{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:58:57Z","timestamp":1790258337611,"version":"4.1.0"},"reference-count":37,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Candida (Candidozyma) auris<\/jats:italic>\n                      (\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      ) poses an urgent public health threat due to its widespread emergence, antimicrobial resistance, and ability to cause severe infections and outbreaks associated with high mortality rates. In this study, we phenotypically and genotypically characterized antifungal susceptibility profiles and used whole-genome sequencing (WGS) to assess overall genetic diversity and to identify clonal clusters. From July 2020 to December 2025, a total of 118\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      isolates from 97 patients were collected at a tertiary hospital in New York City. Antifungal susceptibility testing and WGS were performed on all clinical isolates to characterize their clade-specific antifungal resistance genes and intra-clade genetic variations. Ninety-nine percentage of the\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      isolates demonstrated phenotypic fluconazole resistance. Resistance to echinocandins was observed in 7.6% (9\/118) of isolates, and resistance to amphotericin B was found in 54% (64\/118). WGS confirmed that all 118 isolates belonged to the CDC-defined Clade Ic. Azole resistance mutations in the\n                      <jats:italic toggle=\"yes\">ERG11<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">CDR1<\/jats:italic>\n                      genes were detected in 100% (118\/118) of the isolates, and mutations in the\n                      <jats:italic toggle=\"yes\">TAC1B<\/jats:italic>\n                      gene were present in 92.4% (109\/118) of the isolates, including one case with a unique set of mutations (\n                      <jats:italic toggle=\"yes\">ERG11<\/jats:italic>\n                      -Y132F,\n                      <jats:italic toggle=\"yes\">CDR1<\/jats:italic>\n                      -E709D,\n                      <jats:italic toggle=\"yes\">TAC1B<\/jats:italic>\n                      -A583S). Mutations in the\n                      <jats:italic toggle=\"yes\">FKS1<\/jats:italic>\n                      gene were identified in 5.9% (7\/118) of isolates though these were not consistently linked to echinocandin resistance. Genomic analysis also revealed that individual patients frequently carried the same strain throughout the study. Furthermore, multiple strains emerged simultaneously across the hospital each year. This suggests that numerous patients were likely already colonized upon admission, rather than acquiring the pathogen through intra-hospital transmission. The presence of multiple\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      strains with varying resistance patterns poses significant therapeutic challenges. Genomic typing can help hospitals understand the diversity of their\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      isolates to track their spread, identify potential outbreaks, and ensure the effectiveness of infection control measures.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Candida (Candidozyma) auris<\/jats:italic>\n                        is an emerging, multidrug-resistant fungal pathogen designated by the Centers for Disease Control and Prevention (CDC) as an urgent public threat. Traditionally,\n                        <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                        infections have been considered predominantly nosocomial, with outbreaks typically attributed to a single clonal lineage spreading within healthcare facilities. However, the genomic analysis performed in our study identified multiple distinct clusters of genetic variations within a single clade, suggesting that infections were not derived from a single source. This genomic diversity indicates that many patients may have acquired\n                        <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                        prior to hospital admission. Nevertheless, intra-hospital transmission was evident, as patient-to-patient spread facilitated the dissemination of various clonal lineages within the healthcare environment. These findings underscore the complex epidemiology of\n                        <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                        and highlight the urgent need for stringent infection control measures both within and beyond hospital settings.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01695-26","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:00:39Z","timestamp":1790254839000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Integrated genomic and phenotypic analysis of intra-clade variation in\n                    <i>Candida auris<\/i>\n                    from a New York City tertiary hospital"],"prefix":"10.1128","author":[{"given":"Shivani","family":"Satia","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]},{"name":"Department of Pathology and Genomic Medicine, Houston Methodist Hospital","place":["Houston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Pfeiffer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdullah","family":"Kilic","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]},{"id":[{"id":"https:\/\/ror.org\/0207ad724","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, Wake Forest University School of Medicine","place":["Winston-Salem, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Yoko","family":"Furuya","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medicine, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie C.","family":"Smithgall","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahesh","family":"Mansukhani","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Hsiao","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Shi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rinki","family":"Kumar","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2394-1319","authenticated-orcid":true,"given":"Daniel A.","family":"Green","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0767-6826","authenticated-orcid":true,"given":"Gregory J.","family":"Berry","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4942-7264","authenticated-orcid":true,"given":"Fann","family":"Wu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra2402635"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8020181"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01588-17"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012011"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.12.002"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf8972"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.3390\/jcm13226675"},{"key":"e_1_3_5_9_2","volume-title":"Candida auris","author":"Sikora A","year":"2023","unstructured":"Sikora A, Hashmi MF, Zahra F. 2023. Candida auris. StatPearls Publishing; St, Petersburg, FL, USA."},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1111\/myc.13776"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid3205.250760"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1093\/clinchem\/hvae185"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2417-3_2"},{"key":"e_1_3_5_14_2","unstructured":"Clinical and laboratory standards institute (CLSI). 2017. Reference method for broth dilution antifungal susceptibility testing of yeasts. CLSI Document M27. Clinical and Laboratory Standards Institute. Vol. 4th ed. Wayne Pennsylvania"},{"key":"e_1_3_5_15_2","unstructured":"Centers for Disease Control and Prevention. 2024. Antifungal susceptibility testing for C. Auris. Available from: https:\/\/www.cdc.gov\/candida-auris\/hcp\/laboratories\/antifungal-susceptibility-testing.html"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-024-05913-4"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03957-25"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.3390\/jof7030214"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.02242-21"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01503-19"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1013138"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00238-18"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx480"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012559"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.01585-21"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00300-25"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02659-24"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2023.04.025"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00601-25"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.3390\/jof9050529"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01692-18"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01674-13"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00517-21"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01243-22"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/s44259-025-00102-6"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1013363"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2025.115976"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01695-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01695-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:00:41Z","timestamp":1790254841000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01695-26"}},"subtitle":[],"editor":[{"given":"Renato","family":"Kovacs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,24]]},"references-count":37,"alternative-id":["10.1128\/spectrum.01695-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01695-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,24]]},"assertion":[{"value":"2026-05-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-24","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01695-26"}}