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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\n                  <jats:italic>bla<\/jats:italic>\n                  <jats:sub>CTX-M<\/jats:sub>\n                  and\n                  <jats:italic>bla<\/jats:italic>\n                  <jats:sub>TEM<\/jats:sub>\n                  between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing\n                  <jats:italic>bla<\/jats:italic>\n                  <jats:sub>TEM<\/jats:sub>\n                  and\n                  <jats:italic>bla<\/jats:italic>\n                  <jats:sub>CTX-M<\/jats:sub>\n                  that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including\n                  <jats:italic>Escherichia coli, Klebsiella pneumonia<\/jats:italic>\n                  , and\n                  <jats:italic>Haemophilus influenzae<\/jats:italic>\n                  in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.\n                <\/jats:p>","DOI":"10.1101\/2024.09.12.612745","type":"posted-content","created":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T00:20:15Z","timestamp":1726186815000},"source":"Crossref","is-referenced-by-count":3,"title":["Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5264-7533","authenticated-orcid":false,"given":"Erica R.","family":"Fuhrmeister","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sooyeol","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shruteek A.","family":"Mairal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"McCormack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benard","family":"Chieng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenna M.","family":"Swarthout","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail Harvey","family":"Paulos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sammy M.","family":"Njenga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6193-2221","authenticated-orcid":false,"given":"Amy J.","family":"Pickering","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025060301251244000_2024.09.12.612745v2.1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02724-0\/ATTACHMENT\/4504FC2B-08AE-46D6-BD75-80811DF8B5E6\/MMC1.PDF"},{"key":"2025060301251244000_2024.09.12.612745v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(23)00137-4"},{"key":"2025060301251244000_2024.09.12.612745v2.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-0722-0"},{"key":"2025060301251244000_2024.09.12.612745v2.4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1717295115"},{"key":"2025060301251244000_2024.09.12.612745v2.5","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.5b02566"},{"key":"2025060301251244000_2024.09.12.612745v2.6","unstructured":"Delgado-Baquerizo, M. et al. 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