Evaluation of Automated Platforms for Accurate Identification of Post-COVID-19 Candida auris Isolates

Candida auris has become an important global health threat because of several concerning properties, including resistance to multiple classes of antifungal agents, tendency to cause outbreaks in clinical settings, ability to persist on environmental surfaces, and tolerance to several commonly used disinfectants (Bhargava et al., 2025). In 2009, C. auris was first identified in Japan and is known as a multidrug-resistant (MRD) yeast with great potential to be acquired as a nosocomial infection (Schaefer et al., 2024). In 2019, it was designated as an urgent public health threat by the Centers for Disease Control and Prevention (CDC) due to its growing risk and by the World Health Organization (WHO) as one of the most important fungal pathogens in severely ill people. A higher number of C. auris cases have been attributed to the degree of thermotolerance, ability of transmission among individuals, and lack of infection control practices (Khairat et al., 2021; Bhargava et al., 2025).

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recorded in Wuhan, China, in December 2019, and has risen from an epidemic to a global pandemic. This viral infection has exerted a remarkable impact on the lives of the public health systems, resulting in a large amount of disease burden and millions of cases occurring in China. The first case was identified in Egypt in February 2020 (Gamal et al.,2022; Yassin and Abo-Elyazeed, 2023).

The emergence of new fungal infections appeared in the post pandemic period, with post-COVID-19 infection resulting in a new threat of fungal infectious disease (Melinte et al., 2024). Given the pervasive emergence and spread of C. auris around the world and the global increasing concern over invasive candidiasis, in depth epidemiological aspects and mechanisms of resistance of Candida species in different geographical areas, including Egypt need further research and investigation (Spruijtenburg et al., 2025). This is also relevant in previously infected COVID-19 patients who often have longer hospital stays, receive broader-spectrum antimicrobials and steroids, or may be immunosuppressed, with a consequently increased risk of getting invasive opportunistic infections such as C. auris (Melinte et al., 2024). The spread and incidence of C. auris infections have been dramatically affected by the COVID-19 pandemic, which has caused an exponential surge in cases (Schaefer et al., 2024). There have been reports of a termendous growth in the number of C. auris cases after the pandemic, with values > 200% in some regions. For example, more than 300 clinical cases have been reported in 10 province- level regions in China by the end of 2023 (Bing et al., 2025).

The mortality associated with C. auris infections is exceptionally high, particularly in patients with predisposing risk factors (Bhargava et al., 2025). Host and pathogen factors of COVID-19 combined with inadequate hospital care have created opportunities for the emergence and spread of this fungal global threat with acquired resistance to the mainstream medical antifungals (Schaefer et al., 2024). The global spike in C. auris infections following the COVID-19 pandemic necessitates better surveillance, more knowledge on the pathogenic traits, and innovative preventive methods to counter the two widespread risks (Rahman et al., 2024).

When identifying emerging pathogens such as C. auris, accurate identification of C. auris in the microbiology laboratories is challenging and requires a variety of advanced molecular and automated techniques. Molecular diagnostic tools, such as BioFire FilmArray panels, offer a streamlined sample-to-result approach for the detection of clinically significant Candida species directly from the positive samples (El-Sherif et al., 2022; Widyasari et al., 2023). Automated platforms such as VITEK 2 are valuable as initial screening tools for C. auris isolates (Huma et al., 2023; Patwardhan et al., 2024). As technology continues to progress rapidly, matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF MS) has become a top-tier method for the direct identification of Candida species from the routine cultures. It is frequently used as a benchmark approach for assessing the accuracy of other diagnostic techniques (Bhargava et al., 2025; Park et al., 2025). In addition, healthcare providers often routinely use chromogenic medium, including CHROMagar Candida, for the selection of Candida species, which allows for their discrimination from each other using unique colonies (CDC, 2026). Additionally, C. auris’ ability to grow at 42oC due to its innate natural thermotolerance is one of the differential diagnostic criteria used during their identification procedure (Khairat et al., 2021; Bhargava et al., 2025; CDC, 2026). The addition of these rapid molecular assays to the standard and automated approaches provides an improved diagnostic spectrum for C. auris and allows rapid intervention in acute clinical situations (El-Sherif et al., 2022).

The objective of this study was to critically evaluate and identify the most suitable and cost-effective methodologies and techniques used for the accurate and timely detection of C. auris recovered from diverse laboratory microbial cultures, with a particular emphasis on post-COVID-19 C. auris isolates, given their observed increased prevalence during the pandemic.

This study was conducted as a retrospective observational microbiological study including post-COVID-19 Candida auris isolates collected from routine laboratory microbial cultures at Ain Shams University Specialized Hospital (ASUSH), a tertiary care center in Cairo, Egypt. Candida auris isolates associated with several microbiological records that documented a COVID-19 diagnosis were eligible for inclusion. These isolates were considered eligible when the associated microbiological record indicated that the cultures were processed during the period of active COVID-19 diagnosis or within one month following the documented diagnosis, in accordance with previously published studies (Goravey et al., 2021; Erturk Sengel et al., 2023; El-Zakhem et al., 2023). Only microbiologically confirmed C. auris isolates were included in the study. Isolates identified as Candida species other than C. auris and those isolates where the required microbiological information was incomplete were excluded. Duplicate isolates were excluded according to the predefined study protocol to avoid repeated inclusion of the same isolate.

