Targeted sequencing of <i>Enterobacterales</i> bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.

ABSTRACT: Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient sequence data for effective downstream analysis. CRISPR-Cas9 enrichment is designed to improve the yield of low abundance sequences but has not been thoroughly explored with Oxford Nanopore Technologies (ONT) for use in clinical bacterial epidemiology. We designed CRISPR-Cas9 guide RNAs to enrich the human pathogen Klebsiella pneumoniae, by targeting multi-locus sequence type (MLST) and transfer RNA (tRNA) genes, as well as common antimicrobial resistance (AMR) genes and the resistance-associated integron gene intI1. We validated enrichment performance in 20 K. pneumoniae isolates, finding that guid

SUBMITTER: Cottingham H 

PROVIDER: S-EPMC11834407 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature