scholarly journals Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 101 ◽  
Author(s):  
Himeshi Samarasinghe ◽  
Man You ◽  
Thomas S. Jenkinson ◽  
Jianping Xu ◽  
Timothy Y. James
Keyword(s):  
Fungal Pathogens ◽  
Batrachochytrium Dendrobatidis ◽  
Yeast Species ◽  
Phenotypic Diversity ◽  
Clinical Settings ◽  
Genome Plasticity ◽  
Genetic Changes ◽  
Genomic Plasticity ◽  
Nucleotide Divergence ◽  
Genome Level

Hybridization is increasingly recognized as an important force impacting adaptation and evolution in many lineages of fungi. During hybridization, divergent genomes and alleles are brought together into the same cell, potentiating adaptation by increasing genomic plasticity. Here, we review hybridization in fungi by focusing on two fungal pathogens of animals. Hybridization is common between the basidiomycete yeast species Cryptococcus neoformans × Cryptococcus deneoformans, and hybrid genotypes are frequently found in both environmental and clinical settings. The two species show 10–15% nucleotide divergence at the genome level, and their hybrids are highly heterozygous. Though largely sterile and unable to mate, these hybrids can propagate asexually and generate diverse genotypes by nondisjunction, aberrant meiosis, mitotic recombination, and gene conversion. Under stress conditions, the rate of such genetic changes can increase, leading to rapid adaptation. Conversely, in hybrids formed between lineages of the chytridiomycete frog pathogen Batrachochytrium dendrobatidis (Bd), the parental genotypes are considerably less diverged (0.2% divergent). Bd hybrids are formed from crosses between lineages that rarely undergo sex. A common theme in both species is that hybrids show genome plasticity via aneuploidy or loss of heterozygosity and leverage these mechanisms as a rapid way to generate genotypic/phenotypic diversity. Some hybrids show greater fitness and survival in both virulence and virulence-associated phenotypes than parental lineages under certain conditions. These studies showcase how experimentation in model species such as Cryptococcus can be a powerful tool in elucidating the genotypic and phenotypic consequences of hybridization.

scholarly journals Dear medical mycologists, it is time to look outside the box

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Florent Morio
Keyword(s):  
Clinical Setting ◽  
Fungal Pathogens ◽  
Yeast Species ◽  
The United States ◽  
Clinical Settings ◽  
Candida Auris ◽  
Pathogenic Potential ◽  
Pichia Kudriavzevii ◽  
Wild Yeast

ABSTRACT Opulente et al. (Opulente DA, Langdon QK, Buh KV et al. Pathogenic budding yeasts isolated outside of clinical settings. FEMS Yeast Res 2019;19:foz032) published early this year a study aiming to investigate the diversity of wild yeast species, by collecting 1000 environmental samples coming from different substrates across the United States of America. The main finding of this work is the recovery of 54 strains of budding yeasts of which several are having a pathogenic potential in the clinical setting, such as Candida albicans, C. parapsilosis, C. tropicalis, Nakaseomyces glabrata and Pichia kudriavzevii. These findings, discussed here in light of other recent studies highlighting the role of fungicides in the rise of antifungal resistance in the clinical setting or the emergence of Candida auris, demonstrate that our environment can represent an alternative niche for several opportunistic fungal pathogens that can be a concern for human health.

scholarly journals Virus Infection of Aspergillus fumigatus Compromises the Fungus in Intermicrobial Competition

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 686
Author(s):  
Hasan Nazik ◽  
Ioly Kotta-Loizou ◽  
Gabriele Sass ◽  
Robert H. A. Coutts ◽  
David A. Stevens
Keyword(s):  
Virus Infection ◽  
Aspergillus Fumigatus ◽  
Stress Responses ◽  
Fungal Pathogens ◽  
Clinical Settings ◽  
Virus Infections ◽  
Fungal Strains ◽  
Common Reference ◽  
Strain Virus ◽  
Free Strain

Aspergillus and Pseudomonas compete in nature, and are the commonest bacterial and fungal pathogens in some clinical settings, such as the cystic fibrosis lung. Virus infections of fungi occur naturally. Effects on fungal physiology need delineation. A common reference Aspergillus fumigatus strain, long studied in two (of many) laboratories, was found infected with the AfuPmV-1 virus. One isolate was cured of virus, producing a virus-free strain. Virus from the infected strain was purified and used to re-infect three subcultures of the virus-free fungus, producing six fungal strains, otherwise isogenic. They were studied in intermicrobial competition with Pseudomonasaeruginosa. Pseudomonas culture filtrates inhibited forming or preformed Aspergillus biofilm from infected strains to a greater extent, also seen when Pseudomonas volatiles were assayed on Aspergillus. Purified iron-chelating Pseudomonas molecules, known inhibitors of Aspergillus biofilm, reproduced these differences. Iron, a stimulus of Aspergillus, enhanced the virus-free fungus, compared to infected. All infected fungal strains behaved similarly in assays. We show an important consequence of virus infection, a weakening in intermicrobial competition. Viral infection may affect the outcome of bacterial–fungal competition in nature and patients. We suggest that this occurs via alteration in fungal stress responses, the mechanism best delineated here is a result of virus-induced altered Aspergillus iron metabolism.

scholarly journals Lactoferrin Is Broadly Active against Yeasts and Highly Synergistic with Amphotericin B

2020 ◽  
Vol 64 (5) ◽  
Author(s):  
Kenya E. Fernandes ◽  
Kerry Weeks ◽  
Dee A. Carter
Keyword(s):  
Amphotericin B ◽  
Galleria Mellonella ◽  
Comprehensive Evaluation ◽  
Yeast Species ◽  
Phenotypic Diversity ◽  
Antifungal Drugs ◽  
Fungal Cell ◽  
Content Type ◽  
Iron Saturation ◽  
Capsule Size

ABSTRACT Lactoferrin (LF) is a multifunctional milk protein with antimicrobial activity against a range of pathogens. While numerous studies report that LF is active against fungi, there are considerable differences in the level of antifungal activity and the capacity of LF to interact with other drugs. Here we undertook a comprehensive evaluation of the antifungal spectrum of activity of three defined sources of LF across 22 yeast and 24 mold species and assessed its interactions with six widely used antifungal drugs. LF was broadly and consistently active against all yeast species tested (MICs, 8 to 64 μg/ml), with the extent of activity being strongly affected by iron saturation. LF was synergistic with amphotericin B (AMB) against 19 out of 22 yeast species tested, and synergy was unaffected by iron saturation but was affected by the extent of LF digestion. LF-AMB combination therapy significantly prolonged the survival of Galleria mellonella wax moth larvae infected with Candida albicans or Cryptococcus neoformans and decreased the fungal burden 12- to 25-fold. Evidence that LF directly interacts with the fungal cell surface was seen via scanning electron microscopy, which showed pore formation, hyphal thinning, and major cell collapse in response to LF-AMB synergy. Important virulence mechanisms were disrupted by LF-AMB treatment, which significantly prevented biofilms in C. albicans and C. glabrata, inhibited hyphal development in C. albicans, and reduced cell and capsule size and phenotypic diversity in Cryptococcus. Our results demonstrate the potential of LF-AMB as an antifungal treatment that is broadly synergistic against important yeast pathogens, with the synergy being attributed to the presence of one or more LF peptides.

scholarly journals Chromatin-Mediated Regulation of Genome Plasticity in Human Fungal Pathogens

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 855 ◽  
Author(s):  
Buscaino
Keyword(s):  
Candida Albicans ◽  
Aspergillus Fumigatus ◽  
Cryptococcus Neoformans ◽  
Fungal Pathogens ◽  
Environmental Changes ◽  
Structure And Function ◽  
Model Systems ◽  
Genome Plasticity ◽  
And Function ◽  
Heterochromatin Structure

Human fungal pathogens, such as Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, are a public health problem, causing millions of infections and killing almost half a million people annually. The ability of these pathogens to colonise almost every organ in the human body and cause life-threating infections relies on their capacity to adapt and thrive in diverse hostile host-niche environments. Stress-induced genome instability is a key adaptive strategy used by human fungal pathogens as it increases genetic diversity, thereby allowing selection of genotype(s) better adapted to a new environment. Heterochromatin represses gene expression and deleterious recombination and could play a key role in modulating genome stability in response to environmental changes. However, very little is known about heterochromatin structure and function in human fungal pathogens. In this review, I use our knowledge of heterochromatin structure and function in fungal model systems as a road map to review the role of heterochromatin in regulating genome plasticity in the most common human fungal pathogens: Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans.

