When patients suffer infections related to replaced knee or hip joints, medical teams need to know which bacteria are causing the problem. A promising new method called metagenomic sequencing reads all the DNA in a sample and can identify bacteria without needing them to grow in the lab. This could be faster than standard tests, and might give more complete information. However, these samples usually contain a lot of human DNA, which can “drown out” the bacterial DNA in the sequencing.
We tested a technique called adaptive sampling, which helps the sequencing machine ignore human DNA and focus on bacterial DNA instead. In samples from infected prosthetic joints, adaptive sampling increased the amount of bacterial genetic material we could read by about 1.5 to 2 times. The method didn’t introduce any obvious drawbacks, but the improvement was modest. We also saw some technical issues such low-level contamination that can complicate results.
Overall, adaptive sampling makes sequencing a bit more efficient, but it is not yet accurate, reproducible or powerful enough to replace standard lab tests. It may be a helpful extra tool, and larger studies are needed to confirm its value.
You can read our scientific paper for free here or by clicking the title below.
Teresa L. Street, Philip Bejon, Laura Leach, Sarah Oakley, Bernadette C. Young and Nicholas D. Sanderson. (2025) Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue. Microbial Genomics. 11(9): 001507
