PRELIMINARY FINDINGS ON THE USE OF GENOMIC SEQUENCING TO DIAGNOSE ORTHOPAEDIC INFECTIONS
Authors: Wilkinson Hollie , Cool Paul 
Published: November 2023

Objectives

The objective of this study is to investigate if genomic sequencing is a useful method to diagnose orthopaedic infections. Current methods used to identify the species of bacteria causing orthopaedic infections take considerable time and the results are frequently insufficient for guiding antibiotic treatment. The aim here is to investigate if genomic sequencing is a faster and more reliable method to identify the species of bacteria causing infections. Current methods include a combination of biochemical markers and microbiological cultures which frequently produce false positive results and false negative results.

Methods

Samples of prosthetic fluid were obtained from surgical interventions to treat orthopaedic infections. DNA is extracted from these samples lab and nanopore genomic sequencing is performed. Initial investigations informed that a sequencing time of 15 minutes was sufficient. The resulting genomic sequence data was classified using Basic Local Alignment Tool (BLAST) against the NCBI bacterial database and filtered by only including reads with an identity score of 90 and E-value of 1e-50. An E-value of 1e-50 suggests a high-quality result and is commonly used when analysing genomic data. This data was then filtered in R Studio to identify if any species were associated with orthopaedic infections. The results from genomic sequencing were compared to microbiology results from the hospital to see if the same species had been identified. The whole process from DNA extraction to output took approximately 2 hours, which was faster than parallel microbiological cultures.

Results

In these preliminary analyses, 15 samples have been collected from patients with confirmed/suspected orthopaedic infections. To date, 11 samples from confirmed infected patients have been sequenced and a summary of the findings are presented in the table attached. As well as finding bacteria species to match microbiological cultures, genomic sequencing has also identified bacteria when culture results have been negative, but the patient is known to have an infection due to clinical indication and previous culture results. This example suggests genomic sequencing may have higher sensitivity than microbiological cultures at detecting bacteria causing orthopaedic infections. Results in table indicate the identification of bacteria from genomic sequencing that match microbiological cultures are high quality.

Conclusions

Preliminary data presented using genomic sequencing suggests that the technique may be useful to identify bacterial species causing orthopaedic infections and can do so in a shorter time frame than current microbial methods. The results from genomic sequencing all produced a number of false positive results which hopefully can be reduced by improving the bioinformatic techniques used and increasing the sample number to include individuals without an infection. Further analysis will also look at identifying antibiotic resistance genes in the sequencing data and seeing if this ca be used to predict which patients will and will not respond to antibiotic treatment. The aim at the end of this project is to demonstrate if genomic sequencing is a more sensitive method to identify bacteria causing orthopaedic infections that current methods and if it can be used to guide antibiotic treatment. Include limitations, next steps and bigger picture.

Declaration of Interest

(b) declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported:I declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research project.