Guidance

Investigation in clinical laboratories

Updated 19 March 2025

Note: numbers in round brackets refer to references which can be found in the References section.

Recommendations

As a minimum, perform species-level identification of Candida spp:

• when isolated from:
  • invasive sites
  • critical care units
  • augmented care ^{[footnote 1]} and other ward settings, as determined by local risk assessment ^{[footnote 2]} and screening policy
• when treatment is being considered to guide empirical management

Conduct an organisational risk assessment to identify gaps in laboratory surveillance that may lead to reservoirs of C. auris going undetected.

In an outbreak setting, consider identifying Candida isolates to the species level from hospitalised inpatients and high-risk outpatients as determined by the incident management team, if not already routine.

As a minimum, Candida spp. from invasive sites should be identified to species level, as well as superficial sites from patients being managed in augmented care and other settings (determined by local risk assessment ^{[footnote 2]} and screening policy) including critical care.

Learning from UK outbreak investigations has shown that delays in the recognition of cases have led to transmission of C. auris among patients. An organisational risk assessment should be conducted to identify gaps in laboratory surveillance that could enable undetected reservoirs of C. auris to persist. In addition, consideration should be given to the flagging and processing of high-risk clinical samples from patients transferring from a UK unit with a C. auris outbreak, or those who have had an overnight stay in a healthcare facility abroad in the previous year, so that C. auris infection is not missed.

For screening and clinical samples, laboratory diagnosis is mainly through mycological culture, with polymerase chain reaction (PCR) on direct samples being used for screening in some centres in the UK (17). Diagnostic accuracy has improved following the development of chromogenic media specifically for C. auris and advances in spectral databases of matrix-associated laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) systems. Turnaround times and diagnostic sensitivity may be improved by the use of molecular technologies, particularly for specimens with a high pre-test probability of C. auris colonisation or infection.

Culture-based identification

Recommendations

Perform full identification of suspected isolates using MALDI-TOF MS or a robust molecular method to confirm the identification of C. auris.

Consider C. auris isolate retention of between 3 to 6 months, depending on local resource.

Identification of C. auris has traditionally been challenging using conventional laboratory diagnostic methods. C. auris on microscopy is indistinguishable from most other Candida species. It is a germ tube test negative budding yeast. However, some strains can form rudimentary pseudohyphae on cornmeal agar.

C. auris can grow at temperatures up to 42 degrees Celsius (°C), with the optimal incubation temperature of around 40°C. This characteristic may help differentiate C. auris from many other Candida species when cultured on Sabouraud agar, particularly those it is most commonly misidentified as, such as Candida haemulonii.

A number of novel chromogenic media have been developed to help the detection and identification of C. auris (2, 18). Such media may be particularly useful as a screening tool to identify suspicious colonies from mixed cultures, including the presence of C. albicans, and other non-albicans species depending on the media. Incubation should be continued until chromogenic colour is fully developed.

Confirm suspected C. auris colonies, isolated from chromogenic media, using MALDI-TOF MS or molecular sequencing of the internal transcribed spacer (ITS) or D1/D2 domain of the 28S rDNA. This is advised due to the similarities in colour and colonial morphology between C. auris and certain other Candida species (19). Confirmation of identification is available at the UKHSA MRL, if required. Send pure isolates on Sabouraud slopes accompanied by the appropriate form.

Sample retention of isolates of between 3 to 6 months is advised due to the typically prolonged period between healthcare-associated transmissions, dependant on local resource considerations. This will facilitate further characterisation and investigation of transmission pathways, if required, at a future date.

Biochemical identification

Recommendation

Do not use biochemical methods to identify C. auris.

The use of biochemical identification methods for C. auris is not recommended due to the potential for misidentification or failure to identify the organism. Laboratories are advised to review their databases for currently available biochemical based tests that include C. auris. If C. auris is not present within the database, there is a risk of misclassification of C. auris as a range of other Candida species and genera using biochemical based tests (most commonly as C. haemulonii, C. famata, C. lusitaniae, Rhodotorula glutinis or Saccharomyces cerevisiae).

MALDI-TOF MS identification

Recommendation

Ensure the appropriate version of spectral library is installed to support accurate identification via MALDI-TOF MS.

Recent advances in spectral databases for the 2 main platforms used in laboratories for MALDI-TOF MS, Bruker MALDI Biotyper and bioMérieux VITEK MS, have enabled the accurate identification of C. auris from culture. Recommended thresholds for MALDI scores are associated with improved identification.

For effective identification, pre-analytical formic acid extraction is required (on-target, partial or full extraction protocols can be used) (20).

Molecular identification

Molecular technologies to identify C. auris may be employed in laboratories in addition to culture-based techniques. The advantage of direct molecular techniques for screening is that they do not depend on culture. They are quicker, more sensitive and are rapidly scalable if transmission is detected (21). This potentially enhances IPC team investigations. Most generic Candida PCR assays (whether commercial or in-house) do not target C. auris and cannot be used to detect or identify the organism. However, both commercial and in-house real time PCR assays for C. auris have been developed that provide methods for rapid identification of culture and direct testing of clinical and environmental swabs.

