Crossroads of Antibiotic Resistance and Biosynthesis

Sinigrin reduces the virulence of Staphylococcus aureus by targeting coagulase

Multi-resistant Staphylococcus aureus (S. aureus) infection is a significant global health concern owing to its high mortality and morbidity rates. Coagulase (Coa), a key enzyme that activates prothrombin to initiate host coagulation, has emerged as a promising target for anti-infective therapeutic approaches. This study identified sinigrin as a potent Coa inhibitor that significantly inhibited S. aureus-induced coagulation at concentration as low as 32 mg/L. Additionally, at a higher concentration of 128 mg/L, sinigrin disrupted the self-protection mechanism of S. aureus. Thermal shift and fluorescence-quenching assays confirmed the direct binding of sinigrin to the Coa protein. Molecular docking analysis predicted specific binding sites for sinigrin in the Coa molecule, and point mutation experiments highlighted the importance of Arg-187 and Asp-222 as critical binding sites for both Coa and sinigrin. In vivo studies demonstrated that the combination of sinigrin with oxacillin exhibited greater antibacterial efficacy than oxacillin alone in the treatment of S. aureus-induced pneumonia in mice. Furthermore, sinigrin was shown to reduce bacterial counts and inflammatory cytokine levels in the lung tissues of S. aureus-infected mice. In summary, sinigrin was shown to directly target Coa, resulting in the attenuation of S. aureus virulence, which suggests the potential of sinigrin as an adjuvant for future antimicrobial therapies.

Impact of veterinary pharmaceuticals on environment and their mitigation through microbial bioremediation

Veterinary medications are constantly being used for the diagnosis, treatment, and prevention of diseases in livestock. However, untreated veterinary drug active compounds are interminably discharged into numerous water bodies and terrestrial ecosystems, during production procedures, improper disposal of empty containers, unused medication or animal feed, and treatment procedures. This exhaustive review describes the different pathways through which veterinary medications enter the environment, discussing the role of agricultural practices and improper disposal methods. The detrimental effects of veterinary drug compounds on aquatic and terrestrial ecosystems are elaborated with examples of specific veterinary drugs and their known impacts. This review also aims to detail the mechanisms by which microbes degrade veterinary drug compounds as well as highlighting successful case studies and recent advancements in microbe-based bioremediation. It also elaborates on microbial electrochemical technologies as an eco-friendly solution for removing pharmaceutical pollutants from wastewater. Lastly, we have summarized potential innovations and challenges in implementing bioremediation on a large scale under the section prospects and advancements in this field.

Cerium Dioxide-Dextran Nanocomposites in the Development of a Medical Product for Wound Healing: Physical, Chemical and Biomedical Characteristics

PURPOSE OF THE STUDY

the creation of a dextran coating on cerium oxide crystals using different ratios of cerium and dextran to synthesize nanocomposites, and the selection of the best nanocomposite to develop a nanodrug that accelerates quality wound healing with a new type of antimicrobial effect.

MATERIALS AND METHODS

Nanocomposites were synthesized using cerium nitrate and dextran polysaccharide (6000 Da) at four different initial ratios of Ce(NO3)3x6H2O to dextran (by weight)-1:0.5 (Ce0.5D); 1:1 (Ce1D); 1:2 (Ce2D); and 1:3 (Ce3D). A series of physicochemical experiments were performed to characterize the created nanocomposites: UV-spectroscopy; X-ray phase analysis; transmission electron microscopy; dynamic light scattering and IR-spectroscopy. The biomedical effects of nanocomposites were studied on human fibroblast cell culture with an evaluation of their effect on the metabolic and proliferative activity of cells using an MTT test and direct cell counting. Antimicrobial activity was studied by mass spectrometry using gas chromatography-mass spectrometry against E. coli after 24 h and 48 h of co-incubation.

RESULTS

According to the physicochemical studies, nanocrystals less than 5 nm in size with diffraction peaks characteristic of cerium dioxide were identified in all synthesized nanocomposites. With increasing polysaccharide concentration, the particle size of cerium dioxide decreased, and the smallest nanoparticles (<2 nm) were in Ce2D and Ce3D composites. The results of cell experiments showed a high level of safety of dextran nanoceria, while the absence of cytotoxicity (100% cell survival rate) was established for Ce2D and C3D sols. At a nanoceria concentration of 10-2 M, the proliferative activity of fibroblasts was statistically significantly enhanced only when co-cultured with Ce2D, but decreased with Ce3D. The metabolic activity of fibroblasts after 72 h of co-cultivation with nano composites increased with increasing dextran concentration, and the highest level was registered in Ce3D; from the dextran group, differences were registered in Ce2D and Ce3D sols. As a result of the microbiological study, the best antimicrobial activity (bacteriostatic effect) was found for Ce0.5D and Ce2D, which significantly inhibited the multiplication of E. coli after 24 h by an average of 22-27%, and after 48 h, all nanocomposites suppressed the multiplication of E. coli by 58-77%, which was the most pronounced for Ce0.5D, Ce1D, and Ce2D.

CONCLUSIONS

The necessary physical characteristics of nanoceria-dextran nanocomposites that provide the best wound healing biological effects were determined. Ce2D at a concentration of 10-3 M, which stimulates cell proliferation and metabolism up to 2.5 times and allows a reduction in the rate of microorganism multiplication by three to four times, was selected for subsequent nanodrug creation.

Chiral ligands and photothermal synergistic effects of inorganic nanoparticles for bacteria-killing

As the drawbacks of antibiotics in treating bacterial infections emerged, physical methods such as near-infrared-activated (NIR-activated) bacterial killing, have attracted great interests for their advantages of no resistance, short action time and few side effects. In this manuscript, NIR-activated bacteria-killing performance of chiral copper sulphide nanoparticles (L-/d-CuS NPs) was investigated using linearly polarized light (LPL) and circularly polarized light (CPL) as illumination sources, respectively. Chiral CuS NPs showed enhanced NIR-activated bacteria-killing effect compared with achiral CuS NPs under the same conditions. Moreover, these chiral CuS NPs showed obvious chirality-related antibacterial effect: the bacterial killing was more efficient under CPL activation, and L- and d-CuS NPs had higher antibacterial efficiency under left circularly polarized light (LCPL) and right circularly polarized light (RCPL), respectively. The possible mechanism of bacteria-killing performance for chiral CuS NPs was discussed in detailed. Photothermal bacteria-killing tests of chiral CuS NPs "sealed" in polydimethylsiloxane (PDMS) demonstrated the individual influence of photothermal effect. These observations in this paper could provide ideas for the potential applications of chiral nanostructures with enhanced photothermal effect in efficient bacterial killing.

Naturally Occurring and Widespread Resistance to Bioactive Natural Products

Naturally occurring resistances diminish the effectiveness of antibiotics, and present significant challenges to human health. Human activities are usually considered as the main drivers of the dissemination of antibiotic resistance, however, the origin of the clinical antibiotic resistance can be traced to the environmental microbes, and the clinically relevant resistance determinants have already pre-existed in nature before the antibiotics come into clinic. In this concept, we present the naturally occurring and widespread resistance determinants recently discovered during the biosynthesis study of bioactive compounds. These widely prevalent resistances in environmental microbes, including antibiotic producers and non-producers, advance the understanding of the origin of resistance, and provide prediction for the clinically relevant resistance to aid in the rational design of more effective drug analogues to combat resistance.

Metal-based nanoparticles in antibacterial application in biomedical field: Current development and potential mechanisms

The rise in drug resistance in pathogenic bacteria greatly endangers public health in the post-antibiotic era, and drug-resistant bacteria currently pose a great challenge not only to the community but also to clinical procedures, including surgery, stent implantation, organ transplantation, and other medical procedures involving any open wound and compromised human immunity. Biofilm-associated drug failure, as well as rapid resistance to last-resort antibiotics, necessitates the search for novel treatments against bacterial infection. In recent years, the flourishing development of nanotechnology has provided new insights for exploiting promising alternative therapeutics for drug-resistant bacteria. Metallic agents have been applied in antibacterial usage for several centuries, and the functional modification of metal-based biomaterials using nanotechnology has now attracted great interest in the antibacterial field, not only for their intrinsic antibacterial nature but also for their ready on-demand functionalization and enhanced interaction with bacteria, rendering them with good potential in further translation. However, the possible toxicity of MNPs to the host cells and tissue still hinders its application, and current knowledge on their interaction with cellular pathways is not enough. This review will focus on recent advances in developing metallic nanoparticles (MNPs), including silver, gold, copper, and other metallic nanoparticles, for antibacterial applications, and their potential mechanisms of interaction with pathogenic bacteria as well as hosts.

Preparation and evaluation of oxidized-dextran based on antibacterial hydrogel for synergistic photodynamic therapy

Skin trauma is a widespread, extremely susceptible health issue that affects people all over the world. In this study, an innovative antibacterial hydrogel (ODAA hydrogel) with photosensitizer and antibiotics was developed. Oxidized dextran (ODEX) was used as a carrier to prepare a pH-responsive hydrogel by loading the antibiotic amikacin (AMK) and the photosensitizer hexyl 5-aminolevulinate (HAL) via imine bonds. The ODAA hydrogel has a uniformly distributed cavity structure. The cumulative release rates of HAL and AMK in a simulated inflammatory environment at pH 5.0 were approximately 62.3 % and 71.9 % during 15 days. These results demonstrate the ODAA hydrogel's ability to deliver antibiotics on demand, where the antibiotic content is reduced within the effective range. Regarding the in vitro antibacterial behavior, the combination of HAL and AMK synergistically destroyed the majority of Gram-positive and Gram-negative bacteria through several pathways with broad-spectrum antibacterial effects. ODAA hydrogel has been shown to be biocompatible, nearly non-cytotoxic, and capable of promoting wound healing. It is anticipated that the simultaneous targeted delivery of multiple drugs to lesions in the same carrier at ideal dose ratios for particular therapeutic combinations will produce the most synergistic effects.

Natural products as potential lead compounds to develop new antiviral drugs over the past decade

Virus infection has been one of the main causes of human death since the ancient times. Even though more and more antiviral drugs have been approved in clinic, long-term use can easily lead to the emergence of drug resistance and side effects. Fortunately, there are many kinds of metabolites which were produced by plants, marine organisms and microorganisms in nature with rich structural skeletons, and they are natural treasure house for people to find antiviral active substances. Aiming at many types of viruses that had caused serious harm to human health in recent years, this review summarizes the natural products with antiviral activity that had been reported for the first time in the past ten years, we also sort out the source, chemical structure and safety indicators in order to provide potential lead compounds for the research and development of new antiviral drugs.

Antibiotic resistance in patients with liver cirrhosis: Prevalence and current approach to tackle

Regardless of etiology, complications with bacterial infection in patients with cirrhosis are reported in the range of 25%-46% according to the most recent data. Due to frequent episodes of bacterial infection and repetitive antibiotic treatment, most often with broad-spectrum gram negative coverage, patients with cirrhosis are at increased risk of encountering multidrug resistant bacteria, and this raises concern. In such patients, extended-spectrum beta-lactamase and AmpC-producing Enterobacterales, methicillin- or vancomycin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Pseudomonas aeruginosa, and Acinetobacter baumannii, all of which are difficult to treat, are the most common. That is why novel approaches to the prophylaxis and treatment of bacterial infections to avoid antibiotic resistance have recently been developed. At the same time, our knowledge of resistance mechanisms is constantly updated. This review summarizes the current situation regarding the burden of antibiotic resistance, including the prevalence and mechanisms of intrinsic and acquired resistance in bacterial species that most frequently cause complications in patients with liver cirrhosis and recent developments on how to deal with multidrug resistant bacteria.

Development of an amoxicillin-radix scutellaria extract formulation and evaluation of its pharmacokinetics in pigs

BACKGROUND

A new antibacterial compound powder of amoxicillin (AMO)/Radix Scutellaria extract (RSE) was developed, and its pharmacokinetics were determined in pigs following oral administration.

RESULTS

The MIC ranges of AMO against Escherichia coli, Staphylococcus aureus and Streptococcus were 1-8 μg/mL, 0.5-4 μg/mL and 0.5-64 μg/mL, respectively. The MIC ranges of RSE against E. coli, S. aureus, and Streptococcus were greater than 2.5 mg/mL, 0.156-2.5 mg/mL, and greater than 2.5 mg/mL, respectively. For S. aureus, the combined drug susceptibility test showed that AMO and RSE had an additive or synergistic effect. The results of compatibility test, the excipient screening test and the drug quality control test showed that the formulation had stable quality and uniform properties under the test conditions. Two studies were conducted to investigate the pharmacokinetics of the compound product in pigs. First, the pharmacokinetics of the AMO-RSE powder were compared with those of their respective single products. The results showed no significant change in the main pharmacokinetic parameters when either component was removed from the compound formulation; thus, AMO and RSE have no pharmacokinetic interaction in pigs. Second, pigs were orally administered three different doses of AMO-RSE powder. The Cmax and AUC increased proportionally with increasing p.o. dose; thus, the λz, t1/2λ, MRT, and Tmax were unchanged for the doses of 10, 20, and 30 mg/kg AMO and the doses of 5, 10, and 15 mg/kg BCL, showing that AMO/baicalin in AMO-RSE powder showed linear pharmacokinetic characteristics in pigs.

