Guidance for Detection of Colonization of Candida auris

Candida auris is an emerging multidrug-resistant yeast that can cause invasive infections with high mortality and has been transmitted in healthcare settings. Patients may be asymptomatically colonized with C. auris. Patients with C. auris colonization can spread this yeast to other patients, and colonized patients can develop invasive as well as superficial infections. Identifying persons colonized with C. auris is a key step in containing the spread of C. auris. The instructions below will provide guidance for processing swabs to assess for C. auris colonization.

For this testing, the currently recommended sites are axilla, groin, and sometimes nares. For more information on the screening of patients, including a procedure for the collection of patient swabs, fact sheets for patients, and a sample script for talking with patients about screening, read CDC’s information on screening for laboratory staff and health professionals.

For additional information regarding C. auris, including the latest identification, treatment, and infection control recommendations, visit CDC’s C. auris home page.

All confirmed C. auris specimens should be reported to state and local health departments and CDC at Laboratories are encouraged to submit C. auris isolates to the Antibiotic Resistance (AR) Lab Network.


The techniques for isolation presented here have not been completely validated for diagnostic purposes. Any laboratory wishing to employ these procedures should complete a validation that conforms with their regulatory oversight. None of these tests have been cleared or approved by the FDA. Mention of a specific commercial product does not qualify as an endorsement of the product by the Centers for Disease Control and Prevention.

Real-Time PCR

For those institutions with the resources to do so, real-time PCR is a fast and accurate method for detecting C. auris. Institutions may use this protocol pdf icon[PDF – 11 pages] for screening patients using real-time PCR. There are also other publications that provide protocols for PCR-based identification of C. auris.

Alternatives to PCR

For institutions without the resources to perform real-time PCR, a number of options are available for the screening of patients using culture-based methods. This procedure can be optimized to fit with current laboratory capacity. The following outlines the steps to isolate C. auris from patient swabs.

Suggested equipment/material for culture-based methods

  • Culture collection and transport system that can be used to swab a patient. Examples include:
    • Nylon-flocked swab (BD Eswab collection and transport system; Becton Dickinson and Company, Sparks, MD)
    • Rayon tip swabs (Fisherfinest Amies Charcoal bacteriology culture collection and transport system; Fisher Healthcare, Ontario, Canada)
  • CHROMagar Candida Chromogenic agar
    • There are multiple commercial companies that sell CHROMagar Candida media as well as at least one company that sells powder for making the media in-house
  • 10 µl transfer loops
  • Vortex
  • Stationary Incubator


Communities of Candida

Swabs from patients will contain a complex community of microorganisms including species of Candida and other yeasts. It is necessary to isolate C. auris from this community to obtain accurate species identification.

*Note: All the following culture methods include an incubation step to help grow and isolate C. auris from this community. Incubation should optimally take place at 40°C. Candida auris can grow at temperatures up to 42°C, but 37°C–40°C is optimal to account for temperature fluctuations in the incubator. If a 40°C incubator is not available, 37°C will work.

Strategies for screening non-sterile body sites

There are many methods for processing patient specimens to look for C. auris colonization. This list is not meant to be comprehensive but to give laboratories several options that may be incorporated into their current laboratory workflow.

Salt/Dulcitol enrichment broth

This broth is commercially available from S2 media (Spokane Valley, WA) and Thermo Oxoid (Ontario, Canada), but the recipe has been published hereexternal icon. This broth contains 10% NaCl, which inhibits the growth of most, but not all, yeast species. Candida glabrata is one of the species that can sometimes grow at high salt, and therefore dulcitol is used as a carbon source rather than glucose. C. glabrata cannot assimilate or ferment dulcitol. Although CDC has primarily used this media in broth form, it could also be used as a salt/dulcitol agar plate.

This media is selective but not differential. A differential media such as CHROMagar will still have to be used to differentiate between C. auris and other species that grow on the plates.

Plating directly to salt/dulcitol agar

There are a couple methods for direct plating. The first is to remove the swab and to roll it over the agar plate, covering all surfaces. The second option is to vortex and disperse the pathogen from the swabs before removing liquid from the transport, transfer it to the plate, and then use a spreader to cover all surfaces. The advantage of using liquid from the transport media is that a larger volume can be plated, increasing your chance of recovering C. auris from a patient who is not heavily colonized. The disadvantage is that it may be difficult to pick a single colony from a patient who is highly colonized or who may be colonized by two or more species of yeast.

Again, this media is selective but not differential. A differential media such as CHROMagar will still have to be used to differentiate between C. auris and other species that grow on the plates.

Direct plating may be faster and easier for many laboratories than the salt/dulcitol enrichment broth procedure. However, some laboratories have found direct plating to be less sensitive than the enrichment broth method.

Agar media CHROMagar Candida

There are no conventional agar plates that allow for the differentiation of C. auris.

Chromagar Candida allows the differentiation between C. albicans, C. tropicalis, C. krusei, and everything else. On CHROMagar, C. auris can be differentiated from the most common species, including C. glabrata. However, C. auris does not have a single distinct color on CHROMagar; C. auris can be pink, red, cream, and even purple, as well as a combination of these colors on the same plate (see images). While the manufacturer’s recommended incubation temperature for CHROMagar is 37°C, we have found that incubation at 40°C will inhibit the growth of some other organisms.

This means that all suspect colonies must be identified to species. MALDI-TOF (Bruker Biotyper or bioMérieux VITEK MS), DNA sequencing of marker genes D1/D2 or the ITS region, or whole genome sequencing provide the most accurate species identification.

If using phenotypic methods, an algorithm pdf icon[PDF – 11 pages] can be used to identify C. auris.

Safety considerations

If possible, work with C. auris should be performed in a biological safety cabinet or a glove box to ensure safety and sterility.

C. auris can survive for weeks on surfaces, has reduced susceptibility to quaternary ammonia disinfectants, and can colonize skin. Therefore, strict BSL2 laboratory safety precautions must be followed when working with this organism. Specifically, it is recommended that cultures are processed within BSL2 biosafety cabinet, gloves and lab coats should be worn, and strong hand hygiene should be employed. Since products with C. albicans or fungicidal claims may not be effective against C. auris, 10% bleach or products with EPA approval for C. auris should be used for cleaning the work area. A secondary container should be used when transporting C. auris, and this container should be disinfected after use.