Caracterización molecular y fenotípica del género pseudallescheria y géneros afines

Pseudallescheria es un género de ascomicetos caracterizado por ser polimórfico, ya que pueden presentar hasta tres formas morfológicamente diferentes, una forma sexual o teleomorfo y dos formas asexuales o anamorfos (sinanamorfos). Estas dos formas asexuales se clasifican en los géneros anamórficos Scedosporium y Graphium. Pseudallescheria boydi es la especie más importante del género debido a que es considerado un hongo patógeno emergente capaz de producir infecciones graves especialmente en pacientes inmnusuprimidos. Hasta la presente tesis, el anamorfo de P. boydii era Scedosporium apiospermum. En los últimos años, P. boydii ha sido objeto de diversos estudios moleculares que han mostrado su elevada variabilidad intraespecífica. Otros trabajos han puesto de relieve su variabilidad en cuanto a la respuesta a los antifúngicos así como la diferente virulencia que existe entre sus cepas. Todo ello hacía suponer que en lugar de una sola especie nos hallábamos frente a un complejo de especies. Por esta razón decidimos realizar un estudio molecular y morfológico utilizando numerosas cepas tanto clínicas como ambientales y de diferentes países. Gran parte de las cepas ambientales fueron aisladas por nosotros con la utilización del medio selectivo DRBC con benomilo. El análisis de secuencias parciales del gen de la β-tubulina (dos loci) y la calmodulina y las regiones ITS del ADNr demostraron que P. boydii es un complejo de especies. El análisis combinado de las secuencias de los 4 loci nos permitió la distinción de 8 especies filogenéticas agrupadas en 4 clados diferentes. Los clados 1 y 2 fueron descritos como las nuevas especies Scedosporium aurantiacum y Pseudallescheria minutispora, respectivamente. El clado 5 consistió en 4 subgrupos incorporando las cepas tipos de P. boydii Pseudallescheria angusta, Pseudallescheria ellipsoidea y Pseudallescheria fusoidea. En el caso de los clados 3 y 4 fueron considerados únicamente como especies filogenéticas en este primer estudio. Posteriormente, para facilitar la identificación de estas 8 especies filogenéticas en laboratorios de microbiología clínica, se estudiaron las características morfológicas macro- y microscópicas mas representativas de todas ellas así como su respuesta a 59 pruebas fisiológicas. Para incrementar la robustez de los diferentes clados, aumentamos el número de nuevos aislados y de éstos se secuenció la región TUB del gen de la β-tubulina, el cual previamente demostró ser el marcador molecular más informativo de los 4 evaluados. La combinación de estos estudios permitió distinguir fenotípicamente las mencionadas especies filogenéticas. La nueva especie Scedosporium dehoogii (previamente clado 3) fue descrita y Scedoporium apiospermum (previamente clado 4) y P. boydii fueron consideradas como dos especies diferentes. El nuevo nombre Scedosporium boydii fue propuesto para denominar al anamorfo de la última especie. Scedosporium dehoogii pudo ser separada del resto porque no crece a 40ºC y presenta conidioforos no ramificados. Aunque S. apiospermum fue morfológicamente indistinguible del anamorfo de P. boydii ambas especies pudieron ser separadas por su respuesta a las pruebas de la D-ribosa y por la presencia o ausencia de teleomorfo. Durante la búsqueda de nuevos aislados utilizando el medio DRBC suplementado con benomilo, aislamos un hongo interesante de suelo de Argentina que presentaba una morfología similar a la de Scedosporium. Un estudio más detallado a nivel genético y morfológico nos permitió ver que este hongo era diferente a las especies conocidas de éste y otros géneros relacionados, por lo que propusimos el nuevo género Parascedosporium. Su carácter distintivo es el desarrollo simpodial de los conidios a partir de células conidiógenas denticuladas. Este aislado resultó ser morfológicamente idéntico a Graphium tectonae, por lo que propusimos la nueva combinación Parascedosporium tectonae. El análisis filogenético de las secuencias de 4 regiones de los 3 genes ya trabajados en el primer estudio confirmó nuestra propuesta. En esta tesis también evaluamos la actividad in vitro de 11 antifúngicos (anfotericina B, albaconazol, fluconazol, itraconazol, ketoconazol, posaconazol, ravuconazol, voriconazol, terbinafina, micafungina y flucitosina) utilizando el método de microdilución del CLSI contra 84 aislados pertenecientes a las 8 especies que constituyen el complejo P. boydii. Encontramos diferencias significativas entre las especies, siendo Scedosporium aurantiacum la más resistente. En general, el voriconazol fue el antifúngico más activo, seguido del posaconazol. Otro objetivo de la presente tesis fue comparar la virulencia de alguna de las diferentes especies del complejo utilizando un modelo murino con animales inmunocompetentes e inmunosuprimidos. Se seleccionaron 2 inóculos diferentes, 5x104 conidia/mL (para los animales inmunosuprimidos) y 1x106 conidia/mL (para los animales inmunocompetentes). S. aurantiacum y S. dehoogii fueron significativamente las especies más virulentas, causando la muerte del 80% y 70% de los ratones inmunocompetentes, respectivamente, mientras que el resto de las especies sólo consiguió entre un 0% y un 20% de mortalidad. Finalmente, debido a que ninguna de las cepas estudiadas de la especie más común del complejo, S. apiospermum, había desarrollado la forma sexual, consideramos interesante determinar si se trataba de una especie heterotálica. Para ello, realizamos cruzamientos con 15 cepas de S. apiospermum en todas las combinaciones posibles, incluyendo cruzamientos consigo misma. Algunos cruzamientos entre distintas cepas produjeron ascomas fértiles, mientras que los cruzamientos con subcultivos de una misma cepa resultaron autoestériles. Las cepas pudieron separarse en dos diferentes "mating types". Corroboramos el bi-alelismo del sistema de cruzamiento heterotálico mediante cruzamientos entre las ascosporas