A status of guinea fowl (Numida meleagris) and pheasant (Phasianus colchicus) population transferred from wildlife to the breeding assessed based on the histone H1.c’ polymorphic variation

2019 ◽  
Vol 12 (4) ◽  
pp. 145-151 ◽  
Author(s):  
Andrzej Kowalski
Keyword(s):  
Genetic Drift ◽  
Phenotypic Diversity ◽  
Histone H1 ◽  
Guinea Fowl ◽  
Negative Effects ◽  
Genetic Changes ◽  
Numida Meleagris ◽  
Hardy Weinberg Equilibrium ◽  
First Time ◽  
Heterozygous Phenotype

The genetic changes accompanying a relocation of population to the captivity are mostly adverse and usually associated with deterioration of its status. These alterations are greater in small populations in which a loss of genetic variation limits the capability to adaptation. In this work, a status of small-sized guinea fowl and pheasant population relocated to the breeding is presented. These populations were analyzed based on the polymorphism of histone H1.c’, the protein for the first time identified as a heterogeneous. Histone H1.c’ was resolved in the two-dimensional polyacrylamide gel into the isoform H1.c’1 and H1.c’2, so its heterogeneity corresponds to the presence of homozygous phenotypes c’1 and c’2. Because no histone H1.c’ heterozygous phenotype was found, a significant phenotypic diversity in the guinea fowl ( P = 0.023) and pheasant ( P = 0.018) population was detected, together with its departures from Hardy-Weinberg equilibrium ( P < 0.0001). Both populations characterize an extreme loss of genetic diversity due to complete inbreeding ( F = 1) and an impact of genetic drift which, according to the expected values for guinea fowl (0.192) and pheasant (0.182) population, may strongly diminish allele frequency in the following generations. Thus, condition of populations evaluated based on the histone H1.c’ polymorphic variants, recognized as reasonable informative genetic markers (polymorphism information content of guinea fowl = 0.4 and pheasant = 0.38), corresponds to reduction of genetic variability caused by inbreeding and genetic drift. Therefore, it seems that rearing in the captivity can bring negative effects that favor restriction of animals’ vitality and survival of the population.

scholarly journals Amphibian chytridiomycosis, a lethal pandemic disease caused by the killer fungus Batrachochytrium dendrobatidis: New approaches to host defense mechanisms and techniques for detection and monitoring

Bionatura ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 1628-1636
Author(s):  
Génesis L. Romero-Zambrano ◽  
Stalin A. Bermúdez-Puga ◽  
Alex F. Sánchez-Yumbo ◽  
Jomira K. Yánez-Galarza ◽  
H. Mauricio Ortega-Andrade ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Fungal Pathogens ◽  
Batrachochytrium Dendrobatidis ◽  
Ecological Impacts ◽  
Chytrid Fungus ◽  
Skin Microbiota ◽  
Climatic Effects ◽  
Detection Techniques ◽  
Catastrophic Disease ◽  
Anti Fungal

Chytridiomycosis is a catastrophic disease currently decimating worldwide amphibian populations, caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. Massive species decline to extinction catalyzes radical changes in ecosystems globally, including the largest continuous rainforest ecosystem on Earth, the Amazon rainforest. Innovative research that aims to propose feasible mechanisms of mitigation and the origins of the disease is vital, including studies addressing climatic effects on the expansion of chytridiomycosis. Thus, this publication aims to provide a comprehensive review of: i) the current technologies used for B. dendrobatidis detection and monitoring, and ii) the known Neotropical amphibian's skin microbiota with anti-fungal properties against B. dendrobatidis. Several immunologic and DNA-based methods are discussed to understand the emerging fungal pathogens and their effects on the biosphere, which can help to mitigate the devastating ecological impacts of mass amphibian morbidity. The establishment of rapid and highly accurate B. dendrobatidis detection techniques and methods for monitoring amphibian's cutaneous microbiome is crucial in the fight against chytridiomycosis.

scholarly journals Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples

2020 ◽  
Author(s):  
Caoimhe E. O’Brien ◽  
João Oliveira-Pacheco ◽  
Eoin Ó Cinnéide ◽  
Max A. B. Hasse ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Candida Tropicalis ◽  
Large Scale ◽  
Population Genomics ◽  
Phenotypic Diversity ◽  
Nitrogen Sources ◽  
Asia Pacific ◽  
Phylogenomic Analysis ◽  
Pathogenic Yeast ◽  
A Genome ◽  
Genome Level

AbstractCandida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C. tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates C. tropicalis isolates from clinical and environmental sources from a variety of locations. We show that most C. tropicalis isolates are diploids with approximately 2 - 6 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of C. tropicalis with much higher heterozygosity levels ranging from 36 - 49 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other C. tropicalis isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are MTLa/α heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of C. tropicalis. The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.Author summaryCandida tropicalis is an important fungal pathogen, which is particularly common in the Asia-Pacific and Latin America. There is currently very little known about the diversity of genotype and phenotype of C. tropicalis isolates. By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents. Unlike other Candida species, the hybrids are more common in environmental than in clinical niches, suggesting that for this species, hybridization is not associated with virulence. We also explore the range of phenotypes, and we identify a genomic variant that is required for growth on valine and isoleucine as sole nitrogen sources.

