Current global status of Candida auris an emerging multidrug-resistant fungal pathogen: bibliometric analysis and network visualization.

BACKGROUND: Candida auris is an emerging multidrug-resistant fungal pathogen associated with nosocomial infections and hospital outbreaks worldwide, presenting a serious global health threat. There has been a rapid emergence of scientific research publications focusing on therapeutic compounds, diagnostic techniques, control strategies, prevention, and understanding the epidemiology related to C. auris. OBJECTIVE: This study aims to provide the most up-to-date comprehensive and integrated examination of C. auris research subject and demonstrate that C. auris is indeed a topic of increasing interest. METHODS: The search query "candida-auris" was used as a topic term to find and retrieve relevant data published between 2009 and 15 June 2023, from the Web of Science Core Collection (WoSCC) database. In this work, the bibliometric analysis and network visualization were conducted using VOSviewer software, and Biblioshiny interface accessible through the Bibliometrix R-package on RStudio software. RESULTS: The yearly growth rate percentage (37.91%), along with the strong positive correlations between publications and citations (r = 0.981; p < 0.001), suggests heightened scholarly engagement in this topic. The USA, India, China, and the UK have emerged as pivotal contributors, with the Centers for Disease Control and Prevention (CDC) in the USA being the most productive institution. Current research hotspots in this field mainly focused on identifying and limiting transmission of the clonal strains, epidemiology, antifungal resistance, and in vitro antifungal susceptibility testing. CONCLUSION: This detailed bibliometric analysis in C. auris topic shows that this fungal pathogen has garnered growing attention and attracted progressively more scholars. This paper will help researchers to find without difficulty the relevant articles, research hotspots, influential authors, institutions, and countries related to the topic.

Assessing thermal adaptation of a global sample of Aspergillus fumigatus: Implications for climate change effects.

Aspergillus fumigatus is a common environmental mold and a major cause of opportunistic infections in humans. It's distributed among many ecological niches across the globe. A major virulence factor of A. fumigatus is its ability to grow at high temperature. However, at present, little is known about variations among strains in their growth at different temperatures and how their geographic origins may impact such variations. In this study, we analyzed 89 strains from 12 countries (Cameroon, Canada, China, Costa Rica, France, India, Iceland, Ireland, New Zealand, Peru, Saudi Arabia, and USA) representing diverse geographic locations and temperature environments. Each strain was grown at four temperatures and genotyped at nine microsatellite loci. Our analyses revealed a range of growth profiles, with significant variations among strains within individual geographic populations in their growths across the temperatures. No statistically significant association was observed between strain genotypes and their thermal growth profiles. Similarly geographic separation contributed little to differences in thermal adaptations among strains and populations. The combined analyses among genotypes and growth rates at different temperatures in the global sample suggest that most natural populations of A. fumigatus are capable of rapid adaptation to temperature changes. We discuss the implications of our results to the evolution and epidemiology of A. fumigatus under increasing climate change.

Screening a newly developed common bean germplasm with improved resistance to ashy stem blight in multiple environments.

Ashy stem blight (ASB) caused by the necrotrophic fungus Macrophomina phaseolina (Tassi) Goidanich is an important disease in common bean (Phaseolus vulgaris L.) in the Americas and worldwide. Low to intermediate levels of ASB resistance exist in cultivated and landrace genotypes of the common bean and the tertiary gene pool. However, cultivars with higher levels of resistance are not yet available. Our objectives were to 1) pyramid higher levels of resistance from multiple parent populations within the primary gene pool and 2) compare the response of the newly developed breeding lines (BL) with known sources of resistance. The BL UPR-Mp-22, UPR-Mp-34, UPR-Mp-42, and UPR-Mp-48, known sources of resistance, and susceptible checks were inoculated twice per plant with the PRI21 M. phaseolina isolate in the greenhouse and field trials conducted in Isabela and Lajas, Puerto Rico. None of the genotypes tested were resistant (mean scores 1-3). However, the new black UPR-Mp-42 and white UPR-Mp-48 BL had an intermediate response (mean scores 4-6) compared to white common bean genotypes 'Bella,' NY6020-4, and 'Verano' and black bean TARS-MST1 that were susceptible (scores ≥7) in all environments. Andean genotypes A 195, PRA154, PRA155, and UPR-Mp-22 were intermediate in the greenhouse. In contrast, UPR-Mp-34 had significantly lower scores than BAT 477 that had a susceptible reaction in the greenhouse in Isabela and in the field in Lajas and SEA 5 that was susceptible in all environments. These new BL possess an enhanced ASB resistance and may be used to improve common bean cultivars or germplasms of different market classes.

Special Issue "Sporothrix and Sporotrichosis 2.0".

Sporotrichosis is a chronic fungal disease of humans and other mammals that often affects the skin and subcutaneous tissues and, rarely, deep-seated organs (most frequently in immunocompetent hosts) [...].

A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira".

Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.

Trends towards lower azole susceptibility among 200 Candida tropicalis bloodstream isolates from Brazilian medical centres.

OBJECTIVES: Candida tropicalis is one of the three most frequent species causing candidaemia in Latin America. Despite the high prevalence of C. tropicalis in candidaemia cases in Brazil, little is known about the trends in fluconazole susceptibility over time. The objective of this study was to evaluate temporal trends in azole resistance rates among C. tropicalis bloodstream isolates from patients treated in six Brazilian medical centres over a 12-year period. METHODS: We selected 200 C. tropicalis bloodstream isolates from six medical centres in Brazil collected between 2007 and 2018. Species identification was confirmed by MALDI-TOF/MS. Antifungal susceptibility testing for four antifungal agents was performed by the Clinical and Laboratory Standards Institute (CLSI) microbroth method. RESULTS: Overall, rates of non-susceptibility were 4% and 3.5% to fluconazole and voriconazole, respectively. All isolates were susceptible to amphotericin B and only one isolate was resistant to echinocandins. CONCLUSION: Although we failed to demonstrate statistical differences in the rates of azole resistance documented during the period of analysis, trends towards lower susceptibility to fluconazole and voriconazole were shown.

Genomic characterization of Parengyodontium americanum sp. nov.

Modern genome analysis and phylogenomic methods have increased the number of fungal species, as well as enhanced appreciation of the degree of diversity within the fungal kingdom. In this context, we describe a new Parengyodontium species, P. americanum, which is phylogenetically related to the opportunistic human fungal pathogen P. album. Five unusual fungal isolates were recovered from five unique and confirmed coccidioidomycosis patients, and these isolates were subsequently submitted to detailed molecular and morphological identification procedures to determine identity. Molecular and morphological diagnostic analyses showed that the isolates belong to the Cordycipitaceae. Subsequently, three representative genomes were sequenced and annotated, and a new species, P. americanum, was identified. Using various genomic analyses, gene family expansions related to novel compounds and potential for ability to grow in diverse habitats are predicted. A general description of the genomic composition of this newly described species and comparison of genome content with Beauveria bassiana, Isaria fumosorosea and Cordyceps militaris shows a shared core genome of 6371 genes, and 148 genes that appear to be specific for P. americanum. This work provides the framework for future investigations of this interesting fungal species.

Spatial Quantification of the Population Exposed to Cryptococcus neoformans and Cryptococcus gattii Species Complexes in Europe: Estimating the Immunocompetent and HIV/AIDS Patients Under Risk.

Cryptococcus is an important fungal pathogen worldwide, causing serious clinical manifestations that can affect immunocompetent patients and can be particularly severe for immunocompromised patients. The Cryptococcus gattii s.s. (AFLP4/VGI), Cryptococcus tetragattii (AFLP/VGIV), Cryptococcus neoformans, and Cryptococcus deneoformans have been isolated from both clinical and environmental sources in Europe. We aim to quantify the people in Europe and the entire Mediterranean area who are under risk associated with each of the three fungal pathogens in a spatially explicit way, generating a series of maps and population statistics per country. Niche modeling was applied to estimate the potential distribution of each fungal pathogen, then these models were overlapped with a map of population density to estimate risk levels. The potential number of people per risk level and per country was quantified using a map of population count per pixel. Prevalence of HIV per country was also included in the analysis to quantify the HIV-infected population under potential risk. People under risk associated with exposure to C. gattii species (C. gattii s.s. and C. tetragattii) reached 137.65 million, whereas those exposed to C. neoformans and C. deneoformans were 268.58 and 360.78 million people, respectively. More than a half million HIV-infected patients are exposed to each of the two species of the C. neoformans species complex, and more than 200,000 to the C. gattii species complex. The present results can be useful for public health planning by European governments, focusing on the provision of inputs for a "screen-and-treat" approach, availability of medical resources, and continuous monitoring programs in risk zones.

Expression and purification of the transcription factor StMsn2 from Setosphaeria turcica in Escherichia coli

Background: In Saccharomyces cerevisiae, Msn2, which acts as a key transcription factor downstream the MAPKHOG cascade pathway, also regulates the expression of genes related to stress responses. However, little is known about the regulation mechanisms of the transcription factor in Setosphaeria turcica. Results: In this study, a zinc finger DNA-binding protein, designated as StMSN2, was cloned from S. turcica. Sequencing results showed that StMSN2 had a 1752 bp open reading frame (ORF), which was interrupted by an intron (135 bp) and encoded a putative 538-amino acid protein. Phylogenetic analysis further revealed that StMsn2 was more closely related to Msn2 of Aspergillus parasiticus. StMSN2 was cloned into the pET-28a vector with His (Histidine) tags and induced with 1 mM IPTG (isopropyl-ß-D-thiogalactoside) at 37°C. The recombinant His-tagged StMsn2 was purified, and a band of size approximately 58.8 kDa was obtained. The high specificity of the polyclonal antibody Msn2-2 was detected with the StMsn2 protein from S. turcica and prokaryotic expression system, respectively. Conclusions: A new gene, named StMSN2, with 1617 bp ORF was cloned from S. turcica and characterized using bioinformatics methods. StMsn2 was expressed and purified in a prokaryotic system. A polyclonal antibody, named Msn2-2, against StMsn2 with high specificity was identified.

