{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T18:23:52Z","timestamp":1792607032510,"version":"4.5.0"},"reference-count":30,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T00:00:00Z","timestamp":1689206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:p>\n                    A\n                    <jats:italic>Candida auris<\/jats:italic>\n                    outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200\n                    <jats:italic>C. auris<\/jats:italic>\n                    isolates from patients at several facilities. Genetically distinct subgroups of\n                    <jats:italic>C. auris<\/jats:italic>\n                    were detected from Clade I (3 distinct lineages) and III (1 lineage). Open-source bioinformatic tools were developed and implemented to aid in the epidemiological investigation. The work herein compares three methods for\n                    <jats:italic>C. auris<\/jats:italic>\n                    whole genome analysis: Nullarbor, MycoSNP and a new pipeline TheiaEuk. We also describe a novel analysis method focused on elucidating phylogenetic linkages between isolates within an ongoing outbreak. Moreover, this study places the ongoing outbreaks in a global context utilizing existing sequences provided worldwide. Lastly, we describe how the generated results were communicated to the epidemiologists and infection control to generate public health interventions.\n                  <\/jats:p>","DOI":"10.3389\/fpubh.2023.1198189","type":"journal-article","created":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T05:54:27Z","timestamp":1689314067000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":26,"title":["The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada"],"prefix":"10.3389","volume":"11","author":[{"given":"Andrew","family":"Gorzalski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"Frank J.","family":"Ambrosio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauryn","family":"Massic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle R.","family":"Scribner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danielle Denise","family":"Siao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Hua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip","family":"Dykema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chidinma","family":"Njoku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Libuit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel R.","family":"Sevinsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Van Hooser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Pandori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Hess","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,13]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1111\/j.1348-0421.2008.00083.x","article-title":"Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital","volume":"53","author":"Satoh","year":"2009","journal-title":"Microbiol Immunol"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1093\/cid\/ciw691","article-title":"Simultaneous emergence of multidrug-re-sistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses","volume":"64","author":"Lockhart","year":"2017","journal-title":"Clin Infect Dis"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/978-1-0716-2417-3_17","article-title":"MycoSNP: a portable workflow for performing whole-genome sequencing analysis of Candida auris","volume":"2517","author":"Bagal","year":"2022","journal-title":"Methods Mol Biol"},{"key":"ref4","unstructured":"Tracking Candida auris2022"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1780","DOI":"10.3201\/eid2509.190686","article-title":"Potential fifth clade of Candida auris, Iran, 2018","volume":"25","author":"Chow","year":"2019","journal-title":"Emerg Infect Dis"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.ijantimicag.2019.08.013","article-title":"Control of Candida auris in healthcare institutions: outcome of an International Society for Antimicrobial Chemotherapy expert meeting","volume":"54","author":"Kenters","year":"2019","journal-title":"Int J Antimicrob Agents"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1111\/imj.14612","article-title":"Australian and New Zealand mycoses interest group (ANZMIG), healthcare infection control special interest group (HICSIG); both of the Australasian Society for Infectious Diseases (ASID). 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