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ORTHOPEDICS | Next Generation Sequencing for Orthopedics

The emerging gold standard for diagnosing chronic joint infection

qPCR vs NGS

Second generation 16S/ITS DNA sequencing produces data in vastly larger amounts, at significantly lower cost, in shorter time, and with less manual intervention than previous sequencing methods.

Unlike polymerase chain reaction (PCR), NGS is hypothesis-free and does not rely on a predetermined panel of PCR primer targets. NGS is capable of characterizing all microbial DNA present within a clinical sample and providing a complete picture of the microbial profile, without the need for preconceived ideas of the possible responsible pathogens.

MicroGenDX’s NGS searches against a curated microbial database of over 50,000 species for a match — including bacteria, yeast, and fungi — without the need for additional individual testing.

“We are standing at a very critical historic moment when molecular technologies can help us detect infecting organisms. NGS picks up organisms when cultures are negative and also provide us with the information much faster so during a critical period you are treating the patient with the right antibiotics. Mycobacterm abscesses is not an organism that we usually treat. Not having that information in your hands for 21 days…that could compromise the care of that patient. That is critical information.”

– Dr. Javad Parvizi, Orthopedic Surgeon, Director of Clinical Research at the Rothman Institute

Where does NGS testing fit into your orthopedic practice?


In conjunction with culture, MicroGenDX OrthoKEY Clinic rapidly confirms the likelihood of infection and potential pathogens using synovial biomarkers and NGS.

  • Biofilms on hardware will shed microbes into fluid
  • The more fluid provided, the greater potential for DNA reads – 2ml minimum, 2x8ml maximum
  • Biomarker and resistance gene results in 24-48 hours, NGS sequencing results in 3.5 days
  • Review results on the PJIDx diagnostic app

OrthoKEY Surgery rapidly and accurately identifies multiple species of microbes using synovial biomarkers and NGS.

  • Allows for more targeted post-op antimicrobial selection
  • If a revision is required, antimicrobials for the spacer can be targeted to the exact species
  • Optimal sampling with Captigen flat swab to include as much surface area as possible, avoiding pus and nonviable material
  • Biomarker and resistance gene results in 24-48 hours, NGS sequencing results in 3.5 days
  • Review results on the PJIDx diagnostic app

OrthoKEY Surgery can detect microbes missed by standard culture and reduce potential revision failure.

  • Detects exact species for targeted antimicrobial selection
  • Includes innovative Captigen flat swab to maximize biofilm retrieval and nucleic acid extraction
  • Biomarker and resistance gene results in 24-48 hours, NGS sequencing results in 3.5 days
  • Review results on the PJIDx diagnostic app

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