The study included previously recovered C. auris isolates from positive leftover laboratory cultures, with the associated microbiological records documenting a post-COVID-19 diagnosis. COVID-19 status was determined from the documented laboratory diagnosis accompanying the microbiological record, and the infection was considered as confirmed when a positive SARS-CoV-2 polymerase chain reaction (PCR) result was documented from a respiratory specimen obtained via a nasopharyngeal or an oropharyngeal swab. Isolate’s inclusion and exclusion criteria were predefined before the selection and analysis of the microbiological records and isolates.

The obtained yeast isolates were initially screened for presumptive identification as C. auris based on their ability to grow at an elevated temperature (42 °C) and their characteristic colony morphology on a chromogenic agar medium (Brilliance™ Candida Agar) following the U.S. Centers for Disease Control and Prevention (CDC) guidelines for C. auris identification (CDC, 2026). Yeast isolates that grew at 42 °C and exhibited chromogenic features suggestive of C. auris were subjected to further identification (CDC, 2026).

For all platforms, BACTEC™ culture bottles were incubated in the automated BACTEC™ FX system (BD Diagnostics, Franklin Lakes, NJ, USA) for up to five days, or until a positive growth signal was detected, according to the laboratory’s routine procedures and previously published protocols (Ulrich et al., 2022; Posteraro et al., 2023). Positive BACTEC™ cultures were subsequently processed for C. auris isolation and identification using the diagnostic platforms described below.

Positive BACTEC™ culture bottles were subcultured onto Sabouraud’s Dextrose Agar (SDA) for C. auris recovery. Following growth, the isolates were subjected to identification using the VITEK® 2 Compact system (version 8.01, bioMérieux, Marcy-L’Etoile, France), following the manufacturer’s instructions (Ambaraghassi et al., 2019; CDC, 2024c).

Following obtained positive signals in the BACTEC™ system, the cultures were subcultured onto SDA. The recovered yeast isolates were subsequently identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS, LT2 plus, SAI, UK) using the updated reference database BactoScreen-ID version 2.4 including C. auris spectra as a reference library (Abdolrasouli and Fraser, 2022).

For BioFire® FilmArray® BCID2 (bioMérieux, Marcy-l’Étoile, France), the positive cultures detected by the BACTEC™ FX system were processed according to the manufacturer’s instructions. Following a positive signal, 200 μl aliquots were directly withdrawn from the positive BACTEC™ culture bottles and transferred to the pre-hydrated BCID2 pouch, followed by the addition of the sample buffer. The pouch was then inserted into the FilmArray instrument (Release Version 2, Software Module Version 2.1.273.0). This system performs an automated nucleic acid extraction, multiplex PCR amplification and DNA melting where curve analysis-complete results become available within two hours. The BCID2 system includes C. auris isolates among the array of yeast targets, allowing a rapid identification via molecular means (Zhang et al., 2020; Caméléna et al., 2023; Puumala et al., 2025).

The identification analysis included 37 eligible C. auris isolates and an individual comparison panel of 20 non-C. auris isolates, comprising six C. albicans, six C. tropicalis, four C. famata, and four Nakaseomyces glabratus (formerly C. glabrata). Non-C. auris isolates were included specifically as identification controls and were analyzed separately from the main post-COVID-19 C. auris group. VITEK 2 and MALDI-TOF MS results were compared for all the 57 isolates, whereas BIOFIRE FilmArray BCID2 results were evaluated for 41 positive blood-culture broths, comprising 21 corresponding C. auris-positive cultures and 20 non-C. auris controls. The procedure for each platform is described above.

MALDI-TOF MS was used as the comparator for species assignment. The primary comparison assessed the agreement in classification as C. auris or non-C. auris. Pairwise agreement was calculated as the number of concordant classifications divided by the number evaluated by both platforms and was expressed as a percentage. Species-level agreement was additionally assessed among the VITEK 2, MALDI-TOF MS, and BIOFIRE BCID2 microorganisms included in the panel’s target list. BIOFIRE results reported as C. glabrata were considered equivalent to N. glabratus. Because C. famata is not a BCID2 target, its four isolates were included in the assessment of C. auris detection/non-detection but were excluded from the assessment of a species-level agreement with BIOFIRE. Discordant results were described by the platform and comparator-assigned species. Performance was reported as an observed agreement within the selected collection rather than as an independently established diagnostic accuracy.

Antifungal susceptibility testing (AFST) of all recovered isolates were performed using the VITEK 2® Compact System (bioMérieux, France) with the AST-YS08 test card according to the manufacturer’s instructions. Isolates were subcultured on SDA and incubated at 35–37 °C for 24 h prior to testing. A standardized suspension of a yeast equivalent to a 0.5 McFarland standard was prepared in sterile saline and run on the VITEK 2 system for automated minimum inhibitory concentration (MIC) determination. The panels ran included several antifungals of major therapeutic classes, namely fluconazole, voriconazole (azoles), caspofungin, micafungin (echinocandins), flucytosine and amphotericin B.

