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In New Delhi, India, candidemia affected 15 critically ill coronavirus disease patients admitted to an intensive care unit during April–July 2020. Candida auris accounted for two thirds of cases; case-fatality rate was high (60%). Hospital-acquired C. auris infections in coronavirus disease patients may lead to adverse outcomes and additional strain on healthcare resources.

The whole genome sequencing analysis of 20 T. indotineae strains demonstrate that this new species is distinct clonal offshoot of T. mentagrophytes/T. interdigitale spp. complex. [...]naming of this emerging antifungal-resistant species was essential as it could not be unambiguously identified as either T. mentagrophytes or T. interdigitale based on ITS sequencing, mycological and physiological characteristics. [...]in the last 5 years before labelling T. indotineae as a species de novo, studies based on rDNA ITS region sequencing identified Indian Trichophyton strains as T. mentagrophytes/interdigitale; further, Nenoff and colleagues grouped the strains as T. mentagrophytes Type VIII [3,4,6,26,32]. The BLAST searches of ITS sequences of T. indotineae on NCBI database still show ≥99% sequence similarity with T. mentagrophytes, T. interdigitale, and T. indotineae. [...]to obtain accurate identification (i.e., sequence similarity of 100% with T. indotineae), ITS sequences of well-defined reference strains described by Tang and colleagues [30], importantly, primary T. indotineae strains (NUBS19006 and NUBS19007), should be included in the analysis. Notably, TRB-resistant T. indotineae strains isolated from cases in Germany, Denmark, and Switzerland during 2016 to 2020 exhibited Phe397Leu and Leu393Phe amino acid substitutions that confer resistance to TRB [11,15,22,33]. Since 2018, several cases of clinically resistant tinea corporis with extensive lesions that do not respond to TRB have been reported from France [13,14].

During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.In this Review, Lockhart, Chowdhary and Gold discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, azole-resistant Aspergillus fumigatus and Trichophyton indotineae, with the common thread that all three are currently emerging across the globe and have a high rate of acquired resistance.

About the Authors: Anuradha Chowdhary * E-mail: dranuradha@hotmail.com Affiliation: Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India ORCID http://orcid.org/0000-0002-2028-7462 Cheshta Sharma Affiliation: Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India Jacques F. Meis Affiliations Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands, Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, the Netherlands ORCID http://orcid.org/0000-0003-3253-6080Citation: Chowdhary A, Sharma C, Meis JF (2017) Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. The species exhibits a close phylogenetic relationship to C. haemulonii and is differentiated based on sequence analysis of the D1/D2 domain of the large ribosomal subunit (LSU) of 26S rRNA gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon [23]. [...]Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is considered a more rapid and robust diagnostic technique for C. auris identification [9, 10, 13, 16]. Worldwide reports of Candida auris along with their misidentification using commercial systems and frequency of antifungal resistance. https://doi.org/10.1371/journal.ppat.1006290.t001 Does genetic predisposition make C. auris virulent? A recently published draft genome of C. auris shows that it has a genome size of approximately 12.3 Mb [26, 27]. The emerging Candida auris: characterization of growth phenotype, virulence factors, antifungal activity, and effect of SCY-078, a novel glucan synthesis inhibitor, on growth morphology and biofilm formation. Identification and typing of the emerging pathogen Candida auris by matrix-assisted laser desorption ionisation time of flight mass spectrometry...

  [...]50% of the patients with invasive aspergillosis due to ARAF are known to be azole naïve and the outcome of patients with azole-resistant invasive aspergillosis has been dismal, with a mortality rate of 88% [12]. [...]it would be beneficial to (i) have an active multi-azole susceptibility testing of A. fumigatus to monitor the extent of the problem, (ii) reduce agricultural use of triazole DMI fungicides, and (iii) use combination drug therapy when dealing with infections by A. fumigatus strains to limit the emergence of resistance.

Candida auris , is an emerging fungal pathogen that can cause life-threatening infections in humans. Unlike many other Candida species that colonize the intestine, C . auris most efficiently colonizes the skin. Such colonization contaminates the patient’s environment and can result in rapid nosocomial transmission. In addition, this transmission can lead to outbreaks of systemic infections that have mortality rates between 40% and 60%. C . auris isolates resistant to all known classes of antifungals have been identified and as such, understanding the underlying biochemical mechanisms of how skin colonization initiates and progresses is critical to developing better therapeutic options. With this review, we briefly summarize what is known about horizontal transmission and current tools used to identify, understand, and control C . auris infections.

Candida auris is a recently emerged multidrug-resistant fungal pathogen capable of causing severe infections in hospitalized patients. Despite its recognition as a human pathogen a decade ago, so far the natural ecological niche(s) of C. auris remains enigmatic. Candida auris is a multidrug resistant pathogen that presents a serious global threat to human health. As C. auris is a newly emerged pathogen, several questions regarding its ecological niche remain unexplored. While species closely related to C. auris have been detected in different environmental habitats, little is known about the natural habitat(s) of C. auris . Here, we explored the virgin habitats around the very isolated Andaman Islands in the Indian Ocean for evidence of C. auris . We sampled coastal wetlands, including rocky shores, sandy beaches, tidal marshes, and mangrove swamps, around the Andaman group of the Andaman & Nicobar Islands, Union Territory, in India. Forty-eight samples of sediment soil and seawater were collected from eight sampling sites representing the heterogeneity of intertidal habitats across the east and west coast of South Andaman district. C. auris was isolated from two of the eight sampling sites, a salt marsh and a sandy beach. Interestingly, both multidrug-susceptible and multidrug-resistant C. auris isolates were found in the sample. Whole-genome sequencing analysis clustered the C. auris isolates into clade I, showing close similarity to other isolates from South Asia. Isolation of C. auris from the tropical coastal environment suggests its association with the marine ecosystem. The fact that viable C. auris was detected in the marine habitat confirms C. auris survival in harsh wetlands. However, the ecological significance of C. auris in salt marsh wetland and sandy beaches to human infections remains to be explored. IMPORTANCE Candida auris is a recently emerged multidrug-resistant fungal pathogen capable of causing severe infections in hospitalized patients. Despite its recognition as a human pathogen a decade ago, so far the natural ecological niche(s) of C. auris remains enigmatic. A previous hypothesis suggested that C. auris might be native to wetlands, that its emergence as a human pathogen might have been linked to global warming effects on wetlands, and that its enrichment in that ecological niche was favored by the ability of C. auris for thermal tolerance and salinity tolerance. To understand the mystery of environmental niches of C. auris , we explored the coastal wetland habitat around the very isolated Andaman Islands in the Indian Ocean. C. auris was isolated from the virgin habitats of salt marsh area with no human activity and from a sandy beach. C. auris isolation from the marine wetlands suggests that prior to its recognition as a human pathogen, it existed as an environmental fungus.

Candida spp . infections are a major cause of morbidity and mortality in critically ill patients. Candida auris is an emerging multi-drug-resistant fungus that is rapidly spreading worldwide. Since the first reports in 2009, many isolates across five continents have been identified as agents of hospital-associated infections. Independent and simultaneous outbreaks of C. auris are becoming a major concern for healthcare and scientific community. Moreover, laboratory misidentification and multi-drug-resistant profiles, rarely observed for other non-albicans Candida species, result in difficult eradication and frequent therapeutic failures of C. auris infections. The aim of this review was to provide an updated and comprehensive report of the global spread of C. auris , focusing on clinical and microbiological characteristics, mechanisms of virulence and antifungal resistance, and efficacy of available control, preventive, and therapeutic strategies.

A severe outbreak of highly virulent and multi-resistant dermatophytosis by species in the Trichophyton mentagrophytes / T . interdigitale complex is ongoing in India. The correct identity of the etiologic agent is a much-debated issue. In order to define species limits, a taxonomic study was undertaken combining molecular, morphological, and physiological characteristics as evidence of classification. Molecular characteristics show that T. mentagrophytes s. str . and T. interdigitale s. str . can be distinguished with difficulty from each other, but are unambiguously different from the Indian genotype, T . indotineae by sequences of the HMG gene. The entities were confirmed by multilocus analysis using tanglegrams. Phenotypic characters of morphology and physiology are not diagnostic, but statistically significant differences are observed between the molecular siblings. These properties may be drivers of separate evolutionary trends. Trichophyton mentagrophytes represents the ancestral, homothallic cloud of genotypes with a probable geophilic lifestyle, while T . indotineae and T . interdigitale behave as anthropophilic, clonal offshoots. The origin of T . indotineae , which currently causes a significant public health problem, is zoonotic, and its emergence is likely due to widespread misuse of antifungals.

Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris . Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of health care facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting; therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a short tandem repeat (STR) typing assay for C. auris . STRs in C. auris were identified, and from an initial selection of 23 STRs, 12 were used to develop a STR typing assay. Having shown that the STR typing assay was reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis, we identified five major different C. auris clusters of South American, South Asian, African, East Asian, and Iranian origin. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the South Asian clade. Comparison with WGS demonstrated that isolates with <20 single nucleotide polymorphisms (SNPs) are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers. Altogether, a highly reproducible and specific STR typing assay for C. auris was developed; this assay distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing by >30 SNPs, as determined via WGS, are also separated. This new C. auris -specific genotyping technique is a rapid, reliable, and cost-effective alternative to WGS analysis to investigate outbreaks. IMPORTANCE Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris .