Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses

Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. aurisIMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

Contact lens associated keratitis due to Tintelnotia destructans

We report the first case of Tintelnotia destructans associated keratitis in a contact lens wearer in Australia. Corneal scrape showed fungal elements on direct microscopy leading to a prompt diagnosis of fungal keratitis and early topical and systemic antifungal therapy. The isolate was eventually identified by ITS gene sequencing. This case highlights the importance of accurate identification and antifungal susceptibility testing for the management of fungal keratitis.

Epidemiology and antifungal susceptibility patterns of candidemia from a tertiary centre in Western Australia

Candidemia is a common invasive fungal infection with a high mortality rate. We performed a retrospective audit of candidemia at a tertiary centre in Western Australia, 2005-2014. There were 167 episodes of candidemia due to 173 isolates of Candida. Candida albicans (40.5%), Candida glabrata complex (30.6%), Candida parapsilosis complex (14.4%) were the most common species causing candidemia across the study. Of the tested isolates, 17.7% (11/62) were non-susceptible to fluconazole and 13.6% (9/66) non-susceptible to caspofungin. 22.8% (8/35) C. glabrata complex were fluconazole resistant and 17.1% (6/35) were non-susceptible to caspofungin. Candida glabrata complex was more common in the latter time period, but there were no susceptibility changes over time. In our setting, the prevalence of C. glabrata complex and antifungal non-susceptibility is high, and the prevalence of C. glabrata complex is increasing.

Malignant otitis externa caused by Malassezia sympodialis

BACKGROUND

Malignant otitis externa caused by fungal infections is rare. A review of the literature showed only 9 cases, and the causative fungus in all cases was Aspergillus. This article reports an unusual case caused by Malassezia sympodialis.

METHODS

A 53-year-old man with non-insulin dependent diabetes presented with malignant otitis externa. He deteriorated despite treatment with intravenous antipseudomonal therapy and surgical debridement. Microbiologic tests revealed M. sympodialis. He responded rapidly to intravenous amphotericin.

RESULTS

Systemic human infections caused by M. sympodialis have not been reported. M. furfur systemic infection is rare and has been associated lipid hyperalimentation by means of a central catheter. Only 1 other case of M. fungemia without these associated risk factors has been reported.

CONCLUSIONS

The first case of malignant otitis externa caused by M. sympodialis is presented. It highlights the difficulty of initial biologic diagnosis and the need for lipid-enriched media to grow this fastidious organism.