Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned

Abstract

Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in New York (NY) from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/nonselective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of the internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal gene for C. auris genotyping. Results included (a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates as well as identification of 277 clinical cases and 350 colonized cases from 151 health care facilities, including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, (b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, (c) demonstration of relatively heavier colonization of C. auris in nares than in the axilla/groin, and (d) predominance of the South Asia clade I with intrinsic resistance to fluconazole and elevated MIC to voriconazole (81%), amphotericin B (61%), flucytosine (5FC) (3%), and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

Analysis of a Candida auris Outbreak Provides New Insights into an Emerging Pathogen

“…While numerous studies of individual isolates are vital and will continue to reveal crucial information about some of the characteristics that make this fungus so clinically important, larger studies involving many isolates have the potential to reveal important clinical information. These studies have been few in number; however, in this issue of the Journal of Clinical Microbiology, Zhu et al have described a number of important characteristics concerning the largest United States outbreak of C. auris (20). Their study encompassed a 2-year outbreak from 2016 to 2018 in the New York area and included the analysis of more than 500 clinical isolates, more than 11,000 patient surveillance specimens, and more than 3,500 environmental surveillance specimens.…”

“…This bias suggests differences in clade exposure; however, perhaps there are underlying factors that need to be investigated more closely, such as clade-specific differences in virulence or infection route (person-person route versus environment-person route). Importantly, clade genotyping of C. auris has typically been conducted by whole-genome sequencing, which is not possible for most laboratories; however, Zhu et al (20) found that by using a combination of D1/D2 and ITS sequencing, the strains could be accurately identified and genotyped. Identification was found to be more accurate than either MALDI-TOF MS or Vitek MS; consequently, the sequencing approach should be investigated further as a rapid genotyping method, because laboratories that do not sequence, but can perform PCR, can send amplicons out to sequence to a variety of commercial companies at a small cost.…”

“…Finally, the clinical significance of C. auris is unquestionably drug resistance (for reviews see references 29 and 30). Of 277 clinical isolates, Zhu et al (20) found one that was susceptible to fluconazole, while 81% had elevated MICs to voriconazole. Most were resistant to amphotericin B (61%; MIC Ͼ 2.0 g/ml); however, none were resistant to the echinocandins, as were none of the environmental isolates.…”

Toward point-of-care diagnostics of Candida auris

“…Candida auris is an emerging multidrug-resistant yeast, which presents a serious global health threat. The largest, localized, uninterrupted C. auris outbreak in the US healthcare facilities continues to afflict the New York metro areas (2013-2019) [1], [2]. The New York State Department of Health (NYSDOH) Mycology Laboratory has been serving a crucial role in developing rapid, and high-throughput assays that are sensitive and specific to C. auris, and in processing over 20,000 clinical samples in the state for diagnosis and surveillance purposes [3], [4].…”

Candida aurisIsolates Resistant to Three Classes of Antifungal Medications — New York, 2019

“…As of June 28, 2019, a total of 801 patients with C. auris were detected in New York, identified through clinical cultures (349) or skin or nares screening swabs only (452) (3). Testing of the first available clinical isolates with susceptibilities revealed that 276 of 277 (99.6%) were resistant to fluconazole, 170 of 277 (61.3%) were resistant to amphotericin B, and none was resistant to echinocandins (1,6). Testing of subsequent available isolates obtained from infected patients with susceptibilities revealed 330 of 331 (99.7%) were resistant to fluconazole, US Department of Health and Human Services/Centers for Disease Control and Prevention 210 of 331 (63.4%) were resistant to amphotericin B, and 13 of 331 (3.9%) were resistant to echinocandins (1,6).…”