Clinical Metagenomic Next-Generation Sequencing for Microbial Infections in Trauma
试验速览
- 阶段
- 不适用
- 状态
- 已完成
- 发起方
- 入组人数
- 25
- 试验地点
- 1
- 主要终点
- Microbiome of fracture-related and other trauma-related infection
研究概览
简要总结
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.
详细描述
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.
研究设计
- 研究类型
- Observational
- 观察模型
- Cohort
- 时间视角
- Retrospective
入排标准
- 年龄范围
- 18 Years 至 —（Adult, Older Adult）
- 性别
- All
- 接受健康志愿者
- 否
入选标准
- •Age ≥ 18 years
- •Diagnosis of trauma-related infection
排除标准
- •Participation in an interventional research during the study
- •Patient opposition
- •Absence of bone or soft tissue samples stored at -80°C
结局指标
主要结局
Microbiome of fracture-related and other trauma-related infection
时间窗: 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).
次要结局
- Number of bacteria and their relative abundance according to patients' outcome using the EBJIS (European Bone and Joint Infection) definition(About 6 months)
- Comparison of high throughput sequencing techniques yield(About 3 months)
- Number and nature of virulence or resistance factors among identified OTU (operational Taxonomic Unit)(About 6 months)