A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.

ABSTRACT: Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across parti

SUBMITTER: Dabernig-Heinz J 

PROVIDER: S-EPMC11389150 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature