Outwitting multidrug resistance to antifungals

Synthesis and evaluation of the antifungal and antibiofilm potential of aminochalcones

Candida is a commensal fungus of clinical interest that commonly lives in oral cavity and intestine but can become an opportunist microrganism and cause severe infections. A serie of 10 aminochalcones were designed and synthetized to obtain compounds anti-Candida with potent and broad-spectrum activity. The most active compound J34 demonstrated excellent in vitro activity against Candida albicans, Candida tropicalis, Candida parapsilosis, Candida glabrata and Candida krusei with minimum inhibitory concentration between 1.9 and 7.8 µg/mL. The association of aminochalcone J34 with amphotericin B demonstrated synergistic effect against C. albicans, with Fractional Inhibiroty Concentration Index (FICI) value of 0.5. Subinhibitory concentration of J34 inhibited the C. albicans adhesion to human keratinocytes. Treatment with J34 reduced C. albicans biofilm formation, as well as acts on preformed biofilm in concentration-dependent mode. Time-kill curve demonstrated that J34 had fungicidal action after 12 h of treatment. Preliminary mechanism of action study showed J34 interacts with membrane ergosterol but does not act on fungal cell wall of C. albicans. In additon, in vivo studies using Galleria mellonella indicated low toxic effect of chalcone J34 after 72 h of treatment.

Aspergillus fumigatus escape mechanisms from its harsh survival environments

Aspergillus fumigatus is a ubiquitous pathogenic mold and causes several diseases, including mycotoxicosis, allergic reactions, and systemic diseases (invasive aspergillosis), with high mortality rates. In its ecological niche, the fungus has evolved and mastered many reply strategies to resist and survive against negative threats, including harsh environmental stress and deficiency of essential nutrients from natural environments, immunity responses and drug treatments in host, and competition from symbiotic microorganisms. Hence, treating A. fumigatus infection is a growing challenge. In this review, we summarized A. fumigatus reply strategies and escape mechanisms and clarified the main competitive or symbiotic relationships between A. fumigatus, viruses, bacteria, or fungi in host microecology. Additionally, we discussed the contemporary drug repertoire used to treat A. fumigatus and the latest evidence of potential resistance mechanisms. This review provides valuable knowledge which will stimulate further investigations and clinical applications for treating and preventing A. fumigatus infections. KEY POINTS: • Harsh living environment was a great challenge for A. fumigatus survival. • A. fumigatus has evolved multiple strategies to escape host immune responses. • A. fumigatus withstands antifungal drugs via intrinsic escape mechanisms.

Overcoming multidrug resistance by a singlet oxygen releasing camptothecin-endoperoxide

We made structural modifications on the A-ring of camptothecin (CPT) by incorporating methyl substituents on positions 9 and 12. This allows conversion of the camptothecin-derivative to an endoperoxide (ENDO-CPT). The endoperoxide obtained this way thermally releases singlet oxygen, reverting back to the original 9,12-dimethylcamptothecin (DM-CPT) with a half-life of 1.4 hours at 37 °C. Endoperoxide modification yields a significant improvement in cytotoxicity against MDR-cell lines, compared to both CPT and DM-CPT. It appears that the simultaneous action of singlet oxygen and CPT is highly effective due to the targeting of P-glycoprotein by singlet oxygen.

Azole Combinations and Multi-Targeting Drugs That Synergistically Inhibit Candidozyma auris

Limited antifungal treatment options and drug resistance require innovative approaches to effectively combat fungal infections. Combination therapy is a promising strategy that addresses these pressing issues by concurrently targeting multiple cellular sites. The drug targets usually selected for combination therapy are from different cellular pathways with the goals of increasing treatment options and reducing development of resistance. However, some circumstances can prevent the implementation of combination therapy in clinical practice. These could include the increased risk of adverse effects, drug interactions, and even the promotion of drug resistance. Furthermore, robust clinical evidence supporting the superiority of combination therapy over monotherapy is limited and underscores the need for further research. Despite these challenges, synergies detected with different antifungal classes, such as the azoles and echinocandins, suggest that treatment strategies can be optimized by better understanding the underlying mechanisms. This review provides an overview of multi-targeting combination strategies with a primary focus on Candidozyma auris infections.

Cryo-EM structures of Candida albicans Cdr1 reveal azole-substrate recognition and inhibitor blocking mechanisms

In Candida albicans, Cdr1 pumps azole drugs out of the cells to reduce intracellular accumulation at detrimental concentrations, leading to azole-drug resistance. Milbemycin oxime, a veterinary anti-parasitic drug, strongly and specifically inhibits Cdr1. However, how Cdr1 recognizes and exports azole drugs, and how milbemycin oxime inhibits Cdr1 remain unclear. Here, we report three cryo-EM structures of Cdr1 in distinct states: the apo state (Cdr1Apo), fluconazole-bound state (Cdr1Flu), and milbemycin oxime-inhibited state (Cdr1Mil). Both the fluconazole substrate and the milbemycin oxime inhibitor are primarily recognized within the central cavity of Cdr1 through hydrophobic interactions. The fluconazole is suggested to be exported from the binding site into the environment through a lateral pathway driven by TM2, TM5, TM8 and TM11. Our findings uncover the inhibitory mechanism of milbemycin oxime, which inhibits Cdr1 through competition, hindering export, and obstructing substrate entry. These discoveries advance our understanding of Cdr1-mediated azole resistance in C. albicans and provide the foundation for the development of innovative antifungal drugs targeting Cdr1 to combat azole-drug resistance.

