Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt

Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex

Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and, consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis.

IMPORTANCE

The Mucor species complex comprises a variety of opportunistic pathogens known to cause mucormycosis, a potentially lethal fungal infection with limited therapeutic options. The only effective first-line treatments against mucormycosis consist of liposomal formulations of amphotericin B and the triazoles posaconazole and isavuconazole, all of which target components within the ergosterol biosynthetic pathway. This study uncovered M. circinelloides Erg3 and Erg6a as key enzymes to produce ergosterol, a vital constituent of fungal membranes. Absence of any of those enzymes leads to decreased ergosterol and consequently, resistance to ergosterol-binding polyenes such as amphotericin B. Particularly, losing Erg6a function poses a higher threat as the ergosterol pathway is channeled into alternative sterols similar to cholesterol, which maintain membrane permeability. As a result, erg6a mutants survive within the host and disseminate the infection, indicating that Erg6a deficiency may arise during human infections and confer resistance to the most effective treatment against mucormycoses.

Polystyrene Microplastics Causes Diarrhea and Impairs Intestinal Angiogenesis through the ROS/METTL3 Pathway

Due to the immature intestinal digestion, immunity, and barrier functions, weaned infants are more susceptible to pathogens and develop diarrhea. Microplastics (MPs), pervasive contaminants in food, water, and air, have unknown effects on the intestinal development of weaned infants. This study explored the impact of polystyrene MPs on intestinal development using a weaned piglet model. Piglets in the control group received a basal diet, and those in the experimental groups received a basal diet contaminated with 150 mg/kg polystyrene MPs. The results showed that exposure to polystyrene MPs increased the diarrhea incidence and impaired the intestinal barrier function of weaned piglets. Notably, the exposure led to oxidative stress and inflammation in the intestine. Furthermore, polystyrene MPs-treated weaned piglets showed a reduced level of intestinal angiogenesis. Mechanistically, polystyrene MPs suppressed methyltransferase-like 3 (METTL3) expression by increasing reactive oxygen species (ROS) production, consequently destabilizing angiogenic factors' mRNA and hindering intestinal angiogenesis. In summary, polystyrene MPs contamination in the diet increases diarrhea and compromises intestinal angiogenesis through the ROS/METTL3 pathway, demonstrating their toxic effects on the intestine health of weaned infants.

Identification of Food Spoilage Fungi Using MALDI-TOF MS: Spectral Database Development and Application to Species Complex

Fungi, including filamentous fungi and yeasts, are major contributors to global food losses and waste due to their ability to colonize a very large diversity of food raw materials and processed foods throughout the food chain. In addition, numerous fungal species are mycotoxin producers and can also be responsible for opportunistic infections. In recent years, MALDI-TOF MS has emerged as a valuable, rapid and reliable asset for fungal identification in order to ensure food safety and quality. In this context, this study aimed at expanding the VITEK® MS database with food-relevant fungal species and evaluate its performance, with a specific emphasis on species differentiation within species complexes. To this end, a total of 380 yeast and mold strains belonging to 51 genera and 133 species were added into the spectral database including species from five species complexes corresponding to Colletotrichum acutatum, Colletotrichum gloeosporioides, Fusarium dimerum, Mucor circinelloides complexes and Aspergillus series nigri. Database performances were evaluated by cross-validation and external validation using 78 fungal isolates with 96.55% and 90.48% correct identification, respectively. This study also showed the capacity of MALDI-TOF MS to differentiate closely related species within species complexes and further demonstrated the potential of this technique for the routine identification of fungi in an industrial context.

Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex

Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular pathogenesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3Δ mutations, resulting in ergosterol depletion and consequently, hypersusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycosis.

Characterisation of the surface growth of Mucor circinelloides in cheese agar media using predictive mathematical models

The main objective of this work was to characterise the mycelial growth of Mucor circinelloides, one of the fungal contaminants that appear frequently in the artisan cheese production environment. The study uses primary Baranyi and Huang models to compare their parameters and predict M. circinelloides on cheese-based medium (CBA) under diverse environmental conditions (temperature range from 6 to 37 °C and 0 and 1 % NaCl concentration). However, the Baranyi model consistently estimated longer lag phases and higher surface growth rates (sgr) than the Huang model; both models showed adequate best-fit performance (exactly with the mean coefficient of determination R2 = (0.993 ± 0.020 × 10-1). The groups of primary growth parameters were analysed against temperature using the cardinal model (CM) with the following main outputs. The optimal surface growth rates (sgropt) on CBA were 6.8 and 6.5 mm/d calculated with the Baranyi and Huang models, respectively. They were reduced by approximately 46 % on the surface of the agar medium when 1 % NaCl was added. Topt was estimated in a very narrow range of 32.1-32.5 °C from both primary sgr data sets (0 % and 1 % NaCl). Similarly, Tmax values of 37.2 °C and 37.3 °C were estimated for the Baranyi and Huang models, respectively; however, they decreased at 2 °C in CBA with 1 % NaCl (Tmax = 35.1 °C). The application of CM for sgr provided an estimation of the parameter Tmin with negative values that are considered only as a theoretical output. The results provide insight into the modelling and prediction of fungi growth as a function of time and salt concentration, including the times to detect visible mycelial growth of Mucor circinelloides. The mere quantification of this phenomenon can be useful for practice. Adjusting the frequency of the cheese surface washing step with a salt solution at the early stage of ripening properly can prevent the growth of not only fast fungal growers.

Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis

Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain's economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology.

Molecular mechanisms that govern infection and antifungal resistance in Mucorales

SUMMARYThe World Health Organization has established a fungal priority pathogens list that includes species critical or highly important to human health. Among them is the order Mucorales, a fungal group comprising at least 39 species responsible for the life-threatening infection known as mucormycosis. Despite the continuous rise in cases and the poor prognosis due to innate resistance to most antifungal drugs used in the clinic, Mucorales has received limited attention, partly because of the difficulties in performing genetic manipulations. The COVID-19 pandemic has further escalated cases, with some patients experiencing the COVID-19-associated mucormycosis, highlighting the urgent need to increase knowledge about these fungi. This review addresses significant challenges in treating the disease, including delayed and poor diagnosis, the lack of accurate global incidence estimation, and the limited treatment options. Furthermore, it focuses on the most recent discoveries regarding the mechanisms and genes involved in the development of the disease, antifungal resistance, and the host defense response. Substantial advancements have been made in identifying key fungal genes responsible for invasion and tissue damage, host receptors exploited by the fungus to invade tissues, and mechanisms of antifungal resistance. This knowledge is expected to pave the way for the development of new antifungals to combat mucormycosis. In addition, we anticipate significant progress in characterizing Mucorales biology, particularly the mechanisms involved in pathogenesis and antifungal resistance, with the possibilities offered by CRISPR-Cas9 technology for genetic manipulation of the previously intractable Mucorales species.

