Open Forum Infectious Diseases
BRIEF REPORT
The Emergence and Persistence of
Candida auris in Western New York
With No Epidemiologic Links: A
Failure of Stewardship?
Patrick McGann,1 Francois Lebreton,1 Abhimanyu Aggarwal,2 Jason Stam,1
Rosslyn Maybank,1 Matthew Ficinski,2 Melissa Bronstein,3 Jason W. Bennett,1
and Emil Lesho3
1
Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed
Army Institute of Research, Silver Spring, Maryland, USA, 2Infectious Diseases Department,
Rochester Regional Health, Rochester, New York, USA, and 3Quality and Safety Department,
Rochester Regional Health, Rochester, New York, USA
Reports of Candida auris infection in patients without
epidemiologic links to prior outbreaks are scarce. We
describe the genomic epidemiology of such a case in Western
New York. Before emergence, the patient received >60 days
of excess antibiotics. Candida auris was recovered on near-
patient surfaces after enhanced terminal cleanings.
Keywords. antibiotic stewardship; Candida auris;
outbreak; Western New York.
Candida auris is a fungal pathogen classified as an urgent public
threat due to its association with increased mortality, potential
for developing pan-drug resistance, and its ability to become
entrenched in the hospital environment [1–3]. In fact, a recent
study revealed that surfaces near patients with C auris frequent­
ly become recontaminated within hours of cleaning [4]. The bi­
ology and environmental reservoirs of C auris remain poorly
understood [5]. However, past infections have predominantly
occurred in patients with cancer, feeding tubes, breakdowns
in environmental cleaning and infection control processes, or
with epidemiologic links to other cases [6–8].
In the United States, the first incidence of C auris has been
traced to New York [9], but subsequent reports and surveil­
lance in this region have mainly focused on larger outbreaks
in New York City [3, 6–8]. Reports from rural communities
in Western New York and incident cases without links to other
C auris cases are scarce [10]. We describe an emergence of C
auris in a patient hospitalized at a small community hospital
in Genesee County, New York. Unlike the facility >50 miles
away and described in the 2017 report [10], this patient had
Received 26 November 2022; editorial decision 01 March 2023; accepted 03 March 2023;
published online 6 March 2023
Correspondence: Emil Lesho, DO, FACP, FIDSA, FSHEA, 1425 Portland Avenue, Rochester,
New York 14621 (carolinelesho@yahoo.com); Melissa Bronstein, RN, 1425 Portland Avenue,
Rochester, New York 14621 (melissa.bronstein@rochesterregional.org).
Open Forum Infectious Diseases®
Published by Oxford University Press on behalf of Infectious Diseases Society of America 2023.
This work is written by (a) US Government employee(s) and is in the public domain in the US.
https://doi.org/10.1093/ofid/ofad123
no known epidemiological links to other cases or healthcare
contact outside his immediate community. The main underly­
ing factor appeared to be excess antibiotic exposure.
METHODS
In January 2022, C auris was isolated from a urine culture in a
68-year-old male on the 51st day of hospitalization at a commu­
nity hospital in Western New York. In the 6 months before ad­
mission, he had no healthcare contact or travel outside his
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immediate community in central Genesee County. Before and
during hospitalization he had no identified exposures to other
patients or family members known to be colonized or infected
with C auris. He had no history of (or current malignancy) organ
transplantation, hemodialysis, decubitus ulcers, feeding tubes, or
nursing home stays. He was active and in fair health with a his­
tory of mild vascular dementia. Two days before admission, he
was diagnosed with community-acquired pneumonia and pre­
scribed azithromycin. Upon admission for progressive dyspnea,
he tested positive for severe acute respiratory syndrome corona­
virus 2 and received 6 mg of dexamethasone daily for 10 days
and remdesivir 200 mg once followed by 100 mg daily for 5
days. A chest radiograph showed left lobar consolidation and
the patient received empiric ceftriaxone and azithromycin. He
received no other immunosuppressive therapies. Over the next
week, as a result of worsening respiratory status, he received non­
invasive positive pressure ventilation, followed by 8 days of en­
dotracheal intubation before he was successfully extubated. He
had a peripherally inserted central line in his arm and indwelling
urinary catheter. Both devices were in place for 35 days, 23 of
which occurred before the isolation of the C auris. He also had
intermittent fevers, for which he received 73 days of antimicro­
bial therapy including micafungin, piperacillin-tazobactam, cefe­
pime meropenem, and vancomycin (Table 1). However, the
microbiologic work-up remained negative, including urine,
blood, bronchoalveolar lavage, Legionella antigen and cultures,
and fungal and mycobacterial stains and cultures. Serum procal­
citonin levels also remained within normal limits. On the 22nd
and 24th day of hospitalization, Candida albicans was isolated
from respiratory cultures. On the 51st day of hospitalization,
blood, sputum, and urine cultures were obtained in response
to an episode of fever and hypotension. Due to his altered mental
status, he was unable to report any urinary symptoms. The urine
culture grew azole-resistant C auris identified by mass spectro­
scopy (VITEK MS; Biomérieux, St. Louis, MO) [10] (Table 1).
Identity and susceptibility of the isolate were confirmed accord­
ing to Clinical and Laboratory Standards Institute reference
methodology M27-A4 by the laboratory of New York State
Department of Health, Albany, New York, using MALDI-TOF
BRIEF REPORT • OFID • 1
Table 1. Antibiotic Susceptibilities and Surface Contamination Results

