Microscopy of fungal biofilms

Biofilm-associated metabolism via ERG251 in Candida albicans

Biofilm formation by the fungal pathogen Candida albicans is the basis for its ability to infect medical devices. The metabolic gene ERG251 has been identified as a target of biofilm transcriptional regulator Efg1, and here we report that ERG251 is required for biofilm formation but not conventional free-living planktonic growth. An erg251Δ/Δ mutation impairs biofilm formation in vitro and in an in vivo catheter infection model. In both in vitro and in vivo biofilm contexts, cell number is reduced and hyphal length is limited. To determine whether the mutant defect is in growth or some other aspect of biofilm development, we examined planktonic cell features in a biofilm-like environment, which was approximated with sealed unshaken cultures. Under those conditions, the erg251Δ/Δ mutation causes defects in growth and hyphal extension. Overexpression in the erg251Δ/Δ mutant of the paralog ERG25, which is normally expressed more weakly than ERG251, partially improves biofilm formation and biofilm hyphal content, as well as growth and hyphal extension in a biofilm-like environment. GC-MS analysis shows that the erg251Δ/Δ mutation causes a defect in ergosterol accumulation when cells are cultivated under biofilm-like conditions, but not under conventional planktonic conditions. Overexpression of ERG25 in the erg251Δ/Δ mutant causes some increase in ergosterol levels. Finally, the hypersensitivity of efg1Δ/Δ mutants to the ergosterol inhibitor fluconazole is reversed by ERG251 overexpression, arguing that reduced ERG251 expression contributes to this efg1Δ/Δ phenotype. Our results indicate that ERG251 is required for biofilm formation because its high expression levels are necessary for ergosterol synthesis in a biofilm-like environment.

Effect of 5-Aminolevulinic Acid Photodynamic Therapy on Aspergillus fumigatus Biofilms in Vitro

Aspergillus fumigatus biofilm development results in enhanced pathogenicity and treatment resistance. Most contemporary antibiotics, however, are unable to eliminate biofilms. In recent years, with the application of new photosensitizers and the development of treatment, ALA-PDT (5-aminolevulinic acid photodynamic treatment) has achieved remarkable curative effect in the treatment of fungal infectious diseases; however, no research has been conducted on ALA-PDT against A. fumigatus. This study investigated the inhibitory effect of ALA-PDT at various 5-aminolevulinic acid concentrations and light doses on A. fumigatus planktonic and biofilms in vitro. We found that ALA-PDT may successfully inhibit the development of A. fumigatus biofilm and disintegrate mature biofilm. After ALA-PDT treatment, the adherence rate and vitality dramatically decreased, and the biofilm's structure was severely compromised. Our findings show for the first time that ALA-PDT may be used to prevent the formation of A. fumigatus biofilm and disturb the structure of mature biofilm, and that it could be employed as a therapeutic therapy for A. fumigatus superficial infection.

Tools of the Trade: Image Analysis Programs for Confocal Laser-Scanning Microscopy Studies of Biofilms and Considerations for Their Use by Experimental Researchers

Confocal laser-scanning microscopy (CLSM) is the bedrock of the microscopic visualization of biofilms. Previous applications of CLSM in biofilm studies have largely focused on observations of bacterial or fungal elements of biofilms, often seen as aggregates or mats of cells. However, the field of biofilm research is moving beyond qualitative observations alone, toward the quantitative analysis of the structural and functional features of biofilms, across clinical, environmental, and laboratory conditions. In recent times, several image analysis programs have been developed to extract and quantify biofilm properties from confocal micrographs. These tools not only vary in their scope and relevance to the specific biofilm features under study but also with respect to the user interface, compatibility with operating systems, and raw image requirements. Understanding these considerations is important when selecting tools for quantitative biofilm analysis, including at the initial experimental stages of image acquisition. In this review, we provide an overview of image analysis programs for confocal micrographs of biofilms, with a focus on tool selection and image acquisition parameters that are relevant for experimental researchers to ensure reliability and compatibility with downstream image processing.

Biotechnological applications of biofilms formed by osmotolerant and halotolerant yeasts

Many microorganisms are capable of developing biofilms under adverse conditions usually related to nutrient limitation. They are complex structures in which cells (in many cases of different species) are embedded in the material that they secrete, the extracellular matrix (ECM), which is composed of proteins, carbohydrates, lipids, and nucleic acids. The ECM has several functions including adhesion, cellular communication, nutrient distribution, and increased community resistance, this being the main drawback when these microorganisms are pathogenic. However, these structures have also proven useful in many biotechnological applications. Until now, the most interest shown in these regards has focused on bacterial biofilms, and the literature describing yeast biofilms is scarce, except for pathological strains. Oceans and other saline reservoirs are full of microorganisms adapted to extreme conditions, and the discovery and knowledge of their properties can be very interesting to explore new uses. Halotolerant and osmotolerant biofilm-forming yeasts have been employed for many years in the food and wine industry, with very few applications in other areas. The experience gained in bioremediation, food production and biocatalysis with bacterial biofilms can be inspiring to find new uses for halotolerant yeast biofilms. In this review, we focus on the biofilms formed by halotolerant and osmotolerant yeasts such as those belonging to Candida, Saccharomyces flor yeasts, Schwannyomyces or Debaryomyces, and their actual or potential biotechnological applications. KEY POINTS: • Biofilm formation by halotolerant and osmotolerant yeasts is reviewed. • Yeasts biofilms have been widely used in food and wine production. • The use of bacterial biofilms in bioremediation can be expanded to halotolerant yeast counterparts.

Identifying genetic variants associated with amphotericin B (AMB) resistance in Aspergillus fumigatus via k-mer-based GWAS

Aspergillus fumigatus is one of the most common pathogenic fungi, which results in high morbidity and mortality in immunocompromised patients. Amphotericin B (AMB) is used as the core drug for the treatment of triazole-resistant A. fumigatus. Following the usage of amphotericin B drugs, the number of amphotericin B-resistant A. fumigatus isolates showed an increasing trend over the years, but the mechanism and mutations associated with amphotericin B sensitivity are not fully understood. In this study, we performed a k-mer-based genome-wide association study (GWAS) in 98 A. fumigatus isolates from public databases. Associations identified with k-mers not only recapitulate those with SNPs but also discover new associations with insertion/deletion (indel). Compared to SNP sites, the indel showed a stronger association with amphotericin B resistance, and a significant correlated indel is present in the exon region of AFUA_7G05160, encoding a fumarylacetoacetate hydrolase (FAH) family protein. Enrichment analysis revealed sphingolipid synthesis and transmembrane transport may be related to the resistance of A. fumigatus to amphotericin B. The expansion of variant types detected by the k-mer method increases opportunities to identify and exploit complex genetic variants that drive amphotericin B resistance, and these candidate variants help accelerate the selection of prospective gene markers for amphotericin B resistance screening in A. fumigatus.

Microbial-assisted soil chromium immobilization through zinc and iron-enriched rice husk biochar

Soil chromium toxicity usually caused by the tannery effluent compromises the environment and causes serious health hazards. The microbial role in strengthening biochar for its soil chromium immobilization remains largely unknown. Hence, this study evaluated the effectiveness of zinc and iron-enriched rice husk biochar (ZnBC and FeBC) with microbial combinations to facilitate the chromium immobilization in sandy loam soil. We performed morphological and molecular characterization of fungal [Trichoderma harzianum (F1), Trichoderma viride (F2)] and bacterial [Pseudomonas fluorescence (B1), Bacillus subtilis (B2)] species before their application as soil ameliorants. There were twenty-five treatments having ZnBC and FeBC @ 1.5 and 3% inoculated with bacterial and fungal isolates parallel to wastewater in triplicates. The soil analyses were conducted in three intervals each after 20, 30, and 40 days. The combination of FeBC 3%+F2 reduced the soil DTPA-extractable chromium by 96.8% after 40 days of incubation (DAI) relative to wastewater. Similarly, 92.81% reduction in chromium concentration was achieved through ZnBC 3%+B1 after 40 DAI compared to wastewater. Under the respective treatments, soil Cr(VI) retention trend increased with time such as 40 > 30 > 20 DAI. Langmuir adsorption isotherm verified the highest chromium adsorption capacity (41.6 mg g⁻¹) with FeBC 3% at 40 DAI. Likewise, principal component analysis (PCA) and heat map disclosed electrical conductivity-chromium positive, while cation exchange capacity-chromium and pH-organic matter negative correlations. PCA suggested the ZnBC-bacterial while FeBC-fungal combinations as effective Cr(VI) immobilizers with >70% data variance at 40 DAI. Overall, the study showed that microbes + ZnBC/FeBC resulted in low pH, high OM, and CEC, which ultimately played a role in maximum Cr(VI) adsorption from wastewater applied to the soil. The study also revealed the interrelation and alternations in soil dynamics with pollution control treatments. Based on primitive soil characteristics such as soil metal concentration, its acidity, and alkalinity, the selection criteria can be set for treatments application to regulate the soil properties. Additionally, FeBC with Trichoderma viride should be tested on the field scale to remediate the Cr(VI) toxicity.

Amphotericin B Polymer Nanoparticles Show Efficacy against Candida Species Biofilms

Purpose: Chronic infections of Candida albicans are characterised by the embedding of budding and entwined filamentous fungal cells into biofilms. The biofilms are refractory to many drugs and Candida biofilms are associated with ocular fungal infections. The objective was to test the activity of nanoparticulate amphotericin B (AmB) against Candida biofilms. Methods: AmB was encapsulated in the Molecular Envelope Technology (MET, N-palmitoyl-N-monomethyl-N,N-dimethyl-N,N,N-trimethyl-6-O-glycolchitosan) nanoparticles and tested against Candida biofilms in vitro. Confocal laser scanning microscopy (CLSM) imaging of MET nanoparticles’ penetration into experimental biofilms was carried out and a MET-AmB eye drop formulation was tested for its stability. Results: MET-AmB formulations demonstrated superior activity towards C. albicans biofilms in vitro with the EC50 being ~30 times lower than AmB alone (EC50 MET-AmB = 1.176 μg mL⁻¹, EC50 AmB alone = 29.09 μg mL⁻¹). A similar superior activity was found for Candida glabrata biofilms, where the EC50 was ~10× lower than AmB alone (EC50 MET-AmB = 0.0253 μg mL⁻¹, EC50 AmB alone = 0.289 μg mL⁻¹). CLSM imaging revealed that MET nanoparticles penetrated through the C. albicans biofilm matrix and bound to fungal cells. The activity of MET-AmB was no different from the activity of AmB alone against C. albicans cells in suspension (MET-AmB MIC90 = 0.125 μg mL⁻¹, AmB alone MIC90 = 0.250 μg mL⁻¹). MET-AmB eye drops were stable at room temperature for at least 28 days. Conclusions: These biofilm activity findings raise the possibility that MET-loaded nanoparticles may be used to tackle Candida biofilm infections, such as refractory ocular fungal infections.

First Study of Naturally Formed Fungal Biofilms on the Surface of Intragastric Balloons

BACKGROUND

Intragastric balloon (IGB) is a medical device used in the endoscopic treatment of pre-obesity and obesity. The involvement of IGB with biofilms has been previously reported; however, little is still known. We determine the frequency of biofilms naturally formed on the external surface of IGB, as well as some variables related to IGB types and patients features, species of fungi involved, and biofilm evidence.

METHODS

A retrospective study was conducted based on endoscopies and medical records of patients with explanted IGB between 2015 and 2018, which had masses strongly adhered to the surface of the balloon, suspecting the presence of a biofilm. From 2018, the samples of those masses were investigated seeking biofilm characterization based on mycological and structural aspects.

RESULTS

A total of 149 endoscopies were surveyed; 27 IGBs (18.12%) showed signs suggesting biofilm formation. There was no significant difference between biofilm involvement in IGB and the anthropometric and demographic profile of the patients. On the other hand, there was a significant difference regarding the IGB type, 24.05% of the adjustable IGB were compromised by biofilm, while in non-adjustable IGB, it was 11.43% (p = 0.04; OR 2.45; 95% CI, 0.98-6.12). Candida glabrata was the most isolated fungal species from the well-organized fungal biofilm.

CONCLUSIONS

The frequency of fungal biofilm naturally formed on the external surface of IGB was elevated. The risk of biofilm formation was increased for the adjustable IGB, but it did not relate to the demographic data and anthropometric patient profile.

