The High-Quality Complete Genome Sequence of the Opportunistic Fungal Pathogen Candida vulturna CBS 14366T

Cryptococcal meningitis due to Cryptococcus neoformans VNI in a koala (Phascolarctos cinereus) with progressive neurological disease

Nearly all cases of cryptococcosis in koalas are caused by Cryptococcus gattii species complex. A rare case of meningitis due to Cryptococcus neoformans VNI/AFLP1 (abbreviated VNI) is described in a koala with nasal colonisation by both species complexes. An eight-year-old koala in a wildlife park presented for seizures and returned a positive latex cryptococcal antigen agglutination test. The koala was euthanased due to the severity of disease, and a post-mortem computed tomography study showed mild mucosal thickening of the right nasal turbinates. The necropsy also showed slightly turbid cisternal cerebrospinal fluid and meningeal opacity. Histology revealed severe granulomatous cryptococcal meningitis and paucireactive right cryptococcal rhinitis. Fungal cultures yielded heavy pure growths of C. neoformans from the brain and spinal cord, and comparable heavy growths of both C. neoformans and C. gattii from the nasal cavity. Cryptococcus species complexes were identified by mass spectrometry (MALDI-TOF) and multi-locus sequence typing (MLST). The C. neoformans isolates from the brain, spinal cord and nasal cavity were identical by MLST and classified as sequencing type (ST) 23 and molecular type (MT) VNI. The C. gattii isolates were classified as ST 51 and AFLP4/VGI (abbreviated VGI). This suggests that the meningitis developed as an extension of C. neoformans VNI from nasal cavity colonisation. This is the second documented case of central nervous system (CNS) cryptococcosis due to C. neoformans species complex in a koala and the first in Australia. Despite heavy nasal colonisation by C. gattii, only the C. neoformans isolate progressed to meningitis.

De Novo Genome Assembly and Comparative Genome Analysis of the Novel Human Fungal Pathogen Trichosporon austroamericanum Type-Strain CBS 17435

Trichosporon austroamericanum is a recently described species recognized for its emerging clinical significance in invasive trichosporonosis. In this study, we present the nanopore long-read-based de novo genome assembly of the type-strain CBS 17435. Additionally, we performed genomic comparative analyses with its closest relative, Trichosporon inkin.

Sporothrix davidellisii : A new pathogenic species belonging to the Sporothrix pallida complex

Sporothrix species (Ascomycota, Ophiostomatales) are dimorphic fungi with diverse ecological niches, ranging from mammalian, plant, and insect pathogens to fungicolous organisms. Here, we describe Sporothrix davidellisii (CBS 147636T), a novel pathogenic species within the S. pallida complex isolated from a case of feline sporotrichosis in Melbourne, Australia. Phylogenetic analyses based on ITS, β-tubulin (BT2), calmodulin (CAL), and translation elongation factor 1-α (EF1-α) sequences confirmed its distinctiveness, with ITS sequence identity to its closest relative (S. chilensis) not exceeding 97.6%. The assembled genome is 39.02 Mb (eight contigs) with a 27.2 kb mitochondrial genome and a total of 12,631 predicted genes. Genetic diversity analyses revealed moderate nucleotide variation in the ITS region (π = 0.055), greater diversity in BT2 (π = 0.098), and CAL (π = 0.118), supporting its status as a unique species. Morphological studies revealed distinctive characteristics differentiating S. davidellisii from its nearest relatives, including elongated clavate sympodial conidia and sessile conidia. Notably, S. davidellisii exhibits yeast-like growth at 37°C, forming ellipsoid to ovoid budding cells in liquid media, although cigar-shaped yeasts, characteristic of highly virulent Sporothrix species, are rarely observed. This ability to transition to a yeast-like form, combined with its high-temperature tolerance (growth up to 40°C), underscores its opportunistic pathogenic potential. The pathogenic role of S. davidellisii highlights the importance of monitoring atypical Sporothrix infections in feline hosts, which may serve as environmental sentinels for emerging fungal pathogens. These findings expand the taxonomy of Sporothrix, contributing to our understanding of the evolutionary complexity and zoonotic potential of species within the S. pallida complex.

Mechanism of azole resistance in Candida vulturna, an emerging multidrug resistant pathogen related with Candida haeumulonii and Candida auris

BACKGROUND

Candida vulturna is an emerging pathogen belonging to the Metshnikowiaceae family together with Candida auris and Candida haemulonii species complex. Some strains of this species were reported to be resistant to several antifungal agents.

OBJECTIVES

This study aims to address identification difficulties, evaluate antiungal susceptibilities and explore the molecular mechanisms of azole resistance of Candida vulturna.

METHODS

We studied five C. vulturna clinical strains isolated in three Colombian cities. Identification was performed by phenotypical, proteomic and molecular methods. Antifungal susceptibility testing was performed following CLSI protocol. Its ERG11 genes were sequenced and a substitution was encountered in azole resistant isolates. To confirm the role of this substitution in the resistance phenotype, Saccharomyces cerevisiae strains with a chimeric ERG11 gene were created.

RESULTS

Discrepancies in identification methods are highlighted. Sequencing confirmed the identification as C. vulturna. Antifungal susceptibility varied among strains, with four strains exhibiting reduced susceptibility to azoles and amphotericin B. ERG11 sequencing showed a point mutation (producing a P135S substitution) that was associated with the azole-resistant phenotype.

CONCLUSIONS

This study contributes to the understanding of C. vulturna's identification challenges, its susceptibility patterns, and sheds light on its molecular mechanisms of azole resistance.

Case report and literature review of refractory fungemia caused by Candidavulturna

Candida vulturna is a recently discovered and not widely documented ascomycetous yeast phylogenetically related to the outbreak-causing and multidrug-resistant Candida auris. A middle-aged Japanese man with no discernible immunodeficiency was admitted to hospital with ileal diverticulitis. Following laparoscopic right hemicolectomy against abscess formation on postoperative day (POD) 7, continuous fungemia occurred due to Candida haemulonii, identified using a conventional method by confirming the biochemical phenotype. Micafungin was initiated; however, the fungus was persistently isolated from blood cultures. Eventually, the antifungal agent was changed to a combination of liposomal amphotericin B (L-AMB) and caspofungin (CPFG), which cleared the infection, and no pathogens were detected in the blood cultures on POD 31. Contrast-enhanced computed tomography showed septic emboli in the lungs and spleen; however, no evidence of vasculitis was observed. Moreover, sequential echocardiography did not reveal any signs of infectious endocarditis. Finally, CPFG and L-AMB were administered to the patient for 7 and 9 weeks, respectively, during which the patient's symptoms did not relapse. The strain was later genetically identified as C. vulturna. This case report illustrates a clinical presentation of C. vulturna and provides the diagnostic approach and treatment methods for this pathogen.

Complete Genome Sequence of the Itraconazole Decreased Susceptible Madurella fahalii Type-Strain CBS 129176

Madurella fahalii is a causative agent of the implantation mycosis mycetoma with decreased susceptibility to itraconazole, the preferred therapeutic drug to combat mycetoma. Here, we report the M. fahalii type-strain CBS 129176 genome assembly and annotation to identify a glutamic acid insert near the azole-binding pocket in the Cyp51A protein.

Candida vulturna Outbreak Caused by Cluster of Multidrug-Resistant Strains, China

Candida vulturna belongs to the Candida haemulonii species complex and is phylogenetically related to C. auris. We report a C. vulturna outbreak among persons in Shanxi Province, China, during 2019-2022. Isolates were resistant to multiple antifungal drugs and exhibited enhanced adhesion and biofilm formation properties.

Whole-genome sequencing of Candida haemulonii species complex from Brazil and the United States: Genetic diversity and antifungal susceptibility

Candida haemulonii complex species can be multidrug-resistant and cause infections such as candidemia. This study determined the genetic relationship between isolates from Brazil and the United States through whole-genome sequencing and performed antifungal susceptibility testing to investigate drug resistance. Contrary to what is widely described, most isolates were susceptible to azoles. However, an atypical susceptibility profile was found in 50% of Candida pseudohaemulonii strains, including resistance to the three echinocandins. Isolates from both countries formed distinct clusters with wide genetic diversity. Isolates from three hospitals in Brazil were clonal and involved in candidemia cases, pointing to the importance of improving hospital infection control measures and molecular identification.

A surprising finding: The curious case of a tongue lesion misdiagnosed as paracoccidioidomycosis

BACKGROUND

Paracoccidioidomycosis is an endemic mycosis caused by members of the Paracoccidioides genus. Brazil remains the focus area and, to a lesser extent, the disease has been reported from Argentina, Colombia and Venezuela.

AIMS

A Venezuelan Paracoccidioides brasiliensis strain, isolated from a patient diagnosed with chronic multifocal paracoccidioidomycosis, was subjected to whole genome sequencing to provide more insight about Paracoccidioides outside the endemic focus area.

METHODS

P. brasiliensis strain CBS 118890 was whole genome sequenced using nanopore; library preparation with the 'native barcoding genomic DNA kit' was followed by sequencing on Flongle and MinION flowcells. Batches of strain CBS 118890 were re-identified by sequencing the internal transcribed spacer (ITS) region, and final identification was made based on phylogenetic analysis.