de la progenie F1 de un cruzamiento positivo. Todos estos datos confirmaron que S. apiospermum es una especie heterotálica.Pseudallescheria boydii is a ubiquitous ascomycetous fungus that causes a wide array of human infections that can affect practically all the organs of the body. These infections have been known for a long time, but in recent years, a marked increase in severe invasive infections has been noticed, mainly in immunocompromised hosts. They present a high mortality rate and are difficult to treat. One of the most typical features of this species, which is very rare in other pathogenic fungi, is its ability to develop sexual structures on routine culture media. Until the present thesis Scedosporium apiospermum was considered the anamorph of P. boydii. Recently, it had been demonstrated that high genetic variation exists within P. boydii and other authors had reported considerable differences with respect to growth and sporulation. All these data seemed to suggest that P. boydii was probably a species complex. For this reason we performed a morphological and molecular study involving numerous strains of clinical and environmental origins and from different countries. The analysis of partial sequences of the β-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rDNA gene demonstrated that P. boydii is a species complex. A combined analysis of the sequences of the four loci of 60 strains from different origins showed 8 phylogenetic species within this species, grouped in 5 different clades. The clades 1 and 2 were described as the new species Scedosporium aurantiacum and Pseudallescheria minutispora, respectively. Clade 5 consisted of four subgroups incorporating the ex-type strains of P. boydii, Pseudallescheria angusta, Pseudallescheria ellipsoidea and Pseudallescheria fusoidea, respectively, and clades 3 and 4 remained unnamed. Later, in order to facilitate their identification in the clinical microbiology laboratories we tried to characterize phenotypically those 8 phylogenetic species. In order to increase the robustness of the different clades, we included in this study numerous fresh isolates identified by sequencing the TUB region of the β-tubulin gene, which previously was revealed as the most informative molecular marker of the four evaluated. The most representative macro- and microscopic morphological features of all them were studied and their responses to 59 physiological tests were evaluated. The combination of these studies allowed us to distinguish phenetically the mentioned phylogenetic species. The new species Scedosporium dehoogii (previously clade 3) was described and Scedoporium apiospermum (previously clade 3) and P. boydii were considered two different species The new name Scedosporium boydii was proposed for the anamorph of the latter species. Scedosporium dehoogii can be separated from the rest because it does not growth at 40ºC and present unbranched conidiophores. Although S. apiospermum were morphologically indistinguishable from the anamorph of Pseudallescheria boydii both species can be separated by the response to D-ribose test and by the presence or absence of a teleomorph. During the study of fresh isolates recovered from different geographical areas we recovered an interesting Scedosporium-like fungus from Argentinean soil samples which was proven to be genetically and morphologically different from the known species of Scedosporium and relatives. Diverse morphological and molecular studies confirmed the uniqueness of such fungus and was proposed as the new genus Parascedosporium.. This genus is mainly characterized by producing sympodial conidia from denticulate conidiogenous cells. Further studies demonstrated that such isolate was identical to Graphium tectonae and thus the new combination Parascedosporium tectonae was proposed. In this thesis we also evaluated the in vitro activities of 11 drugs (amphotericin B, albaconazole, fluconazole, itraconazole, ketoconazole, posaconazole, ravuconazole, voriconazole, terbinafine, micafungin and flucytosine) by using the microdilution method following the CLSI guidelines against 84 isolates belonging to the eight species that constitute the Pseudallescheria boydii complex. We found significant differences among the species, with Scedosporium aurantiacum being the most resistant. In general, voriconazole was the most active drug, showing a total geometric mean MIC of 0.61 g/ml, followed by posaconazole. Another objective of the present thesis was to compare the virulence of the different species of the complex using a murine model of disseminated infection by these species. We used two different inocula, i.e., 5x104 conidia/ml and 1x106 conidia/ml, for each fungal strain tested. When mice were infected with the first inoculum animals were immunosuppressed while that those infected with the second inoculum were inmunocompetent. No significant differences in mortality rates were observed (p>0.05) among the species in the immunosupressed animals. In the case of inmunocompetent animals, S. aurantiacum and S. dehoogii were clearly the most virulent species of the complex both showed the highest mean mortality rate (80% and 70%, respectively, versus 0%-20% for the other species). Finally, since none of the strains studied of the most common species of the complex, S. apiospermum, never developed the sexual state we considered of interest to determine if it was a heterothallic species. For this purpose, 15 strains of this species were paired in all possible combinations, including self-pairings to corroborate this hypothesis. All strains were self-sterile and several combinations of strains produced fertile ascomata. The strains could separate in two groups of different mating types. We corroborated the bi-allelic heterothallic mating system suggested by these results with crosses among F1 progeny ascospores from one positive mating test. All these data confirmed that S. apiospermum is a heterothallic species

Genetic Diversity of the Cryptococcus Species Complex Suggests that Cryptococcus gattii Deserves to Have Varieties

The Cryptococcus species complex contains two sibling taxa, Cryptococcus neoformans and Cryptococcus gattii. Both species are basidiomycetous yeasts and major pathogens of humans and other mammals. Genotyping methods have identified major haploid molecular types of C. neoformans (VNI, VNII, VNB and VNIV) and of C. gattii (VGI, VGII, VGIII and VGIV). To investigate the phylogenetic relationships among these haploid genotypes, we selected 73 strains from 2000 globally collected isolates investigated in our previous typing studies, representing each of these genotypes and carried out multigene sequence analyses using four genetically unlinked nuclear loci, ACT1, IDE, PLB1 and URA5. The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type. However, three strains of each species revealed some incongruence between the original molecular type and the sequence-based type obtained here. The topology of the individual gene trees was identical for each clade of C. neoformans but incongruent for the clades of C. gattii indicating recent recombination events within C. gattii. There was strong evidence of recombination in the global VGII population. Both parsimony and likelihood analyses supported three major clades of C. neoformans (VNI/VNB, VNII and VNIV) and four major clades of C. gattii (VGI, VGII, VGIII and VGIV). The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII. MATa was for the first time identified for VGIV. The VNIV and VGII clades are basal to the C. neoformans or the C. gattii clade, respectively. Divergence times among the seven haploid monophyletic lineages in the Cryptococcus species complex were estimated by applying the hypothesis of the molecular clock. The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status

Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater.IMPORTANCE Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic

Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal Pathogen Scedosporium aurantiacum

Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on “Scedosporium/Pseudallescheria Infections” and “Fungal Respiratory Infections in Cystic Fibrosis”.Peer Reviewe

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater understanding of C. gattii evolution in North America and support extensive evolution in, and dispersal from, South America. Importance: Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic

Molecular Phylogeny of the Pseudallescheria boydii Species Complex: Proposal of Two New Species

Pseudallescheria boydii (anamorph Scedosporium apiospermum) is the species responsible for human scedosporiosis, a fungal infection with a high mortality rate and which is difficult to treat. Recently, it has been demonstrated that high genetic variation exists within this species. We have performed a morphological and molecular study involving numerous strains of clinical or environmental origins and from different countries. The analysis of partial sequences of the β-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rRNA gene has demonstrated that P. boydii is a species complex. The combined analysis of the sequences of the four loci of 60 strains has showed the presence of 44 haplotypes in the ingroup. Three species morphologically related to P. boydii sensu stricto, i.e., Pseudallescheria angusta, Pseudallescheria ellipsoidea, and Pseudallescheria fusoidea, which had previously been considered synonyms, could be differentiated genetically from P. boydii in our study. It is relevant that two of the three strains now included in P. ellipsoidea have caused invasive infections. The species Pseudallescheria minutispora and Scedosporium aurantiacum are clearly phylogenetically separated from the other species studied and are here proposed as new. Morphological features support this proposal. All the strains included in S. aurantiacum species have a clinical origin, while those included in P. minutispora are environmental. Further studies are needed to demonstrate whether all the species included in the P. boydii complex have different clinical spectra and antifungal susceptibility

Molecular Epidemiology Reveals Low Genetic Diversity among Cryptococcus neoformans Isolates from People Living with HIV in Lima, Peru, during the Pre-HAART Era

Cryptococcosis, a mycosis presenting mostly as meningoencephalitis, affecting predominantly human immunodeficiency virus (HIV)-infected people, is mainly caused by Cryptococcus neoformans. The genetic variation of 48 C. neoformans isolates, recovered from 20 HIV-positive people in Lima, Peru, during the pre-highly active antiretroviral therapy (HAART) era, was studied retrospectively. The mating type of the isolates was determined by PCR, and the serotype by agglutination and CAP59-restriction fragment length polymorphism (RFLP). Genetic diversity was assessed by URA5-RFLP, PCR-fingerprinting, amplified fragment length polymorphism (AFLP), and multilocus sequence typing (MLST). All isolates were mating type alpha, with 39 molecular type VNI, seven VNII, corresponding to C. neoformans var. grubii serotype A, and two VNIII AD hybrids. Overall, the cryptococcal population from HIV-positive people in Lima shows a low degree of genetic diversity. In most patients with persistent cryptococcal infection, the same genotype was recovered during the follow-up. In four patients with relapse and one with therapy failure, different genotypes were found in isolates from the re-infection and from the isolate recovered at the end of the treatment. In one patient, two genotypes were found in the first cryptococcosis episode. This study contributes data from Peru to the ongoing worldwide population genetic analysis of Cryptococcus