Antifungal susceptibility testing

Recommendations

Perform antifungal susceptibility testing on invasive isolates and isolates from patients requiring treatment. This includes repeat isolates from patients with suspected treatment failure.

Submit C. auris isolates exhibiting resistance to non-azole antifungal agents to a reference laboratory for confirmation and further characterisation.

Susceptibility testing is advised on all C. auris isolates against an antifungal panel appropriate to the site of infection and clinical presentation. As a minimum, invasive isolates and isolates from patients requiring treatment, including repeat isolates from patients with suspected treatment failure, should be prioritised. The minimum panel for bloodstream infections should include amphotericin B, an echinocandin, and voriconazole. 

There are no established minimum inhibitory concentration (MIC) breakpoints for C. auris. Clade-specific differences in MIC and the high proportion of isolates with likely acquired resistance has further complicated this. Established breakpoints for C. albicans are currently being applied for the interpretation of antifungal susceptibility testing of C. auris relative to the test method used. This is the approach currently adopted by the UKHSA MRL in the absence of specific breakpoints ratified by either the Clinical and Laboratory Standards Institute (CLSI) or the European Committee on Antimicrobial Susceptibility Testing (EUCAST).

Where local antifungal susceptibility testing is not available, the UKHSA MRL and other accredited reference services can undertake susceptibility testing for amphotericin B, fluconazole, voriconazole, posaconazole, isavuconazole, anidulafungin, caspofungin, micafungin and flucytosine. The MRL uses CLSI broth microdilution with confirmation of ‘unusual / unexpected’ profiles by E-test. If an isolate is found to be resistant to all these agents, the UKHSA MRL can also test for susceptibility to nystatin and terbinafine.

Due to capacity constraints, only isolates from invasive sites or from patients requiring treatment should be sent to the MRL for susceptibility testing. This also applies to repeat isolates from patients with suspected treatment failure. Diagnostic laboratories are encouraged to develop the capacity to perform antimicrobial susceptibility testing locally to support timely and effective patient management.

Most C. auris isolates described worldwide are resistant to fluconazole, subject to the use of different breakpoints. Testing for susceptibility to amphotericin B remains challenging, with MICs often close to the clinical breakpoints. Multi-drug resistance has been demonstrated at variable rates, including to other azoles, amphotericin B, echinocandins and flucytosine. MIC distribution does, however, vary with geography and by clade.

Using tentative breakpoints established by the US Centers for Disease Control and Prevention (CDC) for epidemiological purposes, approximately 90% of isolates are resistant to fluconazole, 30% to amphotericin B, and less than 5% to echinocandins in the USA (22). It is important to note that these breakpoints are primarily intended for surveillance and may not directly translate to clinical relevance at the individual level. The corresponding values for isolates from India are reported as being 90 to 95%, 7 to 37%, and less than 2%, respectively. Some isolates have also been identified as resistant to 4 classes of antifungal drugs (23). Although resistance to echinocandins remains uncommon, it has been increasingly identified with the expanding use of the drug as first-line therapy.

Experience from the UKHSA MRL indicates that, so far, very few multi-drug resistant strains have been found in the UK. All isolates have been resistant to fluconazole and often cross-resistant to other azoles, with variable resistance to polyenes (approximately 20% for amphotericin B) and echinocandins (approximately 10%). Development of resistance to various antifungals has been observed in previously susceptible isolates, particularly in the context of prolonged antifungal treatment. Non-azole resistance should be confirmed by a reference laboratory.

To date, UK strains remain susceptible to the topical agents nystatin and terbinafine, and it is possible that for the treatment of any future multi-drug resistant strains a regimen incorporating oral terbinafine could be considered.

Clade typing and whole genome sequencing (WGS)

Recommendations

To support outbreak investigation, the following isolates should be referred for WGS:

• sentinel isolates from new centres
• the first 3 to 4 isolates of any outbreak, occurring within a 3-month period of each other
• isolates from protracted outbreaks, particularly after apparent control, to determine whether ongoing transmission is occurring or a novel transmission has taken place

Both clade typing and whole genome sequencing (WGS) are molecular methods used to analyse C. auris strains, however they differ in their scope, resolution and purpose. Clade typing refers to a method used to categorise C. auris isolates into distinct clades or genetic groups. Clades correspond to geographically distinct subpopulations that have been associated with different regions of the world. Clade typing provides limited genetic information and does not provide detailed information about individual strain differences within a clade.

WGS allows for high-resolution genetic analysis of strains, including identification of antifungal resistance mechanisms, phylogenetic studies and supporting epidemiological surveillance and outbreak management. However, analysis of C. auris transmission chains is limited by intra-host variation and its high clonality at the clade level, which can obscure precise transmission networks.

WGS is a limited service at the UKHSA MRL and only isolates meeting the above specified criteria should be referred.

1. Augmented care settings are defined in Box 2 in the UKHSA Framework of actions to contain carbapenemase-producing Enterobacterales. ↩

2. The risk assessment should consider: patient risk factors (including high-risk groups), organisation-specific factors (such as high-risk units), local and regional epidemiology, laboratory capability and capacity, IPC infrastructure, resource availability and outbreak preparedness. ↩ ↩²