Improving Drug Delivery on Candida Albicans Using Geraniol Nanoemulsion

Geraniol (GE) is a monoterpene alcohol with excellent antifungal activity. However, its low solubility and high volatility impair its use. Nanoemulsions (NE) are excellent delivery systems for poorly soluble and volatile drugs, achieving controlled release of the active ingredient. The aim of this study was to improve the delivery of geraniol (GE) incorporated in NE against Candida albicans in order to evaluate the antibiofilm effect and cytotoxicity. Nanoemulsion containing 10% oil phase (cholesterol) (w/w), 10% surfactant (mixture of soy phosphatidylcholine and Brij 58; 1:2) (w/w), and 80% aqueous phase (phosphate buffer) (w/w) was synthesized. Incorporation of GE was carried out by sonication and the final compounds were characterized by hydrodynamic diameter, polydispersity index (PDI), and zeta potential (ZP), in addition to evaluation of physicochemical stability after 6 months and 1 year. The GE-NE effect was evaluated on Candida albicans biofilms and cytotoxic effect was evaluated on immortalized normal oral cell line NOK-Si. The diameter of GE-NE was 232.3 ± 2.7 nm and PDI 0.155 with exhibited homogeneity and stability in solution. GE-NE showed antibiofilm activity at a concentration of 75 μg/mL with reduction of >6.0 log10, and no cytotoxicity against NOK-Si cells at concentrations below 150 μg/mL was observed. GE-NE proved to be a promising candidate for prevention and treatment of fungal diseases.

Candidiasis: From cutaneous to systemic, new perspectives of potential targets and therapeutic strategies

Candidiasis is an infection caused by fungi from a Candida species, most commonly Candida albicans. C. albicans is an opportunistic fungal pathogen typically residing on human skin and mucous membranes of the mouth, intestines or vagina. It can cause a wide variety of mucocutaneous barrier and systemic infections; and becomes a severe health problem in HIV/AIDS patients and in individuals who are immunocompromised following chemotherapy, treatment with immunosuppressive agents or after antibiotic-induced dysbiosis. However, the immune mechanism of host resistance to C. albicans infection is not fully understood, there are a limited number of therapeutic antifungal drugs for candidiasis, and these have disadvantages that limit their clinical application. Therefore, it is urgent to uncover the immune mechanisms of the host protecting against candidiasis and to develop new antifungal strategies. This review synthesizes current knowledge of host immune defense mechanisms from cutaneous candidiasis to invasive C. albicans infection and documents promising insights for treating candidiasis through inhibitors of potential antifungal target proteins.

Calcium Ion Channels in Saccharomyces cerevisiae

Regulating calcium ion (Ca²⁺) channels to improve the cell cycle and metabolism is a promising technology, ensuring increased cell growth, differentiation, and/or productivity. In this regard, the composition and structure of Ca²⁺ channels play a vital role in controlling the gating states. In this review, Saccharomyces cerevisiae, as a model eukaryotic organism and an essential industrial microorganism, was used to discuss the effect of its type, composition, structure, and gating mechanism on the activity of Ca²⁺ channels. Furthermore, the advances in the application of Ca²⁺ channels in pharmacology, tissue engineering, and biochemical engineering are summarized, with a special focus on exploring the receptor site of Ca²⁺ channels for new drug design strategies and different therapeutic uses, targeting Ca²⁺ channels to produce functional replacement tissues, creating favorable conditions for tissue regeneration, and regulating Ca²⁺ channels to enhance biotransformation efficiency.

Myriocin enhances the antifungal activity of fluconazole by blocking the membrane localization of the efflux pump Cdr1

Introduction: Extrusion of azoles from the cell, mediated by an efflux pump Cdr1, is one of the most frequently used strategies for developing azole resistance in pathogenic fungi. The efflux pump Cdr1 is predominantly localized in lipid rafts within the plasma membrane, and its localization is sensitive to changes in the composition of lipid rafts. Our previous study found that the calcineurin signal pathway is important in transferring sphingolipids from the inner to the outer membrane. Methods: We investigated multiple factors that enhance the antifungal activity of fluconazole (FLC) using minimum inhibitory concentration (MIC) assays and disk diffusion assays. We studied the mechanism of action of myriocin through qRT-PCR analysis and confocal microscopy analysis. We tested whether myriocin enhanced the antifungal activity of FLC and held therapeutic potential using a mouse infection model. Results: We found that this signal pathway has no function in the activity of Cdr1. We found that inhibiting sphingolipid biosynthesis by myriocin remarkably increased the antifungal activity of FLC with a broad antifungal spectrum and held therapeutic potential. We further found that myriocin potently enhances the antifungal activity of FLC against C. albicans by blocking membrane localization of the Cdr1 rather than repressing the expression of Cdr1. In addition, we found that myriocin enhanced the antifungal activity of FLC and held therapeutic potential. Discussion: Our study demonstrated that blocking the membrane location and inactivating Cdr1 by inhibiting sphingolipids biogenesis is beneficial for enhancing the antifungal activity of azoles against azole-resistant C. albicans due to Cdr1 activation.

Flipping and other astonishing transporter dance moves in fungal drug resistance

In all domains of life, transmembrane proteins from the ATP-binding cassette (ABC) transporter family drive the translocation of diverse substances across lipid bilayers. In pathogenic fungi, the ABC transporters of the pleiotropic drug resistance (PDR) subfamily confer antibiotic resistance and so are of interest as therapeutic targets. They also drive the quest for understanding how ABC transporters can generally accommodate such a wide range of substrates. The Pdr5 transporter from baker's yeast is representative of the PDR group and, ever since its discovery more than 30 years ago, has been the subject of extensive functional analyses. A new perspective of these studies has been recently provided in the framework of the first electron cryo-microscopy structures of Pdr5, as well as emergent applications of machine learning in the field. Taken together, the old and the new developments have been used to propose a mechanism for the transport process in PDR proteins. This mechanism involves a "flippase" step that moves the substrates from one leaflet of the bilayer to the other, as a central element of cellular efflux.

