Molecular Diagnosis of Invasive Fungal Infections: Species Identification and Quantitative Analysis by Broad-Spectrum PCR Assays.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 5339-5339
Author(s):  
Lenka Baskova ◽  
Sandra Preuner ◽  
Thomas Lion
Keyword(s):  
Quantitative Analysis ◽  
Dna Sequences ◽  
Fungal Pathogens ◽  
Fungal Infections ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Invasive Fungal Infections ◽  
Fungal Genome ◽  
Quantitative Detection ◽  
Correct Identification

Abstract Invasive fungal infections (IFI) play an increasingly important role as life-threatening complications in immunocompromised patients. Early application of antimycotic agents is an essential prerequisite for successful therapy. However, standardized diagnostic techniques permitting rapid, sensitive and, no less importantly, economic screening for the clinically relevant fungi have been lacking. We have developed two different real-time PCR systems for quantitative analysis of pathogenic fungi. The Pan-AC assay* permits in a single reaction the detection of all important Aspergillus and Candida species, which are responsible for the great majority of IFI in immunosuppressed individuals. In view of the increasing incidence of invasive infections caused by hitherto uncommon fungal species, new diagnostic tests with very broad specificity are required. We have therefore developed an additional two-reaction Pan-fungus assay*, which facilitates quantitative detection of a wide spectrum of fungal species (n>50), including also the newly emerging pathogenic fungi. The assays display high sensitivity and show no cross-reactivity with non-fungal pathogens or human DNA sequences. We have established an additional rapid molecular assay based on PCR fragment length analysis of a variable region in the fungal genome permitting rapid identification of the fungal species present, in order to facilitate selection of the most appropriate antifungal treatment. Correct identification of specific fungal pathogens including different Aspergillus, Candida and Fusarium species detected by the above assays in patients with febrile neutropenia has been confirmed by sequence analysis. The new assays are readily applicable to routine clinical diagnosis and provide a rapid and economic approach to the screening and monitoring of invasive fungal infections.

scholarly journals Multiplex PCR Based Strategy for Detection of Fungal Pathogen DNA in Patients with Suspected Invasive Fungal Infections

2020 ◽  
Vol 6 (4) ◽  
pp. 308
Author(s):  
Joana Carvalho-Pereira ◽  
Filipa Fernandes ◽  
Ricardo Araújo ◽  
Jan Springer ◽  
Juergen Loeffler ◽  
...  
Keyword(s):  
Fungal Infections ◽  
Fungal Species ◽  
Cross Reactivity ◽  
Invasive Fungal Infections ◽  
Clinical Samples ◽  
Correct Identification ◽  
Colony Pcr ◽  
Pcr Multiplex ◽  
Pathogen Dna ◽  
Species Specific

A new and easy polymerase chain reaction (PCR) multiplex strategy, for the identification of the most common fungal species involved in invasive fungal infections (IFI) was developed in this work. Two panels with species-specific markers were designed, the Candida Panel for the identification of Candida species, and the Filamentous Fungi Panel for the identification of Aspergillus species and Rhizopusarrhizus. The method allowed the correct identification of all targeted pathogens using extracted DNA or by colony PCR, showed no cross-reactivity with nontargeted species and allowed identification of different species in mixed infections. Sensitivity reached 10 to 1 pg of DNA and was suitable for clinical samples from sterile sites, with a sensitivity of 89% and specificity of 100%. Overall, the study showed that the new method is suitable for the identification of the ten most important fungal species involved in IFI, not only from positive blood cultures but also from clinical samples from sterile sites. The method provides a unique characteristic, of seeing the peak in the specific region of the panel with the correct fluorescence dye, that aids the ruling out of unspecific amplifications. Furthermore, the panels can be further customized, selecting markers for different species and/or resistance genes.

scholarly journals The landscape of toxic intermediates in the metabolic networks of pathogenic fungi reveals targets for antifungal drugs

