Environmental Screening for the <i>Scedosporium apiospermum</i> Species Complex in Public Parks in Bangkok, Thailand

<div><p>The <i>Scedosporium apiospermum</i> species complex, comprising filamentous fungal species <i>S</i>. <i>apiospermum</i> sensu stricto, <i>S</i>. <i>boydii</i>, <i>S</i>. <i>aurantiacum</i>, <i>S</i>. <i>dehoogii</i> and <i>S</i>. <i>minutispora</i>, are important pathogens that cause a wide variety of infections. Although some species (<i>S</i>. <i>boydii</i> and <i>S</i>. <i>apiospermum</i>) have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. <i>Scedosporium</i> species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29%) and 1 of 15 water samples (6.67%) were consistent with that of the <i>S</i>. <i>apiospermum</i> species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the <i>S</i>. <i>apiospermum</i> species complex were identified: <i>S</i>. <i>apiospermum</i> (71 isolates), <i>S</i>. <i>aurantiacum</i> (6 isolates) and <i>S</i>. <i>dehoogii</i> (5 isolates). In addition, 16 sequences could not be assigned to an exact <i>Scedosporium</i> species. According to our environmental survey, the <i>S</i>. <i>apiospermum</i> species complex is widespread in soil in Bangkok, Thailand.</p></div

Sample collection areas in Bangkok, Thailand.

<p>Sample collection areas in Bangkok, Thailand.</p

Colonies of <i>Scedosporium</i> on Scedo-Select III agar after inoculation of 100 μl of soil suspension from each sample and incubation at 35°C for 5 days.

<p>Colonies of <i>Scedosporium</i> on Scedo-Select III agar after inoculation of 100 μl of soil suspension from each sample and incubation at 35°C for 5 days.</p

Maximum-likelihood tree of β-tubulin gene sequences of <i>Scedosporium</i> isolates and reference strains.

<p>The tree recovered under the Tamura–Nei model with the highest log likelihood (−1,599.6719) is shown. The tree is drawn to scale, with branch lengths corresponding to the number of substitutions per site. Bootstrap values ≥ 50% (1,000 replicates) are shown above branches. Accession numbers of <i>Scedosporium</i> sequences retrieved from GenBank are shown in bold; accession numbers of standard strains are underlined. <i>Lomentospora prolificans</i> and <i>Pseudallescheria africana</i> were used as outgroups. Genus abbreviations are as follows: <i>L</i>, <i>Lomentospora</i>; <i>P</i>, <i>Pseudallescheria</i>, <i>S</i>, <i>Scedosporium</i>.</p

Protein domains most frequently found among the 25 top-ranked most promiscuous domains in all the fungal organisms.

<p>Domains marked with an asterisk had been previously identified as promiscuous in animals, plants and fungi <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003733#pcbi.1003733-Basu1" target="_blank">[37]</a>.</p

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

<div><p>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 <i>Aspergillus</i> 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.</p></div

Distribution of protein domains (A), domain architectures (B) and Pfam clans (C) shared between the fungal species included in this study and <i>Homo sapiens</i>.

<p>The category “fungi” refers to the set of 137 organisms analysed.</p

Distribution of Pfam domains and domain architectures per genus.

<p>In parenthesis, the number of species and the number of strains that belong to a given genus are indicated. The area occupied by each genus corresponds to the number of exclusive domain architectures, whereas the colour correlates with the number of exclusive domains present among those architectures (calculated as the number of domains divided by number of domain architectures).</p

Distribution of number of Pfam domains and domain architectures found for selected species.

<p>Distribution of number of Pfam domains and domain architectures found for selected species.</p

Protein domains found exclusively in proteins from the Groups 3 and 4 of clinical isolates.

<p>Protein domains found exclusively in proteins from the Groups 3 and 4 of clinical isolates.</p