New strategies for combating fungal infections: Inhibiting inositol lipid signaling by targeting Sec14 phosphatidylinositol transfer proteins

Virulent fungi represent a particularly difficult problem in the infectious disease arena as these organisms are eukaryotes that share many orthologous activities with their human hosts. The fact that these activities are often catalyzed by conserved proteins places additional demands on development of pharmacological strategies for specifically inhibiting target fungal activities without imposing undesirable secondary effects on the host. While deployment of a limited set of anti-mycotics has to date satisfied the clinical needs for treatment of fungal infections, the recent emergence of multi-drug resistant fungal 'superbugs' now poses a serious global health threat with rapidly diminishing options for treatment. This escalating infectious disease problem emphasizes the urgent need for development of new classes of anti-mycotics. In that regard, Sec14 phosphatidylinositol transfer proteins offer interesting possibilities for interfering with fungal phosphoinositide signaling with exquisite specificity and without targeting the highly conserved lipid kinases responsible for phosphoinositide production. Herein, we review the establishment of proof-of-principle that demonstrates the feasibility of such an approach. We also describe the lead compounds of four chemotypes that directly target fungal Sec14 proteins. The rules that pertain to the mechanism(s) of Sec14 inhibition by validated small molecule inhibitors, and the open questions that remain, are discussed - as are the challenges that face development of next generation Sec14-directed inhibitors.

Reversing Multidrug Resistance by Inducing Mitochondrial Dysfunction for Enhanced Chemo-Photodynamic Therapy in Tumor

Efficiency of standard chemotherapy is dramatically hindered by intrinsic multidrug resistance (MDR). Recently, to amplify therapeutic efficacy, photodynamic therapy (PDT)-induced mitochondrial dysfunction by decorating targeting moieties on nanocarriers has obtained considerable attention. Nevertheless, low targeting efficiency, complex synthesis routes, and difficulty in releasing contents become the major obstacles in further clinical application. Herein, an ingenious liposomal-based nanomedicine (L@BP) was fabricated by encapsulating a mitochondria-anchored photosensitizer (Cy-Br) and paclitaxel (PTX) for realizing enhanced cooperation therapy. At the cellular level, L@BP could hurdle endosomal traps to localize and implement PDT in mitochondria. Intriguingly, the PDT-induced in situ mitochondrial dysfunction led to intracellular ATP reduction, which triggered the downregulated P-glycoprotein transportation capacity and thus resulted in diminishing the efflux of chemotherapeutic agents and increasing drug uptake by drug-resistant cells. The prepared nanomedicine eminently accumulated in the tumor site and acquired enhanced therapeutic efficiency on PTX-resistant lung cancer cells, which possessed great potential in circumventing MDR tumors.

Facile Homobifunctional Imidoester Modification of Advanced Nanomaterials for Enhanced Antibiotic Synergistic Effect

Resistance to antibiotics because of misuse and overuse is one of the greatest public health challenges worldwide. Despite the introduction of advanced nanotechnology in the production of antibiotics, the choice of appropriate medicines is limited due to side effects such as blood coagulation, toxicity, low efficacy, and low biocompatibility; therefore, novel nanomaterial composites are required to counter these repercussions. We first introduce a facile method for synthesizing a homobifunctional imidoester-coated nanospindle (HINS) zinc oxide composite for enhancement of antibiotic efficacy and reduction of toxicity and blood coagulation. The antibiotic efficacy of the composites is twice that of commercialized zinc nanoparticles; in addition, they have good biocompatibility, have increased surface charge and solubility owing to the covalent acylation groups of HI, and produce a large number of Zn⁺ ions and defensive reactive oxygen species (ROS) that effectively kill bacteria and fungi. The synergistic effect of a combination therapy with the HINS composite and itraconazole shows more than 90% destruction of fungi in treatments with low dosage with no cytotoxicity or coagulation evident in intravenous administration in in vitro and in vivo experiments. Thus, HINS composites are useful in reducing the effect of misuse and overuse of antibiotics in the medical field.

Recent progress on anti-Candida natural products

Candida is an intractable life-threatening pathogen. Candida infection is extremely difficult to eradicate, and thus is the major cause of morbidity and mortality in immunocompromised individuals. Morevover, the rapid spread of drug-resistant fungi has led to significant decreases in the therapeutic effects of clinical drugs. New anti-Candida agents are urgently needed to solve the complicated medical problem. Natural products with intricate structures have attracted great attention of researchers who make every endeavor to discover leading compounds for antifungal agents. Their novel mechanisms and diverse modes of action expand the variety of fungistatic agents and reduce the emergence of drug resistance. In recent decades, considerable effort has been devoted to finding unique antifungal agents from nature and revealing their unusual mechanisms, which results in important progress on the development of new antifungals, such as the novel cell wall inhibitors YW3548 and SCY-078 which are being tested in clinical trials. This review will present a brief summary on the landscape of anti-Candida natural products within the last decade. We will also discuss in-depth the research progress on diverse natural fungistatic agents along with their novel mechanisms.

Role of Candida glabrata as nosocomial pathogen and its susceptibility to Fluconazole, Voriconazole, Caspofungin, Micafungin and Amphotericin B

Candida has different types that could cause bloodstream infections. A total number of 150 samples were collected from candidemia patients and examined. The Candida spp. Species isolated from blood samples were analysed. These were identified by culturing the species using different media, namely the chromogenic agar test. Then, the virulence factors of all samples were tested. The Candida glabrata isolates were tested with six commercial antifungal drugs. C. glabrata 67 (44.6%), C. albicans 34 (22.6%), C. krusei 18 (12%), C. tropicalis 17 (11.3%), and C. parasilosis 14 (9.3%). the production of phospholipase ranged between 0.63-0.99 mm. It was found that 96% of the species showed phospholipase activity in aerobic conditions. The protease activities of Candida spp. Isolates were experimentally tested by area of inhibition around the colonies, where 59.3% had the double (++) protease activity, 31.4% with (+) grade, and 9.3% had (–) grade or clear zone around the colony. The hemolytic capacity ranged from 0.69-0.89 in the optimum aerobic environments. Finally, 38.33% of the isolated Candida spp. were positive and 61.67% negative for biofilm formation. Out of the total positive Candida spp. for biofilm formation, 21.73% were strong biofilm producers, and 78.27% were weak. Minimum fungicidal concentration (MFC) of Fluconazole for C. glabrata isolates was not appropriate (NA) due to the occurrence of low inhibition tested for species. Micafungin exhibited the lowest fungicidal activity against C. glabrata ranging from 0.03 - 0.125, while Fluconazole showed the highest.