BSC2 induces multidrug resistance via contributing to the formation of biofilm in Saccharomyces cerevisiae

Biofilm plays an important role in fungal multidrug resistance (MDR). Our previous studies showed that BSC2 is involved in resistance to amphotericin B (AMB) through antioxidation in Saccharomyces cerevisiae. In this study, the overexpression of BSC2 and IRC23 induced strong MDR in S. cerevisiae. BSC2-overexpression affected cellular flocculation, cell surface hydrophobicity, biofilm formation and invasive growth. However, it failed to induce caspofungin (CAS) resistance and affect the invasive growth in FLO mutant strains (FLO11Δ, FLO1Δ, FLO8Δ and TUP1Δ). Furthermore, the overexpression of BSC2 compensated for chitin synthesis defects to maintain the cell wall integrity and significantly reduced the cell morphology abnormality induced by CAS. However, it could not repair the cell wall damage caused by CAS in the FLO mutant strains. Although BSC2 overexpression increased the level of mannose in the cell wall, DPM1 overexpression in both BY4741 and bsc2∆ could confer resistance to CAS and AMB. In addition, BSC2 overexpression significantly increased the mRNA expression of FLO11, FLO1, FLO8 and TUP1. BSC2 may function as a regulator of FLO genes and be involved in cell wall integrity in yeast. Taken together, our data demonstrate that BSC2 induces MDR in a FLO pathway-dependent manner via contributing to the formation of biofilms in S. cerevisiae. TAKE AWAYS: Overexpression of BSC2 induced strong MDR in S. cerevisiae. BSC2 affected cellular flocculation, CSH, biofilm formation and invasive growth. BSC2 could not repair the cell wall damage caused by CAS in the FLO mutants. BSC2 may function as a regulator of FLO genes to maintain cell wall integrity. BSC2 promotes biofilm formation in a FLO pathway-dependent manner to induce MDR.

Whole slide imaging is a high-throughput method to assess Candida biofilm formation

New strategies that enable fast and accurate visualization of Candida biofilms are necessary to better study their structure and response to antifungals agents. Here, we applied whole slide imaging (WSI) to study biofilm formation of Candida species. Three relevant biofilm-forming Candida species (C. albicans ATCC 10231, C. glabrata ATCC 2001, and C. tropicalis ATCC 750) were cultivated on glass coverslips both in presence and absence of widely used antifungals. Accumulated biofilms were stained with fluorescent markers and scanned in both bright-field and fluorescence modes using a WSI digital scanner. WSI enabled clear assessment of both size and structural features of Candida biofilms. Quantitative analyses readily detected reductions in biofilm-covered surface area upon antifungal exposure. Furthermore, we show that the overall biofilm growth can be adequately assessed across both bright-field and fluorescence modes. At the single-cell level, WSI proved adequate, as morphometric parameters evaluated with WSI did not differ significantly from those obtained with scanning electron microscopy, considered as golden standard at single-cell resolution. Thus, WSI allows for reliable visualization of Candida biofilms enabling both large-scale growth assessment and morphometric characterization of single-cell features, making it an important addition to the available microscopic toolset to image and analyse fungal biofilm growth.

Visualizing three-dimensional fungal growth using light sheet fluorescence microscopy

The evaluation of morphology is fundamental to comprehend how fungi grow, develop, and interact with the environment. Although fungal growth has been extensively studied associated to two-dimensional geometries, lack of appropriate experimental tools has limited exploration of the complex three-dimensional (3D) structures exhibited by mycelia in more general contexts. In this paper, we report the construction of a light-sheet fluorescence microscope (LSFM) capable of performing time-lapse visualization of 3D biological structures (4D microscopy), and the use of this instrument to follow the dynamics of fungal growth. LSFM uses scanning of selective plane illumination and digital reconstruction to provide 3D images of the specimen. We describe the optical, electronic, and computational means to implement two-color LSFM, and provide detailed procedures for aligning and testing the setup. We successfully demonstrate use of both autofluorescence and specific tagging to image Trichoderma atroviride and Neurospora crassa strains growing in liquid media, over extended times (~12 h) and volumes (~400 × 1500 × 800 μm³) at single-hypha resolution. The excellent image contrast provided by LSFM enables us to visualize the dynamics of mycelial architecture, interactions among hyphae, and measure rates of 3D apical extension. Altogether, our work shows a powerful imaging tool to perform 3D morphological analysis of fungi, from hyphae to mycelium.