CONCLUSIONS

The combined drug sensitivity test of AMO and RSE against S. aureus showed that the combination was additive or synergistic. Pharmacokinetic studies indicated that AMO and BCL do not interfere with each other in pigs when used in a compound formulation. The pharmacokinetic parameters remained unchanged regardless of the dose for p.o. administration, indicating linear pharmacokinetic properties over the tested dose range. The quality of the AMO-RSE powder was good and stable, providing a foundation for its clinical application in veterinary medicine. Further bioavailability, PK/PD and clinical trials are still needed to determine the final dosage regimen.

Phytochemical characterization, antioxidant and antibacterial activities of crude extracts of Anisomeles malabarica and Coldenia procumbens

The aim of this study was to determine the phytochemical profile, antibacterial and antioxidant activities of crude aqueous leaf extracts of Anisomeles malabarica and Coldenia procumbens. The predominant components present in these crude extracts of test plants identified using gas chromatography-mass spectrometry (GC-MS) analysis in both plant extracts were phytochemicals including flavonoids, tannins, terpenoids, and phenols. The antibacterial activity of crude extracts of these plants against bacterial pathogens including Escherichia coli, Bacillus subtilis, Shigella sp., Salmonella paratyphi A and B, Proteus mirabilis, Proteus vulgaris, Pseudomonas sp. Klebsiella pneumoniae, and Staphylococcus aureus were examined. Data demonstrated that the extracts of A. malabarica and C. procumbens exhibited significant antibacterial activity against B.subtilis and P.vulgaris at the concentration of 50 mg/ml. A. malabarica aqueous extract displayed significant antioxidant activity on 2,2-diphenyl-1-picrylhydrazl (DPPH), fluorescence recovery after photobleaching (FRAP) and hydrogen peroxide (H2O2) free radicals at the concentration of 90 mg/ml. The antioxidant activity was significantly higher with A. malabarica than extract of C. procumbens. Evidence indicates that both plant extracts may possess significant pharmaceutical potential as antibacterial and antioxidant agents.

Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus

Staphylococcus aureus is a zoonotic opportunistic pathogen that represents a significant threat to public health. Previous studies have shown that tannic acid (TA) has an inhibitory effect on a variety of bacteria. In this study, the proteome and transcriptome of S. aureus were analyzed to comprehensively assess changes in genes and proteins induced by TA. Initial observations of morphological changes revealed that TA damaged the integrity of the cell membrane. Next, proteomic and genetic analyses showed that exposure to TA altered the expression levels of 651 differentially expressed proteins (DEPs, 283 upregulated and 368 downregulated) and 503 differentially expressed genes (DEGs, 191 upregulated and 312 downregulated). Analysis of the identified DEPs and DEGs suggested that TA damages the integrity of the cell envelope by decreasing the expression and protein abundance of enzymes involved in the synthesis of peptidoglycans, teichoic acids and fatty acids, such as murB, murQ, murG, fmhX and tagA. After treatment with TA, the assembly of ribosomes in S. aureus was severely impaired by significant reductions in available ribosome components, and thus protein synthesis was hindered. The levels of genes and proteins associated with amino acids and purine synthesis were remarkably decreased, which further reduced bacterial viability. In addition, ABC transporters, which are involved in amino acid and ion transport, were also badly affected. Our results reveal the molecular mechanisms underlying the effects of TA on S. aureus and provide a theoretical basis for the application of TA as an antibacterial chemotherapeutic agent.

A Comprehensive Self-Resistance Gene Database for Natural-Product Discovery with an Application to Marine Bacterial Genome Mining

In the world of microorganisms, the biosynthesis of natural products in secondary metabolism and the self-resistance of the host always occur together and complement each other. Identifying resistance genes from biosynthetic gene clusters (BGCs) helps us understand the self-defense mechanism and predict the biological activity of natural products synthesized by microorganisms. However, a comprehensive database of resistance genes is still lacking, which hinders natural product annotation studies in large-scale genome mining. In this study, we compiled a resistance gene database (RGDB) by scanning the four available databases: CARD, MIBiG, NCBIAMR, and UniProt. Every resistance gene in the database was annotated with resistance mechanisms and possibly involved chemical compounds, using manual annotation and transformation from the resource databases. The RGDB was applied to analyze resistance genes in 7432 BGCs in 1390 genomes from a marine microbiome project. Our calculation showed that the RGDB successfully identified resistance genes for more than half of the BGCs, suggesting that the database helps prioritize BGCs that produce biologically active natural products.

Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil

The extensive use of antibiotics in medicine and agriculture has resulted in the accumulation of antibiotic-resistant microorganisms and antibiotic resistance genes (ARGs) in environments, which threaten human health and contaminate environment. Nematicide avermectin is widely applied to control root-knot nematodes. The effect of five-years application of avermectin on rhizosphere microbiome and resistome of sick tobacco plants in farmland were investigated in present study. The environmental risks of avermectin was assessed adequately. Metagenomic method was used to analyze antibiotic-resistant bacteria and antibiotic resistance genes in the avermectin-treated soil. The abundance and distribution of antibiotic-resistant bacteria and their antibiotic resistance genes were affected by avermectin application. The antibiotic resistant Proteobacteria occupied the highest percentage (36%) in rhizosphere soil and carried 530 ARGs. Opportunistic human pathogens carrying antibiotic resistance genes were enriched in the avermectin-treated soil. Avermectin application increased the counts of many types of antibiotic resistance genes. The relative abundances of genes adeF, BahA, fusH, ileS, and tlrB in the avermectin-treated soil were significantly greater than in the untreated control soil. Different resistance mechanisms were revealed in the avermectin-treated soil. The efflux of antibiotic (670 ARGs), inactivation of antibiotic (475 ARGs), and alteration of antibiotic target (267 ARGs) were the main resistance mechanisms. Rigid control the avermectin dose and use frequency and other pesticides can decrease soil antibiotic resistance genes and protect agricultural products' safety and public health. Overall, application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil, which should be on the alert for environment protection.

Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India

The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.

On the evolution of natural product biosynthesis

Natural products are the raw material for drug discovery programmes. Bioactive natural products are used extensively in medicine and agriculture and have found utility as antibiotics, immunosuppressives, anti-cancer drugs and anthelminthics. Remarkably, the natural role and what mechanisms drive evolution of these molecules is relatively poorly understood. The exponential increase in genome and chemical data in recent years, coupled with technical advances in bioinformatics and genetics have enabled progress to be made in understanding the evolution of biosynthetic gene clusters and the products of their enzymatic machinery. Here we discuss the diversity of natural products, incorporating the mechanisms that govern evolution of metabolic pathways and how this can be applied to biosynthetic gene clusters. We build on the nomenclature of natural products in terms of primary, integrated, secondary and specialised metabolism and place this within an ecology-evolutionary-developmental biology framework. This eco-evo-devo framework we believe will help to clarify the nature and use of the term specialised metabolites in the future.

Bringing resistance modulation to methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) strains using a quaternary ammonium compound coupled with zinc oxide nanoparticles

Nowadays, there are concerns about the inadequacy of new antimicrobials and the rise of antimicrobial resistance. Hence, novel antibacterial agents need to be discovered. In this respect, the use of nanoparticles (NPs) seems promising. Zinc oxide nanoparticles (ZnONPs) are functional and inexpensive NPs that possess antimicrobial characteristics, stability, microbial selectivity, and an easy manufacturing procedure. Imidazolium is one of the quaternary ammonium compounds (QACs) frequently employed as antimicrobial materials in industrial and clinical fields. The present study successfully employed imidazolium to couple with ZnONPs to improve their antimicrobial properties. The antimicrobial activities of ZnONPs doped with imidazolium (IM@ZnONPs) compared to ZnONPs and zinc (Zn) ions against some pathogen microorganism species including Streptococcus aureus (S. aureus), Enterococcus faecalis (E. faecalis), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and Candida albicans (C. albicans) were evaluated by the microdilution method. The minimum inhibitory concentration (MIC) results revealed that the antimicrobial activities of Zn ions, ZnONPs, and IM@ZnONPs were concentration-dependent. Moreover, we found that the nanoparticulate forms of Zn had considerably stronger antibacterial activities, particularly against VRE and MRSA, compared to Zn ions which failed to restrain the microbial strains at the tested microdilutions of this experiment (MIC: ≥512 µg/mL). Interestingly, the incorporation of imidazolium into ZnONPs resulted in significant inhibition of microbial growth in antimicrobial-resistant pathogens at low concentrations (MIC: 32 µg/mL) and effectively improved the monodispersity of the final coated NPs in terms of size and morphology. To sum up, IM@ZnONPs can be a favorable substitute for conventional antimicrobial agents to combat antimicrobial resistance in many fields, including pharmaceuticals, dental materials, and cosmetic products.

Discovery and Biosynthesis of Glycosylated Cycloheximide from a Millipede-Associated Actinomycete

Chemical redundancy of microbial natural products (NPs) underscores the importance to exploit new resources of microorganisms. Insect-associated microbes are prolific but largely underexplored sources of diverse NPs. Herein, we discovered the new compound α-l-rhamnosyl-actiphenol (1) from a millipede-associated Streptomyces sp. ML6, which is the first glycosylated cycloheximide-class natural product. Interestingly, bioinformatics analysis of the ML6 genome revealed that the biosynthesis of 1 involves a cooperation between two gene clusters (chx and rml) located distantly on the genome of ML6. We also carried out in vitro enzymatic glycosylation of cycloheximide using an exotic promiscuous glycosyltransferase BsGT-1, which resulted in the production of an additional cycloheximide glycoside cycloheximide 7-O-β-d-glucoside (5). Although the antifungal and cytotoxic activities of the new compounds 1 and 5 were attenuated relative to those of cycloheximide, our work not only enriches the chemical repertoire of the cycloheximide family but also provides new insights into the structure-activity relationship optimization and ecological roles of cycloheximide.

The Impact of Tetracycline Pollution on the Aquatic Environment and Removal Strategies

Antibacterial drugs are among the most commonly used medications in the world. Tetracycline is a widely used antibiotic for human and animal therapy due to its broad-spectrum activity, high effectiveness, and reasonable cost. The indications for treatment with tetracycline include pneumonia, bone and joint infections, infectious disorders of the skin, sexually transmitted and gastrointestinal infections. However, tetracycline has become a serious threat to the environment because of its overuse by humans and veterinarians and weak ability to degrade. Tetracycline is capable of accumulating along the food chain, causing toxicity to the microbial community, encouraging the development and spread of antibiotic resistance, creating threats to drinking and irrigation water, and disrupting microbial flora in the human intestine. It is essential to address the negative impact of tetracycline on the environment, as it causes ecological imbalance. Ineffective wastewater systems are among the main reasons for the increased antibiotic concentrations in aquatic sources. It is possible to degrade tetracycline by breaking it down into small molecules with less harmful or nonhazardous effects. A range of methods for physical, chemical, and biological degradation exists. The review will discuss the negative effects of tetracycline consumption on the aquatic environment and describe available removal methods.

Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages

Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery.

Conjugates of Chloramphenicol Amine and Berberine as Antimicrobial Agents

In order to obtain antimicrobial compounds with improved properties, new conjugates comprising two different biologically active agents within a single chimeric molecule based on chloramphenicol (CHL) and a hydrophobic cation were synthesized and studied. Chloramphenicol amine (CAM), derived from the ribosome-targeting antibiotic CHL, and the plant isoquinoline alkaloid berberine (BER) are connected by alkyl linkers of different lengths in structures of these conjugates. Using competition binding, double reporter system, and toeprinting assays, we showed that synthesized CAM-Cn-BER compounds bound to the bacterial ribosome and inhibited protein synthesis like the parent CHL. The mechanism of action of CAM-C5-BER and CAM-C8-BER on the process of bacterial translations was similar to CHL. Experiments with bacteria demonstrated that CAM-Cn-BERs suppressed the growth of laboratory strains of CHL and macrolides-resistant bacteria. CAM-C8-BER acted against mycobacteria and more selectively inhibited the growth of Gram-positive bacteria than the parent CHL and the berberine derivative lacking the CAM moiety (CH₃-C8-BER). Using a potential-sensitive fluorescent probe, we found that CAM-C8-BER significantly reduced the membrane potential in B. subtilis cells. Crystal violet assays were used to demonstrate the absence of induction of biofilm formation under the action of CAM-C8-BER on E. coli bacteria. Thus, we showed that CAM-C8-BER could act both on the ribosome and on the cell membrane of bacteria, with the alkylated berberine fragment of the compound making a significant contribution to the inhibitory effect on bacterial growth. Moreover, we showed that CAM-Cn-BERs did not inhibit eukaryotic translation in vitro and were non-toxic for eukaryotic cells.

Linezolid@MOF-74 as a host-guest system with antimicrobial activity

Linezolid (LNZ) is a new-generation synthetic molecule for the antibacterial treatment of severe infections, particularly in infective cases where the bacterial resistance to first-choice drugs is caused by Gram-positive pathogens. In this context, since 2009, some strains resistant to LNZ in patients with long-term treatments have been reported. Therefore, there is a need to use not only new drug molecules with antibacterial activities in the dosage form but also a different approach to pharmacotherapeutic strategies for skin infections, which lead to a reduction in the concentration of biocides. This work explores LNZ hosted at two isostructural MOFs, MOF-74(Zn) and MOF-74(Cu), as promising antimicrobial systems for gradual biocide release within 6 h. These systems reach a lower minimum inhibitory concentration (MIC) in comparison to free LNZ. Even a decreased MIC value is also observed, which is an encouraging result regarding the efficiency of the systems to control concentration-dependent antimicrobial resistance.

Antimicrobial and Antibiofilm Effect of Brazilian Green Propolis Aqueous Extract against Dental Anaerobic Bacteria

Green propolis may represent a promising therapeutic alternative against dental anaerobic pathogens because of its antimicrobial action. This study aimed to evaluate the antimicrobial and antibiofilm actions of Brazilian green propolis aqueous extract (BGP-AqExt) against dental anaerobic bacteria. The minimum inhibitory concentration (MIC) and minimum microbicide concentration (MMC) of the extract were determined against the standard strains (ATCC) of Fusobacterium nucleatum, Parvimonas micra, Prevotella intermedia, Porphyromonas gingivalis and Porphyromonas endodontalis. BGP-AqExt was chemically characterized by high-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis. Antibiofilm action was measured by MTT and crystal violet tests. The data were statistically analyzed by ANOVA and Tukey (5%) tests. The extract had antimicrobial action against all tested anaerobic bacteria, with an MIC value of 55 mg/mL for all bacteria, an MMC of 27.5 mg/mL for F. nucleatum and P. micra and 55 mg/mL for P. intermedia. Chemically, BGP-AqExt is composed of quercetin, gallic acid, caffeic and p-coumaric acid, drupani, kaempferol and Artepillin C. Significant reductions in biomass and metabolic action of biofilms were found after BGP-AqExt application. Therefore, BGP-AqExt has an antimicrobial and antibiofilm effect against dental anaerobic bacteria.

Antibacterial and Anti-Biofilm Activity of Pyrones from a Pseudomonas mosselii Strain

The emergence of drug resistant microbes over recent decades represents one of the greatest threats to human health; the resilience of many of these organisms can be attributed to their ability to produce biofilms. Natural products have played a crucial role in drug discovery, with microbial natural products in particular proving a rich and diverse source of antimicrobial agents. During antimicrobial activity screening, the strain Pseudomonas mosselii P33 was found to inhibit the growth of multiple pathogens. Following chemical investigation of this strain, pseudopyronines A-C were isolated as the main active principles, with all three pseudopyronines showing outstanding activity against Staphylococcus aureus. The analogue pseudopyronine C, which has not been well-characterized previously, displayed sub-micromolar activity against S. aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa. Moreover, the inhibitory abilities of the pseudopyronines against the biofilms of S. aureus were further studied. The results indicated all three pseudopyronines could directly reduce the growth of biofilm in both adhesion stage and maturation stage, displaying significant activity at micromolar concentrations.

Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance

Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.

DNA damage and reticular stress in cytotoxicity and oncotic cell death of MCF-7 cells treated with fluopsin C

Fluopsin C is an antibiotic compound derived from secondary metabolism of different microorganisms, which possesses antitumor, antibacterial, and antifungal activity. Related to fluopsin C antiproliferative activity, the aim of this study was to examine the following parameters: cytotoxicity, genotoxicity, cell cycle arrest, cell death induction (apoptosis), mitochondrial membrane potential (MMP), colony formation, and mRNA expression of genes involved in adaptive stress responses and cellular death utilizing a monolayer. In addition, a three-dimensional cell culture was used to evaluate the effects on growth of tumor spheroids. Fluopsin C was cytotoxic (1) producing cell division arrest in the G₁ phase, (2) elevating expression of mRNA of the CDKN1A gene and (3) decrease in expression of mRNA H2AFX gene. Further, fluopsin C enhanced DNA damage as evidenced by increased expression of mRNA of GADD45A and GPX1 genes, indicating that reactive oxygen species (ROS) may be involved in the observed genotoxic response. Reticulum stress was also detected as noted from activation of the ribonuclease inositol-requiring protein 1 (IRE1) pathway, since a rise in mRNA expression of the ERN1 and TRAF2 genes was observed. During the cell death process, an increase in mRNA expression of the BBC3 gene was noted, indicating participation of this antibiotic in oncotic (ischemic) cell death. Data thus demonstrated for the first time that fluopsin C interferes with the volume of tumor spheroids, in order to attenuate their growth. Our findings show that fluopsin C modulates essential molecular processes in response to stress and cell death.

