Infections of the skin, hair and nails by dermatophyte fungi are common in developed and developing countries alike. However, the species involved and the resulting clinical entities vary both geographically and with time. We have surveyed 15,333 dermatophytes obtained from primary isolations at the Mycology Reference Laboratory, Bristol, UK from 1980 through 2005. Several striking trends in dermatophyte prevalence were apparent over this period. The relative frequencies of isolations of Microsporum canis (cat and dog ringworm), Trichophyton verrucosum (cattle ringworm), T. mentagrophytes var. mentagrophytes (rodent ringworm) and Epidermophyton floccosum (a cause of human groin and foot infections) all decreased by 90%. Conversely, the contributions of T. tonsurans and T. violaceum (two anthropophilic scalp-infecting species) to total dermatophyte isolations increased by 1000% over the same period. Finally, T. rubrum and T. mentagrophytes var. interdigitale, the two common causes of foot infection comprised 80% of all dermatophytes isolated in 1980 and 90% of isolations in 2005. Similar trends in dermatophyte prevalence were evidenced throughout the British Isles, based on the voluntary reporting of isolations from a large number of British laboratories at 5-yearly intervals over the same period. The implications of these changing patterns of dermatophyte species, and the clinical entities they produce are discussed in the context of a review of worldwide dermatophyte isolations over the last three decades, with emphasis on the causal agents of tinea capitis.

COVID-19 associated pulmonary aspergillosis (CAPA) was recently reported as a potential infective complication affecting critically ill patients with acute respiratory distress syndrome following SARS-CoV-2 infection, with incidence rates varying from 8 to 33% depending on the study. However, definitive diagnosis of CAPA is challenging. Standardised diagnostic algorithms and definitions are lacking, clinicians are reticent to perform aerosol-generating bronchoalveolar lavages for galactomannan testing and microscopic and cultural examination, and questions surround the diagnostic sensitivity of different serum biomarkers. Between 11th March and 14th July 2020, the UK National Mycology Reference Laboratory received 1267 serum and respiratory samples from 719 critically ill UK patients with COVID-19 and suspected pulmonary aspergillosis. The laboratory also received 46 isolates of Aspergillus fumigatus from COVID-19 patients (including three that exhibited environmental triazole resistance). Diagnostic tests performed included 1000 (1-3)-β-d-glucan and 516 galactomannan tests on serum samples. The results of this extensive testing are presented here. For a subset of 61 patients, respiratory specimens (bronchoalveolar lavages, tracheal aspirates, sputum samples) in addition to serum samples were submitted and subjected to galactomannan testing, Aspergillus-specific PCR and microscopy and culture. The incidence of probable/proven and possible CAPA in this subset of patients was approximately 5% and 15%, respectively. Overall, our results highlight the challenges in biomarker-driven diagnosis of CAPA especially when only limited clinical samples are available for testing, and the importance of a multi-modal diagnostic approach involving regular and repeat testing of both serum and respiratory samples.

Rapid and accurate identification of yeast isolates from clinical samples is essential, given their innately variable antifungal susceptibility profiles, and the proposal of species-specific antifungal susceptibility interpretive breakpoints. Here we have evaluated the utility of MALDI-ToF MS analysis for the identification of clinical isolates of pathogenic yeasts. A simplified, rapid extraction method, developed in our laboratory, was applied to 6343 isolates encompassing 71 different yeast species, which were then subjected to MALDI-ToF MS analysis using a Bruker Microflex and the resulting spectra were assessed using the supplied Bruker database. In total, 6328/6343 (99.8%) of isolates were correctly identified by MALDI-ToF MS. Our simplified extraction protocol allowed the correct identification of 93.6% of isolates, without the need for laborious full extraction, and a further 394 (6.2%) of isolates could be identified after full extraction. Clinically relevant identifications with both extraction methods were achieved using the supplied Bruker database and did not require the generation of bespoke, in-house databases created using profiles obtained with the adapted extraction method. In fact, the mean LogScores obtained using our method were as robust as those obtained using the recommended, published full extraction procedures. However, an in-house database can provide a useful additional identification tool for unusual or rarely encountered organisms. Finally, the proposed methodology allowed the correct identification of over 75% of isolates directly from the initial cultures referred to our laboratory, without the requirement for additional sub-culture on standardised mycological media.

is a ubiquitous pleomorphic genus comprising at least 40 species, many of which have been associated with superficial, visceral, or systemic infections in humans, other mammals, or cold-blooded animals. In this study, we investigated the potential of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for the identification of species. A total of 89 isolates (including 50 human and 4 animal clinical isolates) stored in the National Collection of Pathogenic Fungi were identified by PCR amplification and sequencing of internal transcribed spacer region 1. Eighty-three of the isolates corresponded to 16 known species within The remaining six isolates are shown by phylogenetic analyses based on four loci to represent two novel species. Four isolates from domestic bathrooms which form a sister species with are described here as sp. nov. The remaining two isolates, both from subcutaneous infections, are distantly related to and are described here as sp. nov. The triazoles and terbinafine exhibited low MICs against all isolates MALDI-TOF MS successfully distinguished all 18 species and identified all isolates after appropriate reference spectra were created and added to commercial databases. Intraspecific mean log scores ranged from 1.786 to 2.584 and were consistently significantly higher than interspecific scores (1.193 to 1.624), with the exception of and , for which there was considerable log score overlap. In summary, MALDI-TOF MS allows the rapid and accurate identification of a wide range of clinically relevant species.

For filamentous fungi (moulds), species-specific interpretive breakpoints and epidemiological cut-off values (ECVs) have only been proposed for a limited number of fungal species–antifungal agent combinations, with the result that clinical breakpoints are lacking for most emerging mould pathogens. In the current study, we have compiled minimum inhibitory concentration (MIC) data for 4869 clinical mould isolates and present full MIC distributions for amphotericin B, itraconazole, voriconazole, posaconazole, and caspofungin with these isolates which comprise 20 species/genera. In addition, we present the results of an assessment of the fungicidal activity of these same five antifungal agents against a panel of 123 mould isolates comprising 16 of the same species.

Candida auris is a serious nosocomial health risk, with widespread outbreaks in hospitals worldwide. Successful management of such outbreaks has depended upon intensive screening of patients to identify those that are colonized and the subsequent isolation or cohorting of affected patients to prevent onward transmission. Here we describe the evaluation of a novel chromogenic agar, CHROMagarTM Candida Plus, for the specific identification of Candida auris isolates from patient samples. Candida auris colonies on CHROMagarTM Candida Plus are pale cream with a distinctive blue halo that diffuses into the surrounding agar. Of over 50 different species of Candida and related genera that were cultured in parallel, only the vanishingly rare species Candida diddensiae gave a similar appearance. Moreover, both the rate of growth and number of colonies of C. auris recovered from swabs of pure and mixed Candida species were substantially increased on CHROMagarTM Candida Plus agar when compared with growth on the traditional mycological isolation medium, Sabouraud dextrose agar. Taken together, the present data suggest that CHROMagarTM Candida Plus agar is an excellent alternative to current conventional mycological media for the screening of patients who are potentially colonized/infected with Candida auris, can be reliably used to identify this emerging fungal pathogen, and should be tested in a clinical setting. Lay Abstract Candida auris is a novel pathogenic yeast that has been associated with large hospital outbreaks across several continents. Affected patients become colonized, predominantly on the skin, with large quantities of C. auris which they then shed into the hospital environment. Identification of C. auris is challenging using routine laboratory methods, and time consuming when patients are colonized with a mixture of different Candida species. Here we demonstrate that a novel chromogenic agar, CHROMagarTM Candida Plus, permits the rapid differentiation of C. auris from a wide range of other yeast species and is potentially ideally suited to screening of patients that are suspected of being colonized or infected with this medically important yeast.

Background Epidemiological cut-off values and clinical interpretive breakpoints have been developed for a number of antifungal agents with the most common Candida species that account for the majority of infections due to pathogenic yeasts species. However, less-common species, for which susceptibility data are limited, are increasingly reported in high-risk patients and breakthrough infections. Methods The UK National Mycology Reference Laboratory performs routine antifungal susceptibility testing of clinical yeast isolates submitted from across the UK. Between 2002 and 2016, >32 000 isolates representing 94 different yeast species were referred to the laboratory. Here we present antifungal susceptibility profiles generated over this period for amphotericin B, fluconazole, voriconazole, itraconazole, anidulafungin and flucytosine against 35 species of uncommon yeast using CLSI methodologies. MIC data were interpreted against epidemiological cut-off values and clinical breakpoints developed with Candida albicans, in order to identify species with unusually skewed MIC distributions that potentially indicate resistance. Results Potential resistance to at least one antifungal agent (>10% of isolates with MICs greater than the epidemiological cut-off or clinical breakpoint) was evidenced for 29/35 species examined here. Four species exhibited elevated MICs with all of the triazole antifungal drugs against which they were tested, and 21 species exhibited antifungal resistance to agents from at least two different classes of antifungal agent. Conclusions This study highlights a number of yeast species with unusual MIC distributions and provides data to aid clinicians in deciding which antifungal regimens may be appropriate when confronted with infections with rarer yeasts.

Eumycetoma, a chronic fungal infection endemic in India, Indonesia, and parts of Africa and South and Central America, follows traumatic implantation of saprophytic fungi and frequently requires radical surgery or amputation in the absence of appropriate treatment. Fungal species that can cause black-grain mycetomas include Madurella spp., Falciformispora spp., Trematosphaeria grisea, Nigrograna mackinnonii, Pseudochaetosphaeronema larense, Medicopsis romeroi, and Emarellia spp. Rhytidhysteron rufulum and Parathyridaria percutanea cause similar subcutaneous infections, but these infections lack the draining sinuses and fungal grains characteristic of eumycetoma. Accurate identification of the agents of subcutaneous fungal infection is essential to guide appropriate antifungal therapy. Since phenotypic identification of the causative fungi is often difficult, time-consuming molecular approaches are currently required. In the study described here we evaluated whether matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry might allow the accurate identification of eumycetoma agents and related fungi. A panel of 57 organisms corresponding to 10 different species from confirmed cases of eumycetoma and subcutaneous pedal masses, previously formally identified by PCR amplification and sequencing of internal transcribed spacer 1 (ITS1), was employed. Representative isolates of each species were used to create reference MALDI-TOF spectra, which were then used for the identification of the remaining isolates in a user-blinded manner. Here, we demonstrate that MALDI-TOF mass spectrometry accurately identified all of the test isolates, with 100%, 90.4%, and 67.3% of isolates achieving log scores greater than 1.8, 1.9, and 2.0, respectively. KEYWORDS black-grain mycetoma, Madurella, Pleosporales, Trematosphaeriaceae, Emarellia, Biatriospora, Rhytidhysteron, Medicopsis, Falciformispora, Exophiala, MALDI-TOF, Pleosporales B lack-grain eumycetoma is an ancient, debilitating fungal infection that is endemic in India, Indonesia, and parts of Africa and South America (1). Disease progression is protracted and results from the traumatic implantation of pigmented saprophytic fungi, usually on exposed body sites. The disease is characterized by a chronic progressive destruction of soft tissue and adjoining structures with associated tumefaction and the formation of purosanguineous sinuses that drain fungal grains (2-5). Without appropriate treatment, the infection eventually progresses to involve the skeletal system, and clinical and mycological cure is unlikely without extensive debridement/ amputation (2-5). The extruded grains are either pale or dark (black), depending on the etiological agent (4, 5). The principal etiological agents described to date include Madurella spp. (Sordariales); a host of fungi classified in the Pleosporales, including