Comparative study of Illumina and Nanopore sequencing for Clostridioides difficile surveillance

Clostridioides difficile is a significant hospital-acquired pathogen, with increasing prevalence in the community. Epidemilogical surveillance is essential to understand C. difficile transmission dynamics, but there is a constant trade-off between accuracy and rapid turnaround time of the results. The project explores the potential of long-read whole genome sequencing (Nanopore) in comparison to Illumina short-read sequencing. Both technologies were used for sequence type designation, virulence factor detection and phylogenetic analysis via core genome MLST. Whille Illumina remains the gold standard for detailed genetic analyses, Nanopore sequencing can still be used as a rapid and reliable tool in outbreak scenarios where timely results are critical for infection control.