Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance

Erica R. Fuhrmeister, Sooyeol Kim, Shruteek A. Mairal, Caroline McCormack, Benard Chieng, Jenna M. Swarthout, Abigail Harvey Paulos, Sammy M. Njenga and Amy J. Pickering ()
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Erica R. Fuhrmeister: University of Washington
Sooyeol Kim: University of California
Shruteek A. Mairal: University of California
Caroline McCormack: University of California
Benard Chieng: Kenya Medical Research Institute
Jenna M. Swarthout: Tufts University
Abigail Harvey Paulos: University of California
Sammy M. Njenga: Kenya Medical Research Institute
Amy J. Pickering: University of California

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: 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 blaCTX-M and blaTEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing blaTEM and blaCTX-M that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumoniae, and Haemophilus influenzae in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.

Date: 2025
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DOI: 10.1038/s41467-025-60491-0

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