With no formal breakpoints established for C. auris, the antifungals were reported using tentative MIC breakpoints provided by the Centers for Disease Control and Prevention together with previously derived derivatisation method-based epidemiological cutoff values (dECOFFs) as well as extrapolated from other species (Ahmed et al., 2025). The CDC tentative breakpoints that implemented included Fluconazole ≥32 μg/ml, amphotericin B ≥2 μg/ml, micafungin ≥4 μg/ml, and caspofungin ≥2 μg/ml (CDC, 2024a). The dECOFFs breakpoints were used for identifying the non-wild-type isolates for voriconazole (1 μg/ml) (Arendrup et al., 2017; Bohner et al., 2023). Flucytosine MICs were interpreted using the Clinical Laboratory Standards Institute (CLSI) breakpoint for other Candida spp. (≥ 32 μg/ml) (CLSI, 2017).

Minimum inhibitory concentrations of 50% of the isolates (MIC50) and Minimum inhibitory concentrations of 90% of the isolates (MIC90) were determined from MIC values ordered from the lowest to the highest, using the observations at ranks [0.50 × n] and [0.90 × n], respectively. MIC summaries for small source-specific groups were considered exploratory.

Jamovi software (version 2.6) was used for statistical analysis. Categorical data are expressed as frequencies and proportions. Antifungal MIC values (both determined values and interpreted in categories) were summarized by reporting the range, MIC50 (the lowest concentration where at least 50% of the isolates show inhibition), and MIC90 (the lowest concentration where at least 90% of the isolate display inhibition). Values falling below or above the testing limits were reported using the original inequality signs. Antifungal susceptibility classifications were presented as numbers and percentages of resistant and susceptible isolates. The distributions of resistant and susceptible isolates for the individual antifungal agents were evaluated using the chi-square goodness-of-fit test against equal expected frequencies. An agreement between the identification platforms was evaluated only among the isolates tested by the corresponding platforms and was reported as the number and percentage of concordant classifications. All tests were two-sided, and a p-value <0.05 was considered statistically significant, values below 0.001 were considered highly significant.

A total of 37 C. auris isolates recovered from routine laboratory cultures were included in this study. Blood cultures accounted for the largest proportion of isolates (21/37, 56.8%), followed by sputum cultures (8/37, 21.6%), bronchoalveolar lavage cultures (6/37, 16.2%), and urine cultures (2/37, 5.4%) (Table 1). Collectively, the isolates recovered from the non-blood cultures represented 43.2% (16/37) of the collection.

Table 1: Distribution of included Candida auris isolates by original culture source.

All 37 C. auris isolates (100%) expressed growth at 42°C. On Brilliance™ Candida Agar, the isolates produced colonies with colors ranging from white or pale pink to lavender. These obtained results supported the presumptive identification of C. auris, with a species identification that was subsequently established using the identification platforms described below (Figure 1).

The identification analysis included 37 C. auris isolates and 20 non-C. auris controls. All 57 isolates were evaluated using VITEK 2 and MALDI-TOF MS, while BIOFIRE FilmArray BCID2 evaluated 41 corresponding positive blood-culture broths, comprising 21 C. auris-positive cultures and 20 non-C. auris controls.

All 37 isolates in the main study group were identified as C. auris by both VITEK 2 and MALDI-TOF MS, demonstrating a complete observed agreement within this group (37/37, 100%). BIOFIRE BCID2 detected C. auris in all 21 corresponding positive blood-culture broths, with concordant identification by VITEK 2 and MALDI-TOF MS for the recovered isolates. Among the 20 non-C. auris controls, MALDI-TOF MS identified six isolates as C. albicans, six as C. tropicalis, four as C. famata, and four as Nakaseomyces glabratus. VITEK 2 reported all 20 controls as C. auris, resulting in no agreement with MALDI-TOF MS within the control group (0/20, 0%). Across the combined 57-isolate collection, VITEK 2, and MALDI-TOF MS agreement was 37/57 (64.9%). All discordances involved a VITEK 2 identification of C. auris and a non-C. auris identification by MALDI-TOF MS.

Table 2: Identification results of VITEK 2 and BIOFIRE FilmArray BCID2 compared to MALDI-TOF MS.

BIOFIRE BCID2 yielded no C. auris detections among the 20 non-C. auris controls. A species-level identifications agreed with MALDI-TOF MS for all 16 controls belonging to species targeted by BIOFIRE BCID2: C. albicans (n= 6), C. tropicalis (n= 6), and N. glabratus, reported as C. glabrata (n= 4). The four C. famata controls were evaluated for the absence of false-positive C. auris detection but were excluded from species-level agreement calculations because C. famata was not a BIOFIRE BCID2 target. Within the shared 41-culture subset, BIOFIRE BCID2 and MALDI-TOF MS displayed a complete observed agreement for C. auris versus non-C. auris classification (41/41, 100%), whereas VITEK 2 agreed with each platform for 21/41 classifications (51.2%). Restricting the BIOFIRE BCID2–MALDI-TOF MS species-level comparison to microorganisms targeted by BIOFIRE BCID2 yielded an agreement for all the 37 eligible cultures (37/37, 100%) (Table 2, Figure 2).

Antifungal susceptibility testing was performed on all 37 C. auris isolates. The overall and culture-source-specific MIC distributions are summarized in Table 3. Fluconazole MICs were 32 µg/ml for all isolates, yielding MIC50 and MIC90 values of 32 µg/ml. All isolates therefore met the CDC tentative resistance threshold for fluconazole (37/37, 100%). Voriconazole MICs ranged from ≤0.12 to 1 µg/ml, with MIC50 and MIC90 values of 0.25 and 0.5 µg/ml, respectively. These results were reported descriptively without assigning clinical susceptibility categories. Amphotericin B MICs ranged from 0.125 to 0.75 µg/ml, with MIC50 and MIC90 values of 0.5 and 0.75 µg/ml, respectively; none of the isolates reached the CDC tentative resistance threshold of ≥2 µg/ml (Figure 3). Flucytosine MICs were ≥64 µg/ml in 34 isolates (91.9%) and ≤1 µg/ml in three isolates (8.1%), resulting in both MIC50 and MIC90 values of ≥64 µg/ml. The 34 isolates with elevated MICs exceeded the exploratory threshold of ≥32 µg/ml specified in the study methodology. This classification was not interpreted as resistance established using a validated C. auris-specific clinical breakpoint. Caspofungin MICs ranged from 0.25 to 2 µg/ml, with MIC50 and MIC90 values of 0.25 and 1 µg/ml, respectively. Three isolates (8.1%) met the CDC tentative resistance threshold of ≥2 µg/ml. Micafungin MICs ranged from 0.12 to 4 µg/ml, with MIC50 and MIC90 values of 0.12 and 4 µg/ml, respectively. Four isolates (10.8%) met the tentative resistance threshold of ≥4 µg/ml.

Table 3: Overall antifungal minimum inhibitory concentration (MIC) distributions and recorded antibiotics susceptibility categories of Candida auris isolates (n = 37).

Where; R/S columns reproduce the recorded classifications, which should not all be interpreted as validated clinical susceptibility categories. ᵃVoriconazole’s recorded susceptible category does not establish a clinical susceptibility; an epidemiological cutoff distinguishes wild-type from non-wild-type isolates. ᵇ Flucytosine classification uses the exploratory ≥32 µg/ml threshold specified in the Methods, not a validated C. auris-specific breakpoint. For the other agents, resistance counts agree with the stated Centers for Disease Control and Prevention (CDC) tentative thresholds; values below those thresholds do not independently establish a clinical susceptibility. Highly significant (p <0.001).

Table 4: Antifungal resistance of Candida auris isolates by source.

By culture source, the isolates meeting the caspofungin resistance threshold were recovered from blood cultures (2/21, 9.5%) and urine cultures (1/2, 50.0%). Isolates meeting the micafungin resistance threshold were also recovered from blood cultures (2/21, 9.5%) and urine cultures (2/2, 100%). No sputum- or bronchoalveolar lavage (BAL)-derived isolates had reached the tentative resistance thresholds for either caspofungin or micafungin. Flucytosine MICs of ≥64 µg/ml were observed in 19/21 blood-derived isolates (90.5%), 2/2 urine-derived isolates (100%), 8/8 sputum-derived isolates (100%), and 5/6 BAL-derived isolates (83.3%). The source-specific findings were interpreted descriptively, particularly for the small non-blood culture groups (Table 4 and Figure 4).

This study included collected post-COVID-19 C. auris isolates, which describes the distribution of C. auris isolates by culture source, phenotypic characteristics, identification results, platform concordance, antifungal susceptibility patterns and MIC distributions. All these findings highlight the importance of rapid molecular diagnosis for prompt initiation of a suitable antifungal therapy and timely infection prevention measures. C. auris was one of the most important MDR yeasts owing to its ability to persist in healthcare environments, cause healthcare-associated outbreaks, and rapidly develop resistance to multiple antifungal agents (Bing et al., 2026). C. auris infection has increased worldwide since the development of COVID-19 pandemic, mainly due to its stay for long time in intensive care unit (ICU), excessive use of broad-spectrum antibiotics, corticosteroid therapy, invasive supportive care, and missing the rules of infection prevention (Ismail et al., 2026). Several studies have also reported a marked increase in the transmission of C. auris during the pandemic, pointing out to the combined effect of overwhelmed healthcare systems and the rise of highly vulnerable patient populations (Jordan et al., 2026; Parnell et al., 2026).

In the present study, C. auris isolates were recovered from different laboratory cultures, confirming its ability to colonize and infect multiple anatomical sites. Blood cultures accounted for more than half of all cases (56.8%), followed by respiratory cultures (37.8%), whereas urinary isolates were relatively uncommon. Many previous reports are in accordance with the current distribution, which have shown that candidemia is the most frequent invasive C. auris infection and remains the main cause of its associated morbidity and mortality (Pappas et al., 2016; Lockhart et al., 2017). Similar epidemiological trends have demonstrated that C. auris has become a very important cause of bloodstream infections in critically ill patients (Caceres et al., 2019; Wang et al., 2024).

The predominance of C. auris isolates recovered from blood cultures observed in this study is likely multifactorial. Infection of acute COVID-19 requires admission in ICU for a long time, central venous catheterization, mechanical ventilation, urinary catheterization, parenteral nutrition, and repeated usage of broad-spectrum antimicrobial agents. All these factors help in fungal colonization and subsequent dissemination in blood (Chowdhary et al., 2020; Kazancioglu et al., 2024). In addition, C. auris has the ability to still alive on hospital surfaces and medical equipment, so the prolonged hospitalization increases the chance of exposure to contaminated healthcare environments and the C. auris spread among the patients (Prestel et al., 2021; Bing et al., 2026).