Transcription Factors Tec1 and Tec2 Play Key Roles in the Hyphal Growth and Virulence of Mucor lusitanicus Through Increased Mitochondrial Oxidative Metabolism

Mucormycosis is a lethal and difficult-to-treat fungal infection caused by fungi of the order Mucorales. Mucor lusitanicus, a member of Mucorales, is commonly used as a model to understand disease pathogenesis. However, transcriptional control of hyphal growth and virulence in Mucorales is poorly understood. This study aimed to investigate the role of Tec proteins, which belong to the TEA/ATTS transcription factor family, in the hyphal development and virulence of M. lusitanicus. Unlike in the genome of Ascomycetes and Basidiomycetes, which have a single Tec homologue, in the genome of Mucorales, two Tec homologues, Tec1 and Tec2, were found, except in that of Phycomyces blakesleeanus, with only one Tec homologue. tec1 and tec2 overexpression in M. lusitanicus increased mycelial growth, mitochondrial content and activity, expression of the rhizoferrin synthetase-encoding gene rfs, and virulence in nematodes and wax moth larvae but decreased cAMP levels and protein kinase A (PKA) activity. Furthermore, tec1- and tec2-overexpressing strains required adequate mitochondrial metabolism to promote the virulent phenotype. The heterotrimeric G beta subunit 1-encoding gene deletant strain (Δgpb1) increased cAMP-PKA activity, downregulation of both tec genes, decreased both virulence and hyphal development, but tec1 and tec2 overexpression restored these defects. Overexpression of allele-mutated variants of Tec1(S332A) and Tec2(S168A) in the putative phosphorylation sites for PKA increased both virulence and hyphal growth of Δgpb1. These findings suggest that Tec homologues promote mycelial development and virulence by enhancing mitochondrial metabolism and rhizoferrin accumulation, providing new information for the rational control of the virulent phenotype of M. lusitanicus.

Mucormycosis in 2023: an update on pathogenesis and management

Mucormycosis (MCR) is an emerging and frequently lethal fungal infection caused by the Mucorales family, with Rhizopus, Mucor, and Lichtheimia, accounting for > 90% of all cases. MCR is seen in patients with severe immunosuppression such as those with hematologic malignancy or transplantation, Diabetes Mellitus (DM) and diabetic ketoacidosis (DKA) and immunocompetent patients with severe wounds. The recent SARS COV2 epidemy in India has resulted in a tremendous increase in MCR cases, typically seen in the setting of uncontrolled DM and corticosteroid use. In addition to the diversity of affected hosts, MCR has pleiotropic clinical presentations, with rhino-orbital/rhino-cerebral, sino-pulmonary and necrotizing cutaneous forms being the predominant manifestations. Major insights in MCR pathogenesis have brought into focus the host receptors (GRP78) and signaling pathways (EGFR activation cascade) as well as the adhesins used by Mucorales for invasion. Furthermore, studies have expanded on the importance of iron availability and the complex regulation of iron homeostasis, as well as the pivotal role of mycotoxins as key factors for tissue invasion. The molecular toolbox to study Mucorales pathogenesis remains underdeveloped, but promise is brought by RNAi and CRISPR/Cas9 approaches. Important recent advancements have been made in early, culture-independent molecular diagnosis of MCR. However, development of new potent antifungals against Mucorales remains an unmet need. Therapy of MCR is multidisciplinary and requires a high index of suspicion for initiation of early Mucorales-active antifungals. Reversal of underlying immunosuppression, if feasible, rapid DKA correction and in selected patients, surgical debulking are crucial for improved outcomes.

Mucormycosis and Its Upsurge During COVID-19 Epidemic: An Updated Review

Although mucormycosis may have reached an epidemic situation during the COVID-19 pandemic, the term was much more familiar even before the COVID-19 period. The year 2020 showed an outbreak of novel coronavirus (SARS-CoV-2) which affected millions of people all over the world. One of the noticeable complications observed to be associated with this disease is mucormycosis. It is an opportunistic infection caused by members of the Order Mucorales existing worldwide and has been commonly reported as a laboratory contaminant for a long time. However, nowadays due to the changes in the host environment, they have been emerging as potent opportunistic pathogens responsible for causing primary infections or coinfections with other diseases eventually resulting in morbidity and even mortality in severe cases. Although immunocompromised patients are more susceptible to this infection, few cases have been reported in immunocompetent individuals. Various risk factors which are responsible for the acquisition of mucormycosis include diabetes mellitus type 2, ketoacidosis, hematological malignancies, organ transplants, and chemotherapy recipients. Among the various etiological agents, Rhizopus is found to be the most common, and rhino-cerebral to be the most frequent clinical presentation. As far as pathogenesis is concerned, host cell invasion, thrombosis, and necrosis are the main events in the progression of this disease. The aim of the present review is to address a complete spectrum of mucormycosis and COVID-19-associated mucormycosis (CAM) in a single article. Both global and Indian scenarios of mucormycosis are taken into account while framing this review.

Epidemiology, Modern Diagnostics, and the Management of Mucorales Infections

Mucormycosis is an uncommon, yet deadly invasive fungal infection caused by the Mucorales moulds. These pathogens are a WHO-assigned high-priority pathogen group, as mucormycosis incidence is increasing, and there is unacceptably high mortality with current antifungal therapies. Current diagnostic methods have inadequate sensitivity and specificity and may have issues with accessibility or turnaround time. Patients with diabetes mellitus and immune compromise are predisposed to infection with these environmental fungi, but COVID-19 has established itself as a new risk factor. Mucorales also cause healthcare-associated outbreaks, and clusters associated with natural disasters have also been identified. Robust epidemiological surveillance into burden of disease, at-risk populations, and emerging pathogens is required. Emerging serological and molecular techniques may offer a faster route to diagnosis, while newly developed antifungal agents show promise in preliminary studies. Equitable access to these emerging diagnostic techniques and antifungal therapies will be key in identifying and treating mucormycosis, as delayed initiation of therapy is associated with higher mortality.