Cell Rupture and Morphogenesis Control of the Dimorphic Yeast Candida albicans by Nanostructured Surfaces

Nanostructured surfaces control microbial biofilm formation by killing mechanically via surface architecture. However, the interactions between nanostructured surfaces (NSS) and cellular fungi have not been thoroughly investigated and the application of NSS as a means of controlling fungal biofilms is uncertain. Cellular yeast such as Candida albicans are structurally and biologically distinct from prokaryotic microbes and therefore are predicted to react differently to nanostructured surfaces. The dimorphic opportunistic fungal pathogen, C. albicans, is responsible for most cases of invasive candidiasis and is a serious health concern due to the rapid increase of drug resistance strains. In this paper, we show that the nanostructured surfaces from a cicada wing alter C. albicans' viability, biofilm formation, adhesion, and morphogenesis through physical contact. However, the fungal cell response to the NSS suggests that nanoscale mechanical interactions impact C. albicans differently than prokaryotic microbes. This study informs on the use of nanoscale architecture for the control of eukaryotic biofilm formation and illustrates some potential caveats with the application of NSS as an antimicrobial means.

Intra-colony channels in E. coli function as a nutrient uptake system

The ability of microorganisms to grow as aggregated assemblages has been known for many years, however their structure has remained largely unexplored across multiple spatial scales. The development of the Mesolens, an optical system which uniquely allows simultaneous imaging of individual bacteria over a 36 mm2 field of view, has enabled the study of mature Escherichia coli macro-colony biofilm architecture like never before. The Mesolens enabled the discovery of intra-colony channels on the order of 10 μm in diameter, that are integral to E. coli macro-colony biofilms and form as an emergent property of biofilm growth. These channels have a characteristic structure and re-form after total mechanical disaggregation of the colony. We demonstrate that the channels are able to transport particles and play a role in the acquisition of and distribution of nutrients through the biofilm. These channels potentially offer a new route for the delivery of dispersal agents for antimicrobial drugs to biofilms, ultimately lowering their impact on public health and industry.

Three-dimensional cellular aggregates formed by Beauveria pseudobassiana in liquid culture with potential for use as a biocontrol agent of the African black beetle (Heteronychus arator)

Beauveria pseudobassiana formed three-dimensional aggregates of cells (CAs) in liquid culture. CAs were formed mainly by blastospores and conidia, distinct from microsclerotia formed through adhesion of hyphae. The formation, germination and sporulation of CAs were studied, as well as the pathogenicity of conidia produced from them against adults of black beetle. After 4 days of culture, CAs were formed, becoming compact and melanised after 10 days of incubation. Electron microscopy showed three-dimensional CAs averaging 431.65 µm in length with irregular shapes and rough surfaces, where cells were trapped within an extracellular matrix. CAs germinated after 2 days of incubation on agar-plates producing hyphae and forming phialides and conidia after 4 days. Produced conidia caused 45% mortality of black beetle adults. CAs germination and sporulation on soil were directly correlated with soil moisture, reaching 80% and 100% germination on the surface of soil with 17% and 30% moisture, respectively. CAs maintained 100% germination after 2 years of storage under refrigeration. These CAs could have a similar function as microsclerotia in nature, acting as resistant structures able to protect internal cells and their ability to sporulate producing infective conidia, suggesting their potential to be used as bioinsecticides to control soil-dwelling insects.

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality

Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality.

All organisms tailor genetic programs to the available nutrients, such as sources of carbon. Here we define two key regulators of the genetic programs for carbon source utilization in the fungal pathogen Candida albicans. The two regulators have many shared roles, yet are partially specialized to control carbon acquisition and metabolism, respectively. In addition, the regulators together control traits associated with pathogenicity, an indication that carbon regulation is integrated into the pathogenicity program. Finally, the regulators help to explain a long-standing riddle—that the central carbon regulator Snf1 is essential for C. albicans viability.

Microbiologically influenced corrosion mechanism of 304L stainless steel in treated urban wastewater and protective effect of silane-TiO2 coating

Microbiologically influenced corrosion (MIC) of bare and silane-TiO₂ sol-gel coated stainless steel (SS) was studied in treated urban wastewater (TUWW). Combining the electrochemical impedance spectroscopy (EIS) and the scanning vibrating electrode technique (SVET) showed that SS surface colonization occurs, at earlier stages, by iron-oxidizing bacteria (IOB), and later by sulphate-reducing bacteria (SRB). The SVET results showed that chemical corrosion process and bacterial respiration led to the depletion of dissolved oxygen, creating a differential aeration cell and thus a localized corrosion phenomenon. Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) showed that the growth of a bacterial biofilm on 304L SS was a dynamic process, stimulating the localized oxidation of SS. To improve corrosion protection, a silane-TiO₂ sol-gel coating for SS is proposed. SEM showed that the coating reduced bacterial adhesion and EIS study demonstrated that the coating improved the barrier properties and corrosion resistance of 304L SS in TUWW over a short period of immersion.

Could Flavonoids Compete with Synthetic Azoles in Diminishing Candida albicans Infections? A Comparative Review Based on In Vitro Studies

Flavonoids are polyphenolic compounds with already confirmed various health benefits. This review will shed light on flavonoids as potential antifungals in Candida albicans infections. C. albicans is an opportunistic pathogen able to cause serious health issues due to numerous virulence factors amplifying its pathogenicity. One of the most important virulence factors is Candida ability to form biofilms which are highly resistant to the treatment of antifungal drugs; making diminishing of this pathogen even more challenging. This review will focus on current knowledge on individual flavonoid compounds having the potential to deal with C. albicans in vitro, with special turn on antibiofilm potential and insight into the mode of action, where available. Majority of the commercial drugs for the treatment of candidiasis belong to azole class, so the activity of flavonoids will be compared with the activity of newly synthetized azole compounds, as well as with azole drugs that are already on the market as official therapeutics. This literature review will provide pros and cons for pushing future research towards exploring novel synthetic azoles or further examination of a wide pallet of natural flavonoids.

The PP2A regulatory subunits, Cdc55 and Rts1, play distinct roles in Candida albicans' growth, morphogenesis, and virulence

Protein phosphatase-2A (PP2A) is a heterotrimeric enzyme composed of a catalytic subunit, a regulatory subunit, and a structural subunit. In Candida albicans, Cdc55 and Rts1 have been identified as possible regulatory subunits of PP2A containing the catalytic subunit Pph21 and structural subunit Tpd3. The Tpd3-Pph21 phosphatase regulates cell morphogenesis and division. However, the functions of Cdc55 and Rts1 remain unclear. Here, we constructed cdc55Δ/Δ and rts1Δ/Δ mutants and found that they exhibit different defects in multiple phenotypes although both show similar hyperphosphorylation of the septin Sep7 and aberrant septin organization. Under yeast growth conditions, the cdc55Δ/Δ mutant grows slowly as pseudohyphae with some cells lacking the nucleus, while rts1Δ/Δ cells are round and enlarged and seem to undergo incomplete cell separation producing multinucleated cells. Strong chitin deposition occurs at the septum of cdc55Δ/Δ cells and on the surface of rts1Δ/Δ cells, which likely contributes to increased susceptibility to caspofungin. Also, cdc55Δ/Δ exhibits severe defects in hyphal and biofilm formation, while rts1Δ/Δ is partially defective. Both mutants show reduced virulence in mice, suggesting that PP2A-B subunits could serve as potential antifungal targets.

Circuit diversification in a biofilm regulatory network

Genotype-phenotype relationships can vary extensively among members of a species. One cause of this variation is circuit diversification, the alteration of gene regulatory relationships among members of a species. Circuit diversification is thought to be a starting point for the circuit divergence or rewiring that occurs during speciation. How widespread is circuit diversification? Here we address this question with the fungal pathogen Candida albicans, which forms biofilms rich in distinctive hyphal cells as a prelude to infection. Our understanding of the biofilm/hyphal regulatory network comes primarily from studies of one clinical isolate, strain SC5314, and its marked derivatives. We used CRISPR-based methods to create mutations of four key biofilm transcription factor genes–BCR1, UME6, BRG1, and EFG1 –in SC5314 and four additional clinical isolates. Phenotypic analysis revealed that mutations in BCR1 or UME6 have variable impact across strains, while mutations in BRG1 or EFG1 had uniformly severe impact. Gene expression, sampled with Nanostring probes and examined comprehensively for EFG1 via RNA-Seq, indicates that regulatory relationships are highly variable among isolates. Our results suggest that genotype-phenotype relationships vary in this strain panel in part because of differences in control of BRG1 by BCR1, a hypothesis that is supported through engineered constitutive expression of BRG1. Overall, the data show that circuit diversification is the rule, not the exception, in this biofilm/hyphal regulatory network.