Respiratory isolates recovered from sputum and bronchoalveolar lavage cultures represent another notable finding. Severe COVID-19 disrupts the local pulmonary immune defenses and causes an extensive epithelial injury, creating favorable conditions for the opportunistic fungal colonization and infection (Salmanton-García et al., 2021; Mina et al., 2022). Mechanical ventilation affects the mucosal integrity and increases the risk of secondary fungal infections in the admitted patients (Bassetti et al., 2020; Bergamasco et al., 2021). Nosocomial transmission contributed by the presence of C. auris either as a colonization or an infection of the lower respiratory tract, warrants a clinical assessment (Prestel et al., 2021; Salmanton-García et al., 2021; Chowdhary et al., 2026).

The recovered urinary isolates were 5.4%, a finding that is consistent with a previous report, which indicated that a urinary infection is less common than a bloodstream one, but it occurs primarily in those patients with a urinary catheterization for a long time and having severe diseases (Cortegiani et al., 2018). Together, these findings illustrate that the combination between severe COVID-19 and the invasive procedures used for its management creates a perfect setting for the opportunistic fungal infections at different body sites (Chowdhary et al., 2020; Kazancioglu et al., 2024).

In this study, C. auris infection following recovery from COVID-19 is likely representative of different characteristics of severe COVID-19 cases, including lymphopenia, loss of CD4+ and CD8+ T-cells, functional exhaustion of immune cells, and dysregulated inflammatory responses with increased cytokine levels (interleukin-6). All these factors compromise the host defense against the opportunistic fungal pathogens (Salehi et al., 2020; Nucci et al., 2021; Bing et al., 2026; Ismail et al., 2026).

Beyond immune dysregulation, disruption of the normal microbiota and reduction in microbial competition due to excessive use of broad-spectrum antibiotic therapy contributes to fungal overgrowth facilitating Candida spp. colonization (Li et al., 2022). The COVID-19 pandemic imposed pressure on the infection prevention programs at the healthcare system level. Overcrowded ICUs, a shortage of personnel, healthcare, and environmental persistence of both SARS-CoV-2 and C. auris created favorable circumstances for hospital transmission and development of many outbreaks worldwide (Eyre et al., 2018; Prestel et al., 2021; Bing et al., 2026). Along these lines, the rates of secondary fungal coinfection-most importantly, candidemia-among COVID-19 hospitalized patients were considerably greater than the hospital-wide population, with candidemia representing one of the deadliest comorbidities because of its associated death rate and challenging treatment approaches (Mirzaei et al., 2020; Jordan et al., 2026; Parnell et al., 2026).

In the present study, the initial laboratory screening was performed as per the CDC recommendations on chromogenic agar, where C. auris generally produces white to pale pink colonies (Ravichandran et al., 2022). The characteristic appearance of C. auris was observed in all 37 isolates, which was consistent with the phenotypic descriptions reported by Ninan et al. (2020); Ravichandran et al. (2022). Though colony morphology is not sufficient to differentiate C. auris from the closely related yeasts, chromogenic media represent a useful and cost-effective screening tool, particularly in laboratories where advanced identification technologies are not readily available. Their values lie in facilitating early recognition and selection of those isolates that require confirmatory testing, not for a definitive identification (CDC, 2026). Furthermore, one phenotypic characteristic of all the isolates was that they all grew at 42 °C, which further emphasizes their exceptional thermostolerance, distinguishing them from most other species in the genus Candida. Extreme thermostolerance is the property that is most strongly associated with the C. auris persistence and environmental success (Borman et al., 2016; Larkin et al., 2017; Casadevall et al., 2019; Jenks et al., 2025). The capacity to grow at temperatures above the normal body temperature has also been attributed to the evolutionary adaptation, allowing C. auris to overcome the mammalian thermal barrier, thereby emerging as a human pathogen (Casadevall et al., 2019; Di Luca et al., 2019; Jackson et al., 2019). Critically, the virulence-associated enzymatic activity is maintained during high temperature conditions further enabling tissue penetration and endurance. (Rossato and Colombo, 2018; Watkins et al., 2022; Semenya et al., 2025).

An accurate identification of a group of 20 non-C. auris controls was included in the identification analysis. All 57 isolates were evaluated by VITEK 2 and MALDI-TOF MS, while 41 corresponding positive blood-culture broths, comprising 21 positive C. auris cultures and 20 non- C. auris controls were evaluated by BIOFIRE FilmArray BCID2. The main study population comprised 37 isolates that were identified by the automated system VITEK 2 system (software version 8.01). The obtained results were confirmed by MALDI-TOF MS, which becomes a standard method for yeast’s identification, as it was accurate, fast, and inexpensive when C. auris-specific spectra were included in a commercial or a curated database (Tan et al., 2019; Ivanova et al., 2023; Jamalian et al., 2023; Hsu and Yassin, 2025). Complete concordance among chromogenic agar, VITEK 2, and MALDI-TOF MS provides reassurance on reliable diagnostic workflow utilized herein. Similar high levels of agreement among automated identification systems and MALDI-TOF MS have been reported by other investigator, emphasizing the importance of updated reference databases for an accurate recognition of this emerging fungal pathogen (Lockhart et al., 2022).

In accordance with the 20 non-C. auris control group, no agreement was observed between VITEK 2, which identified all the control group as C. auris and MALDI-TOF MS, which identified six isolates as C. albicans, six as C. tropicalis, four as C. famata, and four as N. glabratus. The misidentification may be attributed to the fact that C. auris shared deeply overlapping phenotypic characteristics with other Candida species (Ding et al., 2019; Hsu and Yassin, 2025).