Emerging Prospects for Combating Fungal Infections by Targeting Phosphatidylinositol Transfer Proteins

The emergence of fungal “superbugs” resistant to the limited cohort of anti-fungal agents available to clinicians is eroding our ability to effectively treat infections by these virulent pathogens. As the threat of fungal infection is escalating worldwide, this dwindling response capacity is fueling concerns of impending global health emergencies. These developments underscore the urgent need for new classes of anti-fungal drugs and, therefore, the identification of new targets. Phosphoinositide signaling does not immediately appear to offer attractive targets due to its evolutionary conservation across the Eukaryota. However, recent evidence argues otherwise. Herein, we discuss the evidence identifying Sec14-like phosphatidylinositol transfer proteins (PITPs) as unexplored portals through which phosphoinositide signaling in virulent fungi can be chemically disrupted with exquisite selectivity. Recent identification of lead compounds that target fungal Sec14 proteins, derived from several distinct chemical scaffolds, reveals exciting inroads into the rational design of next generation Sec14 inhibitors. Development of appropriately refined next generation Sec14-directed inhibitors promises to expand the chemical weaponry available for deployment in the shifting field of engagement between fungal pathogens and their human hosts.

Candida albicans targets that potentially synergize with fluconazole

Fluconazole has characteristics that make it widely used in the clinical treatment of C. albicans infections. However, fluconazole has only a fungistatic activity in C. albicans, therefore, in the long-term treatment of C. albicans infection with fluconazole, C. albicans has the potential to acquire fluconazole resistance. A promising approach to increase fluconazole's efficacy is identifying potential targets of drugs that can enhance the antifungal effect of fluconazole, or even make the drug fungicidal. In this review, we systematically provide a global overview of potential targets of drugs synergistic with fluconazole in C. albicans, identify new avenues for research on fluconazole potentiation, and highlight the promise of combinatorial strategies with fluconazole in combatting C. albicans infections.

Identification and Predictions Regarding the Biosynthesis Pathway of Polyene Macrolides Produced by Streptomyces roseoflavus Men-myco-93-63

A group of polyene macrolides mainly composed of two constituents was isolated from the fermentation broth of Streptomyces roseoflavus Men-myco-93-63, which was isolated from soil where potato scabs were repressed naturally. One of these macrolides was roflamycoin, which was first reported in 1968, and the other was a novel compound named Men-myco-A, which had one methylene unit more than roflamycoin. Together, they were designated RM. This group of antibiotics exhibited broad-spectrum antifungal activities in vitro against 17 plant-pathogenic fungi, with 50% effective concentrations (EC₅₀) of 2.05 to 7.09 μg/ml and 90% effective concentrations (EC₉₀) of 4.32 to 54.45 μg/ml, which indicates their potential use in plant disease control. Furthermore, their biosynthetic gene cluster was identified, and the associated biosynthetic assembly line was proposed based on a module and domain analysis of polyketide synthases (PKSs), supported by findings from gene inactivation experiments.IMPORTANCE Streptomyces roseoflavus Men-myco-93-63 is a biocontrol strain that has been studied in our laboratory for many years and exhibits a good inhibitory effect in many crop diseases. Therefore, the identification of antimicrobial metabolites is necessary and our main objective. In this work, chemical, bioinformatic, and molecular biological methods were combined to identify the structures and biosynthesis of the active metabolites. This work provides a new alternative agent for the biological control of plant diseases and is helpful for improving both the properties and yield of the antibiotics via genetic engineering.

Roles for Structural Biology in the Discovery of Drugs and Agrochemicals Targeting Sterol 14α-Demethylases

Antifungal drugs and antifungal agrochemicals have significant limitations. These include several unintended consequences of their use including the growing importance of intrinsic and acquired resistance. These problems underpin an increasingly urgent need to improve the existing classes of antifungals and to discover novel antifungals. Structural insights into drug targets and their complexes with both substrates and inhibitory ligands increase opportunity for the discovery of more effective antifungals. Implementation of this promise, which requires multiple skill sets, is beginning to yield candidates from discovery programs that could more quickly find their place in the clinic. This review will describe how structural biology is providing information for the improvement and discovery of inhibitors targeting the essential fungal enzyme sterol 14α-demethylase.

Synthesis, structural characterization, and prospects for new cobalt (II) complexes with thiocarbamoyl-pyrazoline ligands as promising antifungal agents

Candida spp. cause invasive fungal infections. One species, Candida glabrata, may present intrinsic resistance to conventional antifungal agents, thereby increasing mortality rates in hospitalized patients. In this context, metal complexes present an alternative for the development of new antifungal drugs owing to their biological and pharmacological activities demonstrated in studies in the last decades. Accordingly, in this study we have synthesized and characterized two new Co(II) complexes with thiocarbamoyl-pyrazoline ligands to assess their antimicrobial, mutagenic, and cytotoxic potential. For antimicrobial activity, the broth microdilution method was performed against ATCC strains of Candida spp. and fluconazole dose-dependent isolates of C. glabrata obtained from urine samples. The Ames test was used to assess mutagenic potential. The reduction method of the MTS reagent (3 [4,5-dimethylthiazol-2-yl]-5-[3-carboxymethoxyphenyl]-2-[4-sulfophenyl]-2H-tetrazolium) was performed with HeLa, SiHa, and Vero cells to determine cytotoxicity. Both complexes exhibited fungistatic and fungicidal activity for the yeasts used in the study, demonstrating greater potential for C. glabrata ATCC 2001 and the C. glabrata CG66 isolate with a Minimum Inhibitory Concentration MIC from 3.90 to 7.81 μg mL^-1 and fungicidal action from 7.81 to 15.62 μg mL^-1. The complexes inhibited and degraded biofilms by up to 90% and did not present mutagenic and cytotoxic potential at the concentrations evaluated for MIC. Thus, the complexes examined herein suggest promising alternatives for the development of new antifungal drugs.