2021 ◽  
Author(s):  
Jan Ewald ◽  
Paul Mathias Jansen ◽  
Sascha Brunke ◽  
Davina Hiller ◽  
Christian H. Luther ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Metabolic Networks ◽  
Fungal Infections ◽  
Pathogenic Fungi ◽  
Acid Synthesis ◽  
Fungal Species ◽  
Antifungal Drugs ◽  
Random Forest Regression ◽  
Amino Acid Synthesis ◽  
Emergence Of Resistance

The burden of fungal infections for humans, animals and plants is widely underestimated and comprises deadly infections as well as great conomic costs. Despite that, antifungal drugs are scarce and emergence of resistance in fungal strains contributes to a high mortality. To overcome this shortage, we propose toxic intermediates and their controlling enzymes in metabolic pathways as a resource for new targets and provide a web-service, FunTox-Networks to explore the landscape of toxic intermediates in the metabolic networks of fungal pathogens. The toxicity of metabolites is predicted by a new random forest regression model and is available for over one hundred fungal species. Further, for major fungal pathogens, metabolic networks from the KEGG database were enriched with data of toxicity and regulatory effort for each enzyme to support identification of targets. We determined several toxic intermediates in fungal-specific pathways like amino acid synthesis, nitrogen and sulfur assimilation, and the glyoxylate bypass. For the latter, we show experimentally that growth of the pathogen Candida albicans is inhibited when the detoxifying enzymes Mls1 and Hbr2 are deleted and toxic glyoxylate accumulates in the cell. Thus, toxic pathway intermediates and their controlling enzymes represent an untapped resource of antifungal targets.

scholarly journals The Role of Fungi in the Cocoa Production Chain and the Challenge of Climate Change

2021 ◽  
Vol 7 (3) ◽  
pp. 202
Author(s):  
Johannes Delgado-Ospina ◽  
Junior Bernardo Molina-Hernández ◽  
Clemencia Chaves-López ◽  
Gianfranco Romanazzi ◽  
Antonello Paparella
Keyword(s):  
Climate Change ◽  
Fungal Infections ◽  
Close Association ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Mitigation Strategies ◽  
Plant Diseases ◽  
Production Chain ◽  
Cocoa Production

Background: The role of fungi in cocoa crops is mainly associated with plant diseases and contamination of harvest with unwanted metabolites such as mycotoxins that can reach the final consumer. However, in recent years there has been interest in discovering other existing interactions in the environment that may be beneficial, such as antagonism, commensalism, and the production of specific enzymes, among others. Scope and approach: This review summarizes the different fungi species involved in cocoa production and the cocoa supply chain. In particular, it examines the presence of fungal species during cultivation, harvest, fermentation, drying, and storage, emphasizing the factors that possibly influence their prevalence in the different stages of production and the health risks associated with the production of mycotoxins in the light of recent literature. Key findings and conclusion: Fungi associated with the cocoa production chain have many different roles. They have evolved in a varied range of ecosystems in close association with plants and various habitats, affecting nearly all the cocoa chain steps. Reports of the isolation of 60 genera of fungi were found, of which only 19 were involved in several stages. Although endophytic fungi can help control some diseases caused by pathogenic fungi, climate change, with increased rain and temperatures, together with intensified exchanges, can favour most of these fungal infections, and the presence of highly aggressive new fungal genotypes increasing the concern of mycotoxin production. For this reason, mitigation strategies need to be determined to prevent the spread of disease-causing fungi and preserve beneficial ones.

scholarly journals Mitotic Recombination and Adaptive Genomic Changes in Human Pathogenic Fungi

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 901 ◽  
Author(s):  
Asiya Gusa ◽  
Sue Jinks-Robertson
Keyword(s):  
Fungal Pathogens ◽  
Repetitive Sequences ◽  
Pathogenic Fungi ◽  
Genetic Alterations ◽  
Fungal Species ◽  
Chronic Infections ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genomic Changes ◽  
Break Site ◽  
Repair Mechanisms