The traditional culture remained the reference standard method for the diagnosis of candidemia (Timsit et al., 2020; El-Sherif et al., 2022); however, its limitation was a turnaround time. Identification methods, using typical conventional processes, which involve cultures and subcultures for identification, followed by an antifungal susceptibility test, may take a few more days to implement a definitive treatment decision for a patient (Kang et al., 2020). While automated blood culture systems have shortened the time needed to detect a microbial growth, they do not eliminate the need for subsequent identification procedures (Bruins et al., 2004). Furthermore, the conventional biochemical methods have historically misidentified C. auris as a closely related species, potentially delaying an appropriate antifungal therapy and infection control interventions (Altun et al., 2013; Salimnia et al., 2016). To address these diagnostic limitations, the BIOFIRE BCID2 panel was incorporated into 41 corresponding positive blood-culture broths of the current diagnostic workflow. Detection of C. auris occurred in all 21 corresponding positive blood-culture broths. BIOFIRE BCID2 yielded no C. auris detections among the 20 non-C. auris controls. BIOFIRE BCID2 is a multiplex polymerase chain reaction (PCR) assay used for identification of pathogens directly from positive blood culture bottles by simultaneously detecting 43 clinically relevant microorganisms plus relevant antimicrobial resistance genes within an hour. It is one of the first commercially available syndromic assays that received the U.S. Food and Drug Administration/ Conformité Européenne (French for European Conformity) (FDA/CE) approval for the identification of C. auris (Bassetti et al., 2020; Chowdhary et al., 2026). The value of BIOFIRE BCID2 is particularly evident with C. auris, since it is associated with high mortality rates, has frequent MDR rates and substantial breakout potential. Time is critical; thus every one hour that counts before appropriate antifungal treatment and infection prevention measures may be important (Lockhart et al., 2022; Rhoads et al., 2023; Chowdhary et al., 2026).

Quick detection enables appropriate early escalation of antifungals and allows for the early implementation of a patient isolation and contact precautions. It also enhances antimicrobial stewardship by limiting empiric treatment and, thereby, exposure to other antimicrobials. These advantages are especially relevant in intensive care settings, where delayed recognition of C. auris may contribute to ongoing healthcare-associated transmission (Lockhart et al., 2022; Chowdhary et al., 2026).

Recently, the diagnostic performance of BIOFIRE BCID2 has been consistently demonstrated. A multicenter evaluation in the United Arab Emirates has confirmed the significance of BIOFIRE BCID2. Implementation of the BIOFIRE BCID2 yielded a median reduction in the time of diagnosis of Candida pathogens from 92 to 28 h. (p < 0.0001), increased pathogen-detection rates compared to the conventional methods (98.8% versus 87.9%), and was associated with a significantly improved rate of 30-d. survival (17.3% versus 31.6% [p = 0.019]) (Senok et al., 2023). Other multicenter evaluations have displayed high sensitivity and specificity among most of the included microorganisms, including the challenging C. auris, along with an accurate identification of antimicrobial resistance mechanisms (Kim et al., 2024; Aygar and Hoşbul, 2025). Comparable findings have also been reported in Egypt. El-Sherif et al. (2022) reported a sensitivity of 75.8% and a specificity of 98% of identifying pathogens from central line-associated bloodstream infections with the use of BIOFIRE BCID2 compared to the VITEK 2 system. However, the sensitivity and specificity of identifying antimicrobial resistance genes were higher for the BIOFIRE BCID2 (90% and 99.6%, respectively).

Findings of this study further support the incorporation of BIOFIRE BCID2 into the diagnostic workflow with a suspected C. auris candidemia. Given that more than half of all isolates in the present study originated from blood cultures, rapid molecular identification provided clinically meaningful information considerably earlier than the conventional culture-based methods alone. Nevertheless, BIOFIRE BCID2 should be regarded as a complementary rather than a replacement technology. This assay detects only predefined pathogens and resistance markers but does not provide antifungal susceptibility results. Consequently, conventional culturing remains indispensable for isolate recovery, epidemiological investigations, and comprehensive antifungal susceptibility testing, particularly in view of the marked geographic variations in the C. auris resistance profiles (Rhoads et al., 2023). These obtained diagnostic results demonstrated the higher clinical accuracy of BIOFIRE BCID2 and proteomic fingerprinting of MALDI-TOF MS than VITEK 2 in the identification of C. auris, preventing the constant risk of metabolic cross-reactivity. A 100% agreement was observed between BIOFIRE BCID2 panel results and those of MALDI-TOF MS in identifying C. auris (41/41) and identifying species-specific targets (37/37) as expected of an array designed with a gene-target amplification. This array tested the highly conserved sequences in all C. auris isolates.

By focusing on the highly conserved regions, C. auris isolates could be correctly identified; because of this, the BIOFIRE BCID2 panel has an apparent 0% false positive rate compared to the 100% rate observed with VITEK 2, representing an incorrect identification of all the non-C. auris controls and misidentification of the following isolates: C. albicans, C. tropicalis, C. famata and N. glabratus. The use of conventional culturing, phenotype characterization, MALDI-TOF MS, and rapid molecular testing via BIOFIRE BCID2 ensured a robust diagnostic strategy of the C. auris, which compromised species identification and enabled precise antifungal susceptibility testing. Moreover, BIOFIRE BCID2 allowed early C. auris detection, individual patient treatment and infection prevention practices in high-risk environments.

Fluconazole recorded MIC ≥32 µg/ml for all isolates in accordance with the CDC tentative MIC breakpoints. Resistance to fluconazole is attributed to resistance mutation in the Erg11 gene that encodes the target enzyme of azole (CDC, 2024a). The breakpoint of flucytosine was ≥32 µg/ml which was interpreted according to the other Candida species breakpoint (CLSI, 2017). MICs of flucytosine were ≥64 µg/ml in 91.9% of the isolates and ≤1 µg/ml in 8.1% of them, in consistency with a report from Africa (Osaigbovo et al., 2024). MICs were above the exploratory cut-off of ≥32 µg/ml which was not interpreted as an established resistance. Flucytosine MICs were observed in blood, urine, sputum and BAL-derived isolates in 90.5%, 100%, 100%, and 83.3%, respectively. Flucytosine was not effective when used as a monotherapy; however, complete growth inhibition of resistant C. auris was achieved on using combinations of amphotericin B-5-flucytosine and anidulafungin-5-flucytosine at concentrations of 0.25/1 mg/l and 0.008/1 mg/l, respectively (O’Brien et al., 2020a, John et al., 2023). Flucytosine is an anti-Candida drug that enters the fungal cell and inhibits the synthesis of both proteins and DNA (Chowdhary et al., 2018; Osaigbovo et al., 2024).

Antifungal susceptibility testing results recorded 100% resistance to fluconazole and high rates of 91.8% for flucytosine. These findings are in concordance with the global epidemiology of C. auris (Osman et al., 2020; Khairat et al., 2021; Deshkar et al., 2022). Fluconazole resistance typically exceeded 90% across most of the recorded surveillance reports worldwide and was generally considered one of the most definitive features of this emergent pathogen (Ahmad and Alfouzan, 2021; Garcia-Bustos et al., 2021; Ahmad and Asadzadeh, 2023). In contrast, the resistance rates of amphotericin B and echinocandins are variable regionally and amongst the clades of several circulating microorganisms (Maphanga et al., 2021; Yadav et al., 2021; Burrack et al., 2022; Kilburn et al., 2022). In accordance, data from previous surveillance studies in the United States revealed a fluconazole resistance of 90%, amphotericin B of 30%, and echinocandins of 5%. Higher rates of amphotericin B resistance have been observed in New York-New Jersey outbreak (Kilburn et al., 2022). Additionally, similar trends have been documented in South Africa and India where fluconazole resistance reached 90-95%, whereas amphotericin B and echinoncidin resistance remained rare (Maphanga et al., 2021; Yadav et al., 2021). These discrepancies reflect the distribution of the different genetically divergent groups of C. auris, each was associated with a unique susceptibility profile (Maphanga et al., 2021; Yadav et al., 2021; Burrack et al., 2022; Kilburn et al., 2022).

Despite universal resistance to fluconazole, all isolates in the present study remained susceptible to voriconazole (breakpoint 1 μg/ml) (Arendrup et al., 2017; Bohner et al., 2023), which exerted its antifungal activity by inhibiting the biosynthesis of ergosterol. It selectively inhibited 14α-sterol demethylase enzyme of fungal Cytochrome P450 leading to the depletion of ergosterol, disruption of fungal cell membrane integrity, and inhibition of fungal growth (Ghannoum et al., 2002). Similarly, all tested isolates were susceptible to amphotericin B antifungal (breakpoint ≥ 2 μg/ml) that targeted the fungal cell membrane by interacting with ergosterol to form ion channels, which may cause cell death by permitting the release of protons and cations from the cells (Al-Balushi et al., 2018; Rybak et al., 2019).

The voriconazole MICs ranged from ≤ 0.12 to 1 µg /ml with MIC50 of 0.25and MIC90 of 0.5 µg /ml. These results are described in a descriptive manner without any classification into susceptibility categories as the primary objective of the analysis was to characterize the antifungal response patterns of the tested isolates rather than determine their clinical susceptibility or resistance status. MICs of amphotericin B were between 0.125–0.75 µg /ml (MIC50, 0.5 µg/ml; MIC90, 0.75 µg/ml), but no isolate attained MIC ≥2 µg/ml (breakpoint [CDC value]). The echinocandin class displayed the highest susceptible percentage recording 91.8% for caspofungin (≥2 μg/ml breakpoint) and 89.2% for micafungin (≥4 μg/ml) (CDC, 2024a). The mode of action of echinocandine was based on the inhibition of β−1,3-glucan, an essential polysaccharide in the fungal cell wall (Chen et al., 2011; Perlin, 2011).

Isolates derived from blood and urine cultures met the echinocandin resistance threshold by 9.5% and 50.0% for caspofungin and 9.5% and 100% for micafungin, respectively. This susceptibility pattern differed from that reported from several endemic regions and suggested that amphotericin B and echinocandins remained effective therapeutic options in our setting. These results also emphasized the importance of local antifungal susceptibility surveillance, as treatment recommendations should be based on the resistance patterns of the region and not only on the global trends (CDC, 2024c; Wang et al., 2024). Echinocandins are now the first-line therapeutic agents advised for use against invasive C. auris infections according to the WHO. This is based on the fact that most of the clinical isolates have demonstrated a sensitivity towards the echinocandins, in addition to the success of echinocandin-mediated treatment of invasive C. auris infection observed so far (Lepak et al., 2017; Biagi et al., 2019; Kwon et al., 2019). However, a great number of emerging resistant strains has been detected for the last decade as a result of the continued, recurring use, and treatment courses with echinocandins (Biagi et al., 2019). High echinocandin’s susceptibility observed in the current isolates supported their use while waiting for the susceptibility results, with the use of amphotericin B as an alternative treatment. The prevalence of strains that are resistant to multidrugs or all antifungal drugs is rapidly emerging and represents the biggest challenge in terms of treatment of C. auris.