Colletotrichum acutatum M11 can suppress the defence response in strawberry plants.

MAIN CONCLUSION: Colletotrichum acutatum M11 produces a diffusible compound that suppresses the biochemical, physiological, molecular and anatomical events associated with the defence response induced by the plant defence elicitor AsES. The fungal pathogen Colletotrichum acutatum, the causal agent of anthracnose disease, causes important economical losses in strawberry crop worldwide and synthetic agrochemicals are used to control it. In this context, the control of the disease using bioproducts is gaining reputation as an alternative of those toxic and pollutant agrochemicals. However, the success of the strategies using bioproducts can be seriously jeopardized in the presence of biological agents exerting a defence suppression effect. In this report, we show that the response defence induced in plant by the elicitor AsES from the fungus Acremonium strictum can be suppressed by a diffusible compound produced by isolate M11 of C. acutatum. Results revealed that strawberry plants treated with conidia of the isolated M11 or the culture supernatant of the isolate M11 suppress: ROS accumulation (e.g., H2O2, O2·- and NO), cell wall reinforcement (e.g., lignin and callose), and the up-regulation of defence-related genes (e.g., FaPR1, FaCHI23, FaPDF1.2, FaCAT, FaCDPK, FaCML39) induced by the elicitor AsES. Additionally, we show that the defence suppressing effect causes a systemic sensitization of plants. Results presented here highlights the necessity to make an integral study of the microbiome present in soils and plant biosphere before applying defence activation bioproducts to control crop diseases.

The mysterious desert dwellers: Coccidioides immitis and Coccidioides posadasii, causative fungal agents of coccidioidomycosis.

The genus Coccidioides consists of two species: C. immitis and C. posadasii. Prior to 2000, all disease was thought to be caused by a single species, C. immitis. The organism grows in arid to semiarid alkaline soils throughout western North America and into Central and South America. Regions in the United States, with highest prevalence of disease, include California, Arizona, and Texas. The Mexican states of Baja California, Coahuila, Sonora, and Neuvo Leon currently have the highest skin test positive results. Central America contains isolated endemic areas in Guatemala and Honduras. South America has isolated regions of high endemicity including areas of Colombia, Venezuela, Argentina, Paraguay, and Brazil. Although approximately 15,000 cases per year are reported in the United States, actual disease burden is estimated to be in the hundreds of thousands, as only California and Arizona have dedicated public health outreach, and report and track disease reliably. In this review, we survey genomics, epidemiology, ecology, and summarize aspects of disease, diagnosis, prevention, and treatment.

The Still Underestimated Problem of Fungal Diseases Worldwide.

In the past few years, fungal diseases caused estimated over 1.6 million deaths annually and over one billion people suffer from severe fungal diseases (Brown et al., 2012; Anonymous, 2017b). Public health surveillance of fungal diseases is generally not compulsory, suggesting that most estimates are conservative (Casadevall, 2017; Anonymous, 2017a). Fungal disease can also damage plants and crops, causing major losses in agricultural activities and food production (Savary et al., 2012). Animal pathogenic fungi are threatening bats, amphibians and reptiles with extinction (Casadevall, 2017). It is estimated that fungi are the highest threat for animal-host and plant-host species, representing the major cause (approximately 65%) of pathogen-driven host loss (Fisher et al., 2012). In this complex scenario, it is now clear that the global warming and accompanying climate changes have resulted in increased incidence of many fungal diseases (Garcia-Solache and Casadevall, 2010). On the basis of all these factors, concerns on the occurrence of a pandemic of fungal origin in a near future have been raised (Casadevall, 2017). In this context, to stop forgetting and underestimating fungal diseases is mandatory.

Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition.

Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.

Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae.

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission.

Sugarcane smut disease, caused by the biotrophic fungus Sporisorium scitamineum, is characterized by the development of a whip-like structure from the plant meristem. The disease causes negative effects on sucrose accumulation, fiber content and juice quality. The aim of this study was to exam whether the transcriptomic changes already described during the infection of sugarcane by S. scitamineum result in changes at the metabolomic level. To address this question, an analysis was conducted during the initial stage of the interaction and through disease progression in a susceptible sugarcane genotype. GC-TOF-MS allowed the identification of 73 primary metabolites. A set of these compounds was quantitatively altered at each analyzed point as compared with healthy plants. The results revealed that energetic pathways and amino acid pools were affected throughout the interaction. Raffinose levels increased shortly after infection but decreased remarkably after whip emission. Changes related to cell wall biosynthesis were characteristic of disease progression and suggested a loosening of its structure to allow whip growth. Lignin biosynthesis related to whip formation may rely on Tyr metabolism through the overexpression of a bifunctional PTAL. The altered levels of Met residues along with overexpression of SAM synthetase and ACC synthase genes suggested a role for ethylene in whip emission. Moreover, unique secondary metabolites antifungal-related were identified using LC-ESI-MS approach, which may have potential biomarker applications. Lastly, a putative toxin was the most important fungal metabolite identified whose role during infection remains to be established.