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.

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.

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.

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.