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Study

Study Name: Sonication fluids microbial communities from explanted orthopaedic devices in Oxford, United Kingdom

Projects

Biosamples

Organisms

Biosamples: 5 Seq. Projects: 5
STUDY INFORMATION
GOLD Study ID Gs0153828
Study Name Sonication fluids microbial communities from explanted orthopaedic devices in Oxford, United Kingdom
Other Names
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id ERP105215  (Link to NCBI )
Study Title ONT MinION sequencing of prosthetic joint infection sonication fluids
Study Abstract Prosthetic joint infections are clinically difficult to diagnose and treat. Previously we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we compare direct-from-clinical-sample metagenomic Illumina sequencing with Nanopore sequencing, and report a real time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections.DNA was extracted from the sonication fluids of nine explanted orthopaedic devices, including two culture negative controls, and were sequenced on the Oxford Nanopore MinION platform. With high levels of host contamination and unavoidable background lab and kit contamination, a specific analysis pipeline was assembled to overcome the challenges of identifying the true infection pathogen.The majority of DNA classified (>90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological services diagnoses and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within ten minutes from initiation of sequencing. We demonstrate initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data. The high proportion of human DNA in extracts prevents further genotyping, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling.
  
Legacy ER Study ID
Legacy GOLD ID
Added By JGI automated process on 2021-03-17
Last Modified By
PI
Description The goal of this study is to compare direct-from-clinical-sample metagenomic Illumina sequencing with Nanopore sequencing, and report a real time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA
Is HMP
ECOSYSTEM CLASSIFICATION
Ecosystem Engineered
Ecosystem Category Industrial production
Ecosystem Type Engineered product
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
STUDY COMPOSITION
Number of Biosamples 5
Number of Organisms 0
Number of Seq Projects 5
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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