A Review of Modern Methods for the Detection of Foodborne Pathogens

Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to foodborne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. Although extensive reviews of methods for foodborne pathogens detection exist, most are skewed towards bacteria despite the increasing relevance of other pathogens such as viruses. Therefore, this review of foodborne pathogen detection methods is holistic, focusing on pathogenic bacteria, fungi, and viruses. This review has shown that culture-based methods allied with new approaches are beneficial for the detection of foodborne pathogens. The current application of immunoassay methods, especially for bacterial and fungal toxins detection in foods, are reviewed. The use and benefits of nucleic acid-based PCR methods and next-generation sequencing-based methods for bacterial, fungal, and viral pathogens' detection and their toxins in foods are also reviewed. This review has, therefore, shown that different modern methods exist for the detection of current and emerging foodborne bacterial, fungal, and viral pathogens. It provides further evidence that the full utilization of these tools can lead to early detection and control of foodborne diseases, enhancing public health and reducing the frequency of disease outbreaks.

Clonal Dissemination of Antifungal-Resistant Candida haemulonii, China

Candida haemulonii, a relative of C. auris, frequently shows antifungal resistance and is transmissible. However, molecular tools for genotyping and investigating outbreaks are not yet established. We performed genome-based population analysis on 94 C. haemulonii strains, including 58 isolates from China and 36 other published strains. Phylogenetic analysis revealed that C. haemulonii can be divided into 4 clades. Clade 1 comprised strains from China and other global strains; clades 2-4 contained only isolates from China, were more recently evolved, and showed higher antifungal resistance. Four regional epidemic clusters (A, B, C, and D) were identified in China, each comprising ≥5 cases (largest intracluster pairwise single-nucleotide polymorphism differences <50 bp). Cluster A was identified in 2 hospitals located in the same city, suggesting potential intracity transmissions. Cluster D was resistant to 3 classes of antifungals. The emergence of more resistant phylogenetic clades and regional dissemination of antifungal-resistant C. haemulonii warrants further monitoring.

Plain set and stirred yogurt with different additives: implementation of food safety system as quality checkpoints

Hazard Analysis Critical Control Point (HACCP) is a risk management protocol developed to ensure food safety through a precautionary approach that is believed to offer assurances in producing safe food for customers. Yogurt is made in a number of phases, commencing with the collection of raw milk and ending with consumer consumption. While this is happening, major economic and health issues might arise from exposing the manufacturing line to biological, chemical, and/or physical contaminations. As a result, the decision tree approach was used to determine the CCPs during the production of yogurt. Additionally, biological dangers are incorporated as a by-product of the system's implementation performance. In particular, the plain set and nut puree-honey-fortified stirred yogurt manufacturing techniques are highlighted for the first time in this study. The potential manufacturing risks are described for the first time, together with information on how HACCP plans may guard against major risks that could result in the production of yogurt that is not in compliance with established standards.

An old confusion: Entomophthoromycosis versus mucormycosis and their main differences

Fungal diseases were underestimated for many years. And the global burden of fungal infections is substantial and has increased in recent years. Invasive fungal infections have been linked to several risk factors in humans which basically depend on the individual homeostasis of the patients. However, many fungi can infect even apparently healthy people. Knowledge of these pathogens is critical in reducing or stopping morbidity and/or mortality statistics due to fungal pathogens. Successful therapeutic strategies rely on rapid diagnosis of the causative fungal agent and the underlying disease. However, the terminology of the diseases was updated to existing phylogenetic classifications and led to confusion in the definition of mucormycosis, conidiobolomycosis, and basidiobolomycosis, which were previously grouped under the now-uncommon term zygomycosis. Therefore, the ecological, taxonomic, clinical, and diagnostic differences are addressed to optimize the understanding and definition of these diseases. The term "coenocytic hyphomycosis" is proposed to summarize all fungal infections caused by Mucorales and species of Basidiobolus and Conidiobolus.

Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase

Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and β comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.

Two Cases of Post-Traumatic Mucormycosis due to Mucor circinelloides: Salvage Therapy with a Combination of Adjunctive Therapies

Mucormycosis is a rare, emerging angioinvasive infection caused by ubiquitous filamentous fungi. In recent decades, an increase in cutaneous or post-traumatic mucormycosis has been reported. We describe two cases of post-traumatic wound infections with Mucor circinelloides, a mucor species only rarely reported as a cause of post-traumatic mucormycosis. Often considered lethal, management required a combination of medical and surgical therapies to achieve a favorable outcome in both cases.

Differential Gene Expression of Mucor lusitanicus under Aerobic and Anaerobic Conditions

Mucor lusitanicus and some other members of the fungal order Mucorales display the phenomenon of morphological dimorphism. This means that these fungi aerobically produce filamentous hyphae, developing a coenocytic mycelium, but they grow in a multipolar yeast-like form under anaerobiosis. Revealing the molecular mechanism of the reversible yeast-hyphal transition can be interesting for both the biotechnological application and in the understanding of the pathomechanism of mucormycosis. In the present study, transcriptomic analyses were carried out after cultivating the fungus either aerobically or anaerobically revealing significant changes in gene expression under the two conditions. In total, 539 differentially expressed genes (FDR < 0.05, |log2FC| ≥ 3) were identified, including 190 upregulated and 349 downregulated transcripts. Within the metabolism-related genes, carbohydrate metabolism was proven to be especially affected. Anaerobiosis also affected the transcription of transporters: among the 14 up- and 42 downregulated transporters, several putative sugar transporters were detected. Moreover, a considerable number of transcripts related to amino acid transport and metabolism, lipid transport and metabolism, and energy production and conversion were proven to be downregulated when the culture had been transferred into an anaerobic atmosphere.

Metagenomics Approaches for Improving Food Safety: A Review

ABSTRACT

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.

HIGHLIGHTS

New insights on mucormycosis and its association with the COVID-19 pandemic

COVID-19 continues to cause significant fatality worldwide. Glucocorticoids prove to play essential roles in COVID-19 management; however, the extensive use of steroids together with the virus immune dysregulation may increase the danger of secondary infections with mucormycosis, an angioinvasive fungal infection. Unfortunately, a definite correlation between COVID-19 and elevated mucormycosis infection cases is now clear worldwide. In this review, we discuss the historical record and epidemiology of mucormycosis as well as pathogenesis and associated host immune response, risk factors, clinical presentation, diagnosis and treatment. Special emphasis is given to its association with the current COVID-19 pandemic, including latest updates on COVID-19-associated mucormycosis cases globally, with recommendations for efficacious management.

Lactic Acid Bacteria as Biopreservation Against Spoilage Molds in Dairy Products - A Review

Mold spoilage of dairy products such as yogurt is a concern in dairy industry. Not only does it lead to substantial food waste, economic losses, and even brand image damage, but it may also cause public health concern due to the potential production of mycotoxin. Good hygiene practices are necessary to prevent contamination, but contamination may nevertheless occur at the production site and, not least, at the site of the consumer. In recent years, there has been a growing interest from consumers for "clean label" food products, which are natural, less-processed, and free of added, chemical preservatives, and a wish for shelf lives of considerable length in order to minimize food waste. This has sparked an interest in using lactic acid bacteria (LAB) or their metabolites as biopreservatives as a way to limit the growth of spoilage organisms in dairy products. A range of compounds produced by LAB with potential antifungal activity have been described as contributing factors to the inhibitory effect of LAB. More recently, growth inhibition effects caused by specific competitive exclusion have been elucidated. It has also become clear that the sensitivity toward both individual antifungal compounds and competition mechanisms differ among molds. In this review, the main spoilage molds encountered in dairy products are introduced, and an overview of the antifungal activity of LAB against different spoilage molds is presented including the main antifungal compounds derived from LAB cultures and the sensitivity of the spoilage molds observed toward these compounds. The recent findings of the role of competitive exclusion with emphasis on manganese depletion and the possible implications of this for biopreservation are described. Finally, some of the knowledge gaps, future challenges, and trends in the application of LAB biopreservation in dairy products are discussed.

Recent Molecular Tools for the Genetic Manipulation of Highly Industrially Important Mucoromycota Fungi

Mucorales is the largest and most well-studied order of the phylum Mucormycota and is known for its rapid growth rate and various industrial applications. The Mucorales fungi are a fascinating group of filamentous organisms with many uses in research and the industrial and medical fields. They are widely used biotechnological producers of various secondary metabolites and other value-added products. Certain members of Mucorales are extensively used as model organisms for genetic and molecular investigation and have extended our understanding of the metabolisms of other members of this order as well. Compared with other fungal species, our understanding of Mucoralean fungi is still in its infancy, which could be linked to their lack of effective genetic tools. However, recent advancements in molecular tools and approaches, such as the construction of recyclable markers, silencing vectors, and the CRISPR-Cas9-based gene-editing system, have helped us to modify the genomes of these model organisms. Multiple genetic modifications have been shown to generate valuable products on a large scale and helped us to understand the morphogenesis, basic biology, pathogenesis, and host–pathogen interactions of Mucoralean fungi. In this review, we discuss various conventional and modern genetic tools and approaches used for efficient gene modification in industrially important members of Mucorales.

Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri)

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.

Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.

Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis

Fungi of the order Mucorales cause mucormycosis, a lethal infection with an incompletely understood pathogenesis. We demonstrate that Mucorales fungi produce a toxin, which plays a central role in virulence. Polyclonal antibodies against this toxin inhibit its ability to damage human cells in vitro and prevent hypovolemic shock, organ necrosis and death in mice with mucormycosis. Inhibition of the toxin in Rhizopus delemar through RNA interference compromises the ability of the fungus to damage host cells and attenuates virulence in mice. This 17 kDa toxin has structural and functional features of the plant toxin ricin, including the ability to inhibit protein synthesis through its N-glycosylase activity, the existence of a motif that mediates vascular leak and a lectin sequence. Antibodies against the toxin inhibit R. delemar- or toxin-mediated vascular permeability in vitro and cross react with ricin. A monoclonal anti-ricin B chain antibody binds to the toxin and also inhibits its ability to cause vascular permeability. Therefore, we propose the name 'mucoricin' for this toxin. Not only is mucoricin important in the pathogenesis of mucormycosis but our data suggest that a ricin-like toxin is produced by organisms beyond the plant and bacterial kingdoms. Importantly, mucoricin should be a promising therapeutic target.

Oxford nanopore sequencing in clinical microbiology and infection diagnostics

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.

Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues

Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients

Mucormycoses are invasive infections by Rhizopus species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to Rhizopus microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at a median 31.5 days (range: 13-34) post-admission. We performed whole genome sequencing (WGS) on 72 Mucorales isolates (45 R. arrhizus, 19 R. delemar, six R. microsporus, two Lichtheimia species) from these patients, from five patients with community-acquired mucormycosis, and from hospital and regional environments. Isolates were compared by core protein phylogeny and global genomic features, including genome size, guanine-cytosine percentages, shared protein families and paralogue expansions. Patient isolates fell into six core phylogenetic lineages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from two SOT recipients in adjoining hospitals suggested a potential common source exposure. However, isolates from other patients and environmental sites had unique genomes. Many isolates that were indistinguishable by core phylogeny were distinct by one or more global genomic comparisons. Certain clades were recovered throughout the study period, whereas others were found at particular time points. In conclusion, mucormycosis cases could not be genetically linked to a definitive environmental source. Comprehensive genomic analyses eliminated false associations between Mucorales isolates that would have been assigned using core phylogenetic or less extensive genomic comparisons. The genomic diversity of Mucorales mandates that multiple isolates from individual patients and environmental sites undergo WGS during epidemiological investigations. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is probably infeasible.

Identification of Mucor circinelloides antigens recognized by sera from immunocompromised infected mice

BACKGROUND

Mucor circinelloides is an opportunistic fungus capable of causing mucormycosis, a highly aggressive infection of quick spreading. Besides, it also has a high mortality rate due to late diagnosis and difficult treatment.

AIMS

In this study we have identified the most immunoreactive proteins of the secretome and the total protein extract of M. circinelloides using sera from immunocompromised infected mice.

METHODS

The proteins of the secretome and the total extract were analyzed by two-dimensional electrophoresis and the most immunoreactive antigens were detected by Western Blot, facing the sera of immunocompromised infected mice to the proteins obtained in both extracts of M. circinelloides.