Molecular characterization and virulence gene profiling of methicillin-resistant Staphylococcus aureus associated with bloodstream infections in southern China

Methicillin-resistant Staphylococcus aureus (MRSA) causes an enormous illness burden, including skin and soft tissue infections (SSTIs), pneumonia, bloodstream infections (BSI), and sepsis. BSI are associated with significant patient morbidity and mortality worldwide. However, limited information is available on MRSA-related BSI in China. This study aimed to investigate the molecular characterization of 77 MRSA isolates recovered from hospitalized patients with BSI between 2012 and 2020 at three first-class tertiary hospitals in southern China based on multilocus sequence typing (MLST), spa typing, and staphylococcal cassette chromosome mec (SCCmec) typing. Overall, 13 clonal complexes (CCs) were identified, with CC59 and CC5 being the largest clusters, indicating high genetic diversity among BSI-causing MRSA isolates. ST59 was the most prevalent MLST type (22.1%). ST5/ST764-MRSA SCCmec II was the predominant adult MRSA clone, whereas ST59-MRSA SCCmec IV was the most common pediatric MRSA clone. ST5-t2460, ST764-t1084, and ST59-t437 were the most common types of adult MRSA isolates, whereas ST59-t437 and ST59-t172 were the predominant types of children’s MRSA isolates. ST59-SCCmec IV/V represented the most common clone among community acquired-MRSA isolates. ST5/ST764-SCCmec II was the most common type of hospital-associated MRSA isolate. The most prevalent toxin-encoding genes detected were hla, hld, icaA, and clfA (96.1–100%). Forty-three (100%, 43/43) isolates harbored more than 18 of the tested virulence genes in adults and eight virulence genes (23.5%, 8/34) in children. Virulence gene analysis revealed diversity among different clones: the positivity rates for the Panton-Valentine leukocidin (PVL) gene were 55.8 and 35.3% in adult and pediatric MRSA isolates, respectively; the genes seb–sei were present in all adult strains; seb–seg–sei–seo were present in all ST5, ST59, ST15, ST45, and ST22 adult strains; and seg–sei–sem–sen–seo were present in different clones, including ST15, ST45, and ST22 adult MRSA isolates and ST25, ST30, ST546, and ST72 children’s MRSA isolates. Adult MRSA isolates had significantly higher antibiotic resistance rates and virulence gene prevalence than pediatric MRSA isolates. For 8 years, this study provided epidemiological data on the molecular characteristics and virulence genes in different groups of MRSA BSI in China. Our findings may provide critical information for a better understanding of MRSA BSI.

A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria

Understanding antibiotic resistance mechanisms is central to the development of anti‐infective therapies and genomics‐based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less‐explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self‐resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X‐ray crystallography revealed CtaZ as a founding member of a new group of GyrI‐like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand‐optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI‐like domain in self‐resistance and unprecedented thioamide binding, this work aids in uncovering related drug‐resistance mechanisms.

Vertical distribution of antibiotics and antibiotic resistance genes in a representative municipal solid waste landfill, China

The vertical distribution of sulfonamides (SAs), tetracyclines (TCs), macrolides (MLs), and their related antibiotic resistance genes (ARGs) were comprehensively investigated and characterized in a representative municipal solid waste (MSW) landfill in China. The total concentrations of target antibiotics in the MSW landfill were SAs > TCs > MLs. The abundances of mexF (10.78 ± 0.65 log₁₀copies/g) and sul genes (9.15 ± 0.54 log₁₀copies/g) were relatively high, while the tet genes (7.19 ± 0.77 log₁₀copies/g) were the lowest. Both the abundance of antibiotics and genes fluctuated with landfill depth, and the ARGs of the same antibiotics were consistent with depth change. Intl1 and sul genes (sul1, sul2) were tightly connected, and a close relationship also existed between tet genes (tetM, tetQ) and MLs resistance genes (ermB, mefA). High-throughput sequencing showed the dominant genera were Sporosarcina (38%) and Thiobacillus (17%) at sampling points A and C, while the microbial community varied with depth increase at point B were Brevundimonas (20%), Sporosarcina (20%), Pseudomonas (24%), Lysobacter (28%), and Thioalkalimicrobium (14%), respectively. Network analysis further visualized the relationship among antibiotics, genes, and microbial communities and the results indicated the non-random connection among them and the possible host of the target gene. Even at 12.0 m below the landfill surface, the pollution of antibiotics resistance was still serious, which posed difficulties for subsequent landfill remediation and pollution control.

Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery

The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.

A Bombyx mori Infection Model for Screening Antibiotics against Staphylococcus epidermidis

The increasing number of microorganisms that are resistant to antibiotics is prompting the development of new antimicrobial compounds and strategies to fight bacterial infections. The use of insects to screen and test new drugs is increasingly considered a promising tool to accelerate the discovery phase and limit the use of mammalians. In this study, we used for the first time the silkworm, Bombyx mori, as an in vivo infection model to test the efficacy of three glycopeptide antibiotics (GPAs), against the nosocomial pathogen Staphylococcus epidermidis. To reproduce the human physiological temperature, the bacterial infection was performed at 37 °C and it was monitored over time by evaluating the survival rate of the larvae, as well the response of immunological markers (i.e., activity of hemocytes, activation of the prophenoloxidase system, and lysozyme activity). All the three GPAs tested (vancomycin, teicoplanin, and dalbavancin) were effective in curing infected larvae, significantly reducing their mortality and blocking the activation of the immune system. These results corroborate the use of this silkworm infection model for the in vivo studies of antimicrobial molecules active against staphylococci.

Discovery of a Novel Antimicrobial Peptide, Temporin-PKE, from the Skin Secretion of Pelophylax kl. esculentus, and Evaluation of Its Structure-Activity Relationships

Bacterial resistance against antibiotics has led to increasing numbers of treatment failures, and AMPs are widely accepted as becoming potential alternatives due to their advantages. Temporin-PKE is a novel peptide extracted from the skin secretion of Pelophylax kl. esculentus and it displays a strong activity against Gram-positive bacteria, with an extreme cytotoxicity. Incorporating positively charged residues and introducing D-amino acids were the two main strategies adopted for the modifications. The transformation of the chirality of Ile could reduce haemolytic activity, and an analogue with appropriate D-isoforms could maintain antimicrobial activity and stability. The substitution of hydrophobic residues could bring about more potent and broad-spectrum antimicrobial activities. The analogues with Lys were less harmful to the normal cells and their stabilities remained at similarly high levels compared to temporin-PKE. The optimal number of charges was three, and the replacement on the polar face was a better choice. Temporin-PKE-3K exerted dually efficient functions includingstrong antimicrobial and anticancer activity. This analogue showed a reduced possibility for inducing resistance in MRSA and Klebsiella pneumoniae, a rather strong antimicrobial activity in vivo, and it exhibited the highest therapeutic index such that temporin-PKE-3K has the potential to be developed as a clinical drug.

