Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.

ABSTRACT: Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long Klebsiella pneumoniae outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides K. pneumoniae Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing. We offer our masking strategy as a bioinforma

SUBMITTER: Lohde M 

PROVIDER: S-EPMC11610573 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature