Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes
Abstract
Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings 1. 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 regions 2. 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.
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C. auris has an enhanced ability to colonize high-sweat body sites such as the axillae or inguinal crease.
“This suggests an enhanced ability of C. auris to colonize high-sweat body sites, such as the axillae or inguinal crease, which is corroborated by clinical sampling10,19.”
From Adhesin Als4112 promotes Candida auris skin colonization through interactions with keratinocytes and extracellular matrix proteins (2025) · cites this paper as [19]
C. auris can persist in skin tissues for months, often evading detection during routine clinical surveillance.
“suggesting that C. auris can persist in skin tissues for months, often evading detection during routine clinical surveillance [3,12,13].”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [13]
In murine skin, surface colonization turned negative after 2 months, but live C. auris was recovered from deep skin tissue up to 4 months after initial colonization.
“skin surface colonization of the murine skin was shown to turn negative after 2 months, but live C. auris was recovered from deep skin tissue up to 4 months after initial colonization”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [13]
Patients with C. auris skin colonization were frequently co-colonized with multidrug-resistant gram-negative bacteria, including Proteus mirabilis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Providencia stuartii, and Morganella morganii.
“Patients with C. auris skin colonization were frequently co-colonized with multidrug-resistant gram-negative bacteria, including Proteus mirabilis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Providencia stuartii, and Morganella morganii (Fig 2) [12,13].”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [13]
Candida auris can persistently colonize human skin.
“C. auris exhibits a particular tropism for the skin6–8. It is capable of persistent colonization in niches such as the axillae and groin”
From The Wor2 phenotypic switching regulator controls biofilm formation in Candida auris (2026) · cites this paper as [6]
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Ducarmon, Q. R., Terveer, E. M., Nooij, S., Bloem, M. N., Vendrik, K. E. W., Caljouw, M. A. A., Sanders, I. M. J. G., van Dorp, S. M., Wong, M. C., Zwittink, R. D., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00869-z · Cited by 37 · see citing works
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Burgess, M. J., Johnson, J. R., Porter, S. B., Johnston, B., Clabots, C., Lahr, B. D., Uhl, J. R., & Banerjee, R. (2015) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofv011 · Cited by 34 · see citing works
Co-colonization with multiple different species of multidrug-resistant gram-negative bacteria
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GUNC: Detection of Chimerism and Contamination in Prokaryotic GenomesPreprint
Orakov, A. N., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T., & Peer Bork, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.16.422776 · Cited by 24 · see citing works
Rafael Araos, B., Battaglia, T., Ugalde, J. A., Rojas-Herrera, M., Blaser, M. J., & D’Agata, E. M. C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02260 · Cited by 22 · see citing works
Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adultsPreprint
Siranosian, B. A., Brooks, E. F., Andermann, T. M., Rezvani, A. R., Banaei, N., Tang, H., & Bhatt, A. S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.12.435204 · Cited by 13 · see citing works
Genealogical inference and more flexible sequence clustering using iterative-PopPUNKPreprint
Zhao, B., Lees, J. A., Wu, H., Yang, C., & Falush, D. (2023) · Genome Research · doi:10.1101/gr.277395.122 · Cited by 9 · see citing works
Knowledge, Attitude and Practice Regarding Staphylococcus pettenkoferi
Kierzkowska, M., Markowska, K., & Majewska, A. (2022) · Infectious Disease Reports · doi:10.3390/idr14010015 · Cited by 7 · see citing works
Flagged first, then by citations
1 of the 93 references couldn’t be matched to a known paper.
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Recent innovations and challenges in the treatment of fungal infections
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Pathogenicity and virulence of Candida auris
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Antimicrobial resistance and transmission potential of pet-derived Providencia spp. in China
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ZCF4-dependent suppression of MMP-9 drives virulence in fluconazole-resistant Candida auris
Hong, Y.-M., Wang, L., Yin, Z., Zou, Y., Wang, Z., Wang, X., Wu, D., Zeng, X.-K., Zhou, J., Xu, W., et al. (2026) · hLife · doi:10.1016/j.hlife.2026.04.004 · Cited by 2 · see citing works
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Overlooked dissemination risk of resistomes in mining soil environments
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Human keratinocytes and fibroblasts coordinate early cutaneous innate defenses against Candida auris
Seiser, S., Brezovec, H., Penninger, P., Phan-Canh, T., Moser, D., Assen, F. P., Ayub, T., Rademacher, F., Gläser, R., Cerbu, D., et al. (2026) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2026.06.1279 · Cited by 1 · see citing works
Convergent evolution on RBA1 regulates Candidozyma auris host adaptationPreprint
Doorley, L. A., Bella, A. A. L., Jones, S. J., Zhao, G., Asadzadeh, M., Choudhury, Q. J., Ahmad, S., Mokaddas, E. M., Al‐Obaid, I., Alfouzan, W. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.04.692421 · Cited by 1 · see citing works
The Wor2 phenotypic switching regulator controls biofilm formation in Candida auris
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Nursing-home residents’ skin is a source of transmitted harmful and drug-resistant microbes
O’Meara, T. R. (2025) · Nature · doi:10.1038/d41586-025-00306-w
Skin-deep AMR hotspots in nursing homes
Taglialegna, A. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01172-z
Antifungal Effects of the Phloroglucinol Derivative DPPG Against Pathogenic Aspergillus fumigatus
Wang, L., He, J., Feng, H., Li, Q., Song, M., Gou, H., He, Y., & Zhu, K. (2025) · Antibiotics · doi:10.3390/antibiotics14050499
Uncovering fungal pathogens and skin microbiota in rural Malaysia
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EPAS1 regulates host antibacterial defense in response to bacterial quorum sensingPreprint
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Self-citationNo strain, no gain: within-host bacterial microdiversity and human health
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Sleeper agents: asymptomatic Acinetobacter colonization and underlying mechanisms
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- Authors
- Proctor, D. M., Sansom, S. E., Deming, C., Conlan, S., Blaustein, R. A., Atkins, T. K., Program, N. C. S., Mullikin, J., Thomas, J., Young, A., Bouffard, G., Barnabas, B., Brooks, S., Han, J., Buchter, C., Ho, S.-L., Crawford, J., Legaspi, R., Maduro, Q., Marfani, H., Montemayor, C., Riebow, N., Schandler, K., Schmidt, B., Sison, C., Stantripop, M., Black, S., Dekhtyar, M., Masiello, C., McDowell, J., Park, M., Thomas, P., Vemulapalli, M., Dangana, T., Fukuda, C., Thotapalli, L., Kong, H. H., Lin, M. Y., Hayden, M. K., & Segre, J. A.
- Affiliations
- National Institutes of Health (US)
- Rush University Medical Center (US)
- Corresponding author
- Hayden, Mary K.
- Segre, Julia A.
- ORCID
- Venue
- Nature
- Published
- 2025-02-26
- Volume
- 639
- Issue
- 8056
- Pages
- 1016-1023
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W4407957901
- Cited by
- 37
- References
- 93
- Citations by year
- 2026: 21 · 2025: 16
- FWCI
- 24.70
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Health Sciences › Medicine › Infectious Diseases › Infection Control in Healthcare
- Keywords
- Candida auris, ESKAPE pathogens, nursing home residents, skin colonization, antimicrobial resistance, clonal spread, genomic epidemiology, strain-resolved metagenomics, carbapenemase genes, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, multidrug-resistant bacteria, strain sharing
- MeSH terms
- Candida auris, Aged, Aged, 80 and over, Bacteria, Bacterial Proteins, beta-Lactamases, Female, Humans, Male, Nursing Homes, Skin, Metagenomics, Microbiota
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