Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections

Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens

Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.

IMPORTANCE

A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.

Scheffersomyces tanahashii sp. nov., isolated from the cocoon wall of the stag beetle Prosopocoilus astacoides blanchardi

A previous investigation of symbiotic yeasts associated with the stag beetle Prosopocoilus astacoides blanchardi isolated strains of the genus Scheffersomyces from the cocoon walls, larval midgut, larval hindgut and larval tunnels. Phylogenetic analysis of the D1/D2 domains of the LSU rRNA gene sequences revealed identical sequences, indicating that they belonged to the same species, but suggested that the species was new. In this study, sequence analysis and physiological characterization identified a representative strain of these beetle-associated yeasts as a novel species in the genus Scheffersomyces. The sequence similarities of the concatenated LSU domains and internal transcribed spacer regions indicated that strain BCRC 23563T forms a well-supported and distinct species in the xylose-fermenting Scheffersomyces subclade, with the sequences for each gene differing in nt substitutions from those of previously described related species by at least 1.06% and 2.7% respectively. The physiological characteristics of the novel species were also distinct from those of the closely related described species, though it could still process xylose as is expected of stag beetle-associated Scheffersomyces symbionts. Based on the data, a novel yeast species, Scheffersomyces tanahashii sp. nov., is proposed to accommodate this strain. The holotype is BCRC 23563T (ex-type strains NBRC 116731 and NCYC 4470). The MycoBank accession number is 857608.

In the flow of molecular miniaturized fungal diagnosis

The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.

Phaeohyphomycosis Due to Verruconis gallopava: Rare Indolent Pulmonary Infection or Severe Cerebral Fungal Disease?

INTRODUCTION

Phaeohyphomycoses are uncommon and poorly understood opportunistic fungal infections, characterized by a wide spectrum of clinical manifestations ranging from localized skin lesions to disseminated disease. Most frequent genera are Alternaria, Cladophialophora, Exophiala or Curvularia. Less common ones, such as Verruconis gallopava, initially described as responsible of encephalitis of turkeys, pose significant challenges for diagnosis and treatment.

MATERIAL AND METHODS

Following the description of a clinical case, we performed a comprehensive review of 48 cases of V. gallopava infection, a rarely reported species from 1986 to 2024.

RESULTS

Solid organ transplant recipients and patients with hematological malignancies are the population most at-risk. Clinical presentation is nonspecific but can be divided in two main entities, pulmonary and cerebral localizations. This later is associated with a mortality rate over 80% and was significantly more frequently reported in liver transplant recipients (p = 0.03). When tested, ß-D-glucans were positive in all cases. Antifungal susceptibility testing demonstrated low MICs for amphotericin B and all azoles but isavuconazole and fluconazole. Clinical outcomes support the use of amphotericin B, voriconazole, itraconazole and posaconazole as valid treatment options.

DISCUSSION

It is not known whether the cerebral cases are primary or secondary to pulmonary lesions. The indolent pulmonary lesions should prompt a complete work-up including biopsy with pathology and mycology expertise since the differential diagnosis is a cancer lesion.

Multigene phylogeny, bioactive properties, enzymatic and dye decolorization potential of selected marine fungi from brown algae and sponges of Mauritius

Marine fungi represent an important proportion of the microbial diversity in the oceans. They are attractive candidates for biotechnological purposes and industrial applications. Despite an increasing interest in mycology, marine fungi associated with sponges and algae have been poorly studied in Mauritius. The objectives of this study were to: 1) use multigene phylogenetic analyses to identify isolated marine fungi; 2) determine the differences in the antimicrobial and antioxidant properties of the fungal extracts; and 3) assess their enzyme activities and dye decolorization potential. Five fungal isolates viz Aspergillus chevalieri, Aspergillus iizukae, Aspergillus ochraceus, Exserohilum rostratum and Biatriospora sp. were identified based on phylogenetic analyses. There was no significant difference in the antimicrobial properties of the liquid and solid media extracts unlike the antioxidant properties (p < 0.05). The solid media extract of Aspergillus chevalieri (F2-SF) had a minimum inhibitory concentration of 0.156 mg/ml against Staphylococcus aureus while Aspergillus ochraceus (F25-SF) had a minimum inhibitory concentration of 0.313 and 2.5 mg/ml against Enterococcus faecalis and Salmonella typhi. The solid media extract of Biatriospora sp. (F34-SF) had a minimum inhibitory concentration of 0.195 and 1.563 mg/ml against Bacillus cereus, Escherichia coli and Enterobacter cloacae. An IC50 of 78.92 ± 4.71 μg/ml in the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) scavenging assay, ferric reducing antioxidant power (FRAP) value of 11.17 ± 0.20 mM Fe2+/g dry weight extract (DWE) and total phenolic content 360.35 ± 10.31 mg GAE/g DWE was obtained with the solid media extract of Aspergillus chevalieri (F2-SF). Aspergillus ochraceus (F25-SF) and Biatriospora sp. (F34-SF) solid media extracts showed lower IC50 values in the DPPH assay and higher total phenolic content as compared to the liquid media extracts. Aspergillus chevalieri was a good producer of the enzymes DNAse and lipase and had maximum percentage dye decolorization of 79.40 ± 17.72% on Congo red. An enzymatic index ≥ 2 was found for the DNAse and lipase and the maximum percentage dye decolorization of 87.18 ± 3.80% was observed with Aspergillus ochraceus on Methylene blue. Regarding Biatriospora sp., it was a moderate producer of the three enzymes amylase, DNAse and protease and had a maximum dye decolorization potential of 56.29 ± 6.51% on Crystal violet. This study demonstrates that Mauritian marine fungi possess good bioactive properties, enzymatic and dye decolorization potentials, that can potentially be considered for use in pharmaceutical and industrial applications.

Diversity of Leaf Fungal Endophytes from Two Coffea arabica Varieties and Antagonism towards Coffee Leaf Rust

Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.

Identification of Chromoblastomycosis and Phaeohyphomycosis Agents through ITS-RFLP

Chromoblastomycosis (CBM) and phaeohyphomycosis (FEO) are infections caused by melanized filamentous fungal agents, primarily found in tropical and subtropical regions. Both infections pose significant challenges for the correct identification of the causative agent due to their morphological similarity, making conventional methods of morphological analysis highly subjective. Therefore, molecular techniques are necessary for the precise determination of these species. In this regard, this study aimed to contribute to a new methodology based on PCR-RFLP for the identification of agents causing CBM and FEO. Sequences from the Internal Transcribed Spacer (ITS) region were used to identify potential restriction enzyme sites in silico, followed by in vitro validation using the selected restriction enzymes. The obtained results were compared with species identification through morphological analyses and sequencing. The results demonstrated that the PCR-RFLP applied in this study accurately identified two major agents of chromoblastomycosis, Fonsecaea pedrosoi and Fonsecaea monophora, as well as Cladophialophora bantiana and Exophiala dermatitidis, both causative agents of phaeohyphomycosis. In this context, the proposed assay can complement current methods for identifying these species, aiding in diagnosis, and contributing to the proper management of these infections.

Genetic diversity and population differentiation in Earliella scabrosa, a pantropical species of Polyporales

Earliella scabrosa is a pantropical species of Polyporales (Basidiomycota) and well-studied concerning its morphology and taxonomy. However, its pantropical intraspecific genetic diversity and population differentiation is unknown. We initiated this study to better understand the genetic variation within E. scabrosa and to test if cryptic species are present. Sequences of three DNA regions, the nuclear ribosomal internal transcribed spacer (ITS), the large subunit ribosomal DNA (LSU), and the translation elongation factor (EF1α) were analysed for 66 samples from 15 geographical locations. We found a high level of genetic diversity (haplotype diversity, Hd = 0.88) and low nucleotide diversity (π = 0.006) across the known geographical range of E. scabrosa based on ITS sequences. The analysis of molecular variance (AMOVA) indicates that the genetic variability is mainly found among geographical populations. The results of Mantel tests confirmed that the genetic distance among populations of E. scabrosa is positively correlated with the geographical distance, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Based on phylogenetic analyses of combined dataset ITS-LSU-EF1α, the low intraspecific divergences (0-0.3%), and the Automated Barcode Gap Discovery (ABGD) analysis, E. scabrosa can be considered as a single species with five different geographical populations. Each population might be in the process of allopatric divergence and in the long-term they may evolve and become distinct species.

Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management

Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.

Virulence of Beauveria sp. and Metarhizium sp. fungi towards fall armyworm (Spodoptera frugiperda)

The development of effective pest management strategies for Spodoptera frugiperda is a high priority for crop protection across its invasive ranges. Here, we examined six Beauveria and five Metarhizium fungal isolates against this pest. Two Beauveria isolates (B-0571, B-1311) induced high mortality toward 3rd and 6th instar caterpillars and adults. For B-0571 mortality was 82.81 ± 5.75%, 61.46 ± 6.83%, and 93.75 ± 3.61%, and 73.72 ± 2.51%, 71.88 ± 5.41%, and 97.92 ± 2.08% for B-1311, with deaths in caterpillars largely occurring under 24 h (3rd instar control 0.74 ± 0.33%, B-0571 73.96 ± 7.85% and B-1311 62.08 ± 3.67%; 6th instar control 0%, B-0571 66.67% ± 11.02% and B-1311 62.5% ± 9.55%). Infection from both Beauveria isolates fully prevented reproduction in surviving S. frugiperda females. In contrast, all five Metarhizium isolates tested and the remaining four Beauveria isolates exhibited lower virulence. The discovery of two highly virulent Beauveria fungal isolates to S. frugiperda opens avenues to develop novel biological control tools against this highly invasive pest.

Development of reference genes for RT-qPCR analysis of gene expression in Pleurotus pulmonarius for biotechnological applications

Jatropha curcas is an oilseed crop with biorefinery applications. Whilst cake generated following oil extraction offers potential as a protein source for animal feed, inactivation of toxic phorbol esters present in the material is necessary. Pleurotus pulmonarius is a detoxifying agent for jatropha cake with additional potential as animal feed, edible mushroom and for enzyme production. For the characterization of fungal genes involved in phorbol ester degradation, together with other industrial applications, reverse transcription-quantitative PCR (RT-qPCR) is a tool that enables accurate quantification of gene expression. For this, reliable analysis requires reference genes for normalization of mRNA levels validated under conditions employed for target genes. The stability of potential reference genes β-TUB, ACTIN, GAPDH, PHOS, EF1α, TRPHO, LAC, MNP3, MYP and VP were evaluated following growth of P. pulmonarius on toxic, non-toxic jatropha cake and a combined treatment, respectively. NormFinder and geNorm algorithms for expression stability analysis identified PHOS, EF1α and MNP3 as appropriate for normalizing gene expression. Reference gene combinations contrasting in ranking were compared following normalization of relative expression of the CHU_2040 gene, encoding an esterase enzyme potentially involved in phorbol ester degradation. The reference genes for P. pulmonarius will facilitate the elucidation of mechanisms involved in detoxification of phorbol esters as well as analysis of target genes for application in biorefinery models.

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.

Biodeterioration of carbographic ribbon: Isolation, identification of causal agents and forensic implications