RESULTS

Surprisingly, the Venezuelan P. brasiliensis strain CBS 118890 turned out to be a Nannizziopsis species. The batches of this strain were ITS sequenced followed by phylogenetic analysis and resulted in the final identification of Nannizziopsis arthrosporioides.

CONCLUSIONS

Nannizziopsis infections are commonly seen in a wide variety of reptiles, but are particularly rare in human infections. This case underlines the need for molecular characterization of cases that clinically mimic paracoccidioidomycosis but that are serologically negative for Paracoccidioides.

Candida haemulonii Complex and Candida auris: Biology, Virulence Factors, Immune Response, and Multidrug Resistance

There is worldwide concern about the constant increase in infections caused by Candida species that are multiresistant to antifungal drugs. The most common candidiasis is caused by Candida albicans, however, the species of the Candida haemulonii complex and Candida auris are emerging opportunistic pathogens, which isolation from clinical samples has significantly increased in the past years. The special interest in the study of these species lies in their ability to evade the action of antifungal drugs, such as amphotericin B, azoles, and echinocandins. In addition, the phenotypic changes of these species have given them the ability to easily adapt to environmental changes, including the host milieu and immunity. In this paper, a detailed review of the current literature on the C. haemulonii complex and C. auris is shown, analyzing aspects such as biology, immune response, putative virulence factors, infection, treatment, and the current strategies for diagnosis.

Case report: Catheter related blood stream infection caused by Candida vulturna

Candida vulturna is a newly emerging candida species belong to Candida haemulonii species complex of Metschnikowiaceae family. Numerous clinical samples have been reported to isolate C. vulturna since discovery. We report a case of catheter related blood stream infection in which C. vulturna was isolated from blood in patient after prolong antibiotic therapy for recurrent infection of retroperitoneal cyst. The blood isolate was identified to species level by molecular assay targeting D1/D2 regions of 26s rDNA gene. The patient improved with administration of intravenous micafungin despite lack of antifungal susceptibility breakpoints.

Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil

Candida auris has been reported worldwide, but only in December 2020, the first strain from a COVID-19 patient in Brazil was isolated. Here, we describe the genome sequence of this susceptible C. auris strain and performed variant analysis of the genetic relatedness with strains from other geographic localities.

The secreted acid trehalase encoded by the CgATH1 gene is involved in Candida glabrata virulence

BACKGROUND

Candida glabrata yeast is the second cause of candidiasis worldwide. Differs from other yeasts since assimilates only glucose and trehalose (a characteristic used in rapid identification tests for this pathogen) by secreting into the medium a highly active acid trehalase encoded by the CgATH1 gene.

OBJECTIVE

This study aimed to characterise the function of the acid trehalase in the physiopathology of C. glabrata.

METHODS

Gene deletion was performed to obtain a mutant ath1Δ strain, and the ability of the ath1Δ strain to grow in trehalase, or the presence of trehalase activity in the ath1Δ yeast cells, was verified. We also tested the virulence of the ath1Δ strain in a murine model of infection.

FINDINGS

The ath1Δ mutant strain grows normally in the presence of glucose, but loses its ability to grow in trehalose. Due to the high acid trehalase activity present in wild-type cells, the cytoplasmic neutral trehalase activity is only detected in the ath1Δ strain. We also observed a significantly lower virulence of the ath1Δ strain in a murine model of infection with either normal or immunocompromised mice.

MAIN CONCLUSIONS

The acid trehalase is involved in the hydrolysis of external trehalose by C. glabrata, and the enzyme also plays a major virulence role during infectivity.

Understanding the Emergence of Multidrug-Resistant Candida: Using Whole-Genome Sequencing to Describe the Population Structure of Candida haemulonii Species Complex

The recent emergence of a multidrug-resistant yeast, Candida auris, has drawn attention to the closely related species from the Candida haemulonii complex that include C. haemulonii, Candida duobushaemulonii, Candida pseudohaemulonii, and the recently identified Candida vulturna. Here, we used antifungal susceptibility testing and whole-genome sequencing (WGS) to investigate drug resistance and genetic diversity among isolates of C. haemulonii complex from different geographic areas in order to assess population structure and the extent of clonality among strains. Although most isolates of all four species were genetically distinct, we detected evidence of the in-hospital transmission of C. haemulonii and C. duobushaemulonii in one hospital in Panama, indicating that these species are also capable of causing outbreaks in healthcare settings. We also detected evidence of the rising azole resistance among isolates of C. haemulonii and C. duobushaemulonii in Colombia, Panama, and Venezuela linked to substitutions in ERG11 gene as well as amplification of this gene in C. haemulonii in isolates in Colombia suggesting the presence of evolutionary pressure for developing azole resistance in this region. Our results demonstrate that these species need to be monitored as possible causes of outbreaks of invasive infection.