USING NANOPORE SEQUENCING TO DIAGNOSE PROSTHETIC INFECTIONS: PRELIMINARY RESULTS FROM A SINGLE-CENTRE STUDY

Aim Prosthetic joint infection (PJI) is a serious complication following total joint arthroplasty (TJA) and can have devastating consequences if not treated effectively. There is no clear ‘gold standard’ for the diagnosis of PJI, current techniques include blood biochemical markers and microbiological cultures to identify the species of bacteria. Challenges associated with microbiological cultures include inaccurate results and time delays before reporting of results. In the hospital of study, samples of joint fluid and tissue are collected during surgical intervention for PJI and are sent to a partner hospital for microbiological cultures. Results are typically reported back after 7-14 days. Nanopore sequencing is a third-generation genomic sequencing technology designed to facilitate fast, inexpensive, and simple genomic sequencing. This study aims to investigate nanopore sequencing, as a quick and cost-effective method to identify the species of bacteria causing PJI from joint aspirates. Method Joint fluid aspirates were collected during surgical interventions for PJI. DNA was extracted from these samples and sequenced using the MinION device. Sequencing data was classified using Basic Local Alignment Search Tool (BLAST) against the bacterial database. Sequencing data was filtered by quality parameters such as Phred score. 30 samples of fluid were used for nanopore sequencing (26 PJI-positive and 4 controls), based on clinical definitions of infection. Clinical assessments included blood biochemical markers (CRP, ESR), histology, physical signs (e.g., redness, swelling) and multi-disciplinary team (MDT) decision. The MDT decision was used as the clinical decision of infection. Results from nanopore sequencing and microbiological cultures were compared with clinical assessments. Results Contingency tables were made to compare nanopore sequencing with the clinical assessment of patients and to compare microbiological cultures with the clinical decision of patients. Combining the results from nanopore sequencing with microbiological cultures gave an accuracy of 0.89, positive predictive value (PPV) of 0.92, recall (sensitivity) of 0.96 and F1 score of 0.94. The accuracy for microbiological cultures alone was 0.62. Conclusions Nanopore sequencing shows promise as an additional test in diagnosing PJI, particularly when cultures are negative. The advantage for the use of nanopore sequencing in the diagnosis of PJI is the turn-around time of results compared to microbiological cultures. This could have implications with reducing hospital stays, length of treatment and time frames between the first and second stage of a two-stage prosthetic exchange. This may improve patient outcomes and reduced treatment costs. Further studies could solidify its role in routine PJI diagnosis.