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Background Candida auris is an emerging multidrug-resistant yeast that contaminates healthcare environments causing healthcare-associated outbreaks. The mechanisms facilitating contamination are not established. Methods C. auris was quantified in residents’ bilateral axillary/inguinal composite skin swabs and environmental samples during a point-prevalence survey at a ventilator-capable skilled-nursing facility (vSNF A) with documented high colonization prevalence. Environmental samples were collected from all doorknobs, windowsills and handrails of each bed in 12 rooms. C. auris concentrations were measured using culture and C. auris-specific quantitative polymerase chain reaction (qPCR) The relationship between C. auris concentrations in residents’ swabs and associated environmental samples were evaluated using Kendall’s tau-b (τ b) correlation coefficient. Results C. auris was detected in 70/100 tested environmental samples and 31/57 tested resident skin swabs. The mean C. auris concentration in skin swabs was 1.22 × 105 cells/mL by culture and 1.08 × 106 cells/mL by qPCR. C. auris was detected on all handrails of beds occupied by colonized residents, as well as 10/24 doorknobs and 9/12 windowsills. A positive correlation was identified between the concentrations of C. auris in skin swabs and associated handrail samples based on culture (τ b = 0.54, P = .0004) and qPCR (τ b = 0.66, P = 3.83e−6). Two uncolonized residents resided in beds contaminated with C. auris. Conclusions Colonized residents can have high C. auris burdens on their skin, which was positively related with contamination of their surrounding healthcare environment. These findings underscore the importance of hand hygiene, transmission-based precautions, and particularly environmental disinfection in preventing spread in healthcare facilities., Candidaauris causes healthcare-associated outbreaks that are difficult to control. Environmental contamination is common in these settings. At a ventilator-capable skilled-nursing facility, we found environmental contamination was positively related to the colonization burdens on associated residents’ skin.

Candida auris is a fungal pathogen of high concern due to its ability to cause healthcare-associated infections and outbreaks, its resistance to antimicrobials and disinfectants and its persistence on human skin and in the inanimate environment. To inform surveillance and future mitigation strategies, we defined the extent of skin colonization and explored the microbiome associated with C. auris colonization. We collected swab specimens and clinical data at three times points between January and April 2019 from 57 residents (up to ten body sites each) of a ventilator-capable skilled nursing facility with endemic C. auris and routine chlorhexidine gluconate (CHG) bathing. Integrating microbial-genomic and epidemiologic data revealed occult C. auris colonization of multiple body sites not targeted commonly for screening. High concentrations of CHG were associated with suppression of C. auris growth but not with deleterious perturbation of commensal microbes. Modeling human mycobiome dynamics provided insight into underlying alterations to the skin fungal community as a possible modifiable risk factor for acquisition and persistence of C. auris. Failure to detect the extensive, disparate niches of C. auris colonization may reduce the effectiveness of infection-prevention measures that target colonized residents, highlighting the importance of universal strategies to reduce C. auris transmission. Longitudinal skin site sampling of residents in a skilled nursing facility sheds light on persistent niches of the emerging fungal pathogen Candida auris.

Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations.

Early identification of Candida auris is important for timely implementation of infection prevention and control actions. Here, we evaluated performance of the C. auris-specific SYBR Green qPCR assay on a panel of 70 anterior nares swabs. Enrichment broth culture was used as "gold standard". After performing a receiver operating curve (ROC) to optimize signal threshold, we found perfect agreement between culture and qPCR. Additionally, we found no indication of inhibitors in the anterior nares swabs.