RESULTS

Seven antigens were detected in the secretome extract, and two in the total extract, all of them corresponding only to three proteins. The enzyme enolase was detected in both extracts, while triosephosphate isomerase was detected in the secretome, and heat shock protein HSS1 in the total extract.

CONCLUSIONS

In this work the most immunoreactive antigens of the secretome and the total extract of M. circinelloides were identified. The identified proteins are well known fungal antigens and, therefore, these findings can be useful for future research into alternatives for the diagnosis and treatment of mucormycosis.

Understanding Mucormycoses in the Age of "omics"

Mucormycoses are deadly invasive infections caused by several fungal species belonging to the subphylum Mucoromycotina, order Mucorales. Hallmarks of disease progression include angioinvasion and tissue necrosis that aid in fungal dissemination through the blood stream, causing deeper infections and resulting in poor penetration of antifungal agents to the site of infection. In the absence of surgical removal of the infected focus, antifungal therapy alone is rarely curative. Even when surgical debridement is combined with high-dose antifungal therapy, the mortality associated with mucormycoses is >50%. The unacceptably high mortality rate, limited options for therapy and the extreme morbidity of highly disfiguring surgical therapy provide a clear mandate to understand the molecular mechanisms that govern pathogenesis with the hopes of developing alternative strategies to treat and prevent mucormycoses. In the absence of robust forward and reverse genetic systems available for this taxonomic group of fungi, unbiased next generation sequence (NGS)-based approaches have provided much needed insights into our understanding of many aspects of Mucormycoses, including genome structure, drug resistance, diagnostic development, and fungus-host interactions. Here, we will discuss the specific contributions that NGS-based approaches have made to the field and discuss open questions that can be addressed using similar approaches.

Occurrence and species diversity of human-pathogenic Mucorales in commercial food-stuffs purchased in Paris area

Mucormycoses are life-threatening fungal diseases that affect a variety of patients including those with diabetes mellitus or hematological malignancies. The responsible agents, the Mucorales, are opportunistic pathogens originating from the environment such as soil or decaying organic matter. The aim of the present study was to assess the prevalence and diversity of human-pathogenic species of Mucorales in commercially available foodstuffs in France. All food samples were purchased from January 2014 to May 2015 in France. A total of 159 dried food samples including spices and herbs (n = 68), herbal tea (n = 19), cereals (n = 19), vegetables (n = 14), and other foodstuffs (n = 39) were analyzed. Each strain of Mucorales was identified phenotypically, and molecular identification was performed by ITS sequencing. From the 28 (17.6%) samples that were culture-positive for Mucorales, 30 isolates were recovered. Among the isolates, 13 were identified as Rhizopus arrhizus var. arrhizus, 10 R. arrhizus var. delemar, two Rhizopus microsporus, one Lichtheimia corymbifera, three Lichtheimia ramosa, and one Syncephalastrum racemosum. Culture-positive samples originated from different countries (Europe, Asia) and brands. The samples most frequently contaminated by Mucorales were spices and herbs (19/68, 27.9%), followed by herbal tea (2/19, 10.5%), cereals (2/19, 10.5%), other food products (5/39, 12.8%). The present study showed that human-pathogenic Mucorales were frequently recovered from commercially available foodstuffs in France with a large diversity of species. The potential danger represented by Mucorales present in food for immunocompromised patients should be further analyzed.

A lateral flow strip combined with Cas9 nickase-triggered amplification reaction for dual food-borne pathogen detection

Nucleic acid-based detection methods are accurate and rapid, which are widely-used in food-borne pathogen detection. However, traditional nucleic acid-based detection methods usually rely on special instruments, weakening their practicality for on-site tests in resource-limited locations. In this work, we developed a convenient and affordable method for food-borne pathogen detection based on a lateral flow strip combined with Cas9 nickase-triggered isothermal DNA amplification, which allows instrument-free and dual target detection. The genomic DNAs of two most common foodborne pathogens, Salmonella typhimurium and Escherichia coli, were simultaneously amplified in a one-pot reaction using specific sgRNAs and primers. The amplicons of genomic DNAs were double-labelled by digoxin/biotin and FITC/biotin tags, respectively, and directly visualized on a simple lateral flow strip. Our method exhibited a high specificity and sensitivity with a detection limit of 100 copies for genomic DNAs and 100 CFU/mL for bacteria. We believe that this method has potential to provide a convenient and low-cost point-of-care test for pathogen detection in the food quality surveillance.

Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India

Filamentous fungi are important organisms in traditionally prepared amylase and alcohol-producing dry starters in India. We collected 40 diverse types of amylase and alcohol-producing starters from eight states in North East India viz. marcha, thiat, humao, hamei, chowan, phut, dawdim, and khekhrii. The average fungal population was 4.9 × 10⁵ cfu/g with an average of pH 5.3 and 10.7%, respectively. In the present study, 131 fungal isolates were isolated and characterized based on macroscopic and microscopic characteristics and were grouped into 44 representative fungal strains. Based on results of morphological characteristics and ITS gene sequencing, 44 fungal strains were grouped into three phyla represented by Ascomycota (48%), Mucoromycota (38%), and Basidiomycota (14%). Taxonomical keys to species level was illustrated on the basis of morphological characteristics and ITS gene sequencing, aligned to the fungal database of NCBI GenBank, which showed seven genera with 16 species represented by Mucor circinelloides (20%), Aspergillus sydowii (11%), Penicillium chrysogenum (11%), Bjerkandera adusta (11%), Penicillium citrinum (7%), Rhizopus oryzae (7%), Aspergillus niger (5%), Aspergillus flavus (5%), Mucor indicus (5%) Rhizopus microsporus (5%), Rhizopus delemar (2%), Aspergillus versicolor (2%), Penicillium oxalicum (2%), Penicillium polonicum (2%), Trametes hirsuta (2%), and Cladosporium parahalotolerans (2%). The highest Shannon diversity index H was recorded in marcha of Sikkim (H: 1.74) and the lowest in hamei of Manipur (H: 0.69). Fungal species present in these amylolytic starters are morphologically, ecologically and phylogenetically diverse and showed high diversity within the community.

Use of natural resources from Southern Brazil as a strategy to mitigate fungal contamination

Contamination of food by fungi can result in changes in sensory characteristics, as well as rapid reduction in quality and consequently the infeasibility of using contaminated material. In addition, contamination can pose a danger to public health, as in addition to decreasing the availability of nutrients, some fungal species can produce toxic substances. Much research has explored the use of natural resources to prevent or mitigate microbial contamination. Recovery of chemicals from many families from plants and microorganisms has been evaluated. Phenolic compounds are the most studied class on the premise that they have the capacity to inhibit endogenous and exogenous biological degradation processes. In this manuscript, we intend to emphasize the biochemical and experimental evidence of the phenolic compounds present in natural resources from the South of Brazil that have potential to be used in strategies to mitigate the consequences of fungal contamination. The crude phenolic extracts from natural resources (plant portion and microorganisms) of the Southern Brazilian region should be better exploited, to propose strategies to scale up their application in food industries because they have demonstrated an ability to inhibit fungal development without promoting stress and consequent mycotoxin production.

Comparative genomics applied to Mucor species with different lifestyles

BACKGROUND

Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of Mucor annotated genomes is publicly available and mainly correspond to the reference species, Mucor circinelloides, and to medically relevant species. However, the Mucor genus is composed of a large number of ubiquitous species as well as few species that have been reported to specifically occur in certain habitats. The present study aimed to expand the range of Mucor genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the Mucor genus.

RESULTS

In this study, we report four newly sequenced genomes of Mucor isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely Mucor fuscus and Mucor lanceolatus, two species used in cheese production (during ripening), Mucor racemosus, a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and Mucor endophyticus, a plant endophyte. Comparison of these new genomes with those previously available for six Mucor and two Rhizopus (formerly identified as M. racemosus) isolates allowed global structural and functional description such as their TE content, core and species-specific genes and specialized genes. We proposed gene candidates involved in iron metabolism; some of these genes being known to be involved in pathogenicity; and described patterns such as a reduced number of CAZymes in the species used for cheese ripening as well as in the endophytic isolate that might be related to adaptation to different environments and lifestyles within the Mucor genus.

CONCLUSIONS

This study extended the descriptive data set for Mucor genomes, pointed out the complexity of obtaining a robust phylogeny even with multiple genes families and allowed identifying contrasting potentially lifestyle-associated gene repertoires. The obtained data will allow investigating further the link between genetic and its biological data, especially in terms of adaptation to a given habitat.

Outbreak of Saprochaete clavata Sepsis in Hematology Patients: Combined Use of MALDI-TOF and Sequencing Strategy to Identify and Correlate the Episodes

Introduction

New fungal species are increasingly reported in immunocompromised patients. Saprochaete clavata (S. clavata), an ascomycetous fungus formerly called Geotrichum clavatum, is intrinsically resistant to echinocandins and is often misidentified.

Objective

We describe a cluster of seven S. clavata infections in hospitalized hematology patients who developed this rare fungemia within a span of 11 months. Three of the seven patients died. Identification of the isolates was determined only with the Saramis database of VitekMS system and sequencing of the internal transcribed spacer (ITS) region. Clonal relatedness of the isolates was determined by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) analysis; clonal correlation between the strains was investigated by means of phylogenetic analysis, based on single-nucleotide variants (SNPs). Clinical presentation, 1–3 β-D-glucan (BG) and galactomannan (GM) antigen results and analysis of possible sources of contamination are also described with a prospective case–control study of the outbreak.

Results

MALDI-TOF MS-Vitek (bioMerieux, Marcy l’Etoile, France) failed to identify the six isolates, while SARAMIS (bioMerieux, Marcy l’Etoile, France) identified the isolates as S. clavata. Initially, Vitek 2 identified the strains as Geotrichum capitatum in two of the seven cases. Molecular identification gave 99% homology with S. clavata. BG was positive in three out of six patients (range 159 to >523 pg/ml), GM results were always negative. All the isolates were resistant to echinocandins (anidulafungin, micafungin, and caspofungin) and Fluconazole, but susceptible to Flucytosine and Voriconazole. One isolate showed acquired resistance to Flucytosine and Amphotericin B during treatment. Both the correlation-based dendrograms obtained by MALDI-TOF MS (Bruker Daltonics) and MS-Vitek not only clustered six of the seven bloodstream infection (BSI) isolates in the same group, but also showed their strong relatedness. Phylogenetic analysis using SNPrelate showed that the seven samples recorded during the investigation period clustered together. We observed a split between one case and the remainder with a node supported by a z-score of 2.3 (p-value = 0.021) and 16 mutations unique to each branch.

Conclusion

The use of proteomics for identification and evaluation of strain clonality in outbreaks of rare pathogens is a promising alternative to laborious and time-consuming molecular methods, even if molecular whole-genome sequencing (WGS) typing will still remain the reference method for rare emergent pathogens.

A Novel Resistance Pathway for Calcineurin Inhibitors in the Human-Pathogenic Mucorales Mucor circinelloides

Mucormycosis is an emerging lethal fungal infection in immunocompromised patients. Mucor circinelloides is a causal agent of mucormycosis and serves as a model system to understand genetics in Mucorales. Calcineurin is a conserved virulence factor in many pathogenic fungi, and calcineurin inhibition or deletion of the calcineurin regulatory subunit (CnbR) in Mucor results in a shift from hyphal to yeast growth. We analyzed 36 calcineurin inhibitor-resistant or bypass mutants that exhibited hyphal growth in the presence of calcineurin inhibitors or in the yeast-locked cnbRΔ mutant background without carrying any mutations in known calcineurin components. We found that a majority of the mutants had altered sequence in a gene, named here bycA (bypass of calcineurin). bycA encodes an amino acid permease. We verified that both the bycAΔ single mutant and the bycAΔ cnbRΔ double mutant are resistant to calcineurin inhibitor FK506, thereby demonstrating a novel mechanism of resistance against calcineurin inhibitors. We also found that the level of expression of bycA was significantly higher in the wild-type strain treated with FK506 and in the cnbRΔ mutants but was significantly lower in the wild-type strain without FK506 treatment. These findings suggest that bycA is a negative regulator of hyphal growth and/or a positive regulator of yeast growth in Mucor and that calcineurin suppresses expression of the bycA gene at the mRNA level to promote hyphal growth. BycA is involved in the Mucor hypha-yeast transition as our data demonstrate positive correlations among bycA expression, protein kinase A activity, and Mucor yeast growth. Also, calcineurin, independently of its role in morphogenesis, contributes to virulence traits, including phagosome maturation blockade, host cell damages, and proangiogenic growth factor induction during interactions with hosts.IMPORTANCEMucor is intrinsically resistant to most known antifungals, which makes mucormycosis treatment challenging. Calcineurin is a serine/threonine phosphatase that is widely conserved across eukaryotes. When calcineurin function is inhibited in Mucor, growth shifts to a less virulent yeast growth form, which makes calcineurin an attractive target for development of new antifungal drugs. Previously, we identified two distinct mechanisms through which Mucor can become resistant to calcineurin inhibitors involving Mendelian mutations in the gene for FKBP12, including mechanisms corresponding to calcineurin A or B subunits and epimutations silencing the FKBP12 gene. Here, we identified a third novel mechanism where loss-of-function mutations in the amino acid permease corresponding to the bycA gene contribute to resistance against calcineurin inhibitors. When calcineurin activity is absent, BycA can activate protein kinase A (PKA) to promote yeast growth via a cAMP-independent pathway. Our data also show that calcineurin activity contributes to host-pathogen interactions primarily in the pathogenesis of Mucor.

