USING GENOMIC SEQUENCING TO DIAGNOSE ORTHOPAEDIC INFECTIONS

Hollie Wilkinson, Helen McCarthy, Karina Wright, Jade Perry and Paul Cool

Funded by the Orthopaedic Institute

The objective of this study is to investigate if genomic sequencing is a useful method to diagnose orthopaedic infections. Traditional methods used to identify the species of bacteria causing orthopaedic infections take considerable time and the results are frequently insufficient for guiding antibiotic treatment. Current methods include a combination of biochemical markers and microbiological cultures. The aim here is to investigate if genomic sequencing, using a hand-held device (see picture insert) is a faster and more reliable method to identify the species of bacteria causing orthopaedic infections.

Samples of prosthetic fluid are obtained from surgical interventions to treat orthopaedic infections such as revisions or aspirations. Then the DNA is extracted from these samples in the lab and genomic sequencing is performed. This genomic data is analysed to try and identify the bacterial genomes present and therefore, the species of bacteria in the prosthetic fluid sample. The whole process from DNA extraction to output list of bacteria species takes approximately 2 hours, which is considerably faster than microbiological cultures. So far 4 of the samples from confirmed infected patients have been sequenced and the hits for bacteria matching the hospital microbiological culture results have high quality scores associated with them. Further analysis will include looking to identify antibiotic resistance genes in the genomic sequencing data from these clinical samples and see of this information can predict which patients will or will not respond to antibiotic treatment.

The aim is to investigate if genomic sequencing is a faster and more sensitive approach to identifying the species of bacteria causing orthopaedic infections than current methods. This means patients can be diagnosed faster and receive the correct antibiotics sooner, hopefully improving patient outcome from orthopaedic surgery.