scholarly journals Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes

2020 ◽  
Vol 8 (7) ◽  
pp. 1001
Author(s):  
Daniel Vieira ◽  
Soraia Esteves ◽  
Carolina Santiago ◽  
Eduardo Conde-Sousa ◽  
Ticiana Fernandes ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Species ◽  
Phenotypic Diversity ◽  
Population Analysis ◽  
Nuclear Genome ◽  
Reference Sequence ◽  
Evolutionary Analysis ◽  
Novel Approach ◽  
History Of ◽  
First Time

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains’ technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains’ technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.

scholarly journals Tn6603, a Carrier of Tn5053 Family Transposons, Occurs in the Chromosome and in a Genomic Island of Pseudomonas aeruginosa Clinical Strains

2020 ◽  
Vol 8 (12) ◽  
pp. 1997
Author(s):  
Vaheesan Rajabal ◽  
Vilma A. Stanisich ◽  
Steve Petrovski
Keyword(s):  
Genomic Island ◽  
Clinical Settings ◽  
Genome Plasticity ◽  
Clinical Context ◽  
Accessory Gene ◽  
Hypothetical Gene ◽  
Class 1 Integrons ◽  
Resistance Determinants ◽  
Class 1 ◽  
In Trans

Transposons of the Pseudomonasaeruginosa accessory gene pool contribute to phenotype and to genome plasticity. We studied local P. aeruginosa strains to ascertain the encroachment of mer-type res site hunter transposons into clinical settings and their associations with other functional modules. Five different Tn5053 family transposons were detected, all chromosomal. Some were solitary elements; one was in res of Tn1013#, a relative of a reported carrier of int-type res site hunters (class 1 integrons), but most were in res of Tn6603, a new Tn501-related transposon of unknown phenotype. Most of the Tn6603::Tn elements, and some Tn6603 and Tn6603::Tn elements found in GenBank sequences, were at identical sites in an hypothetical gene of P. aeruginosa genomic island PAGI-5v. The island in clonally differing strains was at either of two tRNALys loci, suggesting lateral transfer to these sites. This observation is consistent with the membership of the prototype PAGI-5 island to the ICE family of mobile genetic elements. Additionally, the res site hunters in the nested transposons occupied different positions in the Tn6603 carrier. This suggested independent insertion events on five occasions at least. Tn5053 family members that were mer-/tni-defective were found in Tn6603- and Tn501-like carriers in GenBank sequences of non-clinical Pseudomonas spp. The transposition events in these cases presumably utilized tni functions in trans, as can occur with class 1 integrons. We suggest that in the clinical context, P. aeruginosa strains that carry Tn6603 alone or in PAGI-5v can serve to disseminate functional res site hunters; these in turn can provide the requisite trans-acting tni functions to assist in the dissemination of class 1 integrons, and hence of their associated antibiotic resistance determinants.

scholarly journals Maintenance of phenotypic diversity within a set of virulence encoding genes of the malaria parasite Plasmodium falciparum

2015 ◽  
Vol 12 (113) ◽  
pp. 20150848 ◽  
Author(s):  
Thomas Holding ◽  
Mario Recker
Keyword(s):  
Plasmodium Falciparum ◽  
Malaria Parasite ◽  
Phenotypic Diversity ◽  
Specific Binding ◽  
Surface Proteins ◽  
Dependent Manner ◽  
Empirical Observation ◽  
Parasite Plasmodium Falciparum ◽  
Clinical Protection ◽  
Genome Level

Infection by the human malaria parasite Plasmodium falciparum results in a broad spectrum of clinical outcomes, ranging from severe and potentially life-threatening malaria to asymptomatic carriage. In a process of naturally acquired immunity, individuals living in malaria-endemic regions build up a level of clinical protection, which attenuates infection severity in an exposure-dependent manner. Underlying this shift in the immunoepidemiology as well as the observed range in malaria pathogenesis is the var multigene family and the phenotypic diversity embedded within. The var gene-encoded surface proteins Plasmodium falciparum erythrocyte membrane protein 1 mediate variant-specific binding of infected red blood cells to a diverse set of host receptors that has been linked to specific disease manifestations, including cerebral and pregnancy-associated malaria. Here, we show that cross-reactive immune responses, which minimize the within-host benefit of each additionally expressed gene during infection, can cause selection for maximum phenotypic diversity at the genome level. We further show that differential functional constraints on protein diversification stably maintain uneven ratios between phenotypic groups, in line with empirical observation. Our results thus suggest that the maintenance of phenotypic diversity within P. falciparum is driven by an evolutionary trade-off that optimizes between within-host parasite fitness and between-host selection pressure.

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