Contribution of Metagenomic Sequencing Using Nanopore Technology to the Management of Post-traumatic Bone and Joint Infections
Overview
- Phase
- Not Applicable
- Status
- Active, not recruiting
- Sponsor
- Centre Hospitalier Intercommunal de Toulon La Seyne sur Mer
- Enrollment
- 100
- Locations
- 2
- Primary Endpoint
- Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)
Overview
Brief Summary
The value of next-generation sequencing (NGS) using Nanopore technology has been demonstrated in the case of diabetic patients' wounds or in prosthetic joint infections. The aim of this study is to demonstrate its relevance as a new diagnostic approach for fracture-related infections (FRI).
Bone samples from patient with FRI will be submitted to shotgun metagenomic Next-generation sequencing using Oxford Nanopore Technology (ONT) in order to establish its diagnostic value in this context in comparison with the reference method.
Detailed Description
Tissue samples from patients with FRI used for routine culture and remaining after this step will be retrieved for metagenomic sequencing.
Both DNA extraction and host-DNA depletion steps will be performed. The nanopore ligation sequencing protocol along with native barcoding will be used to carry out DNA library preparation. Sequencing will be run using ONT GridION device. The generated reads will be computerized to be assigned at each taxonomic levels. The results will be compared to those of routine diagnosis to determine NGS concordance with culture.
Study Design
- Study Type
- Observational
- Observational Model
- Cohort
- Time Perspective
- Prospective
Eligibility Criteria
- Ages
- 18 Years to — (Adult, Older Adult)
- Sex
- All
- Accepts Healthy Volunteers
- No
Inclusion Criteria
- •Age ≥ 18 years
- •Diagnosis of fracture-related infection (FRI consensus group)
- •Patient scheduled to undergo a bone and/or soft-tissue biopsy as part of routine care
Exclusion Criteria
- •Patient opposition
- •Patient under a legal protection measure.
Outcomes
Primary Outcomes
Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)
Time Frame: 1 month
Metagenomic sequencing will be used to determine the microbiome of fracture-related infections. Data will be compared with those of reference microbiological identification techniques (culture).
Secondary Outcomes
- Time to obtain final microbiological results by sequencing compared with the reference technique (culture)(1 month)
- Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.(1 month)
- Microbial abundance defined by the number of reads (sequence reads) obtained per phylotype(1 month)