Next generation sequencing for pathogen detection in periprosthetic joint infections

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

The mildly decreased preoperative bilirubin level is a risk factor for periprosthetic joint infection after total hip and knee arthroplasty

“…CRP and ESR are shown to be, as supported by strong evidence, a useful “ruling out” test [ 18 , 19 ]. Synovial fluid tests such as leukocyte count and neutrophil percentage, leukocyte esterase, α-defensin, cultures, and next-generation sequencing for microorganisms can play an important diagnostic role [ 20 – 23 ]. If preoperative evaluation with serum and synovial fluid tests do not secure a diagnosis, the frozen section tissue histopathology may help establish PJI diagnosis [ 24 ].…”

Influence of residual microbial nucleic acid in instruments for hip joint arthroplasty on false-positive results of metagenomic sequencing

“…Even so, the fragment contamination of environmental nucleic acid cannot be well differentiated, resulting in false positives [21]. Most of the interfering fragments found in this study are pathogens that are not common in clinical infections (eg Corynebacterium, Novosphingobium, Sphingomonas), which are relatively easier to distinguish from PJI-infected bacteria.…”

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection

“…Metagenomic sequencing for AMR determinant detection has also been applied to PPT samples for bone and joint infections ( 9 ), with the correct susceptibility inferred in 94.1% of monomicrobial and 76.5% of polymicrobial samples. Recent reviews also highlight the use of metagenomic sequencing for AMR detection ( 35 , 36 ).…”