This study is part of a comprehensive investigation that was performed in regard to a case of alterations on a carbographic ribbon used in a typewriter that was found and seized by inner security operations of the Arma dei Carabinieri, Italy. Thirty-six coded scripts possessing potentially and criminally liable content were present on the tape; however, only the 6th and 7th scripts exhibited alterations of an uncertain nature. The study included sampling that was performed under sterile conditions of a large surface area of carbographic ribbons. A protocol based on physico-chemical, microbiological, and biomolecular tools was established. Preliminary results revealed the presence of fungal contamination that was primarily located on the inner surface of the 6th and 7th scripts on the black carbographic ribbon. One fungal strain was isolated and identified by universal ITS-PCR primer and rDNA sequencing as Alternaria infectoria strain NIS4. Fungal growth was monitored for 3 weeks in the laboratory under different environmental conditions (temperature, open-closed system, and substrate). The A. infectoria NIS4 strain exhibited the best growth at 28°C under a closed system with RH near saturation. We also noted that the fungal growth was abundant at 15°C. Moreover, this fungus (a potential human pathogen) possessed the ability to colonize the surface of the new carbographic ribbon even when using mineral medium; however, this only occurred in a closed system environment and not in open systems due to rapid desiccation. Under our experimental conditions, the A. infectoria NIS4 strain could degrade gelatin as an organic matter present in trace amounts that are often used as a binder in a carbographic ribbon emulsions. The results revealed that the isolated microorganism was the major biological candidate capable of altering the investigated carbographic ribbon; however, these alterations could only occur under favourable environmental conditions.

AIMS

Identify the cause of microbial alterations on a carbographic ribbon in a typewriter used in a hypogean Italian criminal house named "covo."

METHODS AND RESULTS

The isolation and identification of biodeteriogens (Alternaria infectoria NIS4) were performed using both culture-dependent and-independent methods, including ITS regions-primed PCR and rDNA techniques. Environmental scanning electron microscopy (ESEM) and optical observations were also performed. Growth tests and biodeterioration simulation tests on carbographic ribbons at the lab scale were performed under different environmental conditions. The A. infectoria NIS4 strain exhibited biodeterioration activity on carbographic ribbons under environmental conditions that were extremely favourable for growth. A high ability to colonize carbographic ribbon surfaces with fast and abundant growth at both 15°C and 28°C under lab-scale conditions at RH near saturation was observed.

CONCLUSIONS

In this forensic case study, the ability of the isolated micromycetes A. infectoria NIS4 strain to colonize and induce alterations and degradation in a carbographic ribbon stored under indoor environmental conditions was examined. When favourable conditions change over time, the risk of microbial colonization and the damage produced by the fungal biodeterioration processes on the synthetic material objects has been confirmed.

SIGNIFICANCE AND IMPACT OF STUDY

The current study contributes to the knowledge of biodeterioration processes in carbographic ribbon and the responsible agents, and our study provides an example of how environmental microbiology can also aid in forensic studies.

A local Talaromyces atroroseus TRP-NRC isolate: isolation, genetic improvement, and biotechnological approach combined with LC/HRESI-MS characterization, skin safety, and wool fabric dyeing ability of the produced red pigment mixture

Background

During the last decade, enormous research efforts have been directed at identifying potent microorganisms as sustainable green cell factories for eco-friendly pigments. Talaromyces atroroseus has recently been shown to excrete large amounts of azaphilone mycotoxin-free red pigment mixture comprising some known coloring components together with many uncharacterized metabolites. In this study, a new Talaromyces atroroseus isolate was identified via sequencing of the fragment of the nuclear ribosomal gene cluster containing internal transcribed spacers and 5.8S rRNA gene. The parameters that affected the level of pigment production were optimized in uncommon static conditions of culture and genetic improvement, via γ-irradiation, to improve pigment yield. Moreover, chemical characterization using LC/MS and skin safety test of the target pigment mixture were precisely conducted to maximize its benefits as a natural and safe red pigment for wool fabrics.

Results

Molecular identification via the sequencing of the ITS of the rDNA encoding gene cluster revealed that the fungal isolate TRP-NRC was T. atroroseus TRP-NRC (deposited in GenBank under accession number MW282329). In the static conditions of culture, pigment production was dramatically enhanced to 27.36 g/L in an optimum yeast malt peptone medium of 2% mannitol at pH 2−4.5 and 30 °C for 7 days of incubation. Under exposure to a 400-Gy γ-radiation dose, pigment yield was increased to a 3-fold level higher than that recorded for the wild type. Based on the inter-simple sequence repeats (ISSR), as a molecular marker tool, the wild-type T. atroroseus TRP-NRC strain and its mutants were discriminated. The UHPLC/HRESI-MS analytical tool characterized 60 metabolites, including many unknown molecules, at appropriate concentrations. It is worthy to note that four mitorubrin derivatives were identified for the first time in T. atroroseus, i.e., mitorubrinolamine acetate, dihydro-PP-O, mitorobrinal, and mitorubrinol. The range of irritation indexes (0−0.1) demonstrated an adequate skin safety after the direct local application of the pigment mixture. Finally, the pigment mixture exhibited a remarkably good dyeing ability in wool fabrics, with high-fastness properties.