Genome rearrangements and ploidy alterations are important for adaptive change in the pathogenic fungal species Candida and Cryptococcus, which propagate primarily through clonal, asexual reproduction. These changes can occur during mitotic growth and lead to enhanced virulence, drug resistance, and persistence in chronic infections. Examples of microevolution during the course of infection were described in both human infections and mouse models. Recent discoveries defining the role of sexual, parasexual, and unisexual cycles in the evolution of these pathogenic fungi further expanded our understanding of the diversity found in and between species. During mitotic growth, damage to DNA in the form of double-strand breaks (DSBs) is repaired, and genome integrity is restored by the homologous recombination and non-homologous end-joining pathways. In addition to faithful repair, these pathways can introduce minor sequence alterations at the break site or lead to more extensive genetic alterations that include loss of heterozygosity, inversions, duplications, deletions, and translocations. In particular, the prevalence of repetitive sequences in fungal genomes provides opportunities for structural rearrangements to be generated by non-allelic (ectopic) recombination. In this review, we describe DSB repair mechanisms and the types of resulting genome alterations that were documented in the model yeast Saccharomyces cerevisiae. The relevance of similar recombination events to stress- and drug-related adaptations and in generating species diversity are discussed for the human fungal pathogens Candida albicans and Cryptococcus neoformans.

Identification and in Vitro Susceptibility Pattern of Fungal Pathogens in Immunocompromised Patients with invasive Fungal Infections

2021 ◽  
Vol 30 (3) ◽  
pp. 127-134
Author(s):  
Shaimaa A.S. Selem ◽  
Neveen A. Hassan ◽  
Mohamed Z. Abd El-Rahman ◽  
Doaa M. Abd El-Kareem
Keyword(s):  
Intensive Care ◽  
Fungal Infection ◽  
Fungal Pathogens ◽  
Fungal Infections ◽  
Antifungal Susceptibility ◽  
Invasive Fungal Infections ◽  
Immunocompromised Patients ◽  
University Hospitals ◽  
Vitek 2

Background: In intensive care units, invasive fungal infections have become more common, particularly among immunocompromised patients. Early identification and starting the treatment of those patients with antifungal therapy is critical for preventing unnecessary use of toxic antifungal agents. Objective: The aim of this research is to determine which common fungi cause invasive fungal infection in immunocompromised patients, as well as their antifungal susceptibility patterns in vitro, in Assiut University Hospitals. Methodology: This was a hospital based descriptive study conducted on 120 patients with clinical suspicion of having fungal infections admitted at different Intensive Care Units (ICUs) at Assiut University Hospitals. Direct microscopic examination and inoculation on Sabouraud Dextrose Agar (SDA) were performed on the collected specimens. Isolated yeasts were classified using phenotypic methods such as chromogenic media (Brilliance Candida agar), germ tube examination, and the Vitek 2 system for certain isolates, while the identification of mould isolates was primarily based on macroscopic and microscopic characteristics. Moulds were tested in vitro for antifungal susceptibility using the disc diffusion, and yeast were tested using Vitek 2 device cards. Results: In this study, 100 out of 120 (83.3%) of the samples were positive for fungal infection. Candida and Aspergillus species were the most commonly isolated fungal pathogens. The isolates had the highest sensitivity to Amphotericin B (95 %), followed by Micafungin (94 %) in an in vitro sensitivity survey. Conclusion: Invasive fungal infections are a leading cause of morbidity and mortality in immunocompromised patients, with Candida albicans being the most frequently isolated yeast from various clinical specimens; however, the rise in resistance, especially to azoles, is a major concern.

scholarly journals Prophylaxis of Invasive Fungal Infections: A Review of the Use of Posaconazole

2009 ◽  
Vol 1 ◽  
pp. CMT.S1948
Author(s):  
Curtis D. Collins ◽  
Jeannina A. Smith ◽  
Daniel R. Kaul
Keyword(s):  
At Risk ◽  
Fungal Pathogens ◽  
Fungal Infections ◽  
Case Reports ◽  
Case Series ◽  
Individual Case ◽  
Invasive Fungal Infections ◽  
Cost Of Care ◽  
Therapeutic Drug ◽  
Patients At Risk

