The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

Elevated incidence of blastomycosis in Ontario calls for diagnostic vigilance.

Trichophyton indotineae is an emerging fungal pathogen capable of causing extensive recalcitrant dermatophytosis exacerbated by frequently retained terbinafine resistance. Cases of dermatophytosis due to T. indotineae have increased dramatically in India in recent years. Other countries have reported imported infection cases, causing public health concerns over the potential global spread of this drug-resistant pathogen. We describe T. indotineae from 47 clinical cases in Ontario, Canada, from 2014 to 2023, based on 50 isolates received by the provincial public health laboratory. Although detected in Ontario as early as 2014, cases increased sharply in 2022–2023. The majority of cases were found in 20 to 64-year-olds (83.0%). Cases from 2022 to 2023 were noted in only 8 of 34 public health units, clustering in large urban centers. Based on genomic epidemiology, Ontario isolates were genetically similar to isolates from other countries. Neither temporal nor geographic clustering based on country or public health unit was observed, suggesting Ontario cases represented recent introductions from endemic regions, although limited local transmission cannot be ruled out. Genome diversity (4.4 × 10 ⁻⁶ ) was extremely low, consistent with the hypothesized recent emergence and clonal population structure of T. indotineae . Most (71.4%) cases were terbinafine-resistant, with isolates exhibiting either the L393F/L393S ( n = 3) or F397L ( n = 27) squalene epoxidase substitution. Decreased susceptibility to itraconazole or voriconazole was found among 23.7% of isolates and was frequently associated with CYP51B gene duplication. Terbinafine-resistant T. indotineae infections are escalating in Ontario, meriting enhanced laboratory detection methods and public health efforts to increase the awareness of recalcitrant dermatophytoses in order to promptly initiate appropriate treatment and control transmission. IMPORTANCE: Cases of dermatophytosis caused by emerging pathogen Trichophyton indotineae are increasing worldwide. Many are resistant to first-line treatment option terbinafine, resulting in difficult-to-treat cases. We describe the emergence of cases of T. indotineae infections in Ontario, Canada. The incidence in primarily urban centers increased dramatically in 2022–2023, with a large percentage of isolates resistant to terbinafine. Decreased susceptibility to azoles was also observed for some isolates, raising concern over the potential evolution of multi-drug resistance. Ontario T. indotineae isolates were genetically similar to those from disparate locales worldwide, signifying the global nature of this public health concern. Together with other reports, this study serves to raise public health awareness to promote better laboratory detection procedures, prompt appropriate treatment of recalcitrant dermatophytoses, and inform infection prevention and control measures.

Staphylococcus argenteus is a newly described species, formerly known as S. aureus clonal complex 75 (CC75). Here, we describe the largest collection of S. argenteus isolates in North America, highlighting identification challenges.

Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses.

To understand the epidemiology and susceptibility patterns of yeast infections in Ontario, Canada, we examined 4,715 clinical yeast isolates submitted to our laboratory for antifungal susceptibility testing from 2014 to 2018. Candida albicans was the most frequently submitted species (43.0%), followed by C. glabrata (21.1%), C. parapsilosis (15.0%), and C. tropicalis (6.2%). Twenty-three other Candida spp.