Conclusions

Because of its sustainable and economic production, the target red pigment mixture may be applied in the future in textile, food, cosmetics, or different pharmaceutical industries after extensive conventional safety and toxicity studies, which are currently under consideration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00335-2.

Genetic and Phenotypic Characterization of the Fungal Pathogen Cytospora plurivora from Western Colorado Peach Orchards and the Development of a ddPCR Assay for Detection and Quantification

Cytospora canker is one of the most important diseases affecting peach production in Colorado, yet previous efforts to characterize Cytospora species diversity in Colorado have relied exclusively on morphological traits. Recently, several new Cytospora species were described from peach orchards within the United States using molecular and morphological data, prompting the need to reexamine Cytospora spp. present on peach trees in Colorado. A total of 137 isolates of Cytospora spp. were collected from eight orchards in western Colorado. Isolates were sequenced at the internal transcribed spacer region and elongation factor 1-α and assessed with reference sequences in phylogenetic analyses. All isolates from western Colorado peach trees resolved with the newly described Cytospora plurivora. In addition to molecular characterization, temperature growth and virulence assays were conducted to assess phenotypic variation among the isolates from western Colorado. Variation across isolates was found both in growth at different temperatures and in virulence. Ancestral state reconstruction analyses resolved the most virulent (and most often collected) haplotypes together in a well-supported clade from which a single monophyletic origin of high virulence can be inferred. Finally, a droplet digital PCR assay was developed for use in ongoing and future studies to detect and quantify C. plurivora from field and laboratory samples.

The developed molecular biological identification tools for mycetoma causative agents: An update

Mycetoma is a chronic granulomatous inflammatory disease that is caused either by bacteria or fungi. Bacterial mycetoma (actinomycetoma) can be caused by various causative agents of the genera Nocardia, Streptomyces and Actinomadura. On the other hand, fungal mycetoma (eumycetoma) is most commonly caused by causative agents belonging to the genera Madurella, Scedosporium and Falciformispora. Early and accurate diagnosis of the causative organisms can guide proper patient management and treatment. To allow rapid and accurate species identification, different molecular techniques were developed over the past decades. These techniques can be protein based (MALDI-TOF MS) as well as DNA based (Sequencing, PCR and isothermal amplification methods). In this review, we provide an overview of the different molecular techniques currently in use and identify knowledge gaps, which need to be addressed before we can implement molecular diagnostics for mycetoma in different clinical settings.

Plant associated fungal endophytes as a source of natural bioactive compounds

Endophytes are a potent source of bioactive compounds that mimic plant-based metabolites. The relationship of host plant and endophyte is significantly associated with alteration in fungal colonisation and the extraction of endophyte-derived bioactive compounds. Screening of fungal endophytes and their relationship with host plants is essential for the isolation of bioactive compounds. Numerous bioactive compounds with antioxidant, antimicrobial, anticancer, and immunomodulatory properties are known to be derived from fungal endophytes. Bioinformatics tools along with the latest techniques such as metabolomics, next-generation sequencing, and metagenomics multilocus sequence typing can potentially fill the gaps in fungal endophyte research. The current review article focuses on bioactive compounds derived from plant-associated fungal endophytes and their pharmacological importance. We conclude with the challenges and opportunities in the research area of fungal endophytes.

Cyphellophora laciniata: A new etiological agent of chromoblastomycosis

Chromoblastomycosis is a chronic subcutaneous mycosis caused by traumatic inoculation of dematiaceous fungi especially in tropical and subtropical areas. Cyphellophora genus include melanized fungi reported as etiological agents of skin and nail infections. We report a 60-year-old male from the south of Mexico with a 40-year history of chromoblastomycosis caused by Cyphellophora laciniata. The isolated fungus was identified by sequencing of the internal transcribed spacer region of rDNA. The patient was treated with itraconazole and cryosurgery with unsatisfactory results.

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.

Identification of molds with MALDI-TOF mass spectrometry: performance of the newly developed MSI-2 application in comparison with the Bruker filamentous fungi database and MSI-1

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) represents a promising tool for the rapid and efficient identification of molds, but improvements are still necessary to achieve satisfactory results when identifying cryptic species. Here, we aimed to validate a new web application, MSI-2, which replaces MSI-1, an application that was built and deployed online in 2017. For the evaluation, we gathered 633 challenging isolates obtained from daily hospital practice that were first identified with DNA-based methods, and we submitted their corresponding mass spectra to three identification programs (Bruker, MSI-1 and MSI-2). The MSI-2 application had a better identification performance at the species level than MSI-1 and Bruker, reaching 83.25% correct identifications compared with 63.19% (MSI-1), 38.07% (Bruker with 1.7 threshold) and 21.8% (Bruker with 2.0 threshold). The MSI-2 application performed especially well for Aspergillus and Fusarium species, including for many cryptic species, reaching 90% correct identifications for Aspergillus species and 78% for Fusarium species compared to 69% and 43% with MSI-1. Such improvement may have a positive impact on patient management by facilitating the identification of cryptic species potentially associated with a specific antifungal resistance profile.

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

Antifungal Susceptibility Testing and Identification

The requirement for antifungal susceptibility testing is increasing given the availability of new drugs, increasing populations of individuals at risk for fungal infection, and emerging multiresistant fungi. Rapid and accurate fungal identification remains at the forefront of laboratory efforts to guide empiric therapy. Antifungal susceptibility testing methods have greatly improved, but are subject to variation in results between methods. Careful standardization, validation, and extensive training of users is essential to ensure susceptibility results are clinically useful and interpreted appropriately. Interpretive criteria for many drugs and species are still lacking, but this will continue to evolve.

Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding

Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world's wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Among these samples, we successfully obtained the DNA barcode sequences from 2198 samples. Sequence comparisons revealed that these 2198 samples likely belonged to 159 known species in 56 different genera, 31 families, 11 orders, 2 classes, and 2 phyla. Significantly, 51.13% of these samples had sequence similarities to known species at lower than 97%, likely representing new taxa. Further phylogenetic analyses on several common mushroom groups including 1536 internal transcribed spacer (ITS) sequences suggested the existence of 20 new (cryptic) species in these groups. The extensive new and cryptic species diversity in wild mushroom markets in Yunnan calls for greater attention for the conservation and utilization of these resources. Our results on both the distinct barcode sequences and the distributions of these sequences should facilitate new mushroom species discovery and forensic authentication of high-valued mushrooms and contribute to the scientific inventory for the management of wild mushroom markets.

DNA barcode, multiplex PCR and qPCR assay for diagnosis of pathogens infecting pulse crops to facilitate safe exchange and healthy conservation of germplasm

