Case Patients

Figure 1. Figure 1. Detection of Candida auris and Rates of Screening. In Panel A, red indicates patients who had had exposure to the neurosciences intensive care unit (ICU) before diagnosis of C. auris infection or colonization, blue indicates patients who had had exposure to the neurosciences ward but not to the neurosciences ICU, and green indicates patients who had had exposure to neither unit. The timing of the removal of reusable temperature probes is shown. The data in Panel B are deduplicated to unique patient screening days — that is, in instances in which multiple swabs were obtained from a single patient on the same day, this is represented as a single data point, shown as positive if any of the swabs were positive. A full list of infection-control interventions is provided in Table S3 in the Supplementary Appendix.

A total of 70 patients were identified as being colonized or infected with C. auris between February 2, 2015, and August 31, 2017 (Figure 1A); 66 patients (94%) had been admitted to the neurosciences ICU before the diagnosis, with a median stay of 8.4 days in the ICU before diagnosis (interquartile range, 4.6 to 13.4). Three other patients had been admitted to the adjacent neurosciences ward before diagnosis. The final patient had had no exposure to the neurosciences ward or ICU; the diagnosis in this patient was made in 2015, which predated most cases.

Invasive C. auris infections developed in 7 patients: 4 had candidemia, and 3 had central nervous system device-associated meningitis (1 with candidemia); an orthopedic-device infection was found in the patient without exposure to the neurosciences ward or ICU. Five infections occurred before patient screening started. There were no invasive infections noted after November 2016. One patient with an invasive infection died 229 days after the collection of the last invasive isolate from that patient, with subsequent sterile blood and cerebrospinal fluid cultures; the death was therefore judged to not be attributable to C. auris infection.

Patient Screening

Culture was performed on 9153 screening swabs obtained from patients, representing 2872 unique patient-days of screening among 900 patients (Figure 1B). Of the 2872 screening swabs from a given day and patient, 267 (9.3%) yielded one or more C. auris isolates, in 62 unique patients (8 case patients who were colonized or infected were identified before the screening period from clinical samples). The acquisition rate during the screening period was 2.9 cases per 100 neurosciences ICU inpatient–days at risk.

One or more negative C. auris screening results without any positive results were found in 838 patients; 363 of these patients had been admitted to the neurosciences ICU before their last negative screening result. The electronic patient records for 2 patients were incomplete; these patients were excluded from the analysis, which left 361 controls for the determination of risk factors for C. auris acquisition in the neurosciences ICU.

Risk Factors for Colonization or Infection

The median age was 52 years (interquartile range, 42 to 64) among the 66 case patients and 56 years (interquartile range, 44 to 67) among the 361 controls; 44 case patients (67%) and 188 controls (52%) were male. The most common primary diagnoses among both case patients and controls were trauma and intracranial bleeding (Table S1 in the Supplementary Appendix).

Table 1. Table 1. Multivariable Predictors of Candida auris Colonization.

In multivariable models, the risk of colonization or infection initially increased with length of stay in the neurosciences ICU before declining again among patients with longer stays (P=0.001) (Table 1, and Fig. S1 in the Supplementary Appendix). Similarly, the risk of colonization was greatest in association with high-normal to moderately elevated neutrophil counts (P=0.01) (Fig. S2 in the Supplementary Appendix). The risk of colonization or infection was also associated with any skin-surface axillary temperature monitoring with the use of reusable probes (odds ratio, 6.80; 95% confidence interval [CI], 2.96 to 15.63; P<0.001). These temperature probes were used in 57 case patients (86%) and 122 controls (34%). There was some evidence that the risk of colonization or infection was higher among patients with lower serum albumin levels (P=0.06), a higher body temperature (P=0.08), and higher serum sodium levels (P=0.07). Systemic fluconazole treatment was also associated with an increased risk (odds ratio, 10.3; 95% CI, 1.64 to 65.2; P=0.01), although only 3 case patients (5%) received antifungal agents before colonization or infection.

Environmental Screening and Infection-Control Response

A total of 128 environmental samples were obtained in November 2016, February 2017, and April 2017. C. auris was rarely detected in the general environment or air (one settle plate was found to be positive). However, the organism was detected from reusable patient-monitoring equipment (axillary temperature probes and a pulse oximeter) and a patient hoist (Table S2 in the Supplementary Appendix). All skin-surface temperature probes (Fig. S3 in the Supplementary Appendix) were withdrawn from use on April 11, 2017. However, they came back into use during the annual leave of a senior nurse, and acquisitions of infection and colonization continued (Figure 1). All probes were comprehensively withdrawn from the neurosciences ICU on April 24, 2017, and cultured — five that had been in recent use and five that had been in storage. C. auris was isolated from four probes that are presumed to be those that had recently been in use. No other candida species were isolated from any probe. After the removal of the temperature probes, four additional cases were identified up to the end of the study (August 31, 2017), the last on July 17, 2017. Additional measures for the prevention and control of infection were implemented (Table S3 in the Supplementary Appendix).

Antifungal Susceptibility Testing

The first isolate from each patient and all the invasive isolates underwent antifungal susceptibility testing; 79 of 79 (100%), 78 of 80 (98%), and 66 of 73 (90%) isolates were resistant to fluconazole, voriconazole, and posaconazole, respectively, on the basis of breakpoints established for C. albicans (Table S4 in the Supplementary Appendix). A total of 14 of 79 isolates (18%) were amphotericin-resistant. No micafungin or flucytosine resistance was identified.

Survival and Carriage Duration

The crude mortality rate was similar among case patients and controls. Among patients for whom data on 30-day vital status were ascertainable at the end of the study, 30-day mortality was 17% (11 of 66) among case patients and 16% (52 of 331) among controls (P=0.85 by Fisher’s exact test). Among those for whom 90-day vital status was ascertainable, 90-day mortality was 20% (13 of 64) and 20% (44 of 221), respectively (P=1.00).

A total of 60 case patients (58 colonized and 2 infected) had screening samples sent on at least 1 day, with a median number of distinct screening days per patient of 7 (interquartile range, 4 to 13; range, 1 to 30) (Fig. S4 in the Supplementary Appendix). The axilla was often colonized first: among case patients, the first positive screening result was from the axilla in 22 of 60 patients (37%), from another site (groin or urine) in 21 of 60 (35%), and from both the axilla and one or more other sites in 17 of 60 (28%); on subsequent screening days, these sites were positive in 34 of 207 (16%), 66 of 207 (32%), and 107 of 207 (52%), respectively (P<0.001).

Figure 2. Figure 2. Duration of C. auris Colonization. Panel A shows the proportion of patients with clearance of C. auris colonization according to the number of days since their first positive screening result, with death without clearance treated as a competing risk. Because any one screen was imperfectly sensitive, clearance of colonization was defined as two consecutive negative screening results, timed from the day of the first negative screening result. Of the 21 patients whose colonization was cleared, 7 had a subsequent relapse (details, including whole-genome sequence comparisons, are provided in Table S5 in the Supplementary Appendix). A graph constructed under an alternative definition of three consecutive negative screening results is provided in Figure S5 in the Supplementary Appendix; of the 11 patients whose colonization was cleared according to this definition, 2 had a relapse. Panel B shows the proportion of next screening results found to be positive according to the number of consecutive previous negative screening results in the same patient. 𝙸 bars indicate the 95% confidence intervals calculated from exact binomial distributions.

To estimate the sensitivity of a single screen, we considered patients who underwent screening twice within 2 days, assuming that loss of colonization was minimal within this time window: 62 of 79 screening samples (78%) obtained 1 to 2 days after a positive screen were positive. Because a single screen was imperfectly sensitive, we defined clearance of colonization as either two or three consecutive negative screening results, treating death while colonized as a competing risk. The median duration of carriage among patients remaining alive was 61 days (interquartile range, 33 to not estimable) when two consecutive negative screening results were used to define clearance of colonization and was 82 days (interquartile range, 37 to not estimable), when three consecutive negative results were used (Figure 2A, and Figs. S5 and S6 in the Supplementary Appendix). After a positive screening result, 175 of 234 next screening results (75%) were positive; after one, two, and three negative screening results, 23 of 49 (47%), 7 of 21 (33%), and 1 of 12 (8%) next screening results, respectively, were positive (Figure 2B, and Table S5 in the Supplementary Appendix).

Sequence Analysis

Figure 3. Figure 3. Maximum-Likelihood Phylogeny Comparing Outbreak Sequences with a Previously Sequenced Global Collection. Shown are 78 outbreak sequences as compared with previously sequenced strains from Lockhart et al.,5 plus four additional Indian isolates.16 SNP denotes single-nucleotide polymorphism.

A total of 78 isolates were available for whole-genome sequencing: 72 screening or invasive isolates from 37 patients, plus 6 environmental isolates from five temperature probes and one hoist. All sequences fell within the South African C. auris clade (Figure 3). The rate of C. auris evolution was 5.75 mutations per genome per year (95% highest posterior density interval, 4.49 to 7.11) (Fig. S7 in the Supplementary Appendix). The sequences formed a single subclade, estimated to have emerged in April 2013 (95% highest posterior density interval, August 2012 to December 2013).

Figure 4. Figure 4. Time-Scaled Bayesian Phylogeny of 104 Unique Outbreak Sequences Obtained from 78 Isolates. Samples from patients are labeled with a p, and environmental samples are labeled with their source (temperature [temp] probe or hoist). Samples with an asterisk (*) denote mixed infections detected within a single isolate pool obtained from 6 to 12 colonies. The locations of patients’ beds before and after the date of each patient’s first positive sample are shown on the right. Within the neurosciences ICU, beds are arranged in a circular layout, such that bed 1 is adjacent to beds 16 and 2, bed 2 is adjacent to beds 1 and 3, and so on. Beds 1 through 13 are in an open-plan configuration, and beds 14 through 16 are in separate side rooms. NA denotes not applicable.

We identified 40 unique sequences that differed from another sequence by at least 1 SNP. When a probabilistic method was used to identify isolates containing mixtures of these unique sequences, we found that 52 of 78 samples (67%) had no evidence of mixed colonization or infection within the 6 to 12 colonies sequenced, and 26 of 78 (33%) contained 2 of the unique sequences; 7 mixed sequences differed by 5 or fewer SNPs, 7 by 6 to 14 SNPs, and 12 by 30 or more SNPs (Table S6 in the Supplementary Appendix). Allowing for the mixed colonizations or infections, 104 sequences were identified in the 78 patient or environmental samples (Figure 4, and Fig. S8 in the Supplementary Appendix). Three temperature-probe samples were also found to have mixed colonization.

Sequences from isolates obtained from reusable patient equipment were found throughout the phylogenetic tree of sequenced patient isolates (Figure 4), including close matches between patient and temperature-probe samples; for example, Patients 24 and 32 had mixed colonization similar to that found on Temperature Probes 1 and 2. Conversely, transmission between patients in nearby beds could not explain the transmission pattern (Figure 4). There was no evidence that patients with closely genetically related sequences were likely to be in nearby beds (P=0.34 for trend) (Fig. S9 in the Supplementary Appendix).

We investigated whether mixed colonization was likely to have resulted from simultaneous acquisition of multiple strains or from serial acquisitions of strains over time. Considering sequences that differed from each other by more than 5 SNPs as distinct genotypes, we found that 8 of 37 patients (22%) had mixed colonization or infection at their first positive screening result, as compared with 9 of 35 (26%) at any subsequent time point. There was no evidence that samples that were obtained closer in time to the first positive sample were more likely to be mixed than those obtained later (P=0.62 by rank-sum test).