Outbreaks of Mucorales and the Species Involved

The order Mucorales is an ancient group of fungi classified in the subphylum Mucoromycotina. Mucorales are mainly fast-growing saprotrophs that belong to the first colonizers of diverse organic materials and represent a permanent part of the human environment. Several species are able to cause human infections (mucormycoses) predominantly in patients with impaired immune system, diabetes, or deep trauma. In this review, we compiled 32 reports on community- and hospital-acquired outbreaks caused by Mucorales. The most common source of mucoralean outbreaks was contaminated medical devices that are responsible for 40.7% of the outbreaks followed by contaminated air (31.3%), traumatic inoculation of soil or foreign bodies (9.4%), and the contact (6.2%) or the ingestion (6.2%) of contaminated plant material. The most prevalent species were Rhizopus arrhizus and R. microsporus causing 57% of the outbreaks. The genus Rhizomucor was dominating in outbreaks related to contaminated air while outbreaks of Lichtheimia species and Mucor circinelloides were transmitted by direct contact. Outbreaks with the involvement of several species are reported. Subtyping of strains revealed clonality in two outbreaks and no close relation in two other outbreaks. Based on the existing data, outbreaks of Mucorales can be caused by heterogeneous sources consisting of different strains or different species. Person-to-person transmission cannot be excluded because Mucorales can sporulate on wounds. For a better understanding and prevention of outbreaks, we need to increase our knowledge on the physiology, ecology, and population structure of outbreak causing species and more subtyping data.

Drug-Resistant Epimutants Exhibit Organ-Specific Stability and Induction during Murine Infections Caused by the Human Fungal Pathogen Mucor circinelloides

The emerging fungal pathogen Mucor circinelloides causes a severe infection, mucormycosis, which leads to considerable morbidity and mortality. Treatment of Mucor infection is challenging because Mucor is inherently resistant to nearly all clinical antifungal agents. An RNAi-dependent and reversible mechanism of antifungal resistance, epimutation, was recently reported for Mucor. Epimutation has not been studied in vivo, and it was unclear whether it would contribute to antifungal resistance observed clinically. We demonstrate that epimutation can both be induced and reverted after in vivo passage through a mouse; rates of both induction and reversion are higher after brain infection than after infection of other organs (liver, spleen, kidneys, or lungs). Elucidating the roles played by epimutation in drug resistance and infection will improve our understanding of Mucor and other fungal pathogens and may have implications for antifungal treatment.

The environmentally ubiquitous fungus Mucor circinelloides is a primary cause of the emerging disease mucormycosis. Mucor infection is notable for causing high morbidity and mortality, especially in immunosuppressed patients, while being inherently resistant to the majority of clinically available antifungal drugs. A new, RNA interference (RNAi)-dependent, and reversible epigenetic mechanism of antifungal resistance—epimutation—was recently discovered in M. circinelloides. However, the effects of epimutation in a host-pathogen setting were unknown. We employed a systemic, intravenous murine model of Mucor infection to elucidate the potential impact of epimutation in vivo. Infection with an epimutant strain resistant to the antifungal agents FK506 and rapamycin revealed that the epimutant-induced drug resistance was stable in vivo in a variety of different organs and tissues. Reversion of the epimutant-induced drug resistance was observed to be more rapid in isolates from the brain than in isolates recovered from the liver, spleen, kidney, or lungs. Importantly, infection with a wild-type strain of Mucor led to increased rates of epimutation after strains were recovered from organs and exposed to FK506 stress in vitro. Once again, this effect was more pronounced in strains recovered from the brain than from other organs. In summary, we report the rapid induction and reversion of RNAi-dependent drug resistance after in vivo passage through a murine model, with pronounced impact in strains recovered from brain. Defining the role played by epimutation in drug resistance and infection advances our understanding of Mucor and other fungal pathogens and may have implications for antifungal therapy.

A polyphasic approach to characterize Weissella cibaria and Weissella confusa strains

AIM

To study Weissella cibaria and Weissella confusa strains, lactic acid bacteria (LAB) members naturally present in food products, but not yet included in Qualified Presumption of Safety (QPS) list of European Food Safety Authority (EFSA).

METHODS AND RESULTS

We carried out a comparative genome analysis of 23 sequenced W. cibaria and 7 W. confusa genomes, in parallel with a physiological and functional characterization of several strains previously isolated from sourdough-like maize bran fermentation. The genome analysis revealed the absence of dedicated pathogenicity factors. Some putative virulence genes found in Weissella genomes were also present in other LAB strains, considered safe by EFSA and commonly used as probiotics. The physiological tests carried out on our strains corroborated the genomic results. Moreover, the following functional traits of interest to application in the food sector were identified: the majority of tested strains displayed high acidification rate, high reducing ability, production of exopolysaccharides (EPS), arabinoxylan degradation ability, growth in the presence of fructo-oligosaccharides (FOS), bile and gastric juice tolerance, and antifungal activity.

CONCLUSIONS

These results provide evidence for the possible use of selected strains of W. cibaria and W. confusa in the food sector.

SIGNIFICANCE AND IMPACT OF THE STUDY

This polyphasic study adds to the body of knowledge on the functional and applicable characteristics of these controversial species of LAB. This knowledge contributes to design new selected cultures included in the QPS list required for food applications.

