{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T05:02:28Z","timestamp":1785301348972,"version":"3.55.0"},"reference-count":73,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008908","name":"Universit\u00e1 degli Studi di Messina","doi-asserted-by":"publisher","award":["CT_GOM_2024_2025"],"award-info":[{"award-number":["CT_GOM_2024_2025"]}],"id":[{"id":"10.13039\/501100008908","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Magnusiomyces clavatus<\/jats:italic>\n                      is an emerging fungal pathogen primarily infecting immunocompromised patients hospitalized in hematological wards. Its remarkable genetic homogeneity makes high-resolution phylogenetic analysis challenging, hindering efforts to accurately discriminate strains and complicating epidemiological surveillance, particularly in the context of hospital outbreaks.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this study, we provide the most comprehensive phylogenomic framework to date for this species by analyzing a dataset of 62 whole-genome sequences, including four novel genomes from clinical and environmental strains recovered in a large hospital in southern Italy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Using a pangenome graph-based variant calling strategy on 1,624 high-quality single nucleotide polymorphisms, we delineated eight genetically distinct clades (A-H) that accurately reflect the geo-epidemiological history of this fungus. Population structure analysis revealed significant genetic differentiation among geographically separated populations, suggesting localized diversification. Furthermore, only the\n                      <jats:italic>MAT\u03b1<\/jats:italic>\n                      idiomorph was identified across strains, supporting the highly clonal nature of\n                      <jats:italic>M. clavatus<\/jats:italic>\n                      . Finally, comparative mitogenomic analysis revealed 43 conserved translational bypass (byps) elements and identified four possible mitotypes based on presence or absence of specific inverted regions.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This work provides a robust, high-resolution framework for future genomic epidemiology studies and outbreak investigations of this important emerging fungal pathogen.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1872401","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T04:35:10Z","timestamp":1785299710000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic epidemiology and phylogenomics of Magnusiomyces clavatus: a comparative analysis of novel italian and publicly available genomes"],"prefix":"10.3389","volume":"16","author":[{"given":"Gabriele","family":"Rigano","sequence":"first","affiliation":[{"name":"Department of Biology, University of Rome \u201cTor Vergata\u201d","place":["Rome, Italy"]},{"name":"Department of Physics, PhD programme in Space Science and Technology, University of Trento","place":["Trento, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Letterio","family":"Giuffr\u00e8","sequence":"additional","affiliation":[{"name":"Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina","place":["Messina, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastiano","family":"Strangio","sequence":"additional","affiliation":[{"name":"Medical Directorate, Hygiene and Preventive Medicine Unit, Great Metropolitan Hospital \u201cBianchi-Melacrino-Morelli\u201d","place":["Reggio Calabria, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giuseppe","family":"Criseo","sequence":"additional","affiliation":[{"name":"Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina","place":["Messina, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giuliana Lo","family":"Cascio","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma","place":["Parma, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caterina","family":"Alati","sequence":"additional","affiliation":[{"name":"Department of Hemato-Oncology and Radiotherapy, Hematology and Stem Cell Transplantation and Cellular Therapies Unit (CTMO), Great Metropolitan Hospital \u201cBianchi-Melacrino-Morelli\u201d","place":["Reggio Calabria, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonietta","family":"Meliad\u00f2","sequence":"additional","affiliation":[{"name":"Clinical Microbiology and Virology Unit, Great Metropolitan Hospital \u201cBianchi-Melacrino-Morelli\u201d","place":["Reggio Calabria, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo","family":"Martino","sequence":"additional","affiliation":[{"name":"Department of Hemato-Oncology and Radiotherapy, Hematology and Stem Cell Transplantation and Cellular Therapies Unit (CTMO), Great Metropolitan Hospital \u201cBianchi-Melacrino-Morelli\u201d","place":["Reggio Calabria, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luigi","family":"Principe","sequence":"additional","affiliation":[{"name":"Clinical Microbiology and Virology Unit, Great Metropolitan Hospital \u201cBianchi-Melacrino-Morelli\u201d","place":["Reggio Calabria, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orazio","family":"Romeo","sequence":"additional","affiliation":[{"name":"Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina","place":["Messina, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1700147","article-title":"Ribosome rearrangements at the onset of translational bypassing","volume":"3","author":"Agirrezabala","year":"2017","journal-title":"Sci. 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