Genome Anatomy of <i>Pyrenochaeta unguis-hominis</i> UM 256, a Multidrug Resistant Strain Isolated from Skin Scraping

<div><p><i>Pyrenochaeta unguis-hominis</i> is a rare human pathogen that causes infection in human skin and nail. <i>P</i>. <i>unguis-hominis</i> has received little attention, and thus, the basic biology and pathogenicity of this fungus is not fully understood. In this study, we performed in-depth analysis of the <i>P</i>. <i>unguis-hominis</i> UM 256 genome that was isolated from the skin scraping of a dermatitis patient. The isolate was identified to species level using a comprehensive multilocus phylogenetic analysis of the genus <i>Pyrenochaeta</i>. The assembled UM 256 genome has a size of 35.5 Mb and encodes 12,545 putative genes, and 0.34% of the assembled genome is predicted transposable elements. Its genomic features propose that the fungus is a heterothallic fungus that encodes a wide array of plant cell wall degrading enzymes, peptidases, and secondary metabolite biosynthetic enzymes. Antifungal drug resistance genes including <i>MDR</i>, <i>CDR</i>, and <i>ERG11/CYP51</i> were identified in <i>P</i>. <i>unguis-hominis</i> UM 256, which may confer resistance to this fungus. The genome analysis of <i>P</i>. <i>unguis-hominis</i> provides an insight into molecular and genetic basis of the fungal lifestyles, understanding the unrevealed biology of antifungal resistance in this fungus.</p></div

Classifications of fungal isolates.

<p>Bayesian tree generated with general time reversible (GTR) model space based on unique ITS1-5.8S-ITS2 gene sequences with two strains of <i>Saccharomyces boulardii</i> as out-group. Isolate sequence duplicates are listed in parentheses next to their representative. Clinical isolates from UMMC used in this study are printed in bold. Bayesian posterior probability values for every clustering are printed on each node.</p

<i>MAT1-2-1</i> gene of <i>P</i>. <i>unguis-hominis</i> UM256.

<p>Genes constituting the MAT locus: <i>MAT1-2-1</i> (UM256_7301), DNA lyase, <i>Apn2</i> (UM 256_7302) and cytochrome C oxidase subunit Vla, <i>Cox13</i> (UM256_7303).</p

List of <i>Pyrenochaeta</i> spp. fungus sequences (ITS, SSU, and LSU) obtained from NCBI and Q-bank for phylogenetic trees.

<p>List of <i>Pyrenochaeta</i> spp. fungus sequences (ITS, SSU, and LSU) obtained from NCBI and Q-bank for phylogenetic trees.</p

Microscopic features of dematiaceous fungi.

<p>(A-D) Macroconidia of <i>Curvularia</i>, <i>Bipolaris</i>, <i>Exserohilum</i> and <i>Alternaria</i> (E) Arthroconidia of <i>Neosyctalidium</i> (F) Globose chain conidia and ramoconidia of <i>Cladosporium</i> (G) conidia of <i>Daldinia</i> (H) Dark conidia of <i>Nigrospora</i> (I) <i>Chaetomium</i> perithecium covered with long setae and dark ascospores (J) Spine-like conidiophore and hyaline conidia of <i>Exophiala</i> (K) <i>Ochroconis</i> two-celled clavate conidia with cylindrical conidiophore. <i>Bars</i> 20 µm.</p

<i>In vitro</i> susceptibility of dematiaceous fungal isolates to antifungal agents, grouped according to MIC^a categories.

a<p>minimum inhibitory concentration.</p>b<p>Number of fungal isolates.</p>c<p>Amphotericin B.</p>d<p>Ketoconazole.</p>e<p>Fluconazole.</p>f<p>Itraconazole.</p>g<p>Voriconazole.</p>h<p>Posaconazole.</p>i<p>Anidulafungin.</p>j<p>Caspofungin.</p><p>MIC categories:</p><p>Category A: ≤1 µg/mL (FLC: ≤1 µg/mL).</p><p>Category B: >1–32 µg/mL (FLC: >1–256 µg/mL).</p><p>Category C: >32 µg/mL (FLC: >256 µg/mL).</p

Amino acid substitution detected in <i>ERG 11/CYP51</i> genes of <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>Amino acid substitution detected in <i>ERG 11/CYP51</i> genes of <i>P</i>. <i>unguis-hominis</i> UM 256.</p

Phylogenomic analysis of <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>The phylogenomic tree was constructed with total of 23 fungi including four from Sordariomycetes, nine from Dothideomycetes, eight from Eurotiomycetes and two outgroups from the Saccharomycetes (<i>C</i>. <i>albicans</i> and <i>S</i>. <i>cerevisiae</i>).</p

KOG and KEGG classifications of proteins in <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>(A) KOG class annotation distribution of <i>P</i>. <i>unguis-hominis</i> UM 256 genome. A: RNA processing and modification; B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Post-translational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; W: Extracellular structures; X: Unnamed protein and Z: Cytoskeleton. (B) Distribution of predicted proteins from <i>P</i>. <i>unguis-hominis</i> UM 256 genome that involved in metabolic pathway by KEGG database.</p

Bayesian phylogenetic tree of <i>Pyrenochaeta</i> sp. based on the combined genes of ITS, SSU and LSU sequenced data.

<p>The phylogenetic tree were constructed with 12 <i>Pyrenochaeta</i> species. The tree is rooted with <i>C</i>. <i>hispidulum</i> and <i>S</i>. <i>terrestris</i> as outgroup. The numbers on the nodes indicate Bayesian posterior probabilities.</p