Fluconazole analogues with metal-binding motifs impact metal-dependent processes and demonstrate antifungal activity in Candida albicans

Azole antifungals are an important class of antifungal drugs due to their low cost, ability to be administered orally, and broad-spectrum activity. However, their widespread and long-term use have given rise to adaptation mechanisms that render these compounds less effective against common fungal pathogens, including Candida albicans. New antifungals are desperately needed as drug-resistant strains become more prevalent. We recently showed that copper supplementation potentiates the activity of the azole antifungal fluconazole against the opportunistic fungal pathogen C. albicans. Here, we report eight new azole analogues derived from fluconazole in which one triazole group has been replaced with a metal-binding group, a strategy designed to enhance potentiation of azole antifungal activity by copper. The bioactivity of all eight compounds was tested and compared to that of fluconazole. Three of the analogues showed activity against C. albicans and two had lower levels of trailing growth. One compound, Flu-TSCZ, was found to impact the levels, speciation, and bioavailability of cellular metals.

Cationic chitosan derivatives as potential antifungals: A review of structural optimization and applications

The increasing resistance of pathogen fungi poses a global public concern. There are several limitations in current antifungals, including few available fungicides, severe toxicity of some fungicides, and drug resistance. Therefore, there is an urgent need to develop new antifungals with novel targets. Chitosan has been recognized as a potential antifungal substance due to its good biocompatibility, biodegradability, non-toxicity, and availability in abundance, but its applications are hampered by the low charge density results in low solubility at physiological pH. It is believed that enhancing the positive charge density of chitosan may be the most effective approach to improve both its solubility and antifungal activity. Hence, this review mainly focuses on the structural optimization strategy of cationic chitosan and the potential antifungal applications. This review also assesses and comments on the challenges, shortcomings, and prospect of cationic chitosan derivatives as antifungal therapy.

Comparative Transcriptomics Reveals Features and Possible Mechanisms of Glucose-Mediated Soil Fungistasis Relief in Arthrobotrys oligospora

Soil-borne pest diseases result in large annual agricultural losses globally. Fungal bio-control agents are an alternative means of controlling pest diseases; however, soil fungistasis limits the effect of fungal agents. Nutrients can relieve soil fungistasis, but the mechanisms behind this process remain poorly understood. In this study, we determined and quantified the transcriptomes of Arthrobotrys oligospora, a nematode-trapping fungus, derived from samples of fresh conidia, germinated conidia, soil fungistatic conidia, and glucose-relieved conidia. The transcriptomes of fungistatic and glucose-relieved conidia were significantly different from those of the other two conidia samples. KEGG pathway analyses showed that those genes upregulated in fungistatic and glucose-relieved conidia were mainly involved in translation and substance metabolism, and the downregulated genes were mainly involved in MAPK pathway, autophagy, mitophagy, and endocytosis. As being different from the transcriptome of fungistatic conidia, upregulated genes in the transcriptome of glucose-relieved conidia are also related to replication and repair, spliceosome, oxidative phosphorylation, autophagy, and degradation pathway (lysosome, proteasome, and RNA degradation). And the upregulated genes resulted from comparison of glucose-relieved conidia and fungistatic conidia were enriched in metabolic pathways, cycle, DNA replication, and repair. The differentially splicing events in the transcriptome of glucose-relieved conidia are far more than that of other two transcriptomes, and genes regulated by differentially splicing were analyzed through KEGG pathway analysis. Furthermore, autophagy genes were proved to play important role in resisting soil fungistasis and glucose-mediated soil fungistasis relief. These data indicate that, in addition to being a carbon and energy source for conidia germination, glucose may also help to relieve soil fungistasis by activating many cellular processes, including autophagy, DNA replication and repair, RNA alternative splicing, and degradation pathways.

Deacylation of Echinocandin B by Streptomyces species: a novel method for the production of Echinocandin B nucleus

Anidulafungin, a new class of antifungal agent used for the treatment of chronic fungal infections, is derived from Echinocandin B nucleus, an intermediate metabolite of Echinocandin B produced by Aspergillus nidulans. The enzyme acylase plays a key role in the bioconversion of Echinocandin B to Echinocandin B nucleus. In the present study, a rapid screening method was used to select an actinomycete capable of producing Echinocandin B acylase. Out of 140 actinomycetes screened for the production of acylase by preliminary qualitative plate assay, 53 were selected. The selected isolates were subjected to quantitative assay under submerged fermentation for the bioconversion of Echinocandin B to Echinocandin B nucleus. Among 53 strains of actinomycetes, two strains (BICC-8848 and BICC-8547) exhibited higher degree of acylase activity. Various physico-chemical parameters were optimised for maximum bioconversion of ECB to ECB nucleus. It was found that the conditions viz. pH 7.0, temperature 26 °C and substrate concentration of about 4 g/L supported higher degree of bioconversion. It was also observed that, as the medium volume increased to 500 mL, the conversion rate was also increased by more than two-folds.

Antioxidant, antihypertensive, anti-hyperglycemic, and antimicrobial activity of aqueous extracts from twelve native plants of the Yucatan coast

Looking for a biotechnical potential, aqueous extracts of leaves of 12 native species used in the Mayan traditional medicine of the coastal dune and mangrove of Yucatan (Mexico) were selected to evaluate their biological activities. Rhizophora mangle and Manilkara zapota showed the highest free radical scavenging activity (3.94 ± 0.19 and 6.42 ± 0.32 μg/mL, respectively), and the highest antihypertensive activity was obtained from Solanum donianum (0.38 μg/mL). The anti-hyperglycemic activity of these species was also tested; the highest activities were registered with R. mangle. The antimicrobial activity of Malvaviscus arboreus, S. donianum, M. zapota, and R. mangle at 10% (w/v) was positive against six human pathogenic bacteria and Bonellia macrocarpa against one pathogenic fungus. Solanum donianum, M. zapota, B. macrocarpa, and R. mangle were positive against two pathogenic plant fungi. These results show that the aqueous extracts of five native plants of the Yucatan coast have potential as antioxidants, ACE inhibitors, α-amylase and α-glucosidase inhibitors, and as antimicrobials, which make their exploration for utilization in the agricultural and pharmaceutical industries a possibility.

