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.
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 Type
OBSERVATIONAL
Enrollment
100
Samples shall be submitted to high throughput sequencing using both illumine MiSeq and Oxford Nanopore Technologies.
IHU, service des maladies infectieuses chroniques
Marseille, Bouches-du-Rhône, France
Military Teaching Hospital Sainte Anne
Toulon, VAR, France
Concordance between the microbiological documentation obtained by sequencing and that of the reference technique (culture)
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).
Time frame: 1 month
Time to obtain final microbiological results by sequencing compared with the reference technique (culture)
Duration (in days) for definitive microbiological diagnosis using both culture and NGS-based protocols.
Time frame: 1 month
Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.
Number of cases in which an adjustment of targeted antibiotic therapy would be made based on NGS results.
Time frame: 1 month
Microbial abundance defined by the number of reads (sequence reads) obtained per phylotype
To describe the microbiome of fracture related infection in terms of microbial diversity and abundance in order to discuss both raw reads number and relative abundance roles when considering NGS results in this context.
Time frame: 1 month
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