Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples

Global characteristics and trends in research on Candida auris

Introduction

Candida auris, a fungal pathogen first reported in 2009, has shown strong resistance to azole antifungal drugs and has caused severe nosocomial outbreaks. It can also form biofilms, which can colonize patients' skin and transmit to others. Despite numerous reports of C. auris isolation in various countries, many studies have reported contradictory results.

Method

A bibliometric analysis was conducted using VOSviewer to summarize research trends and provide guidance for future research on controlling C. auris infection. The analysis revealed that the United States and the US CDC were the most influential countries and research institutions, respectively. For the researchers, Jacques F. Meis published the highest amount of related articles, and Anastasia P. Litvintseva's articles with the highest average citation rate. The most cited publications focused on clade classification, accurate identification technologies, nosocomial outbreaks, drug resistance, and biofilm formation. Keyword co-occurrence analysis revealed that the top five highest frequencies were for 'drug resistance,' 'antifungal susceptibility test,' 'infection,' 'Candida auris,' and 'identification.' The high-frequency keywords clustered into four groups: rapid and precise identification, drug resistance research, pathogenicity, and nosocomial transmission epidemiology studies. These clusters represent different study fields and current research hotspots of C. auris.

Conclusion

The bibliometric analysis identified the most influential country, research institution, and researcher, indicating current research trends and hotspots for controlling C. auris.

Diagnosis of invasive fungal infections: challenges and recent developments

BACKGROUND

The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow.

MAIN TEXT

A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections.

CONCLUSION

The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.

Strategies to Prevent Transmission of Candida auris in Healthcare Settings

Purpose of Review

Candida auris, a recently recognized yeast pathogen, has become a major public health threat due to the problems associated with its accurate identification, intrinsic and acquired resistance to antifungal drugs, and its potential to easily contaminate the environment causing clonal outbreaks in healthcare facilities. These outbreaks are associated with high mortality rates particularly among older patients with multiple comorbidities under intensive care settings. The purpose of this review is to highlight strategies that are being adapted to prevent transmission of C. auris in healthcare settings.

Recent Findings

Colonized patients shed C. auris into their environment which contaminates surrounding equipment. It resists elimination even by robust decontamination procedures and is easily transmitted to new patients during close contact resulting in outbreaks. Efforts are being made to rapidly identify C. auris-infected/C. auris-colonized patients, to determine its susceptibility to antifungals, and to perform effective cleaning and decontamination of the environment and isolation of colonized patients to prevent further transmission.

Summary

Rapid and accurate identification of hospitalized patients infected/colonized with C. auris, rapid detection of its susceptibility patterns, and appropriate use of infection control measures can help to contain the spread of this highly pathogenic yeast in healthcare settings and prevent/control outbreaks.

Development and Validation of Specific Conventional PCR and Real-Time PCR Assays for Rapid Detection/Identification of C. auris from Yeast Isolates and Clinical Specimens

BACKGROUND

The accurate occurrence rate of C. auris infections is still not clear, mainly due to defects in detection and identification tools routinely used. In this study, we used conventional PCR and real-time PCR assays for sensitive and specific detection/identification of C. auris from either yeast isolates or clinical specimens collected from various patients in different parts of Iran. Our survey is the first large scale study rating the incidence of C. auris infections in Iran.

METHODS

A total of 439 yeast isolates and 590 clinical specimens were screened by specific C. auris-PCR, targeting the ITS region. The validity of positive samples was assessed by sequencing.

RESULTS

Four out of 590 clinical specimens (0.68%) were positive by conventional PCR, while in real-time PCR performed on 100 clinical samples, including those four samples positive in conventional samples, 6 samples were positive. A complete agreement of the identification of positive cases with sequencing results was documented. Among 439 culture isolate, none was positive for C. auris. After following up and resampling of the patients with positive PCR, only one specimen showed positive culture for C. auris, which was confirmed by sequencing.