Much of what we know about microbial pathogens is derived from in-depth analysis of one or a few standard laboratory strains. This statement is especially true for the fungal pathogen Candida albicans, because most studies have centered on strain SC5314 and its genetically marked derivatives. Here we examine the functional impact of mutations of four key biofilm regulators across five different clinical isolates. We observe that functional impact of the mutations, based on biological phenotypes and gene expression effects, varies extensively among the isolates. Our results support the idea that gene function should be validated with multiple strain isolates. In addition, our results indicate that a core regulatory network, which comprises regulatory relationships common to multiple isolates, may be enriched for functionally relevant genes.

Evaluating Efficacy of Antimicrobial and Antifouling Materials for Urinary Tract Medical Devices: Challenges and Recommendations

In Europe, the mean incidence of urinary tract infections in intensive care units is 1.1 per 1000 patient-days. Of these cases, catheter-associated urinary tract infections (CAUTI) account for 98%. In total, CAUTI in hospitals is estimated to give additional health-care costs of £1-2.5 billion in the United Kingdom alone. This is in sharp contrast to the low cost of urinary catheters and emphasizes the need for innovative products that reduce the incidence rate of CAUTI. Ureteral stents and other urinary-tract devices suffer similar problems. Antimicrobial strategies are being developed, however, the evaluation of their efficacy is very challenging. This review aims to provide considerations and recommendations covering all relevant aspects of antimicrobial material testing, including surface characterization, biocompatibility, cytotoxicity, in vitro and in vivo tests, microbial strain selection, and hydrodynamic conditions, all in the perspective of complying to the complex pathology of device-associated urinary tract infection. The recommendations should be on the basis of standard assays to be developed which would enable comparisons of results obtained in different research labs both in industry and in academia, as well as provide industry and academia with tools to assess the antimicrobial properties for urinary tract devices in a reliable way.

Rapid Gene Concatenation for Genetic Rescue of Multigene Mutants in Candida albicans

Our understanding of new genes is often built upon the knowledge of well-characterized genes. One avenue toward revealing such connections involves creation of strains with mutations in two or more defined genes to permit genetic interaction analysis. Strain manipulations can yield unexpected mutations at loci outside the defined targeted genes. In this report, we describe a method for rapid validation of multigene mutants, thus allowing an appraisal of the contribution of the defined targeted genes to the strain’s phenotype.

The biological function of a gene is often probed through its interactions with other genes. This general approach has been especially useful to build knowledge about poorly understood genes upon the bedrock of well-characterized genes. Genetic interaction analysis requires the construction of strains with mutations in two or more genes. Single-gene mutants of microbial pathogens are generally validated through introduction of a wild-type copy of the affected gene to create a complemented or reconstituted strain, followed by testing for restoration of a wild-type phenotype. This practice, formalized as one of Falkow’s “molecular Koch’s postulates” ensures that the phenotype of the mutant depends upon the known mutation. However, multigene mutants are seldom validated because of the labor required to assemble multiple genomic segments into a vector that can be introduced into the mutant strain. We present here an approach, concatemer assembly for rescue of mutant abilities (CARMA), that circumvents this impediment through an in vivo recombinational assembly strategy that does not require cloning at all. Our results show that CARMA allows genetic rescue of two double-gene mutant strains of the fungal pathogen Candida albicans.

IMPORTANCE Our understanding of new genes is often built upon the knowledge of well-characterized genes. One avenue toward revealing such connections involves creation of strains with mutations in two or more defined genes to permit genetic interaction analysis. Strain manipulations can yield unexpected mutations at loci outside the defined targeted genes. In this report, we describe a method for rapid validation of multigene mutants, thus allowing an appraisal of the contribution of the defined targeted genes to the strain’s phenotype.