Total DOT Before Isolation Minimum Inhibitory/Concentration No. Surfaces PCR Positive Culture Positive
Drug of C. auris (mcg/mL) Interpretation Location Tested n (%) n (%)

AZM 3 … … After Terminal Cleaning

FEP 7 … … ICU 9 6 (66) 0
MEM 16 … … Ward 8 6 (75) 2 (25)
MFG 15 … … … After Directly Observed Recleaning
TZP 8 … … ICU 9 0 0
VAN 17 … … Ward 8 0 0
Total 73 … … … … … …
FLC … >256 R … … …
VRC … 1 U … … …
ICT … 0.06 U … … … …
ISA … 0.25 U … … … …

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CAS … 0.06 S … … … …
MFG … 0.12 S … … … …
AFG … 2 S … … … …
AMB … 0.06 S … … … …
Abbreviations: AFG, anidulafungin; AMB, amphotericin B; AZM, aztreonam; CAS, caspofungin; DOT, days of therapy; FEP, cefepime; FLC, fluconazole; ICT, itraconazole; ICU, intensive care
unit; ISA, isavuconazole; MEM, meropenem; MFG, micafungin; PCR, polymerase chain reaction; R, resistant; S, susceptible; TZP, piperacillin tazobactam; U, uninterpretable; VAN,
vancomycin; VRC, voriconazole.

Figure 1. Core genome phylogeny and pairwise single-nucleotide polymorphism (SNP) distance matrix. (A) Core genome phylogeny for 5 Candida auris isolates from a
hospital network in Western New York and 2 reference isolates from India. Phylogenetic tree was built using the GTR-GAMMA model in RAxML v8.2.11 and a core genome
alignment from panseq (fragmentation size of 500 base pairs to find sequences with ≥95% identity in ≥95% of the isolates). Genomes of reference strains CA-VPCI (GenBank
accession number PRJEB9463) and CA-6684 (GenBank accession number PRJNA267757) were obtained from public databases, and newly generated genomes were depos­
ited under GenBank accession PRJNA903931. The carriage of a K143R substitution in ERG11 is indicated (closed circle). (B) Pairwise SNP distance matrix (obtained from
whole-genome SNP analysis using snippy and snp-dist) for 5 highly genetically related isolates from Western New York.

MS (Bruker, Bremen, Germany) and custom TREK frozen broth
microdilution panels (Thermo Fisher Scientific, Marietta, OH)
and by Etest as recommended by the manufacturer (AB
Biodisk; bioMérieux, Solna, Sweden) [8, 11]. No further C auris
was isolated from this patient.
Outbreak Response
This isolate (MRSN101498) was forwarded to the
Multidrug-Resistant Organism Repository and Surveillance
Network (MRSN), where it underwent whole-genome se­
quencing on a Miseq benchtop sequencer, as previously de­
scribed [10]. Laboratory records were queried for other C
auris results during the previous 12 months. During admission,
the patient occupied 4 different rooms in the intensive care unit
(55 days), followed by 12 days on the medical surgical ward
(Supplementary Figure 1). The index patient’s roommate was
relocated and the room was closed to further patients. After dis­
charge, the room was terminally cleaned with hydrogen perox­
ide and peracetic acid (Oxicide), then treated with ultraviolet-C
light. It remained closed until results of environmental cultures,
taken as previously described [8, 10], were available. All 4 pa­
tients who had either spent more than 24 hours in the same
room with the index patient or in immediately adjacent rooms
were placed on enhanced contact precautions and underwent

