Biology subjects

Hagen, F.

Publications and source records attributed to Hagen, F..

9 recordsLinked to original sources

bioRxiv2025

Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology

Sporotrichosis is a globally distributed subcutaneous mycosis caused mainly by Sporothrix brasiliensis, S. schenckii, and S. globosa. Cat-transmitted sporotrichosis, primarily caused by S. brasiliensis in South America and to a lesser extent by S. schenckii in Southeast Asia, is emerging as a significant public health concern, due its outbreak potential. Itraconazole is the first-choice drug for treatment of human and cats, but reduced susceptibility has been reported based on previously proposed epidemiological cut-off values (ECVs). To support resistance surveillance, we aimed to establish CLSI-endorsed ECVs for these clinically relevant Sporothrix species. A total of 3,588 minimum inhibitory concentration (MIC) values for seven antifungal agents (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, olorofim, and terbinafine) were obtained from 19 international laboratories. Four of seven antifungals met the CLSI M57 guidelines criteria to determine the ECV. Established ECVs for amphotericin B were found to be high with 8 {micro}g/mL for S. brasiliensis and S. globosa, and 4 {micro}g/mL for S. schenckii. Itraconazole ECVs were 4 {micro}g/mL for S. brasiliensis and S. schenckii. Posaconazole ECVs were 4 {micro}g/mL for all three species (tentative for S. globosa), while the terbinafine ECV for S. brasiliensis was 0.12 {micro}g/mL. Olorofim demonstrated good in vitro activity, particularly against S. brasiliensis. Overall, this study establishes validated ECVs for key antifungals against Sporothrix species and identifies a low prevalence of non-wild type (NWT) isolates, supporting ongoing antifungal resistance monitoring.

microbiology↗

bioRxiv2025

Limited genetic diversity among Malassezia furfur isolates during two one-year neonatal and pediatric bloodstream infection surveys confirms preference for one specific IGS1 genotype in deep-seated infections

In recent years, multiple reports indicated that Malassezia fungemia may be of emerging concern in immunocompromised patients and neonates. In combination with observations of reduced antifungal susceptibility, this highlights the need for a better understanding of the extent of Malassezia etiology in deep seated infections. The use of media without lipid supplementation in most clinics underlines the likelihood of underdiagnosis. Here, we utilize multiple genetic markers to explore the genetic diversity of number one Malassezia fungemia species Malassezia furfur, observed from two one-year surveys investigating neonatal and pediatric bloodstream infections. All strains isolated from skin and deep seated neonatal or pediatric sites belong to IGS1-genotype A, except for nine isolates from one pediatric patient. This confirms previous observations of a preferential genotype for deep seated body sites. The mitochondrial cox3-nad3 intergenic region provided additional typing resolution, and including ITS, translation elongation factor 1-, chitin synthase 2, and the mating type, 16 genotypes (MF1-16) could be distinguished among all isolates from both surveys and reference isolates. These results present a promising MLST scheme that requires further testing. We observed a decreased genetic variation of M. furfur isolates among NICU and pediatric surgery patients over the course of 5 years and showed that the skin likely serves as a reservoir for resident M. furfur strains from where they can enter the bloodstream, causing infections among susceptible patient groups. Overall, reduced susceptibility for amphotericin B and specifically fluconazole was observed.

genetics↗

bioRxiv2024

Investigating the genetic relationship of Trichosporon asahii isolates using a newly developed microsatellite typing assay

The basidiomycetous yeast-like fungus Trichosporon asahii is increasingly encountered in the clinic and has been known to cause nosocomial infections. Here, we aim to develop a microsatellite typing tool to investigate the genetic relatedness of Trichosporon asahii isolates. Six microsatellite markers were selected from a nanopore long-read sequencing de novo assembled genome of the T. asahii type-strain CBS 2479. PCR reactions amplified three di-, tri-, or tetranucleotide repeats, respectively. All six microsatellite markers were used to analyze 111 T. asahii isolates, including single and related-patient isolates from clinical and environmental sources. Each marker exhibited between 11 and 37 alleles in this population, resulting in 71 different microsatellite genotypes. The Simpsons diversity index ranged from 0.6452 to 0.8280 for the individual markers, and for the combined set of microsatellites 0.9793, indicating the high discriminatory power of the reported panel. In summary, this panel combines high reproducibility and specificity, making it suitable for use in epidemiological studies of T. asahii and in investigations of potential outbreaks caused by this pathogen.

molecular biology↗

bioRxiv2024

Aspergillus species in Iceland: species distribution and cyp51A mutation testing in a 7.5-year clinical isolate collection

Introduction.Among challenges in diagnosing and treating aspergillosis are Aspergillus species identification, which can inform therapeutic choices, and detection of antifungal resistance. Increasing rates of triazole resistance have been reported for the most common species, Aspergillus fumigatus. Methods.A collection of clinical Aspergillus isolates cultured during 2014-2021, previously identified morphologically, were tested with the AsperGenius qPCR-kit for identification of A. fumigatus and Aspergillus flavus and the presence of a cyp51A mutation encoding azole resistance (TR34/L98H and Y121F/T289A); other species were identified with calmodulin sequencing. Results.Identification of the 312 isolates (224 patients) tested revealed 19 species in nine Aspergillus sections. Rare or cryptic species were identified in 48 isolates (44 patients). Thirty-one isolates had been assigned an incorrect species name when initially cultured. The TR34/L98H and Y121F/T289A mutations were not found in any of the 202 A. fumigatus isolates tested. Discussion.In this first study on clinical Aspergillus isolates in Iceland the proportion of cryptic and rare species was on par with findings from other countries. In contrast, unlike other studies we did not find the most common azole resistance-related mutations in A. fumigatus, possibly due to the absence of significant environmental antifungal pressure in the local agriculture.

microbiology↗

bioRxiv2024

Typing of feces-derived Candida albicans strains using a novel seven-locus microsatellite panel reveals associations with yeast phenotype in individuals with inflammatory bowel disease

Inflammatory diseases of the human gastrointestinal tract are affected by the microbes that reside in the mucosal surfaces along this tract. Patients with inflammatory bowel diseases (IBD) have altered bacterial and fungal intestinal compositions, including higher levels of fecal Candida yeasts. Ongoing research indicates that genetic and phenotypic diversity of Candida albicans may be linked with disease severity. In this study, we set out to investigate feces-derived C. albicans strains from individuals with Crohns disease, ulcerative colitis, and healthy volunteers through microsatellite-based genotyping and phenotypic assays. A seven-locus microsatellite panel was applied, of which six loci were newly developed. Combined interpretation of minimum spanning networks and principal component analysis (PCA) led to indications that there is no specific lineage of C. albicans that is associated with IBD, but rather that the three study populations do have distinguishable distributions of genotypes. In addition, phenotypic characterization by means of enzyme release assays revealed trends between genotypes and virulence-related enzyme activity. Furthermore, correlations were observed between the clinical inflammation biomarker fecal calprotectin and serum anti- Saccharomyces cerevisiae antibodies, as well as between lipase activity of feces-derived C. albicans strains and serum 1,3-{beta}-glucan levels. We thus show that microsatellite typing can describe genetic diversity of feces-derived C. albicans strains, and that phenotypic diversity of these strains may indeed correlate with fungal genotype or disease. This study opens further possibilities to investigate fecal fungi in relation to severity of inflammation in IBD or in other (intestinal) diseases.

microbiology↗

bioRxiv2024

Fungal pathogens exposed - genomic and phenotypic insights into Candida auris and its relatives of the Candida haemulonii species complex