Summary Background Transmission of multidrug-resistant Candida auris infection has been reported in the USA. To better understand its emergence and transmission dynamics and to guide clinical and public health responses, we did a molecular epidemiological investigation of C auris cases in the USA. Methods In this molecular epidemiological survey, we used whole-genome sequencing to assess the genetic similarity between isolates collected from patients in ten US states (California, Connecticut, Florida, Illinois, Indiana, Maryland, Massachusetts, New Jersey, New York, and Oklahoma) and those identified in several other countries (Colombia, India, Japan, Pakistan, South Africa, South Korea, and Venezuela). We worked with state health departments, who provided us with isolates for sequencing. These isolates of C auris were collected during the normal course of clinical care (clinical cases) or as part of contact investigations or point prevalence surveys (screening cases). We integrated data from standardised case report forms and contact investigations, including travel history and epidemiological links (ie, patients that had shared a room or ward with a patient with C auris ). Genetic diversity of C auris within a patient, a facility, and a state were evaluated by pairwise differences in single-nucleotide polymorphisms (SNPs). Findings From May 11, 2013, to Aug 31, 2017, isolates that corresponded to 133 cases (73 clinical cases and 60 screening cases) were collected. Of 73 clinical cases, 66 (90%) cases involved isolates related to south Asian isolates, five (7%) cases were related to South American isolates, one (1%) case to African isolates, and one (1%) case to east Asian isolates. Most (60 [82%]) clinical cases were identified in New York and New Jersey; these isolates, although related to south Asian isolates, were genetically distinct. Genomic data corroborated five (7%) clinical cases in which patients probably acquired C auris through health-care exposures abroad. Among clinical and screening cases, the genetic diversity of C auris isolates within a person was similar to that within a facility during an outbreak (median SNP difference three SNPs, range 0–12). Interpretation Isolates of C auris in the USA were genetically related to those from four global regions, suggesting that C auris was introduced into the USA several times. The five travel-related cases are examples of how introductions can occur. Genetic diversity among isolates from the same patients, health-care facilities, and states indicates that there is local and ongoing transmission. Funding US Centers for Disease Control and Prevention

Candida auris is a newly emerging species that was first identified in Asia in 2009 but has rapidly spread across the world. C. auris differs from most other Candida species in that antifungal resistance is the norm rather than the exception, it is a commensal of human skin rather than the human gut, and it can be easily transmitted from person to person in a health care setting. This review discusses the emergence of C. auris , global epidemiology, identification, antifungal susceptibility testing, and precautions to be taken when it is identified from a patient specimen.

November 11, 2016/65(44);1234-1237. What is already known about this topic? Candida auris is an emerging pathogenic fungus that has been reported from at least a dozen countries on four continents during 2009-2015. The organism is difficult to identify using traditional biochemical methods, some isolates have been found to be resistant to all three major classes of antifungal medications, and C. auris has caused health care-associated outbreaks. What is added by this report? This is the first description of C. auris cases in the United States. C. auris appears to have emerged in the United States only in the last few years, and U.S. isolates are related to isolates from South America and South Asia. Evidence from U.S. case investigations suggests likely transmission of the organism occurred in health care settings. What are the implications for public health practice? It is important that U.S. laboratories accurately identify C. auris and for health care facilities to implement recommended infection control practices to prevent the spread of C. auris. Local and state health departments and CDC should be notified of possible cases of C. auris and of isolates of C. haemulonii and Candida spp. that cannot be identified after routine testing.

Candida auris is an emerging multidrug-resistant fungal pathogen. Since first reported in 2009, C. auris has caused healthcare outbreaks around the world, often involving high mortality. Identification of C. auris has been a major challenge as many common conventional laboratory methods cannot accurately detect it. Early detection and implementation of infection control practices can prevent its spread. The aim of this review is to describe recommendations for the detection and control of C. auris in healthcare settings.

