Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance.

ABSTRACT: Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs bla _CTX-M and bla _TEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing bla _TEM and bla _CTX-M that are shared between

SUBMITTER: Fuhrmeister ER 

PROVIDER: S-EPMC11419053 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature