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Published on: December 3, 2017
Nanopore 16S amplicon sequencing enables rapid detection of pathogen in knee periprosthetic joint infection
Hyuk-Soo Han1, Du Hyun Ro1, Jeehyeok Chung1
1Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea.
Objectives:
We investigated whether nanopore 16S amplicon sequencing is capable of bacterial identification in patients with knee prosthetic joint infection (PJI), and we compared its efficacy with conventional culture studies.
Methods:
In total, 36 patients who had clinical manifestation suspected of PJI were enrolled in this study. To begin, synovial fluids were aspirated from the affected knee using aseptic technique and tissues specimens were obtained during the surgery. Next, DNA was extracted from the synovial fluid or tissues, and 16S rDNA PCR was performed. In PCR positive cases, nanopore amplicon sequencing was then performed for up to 3 h. The results of amplicon sequencing were compared to those of conventional culture studies.
Results:
Of the 36 patients enrolled, 22 were classified as true infections according to the MSIS criteria whereas 14 were considered uninfected. Among the 22 PJI cases, 19 cases were culture positive (CP-PJI) while three cases were culture negative (CN-PJI). In 14 of 19 (73.7 %) CP- PJI cases, 16S sequencing identified concordant bacteria with conventional culture studies with a significantly shorter turnaround time. In some cases, nanopore 16S sequencing was superior to culture studies in the species-level identification of pathogen and detection of polymicrobial infections. Altogether, in the majority of PJI candidate patients (32 of 36, 88.9 %), 16S sequencing achieved identical results to cultures studies with a significantly reduced turnaround time (100.9 ± 32.5 h vs. 10.8 ± 7.7 h, p < 0.001).
Conclusions:
Nanopore 16S sequencing was found to be particularly useful for pathogen identification in knee PJI. Although the sensitivity was not superior to culture studies, the nanopore 16S sequencing was much faster, and species-level identification and detection of polymicrobial infections were superior to culture studies.
Insights
Nanopore 16S sequencing rapidly identifies bacteria in knee prosthetic joint infections (PJI), offering faster results and superior species-level identification compared to traditional cultures. This method aids in diagnosing polymicrobial infections more effectively.
Area of Science:
- Microbiology
- Infectious Diseases
- Medical Diagnostics
Background:
- Prosthetic joint infection (PJI) is a serious complication following knee replacement surgery.
- Accurate and rapid bacterial identification is crucial for effective PJI management.
- Conventional culture methods can be slow and may fail to detect all causative pathogens.
Purpose of the Study:
- To evaluate the capability of nanopore 16S amplicon sequencing for bacterial identification in knee PJI.
- To compare the diagnostic efficacy of nanopore sequencing with conventional culture studies.
Main Methods:
- Synovial fluid and tissue samples were collected from 36 patients with suspected knee PJI.
- DNA was extracted, followed by 16S rDNA PCR and subsequent nanopore amplicon sequencing.
- Results were compared against conventional bacterial culture studies.
Main Results:
- Nanopore 16S sequencing achieved concordant results with culture studies in 73.7% of culture-positive PJI cases.
- The sequencing method demonstrated a significantly shorter turnaround time (10.8 ± 7.7 h vs. 100.9 ± 32.5 h).
- Nanopore sequencing showed superiority in species-level identification and detecting polymicrobial infections.
Conclusions:
- Nanopore 16S sequencing is a valuable tool for pathogen identification in knee PJI.
- While not more sensitive than culture, it offers significant speed advantages.
- Its enhanced ability for species-level and polymicrobial detection improves diagnostic accuracy in PJI.