Candida auris is an emerging fungal pathogen of rising concern due to its increasing incidence, its ability to cause healthcare-associated outbreaks and antifungal resistance. Genomic analysis revealed that early cases of C. auris that were detected contemporaneously were geographically stratified into four major clades. Clade II, also termed East Asian clade, consists of the initial isolates described from cases of ear infection, is less frequently resistant to antifungal drugs and to date, the isolates from this group have not been associated with outbreaks. Here, we generate nearly complete genomes (“telomere-to-telomere”) of an isolate of this clade and of the more widespread Clade IV. By comparing these to genome assemblies of the other two clades, we find that the Clade II genome appears highly rearranged, with 2 inversions and 9 translocations resulting in a substantially different karyotype. In addition, large subtelomeric regions have been lost from 10 of 14 chromosome ends in the Clade II genomes. We find that shorter telomeres and genome instability might be a consequence of a naturally occurring loss-of-function mutation in DCC1 exclusively found in Clade II isolates, resulting in a hypermutator phenotype. We also determine that deleted subtelomeric regions might be linked to clade-specific adaptation as these regions are enriched in Hyr/Iff-like cell surface proteins, novel candidate cell surface proteins, and an ALS-like adhesin. The presence of these cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggests an explanation for the different phenotypes observed between clades.IMPORTANCECandida auris was unknown prior to 2009 and since then it has quickly spread around the world, causing outbreaks in healthcare facilities and representing a high fraction of candidemia cases in some regions. The emergence of C. auris is a major concern, since it is often multidrug-resistant, easily spread between patients, and causes invasive infections. While isolates from three global clades cause invasive infections, isolates from Clade II primarily cause ear infections and have not been implicated in outbreaks, though cases of Clade II infections have been reported on different continents. Here, we describe genetic differences between Clade II and Clades I, III and IV, including a loss-of-function mutation in a gene associated with telomere length maintenance and genome stability, and the loss of cell wall proteins involved in adhesion and biofilm formation, that may suggest an explanation for the lower virulence and potential for transmission of Clade II isolates.

Candida auris, an emerging fungus that can cause invasive infections, is associated with high mortality and is often resistant to multiple antifungal drugs. C. auris was first described in 2009 after being isolated from external ear canal discharge of a patient in Japan (1). Since then, reports of C. auris infections, including bloodstream infections, have been published from several countries, including Colombia, India, Israel, Kenya, Kuwait, Pakistan, South Africa, South Korea, Venezuela, and the United Kingdom (2-7). To determine whether C. auris is present in the United States and to prepare for the possibility of transmission, CDC issued a clinical alert in June 2016 informing clinicians, laboratorians, infection control practitioners, and public health authorities about C. auris and requesting that C. auris cases be reported to state and local health departments and CDC (8). This report describes the first seven U.S. cases of C. auris infection reported to CDC as of August 31, 2016. Data from these cases suggest that transmission of C. auris might have occurred in U.S. health care facilities and demonstrate the need for attention to infection control measures to control the spread of this pathogen.

Candida auris is a multidrug-resistant pathogenic yeast whose recent emergence is of increasing public-health concern. C. auris can colonise multiple body sites, including patients' skin, and survive for weeks in the health care environment, facilitating patient-to-patient transmission and fueling health care-associated outbreaks. Rapid and accurate detection of C. auris colonisation is essential for timely implementation of infection control measures and to prevent transmission. Currently, axilla/groin composite swabs, used to assess colonisation status, are processed using a culture-based method that is sensitive and specific but requires 14 days. This delay limits the opportunity to respond and highlights the need for a faster alternative. The culture-independent T2 Magnetic Resonance (T2MR) system is a rapid diagnostic platform shown to detect target pathogens of interest from unprocessed blood samples in

Background Candida auris is a multidrug-resistant yeast associated with hospital outbreaks worldwide. During 2015-2016, multiple outbreaks were reported in Colombia. We aimed to understand the extent of contamination in healthcare settings and to characterize the molecular epidemiology of C. auris in Colombia. Methods We sampled patients, patient contacts, healthcare workers, and the environment in 4 hospitals with recent C. auris outbreaks. Using standardized protocols, people were swabbed at different body sites. Patient and procedure rooms were sectioned into 4 zones and surfaces were swabbed. We performed whole-genome sequencing (WGS) and antifungal susceptibility testing (AFST) on all isolates. Results Seven of the 17 (41%) people swabbed were found to be colonized. Candida auris was isolated from 37 of 322 (11%) environmental samples. These were collected from a variety of items in all 4 zones. WGS and AFST revealed that although isolates were similar throughout the country, isolates from the northern region were genetically distinct and more resistant to amphotericin B (AmB) than the isolates from central Colombia. Four novel nonsynonymous mutations were found to be significantly associated with AmB resistance. Conclusions Our results show that extensive C. auris contamination can occur and highlight the importance of adherence to appropriate infection control practices and disinfection strategies. Observed genetic diversity supports healthcare transmission and a recent expansion of C. auris within Colombia with divergent AmB susceptibility.

Candida auris is an emerging multidrug-resistant yeast first described in 2009 that has since caused healthcare-associated outbreaks of severe human infections around the world. In some hospitals, it has become a leading cause of invasive candidiasis. C. auris is markedly different from most other pathogenic Candida species in its genetics, antifungal resistance, and ability to spread between patients. The reasons why this fungus began spreading widely in the last decade remain a mystery. We examine available data on C. auris and related species, including genomic epidemiology, phenotypic characteristics, and sites of detection, to put forth hypotheses on its possible origins. C. auris has not been detected in the natural environment; related species have been detected in in plants, insects, and aquatic environments, as well as from human body sites. It can tolerate hypersaline environments and higher temperatures than most Candida species. We explore hypotheses about the pre-emergence niche of C. auris, whether in the environmental or human microbiome, and speculate on factors that might have led to its spread, including the possible roles of healthcare, antifungal use, and environmental changes, including human activities that might have expanded its presence in the environment or caused increased human contact.

Background Candida auris is an often multidrug-resistant yeast that causes invasive infections and, unlike most Candida species, spreads in healthcare facilities. CDC released a clinical alert in June 2016 requesting reporting of C. auris cases. We investigated cases to contain transmission and inform prevention measures for this novel organism. Methods Clinical cases were defined as C. auris from any clinical specimen from a patient in the United States. Response to cases included implementation of infection control measures, enhanced cleaning and disinfection, and testing of close contacts for C. auris colonisation (isolation from a person’s axilla or groin was defined as a screening case). Microbiology records were reviewed at reporting facilities for missed cases. All isolates were forwarded to CDC for confirmation, antifungal susceptibility testing, and whole-genome sequencing (WGS). Results As of April 13, 2017, 61 clinical cases of C. auris were reported from six states: New York (39), New Jersey (15), Illinois (4), Indiana (1), Maryland (1), and Massachusetts (1). All but two occurred since 2016 (Figure). An additional 32 screening cases were identified among contacts. Median age of clinical case-patients was 70 years (range 21–96); 56% were male. Nearly, all had underlying medical conditions and extensive exposure to healthcare facilities before infection. Most clinical isolates were from blood (38, 62%), followed by urine (8, 13%) and respiratory tract (5, 8%). Among the first 35 isolates, 30 (86%) were resistant to fluconazole, 15 (43%) to amphotericin B, and one (3%) to caspofungin. No isolate was resistant to all three. WGS revealed isolates from each state were highly related and different from other states, suggestive of transmission. Microbiology record reviews did not identify additional cases before 2016. Conclusion C. auris is an emerging pathogen, with similarities to multidrug-resistant bacteria, that has been transmitted in US healthcare settings. CDC and public health partners are committed to prompt and aggressive action through investigation of cases and heightened infection control practices to halt its spread. Disclosures All authors: No reported disclosures.

Background Candida auris can be transmitted in healthcare settings, and patients can become asymptomatically colonized, increasing risk for invasive infection and transmission. We investigated an ongoing C. auris outbreak at a 30-bed long-term acute care hospital to identify colonization for C. auris prevalence and risk factors. Methods During February–June 2017, we conducted point prevalence surveys every 2 weeks among admitted patients. We abstracted clinical information from medical records and collected axillary and groin swabs. Swabs were tested for C. auris. Data were analyzed to identify risk factors for colonization with C. auris by evaluating differences between colonized and noncolonized patients. Results All 101 hospitalized patients were surveyed, and 33 (33%) were colonized with C. auris. Prevalence of colonization ranged from 8% to 38%; incidence ranged from 5% to 20% (figure). Among colonized patients with available data, 19/27 (70%) had a tracheostomy, 20/31 (65%) had gastrostomy tubes, 24/33 (73%) ventilator use, and 12/27 (44%) had hemodialysis. Also, 31/33 (94%) had antibiotics and 13/33 (34%) antifungals during hospitalization. BMI for colonized patients (mean = 30.3, standard deviation (SD) = 10) was higher than for noncolonized patients (mean = 26.5, SD = 7.9); t = −2.1; P = 0.04). Odds of colonization were higher among Black patients (33%) vs. White patients (16%) (odds ratio [OR] 3.5; 95% confidence interval [CI] 1.3–9.8), and those colonized with other multidrug-resistant organism (MDRO) (72%) vs. noncolonized (44%) (OR 3.2; CI 1.3–8.0). Odds of death were higher among colonized patients (OR 4.6; CI 1.6—13.6). Conclusion Patients in long-term acute care facilities and having high prevalences of MDROs might be at risk for C. auris. Such patients with these risk factors could be targeted for enhanced surveillance to facilitate early detection of C. auris. Infection control measures to reduce MDROs’ spread, including hand hygiene, contact precautions, and judicious use of antimicrobials, could prevent further C. auris transmission. Acknowledgements The authors thank Janet Glowicz and Kathleen Ross. Disclosures All authors: No reported disclosures.

Background In 2016, Candida auris was first reported in the United States, with 2 Illinois patients among the first cases. In response, the state and 3 Chicago-area health departments (HDs) investigated clinical cases and performed point prevalence surveys (PPSs) to identify colonized cases. Methods Clinical cases had positive C. auris cultures obtained for clinical care; colonized cases had positive surveillance cultures during PPSs. In August 2016–January 2018, PPSs were performed in Chicago-area acute care hospital (ACH) intensive care units, long-term acute-care hospitals (LTACHs), and high-acuity floors of skilled nursing facilities (SNFs) and SNFs caring for ventilated patients (vSNFs). Facility and HD staff obtained composite axilla/groin swabs from assenting patients to detect colonization. Facilities with an epidemiologic link to a clinical case or a shared patient population with a facility housing a clinical case were prioritized for PPSs. Results During May 2016–January 2018, Chicago-area facilities reported 24 clinical cases, including 10 bloodstream infections. HDs performed 33 PPSs at 20 facilities (5 ACHs, 5 LTACHs, 3 SNFs, and 7 vSNFs) during August 2016–January 2018. Of 1,364 patients screened, 92 (6.7%) were colonized with C. auris; 10 (50%) facilities had ≥1 colonized patient. A significantly higher proportion screened positive from September 2017 to January 2018 (84/822, 10.2%) than in August 2016–August 2017 (8/542, 1.5%; z-test P < 0.01). Prevalence of C. auris colonization was highest in vSNFs (median: 7.7%; range: 0%–43.3%), compared with ACHs (0%; 0%–6.3%), LTACHs (0%; 0%–14.3%), and SNFs (0%, 0%–1.5%). PPSs in vSNFs identified 91% (84/92) of colonized cases. Among 5 vSNFs with repeat PPSs, 4 had higher prevalence on repeat screening (median: 26.1%; range: 0%–43.3%) than at baseline (1.2%; 0%–17.0%). Conclusion C. auris has rapidly emerged in the Chicago area. Increasing prevalence of C. auris colonization during repeat PPSs indicates transmission and amplification within vSNFs. To prevent spread, state and local HDs provided infection control recommendations, disseminated health alerts, and recommended placing vSNF patients from high-acuity floors on transmission-based precautions. Disclosures All authors: No reported disclosures.