Context Seq: Cas9 targeted sequencing for ARG identification in genomic context

We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya.