EUCAST and CLSI: How to Assess in Vitro Susceptibility and Clinical Resistance

There are two different approved reference procedures based on microdilution techniques for antifungal susceptibility testing (AFST) of fungal species, the CLSI and the EUCAST procedures. Although there have always been some methodological differences between them, AFST results are comparable. In addition, current breakpoints values of antifungal compounds to interpret AFST results set by both institutions are very similar with some exceptions. Experts advised AFST should be done with validated commercial techniques for a routine daily practice and discrepant results should be confirmed by reference procedures particularly for isolates with borderline/resistant MIC values. Reference methods by EUCAST and CLSI should be also used in periodical epidemiological studies, to evaluate new antifungal agents, new methods of AFST and to know the susceptibility profile of rare and emerging fungal species.     

Ecology of <Emphasis Type="Italic">Scedosporium</Emphasis> Species: Present Knowledge and Future Research

The genus Scedosporium, which comprises at least five clinically relevant species, i.e. Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum, Scedosporium dehoogii and Scedosporium minutisporum, ranks the second among the filamentous fungi colonizing the airways of patients with cystic fibrosis (CF). This colonization of the airways is thought to contribute to the inflammatory reaction leading to a progressive deterioration of the lung function. Additionally, these colonizing fungi may lead to severe disseminated infections in case of lung transplantation. Therefore, considering the low susceptibility of Scedosporium species to all current antifungal drugs, preventive measures should be defined to reduce the risk of exposure to these fungi for non-colonized CF patients. With this in mind, several studies have been conducted to elucidate the ecology of these fungi and to define possible sources of patient contamination. This review will summarize the major outcomes of those studies, including: the clear demonstration that ecological niches of Scedosporium species are strongly impacted by human activities, and the ability of Scedosporium species to degrade aliphatic and aromatic pollutants which supports the high occurrence of these species in contaminated soils and polluted waters and makes them promising candidates for bioremediation purposes. Finally, prospects for future research in this field are proposed.     

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets.     

Eighty Years of <Emphasis Type="Italic">Mycopathologia</Emphasis>: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens

Mycopathologia was founded in 1938 to ‘diffuse the understanding of fungal diseases in man and animals among mycologists.’ This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5–5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of ‘classic papers’ since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host–pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other’s language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.     

Wild Boar (Sus scrofa) as Reservoir of Zoonotic Yeasts: Bioindicator of Environmental Quality

Mycopathologia - Wildlife animals are recognized as reservoirs for zoonotic fungi and their faeces might play an important role in introducing pathogens into the environment. Thought wild boar (Sus...     

Diversity of coelomycetous fungi in human infections: A 10-y experience of two European reference centres

The coelomycetous fungi are difficult to properly identify from their phenotypic characterization and their role as etiologic agents of human infections is not clear. We studied the species distribution of these fungi among clinical isolates that had been collected and stored over a ten-year period in two European reference laboratories (France and Spain). We identified phenotypically and molecularly 97 isolates by sequencing the D1-D2 fragment of the 28S nrRNA (LSU) gene and we provided the in vitro antifungal susceptibility pattern of seven antifungals against 46 isolates. Species of the orders Pleosporales and Glomerellales were present in both collections, and Botryosphaeriales and Diaporthales only in the French one. The most prevalent species were Medicopsis romeroi, Neocucurbitaria keratinophila, Neocucurbitaria unguis-hominis and Paraconiothyrium cyclothyrioides, which had been recovered primarily from superficial tissues. The Didymellaceae was the most common family represented, with 27 isolates distributed into five genera. Most of the isolates tested were susceptible to antifungals, and only the geometric mean (GM) and minimal inhibitory concentration (MIC) values of itraconazole and caspofungin had higher values. This study provides a good picture of the great diversity of coelomycetous fungi in the European clinical context, and the basis for future studies on this interesting but neglected group of fungi.     

Case Series Study of Invasive Pulmonary Aspergillosis

Diagnosis of invasive pulmonary aspergillosis (IPA) is challenging. The objective of the study was to assess the value of microbiological tests to the diagnosis of IPA in the absence of non-specific radiological data. A retrospective study of 23 patients with suspicion of IPA and positivity of some microbiological diagnostic tests was performed. These tests included conventional microbiological culture, detection of Aspergillus galactomannan (GM) antigen and in some patients (1 → 3)-β-d-glucan (BDG) and Aspergillus fumigatus DNA using the LightCycler^® SeptiFast test. In 10 patients with hematological malignancy, 6 cases were considered ‘probable’ and 4 ‘non-classifiable.’ In 8 patients with chronic lung disease, 7 cases were classified as ‘probable’ and 1 as ‘proven,’ and in 5 patients with prolonged ICU stay (>7 days), there were 2 ‘proven’ cases, 2 ‘non-classifiable’ and 1 putative case. Microbiological culture was positive in 17 cases and 18 Aspergillus spp. were isolated (one mixed culture). A. fumigatus was the most frequent (44.4%) followed by A. tubingensis. The Aspergillus galactomannan (GM) antigen assay was positive in 21 cases (91.3%). The GM antigen and the (1 → 3)-β-d-glucan (BDG) assays were both performed in 12 cases (52.2%), being positive in 9. The SeptiFast test was performed in 7 patients, being positive in 4. In patients with non-classifiable pulmonary aspergillosis and one or more positive microbiological tests, radiological criteria may not be considered a limiting factor for the diagnosis of IPA.