CONCLUSION

C. auris is not a common cause of systemic or superficial fungal infections in Iran, and a few detected positive cases can be considered as a commensal, colonizer, or infecting yeast which may potentially emerge in some clinical and therapeutical conditions. Mycological and phenotypical assays are not sensitive approaches for isolation/identification of C. auris, unless a specific and sensitive molecular-based method is applied.

A Portable Droplet Magnetofluidic Device for Point-of-Care Detection of Multidrug-Resistant Candida auris

Candida auris is an emerging multidrug-resistant fungal pathogen that can cause severe and deadly infections. To date, C. auris has spurred outbreaks in healthcare settings in thirty-three countries across five continents. To control and potentially prevent its spread, there is an urgent need for point-of-care (POC) diagnostics that can rapidly screen patients, close patient contacts, and surveil environmental sources. Droplet magnetofluidics (DM), which leverages nucleic acid-binding magnetic beads for realizing POC-amenable nucleic acid detection platforms, offers a promising solution. Herein, we report the first DM device—coined POC.auris—for POC detection of C. auris. As part of POC.auris, we have incorporated a handheld cell lysis module that lyses C. auris cells with 2 min hands-on time. Subsequently, within the palm-sized and automated DM device, C. auris and control DNA are magnetically extracted and purified by a motorized magnetic arm and finally amplified via a duplex real-time quantitative PCR assay by a miniaturized rapid PCR module and a miniaturized fluorescence detector—all in ≤30 min. For demonstration, we use POC.auris to detect C. auris isolates from 3 major clades, with no cross reactivity against other Candida species and a limit of detection of ∼300 colony forming units per mL. Taken together, POC.auris presents a potentially useful tool for combating C. auris.

Tools for detecting a "superbug": updates on Candida auris testing

Candida auris is an emerging yeast species that has the unique characteristics of patient skin colonization and rapid transmission within healthcare facilities and the ability to rapidly develop antifungal resistance. When C. auris first started appearing in clinical microbiology laboratories, it could only be identified using DNA sequencing. In the decade since its first identification outside of Japan there have been many improvements in the detection of C. auris. These include the expansion of MALDI-TOF databases to include C. auris, the development of both laboratory-developed tests and commercially available kits for its detection, and special CHROMagar for identification from laboratory specimens. Here we discuss the current tools and resources that are available for C. auris identification and detection.

Isolation of Candida auris in Clinical Specimens

Candida auris is a multidrug-resistant yeast causing healthcare-associated outbreaks of blood stream infections worldwide. Currently, C. auris isolation and identification is complicated by issues such as misidentification and long turnaround time associated with application of commonly used diagnostic tools. Based on phenotypic characteristics, differentiation of C. auris from related Candida haemulonii complex spp. is problematic. Candida auris can be misidentified using biochemical-based systems such as VITEK 2 YST, API 20C, BD Phoenix yeast identification system, and MicroScan. C. auris growth at 42 °C and in the presence of 10% NaCl helps in presumptive identification of this yeast from related Candida haemulonii complex spp. A new CHROMagar™ Candida Plus agar is an excellent alternative to current conventional mycological media for the screening of patients colonized/infected with Candida auris. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) can differentiate C. auris from other Candida species, but not all the reference databases included in MALDI-TOF devices allow for detection. Currently, accurate identification of C. auris can be performed using the updated FDA-approved libraries or "research use-only" libraries. Molecular techniques have greatly enhanced the diagnosis of C. auris. Sequencing of rDNA genetic loci, namely, internal transcribed spacer and D1/D2 region of large subunit (LSU), and PCR/qPCR assays has successfully been applied for identification of C. auris. Real-time PCR assays bear incomparable potential of being the most efficient tool for high-throughput screening of surveillance samples. If properly validated, they can deliver the diagnostic result within several hours, since the DNA can be isolated directly from the patient specimen without the need of obtaining a colony. In this chapter we detailed the isolation of Candida auris from various clinical specimens and its currently available identification methods and hitches.

