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Certain\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    lineages dominate the global spread of AMR, but the extent of their host specificity and its impact on transmission remains unclear. Here, 1,198\n                    <jats:italic>E. coli<\/jats:italic>\n                    isolates from cattle, chickens, humans, and pigs across Germany, the UK, Spain, and Vietnam were classified for host-association using a phylogeny-based bioinformatic approach, with non-host-associated isolates defined as \u2018generalists\u2019. To validate this classification, 17 extended-spectrum beta-lactamase (ESBL)-producing isolates representing host-associated or generalist clusters were administered as a cocktail to three groups of weaner pigs, either untreated or treated with amoxicillin or ceftiofur. Bacterial shedding was monitored via culture and isolate-specific PCR up to 56 days post-inoculation. Colonization occurred within 24\u00a0h, with shedding peaking early and declining over time. Only 12 of 17 isolates were recovered post-inoculation; four were persistently detected, including one pig-associated, one bovine, one chicken, and one generalist isolate. These findings suggest limitations in the classification approach, possible low host selectivity in pigs, and\/or incomplete knowledge of colonization mechanisms. Nonetheless, the model successfully identified isolates capable of stable colonization, supporting its utility for studying AMR\n                    <jats:italic>E. coli<\/jats:italic>\n                    host adaptation.\n                  <\/jats:p>","DOI":"10.1038\/s41598-026-53668-0","type":"journal-article","created":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T09:44:06Z","timestamp":1781084646000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Intestinal colonization of weaner pigs by extended-spectrum-\u03b2-lactamase-encoding Escherichia coli classified for differential host-association using a phylogenetics-based approach"],"prefix":"10.1038","volume":"16","author":[{"given":"M.","family":"Ferrandis-Vila","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Mamerow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Bootsma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B.","family":"van der Putten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"Oldenkamp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Weber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. 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These isolates were originally collected for other research purposes, and their sequences have been published previously in Tiwari et al. (see ref. #6). All methods were carried out in accordance with relevant guidelines and regulations. According to the University of Surrey Ethics Committee, the human\n                      E. coli\n                      isolates provided to the authors were fully anonymized at the point of transfer and were not accompanied by any patient or clinical data. In accordance with UK regulations and University of Surrey policies, the use of anonymized bacterial isolates without associated patient data does not constitute human subject research and therefore, does not require ethical approval or informed consent. Consequently, no additional ethical approval or informed consent was required for the use of these isolates in this study.\n                      Animal experiment\n                      : The experimental animal study involving pigs was approved by the competent authority (State Office for Agriculture, Food Safety and Fisheries of Mecklenburg-Western Pomerania, Rostock, Germany) under the reference no. 7221.3\u20131\u2013034\/19\u20131. All experiments involving animals were performed according to the guidelines for the care and use of experimental animals established by the State Office for Agriculture, Food Safety and Fisheries of Mecklenburg-Western Pomerania. The study was carried out in compliance with the ARRIVE guidelines.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}}],"article-number":"18020"}}