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Background: Environmental contamination is suspected to play an important role in Candida auris transmission. Understanding speed and risks of contamination after room disinfection could inform environmental cleaning recommendations., Methods: We conducted a prospective multicenter study of environmental contamination associated with C. auris colonization at 6 ventilator-capable skilled nursing facilities and 1 acute care hospital in Illinois and California. Known C. auris carriers were sampled at 5 body sites followed by sampling of nearby room surfaces before disinfection and at 0, 4, 8, and 12 hours after disinfection. Samples were cultured for C. auris and bacterial multidrug-resistant organisms (MDROs). Odds of surface contamination after disinfection were analyzed using multilevel generalized estimating equations., Results: Among 41 known C. auris carriers, colonization was detected most frequently on palms/fingertips (76%) and nares (71%). C. auris contamination was detected on 32.2% (66/205) of room surfaces before disinfection and 20.5% (39/190) of room surfaces by 4 hours after disinfection. A higher number of C. auris-colonized body sites was associated with higher odds of environmental contamination at every time point following disinfection, adjusting for facility of residence. In the rooms of 38 (93%) C. auris carriers co-colonized with a bacterial MDRO, 2%-24% of surfaces were additionally contaminated with the same MDRO by 4 hours after disinfection., Conclusions: C. auris can contaminate the healthcare environment rapidly after disinfection, highlighting the challenges associated with environmental disinfection. Future research should investigate long-acting disinfectants, antimicrobial surfaces, and more effective patient skin antisepsis to reduce the environmental reservoir of C. auris and bacterial MDROs in healthcare settings., Competing Interests: Potential conflicts of interest. G. M. G., R. D. S., R. S., R. P., S. S. H., and M. K. H. have the following disclosures: Conducted studies where participating healthcare facilities received contributed antiseptic and cleaning products from Medline Industries, Inc., and Xttrium Laboratories. Companies had no role in the design, conduct, or analysis of these studies. The remaining authors have no conflicts to declare. K. B. reports other financial or nonfinancial interests: Conducted studies where participating hospitals/nursing homes received cleaning and antiseptic product from Medline Industries (payment to institution). G. M. G. also reports the following grants or contracts to institution: NIAID 5F31AI172386-02: Endemic and Emerging Multidrug Resistant Organisms in Nursing Homes: A Neglected Clinical Setting and 1P01AI172725: MDRO Carriage, Transmission, Sequelae, and Prevention in Nursing Homes. M. K. H. reports a position as unpaid volunteer position as President SHEA Board of Trustees and the following grants or contracts to institution: CDC BAA 75D301-19-67835 Evaluating emergence of resistance and changes in clinical pathogens following introduction of chlorhexidine bathing. S. S. H., R. S., J. S., and R. D. S. report grants or contracts to institution: 1P01AI172725: MDRO Carriage, Transmission, Sequelae, and Prevention in Nursing Homes. S. E. S. reports the following grants or contracts to institution: NIH—1R01AI175227-01 (Subaward from University of Michigan) and Cohn Fellowship Intramural Career Development Grant (Rush University Medical Center); travel stipend to cover travel costs to present at IDWeek 2022 from Society for Healthcare Epidemiology of America. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.