Clinical and environmental aspergillus: Morphological and molecular characterization, phylogeny, and antifungal susceptibility profile

• Autores: Joao Paulo Zen Siqueira
• Directores de la Tesis: Josepa Gené Díaz (dir. tes.), Josep Guarro Artigas (dir. tes.), Dania García Sánchez (dir. tes.)
• Lectura: En la Universitat Rovira i Virgili ( España ) en 2017
• Idioma: español
• Tribunal Calificador de la Tesis: Ma. Lourdes Abarca Salat (presid.), Alberto Stchigel (secret.), Ana Alastruey-Izquierdo (voc.)
• Programa de doctorado: Programa de Doctorado en Biomedicina por la Universidad Rovira i Virgili
• Materias:
  • Ciencias de la vida
    • Microbiología
      • Hongos
      • Mohos
    • Biología molecular
• Enlaces
  • Tesis en acceso abierto en:  hdl.handle.net  TDX 
• Resumen

  • Aspergillus is one of the most common and ubiquitous genus of Ascomycetes, inhabiting a great diversity of environmental substrates. Some of them are known as opportunistic human pathogens, responsible for over hundreds of thousands of life-threatening infections per year worldwide. The advances in modern medicine contribute to an increasing population with altered immune function and, consequently, at risk of these type of fungal infections. The main agent of aspergillosis is A. fumigatus; however, changes in the epidemiology are being observed. Recent studies show that those changes seem to favor more resistant and/or cryptic species. Accurate identification of an Aspergillus to the species level is important when dealing with infections refractory to antifungal therapy, for investigation of outbreaks, or when performing epidemiologic studies. Improvement of the identification methods, especially the sequence-based, allowed detecting Aspergillus species with greater confidence, helping to uncover species never associated to clinical specimens before and may be one of the reasons for the mentioned epidemiological changes. Aspergillus species may have positive and negative impacts in many fields, including fungal taxonomy, food and indoor mycology, biotechnology, ecology, medical mycology, and genomics; and in all of them the correct identification is a crucial step. Recent reports prove that the diversity of the genus is yet being discovered and there are numerous potential new species to be described in a variety of substrates. The main objective of this thesis was to contribute to the better knowledge of genus Aspergillus, exploring the species diversity of the less studied Aspergillus sections from clinical and environmental sources. A total of 433 isolates, obtained from different sources (clinical samples, soil, dung, plant debris), were included in the different studies of this thesis. The identification of the isolates was carried out by using multilocus phylogenetic analyses, including sequences of the ITS region and portions of the β-tubulin, calmodulin, and RNA polymerase II second largest subunit genes. Phenotypic characterization was also performed according to the methodology commonly used for this group of fungi. When relevant, clinical isolates were submitted to antifungal susceptibility testing against the main drugs available. In summary, 98 species of Aspergillus were identified, 49 from clinical samples (248 isolates), 48 from soil (92 isolates), 48 from herbivore dung (82 isolates), and 10 from plant debris (10 isolates). The most frequent sections among those considered poorly studied sections of Aspergillus in the clinical setting were Nidulantes (including members of the former Versicolores section), with 84 isolates and 14 species; Circumdati, 35 isolates and seven species; Aspergillus, 25 isolates and five species; and Usti, 19 isolates and two species. Eight species were isolated from clinical samples for the first time and three were proposed as new. The antifungal drugs, in general, showed good activity against the isolates tested. The most noticeable exception was the reduced activity of amphotericin B against members of section Circumdati. Regarding the environmental isolates, 14 new species were proposed based on phenotypic and molecular data; five belonging to the section Terrei (three from herbivore dung and two from soil); four to the section Candidi (all from dung); two to the section Nidulantes (both from soil); and one in each of the sections Flavipedes, Cremei, and Usti (all from dung)