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Novel Diagnostics in Revision Arthroplasty: Implant Sonication and Multiplex Polymerase Chain Reaction
Published on: December 3, 2017
Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic
Hyo-Lim Hong1,2, Laure Flurin1,3, Matthew J Thoendel4
1Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA.
Background:
Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure.
Methods:
A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq.
Results:
A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83).
Conclusions:
16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.
Insights
Targeted metagenomic sequencing (tNGS) of 16S rRNA genes shows promise for diagnosing periprosthetic joint infections (PJI) in joint fluid. This method offers similar performance to shotgun metagenomic sequencing (sNGS) and can identify pathogens missed by traditional cultures.
Area of Science:
- Microbiology
- Genomics
- Orthopedic Surgery
Background:
- Periprosthetic joint infection (PJI) diagnosis relies on methods with variable accuracy.
- Next-generation sequencing (NGS) offers potential but requires further clinical validation.
- Shotgun metagenomic sequencing (sNGS) can detect pathogens missed by culture but is complex and costly.
Purpose of the Study:
- To compare 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) with sNGS for microbial detection in failed total hip arthroplasty (THA) and total knee arthroplasty (TKA).
- To evaluate the diagnostic utility of tNGS in culture-negative PJI cases.
Main Methods:
- Sonicate fluid samples from 395 patients with THA or TKA failure were analyzed.
- Samples were tested using culture, sNGS, and 16S rRNA gene-based tNGS (targeting V1-V3 regions).
- tNGS involved DNA extraction, PCR amplification, and Illumina MiSeq sequencing.
Main Results:
- tNGS demonstrated higher positive percent agreement than culture for PJI diagnosis (72.1% vs 52.9%, P < .001).
- tNGS identified potential pathogens in 48.0% of culture-negative PJI cases.
- The positive percent agreement of tNGS was comparable to sNGS (72.1% vs 73.1%, P = .83).
Conclusions:
- 16S rRNA gene-based tNGS is a viable diagnostic tool for identifying PJI pathogens in sonicate fluid.
- tNGS performs similarly to sNGS and is effective in detecting pathogens in culture-negative cases.
- tNGS shows potential for improving PJI diagnosis in patients with failed THA and TKA.
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