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Gut microbiomes and fluoroquinolone-resistant <jats:italic>Escherichia coli<\/jats:italic> isolates were sequenced, and mobile genetic elements adjacent to the \u03b2-lactamase (<jats:italic>bla<\/jats:italic>) and transferable quinolone resistance (<jats:italic>qnr<\/jats:italic>) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of <jats:italic>bla<\/jats:italic> and <jats:italic>qnr<\/jats:italic>, the prevalence rates between chickens and patients with CDI were the most similar (R<jats:sup>2<\/jats:sup>\u2009=\u20090.46); <jats:italic>bla<\/jats:italic><jats:sub>TEM<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>OXA<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>CTX-M<\/jats:sub>, and <jats:italic>qnrS<\/jats:italic> were highly prevalent in both groups. According to genomic and phylogenetic analyses, <jats:italic>bla<\/jats:italic><jats:sub>CTX-M<\/jats:sub> and <jats:italic>bla<\/jats:italic><jats:sub>OXA<\/jats:sub> expressed lineage specificity to either humans or livestock, while <jats:italic>qnrS<\/jats:italic> and <jats:italic>bla<\/jats:italic><jats:sub>TEM<\/jats:sub> displayed a shared lineage between humans and livestock. A <jats:italic>qnrS1<\/jats:italic> mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to \u03b2-lactams and quinolones. <jats:italic>QnrS<\/jats:italic> and <jats:italic>bla<\/jats:italic><jats:sub>TEM<\/jats:sub> displayed especially strong co-occurrence between the guts of humans and livestock.<\/jats:p>","DOI":"10.1038\/s41598-023-48221-2","type":"journal-article","created":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T18:02:11Z","timestamp":1701194531000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Comparative analyses of the faecal resistome against \u03b2-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing"],"prefix":"10.1038","volume":"13","author":[{"given":"Jieun","family":"Kim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youna","family":"Cho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suk-Kyung","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mi-Ran","family":"Seo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jang Won","family":"Sohn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bongyoung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mina","family":"Rho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyunjoo","family":"Pai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,11,28]]},"reference":[{"issue":"8","key":"48221_CR1","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1038\/s41564-018-0192-9","volume":"3","author":"P Munk","year":"2018","unstructured":"Munk, P. et al. 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