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Using nanopore sequencing to identify bacterial infection in joint replacements: a preliminary study
Hollie Wilkinson1,2, Jamie McDonald3, Helen S McCarthy1,2
1Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK.
Briefings in Functional Genomics
|March 31, 2024
Summary
Third-generation genomic sequencing accurately identifies bacteria causing prosthetic joint infections (PJIs) during revision surgery. While rapid bacterial identification is feasible, predicting antibiotic resistance requires further research.
Area of Science:
- Microbiology
- Genomics
- Orthopedic Surgery
Background:
- Prosthetic joint infections (PJIs) are a significant complication following joint replacement surgery.
- Accurate and rapid identification of causative bacteria is crucial for effective treatment.
- Current diagnostic methods, such as microbiological cultures, can be time-consuming.
Purpose of the Study:
- To evaluate the utility of third-generation genomic sequencing for identifying bacterial species in PJIs during revision surgery.
- To assess the feasibility of rapid bacterial identification using Nanopore sequencing.
- To explore the potential of genomic data for predicting antibiotic resistance in PJIs.
Main Methods:
- Prosthetic fluid samples were collected from patients undergoing revision surgery for PJIs and controls.
- Genomic sequencing was performed using Oxford Nanopore Technologies' MinION device.
- Bioinformatic pipelines (BLAST, Kraken2, MDS) and computational tools (ResFinder, AMRFinderPlus, CARD) were employed for bacterial identification and resistance prediction.
Main Results:
- Bioinformatic analysis pipelines successfully identified bacteria, consistent with standard microbiological cultures.
- Nanopore sequencing and genomic classification were completed within the surgical timeframe (2-3 hours).
- Antibiotic resistance prediction was not achieved within the clinically relevant timeframe, likely due to short read length and low read depth.
Conclusions:
- Genomic sequencing is a viable method for identifying bacterial species in infected joint replacements.
- The rapid turnaround time of Nanopore sequencing is suitable for intraoperative use.
- Further optimization is needed to enable timely prediction of antibiotic resistance using genomic sequencing.
