primary outcomes:
measure: Microbiome of fracture-related and other trauma-related infection
timeFrame: About 2 months
Secondary outcomes:
measure: Comparison of high throughput sequencing techniques yield
timeFrame: About 3 months
measure: Number and nature of virulence or resistance factors among identified OTU (operational Taxonomic Unit)
timeFrame: About 6 months
measure: Number of bacteria and their relative abundance according to patients' outcome using the EBJIS (European Bone and Joint Infection) definition
timeFrame: About 6 months
Other outcomes:
Locations:
city: Toulon
country: France
facility: Military Teaching Hospital Sainte Anne
state: Var
Study officials:
affiliation: Military Teaching Hospital Sainte Anne
name: David LACÔTE-DELARBRE, MD
role: STUDY_DIRECTOR
References:
citation: 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.
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.
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.
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.
citation: 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 Sep;110(1):116411. doi: 10.1016/j.diagmicrobio.2024.116411. Epub 2024 Jun 22.