2 • OFID • BRIEF REPORT

surveillance culturing of nares, axilla, and groin. Their rooms
and equipment were terminally cleaned in the same manner.
All staff and trainees who had contact with the patient were in­
terviewed. None were found to have possible links to other C
auris cases. Department of Health representatives examined
the patient’s home and interrogated the patient’s family and
ruled those out as potential sources of infection. Two infectious
disease physicians separately reviewed the patient’s medical re­
cord to determine appropriateness of antibiotic usage. Excess
or inappropriate antibiotic days were determined by the total
days of antibiotic received before the emergence of C auris
and not supported by culture or other microbiologic data, mi­
nus 3 days allowed for empiric treatment for each unexplained
fever or fever not attributed to coronavirus disease 2019.
RESULTS
Candida auris had not been isolated at the facility in the past
year. All exposed patient samples were negative for C auris.
Environmental cultures from nearby rooms and surfaces
were negative. However, as in the report by Sansom et al [4]
in the rooms that the index patient occupied, up to 75%
of surfaces tested after terminal cleaning had detectable
nucleic acid, and 25% had cultivable C auris (Table 1 and
Supplementary Figures 2 and 3). Both physician reviewers in­
dependently concluded that the patient received at least 60 ex­
cess or inappropriate days of broad-spectrum antibiotics
including 15 days of micafungin, before the appearance of C
auris (Table 1).
A comparison of the MRSN101498 genome sequence with
known reference strains obtained from National Center for
Biotechnology Information (NCBI) revealed that MRSN101498
was most closely genetically related to the 2013 Indian CA-6684
strain, differing by 209 variable sites across the 11 753 726 base
pair core genome alignment (Figure 1). It is notable that the
MRSN101498 carried the K143R mutation in ERG11 that has
been linked to increased triazole resistance in C albicans. This mu­
tation is absent in the closely related CA-6684 but found in the
more distantly related Indian 2105 VPCI reference strain
(Figure 1). Furthermore, whole-genome single-nucleotide poly­
morphism (SNP) analysis revealed that MRSN101498 was also
highly genetically related to 4 previous isolates involved in an out­
break in March 2017 from a hospital 47 miles to the northeast in
Rochester, New York, differing by just 39–43 SNPs across the en­
tire 12.4 Mb genome (Figure 1). This amount of genetic differenc­
es, accumulated over 5 years, is in agreement with the estimated
evolution rate of C auris (5.75 mutations per genome per year)
[2] and suggests all 5 isolates from Western New York shared a
recent common ancestor. In addition, similar to the most recent
MRSN101498 isolate, the 4 earlier outbreak isolates from
Rochester, New York carried an identical SNP causing the
K143R substitution in the ERG11 gene. (Genomic data are
available at GenBank for Bioproject, PRJNA903931; https://
www.ncbi.nlm.nih.gov/bioproject/PRJNA903931.)
DISCUSSION
This report is noteworthy for several reasons. First, unlike prior
reports, there were no exposures or epidemiologic links to
known cases. Second, reports from rural community hospitals
are uncommon and may represent surveillance “blind spots”.
Third, it highlights important knowledge gaps pertaining to
unrecognized reservoirs of C auris [5]. Despite these genomic
results, the potential reservoir(s) of MRSN101498 in Western
New York remain unclear. Both hospitals had previously im­
plemented sporicidal (not quaternary ammonium) disinfec­
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tants for environmental cleaning as part of Clostridioides
difficile reduction measures, because quaternary ammonium
is known to be less effective against C difficile and C auris
[2]. However, nucleic acid and cultivable C auris were recov­
ered from near-patient surfaces in rooms that housed the index
after repeated terminal cleanings. It was not until terminal
cleaning was performed under direct observation by infection
preventionists (IPs) that no cultivable C auris and C auris nu­
cleic acid was detected. All terminal cleaning protocols were the
same, and all included ultraviolet irradiation and sporicidal
cleaning agent as described earlier. The only difference during
the cleanings after which no C auris was recovered was the di­
rect observation by the IP that occurred during those cleaning
process. Unlike previous outbreaks in New York, there were no
infection control lapses or use of quaternary ammonium for
disinfection [2, 6, 12]. Furthermore, the patient had no epide­
miologic links to the Rochester facility involved in the 2017
outbreak, nor did any of the staff.
CONCLUSIONS
This case underscores the potential role antibiotic exposure
may play in the emergence of C auris and the challenges it poses
to cleaning and disinfection. We propose that detailed antibiot­
ic exposure and cleaning regimens be included in future out­
break reports of drug-resistant pathogens.
Supplementary Data
Supplementary materials are available at Open Forum Infectious Diseases
online. Consisting of data provided by the authors to benefit the reader, the
posted materials are not copyedited and are the sole responsibility of the
authors, so questions or comments should be addressed to the correspond­
ing author.
Acknowledgments
Author contributions. PM, MB, and EL contributed to conception and
design; MB, MF, and AA contributed to data collection; FL, JS, RM, and
JWB contributed to data analysis; all authors contributed to manuscript
preparation and revision.
Potential conflicts of interest. All authors: No reported conflicts of
interest.
BRIEF REPORT • OFID • 3
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