Fungal Lanosterol 14α-demethylase: A target for next-generation antifungal design

The cytochrome P450 enzyme lanosterol 14α-demethylase (LDM) is the target of the azole antifungals used widely in medicine and agriculture as prophylaxis or treatments of infections or diseases caused by fungal pathogens. These drugs and agrochemicals contain an imidazole, triazole or tetrazole substituent, with one of the nitrogens in the azole ring coordinating as the sixth axial ligand to the LDM heme iron. Structural studies show that this membrane bound enzyme contains a relatively rigid ligand binding pocket comprised of a deeply buried heme-containing active site together with a substrate entry channel and putative product exit channel that reach to the membrane. Within the ligand binding pocket the azole antifungals have additional affinity determining interactions with hydrophobic side-chains, the polypeptide backbone and via water-mediated hydrogen bond networks. This review will describe the tools that can be used to identify and characterise the next generation of antifungals targeting LDM, with the goal of obtaining highly potent broad-spectrum fungicides that will be able to avoid target and drug efflux mediated antifungal resistance.

Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics

Efflux pumps play a major role in the increasing antimicrobial resistance rendering a large number of drugs of no use. Large numbers of pathogens are becoming multidrug resistant due to inadequate dosage and use of the existing antimicrobials. This leads to the need for identifying new efflux pump inhibitors. Design of novel targeted therapies using inherent complexity involved in the biological network modeling has gained increasing importance in recent times. The predictive approaches should be used to determine antimicrobial activities with high pathogen specificity and microbicidal potency. Antimicrobial peptides, which are part of our innate immune system, have the ability to respond to infections and have gained much attention in making resistant strain sensitive to existing drugs. In this review paper, we outline evidences linking host-directed therapy with the efflux pump activity to infectious disease.

Azole Resistance Reduces Susceptibility to the Tetrazole Antifungal VT-1161

Tetrazole antifungals designed to target fungal lanosterol 14α-demethylase (LDM) appear to be effective against a range of fungal pathogens. In addition, a crystal structure of the catalytic domain of Candida albicans LDM in complex with the tetrazole VT-1161 has been obtained. We have addressed concern about artifacts that might arise from crystallizing VT-1161 with truncated recombinant CYP51s and measured the impact on VT-1161 susceptibility of genotypes known to confer azole resistance. A yeast system was used to overexpress recombinant full-length Saccharomyces cerevisiae LDM with a C-terminal hexahistidine tag (ScLDM6×His) for phenotypic analysis and crystallographic studies with VT-1161 or with the widely used triazole drug posaconazole (PCZ). We determined the effect of characterized mutations in LDM on VT-1161 activity and identified drug efflux pumps from fungi, including key fungal pathogens, that efflux VT-1161. The relevance of these yeast-based observations on drug efflux was verified using clinical isolates of C. albicans and Candida glabrata VT-1161 binding elicits a significant conformational difference between the full-length and truncated enzymes not found when posaconazole is bound. Susceptibility to VT-1161 is reduced by ATP-binding cassette (ABC) and major facilitator superfamily (MFS) drug efflux pumps, the overexpression of LDM, and mutations within the drug binding pocket of LDM that affect interaction with the tertiary alcohol of the drug.

Heterologous Expression of Full-Length Lanosterol 14α-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provides Tools for Antifungal Discovery

Targeting lanosterol 14α-demethylase (LDM) with azole drugs provides prophylaxis and treatments for superficial and disseminated fungal infections, but cure rates are modest for immunocompromised patients and individuals with comorbidities. The efficacy of azole drugs has also been reduced due to the emergence of drug-resistant fungal pathogens. We have addressed these problems by expressing in Saccharomyces cerevisiae functional, hexahistidine-tagged, full-length Candida albicans LDM (CaLDM6×His) and Candida glabrata LDM (CgLDM6×His) for drug discovery purposes and determining their X-ray crystal structures. Compared with S. cerevisiae overexpressing LDM6×His (ScLDM6×His), the reduced susceptibility of CgLDM6×His to all azole drugs tested correlated with its level of overexpression. In contrast, the reduced susceptibility to short-tailed (fluconazole and voriconazole) but not medium-tailed (VT-1161) or long-tailed azoles (itraconazole and posaconazole) indicates CaLDM6×His works best when coexpressed with its cognate NADPH-cytochrome P450 reductase (CaNcp1A) rather than the host reductase (ScNcp1). Overexpression of LDM or Ncp1 modified the ergosterol content of yeast and affected growth inhibition by the polyene antibiotic amphotericin B. Affinity-purified recombinant Candida LDMs bind carbon monoxide and show tight type II binding of a range of azole drugs, including itraconazole, posaconazole, fluconazole, and voriconazole. This study provides a practical basis for the phenotype-, biochemistry-, and structure-directed discovery of novel antifungals that target LDMs of fungal pathogens.

The Paralogous Genes PDR18 and SNQ2, Encoding Multidrug Resistance ABC Transporters, Derive From a Recent Duplication Event, PDR18 Being Specific to the Saccharomyces Genus

Pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters play a key role in the simultaneous acquisition of resistance to a wide range of structurally and functionally unrelated cytotoxic compounds in yeasts. Saccharomyces cerevisiae Pdr18 was proposed to transport ergosterol at the plasma membrane, contributing to the maintenance of adequate ergosterol content and decreased levels of stress-induced membrane disorganization and permeabilization under multistress challenge leading to resistance to ethanol, acetic acid and the herbicide 2,4-D, among other compounds. PDR18 is a paralog of SNQ2, first described as a determinant of resistance to the chemical mutagen 4-NQO. The phylogenetic and neighborhood analysis performed in this work to reconstruct the evolutionary history of ScPDR18 gene in Saccharomycetaceae yeasts was focused on the 214 Pdr18/Snq2 homologs from the genomes of 117 strains belonging to 29 yeast species across that family. Results support the idea that a single duplication event occurring in the common ancestor of the Saccharomyces genus yeasts was at the origin of PDR18 and SNQ2, and that by chromosome translocation PDR18 gained a subtelomeric region location in chromosome XIV. The multidrug/multixenobiotic phenotypic profiles of S. cerevisiae pdr18Δ and snq2Δ deletion mutants were compared, as well as the susceptibility profile for Candida glabrata snq2Δ deletion mutant, given that this yeast species has diverged previously to the duplication event on the origin of PDR18 and SNQ2 genes and encode only one Pdr18/Snq2 homolog. Results show a significant overlap between ScSnq2 and CgSnq2 roles in multidrug/multixenobiotic resistance (MDR/MXR) as well as some overlap in azole resistance between ScPdr18 and CgSnq2. The fact that ScSnq2 and ScPdr18 confer resistance to different sets of chemical compounds with little overlapping is consistent with the subfunctionalization and neofunctionalization of these gene copies. The elucidation of the real biological role of ScSNQ2 will enlighten this issue. Remarkably, PDR18 is only found in Saccharomyces genus genomes and is present in almost all the recently available 1,000 deep coverage genomes of natural S. cerevisiae isolates, consistent with the relevant encoded physiological function.

Tetrandrine enhances the antifungal activity of fluconazole in a murine model of disseminated candidiasis

BACKGROUND

Tetrandrine (TET), a bis-benzylisoquinoline alkaloid isolated from the Chinese medicinal herb Stephaniae tetrandrae, has a long history in Chinese clinical applications as an anti-inflammatory or anti-arrhythmic agent in the treatment of diverse diseases. In our previous study, TET exhibited the synergisitic action on azoles against pathogenic fungi.

PURPOSE

In the current study, we examined whether TET can enhance the antifungal activity of FLC against disseminated candidiasis in mice.

METHODS

BALB/c mice were inoculated intravenously with FLC-sensitive or FLC-resistant strains of Candida albicans, randomized and treated intraperitoneally with different doses of TET and/or FLC daily for 7 days. The treatment effectiveness, fungal burdens and the levels of the IFN-γ, IL-10, TGF-β1 and IL-17A are determined in serum by ELISA and in the kidney by Real-time RT-PCR methods.

RESULTS

We found that treatment with 45, 30 and 15 mg/kg of TET, enhanced the antifungal activities of a sub-critical dose (0.4 or 5 mg/kg) and minimal dose (0.8 or 10 mg/kg) of FLC against FLC-sensitive and FLC-resistant (respectively) infected mice. In the resistant strains the resistance mechanisms included MDR1 overexpression-and CDR1/CDR2 overexpression. Furthermore, when animals were treated with a sub-high dose (1.6-3.2 and 20-30 mg/kg) of FLC in the presence of fixed amounts of TET at 45, 30 and 15 mg/kg, the therapeutic doses of FLC could be substantially reduced in all strains tested. The findings in infected animal are consistent with the conclusion that TET exerts a synergistic effect on FLC against C. albicans by fractional inhibitory concentration index (FICI) and time-killing test in vitro.

CONCLUSION

In summary, our data indicate that TET will enhance the antifungal activity of FLC against C. albicans infection in disseminated mice model.

Pdr18 is involved in yeast response to acetic acid stress counteracting the decrease of plasma membrane ergosterol content and order

Saccharomyces cerevisiae has the ability to become less sensitive to a broad range of chemically and functionally unrelated cytotoxic compounds. Among multistress resistance mechanisms is the one mediated by plasma membrane efflux pump proteins belonging to the ABC superfamily, questionably proposed to enhance the kinetics of extrusion of all these compounds. This study provides new insights into the biological role and impact in yeast response to acetic acid stress of the multistress resistance determinant Pdr18 proposed to mediate ergosterol incorporation in plasma membrane. The described coordinated activation of the transcription of PDR18 and of several ergosterol biosynthetic genes (ERG2-4, ERG6, ERG24) during the period of adaptation to acetic acid inhibited growth provides further support to the involvement of Pdr18 in yeast response to maintain plasma membrane ergosterol content in stressed cells. Pdr18 role in ergosterol homeostasis helps the cell to counteract acetic acid-induced decrease of plasma membrane lipid order, increase of the non-specific membrane permeability and decrease of transmembrane electrochemical potential. Collectively, our results support the notion that Pdr18-mediated multistress resistance is closely linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties.

KIX domain of AtMed15a, a Mediator subunit of Arabidopsis, is required for its interaction with different proteins

Med15 is an important subunit of Mediator Tail module and is characterized by a KIX domain present towards amino terminal. In yeast and metazoans, Med15 KIX domain has been found to interact with various transcription factors regulating several processes including carbohydrate metabolism, lipogenesis, stress response and multidrug resistance. Mechanism of Med15 functioning in Arabidopsis is largely unknown. In this study, interactome of KIX domain of Arabidopsis Med15, AtMed15a, was characterized. We found 45 proteins that interact with AtMed15a KIX domain, including 11 transcription factors, 3 single strand nucleic acid-binding proteins and 1 splicing factor. The third helix of the KIX domain was found to be involved in most of the interactions. Mapping of the regions participating in the interactions revealed that the activation domain of a transcription factor, UKTF1 interacted with AtMed15a KIX domain. Thus, our results suggest that in Arabidopsis, activation domain of transcription factors target KIX domain of AtMed15a for their transcriptional responses.

Toward Generalization of Iterative Small Molecule Synthesis

Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the "building block approach", i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach.

The binding mechanism between azoles and FgCYP51B, sterol 14α-demethylase of Fusarium graminearum

BACKGROUND

Fusarium graminearum is the main pathogen of Fusarium head blight (FHB), a worldwide plant disease and a major disease of wheat in China. Control of FHB is mainly dependent on the application of demethylase inhibitor (DMI) fungicides. Fungal sterol 14α-demethylase enzymes (CYP51) are the main target for DMI fungicides. A molecular modeling study and biological evaluation were performed to investigate the binding mechanism between azoles and CYP51B in F. graminearum.

