Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.

Xin Huang,Snigdha Vallabhaneni,Susan S Huang,Clay Deming,Brendan R Jackson,Julia A Segre,Gabrielle M Gussin,Tom Chiller,Sean Conlan,Heidi H Kong,Diana M Proctor,Pamela J Thomas,Kaitlin Forsberg,Meghan L Bentz,Anastasia P Litvintseva,Rory M Welsh,Vincent B Young

doi:10.1128/msphere.00287-21

Abstract

ABSTRACTCandida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris.IMPORTANCECandida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.

Highlights

IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections
When patients colonized with Candida auris were identified in Illinois and New York health care facilities in 2017, local health departments launched point prevalence surveillance surveys to identify any additional residents colonized by C. auris
Candida auris has rapidly emerged as a serious threat for vulnerable patients with immunodeficiency and/or other preexisting conditions, especially in long-term care facilities, such as long-term post-acute care hospitals and nursing homes, with recent clusters occurring in acute care facilities [30, 31]

Summary

Introduction

IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Long-term acute care facilities and nursing homes with ventilator beds are vulnerable to C. auris outbreaks since residents stay for long periods of time and have complex care needs. These facilities often do not have the infection control resources or structural protections (e.g., single-occupancy rooms) that are available in short-stay acute care hospitals. These factors underlie the increased risk to residents of health care-associated microbial infections, often by multidrug-resistant pathogens [20]

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Results

Conclusion