Candida auris from colonisation to candidemia: A four-year study

Short-term evolution and dispersal patterns of fluconazole-resistance in Candida auris clade III

The rapid increase in infections caused by the emerging fungal pathogen Candida auris is of global concern, and understanding its expansion is a priority. The phylogenetic diversity of the yeast is clustered in five major clades, among which clade III is particularly relevant, as most of its strains exhibit resistance to fluconazole, reducing the therapeutic alternatives and provoking outbreaks that are difficult to control. In this study, we have investigated the phylogenetic structure of clade III by analyzing a global collection of 566 genomes. We have identified three subgroups within clade III, among which two are genetically most closely related. Moreover, we have estimated the evolutionary rate of clade III to be 2.25e-7 s/s/y (2.87 changes per year). We found that one of these subgroups shows intrinsic resistance to fluconazole and is responsible for the majority of cases within this clade globally. We inferred that this subgroup may have originated around December 2010 (95% High Probability Density (HPD): April 2010-June 2011), and since then it has spread across continents, generating multiple large outbreaks, each with a unique pattern of transmission and dissemination. These results highlight the remarkable ability of the pathogen to adapt to its environment and its rapid global spread, underscoring the urgent need to address this epidemiological challenge effectively.IMPORTANCEThe number of cases affected by Candida auris has increased worryingly worldwide. Among the currently recognized clades, clade III has the highest proportion of fluconazole-resistant cases and is spreading very rapidly, causing large nosocomial outbreaks across the globe. By analyzing complete fungal genomes from around the world, we have confirmed the origin of this clade and unraveled its dispersal patterns in the early 2010s. This finding provides knowledge that may be helpful to the public health authorities for the control of the disease.

Cerebrospinal Drain Infection by Candida auris: A Case Report and Review of the Literature

Candida auris is notorious for its ability to spread within healthcare environments, particularly in intensive care units (ICUs), posing significant challenges for clinicians as treatment options become limited. This is especially concerning in the context of central nervous system (CNS)-invasive infections. While rare, its involvement in nosocomial brain ventriculitis presents substantial diagnostic and therapeutic challenges, with no established guidelines for managing CNS infections caused by Candida auris. This report presents a case of Candida auris ventriculitis in an ICU patient and offers a comprehensive and targeted literature review, emphasizing diagnostic approaches, treatment strategies, and the clinical complexities of managing this emerging pathogen in CNS infections.

First report of Candida auris in Guangdong, China: clinical and microbiological characteristics of 7 episodes of candidemia

Candida auris is an emerging multidrug-resistant fungal pathogen worldwide. To date, it has not been reported in Guangdong, China. For the first time, we reported 7 cases of C. auris candidemia from two hospitals in Guangdong. The clinical and microbiological characteristics of these cases were investigated carefully. Two geographic clades, i.e. III and I, were found popular in different hospitals by whole genome sequencing analyses. All C. auris isolates from bloodstream were resistant to fluconazole, 5 of which belonged to Clade III harbouring VF125AL mutation in the ERG11 gene. The isolates with Clade I presented Y132F mutation in the ERG11 gene as well as resistance to amphotericin B. All isolates exhibited strong biofilm-forming capacity and non-aggregative phenotype. The mean time from admission to onset of C. auris candidemia was 39.4 days (range: 12 - 80 days). Despite performing appropriate therapeutic regimen, 42.9% (3/7) of patients experienced occurrences of C. auris candidemia and colonization after the first positive bloodstream. C. auris colonization was still observed after the first C. auris candidemia for 81 days in some patient. Microbiologic eradication from bloodstream was achieved in 85.7% (6/7) of patients at discharge. In conclusion, this study offers a crucial insight into unravelling the multiple origins of C. auris in Guangdong, highlighting great challenges in clinical prevention and control.

Factors Associated With Poor Clinical and Microbiologic Outcomes in Candida auris Bloodstream Infection: A Multicenter Retrospective Cohort Study

BACKGROUND

Candida auris has become a growing concern worldwide because of increases in incidence of colonization and reports of invasive infections. There are limited data on clinical factors associated with poor outcomes in patients with C. auris bloodstream infection (BSI).

METHODS

We assembled a multicenter retrospective cohort of patients with C. auris BSI from 2 geographics areas in US healthcare settings. We collected data on demographic, clinical, and microbiologic characteristics to describe the cohort and constructed multivariate logistic regression models to understand risk factors for 2 clinical outcomes, all-cause mortality during facility admission, and blood culture clearance.

RESULTS

Our cohort consisted of 187 patients with C. auris BSI (56.1% male, 55.6% age >65 years); 54.6% died by facility discharge and 66.9% (of 142 with available data) experienced blood culture clearance. Pitt bacteremia score at infection onset was associated with mortality (odds ratio [95% confidence interval]: 1.19 [1.01-1.40] per 1-point increase). Hemodialysis was associated with a reduced odds of microbiologic clearance (0.15 [0.05-0.43]) and with mortality (3.08 [1.27-7.50]).

CONCLUSIONS

The Pitt bacteremia score at the onset of C. auris BSI may be a useful tool in identifying patients at risk for mortality. Targeted infection prevention practices in patients receiving hemodialysis may be useful to limit poor outcomes.

Antibiofilm activity of truncated Staphylococcus aureus phenol soluble modulin α2 (SaΔ1Δ2PSMα2) against Candida auris in vitro and in an animal model of catheter-associated infection

Candida auris has emerged as a major multidrug-resistant nosocomial pathogen. The organism exhibits a persistent colonising phenotype, and causes recalcitrant infections often strongly linked to biofilm formation. Alternate strategies are urgently needed to combat this yeast and its biofilm-associated phenotype. This work aimed to evaluate the efficacy of select staphylococcal phenol soluble modulins (PSMs), namely, a truncated version of Staphylococcus aureus PSMα2 shortened by two amino acids at the N-terminal (SaΔ1Δ2PSMα2) and Staphylococcus epidermidis PSMδ against C. auris in vitro and in vivo. The antifungal and antibiofilm activity was tested by broth microdilution and XTT dye reduction assay. Combination effect with antifungal drugs was determined by fractional inhibitory concentration test. The efficacy of combination therapy using SaΔ1Δ2PSMα2 with amphotericin B or caspofungin was evaluated in murine model of C. auris catheter-associated infection. Based on antifungal activity, antibiofilm activity and cytotoxicity data, SaΔ1Δ2PSMα2 exhibited promising activity against C. auris biofilms. Nearly 50 % inhibition in biofilm formation was noted with 0.5-2 μM of the peptide against multiple clinical and C. auris colonizing isolates. It was synergistic with amphotericin B (ΣFIC = 0.281) and caspofungin (ΣFIC = 0.047) in vitro, and improved the activity of voriconazole in voriconazole-resistant C. auris. Combination therapy using amphotericin B or caspofungin (1 μg/ml) with SaΔ1Δ2PSMα2 resulted in 99.5 % reduction in C. auris biofilm in murine model, even when the peptide was used at a concentration that was neither fungicidal nor antibiofilm (0.125 μM; ≈0.26 μg/ml). The study provides insight into the potential utility of SaΔ1Δ2PSMα2-antifungal drug combination against C. auris biofilm-associated infections.

Evaluation of the Eazyplex®Candida ID LAMP Assay for the Rapid Diagnosis of Positive Blood Cultures

Rapid molecular assays can be used to identify Candida pathogens directly from positive blood cultures (BCs) in a timely manner compared to standard methods using subcultures. In this study, the eazyplex®Candida ID assay, which is based on loop-mediated amplification (LAMP) and is currently for research use only, was evaluated for the identification of the most common fungal species. A total of 190 BCs were analysed. Sensitivity and specificity were 93.88% and 99.26% for C. albicans, 89.13% and 100% for Nakaseomyces glabratus (N. glabratus), 100% and 100% for Pichia kudravzevii (P. kudriavzevii), 100% and 100% for C. tropicalis, and 100% and 99.44% for C. parapsilosis. Sample preparation took approximately 11 min and positive amplification results were obtained between 8.5 and 19 min. The eazyplex®Candida ID LAMP assay is an easy-to-use diagnostic tool that can optimise the management of patients with candidemia.

Candida auris: Understanding the dynamics of C. auris infection versus colonization

Candida auris is a pathogen of growing public health concern worldwide. However, risk factors contributing to C. auris infection in patients colonized with C. auris remain unclear. Understanding these risk factors is crucial to prevent colonization-to-infection transition and devise effective preventive strategies. This study aimed to investigate risk factors associated with C. auris infection compared to colonization. The study included 97 patients who acquired laboratory-confirmed C. auris in either matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry or VITEK 2 system from October 2019 to June 2023. Baseline demographics and known risk factors associated with C. auris infection were collected from electronic medical records. The infection group had C. auris from a sterile site or non-sterile site with evidence of infection. The colonization group was followed up for a median of 30 days for any signs of infection. Associations between relevant variables and C. auris infection were assessed using multivariable logistic regression. The infection group (n = 31) was more likely to be bedbound, with longer hospital stays and more arterial catheters. Chronic kidney disease (odds ratio [OR] 45.070), carriage of multidrug-resistant organisms (OR 64.612), and vasopressor use for > 20 days (OR 68.994) were associated with C. auris infection, after adjusting for sex, age, and prior colonization with C. auris. Chronic kidney disease, carriage of multidrug-resistant organisms, and prolonged vasopressor use emerged as significant risk factors for C. auris infection compared to colonization. They could be used to predict C. auris infection early in patients colonized with C. auris.

Evaluation of Etest and MICRONAUT-AM Assay for Antifungal Susceptibility Testing of Candida auris: Underestimation of Fluconazole Resistance by MICRONAUT-AM and Overestimation of Amphotericin B Resistance by Etest

Multidrug-resistant Candida auris has recently caused major outbreaks in healthcare facilities. Rapid and accurate antifungal susceptibility testing (AST) of C. auris is crucial for proper management of invasive infections. The Commercial Sensititre Yeast One and Vitek 2 methods underestimate or overestimate the resistance of C. auris to fluconazole and amphotericin B (AMB). This study evaluated the AST results of C. auris against fluconazole and AMB by gradient-MIC-strip (Etest) and broth microdilution-based MICRONAUT-AM-EUCAST (MCN-AM) assays. Clinical C. auris isolates (n = 121) identified by phenotypic and molecular methods were tested. Essential agreement (EA, ±1 two-fold dilution) between the two methods and categorical agreement (CA) based on the Centers for Disease Control and Prevention's (CDC's) tentative resistance breakpoints were determined. Fluconazole resistance-associated mutations were detected by PCR-sequencing of ERG11. All isolates identified as C. auris belonged to South Asian clade I and contained the ERG11 Y132F or K143R mutation. The Etest-MCN-AM EA was poor (33%) for fluconazole and moderate (76%) for AMB. The CA for fluconazole was higher (94.2%, 7 discrepancies) than for AMB (91.7%, 10 discrepancies). Discrepancies were reduced when an MCN-AM upper-limit value of 4 µg/mL for fluconazole-susceptible C. auris and an Etest upper-limit value of 8 µg/mL for the wild type for AMB were used. Our data show that resistance to fluconazole was underestimated by MCN-AM, while resistance to AMB was overestimated by Etest when using the CDC's tentative resistance breakpoints of ≥32 µg/mL for fluconazole and ≥2 µg/mL for AMB. Method-specific resistance breakpoints should be devised for accurate AST of clinical C. auris isolates for proper patient management.

Clinical and microbiological characteristics of a hospital outbreak of Candida auris in a referral hospital in Lima, Peru

BACKGROUND

Candida auris, a multidrug-resistant fungal pathogen, has received considerable attention owing to its recent surge, especially in South America, which coincides with the ongoing global COVID-19 pandemic. Understanding the clinical and microbiological characteristics of outbreaks is crucial for their effective management and control.

OBJECTIVE

This retrospective observational study aimed to characterize a C. auris outbreak at a Peruvian referral hospital between January 2021 and July 2023.

METHODS

Data were collected from hospitalized patients with positive C. auris culture results. Microbiological data and antifungal susceptibility test results were analysed. Additionally, infection prevention and control measures have been described. Statistical analysis was used to compare the characteristics between the infected and colonized patients.

RESULTS

Thirty-three patients were identified, mostly male (66.7%), with a median age of 53 years. Among them, 18 (54.5%) were colonized, and 15 (45.5%) were infected. Fungemia was the predominant presentation (80%), with notable cases of fungemia in tuberculosis patients with long-stay devices for parenteral anti-tuberculosis therapy. Seventy-five percent of the isolates exhibited fluconazole resistance. Echinocandins were the primary treatment, preventing fungemia recurrence within 30 days. Infected patients had significantly longer hospital stays than colonized patients (100 vs. 45 days; p = .023). Hospital mortality rates were 46.7% and 25% in the infected and fungemia patients, respectively. Simultaneous outbreaks of multidrug-resistant bacteria were documented.

CONCLUSIONS

This study underscores the severity of a C. auris outbreak at a referral hospital in Peru, highlighting its significant impact on patient outcomes and healthcare resources. The high prevalence of fluconazole-resistant isolates, leading to prolonged hospital stay and high mortality rates, particularly in cases of fungemia, underscores the critical need for effective infection prevention and control strategies.

