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Next generation sequencing for pathogen detection in periprosthetic joint infections
Pier F Indelli1, Stefano Ghirardelli2, Bruno Violante2
1Department of Orthopaedic Surgery, Stanford University, Stanford, California, USA.
Abstract:
Periprosthetic joint infections (PJI) represent one of the most catastrophic complications following total joint arthroplasty (TJA). The lack of standardized diagnostic tests and protocols for PJI is a challenge for arthroplasty surgeons.Next generation sequencing (NGS) is an innovative diagnostic tool that can sequence microbial deoxyribonucleic acids (DNA) from a synovial fluid sample: all DNA present in a specimen is sequenced in parallel, generating millions of reads. It has been shown to be extremely useful in a culture-negative PJI setting.Metagenomic NGS (mNGS) allows for universal pathogen detection, regardless of microbe type, in a 24-48-hour timeframe: in its nanopore-base variation, mNGS also allows for antimicrobial resistance characterization.Cell-free DNA (cfDNA) NGS, characterized by lack of the cell lysis step, has a fast run-time (hours) and, together with a high sensitivity and specificity in microorganism isolation, may provide information on the presence of antimicrobial resistance genes.Metagenomics and cfDNA testing have reduced the time needed to detect infecting bacteria and represent very promising technologies for fast PJI diagnosis.NGS technologies are revolutionary methods that could disrupt the diagnostic paradigm of PJI, but a comprehensive collection of clinical evidence is still needed before they become widely used diagnostic tools. Cite this article: EFORT Open Rev 2021;6:236-244. DOI: 10.1302/2058-5241.6.200099.
Insights
Next-generation sequencing (NGS) offers rapid diagnosis for periprosthetic joint infections (PJI), a severe complication of total joint arthroplasty (TJA). This technology, including metagenomic and cell-free DNA sequencing, shows promise for faster and more accurate PJI detection.
Area of Science:
- Orthopedic Surgery
- Infectious Diseases
- Molecular Diagnostics
Background:
- Periprosthetic joint infections (PJI) are severe complications following total joint arthroplasty (TJA).
- Current diagnostic methods for PJI lack standardization and can be challenging, particularly in culture-negative cases.
- There is a critical need for rapid and accurate diagnostic tools for PJI.
Purpose of the Study:
- To evaluate the potential of next-generation sequencing (NGS) technologies for the diagnosis of PJI.
- To explore the capabilities of metagenomic NGS (mNGS) and cell-free DNA (cfDNA) NGS in identifying pathogens and antimicrobial resistance in PJI cases.
- To assess the impact of these innovative technologies on the diagnostic paradigm of PJI.
Main Methods:
- Review of next-generation sequencing (NGS) applications in PJI diagnosis.
- Discussion of metagenomic NGS (mNGS) for universal pathogen detection and antimicrobial resistance characterization.
- Analysis of cell-free DNA (cfDNA) NGS for rapid microorganism isolation and resistance gene identification.
Main Results:
- NGS technologies can sequence microbial DNA from synovial fluid, proving useful in culture-negative PJI.
- mNGS provides universal pathogen detection within 24-48 hours and can characterize antimicrobial resistance.
- cfDNA NGS offers a fast, sensitive, and specific method for microorganism detection and resistance gene identification.
Conclusions:
- Metagenomics and cfDNA NGS represent promising technologies for the rapid diagnosis of PJI.
- These NGS methods significantly reduce the time required for bacterial detection compared to traditional methods.
- While revolutionary, further clinical evidence is necessary before widespread adoption of NGS for PJI diagnosis.
