P049

1:National Reference Laboratory for Mycobacteriology, Hungary

Timely and accurate molecular epidemiological investigation is critical in controlling Mycobacterium tuberculosis (MTB) transmission. Whole-genome sequencing (WGS) has become a key tool in identifying transmission clusters, traditionally relying on short-read platforms, such as Illumina, due to their high accuracy. However, rapid sequencing technologies, like Oxford Nanopore, offer significantly faster turnaround times, making them attractive for real-time surveillance. Despite this advantage, several studies have raised concerns about the specificity and reliability of Nanopore data in the context of MTB genotyping, highlighting the importance for direct comparison.

This study aimed to evaluate whether Nanopore sequencing can identify the same transmission clusters as Illumina WGS when applied to MTB isolates. The analysis involved 20 MTB strains, isolated in Hungary, including epidemiologically linked cases. Each isolate was sequenced using both Illumina and Nanopore platforms. SNP-based phylogenetic analyses and clustering assessments were performed to determine concordance between the technologies.

Our results provide insights into the comparability of these sequencing approaches for MTB cluster identification, highlighting the strengths and limitations of Nanopore sequencing in high-resolution genotyping and underscoring its potential role in complementing traditional methods, especially where rapid decision-making is of primary concern for public health interventions.