Tackling antimicrobial stewardship through synergy and antimicrobial peptides

The unrestricted use of antibiotics has led to rapid development of antibiotic resistance (AR) and renewed calls to address this serious problem. This review summarizes the most common mechanisms of antibiotic action, and in turn antibiotic resistance, as well as pathways to mitigate the harm. Focus is then turned to emerging antibiotic strategies, including antimicrobial peptides (AMPs), with a discussion of their modes of action, biochemical features, and potential challenges for their use as antibiotics. The role of synergy in antimicrobials is also examined, with a focus on the synergy of AMPs and other emerging interactions with synergistic potential.

Promising antimicrobials from Phoma spp.: progress and prospects

The increasing multidrug-resistance in pathogenic microbes and the emergence of new microbial pathogens like coronaviruses have necessitated the discovery of new antimicrobials to treat these pathogens. The use of antibiotics began after the discovery of penicillin by Alexander Fleming from Penicillium chrysogenum. This has attracted the scientific community to delve deep into the antimicrobial capabilities of various fungi in general and Phoma spp. in particular. Phoma spp. such as Phoma arachidicola, P. sorghina, P. exigua var. exigua, P. herbarum, P. multirostrata, P. betae, P. fimeti, P. tropica, among others are known to produce different bioactive metabolites including polyketides, macrosporin, terpenes and terpenoids, thiodiketopiperazines, cytochalasin derivatives, phenolic compounds, and alkaloids. These bioactive metabolites have already demonstrated their antimicrobial potential (antibacterial, antifungal, and antiviral) against various pathogens. In the present review, we have discussed the antimicrobial potential of secondary metabolites produced by different Phoma species. We have also deliberated the biogenic synthesis of eco-friendly antimicrobial silver nanoparticles from Phoma and their role as potential antimicrobial agents.

Growing multidrug-resistance and emerging pathogens need new antimicrobial drugs

Different species of Phoma produce antimicrobial metabolites

Phoma spp. are potential synthesizers of silver nanoparticles demonstrating antimicrobial activity.

Penicillin-Binding Proteins, β-Lactamases, and β-Lactamase Inhibitors in β-Lactam-Producing Actinobacteria: Self-Resistance Mechanisms

The human society faces a serious problem due to the widespread resistance to antibiotics in clinical practice. Most antibiotic biosynthesis gene clusters in actinobacteria contain genes for intrinsic self-resistance to the produced antibiotics, and it has been proposed that the antibiotic resistance genes in pathogenic bacteria originated in antibiotic-producing microorganisms. The model actinobacteria Streptomyces clavuligerus produces the β-lactam antibiotic cephamycin C, a class A β-lactamase, and the β lactamases inhibitor clavulanic acid, all of which are encoded in a gene supercluster; in addition, it synthesizes the β-lactamase inhibitory protein BLIP. The secreted clavulanic acid has a synergistic effect with the cephamycin produced by the same strain in the fight against competing microorganisms in its natural habitat. High levels of resistance to cephamycin/cephalosporin in actinobacteria are due to the presence (in their β-lactam clusters) of genes encoding PBPs which bind penicillins but not cephalosporins. We have revised the previously reported cephamycin C and clavulanic acid gene clusters and, in addition, we have searched for novel β-lactam gene clusters in protein databases. Notably, in S. clavuligerus and Nocardia lactamdurans, the β-lactamases are retained in the cell wall and do not affect the intracellular formation of isopenicillin N/penicillin N. The activity of the β-lactamase in S. clavuligerus may be modulated by the β-lactamase inhibitory protein BLIP at the cell-wall level. Analysis of the β-lactam cluster in actinobacteria suggests that these clusters have been moved by horizontal gene transfer between different actinobacteria and have culminated in S. clavuligerus with the organization of an elaborated set of genes designed for fine tuning of antibiotic resistance and cell wall remodeling for the survival of this Streptomyces species. This article is focused specifically on the enigmatic connection between β-lactam biosynthesis and β-lactam resistance mechanisms in the producer actinobacteria.

An Anti-MRSA Phage From Raw Fish Rinse: Stability Evaluation and Production Optimization

Accumulating evidence has denoted the danger of resistance in tenacious organisms like methicillin-resistant Staphylococcus aureus (MRSA). MRSA, a supple bacterium that adopts a variety of antibiotic resistance mechanisms, is the cause of multiple life-threatening conditions. Approaching a post-antibiotic era, bacteria-specific natural predators, bacteriophages, are now given the chance to prove eligible for joining the antibacterial weaponry. Considering the foregoing, this study aimed at isolating bacteriophages with promising anti-MRSA lytic activity, followed by characterization and optimization of the production of the bacteriophage with the broadest host range. Five phages were isolated from different environmental sources including the rinse of raw chicken egg, raw milk, and, remarkably, the raw meat rinses of chicken and fish. Examined for lytic activity against a set of 23 MRSA isolates collected from various clinical specimens, all five phages showed relatively broad host ranges with the bacteriophage originally isolated from raw fish rinse showing lytic activity against all the isolates tested. This phage is suggested to be a member of Siphoviridae family, order Caudovirales, as revealed by electron microscopy. It also exhibited good thermal stability and viability at different pH grades. Moreover, it showed reasonable stability against UV light and all viricidal organic solvents tested. Optimization using D-optimal design by response surface methodology was carried out to enhance the phage yield. The optimum conditions suggested by the generated model were a pH value of 7, a carbon source of 0.5% w/v sucrose, and a nitrogen source of 0.1% w/v peptone, at a temperature of 28°C and a bacterial inoculum size of 107 CFU/ml, resulting in a 2 log-fold increase in the produced bacteriophage titer. Overall, the above findings indicate the lytic ability inflicted by this virus on MRSA. Apparently, its stability under some of the extreme conditions tested implies its potential to be a candidate for pharmaceutical formulation as an anti-MRSA therapeutic tool. We hope that bacteriophages could tip the balance in favor of the human front in their battle against multidrug-resistant pathogens.

The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin

Bacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic‐producing bacteria. In this work, we characterize the self‐resistance protein Ecm16 encoded by echinomycin‐producing bacteria. Ecm16 is a structural homolog of the nucleotide excision repair protein UvrA. Expression of ecm16 in the heterologous system Escherichia coli was sufficient to render resistance against echinomycin. Ecm16 binds DNA (double‐stranded and single‐stranded) using a nucleotide‐independent binding mode. Ecm16’s binding affinity for DNA increased by 1.7‐fold when the DNA is intercalated with echinomycin. Ecm16 can render resistance against echinomycin toxicity independently of the nucleotide excision repair system. Similar to UvrA, Ecm16 has ATPase activity, and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other's function. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin.

