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

Author

Listed:
  • Erica R. Fuhrmeister

    (University of Washington
    University of California
    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
    University of California
    Chan Zuckerberg Biohub)

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.

Suggested Citation

  • Erica R. Fuhrmeister & Sooyeol Kim & Shruteek A. Mairal & Caroline McCormack & Benard Chieng & Jenna M. Swarthout & Abigail Harvey Paulos & Sammy M. Njenga & Amy J. Pickering, 2025. "Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60491-0
    DOI: 10.1038/s41467-025-60491-0
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    References listed on IDEAS

    as
    1. An-Ni Zhang & Jeffry M. Gaston & Chengzhen L. Dai & Shijie Zhao & Mathilde Poyet & Mathieu Groussin & Xiaole Yin & Li-Guan Li & Mark C. M. Loosdrecht & Edward Topp & Michael R. Gillings & William P. H, 2021. "An omics-based framework for assessing the health risk of antimicrobial resistance genes," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
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