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Use of Whole Genome Sequencing to Investigate Potential Sources of Candidozyma auris Transmission in a University Hospital

Published online by Cambridge University Press:  23 June 2026

Jose Andres Portillo
Affiliation:
University Hospitals
Jennifer Cadnum
Affiliation:
Cleveland VA Medical Center
Munok Hwang
Affiliation:
Central Texas VA Research Foundation
Hosoon Choi
Affiliation:
Central Texas Veterans Health Care System
Piyali Chatterjee
Affiliation:
Central Texas Veterans Health Care System
Chetan Jinadatha
Affiliation:
Central Texas Veterans Health Care System
Tina Lewis
Affiliation:
University Hospitals Health System
Jay Krishnan
Affiliation:
University Hospitals, Case Western Reserve University
Curtis Donskey
Affiliation:
Cleveland VA Medical Center
Elie Saade
Affiliation:
Case Western Reserve University

Abstract

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Background: Candidozyma auris is an emerging multidrug-resistant pathogen characterized by environmental persistence and healthcare-associated transmission. Genomic epidemiology can help clarify transmission networks linking clinical isolates, shared equipment, and contaminated surfaces. Methods: We integrated environmental surveillance culturing with whole-genome sequencing (WGS) to characterize environmental reservoirs and genomic diversity of C. auris at University Hospitals Cleveland Medical Center, a tertiary-care hospital. Environmental surveillance samples were collected from high-touch surfaces, shared equipment, and other environmental sites within patient care areas and C. auris clinical isolates were obtained. All C. auris isolates underwent whole-genome sequencing. Dendrograms were constructed using single nucleotide polymorphism (SNP) distances to assess genetic relatedness (isolates with <13 SNP differences were considered related) and evaluate overlap between clinical and environmental isolates to infer transmission-relevant patterns. Results: Two genetically distinct C. auris clades, Clade III and Clade IV, circulated concurrently in April to May 2025. Three patients were infected with genomically related Clade III isolates (Figure 1.A) and 3 were infected with related Clade IV isolates (Figure 1.B). For both clades, multiple related isolates were present in the environment, including patient room surfaces, portable equipment, floors, and shoes of personnel. For Clade III, a distinct isolate (31 SNP difference from prior isolates) was detected in the environment in June 2025 with no concurrent clinical isolates. Conclusions: Our findings are consistent with previous evidence that high-touch surfaces and portable equipment frequently become contaminated with C. auris and suggest that floors and shoes may be an underappreciated source of dissemination. Integrating environmental surveillance with whole-genome sequencing can help identify likely reservoirs, clarify transmission dynamics, and guide targeted infection prevention interventions.

A dendrogram showing the relatedness of Clade III and Clade IV Candidozyma auris isolates from patients and the environment.

Information

Type
Emerging Pathogens
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
© The Author(s), 2026. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America