Identification of Prosthetic Joint Pathogens Directly in Clinical Specimens by Metagenomic Shotgun Sequencing

Background: Detection and identification of prosthetic joint infection (PJI) pathogens is important for management of these difficult to treat infections. Metagenomic shotgun sequencing is a powerful tool with the potential to change how many infections, including PJIs, are diagnosed, as it allows direct detection and identification of microorganisms from clinical specimens. We sought to develop a metagenomics approach to evaluate the microbiology of arthroplasty components removed due to infection or aseptic failure (AF).

Methods: Dislodged surface materials from the surfaces of resected joint arthroplasty components (sonicate fluid) were collected. Human DNA was removed using the MolYsis basic kit prior to DNA extraction, whole genome amplification, and shotgun sequencing. Pathogen identification was performed using a pipeline incorporating LMAT and MetaPhlAn2 software. A total of 174 prosthetic joints (from 95 and 79 patients with PJI and AF, respectively) were tested.

Results: Metagenomic analysis identified the known pathogens in 60 out of 63 culture-positive PJIs. Additional potential pathogens not identified by culture were detected in seven culture-positive PJI cases. Potential pathogens were identified in five out of 32 culture-negative PJIs and three out of 79 AF’s. Identified potential pathogens not recovered in culture included Staphylococcus, Streptococcus, Clostridium, Corynebacterium, Peptoniphilus, and Candida species. In most cases, pathogens were sequenced at sufficient depth (average depth 560x, median 110x) to allow draft genome assembly for identification of clinically-relevant genes (such as those mediating antibiotic resistance) as well as to perform single nucleotide polymorphism (SNP) analysis.

Conclusion: Metagenomic shotgun sequencing performed directly on clinical specimens allows for reliable detection and identification of PJI pathogens recovered in culture as well as identification of additional pathogens in 13% of culture-negative PJI cases. The role of the microorganisms detected in the AF cases remains to be defined.