{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:10:59Z","timestamp":1785409859662,"version":"3.56.0"},"reference-count":30,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,12,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Coccidioidomycosis (Valley fever), caused by the fungal pathogen\n                      <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                      , is increasing in incidence across the western United States and parts of the Americas. However, genomic data from low-incidence regions remain scarce, limiting our understanding of the pathogen\u2019s dispersal and evolution. To address this gap, we prospectively collected\n                      <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                      -positive clinical isolates submitted to a national diagnostic laboratory between January 2023 and November 2024. We performed whole-genome sequencing on 27 clinical isolates from Utah, Colorado, and Nevada\u2014states with no previously available\n                      <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                      genomes\u2014and sequenced an additional 22 isolates from California. For Utah patients, we also reviewed medical records to assess potential travel history. Among the 27 newly sequenced isolates, three were identified as\n                      <jats:italic toggle=\"yes\">Coccidioides immitis<\/jats:italic>\n                      and 24 as\n                      <jats:italic toggle=\"yes\">Coccidioides posadasii<\/jats:italic>\n                      . The\n                      <jats:italic toggle=\"yes\">C. immitis<\/jats:italic>\n                      isolates, all from a single Utah patient, were linked to recent travel to southern California. In contrast,\n                      <jats:italic toggle=\"yes\">C. posadasii<\/jats:italic>\n                      isolates from Utah, Colorado, and Nevada were phylogenetically diverse and dispersed across the species tree. Ancestral state reconstructions suggested multiple independent introductions: at least seven into Utah, two into Nevada, and seven into Colorado. The\n                      <jats:italic toggle=\"yes\">C. immitis<\/jats:italic>\n                      clade likely originated in California (likelihood = 0.96), while\n                      <jats:italic toggle=\"yes\">C. posadasii<\/jats:italic>\n                      traces to Arizona (likelihood = 0.99). These results reveal a complex dispersal history of\n                      <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                      in the western United States, driven by recurrent introductions rather than a single emergence event. Our study underscores the need for continued genomic surveillance in underrepresented regions to fully capture the evolutionary dynamics of this emerging fungal pathogen.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Valley fever is a fungal disease caused by\n                        <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                        species, primarily found in arid regions of the western United States and parts of Central and South America. While most genomic studies focus on high-incidence areas, the evolutionary dynamics of the fungus in low-incidence states remain poorly understood. In this study, we analyzed clinical\n                        <jats:italic toggle=\"yes\">Coccidioides<\/jats:italic>\n                        isolates from Utah, Colorado, and Nevada\u2014states with reported cases but limited genomic data. Using whole-genome sequencing and phylogenetic analysis, we found evidence of multiple introductions into each state, likely from neighboring high-incidence regions such as Arizona and California. In Utah, we detected both\n                        <jats:italic toggle=\"yes\">Coccidioides immitis<\/jats:italic>\n                        and\n                        <jats:italic toggle=\"yes\">Coccidioides posadasii<\/jats:italic>\n                        , though the\n                        <jats:italic toggle=\"yes\">C. immitis<\/jats:italic>\n                        case was associated with recent travel. Only\n                        <jats:italic toggle=\"yes\">C. posadasii<\/jats:italic>\n                        was found in Colorado and Nevada. These findings support ongoing dispersal rather than a single introduction and highlight the need for expanded genomic surveillance beyond traditionally endemic regions.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01822-25","type":"journal-article","created":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T14:09:54Z","timestamp":1761314994000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["<i>Coccidioides<\/i>\n                    genomes from low-incidence states reveal complex migration history across the western United States"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2952-8816","authenticated-orcid":true,"given":"Emanuel M.","family":"Fonseca","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03r0ha626","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Epidemiology, University of Utah","place":["Salt Lake City, USA"]},{"name":"Elfa Analytics","place":["Ponte Nova, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanaya","family":"Fox","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03r0ha626","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Epidemiology, University of Utah","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrienne L.","family":"Carey","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Utah School of Medicine","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3439-4517","authenticated-orcid":false,"given":"Bridget","family":"Barker","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0272j5188","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, Northern Arizona University","place":["Flagstaff, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Marchetti","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03r0ha626","id-type":"ROR","asserted-by":"publisher"}],"name":"Eccles Institute of Human Genetics, University of Utah","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Hirschi","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Utah School of Medicine","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9790-277X","authenticated-orcid":true,"given":"Kimberly E.","family":"Hanson","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Utah School of Medicine","place":["Salt Lake City, USA"]},{"id":[{"id":"https:\/\/ror.org\/03r0ha626","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, Division of Clinical Microbiology, University of Utah and ARUP Laboratories","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0065-2204","authenticated-orcid":false,"given":"Katharine S.","family":"Walter","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03r0ha626","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Epidemiology, University of Utah","place":["Salt Lake City, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.2147\/CLEP.S34434"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw360"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2018.1509667"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2901.220771"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1289\/ehp.7786"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1029\/2019GH000209"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","unstructured":"Camponuri SK Heaney AK Cooksey GS Vugia DJ Jain S Swain DL Balmes J Remais JV Head JR. 2024. 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