Long-read 16S rRNA gene sequencing enhances diagnostic resolution of bacterial infections
Sequencing of the 16S rRNA gene is a valuable complement to traditional culture-based diagnostics for bacterial infections. This analysis has historically been performed using the Sanger sequencing method. Uppsala University Hospital is now implementing long-read 16S rRNA gene sequencing in clinical routine. This transition allows for faster, more scalable, and cost-effective detection of multiple bacterial species within the same sample.
Ida Karlsson, Bioinformatician at Clinical Genomics. Photo: Ulrika Gunnarsson
The method utilizes Oxford Nanopore Technologies (ONT) sequencing. At the Clinical Microbiology Laboratory, the 16S rRNA gene sequencing workflow has been validated for clinical diagnostics and optimized to allow parallel processing with other diagnostic targets in the same sequencing run, increasing scalability and cost efficiency.
The bioinformatic analysis pipeline was developed in collaboration with Clinical Genomics Uppsala. Long-read sequencing enables the generation of almost full-length 16S rRNA gene sequences, which enhances bacterial species identification.
Initial diagnostic applications include analysis of bacterial DNA from tissue and sonicated fluids. Additional sample types will be validated and incorporated into the workflow over time.
Amplicon sequencing, including targets such as the bacterial 16S rRNA gene, eukaryotic 18S rRNA gene, ITS regions, and genes associated with virulence or antibiotic resistance, is also available for research use and can be ordered through Clinical Genomics Uppsala.