The Use of Galleria mellonella Larvae to Study the Pathogenicity and Clonal Lineage-Specific Behaviors of the Emerging Fungal Pathogen Candida auris

Candida species are the most common fungal causes of disseminated infections in humans. Although such infections are associated with high morbidity and mortality, it is widely accepted that virulence, antifungal susceptibility, and disease outcome vary according to individual Candida species. In this respect, the emerging pathogen Candida auris has received much attention due to its propensity to cause widespread nosocomial outbreaks, to exhibit high virulence in several infection models, and to develop resistance to multiple classes of antifungal drugs. Although mammalian models of infection have long been viewed as the gold standard for studies on fungal virulence, comparative pathogenicity, and evaluation of antifungal drug efficacy, the larvae of the greater wax moth Galleria mellonella have shown considerable promise as an alternative invertebrate model of infection. Galleria larvae are inexpensive, are easily maintained in the laboratory, tolerate incubation at human physiological temperatures, possess cellular and humoral immune systems that share many features with mammals, and allow investigation of pathogenicity/virulence using multiple different reading endpoints. Here, I describe in detail the methods that can be used to study the virulence/pathogenicity of Candida auris in G. mellonella.

Emerging Status of Multidrug-Resistant Bacteria and Fungi in the Arabian Peninsula

Simple Summary

The incidence and developing status of multidrug-resistant bacteria and fungi, as well as their related mortality, is reviewed by a systematic published literature search from nine countries in the Arabian Peninsula. In order to analyse the emerging status and mortality, a total of 382 research articles were selected from a comprehensive screening of 1705 papers. More than 850 deaths reported since 2010 in the Arabian Peninsula due to the infection of multidrug-resistant bacteria and fungi. Multidrug-resistant bacteria Acinetobacter baumannii, Mycobacterium tuberculosis, Staphylococcus aureus, and fungi Candida auris are the most prevalent and causing high deaths. To control these infections and associated deaths in the Arabian Peninsula, continuous preventive measures, accurate methods for early diagnosis of infection, active surveillance, constant monitoring, developing vaccines, eradicating multidrug resistance modulators, and data sharing among countries are required.

Abstract

We aimed to identify the prevalence and emerging status of multidrug-resistant bacteria and fungi and their associated mortality in nine countries in the Arabian Peninsula. Original research articles and case studies regarding multidrug-resistant bacteria and fungi in the Arabian Peninsula, published during the last 10 years, were retrieved from PubMed and Scopus. A total of 382 studies were included as per the inclusion and exclusion criteria, as well as the PRISMA guidelines, from a thorough screening of 1705 articles, in order to analyse the emerging status and mortality. The emerging nature of >120 multidrug-resistant (MDR) bacteria and fungi in the Arabian Peninsula is a serious concern that requires continuous monitoring and immediate preventive measures. More than 50% (n = 453) of multidrug-resistant, microbe-associated mortality (n = 871) in the Arabian Peninsula was due to MDR Acinetobacter baumannii, Mycobacterium tuberculosis and Staphylococcus aureus infection. Overall, a 16.51% mortality was reported among MDR-infected patients in the Arabian Peninsula from the 382 articles of this registered systematic review. MDR A. baumannii (5600 isolates) prevailed in all the nine countries of the Arabian Peninsula and was one of the fastest emerging MDR bacteria with the highest mortality (n = 210). A total of 13,087 Mycobacterium tuberculosis isolates were reported in the region. Candida auris (580 strains) is the most prevalent among the MDR fungal pathogen in the Arabian Peninsula, having caused 54 mortalities. Active surveillance, constant monitoring, the development of a candidate vaccine, an early diagnosis of MDR infection, the elimination of multidrug resistance modulators and uninterrupted preventive measures with enhanced data sharing are mandatory to control MDR infection and associated diseases of the Arabian Peninsula. Accurate and rapid detection methods are needed to differentiate MDR strain from other strains of the species. This review summarises the logical relation, prevalence, emerging status and associated mortality of MDR microbes in the Arabian Peninsula.

So Many Diagnostic Tests, So Little Time: Review and Preview of Candida auris Testing in Clinical and Public Health Laboratories

The recognition of a new yeast, Candida auris, in 2009 in East Asia, and its rapid global spread, was a reminder of the threats posed by multidrug-resistant fungal pathogens. C. auris had likely remained unrecognized for a long time as accurate tests were not available. The laboratory community responded to the C. auris challenge by publishing 35 new or revised diagnostic methods between 2014 and early 2021. The commercial sector also modified existing diagnostic devices. These C. auris diagnostic tests run the gamut from traditional culture-based differential and selective media, biochemical assimilations, and rapid protein profiles, as well as culture-independent DNA-based diagnostics. We provide an overview of these developments, especially the tests with validation data that were subsequently adopted for common use. We share a workflow developed in our laboratory to process over 37,000 C. auris surveillance samples and 5,000 C. auris isolates from the outbreak in the New York metropolitan area. Our preview covers new devices and diagnostic approaches on the horizon based on microfluidics, optics, and nanotechnology. Frontline laboratories need rapid, cheap, stable, and easy-to-implement tests to improve C. auris diagnosis, surveillance, patient isolation, admission screening, and environmental control. Among the urgent needs is a lateral flow assay or similar device for presumptive C. auris identification. All laboratories will benefit from devices that allow rapid antifungal susceptibility testing, including detection of mutations conferring drug resistance. Hopefully, multiplex test panels are on the horizon for synergy of C. auris testing with ongoing surveillance of other healthcare-associated infections. C. auris genome analysis has a proven role for outbreak investigations, and diagnostic laboratories need quick access to regional and national genome analysis networks.

Fluorescent toys 'n' tools lighting the way in fungal research

Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.

Metagenomic Sequencing for Direct Identification of Candida auris Colonization

Candida auris is an emerging multidrug-resistant yeast that is associated with skin colonization and deadly bloodstream infections, especially in ventilator skilled nursing facilities. An ongoing question is how this organism colonizes the skin of these patients and whether the skin microbiome provides a measure of colonization resistance against C. auris. Now, Huang et al. (X. Huang, R. M. Welsh, C. Deming, D. M. Proctor, et al., mSphere 6:e00287-21, 2021, https://doi.org/10.1128/mSphere.00287-21) demonstrate a method for shotgun metagenomic analysis of the skin to generate a profile of fungal colonization that is highly correlative with culture-based methods. These methods are likely to assist in the diagnosis of C. auris and the identification of microbiome-associated risk factors that predict invasive disease.

Candida auris: Epidemiology, Diagnosis, Pathogenesis, Antifungal Susceptibility, and Infection Control Measures to Combat the Spread of Infections in Healthcare Facilities

Candida auris, a recently recognized, often multidrug-resistant yeast, has become a significant fungal pathogen due to its ability to cause invasive infections and outbreaks in healthcare facilities which have been difficult to control and treat. The extraordinary abilities of C. auris to easily contaminate the environment around colonized patients and persist for long periods have recently resulted in major outbreaks in many countries. C. auris resists elimination by robust cleaning and other decontamination procedures, likely due to the formation of 'dry' biofilms. Susceptible hospitalized patients, particularly those with multiple comorbidities in intensive care settings, acquire C. auris rather easily from close contact with C. auris-infected patients, their environment, or the equipment used on colonized patients, often with fatal consequences. This review highlights the lessons learned from recent studies on the epidemiology, diagnosis, pathogenesis, susceptibility, and molecular basis of resistance to antifungal drugs and infection control measures to combat the spread of C. auris infections in healthcare facilities. Particular emphasis is given to interventions aiming to prevent new infections in healthcare facilities, including the screening of susceptible patients for colonization; the cleaning and decontamination of the environment, equipment, and colonized patients; and successful approaches to identify and treat infected patients, particularly during outbreaks.

Development and standardization of a specific real-time PCR assay for the rapid detection of Candida auris

Candida auris is an emerging multiresistant pathogen causing nosocomial fungal infection. Specific detection and identification are necessary. Our goal is to develop a new qPCR system that enables rapid detection of C. auris, based on a GPI (glycosyl-phosphatidylinositol) protein-encoding gene. This system is reproducible and sensitive with a limit of detection of 13 C. auris CFU/qPCR reaction. The 100% specificity of this system is confirmed on 2073 clinical and environmental samples, 50 different bacterial species, and 9 Candida spp. (70 strains). This system is suitable to correctly identify C. auris infections and to trace its source.

Molecular Diagnosis of Yeast Infections

PURPOSE OF REVIEW

The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing).

RECENT FINDINGS

Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny.

SUMMARY

Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.

Candida duobushaemulonii: An Old But Unreported Pathogen

Candidiasis caused by species of the Candida haemulonii complex (Candida haemulonii and Candida duobushaemulonii) and closely related species, Candida auris and Candida pseudohaemulonii are increasing. These species often show reduced susceptibility to antifungal drugs, such as azoles and amphotericin B or, less frequently, echinocandins. However, conventional phenotypic identification methods are unable to accurately differentiate these species and, therefore, their prevalence may have been underestimated. In this study, 150 isolates that were probably misidentified were reanalyzed using two novel PCR approaches. We found that one isolate previously identified in 1996 as Candida intermedia was C. duobushaemulonii, being one of the oldest isolates of this species described to date. We also found that this isolate had reduced susceptibility to fluconazole, itraconazole, and amphotericin B.

Identification of Candida auris and related species by multiplex PCR based on unique GPI protein-encoding genes

BACKGROUND

The pathogen Candida auris is rapidly gaining clinical importance because of its resistance to antifungal treatments and its persistence in hospital environments. Early and accurate diagnosis of C. auris infections is crucial, and however, the fungus has often been misidentified by commercial systems.

OBJECTIVES

To develop conventional and real-time PCR methods for accurate and rapid identification of C. auris and its discrimination from closely related species by exploiting the uniqueness of certain glycosylphosphatidylinositol (GPI)-modified protein-encoding genes.

METHODS

Species-specific primers for two unique putative GPI protein-encoding genes per species were designed for C. auris, C. haemulonii, C. pseudohaemulonii, C. duobushaemulonii, C. lusitaniae and C. albicans. Primers were blind tested for their specificity and efficiency in conventional and real-time multiplex PCR set-up.

RESULTS

All primers combinations showed excellent species specificity. In multiplex mode, correct identification was aided by different-sized amplicons for each species. Efficiency of the C. auris primers was validated using a panel of 155 C. auris isolates, including all known genetically diverse clades. In real-time multiplex PCR, different melting points of the amplicons allowed the distinction of C. auris from four related species. C. auris limit of detection was 5 CFU/reaction with a threshold value of 32. The method was also able to detect C. auris in spiked blood and serum.

CONCLUSIONS

PCR identification based on unique GPI protein-encoding genes allows for accurate and rapid species identification of C. auris and related species without need for expensive equipment when applied in conventional PCR set-up.

Candida auris Direct Detection from Surveillance Swabs, Blood, and Urine Using a Laboratory-Developed PCR Method

Candida auris is an emerging fungal pathogen with cases reported in countries around the world and in 19 states within the United States as of August 2020. The CDC has recommended that hospitals perform active surveillance upon admission for patients with the appropriate risk factors. Currently, active surveillance requires that local hospitals send surveillance swabs to a public health laboratory for analysis. In this work, a real-time PCR assay was developed for the specific detection of C. auris from surveillance swabs, blood, and urine to enable rapid detection of this pathogen. The assay uses commercially available primers and reporter probes and it was verified on the LightCycler 480 PCR platform. Contrived specimens and prospectively collected composite groin/axilla surveillance swabs were used to validate the assay. The performance of the PCR assay on surveillance swabs was also compared to a second PCR assay targeting C. auris that was performed at the Minnesota Department of Health–Public Health Laboratory (MDH-PHL). Our PCR assay is able to detect and differentiate C. auris from closely related Candida species such as C. duobushaemulonii, C. haemulonii, and C. pseudohaemulonii on the basis of melting curve temperature differences.

Diagnosis of Breakthrough Fungal Infections in the Clinical Mycology Laboratory: An ECMM Consensus Statement

Breakthrough invasive fungal infections (bIFI) cause significant morbidity and mortality. Their diagnosis can be challenging due to reduced sensitivity to conventional culture techniques, serologic tests, and PCR-based assays in patients undergoing antifungal therapy, and their diagnosis can be delayed contributing to poor patient outcomes. In this review, we provide consensus recommendations on behalf of the European Confederation for Medical Mycology (ECMM) for the diagnosis of bIFI caused by invasive yeasts, molds, and endemic mycoses, to guide diagnostic efforts in patients receiving antifungals and support the design of future clinical trials in the field of clinical mycology. The cornerstone of lab-based diagnosis of breakthrough infections for yeast and endemic mycoses remain conventional culture, to accurately identify the causative pathogen and allow for antifungal susceptibility testing. The impact of non-culture-based methods are not well-studied for the definite diagnosis of breakthrough invasive yeast infections. Non-culture-based methods have an important role for the diagnosis of breakthrough invasive mold infections, in particular invasive aspergillosis, and a combination of testing involving conventional culture, antigen-based assays, and PCR-based assays should be considered. Multiple diagnostic modalities, including histopathology, culture, antibody, and/or antigen tests and occasionally PCR-based assays may be required to diagnose breakthrough endemic mycoses. A need exists for diagnostic tests that are effective, simple, cheap, and rapid to enable the diagnosis of bIFI in patients taking antifungals.

Diagnostic Mycology: Xtreme Challenges

Developing any diagnostic assay that receives United States Food and Drug Administration (FDA) approval can be a slow and difficult process. FDA-approved assays for fungal diagnosis are generally few in number and are focused mainly on diagnosing candidiasis, which is caused by several species of Candida, in addition to a limited number of systemic mycotic agents. While all microbial diagnostic assays face challenges before they are FDA approved and reach the market, there are a number of challenges to fungal diagnostic assay development that have been difficult hurdles to overcome. These hurdles include template preparation, fungal morphology, how many fungi should be identified in a single assay (scope), taxonomy and nomenclature, discriminating colonizers from invasive infection, combining identification with antifungal susceptibility, and navigating the administrative hurdles required to integrate an assay into a clinical laboratory. Some of these challenges are easier to overcome than others, but all seem to be particularly difficult for fungal diagnostic assays.

Candida auris, an Agent of Hospital-Associated Outbreaks: Which Challenging Issues Do We Need to Have in Mind?

The emergence of Candida auris is considered as one of the most serious problems associated with nosocomial transmission and with infection control practices in hospital environment. This multidrug resistant species is rapidly spreading worldwide, with several described outbreaks. Until now, this species has been isolated from different hospital surfaces, where it can survive for long periods. There are multiple unanswered questions regarding C. auris, such as prevalence in population, environmental contamination, effectiveness of infection prevention and control, and impact on patient mortality. In order to understand how it spreads and discover possible reservoirs, it is essential to know the ecology, natural environment, and distribution of this species. It is also important to explore possible reasons to this recent emergence, namely the environmental presence of azoles or the possible effect of climate change on this sudden emergence. This review aims to discuss some of the most challenging issues that we need to have in mind in the management of C. auris and to raise the awareness to its presence in specific indoor environments as hospital settings.

Candida auris: A Review of Recommendations for Detection and Control in Healthcare Settings

Candida auris is an emerging multidrug-resistant fungal pathogen. Since first reported in 2009, C. auris has caused healthcare outbreaks around the world, often involving high mortality. Identification of C. auris has been a major challenge as many common conventional laboratory methods cannot accurately detect it. Early detection and implementation of infection control practices can prevent its spread. The aim of this review is to describe recommendations for the detection and control of C. auris in healthcare settings.

Identification of Candida auris by Use of the Updated Vitek 2 Yeast Identification System, Version 8.01: a Multilaboratory Evaluation Study

Candida auris is an emerging multidrug-resistant yeast that has been systematically incorrectly identified by phenotypic methods in clinical microbiology laboratories. The Vitek 2 automated identification system (bioMérieux) recently included C. auris in its database (version 8.01). We evaluated the performance of the Vitek 2 YST ID card to identify C. auris and related species. A panel of 44 isolates of Candida species (C. auris, n = 35; Candida haemulonii, n = 5; Candida duobushaemulonii, n = 4) were tested by three different hospital-based microbiology laboratories. Among 35 isolates of C. auris, Vitek 2 yielded correct identification in an average of 52% of tested samples. Low-discrimination (LD) results with an inability to distinguish between C. auris, C. duobushaemulonii, and Candida famata were obtained in an average of 27% of samples. Incorrect identification results were obtained in an average of 21% of samples, the majority (91%) of which were reported as C. duobushaemulonii and the remaining 9% of which were reported as Candida lusitaniae /C. duobushaemulonii. The proportion of correct identification was not statistically different across different centers (P = 0.78). Stratification by genetic clades demonstrated that 100% (n = 8) of the strains of the South American clade were correctly identified compared to 7% (n = 10) and 0% (n = 4) from the African and East Asian clades, respectively. None of the non-auris Candida strains (n = 9) were incorrectly identified as C. auris Our results show that the Vitek 2 (version 8.01) yeast identification system has a limited ability to correctly identify C. auris These data suggest that an identification result for C. duobushaemulonii should warrant further testing to rule out C. auris The overall performance of the Vitek 2 seems to differ according to C. auris genetic clade, with the South American isolates yielding the most accurate results.

Identification of Mycoses in Developing Countries

Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.

A Rapid and Automated Sample-to-Result Candida auris Real-Time PCR Assay for High-Throughput Testing of Surveillance Samples with the BD Max Open System

The multidrug-resistant yeast pathogen Candida auris continues to cause outbreaks and clusters of clinical cases worldwide. Previously, we developed a real-time PCR assay for the detection of C. auris from surveillance samples (L. Leach, Y. Zhu, and S. Chaturvedi, J Clin Microbiol 56:e01223-17, 2018, https://doi.org/10.1128/JCM.01223-17). The assay played a crucial role in the ongoing investigations of the C. auris outbreak in New York City. To ease the implementation of the assay in other laboratories, we developed an automated sample-to-result real-time C. auris PCR assay using the BD Max open system. We optimized sample extraction at three different temperatures and four incubation periods. Sensitivity was determined using eight pools of patient samples, and specificity was calculated using four clades of C. auris and closely and distantly related yeasts. Three independent extractions and testing of two patient sample pools in quadruplicate yielded assay precision. BD Max optimum assay conditions were as follows: DNA extraction at 75°C for 20 min and the use of PerfeCTa multiplex quantitative PCR (qPCR) ToughMix. The limit of detection (LOD) of the assay was one C. auris CFU/PCR. We detected all four clades of C. auris without cross-reactivity to other yeasts. Of the 110 patient surveillance samples tested, 50 were positive for C. auris using the BD Max system with 96% clinical sensitivity and 94% accuracy compared to the results of the manual assay. The BD Max assay allows high-throughput C. auris screening of 180 surveillance samples in a 12-h workday.

Molecular Diagnostics in the Times of Surveillance for Candida auris

Recently, global health professionals have been significantly challenged by the emergence of Candida auris and its propensity to colonize human skin, persist in the healthcare environment, and cause healthcare-associated outbreaks. Additionally, C. auris isolates are often characterized by elevated minimal inhibitory concentration (MIC) values for antifungal drugs. Thus, rapid detection and accurate identification of C. auris together with an assessment of potential antifungal drug resistance has become essential for effective patient management, and infection prevention and control in healthcare facilities. Surprisingly, almost all of the commonly available diagnostic tools rely on recovery (growth) of yeast colonies from collected samples, which delays the diagnostic result by several days or longer. To circumvent these issues, molecular-based DNA amplification assays have been developed to identify C. auris DNA directly from patient samples. Moreover, allele discriminating detection probes can be used to rapidly assess validated mechanisms of echinocandin and azole resistance.

Identification of Drug Resistant Candida auris

Candida auris is a multidrug resistant yeast, recognized as a cause of invasive infections and health care associated outbreaks around the world. C. auris is of great public health concern, due to its propensity for drug resistance, mode and pace of its transmission, and the possibility that biologic and epidemiologic factors could exacerbate worldwide emergence of C. auris infections. Currently, outbreak response is complicated by limited treatment options and inadequate disinfection strategies, as well as by issues (misidentification, long turnaround time) associated with application of commonly used diagnostic tools. Misdiagnosis of C. auris is common since many diagnostic platforms available in clinical and public health laboratories depend on reference databases that have not fully incorporated C. auris. Moreover, the correlation between minimal inhibitory concentration values (MICs) and clinical outcomes is poorly understood resulting in the absence of C. auris-specific breakpoints. New, accurate and fast diagnostic methods have emerged to facilitate effective patient management and improve infection control measures, ultimately reducing the potential for C. auris transmission. This review provides an overview of available C. auris detection/identification and antifungal susceptibility determination methods and discusses their advantages and limitations. A special emphasis has been placed on culture-independent methods that have recently been developed and offer faster turnaround times.

A TaqMan Probe-Based Real-Time PCR Assay for the Rapid Identification of the Emerging Multidrug-Resistant Pathogen Candida auris on the BD Max System

Candida auris is an emerging multidrug-resistant fungal pathogen that has been associated with nosocomial bloodstream and deep wound infections causing a high mortality rate mainly in intensive care unit (ICU) patients. Laboratories currently rely on phenotypic testing using commercial automated systems for identification of yeasts; however, this technique has often led to misidentification of C. auris to other closely related species. We developed and validated a TaqMan-based real-time PCR assay on the BD Max platform targeting ribosomal DNA (rDNA) region nucleotide sequences to quickly and accurately test for C. auris infection from culture and clinical specimens. The assay is highly specific, reproducible, and sensitive, allowing detection of as low as 1 C. auris CFU per reaction within 3 h.

Attack, Defend and Persist: How the Fungal Pathogen Candida auris was Able to Emerge Globally in Healthcare Environments

Within a decade after its first description, the multidrug-resistant yeast Candida auris has emerged globally as a nosocomial pathogen causing difficult to control outbreaks. This, together with the alarmingly high mortality rate of up to 66% associated with C. auris candidemia, calls for a better understanding of its virulence traits and routes of transmission. Unlike other clinically relevant Candida species, C. auris seems to have the unique ability to be easily transmitted between patients. Although initially thought to express fewer virulence traits than Candida albicans, recent genomic insights suggest C. auris to possess these traits to a much more similar extent. This review highlights the virulence traits C. auris expresses to attack the host, defend itself against antimicrobial agents and to persist within the healthcare environment.