In a recent interview with GenomeWeb, Robin Patel, M.D., Director of the Infectious Diseases Research Laboratory at the Mayo Clinic, described a metagenomic sequencing approach her lab is testing to identify potential infections in patients whose joint replacements fail.
According to Dr. Patel, the technique is still too time-consuming and expensive to be used clinically for diagnostic purposes, but as technology improves and costs decline, she envisions eventually implementing a next-generation sequencing-based approach potentially for tricky cases of replacement failures.
Based on research from the U.S. Centers for Disease Control and Prevention, in 2010, nearly 700,000 knee replacements and more than 310,000 hip replacements were performed in the U.S. By 2030, the American Academy of Orthopaedic Surgeons predicts that there will be nearly 3.5 million knee replacements and more than 500,000 hip replacements.
Dr. Patel said that these surgeries are typically extremely beneficial, enabling people who suffered from "limited mobility and lots of pain" to become active again. But, approximately 1 percent of hip replacements and 2% of knee replacements become infected over a 10-year period. Infections develop in the biofilms on the surface of the implant and do not result in typical symptoms associated with infection, she said. In addition, they can be slow to manifest, and therefore, slow to diagnose and intervene.
The current gold standard to diagnose microbial infections relies on culturing organisms extracted from the biofilm of the prosthetic. Dr. Patel's lab at Mayo has come up with enhanced culturing techniques to help improve on diagnostic rates, but sensitivity of those approaches still hovers around 73%. The group also tested a PCR panel, which only boosted sensitivity to 77%.
In order to try and improve sensitivity as well as to identify the up to one-third of cases that have polymicrobial infections, her group decided to test metagenomic sequencing approaches.
According to Dr. Patel, the main challenge with metagenomic sequencing is to reduce the amount of background DNA, the majority of which is human DNA, and amplify the microbial DNA.
Read the full article to learn more about how Mayo Clinic is using metagenomic sequencing for infections in joint replacement.