ToxGen: An improved reference database for the identification of type B-trichothecene genotypes in Fusarium

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype´s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort.Fil: Kulik, Tomasz. Uniwersytet Warminsko-mazurski W Olsztynie;Fil: Abarenkov, Kessy. University Of Tartu.; EstoniaFil: Busko, Maciej. Poznań University of Life Sciences; PoloniaFil: Bilska, Katarzyna. University of Warmia and Mazury; PoloniaFil: van Diepeningen, Anne D.. University of Amsterdam; Países BajosFil: Ostrowska-Kolodziejczak, Anna. Poznań University of Life Science; PoloniaFil: Krawczyk, Katarzyna. University of Warmia and Mazur; PoloniaFil: Brankovics, Balázs. CBS-KNAW Fungal Biodiversity Centre; Países Bajos. University of Amsterdam; Países BajosFil: Stenglein, Sebastian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Cientifico Tecnolológico Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología. Laboratorio de Biología Funcional y Biotecnología; ArgentinaFil: Sawicki, Jakub. University of Warmia and Mazury; PoloniaFil: Perkowski, Juliusz. Poznań University of Life Sciences; Poloni

Emerging pan-resistance in <i>Trichosporon </i>species:a case report

BACKGROUND: Trichosporon species are ubiquitously spread and known to be part of the normal human flora of the skin and gastrointestinal tract. Trichosporon spp. normally cause superficial infections. However, in the past decade Trichosporon spp. are emerging as opportunistic agents of invasive fungal infections, particularly in severely immunocompromised patients. Clinical isolates are usually sensitive to triazoles, but strains resistant to multiple triazoles have been reported. CASE PRESENTATION: We report a high-level pan-azole resistant Trichosporon dermatis isolate causing an invasive cholangitis in a patient after liver re-transplantation. This infection occurred despite of fluconazole and low dose amphotericin B prophylaxis, and treatment with combined liposomal amphotericin B and voriconazole failed. CONCLUSION: This case and recent reports in literature show that not only bacteria are evolving towards pan-resistance, but also pathogenic yeasts. Prudent use of antifungals is important to withstand emerging antifungal resistance

Emergence of fusarioses in a university hospital in Turkey during a 20-year period

Fusarium species have started appearing increasingly as the main cause of infections, particularly in immunocompromised patients. In this study, we aimed to present the first epidemiological data from Turkey, analyze fusariosis cases that have been monitored in a university hospital during the past 20 years, identify the responsible Fusarium species, and determine antifungal susceptibilities. A total of 47 cases of fusariosis was included in the study. Fusarium isolates were identified by multilocus sequence typing (MLST). Antifungal susceptibility was tested by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) methodology. Of the Fusarium infections, 23.4 % were superficial, 44.7 % were locally invasive, and 31.9 % were disseminated. A significant increase was observed over the years. The Fusarium fujikuroi species complex (FFSC) proved to be the most frequent agent group (17 cases; 51.5 %), followed by the Fusarium solani species complex (FSSC) (14 cases; 42.4 %), the Fusarium dimerum species complex (FDSC), and the Fusarium oxysporum species complexes (FOSC) (one case each). Amphotericin B had the highest in vitro activity against all species. Voriconazole and posaconazole showed interspecies variability across and within Fusarium species complexes. In conclusion, our data support the fact that regional differences exist in the distribution of the Fusarium species and that species-specific differences are observed in antifungal susceptibility patterns. The monitoring of local epidemiological data by determining fungal identity and susceptibility are of importance in guiding the clinical follow-up of patients.Türk Mikrobiyoloji DerneğiMinistry of Health, Muscat, Oma

First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations

The Amsterdam Declaration on Fungal Nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented