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Although several studies have reported genomic characteristics of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              , limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              from different sources. While endosymbionts exert a significant influence on the phenotypes of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              , including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              , as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              strains suggested that genomic exchanges between\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the\n              <jats:italic>adeF<\/jats:italic>\n              ,\n              <jats:italic>amrA<\/jats:italic>\n              , and\n              <jats:italic>amrB<\/jats:italic>\n              genes exchange events, potentially contribute to\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              drug resistance. In conclusion, this study elucidated the adaptation of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              to different ecological niches and the influence of gene exchange on the evolution of ocular\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              causes a serious blinding keratopathy,\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific\n              <jats:italic>Acanthamoeba<\/jats:italic>\n              keratitis cases.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/msphere.00548-24","type":"journal-article","created":{"date-parts":[[2024,10,1]],"date-time":"2024-10-01T16:01:22Z","timestamp":1727798482000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["Comparative genomic analysis of\n            <i>Acanthamoeba<\/i>\n            from different sources and horizontal transfer events of antimicrobial resistance genes"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-7551-0407","authenticated-orcid":false,"given":"Xinyi","family":"Ling","sequence":"first","affiliation":[{"name":"Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of 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