Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes

Diana M. Proctor, Sarah E. Sansom, Clay Deming, Sean Conlan, Ryan A. Blaustein, Thomas K. Atkins, Thelma Dangana, Christine Fukuda, Lahari Thotapalli, Heidi H. Kong, Michael Y. Lin, Mary K. Hayden () and Julia A. Segre ()
Additional contact information
Diana M. Proctor: National Institutes of Health
Sarah E. Sansom: Rush University Medical Center
Clay Deming: National Institutes of Health
Sean Conlan: National Institutes of Health
Ryan A. Blaustein: National Institutes of Health
Thomas K. Atkins: National Institutes of Health
Thelma Dangana: Rush University Medical Center
Christine Fukuda: Rush University Medical Center
Lahari Thotapalli: Rush University Medical Center
Heidi H. Kong: National Institutes of Health
Michael Y. Lin: Rush University Medical Center
Mary K. Hayden: Rush University Medical Center
Julia A. Segre: National Institutes of Health

Nature, 2025, vol. 639, issue 8056, 1016-1023

Abstract: Abstract Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings1. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions2. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.

Date: 2025
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DOI: 10.1038/s41586-025-08608-9

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