{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T17:41:05Z","timestamp":1793986865520,"version":"4.8.0"},"reference-count":48,"publisher":"American Society for Microbiology","issue":"11","license":[{"start":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T00:00:00Z","timestamp":1732060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/ASMCopyrightv2"},{"start":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T00:00:00Z","timestamp":1732060800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"MOST | National Key Research and Development Program of China","award":["2021YFC2301000"],"award-info":[{"award-number":["2021YFC2301000"]}]},{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82304963"],"award-info":[{"award-number":["82304963"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32300084"],"award-info":[{"award-number":["32300084"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"\u5317\u4eac\u5e02\u79d1\u5b66\u6280\u672f\u59d4\u5458\u4f1a | Natural Science Foundation of Beijing Municipality","award":["IS23089"],"award-info":[{"award-number":["IS23089"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2024,11,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              <jats:italic>Candida auris,<\/jats:italic>\n              an emerging fungal pathogen characterized by multidrug resistance and high-mortality nosocomial infections, poses a serious global health threat. However, the precise and rapid identification and characterization of\n              <jats:italic>C. auris<\/jats:italic>\n              remain a challenge. Here, we employed Raman spectroscopy combined with machine learning to identify\n              <jats:italic>C. auris<\/jats:italic>\n              isolates and its closely related species as well as to predict antifungal resistance and key virulence factors at the single-cell level. The average accuracy of identification among all\n              <jats:italic>Candida<\/jats:italic>\n              species was 93.33%, with an accuracy of 98% for the clinically simulated samples. The drug susceptibility of\n              <jats:italic>C. auris<\/jats:italic>\n              to fluconazole and amphotericin B was 99% and 94%, respectively. Furthermore, the phenotypic prediction of\n              <jats:italic>C. auris<\/jats:italic>\n              yielded an accuracy of 100% for aggregating cells and 97% for filamentous cells. This proof-of-concept methodology not only precisely identifies\n              <jats:italic>C. auris<\/jats:italic>\n              at the clade-specific level but also rapidly predicts the antifungal resistance and biological characteristics, promising a valuable medical diagnostic tool to combat this multidrug-resistant pathogen in the future.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Currently, combating\n              <jats:italic>Candida auris<\/jats:italic>\n              infections and transmission is challenging due to the lack of efficient identification and characterization methods for this species. To address these challenges, our study presents a novel approach that utilizes Raman spectroscopy and artificial intelligence to achieve precise identification and characterization of\n              <jats:italic>C. auris<\/jats:italic>\n              at the singe-cell level. It can accurately identify a single cell from the four\n              <jats:italic>C. auris<\/jats:italic>\n              clades. Additionally, we developed machine learning models designed to detect antifungal resistance in\n              <jats:italic>C. auris<\/jats:italic>\n              cells and differentiate between two distinct phenotypes based on the single-cell Raman spectrum. We also constructed prediction models for detecting aggregating and filamentous cells in\n              <jats:italic>C. auris<\/jats:italic>\n              , both of which are closely linked to its virulence. These results underscore the merits of Raman spectroscopy in the identification and characterization of\n              <jats:italic>C. auris<\/jats:italic>\n              , promising improved outcomes in the battle against\n              <jats:italic>C. auris<\/jats:italic>\n              infections and transmission.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/aem.01025-24","type":"journal-article","created":{"date-parts":[[2024,10,29]],"date-time":"2024-10-29T13:00:27Z","timestamp":1730206827000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":16,"title":["Application of Raman spectroscopy and machine learning for\n            <i>Candida auris<\/i>\n            identification and characterization"],"prefix":"10.1128","volume":"90","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3966-942X","authenticated-orcid":false,"given":"Junjing","family":"Xue","sequence":"first","affiliation":[{"name":"Shandong First Medical University &amp; Shandong Academy of Medical Sciences, Shandong, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huizhen","family":"Yue","sequence":"additional","affiliation":[{"name":"Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China"},{"name":"Beijing Key Laboratory of Basic Research With Traditional Chinese Medicine on Infectious Diseases, Beijing Institute of Chinese Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weilai","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanying","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4761-7548","authenticated-orcid":false,"given":"Guanghua","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China"},{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8251-2306","authenticated-orcid":false,"given":"Yu Vincent","family":"Fu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China"},{"name":"Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004404"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00960-9"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1348-0421.2008.00083.x"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00029-17"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/myc.12904"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40560-018-0342-4"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.3390\/jof7010031"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw691"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/mmy\/myaa116"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011239"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S402754"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(24)00101-0"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01624-18"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0223433"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2018.09.014"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02202-16"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw696"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2017.1364992"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/jbio.202100312"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.talanta.2022.123383"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.3c00047"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-20850-z"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.talanta.2022.123807"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1039\/c7an01371j"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1039\/c8an02212g"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1039\/d0cs01019g"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.03.030"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01466-20"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/jemt.20229"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2004.0008"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00189-16"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00371-20"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bjc.6603102"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10103-014-1635-z"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics12122944"},{"key":"e_1_3_4_37_2","first-page":"245","volume-title":"Infrared and NIR Raman spectroscopy in medical microbiology","author":"Naumann D","year":"1998","unstructured":"Naumann D. 1998 Infrared and NIR Raman spectroscopy in medical microbiology, p 245\u2013257"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.saa.2004.11.017"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0213621"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules13102608"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac00101a001"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.3c09563"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1002\/jrs.1107"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41426-018-0187-x"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00055-24"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.9b04946"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.1076965"},{"key":"e_1_3_4_48_2","volume-title":"Reference method for Broth dilution antifungal susceptibility testing of yeasts","author":"CLSI","year":"2017","unstructured":"CLSI. 2017. Reference method for Broth dilution antifungal susceptibility testing of yeasts"},{"key":"e_1_3_4_49_2","volume-title":"Antifungal susceptibility testing for C. auris","author":"Prevention CfDCa","year":"2024","unstructured":"Prevention CfDCa. 2024. Antifungal susceptibility testing for C. auris"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/aem.01025-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/aem.01025-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T14:07:46Z","timestamp":1732111666000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/aem.01025-24"}},"subtitle":[],"editor":[{"given":"Irina S.","family":"Druzhinina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,11,20]]},"references-count":48,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2024,11,20]]}},"alternative-id":["10.1128\/aem.01025-24"],"URL":"https:\/\/doi.org\/10.1128\/aem.01025-24","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,20]]},"assertion":[{"value":"2024-06-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-09-23","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-10-29","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01025-24"}}