Invasive fungal infections (IFIs) cause significant morbidity, mortality, and increased cost of care in patients with hematological malignancies, prolonged (i.e. >7-10 days) treatment induced neutropenia, and other disease states causing underlying immunosuppression. One strategy often used to combat the development of invasive infections is the use of antifungal agents as prophylaxis in at risk patients. Posaconazole is an oral triazole with a useful spectrum of activity against many fungal pathogens of concern in patients at risk for the development of IFIs. Posaconazole is only available in oral formulation and therapeutic drug monitoring may provide value due to variable absorption and serum concentrations. Clinical efficacy and pharmacoeconomic data have demonstrated the utility of posaconazole in the treatment of oropharyngeal candidiasis and for prophylaxis in patients at risk for development of IFIs. Several organizations or expert groups involved in developing guidelines for the management of IFIs recommend posaconazole anti-fungal prophylaxis in patients with AML or MDS and chemotherapy induced neutropenia or significant GVHD. In addition, nonrandomized studies (largely of salvage therapy) and case series suggest that posaconazole may be effective as treatment for invasive aspergillosis, zygomycosis, and coccidiomycosis. Further, small case series or individual case reports suggest activity against other less commonly encountered filamentous fungi and Histoplasma.

scholarly journals The Mechanisms of Mating in Pathogenic Fungi—A Plastic Trait

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 831
Author(s):  
Jane Usher
Keyword(s):  
Fungal Pathogens ◽  
Crop Yields ◽  
Fungal Infections ◽  
Pathogenic Fungi ◽  
Yeast Saccharomyces Cerevisiae ◽  
Closely Related Species ◽  
Sexual And Asexual Reproduction ◽  
Target Dna ◽  
High Degree ◽  
The Impact

The impact of fungi on human and plant health is an ever-increasing issue. Recent studies have estimated that human fungal infections result in an excess of one million deaths per year and plant fungal infections resulting in the loss of crop yields worth approximately 200 million per annum. Sexual reproduction in these economically important fungi has evolved in response to the environmental stresses encountered by the pathogens as a method to target DNA damage. Meiosis is integral to this process, through increasing diversity through recombination. Mating and meiosis have been extensively studied in the model yeast Saccharomyces cerevisiae, highlighting that these mechanisms have diverged even between apparently closely related species. To further examine this, this review will inspect these mechanisms in emerging important fungal pathogens, such as Candida, Aspergillus, and Cryptococcus. It shows that both sexual and asexual reproduction in these fungi demonstrate a high degree of plasticity.

scholarly journals Epidemiology and identification of potential fungal pathogens causing invasive fungal infections in a tertiary care hospital in northeast Thailand

2014 ◽  
Vol 52 (8) ◽  
pp. 810-818 ◽  
Author(s):  
Kiatichai Faksri ◽  
Wanlop Kaewkes ◽  
Kunyaluk Chaicumpar ◽  
Prajuab Chaimanee ◽  
Suwin Wongwajana
Keyword(s):  
Fungal Pathogens ◽  
Tertiary Care Hospital ◽  
Fungal Infections ◽  
Tertiary Care ◽  
Invasive Fungal Infections ◽  
Care Hospital ◽  
Northeast Thailand

scholarly journals Neutrophil and Eosinophil DNA Extracellular Trap Formation: Lessons From Pathogenic Fungi

2021 ◽  
Vol 12 ◽  
Author(s):  
Juliana da Costa Silva ◽  
Glaucia de Azevedo Thompson-Souza ◽  
Marina Valente Barroso ◽  
Josiane Sabbadini Neves ◽  
Rodrigo Tinoco Figueiredo
Keyword(s):  
Fungal Pathogens ◽  
Fungal Infections ◽  
Pathogenic Fungi ◽  
Allergic Diseases ◽  
Extracellular Vesicle ◽  
Fungal Colonization ◽  
Polymorphonuclear Cells ◽  
Effector Cells ◽  
Inflammatory Stimuli ◽  
Extracellular Trap

