Diagnosing prosthetic joint infections using bacterial genomic sequences
An infection following surgery can occur in some patients when they receive a replacement joint such as a knee or hip joint. Although not very common, these infections may be take months to treat with drugs. Sometimes the treatment does not work and then patients may need more surgery.
The cause of the infections is usually small numbers of bacteria inside the joint. It is difficult to find and identify these bacteria so surgeons collect tissue samples from around the site of the infection, or remove the whole joint. These samples go to a microbiology laboratory to try to grow (culture) any organisms that could cause infection, so that they can be identified. This method does not always find the cause of infection as the patient may have already received antibiotics or the bacteria may be difficult to grow in the lab.
Instead of growing the bacteria, detecting its genome (DNA) could identify which bacteria is causing the infection. This approach, which aims to find DNA from any organisms present in a patient sample, is called Metagenomic Sequencing. This study examines whether we can identify bacterial infections in joints using this method, instead of trying to grow the bacteria. When the joint is removed during surgery, it is put in salt water (saline). We try to dislodge bacteria that might be stuck to the joint using a method called sonication, which uses sound waves to vibrate the joint. The bacteria that come from the joint go into the saline. Then, by spinning the saline (now called sonication fluid) very fast we can remove the bacteria from the saline and break the bacterial cell walls to sequence the DNA. There may be many types of bacterial DNA in this mix but using the genetic code we can identify what is in the sample.
Our study compares growing bacteria from sonication fluids to metagenomic sequencing, and shows that metagenomic sequencing provides accurate diagnosis of infections in the joints. Overall, sequencing correctly finds the presence of an infection nine times out of ten and identifies what species of bacteria was causing the infection (which helps doctors to choose the best antibiotic treatment). Because DNA from all the bacteria on the joint is sequenced, the method also identifies some species that did not grow in the microbiology laboratory. Some of these species are ones we know are difficult to grow in a lab, or from patients who had already received antibiotics – making them likely causes of infection that the traditional culture methods had missed.
Our study demonstrates that sequencing can be used to identify prosthetic joint infections directly from sonication fluid, and leads the way for other studies that aim to diagnose infections directly from different kinds of clinical samples.
The full article can be accessed at: http://jcm.asm.org/content/early/2017/05/04/JCM.00462-17.long