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

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年7月3日

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  • Erica R. Fuhrmeister,
  • Sooyeol Kim,
  • Shruteek A. Mairal,
  • Caroline McCormack,
  • Benard Chieng,
  • Jenna M. Swarthout,
  • Abigail Harvey Paulos,
  • Sammy M. Njenga,
  • Amy J. Pickering

摘要

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.