Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like <i>Burkholderia pseudomallei</i>.

ABSTRACT: Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-read (SR) sequencing. Oxford Nanopore long-read sequencing (ONT-LR), which allows fast on-site analysis with comparatively low costs, could provide an alternative. Despite ONT-LR raw read accuracy improvement, evidence for methylation-based errors accumulates. PCR-based library preparation, suggested as a solution, presumably poses difficulties for GC-rich bacteria. We challenged ONT-LR-based cgMLST using the highly GC-rich pathogen Burkholderia pseudomallei to develop a clinically applicabl

SUBMITTER: Weigl S 

PROVIDER: S-EPMC11898673 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature