Samples were collected in a 70-bed ventilator-capable unit of a 300-bed SNF (vSNF A) in Chicago, Illinois, USA, in October 2018. The first C. auris colonization case at this facility was identified in March 2017 during a point-prevalence survey (PPS) that was performed using culture. Six subsequent PPSs occurring during March 2017– September 2018 were also performed using culture and documented a rise in C. auris colonization prevalence on the ventilator-capable floor, reaching 71% [13]. At the time of sampling, this facility was a participant in a heightened infection prevention and control (IPC) program designed to control the spread of multidrug-resistant organisms (MDROs) through a bundle of interventions that included cohorting residents colonized by the same MDRO, increased alcohol-based hand rub availability, dedicating a full time environmental service staff member to disinfecting the vSNF unit with a sporicidal agent, and daily bathing of residents with 2% chlorhexidine gluconate (CHG) wipes [13]. At the time of this study, the C. auris colonization status of many residents was already determined from the previous PPS. These previous results were taken into consideration when describing the distribution of C. auris in the facility.

Screening of residents for C. auris was performed as part of the ongoing surveillance and IPC efforts by Chicago Department of Public Health. Bilateral axillary/inguinal composite skin swabs were collected from residents on vSNF A using a single BD Eswab in 1 mL of liquid AMIES Medium (#220245, BD Diagnostics). Residents were screened regardless of whether they had previously been positive for C. auris. Residual material from these samples was used to quantify C. auris colonization burdens as approved by Centers for Disease Control and Prevention’s (CDC’s) human subjects internal review board.

On the same day, environmental samples were collected from 12 rooms from the following surfaces: the windowsills, the inside and outward facing doorknobs, and the left and right handrails of each bed. Prior colonization data were referenced when rooms were selected such that at least 1 room without a known C. auris colonized resident was included. Samples were collected from defined surface areas using 3M^TM Cellulose Sponge-Sticks with neutralizing buffer (3M Healthcare, St. Paul, MN). The quantity of C. auris recovered was normalized by dividing the number of cells detected by the surface area sampled and expressed as cells/100 cm². The time when the surfaces were last cleaned and disinfected was unknown. Both resident and environmental samples were stored at 4°C and tested within 72 hours after collection as described below.

All patient samples were processed with the Taqman quantitative polymerase chain reaction (qPCR) [20], a most probable number (MPN) culture method, and an enrichment broth culture method, providing quantitative culture-independent results, quantitative culture-dependent results, as well as a qualitative gold-standard culture result, respectively [17, 21, 22]. Environmental samples were preprocessed by homogenizing with a Stomacher® 400 Circulator (Seward, West Sussex, UK), before testing with the Taqman qPCR, enrichment broth and direct dilution plating. The percent recovery (%R) of environmental sampling was determined based on controlled laboratory experiments with pre-inoculated coupons and is further described in the Supplementary Material-methods. Detailed descriptions of sample processing methods are also described in the Supplementary Material.

The relationship between C. auris concentrations in resident skin swabs and associated handrail samples was evaluated using Kendall’s tau-b (τ _b) coefficient of rank correlation and the corresponding nonparametric rank test. It is an alternative to the Spearman rank-order correlation coefficient and is recommended in situations with small sample size and many tied ranks [23]. Data analysis and figures were generated using R 4.0.2 and Python 3.7 software.

Fifty-seven (82.6%) of 69 residents on the ventilator-capable floor of vSNF A were screened for C. auris skin colonization. Eight refused screening, and 4 were not present at the time of sampling. Twenty (35.1%) of the screened residents were found to be C. auris positive by both culture and qPCR; 11 residents were identified as positive by qPCR but not culture. Thus, a total of 31 (54.4%) residents were positive at the time of sampling. All culture-positive residents were also positive by qPCR. Of the 11 qPCR-positive but culture-negative residents, 9 were known to be C. auris culture-positive from prior PPS. One resident had been sampled 7 times since March 2017 and had been consistently negative by culture. The remaining single culture-negative but qPCR-positive resident had no prior C. auris screening history.

Fourteen of the 30 occupied rooms on the floor (46.6%) housed at least 1 resident that was culture-positive, and an additional 4 rooms had at least 1 qPCR-positive resident (18 rooms, 60.0% total; Figure 1).

The mean concentration of C. auris in culture-positive skin swabs was 1.2 × 10⁵ MPN/mL (range 7.1–1.0 × 10⁶), while the mean concentration interpolated from qPCR C_q values was 1.1 × 10⁶ cells/mL (range 410–9.7 × 10⁶).

A total of 100 environmental samples were collected from the windowsills, doorknobs, and handrails of the resident beds in 12 rooms. Fifty environmental samples were culture-positive, and 70 were qPCR-positive. All culture-positive samples were qPCR-positive except for the outward facing doorknob in room A18, which was culture-positive but qPCR-negative. The mean concentration of C. auris in culture-positive environmental samples was 92 colony-forming units (CFU)/100 cm² (range 2.4–970), and the mean concentration interpolated from qPCR was 4.0 × 10⁴ cells/100 cm² (range 460–4.50 × 10⁵; Table 1).

The percent of C. auris AR 0385 cells recovered from spiked textured plastic surfaces with the sponge sampling method ranged from 1.4 % to 3.7%, with the mean recovery found to be 2.3% (SD 0.008). Overgrowth of other organisms was not observed on any plates.

Environmental sampling was conducted in 12 rooms that housed 28 residents: 12 residents were positive by both culture and qPCR, 5 were culture-negative but positive by qPCR, and the remaining 11 were negative. Overall, 17 C. auris-positive residents were housed in 8 of the 12 sampled rooms. The remaining 4 rooms were occupied by C. auris negative residents, and 1 resident in room A07 who was not tested (Figure 1). Environmental contamination with C. auris was detected in all 8 rooms with C. auris positive residents, as well as in 2 of the 4 rooms occupied by C. auris negative residents (Figure 1).

All 12 C. auris culture-positive residents with associated environmental samples had at least one culture-positive handrail; 10 of these (83.3%) were culture-positive for both handrails. All handrails of culture-positive residents were also qPCR-positive. Similarly, for the 5 beds occupied by residents that were qPCR-positive but culture-negative, all 10 associated handrails were qPCR-positive, 6 of which were also culture-positive. Therefore, when culture and qPCR results were considered collectively, C. auris contamination was detected on both handrails of all beds associated with all 17 C. auris positive residents (Figure 1).

The concentrations of C. auris in residents’ skin swabs were positively related to the averaged concentration recovered from the left and right handrails of their beds (Figure 2). This relationship was observed when using data from both culture-dependent (τ _b = 0.536, P = .0004) as well as qPCR (τ _b = 0.657, P = 3.832e⁻⁶) approaches. Similarly, a positive association was found when the left and right handrails were evaluated individually as well as collectively as independent samples (P < .0001, Supplementary Figure 1). Even though the range of C. auris concentrations observed on all handrails ranged over several orders of magnitude, left-right handrail pairs from the same bed were generally similar in concentration (Figure 3).

In addition to the 17 C. auris positive beds that were occupied by C. auris colonized residents, we found 3 beds, where both handrails were culture-positive despite being occupied by residents who screened negative for C. auris (Figure 1, Room A00 Bed B, Room A02 Bed B, and Room A21 Bed C). Review of facility records indicated the occupant of Bed C in Room A21 had previously been reported colonized. In contrast, the occupants of Bed B in Room A00 and Bed B in Room A02 had both been sampled numerous times and have no prior record of C. auris colonization. The facility records indicate that both residents were recently relocated into these rooms, which were previously occupied by C. auris colonized residents as recently as early 1 month prior for Bed B in room A00 and 2 months prior for Bed B in Room A02.