A new species concept for the clinically relevant Mucor circinelloides complex

Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides complex – MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus.

The geographical region of origin determines the phagocytic vulnerability of Lichtheimia strains

Mucormycoses are life-threatening infections that affect patients suffering from immune deficiencies. We performed phagocytosis assays confronting various strains of Lichtheimia species with alveolar macrophages, which form the first line of defence of the innate immune system. To investigate 17 strains from four different continents in a comparative fashion, transmitted light and confocal fluorescence microscopy was applied in combination with automated image analysis. This interdisciplinary approach enabled the objective and quantitative processing of the big volume of image data. Applying machine-learning supported methods, a spontaneous clustering of the strains was revealed in the space of phagocytic measures. This clustering was not driven by measures of fungal morphology but rather by the geographical origin of the fungal strains. Our study illustrates the crucial contribution of machine-learning supported automated image analysis to the qualitative discovery and quantitative comparison of major factors affecting host-pathogen interactions. We found that the phagocytic vulnerability of Lichtheimia species depends on their geographical origin, where strains within each geographic region behaved similarly, but strongly differed amongst the regions. Based on this clustering, we were able to also classify clinical isolates with regard to their potential geographical origin.

A Revised Species Concept for Opportunistic Mucor Species Reveals Species-Specific Antifungal Susceptibility Profiles

Recently, the species concept of opportunistic Mucor circinelloides and its relatives has been revised, resulting in the recognition of its classical formae as independent species and the description of new species. In this study, we used isolates of all clinically relevant Mucor species and performed susceptibility testing using the EUCAST reference method to identify potential species-specific susceptibility patterns. In vitro susceptibility profiles of 101 mucoralean strains belonging to the genus Mucor (72), the closely related species Cokeromyces recurvatus (3), Rhizopus (12), Lichtheimia (10), and Rhizomucor (4) to six antifungals (amphotericin B, natamycin, terbinafine, isavuconazole, itraconazole, and posaconazole) were determined. The most active drug for all Mucorales was amphotericin B. Antifungal susceptibility profiles of pathogenic Mucor species were specific for isavuconazole, itraconazole, and posaconazole. The species formerly united in M. circinelloides showed clear differences in their antifungal susceptibilities. Cokeromyces recurvatus, Mucor ardhlaengiktus, Mucor lusitanicus (M. circinelloides f. lusitanicus), and Mucor ramosissimus exhibited high MICs to all azoles tested. Mucor indicus presented high MICs for isavuconazole and posaconazole, and Mucor amphibiorum and Mucor irregularis showed high MICs for isavuconazole. MIC values of Mucor spp. for posaconazole, isavuconazole, and itraconazole were high compared to those for Rhizopus and the Lichtheimiaceae (Lichtheimia and Rhizomucor). Molecular identification combined with in vitro susceptibility testing is recommended for Mucor species, especially if azoles are applied in treatment.

A Guide to Investigating Suspected Outbreaks of Mucormycosis in Healthcare

This report serves as a guide for investigating mucormycosis infections in healthcare. We describe lessons learned from previous outbreaks and offer methods and tools that can aid in these investigations. We also offer suggestions for conducting environmental assessments, implementing infection control measures, and initiating surveillance to ensure that interventions were effective. While not all investigations of mucormycosis infections will identify a single source, all can potentially lead to improvements in infection control.

Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model

Mucor circinelloides is a pathogenic fungus and etiologic agent of mucormycosis. In 2013, cases of gastrointestinal illness after yogurt consumption were reported to the US FDA, and the producer found that its products were contaminated with Mucor. A previous study found that the Mucor strain isolated from an open contaminated yogurt exhibited virulence in a murine systemic infection model and showed that this strain is capable of surviving passage through the gastrointestinal tract of mice. In this study, we isolated another Mucor strain from an unopened yogurt that is closely related but distinct from the first Mucor strain and subsequently examined if Mucor alters the gut microbiota in a murine host model. DNA extracted from a ten-day course of stool samples was used to analyze the microbiota in the gastrointestinal tracts of mice exposed via ingestion of Mucor spores. The bacterial 16S rRNA gene and fungal ITS1 sequences obtained were used to identify taxa of each kingdom. Linear regressions revealed that there are changes in bacterial and fungal abundance in the gastrointestinal tracts of mice which ingested Mucor. Furthermore, we found an increased abundance of the bacterial genus Bacteroides and a decreased abundance of the bacteria Akkermansia muciniphila in the gastrointestinal tracts of exposed mice. Measurements of abundances show shifts in relative levels of multiple bacterial and fungal taxa between mouse groups. These findings suggest that exposure of the gastrointestinal tract to Mucor can alter the microbiota and, more importantly, illustrate an interaction between the intestinal mycobiota and bacteriota. In addition, Mucor was able to induce increased permeability in epithelial cell monolayers in vitro, which might be indicative of unstable intestinal barriers. Understanding how the gut microbiota is shaped is important to understand the basis of potential methods of treatment for gastrointestinal illness. How the gut microbiota changes in response to exposure, even by pathogens not considered to be causative agents of food-borne illness, may be important to how commercial food producers prevent and respond to contamination of products aimed at the public. This study provides evidence that the fungal microbiota, though understudied, may play an important role in diseases of the human gut.

Animal Models to Study Mucormycosis

Mucormycosis is a rare but often fatal or debilitating infection caused by a diverse group of fungi. Animal models have been crucial in advancing our knowledge of mechanisms influencing the pathogenesis of mucormycoses, and to evaluate therapeutic strategies. This review describes the animal models established for mucormycosis, summarizes how they have been applied to study mucormycoses, and discusses the advantages and limitations of the different model systems.

Fulminant mucormycosis after a traffic accident: a case report

Mucormycosis is a rare fungal infection in immunocompetent patients, whereas in immunocompromised, it may be systemic and disseminated infection associated with high mortality. Mucormycosis is one of the most rapidly progressing and fulminant forms of fungal infections; Mucor circinelloides is rarely isolated species, also from immunocompromised patients. The reported case of mucormycosis after a traffic accident indicates that it may be the result of a contamination of wound by M. circinelloides coming from the environment. The fungal strain was identified by phenotypic methods and confirmed by molecular methods. Etest method was used for susceptibility testing of the fungal strain. No mycotoxins were detected in the analyzed sample. The infection was successfully treated with amphotericin B, but amputation of the lower limb was necessary.