Candida auris showed the world the ability of fungi to rapidly emerge as an urgent threat to public health. Close relatives of the Candida haemulonii complex exhibit also a similar multi-drug resistant nature and are increasingly reported as nosocomial pathogens. Here, we analyze both complete genomes assemblies and extensive phenotypic data for the five C. auris clades and pathogenic and non-pathogenic species related to the C. haemulonii species complex. First, we resolved the phylogeny of the species complex. Next, comparing C. auris to its pathogenic and non-pathogenic relatives we identified a pathogenic potential for the whole C. haemulonii species complex by shared gene content and phenotypic traits linked to drug resistance and virulence. In vivo virulence assays using the Galleria mellonella fungal infection model show that C. auris strains are significantly more virulent than any of the sibling species in the C. haemulonii complex. Phenotypic analysis links the increased virulence of C. auris to a more stress resistant phenotype compared to its siblings.

microbiology↗

bioRxiv2023

A yeast love triangle: multiple hybridizations shape genome evolution in the Pichia cactophila species complex.

Hybrids are chimeric organisms carrying genetic material from at least two divergent parental lineages. Hybridization can contribute to the emergence of novel lineages with unique phenotypic traits that may facilitate their adaptation to new environments. In recent years, genomic analyses have revealed the hybrid nature of several opportunistic human pathogenic yeasts. One of them is Candida inconspicua, a member of the Pichia cactophila species complex, for which all sequenced strains are hybrids isolated from Europe with so far unknown parentals. It has been recently proposed that C. inconspicua and P. cactophila s.s. should be ranked as the same species due to their genetic similarity. To obtain a better understanding of the evolution of this clade, we sequenced the genomes of the P. cactophila type strain, of its close-relative Pichia pseudocactophila, and of a putative C. inconspicua clinical isolate from Alaska and compared them with the previously sequenced genomes of Pichia norvegensis, C. inconspicua and the recently described Pichia galeolata. Our results show evidence for the existence of distinct hybrid lineages within this clade and suggest an intricate scenario of recurrent hybridizations in this species complex, some of them giving rise to lineages with the ability to infect humans. Given their different hybridization histories, we propose that C. inconspicua, P. cactophila, and the new clinical isolate from Alaska should represent three distinct species and suggest the name Pichia alaskaensis for the new taxon. Moreover, the name C. inconspicua is recombined in the genus Pichia as P. inconspicua. Our results clarify the evolutionary relationships within the P. cactophila species complex and underscore the importance of non-vertical evolution.

microbiology↗

bioRxiv2022

Candida khanbhai sp. nov., a new clinically relevant yeast within the Candida haemulonii species complex

Invasive fungal infections caused by non-albicans Candida species are increasingly reported. Recent advances in diagnostic and molecular tools enabled better identification and detection of these emerging pathogenic yeasts. Several of these emerging species belong to the Candida haemulonii species complex, which attracted much attention due to the rapid global emergence of its multi-drug resistant member Candida auris. Here, we describe a new clinically relevant yeast isolated from geographically distinct regions, representing the proposed novel species Candida khanbhai, member of the C. haemulonii species complex. Moreover, several members of the C. haemulonii species complex were observed to be invalidly described, including Candida auris and Candida vulturna. Hence, the opportunity was taken to correct this here, formally validating the names of various yeast species.

microbiology↗

bioRxiv2017

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype A/A) and of hybrids with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil revealed that the previously African VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen.\n\nAuthor SummaryCryptococcus neoformans var. grubii is a human fungal pathogen of immunocompromised individuals that has global clinical impact, causing half a million deaths per year. Substantial genetic substructure exists for this pathogen, with two lineages found globally (VNI, VNII) whereas a third has appeared confined to sub-Saharan Africa (VNB). Here, we utilized genome sequencing of a large set of global isolates to examine the genetic diversity, hybridization, and biogeography of these lineages. We found that while the three major lineages are well separated, recombination between the lineages has occurred, notably resulting in hybrid isolates with segmented ancestry across the genome. In addition, we showed that isolates from South America are placed within the VNB lineage, formerly thought to be confined to Africa, and that there is phylogenetic separation between these geographies that substantially expands the diversity of these lineages. Our findings provide a new framework for further studies of the dynamics of natural populations of C. neoformans var. grubii.

genomics↗