Differential Gene Expression of Malaria Parasite in Response to Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG).

Innovative strategies to control malaria are urgently needed. Exploring the interplay between sp. parasites and host red blood cells (RBCs) offers opportunities for novel antimalarial interventions.

Origin of fungal hybrids with pathogenic potential from warm seawater environments.

Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C.

in Intensive Care Setting: The First Case Reported in Portugal.

is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of in Portugal, which was associated with a patient transferred from Angola to an ICU in Portugal for liver transplantation after a SARS-CoV-2 infection. was isolated during the course of bronchoalveolar lavage, and it was subjected to antifungal susceptibility testing and whole-genome sequence analysis.

ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data.

Background: Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce.

Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens.

Background: Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions.

Pathogenic , spp. and spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization.

Human-wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of (Shiga toxin-producing (STEC) and non-STEC), spp. and spp.

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies.

Background: Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors.

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus.

The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. ). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin.

Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex.

Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C.

Multiple Hybridization Events Punctuate the Evolutionary Trajectory of .

species are important fungal skin commensals and are part of the normal microbiota of humans and other animals. However, under certain circumstances these fungi can also display a pathogenic behavior. For example, is a common commensal of human skin and yet is often responsible for skin disorders but also systemic infections.

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.

Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis.

Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans.

Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn.

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans.

Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis.

Differential Expression of Fungal Genes Determines the Lifestyle of Strains During Colonization.

The fungal genus comprises species and strains with different lifestyles on plants, such as , which has served as model for the characterization of basal and nonhost resistance to necrotrophic fungi. We have sequenced, annotated, and compared the genomes and transcriptomes of three strains with different lifestyles on , namely, PcBMM, a natural pathogen of wild-type plants (Col-0), Pc2127, a nonpathogenic strain on Col-0 but pathogenic on the immunocompromised mutant, and P0831, which was isolated from a natural population of and is shown here to be nonpathogenic and to grow epiphytically on Col-0 and plants. The genomes of these strains are very similar and do not differ in the number of genes with pathogenesis-related functions, with the exception of secreted carbohydrate-active enzymes (CAZymes), which are up to five times more abundant in the pathogenic strain PcBMM.

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans.

Background: Opportunistic yeast pathogens of the genus Candida are an important medical problem. Candida albicans, the most prevalent Candida species, is a natural commensal of humans that can adopt a pathogenic behavior. This species is highly heterozygous and cannot undergo meiosis, adopting instead a parasexual cycle that increases genetic variability and potentially leads to advantages under stress conditions.

HaploTypo: a variant-calling pipeline for phased genomes.

Summary: An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available.

Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: (syn. ) and (syn. ).

Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. (syn.

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Uncovers Its Hybrid Origin.

Fungal infections such as those caused by species are increasingly common complications in immunocompromised patients. The list of causative agents of candidiasis is growing and comprises a set of emerging species whose relative global incidence is rare but recurrent. This is the case of , which prevalence has increased 10-fold over the last years.

Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications.

Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data.

Hybridization and emergence of virulence in opportunistic human yeast pathogens.

Hybridization between different species can result in the emergence of new lineages and adaptive phenotypes. Occasionally, hybridization in fungal organisms can drive the appearance of opportunistic lifestyles or shifts to new hosts, resulting in the emergence of novel pathogens. In recent years, an increasing number of studies have documented the existence of hybrids in diverse yeast clades, including some comprising human pathogens.

Comparative morphological and molecular analysis confirms the presence of the West Nile virus mosquito vector, Culex univittatus, in the Iberian Peninsula.

Background: Culex univittatus and Culex perexiguus mosquitoes (Diptera: Culicidae) are competent arbovirus vectors, but with unclear morphological differentiation. In Europe, and in the Iberian Peninsula in particular, the presence of either or both species is controversial. However, in order to conduct adequate surveillance for arboviruses in this region, it is crucial to clarify whether Cx.