{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T19:53:13Z","timestamp":1790970793742,"version":"4.1.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["5R01AI148259"],"award-info":[{"award-number":["5R01AI148259"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U19AI181767"],"award-info":[{"award-number":["U19AI181767"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["F31-AI186288"],"award-info":[{"award-number":["F31-AI186288"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2217116"],"award-info":[{"award-number":["2217116"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["T32-HG000040"],"award-info":[{"award-number":["T32-HG000040"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence and resistance spread must be better understood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 long-term acute care hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics\/exposures and these 2 pathways: resistance due to predicted within-host emergence of resistance and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https:\/\/github.com\/kylegontjes\/phyloAMR).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant K. pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to 5 antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and novel beta-lactam\/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (eg, stage IV + decubitus ulcers) and indwelling medical devices (eg, gastrostomy tubes) were detected as unique risk factors for resistance spread.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiaf478","type":"journal-article","created":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T12:10:58Z","timestamp":1757679058000},"page":"e992-e1002","source":"Crossref","is-referenced-by-count":9,"title":["Phylogenetic Context of Antibiotic Resistance Provides Insights into the Dynamics of Resistance Emergence and Spread"],"prefix":"10.1093","volume":"232","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8671-7990","authenticated-orcid":false,"given":"Kyle J","family":"Gontjes","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, Michigan ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1850-5598","authenticated-orcid":false,"given":"Aryan","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, Michigan ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1924-8941","authenticated-orcid":false,"given":"Sarah E","family":"Sansom","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center , Chicago, Illinois ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0952-169X","authenticated-orcid":false,"given":"James D","family":"Boyko","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, Michigan ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2035-9531","authenticated-orcid":false,"given":"Stephen A","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, Michigan ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4772-2409","authenticated-orcid":false,"given":"Ebbing","family":"Lautenbach","sequence":"additional","affiliation":[{"name":"Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Department of Medicine, Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8409-278X","authenticated-orcid":false,"given":"Evan","family":"Snitkin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, Michigan ,","place":["USA"]},{"name":"Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School , Ann Arbor, Michigan 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