The DNA barcodes were developed from ITS region for the identification of fungal plant pathogens namely, Alternaria alternata and A. tenuissima both causing leaf spots, Ascochyta rabiei causing Ascochyta blight, Fusarium oxysporum f. sp. ciceris causing wilt, Macrophomina phaseolina causing dry root rot, Rhizoctonia solani causing web blight and wet root rot, Sclerotium (Athelia) rolfsii causing collar rot, Sclerotinia sclerotiorum causing stem rot and Cercospora canescens and Pseudocercospora cruenta both causing leaf spots in pulse crops. Barcode compliance for A. alternata (DBTPQ001-18), A. tenuissima (DBTPQ002-18), A. rabiei (DBTPQ003-18), F. oxysporum f. sp. ciceris (DBTPQ004-18), M. phaseolina (DBTPQ005-18), R. solani (DBTPQ006-18), S. rolfsii (DBTPQ007-18), S. sclerotiorum (DBTPQ008-18), C. canescens (DBTPQ009-18) and P. cruenta (DBTPQ029-20) have been generated based on the Barcode of Life Data System (BOLD) system. In addition to ITS, other genomic regions were also explored and on the basis of sequence variation they were ranked as TEF-α > SSU > LSU > β-tubulin. These genes could be considered for secondary barcode and phylogenetic relatedness. ITS-based markers for the detection of A. alternata (BAA2aF and BAA2aR) and R. solani (BRS17cF and BRS17cR) were developed which provided 400 bp and 220 bp amplicons, respectively. While, for F. oxysporum f. sp. ciceris, COX1-based marker (FOCox1F and FOCox3R) was developed which amplified 150 bp. The markers proved highly specific and sensitive with detection limit of 0.0001 ng of template DNA using qPCR and simultaneously detected these three pathogens. The DNA barcodes and diagnostics developed are suitable for quick and reliable detection of these pathogens during quarantine processing and field diagnostics.

DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance

DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.

Delimitation and phylogeny of Dictyochaeta, and introduction of Achrochaeta and Tubulicolla, genera nova

Dictyochaeta (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in Chaetosphaeria. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (RPB2), translation elongation factor 1-α (TEF1-α), and β-tubulin (TUB2), along with comparative morphological and cultivation studies, are used to reevaluate the concept of Dictyochaeta and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and TEF1-α, together with TUB2, facilitated accurate identification of Dictyochaeta species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that D. fuegiana, the type species, is a complex of three distinct species including D. querna and the newly described D. stratosa. Besides, a new species, D. detriticola, and two new combinations, D. callimorpha and D. montana, are proposed. An epitype of D. montana is selected. Dictyochaeta includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. Dictyochaeta is shown to be distantly related to the morphologically similar Codinaea, which is resolved as paraphyletic. Chaetosphaeria talbotii with a Dictyochaeta anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from Dictyochaeta, and a new genus Achrochaeta is proposed. Multigene phylogenetic analysis revealed that D. cylindrospora belongs to the Vermiculariopsiellales, and a new genus Tubulicolla is introduced.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

In vitro antifungal susceptibilities of six antifungal drugs against clinical Candida glabrata isolates according to EUCAST

Background and Purpose:

Candida glabrata is the second cause of candidiasis. The mortality rate of C. glabrata infections is about 40%; accordingly, it may be life threatening, especially in immunocompromised hosts. Regarding this, the current study was conducted to evaluate the regional patterns of the antifungal susceptibility of clinical C. glabrataisolated from the patients referring to the health centers located in Ahvaz, Iran

Materials and Methods:

In this study, a total of 30 clinical strains of C. glabrata isolates were recovered from different body sites (i.e., vagina, mouth, and urine). Phenotypic characteristics and molecular methods were used to identify the isolates. The minimum inhibitory concentration (MIC) was determined according to the European Committee on Antimicrobial Susceptibility Testing

Results:

Our findings demonstrated that 20%, 80%, and 6.7% of the isolates were resistant to amphotericin B, terbinafine, and posaconazole, respectively, while all the isolates were found to be fluconazole susceptible dose dependent and susceptible to voriconazole and caspofungin

Conclusion:

Our study suggested that voriconazole had high potency against C. glabrata isolates. Consequently, this antifungal agent can be an alternative drug in the treatment of resistant patients. These results can be helpful for the successful treatment of patients in different regions

Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA

Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known as prokaryotes, and Fungi, the Oomycetes and other protists, collectively referred to as fungi. The prokaryotes and fungi are the most commonly studied microbes from plants, and we introduce the most relevant concepts of prokaryote and fungal taxonomy and nomenclature. We first explain how prokaryote and fungal species are defined, delimited, and named, and then summarize the criteria and methods used to identify prokaryote and fungal organisms to species.

A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?

Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.