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Here we assessed <jats:italic>Escherichia coli<\/jats:italic> strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five <jats:italic>E. coli<\/jats:italic> colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. <jats:italic>E. coli<\/jats:italic> isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. <jats:italic>E. coli<\/jats:italic>-contaminated stored drinking water was associated with higher human\u2013human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.<\/jats:p>","DOI":"10.1038\/s41564-025-01986-w","type":"journal-article","created":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T09:03:30Z","timestamp":1746090210000},"page":"1198-1209","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7234-4721","authenticated-orcid":false,"given":"Daehyun D.","family":"Kim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenna M.","family":"Swarthout","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9132-7249","authenticated-orcid":false,"given":"Colin J.","family":"Worby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benard","family":"Chieng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Mboya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7857-9145","authenticated-orcid":false,"given":"Ashlee M.","family":"Earl","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":"297","published-online":{"date-parts":[[2025,5,1]]},"reference":[{"key":"1986_CR1","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1016\/S0140-6736(05)71877-8","volume":"365","author":"J Bryce","year":"2005","unstructured":"Bryce, J., Boschi-Pinto, C., Shibuya, K. & Black, R. 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