Spectrum and management of rare Candida/yeast infections in Kuwait in the Middle East

Invasive fungal infections (IFIs) are associated with high mortality rates and mostly affect patients with compromised immunity. The incidence of IFIs is increasing worldwide with the expanding population of susceptible patients. Candida and other yeast infections represent a major component of IFIs. Rare Candida/yeast infections have also increased in recent years and pose considerable diagnostic and management challenges as they are not easily recognized by routine phenotypic characteristic-based diagnostic methods and/or by the automated yeast identification systems. Rare Candida/yeasts also exhibit reduced susceptibility to antifungal drugs making proper management of invasive infections challenging. Here, we review the diagnosis and management of 60 cases of rare Candida/yeast IFIs described so far in Kuwait, an Arabian Gulf country in the Middle East. Interestingly, majority (34 of 60, 56.7%) of these rare Candida/yeast invasive infections occurred among neonates or premature, very-low-birth-weight neonates, usually following prior bacteremia episodes. The clinical details, treatment given, and outcome were available for 28 of 34 neonates. The crude mortality rate among these neonates was 32.2% as 19 of 28 (67.8%) survived the infection and were discharged in healthy condition, likely due to accurate diagnosis and frequent use of combination therapy. Physicians treating patients with extended stay under intensive care, on mechanical ventilation, receiving broad spectrum antibiotics and with gastrointestinal surgery/complications should proactively investigate IFIs. Timely diagnosis and early antifungal treatment are essential to decrease mortality. Understanding the epidemiology and spectrum of rare Candida/yeast invasive infections in different geographical regions, their susceptibility profiles and management will help to devise novel diagnostic and treatment approaches and formulate guidelines for improved patient outcome.

Whole genome sequencing analysis demonstrates therapy-induced echinocandin resistance in Candida auris isolates

Candida auris is an emerging, multidrug-resistant yeast, causing outbreaks in healthcare facilities. Echinocandins are the antifungal drugs of choice to treat candidiasis, as they cause few side effects and resistance is rarely found. Previously, immunocompromised patients from Kuwait with C. auris colonisation or infection were treated with echinocandins, and within days to months, resistance was reported in urine isolates. To determine whether the development of echinocandin resistance was due to independent introductions of resistant strains or resulted from intra-patient resistance development, whole genome sequencing (WGS) single-nucleotide polymorphism (SNP) analysis was performed on susceptible (n = 26) and echinocandin-resistant (n = 6) isolates from seven patients. WGS SNP analysis identified three distinct clusters differing 17-127 SNPs from two patients, and the remaining isolates from five patients, respectively. Sequential isolates within patients had a maximum of 11 SNP differences over a time period of 1-10 months. The majority of isolates with reduced susceptibility displayed unique FKS1 substitutions including a novel FKS1M690V substitution, and nearly all were genetically related, ranging from only three to six SNP differences compared to susceptible isolates from the same patient. Resistant isolates from three patients shared the common FKS1S639F substitution; however, WGS analysis did not suggest a common source. These findings strongly indicate that echinocandin resistance is induced during antifungal treatment. Future studies should determine whether such echinocandin-resistant strains are capable of long-term colonisation, cause subsequent breakthrough candidiasis, have a propensity to cross-infect other patients, or remain viable for longer time periods in the hospital environment.

An Autochthonous Susceptible Candida auris Clade I Otomycosis Case in Iran

Candida auris is a newly emerging multidrug-resistant fungal pathogen considered to be a serious global health threat. Due to diagnostic challenges, there is no precise estimate for the prevalence rate of this pathogen in Iran. Since 2019, only six culture-proven C. auris cases have been reported from Iran, of which, five belonged to clade V and one to clade I. Herein, we report a case of otomycosis due to C. auris from 2017 in a 78-year-old man with diabetes mellitus type II without an epidemiological link to other cases or travel history. Short tandem repeat genotyping and whole genome sequencing (WGS) analysis revealed that this isolate belonged to clade I of C. auris (South Asian Clade). The WGS single nucleotide polymorphism calling demonstrated that the C. auris isolate from 2017 is not related to a previously reported clade I isolate from Iran. The presence of this retrospectively recognized clade I isolate also suggests an early introduction from other regions or an autochthonous presence. Although the majority of reported C. auris isolates worldwide are resistant to fluconazole and, to a lesser extent, to echinocandins and amphotericin B, the reported clade I isolate from Iran was susceptible to all antifungal drugs.

A Candida auris-specific adhesin, Scf1, governs surface association, colonization, and virulence

Candida auris is an emerging fungal pathogen responsible for health care-associated outbreaks that arise from persistent surface and skin colonization. We characterized the arsenal of adhesins used by C. auris and discovered an uncharacterized adhesin, Surface Colonization Factor (Scf1), and a conserved adhesin, Iff4109, that are essential for the colonization of inert surfaces and mammalian hosts. SCF1 is apparently specific to C. auris, and its expression mediates adhesion to inert and biological surfaces across isolates from all five clades. Unlike canonical fungal adhesins, which function through hydrophobic interactions, Scf1 relies on exposed cationic residues for surface association. SCF1 is required for C. auris biofilm formation, skin colonization, virulence in systemic infection, and colonization of inserted medical devices.