RESULTS

A homology model based on the crystal structure of Aspergillus fumigatus was built. Molecular docking and molecular dynamics (MD) simulations were then used to identify the optimum binding mode of propiconazole (PRP), diniconazole (DIN), triadimenol (TRL), tebuconazole (TEC) and triadimefon (TRN) with FgCYP51B. Furthermore, the binding free energy of the five protein-inhibitor complexes was calculated using molecular mechanics generalized Born surface area and Poisson-Boltzmann surface area (MM-GB/PBSA) methods. Key residues in the selective binding of azoles to FgCYP51B were recognized by per-residue free energy decomposition analysis. The five ligands have a similar binding mode in the active pocket. The binding free energy to the enzyme for inhibitors PRP and TEC is more favorable than that of TRN, TRL and DIN. Furthermore, the amino acid residues Phe511, Val136, Ile374, Ala308, Ser312 and Try137 of FgCYP51B are key residues interacting with azoles fungicides. From the experimental evaluation, the 50% effective concentration (EC₅₀ ) values for PRP, TEC, DIN, TRL and TRN are 0.024, 0.047, 0.148, 0.154 and 0.474 mg L^-1 , respectively. These five molecules exhibit potential inhibitory activity against CYP51B protein from F. graminearum.

CONCLUSION

Azole fungicides for FgCYP51B should possess more hydrophobic groups interacting with residues Phe511, Val136, Ile374, Ala308, Ser312 and Tyr137. PRP and TEC are preferable for the control of FHB than DIN, TRL and TRN. © 2017 Society of Chemical Industry.

Synthesis and biological evaluation of new fluconazole β-lactam conjugates linked via 1,2,3-triazole

Novel fluconazole conjugates with potent antifungal activity are reported here. They were also found to be non-hemolytic and non-cytotoxic.

Quinone derivatives isolated from the endolichenic fungus Phialocephala fortinii are Mdr1 modulators that combat azole resistance in Candida albicans

One of the main azole-resistance mechanisms in Candida pathogens is the upregulation of drug efflux pumps, which compromises the efficacy of azoles and results in treatment failure. The combination of azole-antifungal agents with efflux pump inhibitors represents a promising strategy to combat fungal infection. High-throughput screening of 150 extracts obtained from endolichenic fungal cultures led to the discovery that the extract of Phialocephala fortinii exhibits potent activity for the reversal of azole resistance. From P. fortinii cultures, a total of 15 quinone derivatives, comprising 11 new derivatives and 4 known compounds, were obtained. Among these compounds, palmarumycin P3 (3) and phialocephalarin B (8) specifically modulate the expression of MDR1 to inhibit the activity of drug efflux pumps and therefore reverse azole resistance. The present study revealed Mdr1 targeting as an alternative mechanism for the discovery of new agents to fight antifungal drug resistance.

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.

The putative ABC transporter encoded by the orf19.4531 plays a role in the sensitivity of Candida albicans cells to azole antifungal drugs

ATP-binding cassette (ABC) transporters constitute a large superfamily of integral membrane proteins in prokaryotic and eukaryotic cells. In the human fungal pathogen Candida albicans, there are 28 genes encoding ABC transporters and many of them have not been characterized so far. The orf19.4531 (also known as IPF7530) encodes a putative ABC transporter. In this study, we have demonstrated that disruption of orf19.4531 causes C. albicans cells to become tolerant to azoles, but not to polyene antifungals and terbinafine. Therefore, the protein encoded by orf19.4531 is involved in azole sensitivity and we name it as ROA1, the regulator of azole sensitivity 1 gene. Consistently, we show that the expression of ROA1 is responsive to treatment of either fluconazole or ketoconazole inC. albicans In addition, through a GFP tagging approach, Roa1 is localized in a small punctuate compartment adjacent to the vacuolar membrane. However, ROA1 is not essential for the in vitro filamentation of C. albicans cells.

Taming Amphotericin B

A strategy is introduced for enhancing the cellular selectivity of Amphotericin B (AmB) and other classes of membrane-disrupting agents. This strategy involves attaching the agent to a molecular umbrella to minimize the disruptive power of aggregated forms. Based on this approach, AmB has been coupled to a molecular umbrella derived from one spermidine and two cholic acid molecules and found to have antifungal activities approaching that of the native drug. However, in sharp contrast to AmB, the hemolytic activity and the cytotoxcity of this conjugate toward HEK293 T cells have been dramatically reduced.

A subgroup of MATE transporter genes regulates hypocotyl cell elongation in Arabidopsis

The growth of higher plants is under complex regulation to ensure the elaboration of developmental programmes under a changing environment. To dissect these regulatory circuits, we carried out genetic screens for Arabidopsis abnormal shoot (abs) mutants with altered shoot development. Here, we report the isolation of two dominant mutants, abs3-1D and abs4-1D, through activation tagging. Both mutants showed a 'bushy' loss of apical dominance phenotype. ABS3 and ABS4 code for two closely related putative Multidrug and Toxic Compound Extrusion (MATE) family of efflux transporters, respectively. ABS3 and ABS4, as well as two related MATE genes, ABS3-Like1 (ABS3L1) and ABS3L2, showed diverse tissue expression profiles but their gene products all localized to the late endosome/prevacuole (LE/PVC) compartment. The over-expression of these four genes individually led to the inhibition of hypocotyl cell elongation in the light. On the other hand, the quadruple knockout mutant (mateq) showed the opposite phenotype of an enhanced hypocotyl cell elongation in the light. Hypocotyl cell elongation and de-etiolation processes in the dark were also affected by the mutations of these genes. Exogenously applied sucrose attenuated the inhibition of hypocotyl elongation caused by abs3-1D and abs4-1D in the dark, and enhanced the hypocotyl elongation of mateq under prolonged dark treatment. We determined that ABS3 genetically interacts with the photoreceptor gene PHYTOCHROME B (PHYB). Our results demonstrate that ABS3 and related MATE family transporters are potential negative regulators of hypocotyl cell elongation and support a functional link between the endomembrane system, particularly the LE/PVC, and the regulation of plant cell elongation.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.