Fungal infections represent a worldwide health problem. Fungal pathogens are responsible for a variety of conditions, including superficial diseases, allergic pathologies and potentially lethal invasive infections. Neutrophils and eosinophils have been implicated as effector cells in several pathologies. Neutrophils are major effector cells involved in the control of fungal infections and exhibit a plethora of antifungal mechanisms, such as phagocytosis, reactive oxygen species production, degranulation, extracellular vesicle formation, and DNA extracellular trap (ET) release. Eosinophils are polymorphonuclear cells classically implicated as effector cells in the pathogenesis of allergic diseases and helminthic infections, although their roles as immunomodulatory players in both innate and adaptive immunity are currently recognized. Eosinophils are also endowed with antifungal activities and are abundantly found in allergic conditions associated with fungal colonization and sensitization. Neutrophils and eosinophils have been demonstrated to release their nuclear and mitochondrial DNA in response to many pathogens and pro-inflammatory stimuli. ETs have been implicated in the killing and control of many pathogens, as well as in promoting inflammation and tissue damage. The formation of ETs by neutrophils and eosinophils has been described in response to pathogenic fungi. Here, we provide an overview of the mechanisms involved in the release of neutrophil and eosinophil ETs in response to fungal pathogens. General implications for understanding the formation of ETs and the roles of ETs in fungal infections are discussed.

scholarly journals Cryphonectriaceae on Myrtales in China: phylogeny, host range, and pathogenicity

2020 ◽  
Vol 45 (1) ◽  
pp. 101-131 ◽  
Author(s):  
W. Wang ◽  
G.Q. Li ◽  
Q.L. Liu ◽  
S.F. Chen
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Fungal Pathogens ◽  
Southern China ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Psidium Guajava ◽  
Fungal Species ◽  
Canker Disease

Plantation-grown Eucalyptus (Myrtaceae) and other trees residing in the Myrtales have been widely planted in southern China. These fungal pathogens include species of Cryphonectriaceae that are well-known to cause stem and branch canker disease on Myrtales trees. During recent disease surveys in southern China, sporocarps with typical characteristics of Cryphonectriaceae were observed on the surfaces of cankers on the stems and branches of Myrtales trees. In this study, a total of 164 Cryphonectriaceae isolates were identified based on comparisons of DNA sequences of the partial conserved nuclear large subunit (LSU) ribosomal DNA, internal transcribed spacer (ITS) regions including the 5.8S gene of the ribosomal DNA operon, two regions of the β-tubulin (tub2/tub1) gene, and the translation elongation factor1-alpha (tef1) gene region, as well as their morphological characteristics. The results showed that eight species reside in four genera of Cryphonectriaceae occurring on the genera Eucalyptus, Melastoma (Melastomataceae), Psidium (Myrtaceae), Syzygium (Myrtaceae), and Terminalia (Combretaceae) in Myrtales. These fungal species include Chrysoporthe deuterocubensis, Celoporthe syzygii, Cel. eucalypti, Cel. guang-dongensis, Cel. cerciana, a new genus and two new species, as well as one new species of Aurifilum. These new taxa are hereby described as Parvosmorbus gen. nov., Par. eucalypti sp. nov., Par. guangdongensis sp. nov., and Aurifilum terminali sp. nov. Pathogenicity tests showed that the eight species of Cryphonectriaceae are pathogenic to two Eucalyptus hybrid seedlings, Melastoma sanguineum branches, and Psidium guajava and Syzygium jambos seedlings. Theoveralldatashowedthat Chr. deuterocubensis is the most aggressive, followed by Par. eucalypti. Significant differences in tolerance were observed between the two tested Eucalyptus hybrid genotypes, suggesting that disease-tolerant genotypes can be selected for disease management in the Eucalyptus industry.

Sign in / Sign up

Export Citation Format

Share Document