Even though pan-resistant strains are currently sporadic, they have been reported in several countries and leads to a high death rate due to limitations in the number of treatment alternatives (Lockhart et al., 2019). The combination of antifungal drug therapy has therefore attracted considerable attention. Many antifungal combinations were reported to be synergistic, including flucytosine and amphotericin B, or echinocandins, caspofungin and posaconazole, anidulafungin and flucytosine or manogepix (O’Brien et al., 2020b; Balla et al., 2022; John et al., 2023). Several emerging antifungals such as fosmanogepix which showed well-known effects in vitro and in early stages of clinical trials, and rezafungin, a long-acting echinocandin, which has favorable pharmacokinetic properties along with a high antifungal activity in clinical trials, have gained remarkable attention as prospective agents for MDR C. auris infection (Tóth et al., 2019; Ham et al., 2021; Vazquez et al., 2023; CDC, 2024b).

Several strengths improve the significance of the present study. It provides one of the few detailed evaluations of post-COVID-19 laboratory-confirmed C. auris infection, integrating comprehensive clinical data with phenotypic identification, MALDI-TOF MS confirmation, rapid molecular diagnosis using the BIOFIRE BCID2 panel, and antifungal susceptibility testing. This integrated diagnostic approach allowed timely identification of bloodstream infections while providing a clinically relevant susceptibility data that may help inform the local treatment strategies.

The study also has several limitations. First, the relatively small number of candidemia cases that reduced the statistical power. Second, molecular typing was not performed; thus, prevalent strains of C. auris and transmission of strains within the healthcare setting have not been analyzed. Follow-up research studies using advanced approaches, such as whole-genome sequencing (WGS) with comprehensive patient samples, will allow the detailed epidemiologic definition of regional patterns, routes of transmission, mechanisms of antifungal resistance and clinical outcomes (Parnell et al., 2026).

Candida auris has become an important opportunistic pathogen among patients recovering from COVID-19 infection, particularly those with prolonged hospitalization and intensive care exposure. The findings demonstrate substantial differences in the performance of the evaluated identification platforms for C. auris. Vitek 2 correctly identified the main 37 isolates of the study as C. auris but misidentified all 20 non-C. auris control as C. auris. In contrast, MALDI-TOF MS showed complete discrimination between C. auris and non-C. auris isolates in the evaluated collection. BIOFIRE BCID2 demonstrated 100% agreement with MALDI-TOF MS for C. auris versus non-C. auris classification in the shared 41-culture subset and showed complete species-level agreement for microorganisms targeted by the panel. These findings indicate that BIOFIRE BCID2 and MALDI-TOF MS provided more specific identification than VITEK 2 in this study, particularly for distinguishing C. auris from closely related or other yeast species. The antifungal susceptibility results demonstrated a concerning pattern of reduced susceptibility among the C. auris isolates. The observed resistance profile, characterized by universal fluconazole resistance but with preserved susceptibility to amphotericin B and echinocandins, supported the current treatment recommendations and emphasized the importance of a continued local resistance surveillance. Overall, these findings highlight the value of integrating rapid molecular diagnostics with conventional microbiological methods to improve patient management, strengthen infection prevention strategies, and optimize antifungal stewardship in healthcare settings where C. auris continues to emerge. Accordingly, confirmation of suspected C. auris isolates using a reliable reference method, particularly when identified by VITEK 2, is recommended. Rapid molecular blood-culture testing such as BIOFIRE BCID2 may further facilitate early recognition and appropriate infection-control responses. Routine antifungal susceptibility testing and ongoing laboratory and infection-control surveillance should be maintained to detect emerging resistance and support appropriate clinical management.

The novelty of this study lies in using a novel strategy for enabling a timely recognition of bloodstream infection using the BioFire® BCID2 panel in combination with conventional microbiological methods for the early and accurate diagnosis of C. auris, improvement of patient’s management, infection control, and antifungal stewardship.

Fatma Ahmed: Methodology, formal analysis, resources, data curation.

Iman M. El-Kholy: Conceptualization, methodology, validation, investigation, review and editing, visualization, supervision, project administration.

Nadia A. Elkady: Methodology, formal analysis, writing original draft, writing review and editing, project administration.

Adel A. El-Mehalawy: Conceptualization, review and editing, supervision, project administration.

Dalia A.M. Abdou: Conceptualization, methodology, validation, investigation, data curation, writing original draft, writing review and editing, project administration.

All authors reviewed and approved the final manuscript.

The authors declare that no generative AI and AI assisted technology was used in the creation of the text of the manuscript.

The Institutional Research Ethics Committee of the Faculty of Science, Ain Shams University, reviewed and approved the study protocol with an approval number ASU-SCI/MICR/2026/08/02

The authors have declared no conflicts of interest.