The panorama of antibiotics and the related antibiotic resistance genes (ARGs) in landfill leachate

Landfill leachate is an important source and sink of antibiotics and antibiotic resistance genes (ARGs), which poses a potential threat to human health and ecological environment. Ten antibiotics and 8 ARGs in leachates collected from Zhejiang Province, China, were systematically investigated. The effects of multiple factors were considered: leachate age, season when the leachate was sampled (dry or rainy), heavy metal concentrations, and leachate quality parameters. Leachate age was crucial to the profile of the detectable antibiotics and ARGs. The total concentration of antibiotics were in the order of macrolides > sulfonamides > tetracyclines and they decreased significantly with leachate age. Similarly, fewer ARGs were harbored in aged leachate; the order of abundance of the ARGs was mexF (11.92 ± 0.22 log₁₀ gene copies/L) > sul2 > Intl1 > sul1 > ermB > mefA > tetM > tetQ (9.57 ± 1.32 log₁₀ gene copies/L). The extreme abundances (i.e., the maxima and minima) of ARGs relating to the same class of antibiotic were always surprisingly similar and appeared in leachate of the same age. Seasonal variation greatly affected the concentrations of antibiotics in the leachate-the concentration difference between the dry and rainy seasons could reach two orders of magnitude. Heavy metal concentrations and leachate quality parameters also had important effects on the distribution of antibiotics and ARGs. Overall, the profile of antibiotics and ARGs in leachates was influenced by numerous factors, and the pollution of antibiotics and ARGs may be reduced and controlled by adjusting the environmental factors.

Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens

Phylogenetically diverse bacteria can carry out chloramphenicol reduction, but only a single enzyme has been described that efficiently catalyzes this reaction, the NfsB nitroreductase from Haemophilus influenzae strain KW20. Here, we tested the hypothesis that some NfsB homologs function as housekeeping enzymes with the potential to become chloramphenicol resistance enzymes. We found that expression of H. influenzae and Neisseria spp. nfsB genes, but not Pasteurella multocida nfsB, allows Escherichia coli to resist chloramphenicol by nitroreduction. Mass spectrometric analysis confirmed that purified H. influenzae and N. meningitides NfsB enzymes reduce chloramphenicol to amino-chloramphenicol, while kinetics analyses supported the hypothesis that chloramphenicol reduction is a secondary activity. We combined these findings with atomic resolution structures of multiple chloramphenicol-reducing NfsB enzymes to identify potential key substrate-binding pocket residues. Our work expands the chloramphenicol reductase family and provides mechanistic insights into how a housekeeping enzyme might confer antibiotic resistance. IMPORTANCE The question of how new enzyme activities evolve is of great biological interest and, in the context of antibiotic resistance, of great medical importance. Here, we have tested the hypothesis that new antibiotic resistance mechanisms may evolve from promiscuous housekeeping enzymes that have antibiotic modification side activities. Previous work identified a Haemophilus influenzae nitroreductase housekeeping enzyme that has the ability to give Escherichia coli resistance to the antibiotic chloramphenicol by nitroreduction. Herein, we extend this work to enzymes from other Haemophilus and Neisseria strains to discover that expression of chloramphenicol reductases is sufficient to confer chloramphenicol resistance to Es. coli, confirming that chloramphenicol reductase activity is widespread across this nitroreductase family. By solving the high-resolution crystal structures of active chloramphenicol reductases, we identified residues important for this activity. Our work supports the hypothesis that housekeeping proteins possessing multiple activities can evolve into antibiotic resistance enzymes.

Phytolectin conjugated positively charged fatty acid amide impairs virulence factors and inhibits cross-kingdom biofilm formation of Candida albicans and uropathogenic Escherichia coli

AIM

Polymicrobial biofilm encasing cross-kingdom microorganisms are apparent in medicine, which imposes serious resistance to conventional antimicrobial treatment. The objective of the study was to explore Butea monosperma seed lectin (BMSL) conjugated antimicrobial lipid, 2-((N-(2-hydroxyethyl)palmitamido)methyl)-1-methylpyridin-1-ium iodide (cN16E) to inhibit mixed-species biofilm of uropathogenic Escherichia coli-Candida albicans.

METHODS AND RESULTS

Antimicrobial activity and antibiofilm of cN16E and cN16E-BMSL conjugate (BcN16E) were analyzed against single- and mixed microbial cultures. The minimum inhibitory concentration (MIC) indicates that the MIC of cN16E-BMSL conjugate (BcN16E) against cohabiting UPEC-C. albicans was eightfold lower than the cN16E. BcN16E affects membrane integrity to elicit antimicrobial activity. BcN16E inhibits the dual-species biofilm even with 16 times lower MIC of cN16E. BcN16E impairs the biofilm-associated virulence factors which include extracellular polysaccharides, cell surface hydrophobicity, swimming, swarming motilities, hyphal filamentous morphology, curli formation, and hemolysin activity. As a proof of concept, we demonstrated BcN16E ability to inhibit dual-species biofilm formation on a urinary catheter.

CONCLUSION

The study revealed that the BcN16E is better than cN16E in impairing biofilm-associated virulence factors and exerting antimicrobial activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings emphasize that phytolectin has the potential to enhance the anti-virulence strategies of antimicrobials against cross-kingdom biofilm-related infections.

Multifunctional P450 Monooxygenase CftA Diversifies the Clifednamide Pool through Tandem C-H Bond Activations

Polycyclic tetramate macrolactams (PTMs) are a class of structurally complex hybrid polyketide-nonribosomal peptide (PK-NRP) natural products produced by diverse bacteria. Several PTMs display pharmaceutically interesting bioactivities, and the early stages of PTM biosynthesis involving polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymology are well studied. However, the timing and mechanisms of post PKS-NRPS oxidations by P450 monooxygenases encoded in PTM biosynthetic gene clusters (BGCs) remain poorly characterized. Here we demonstrate that CftA, encoded in clifednamide-type PTM BGCs, is a multifunctional P450 monooxygenase capable of converting the C29-C30 ethyl side chain of ikarugamycin to either a C29-C30 methyl ketone or a C29-C30 hydroxymethyl ketone through C-H bond activation, resulting in the formation of clifednamide A or clifednamide C, respectively. We also report the complete structure of clifednamide C solved via multidimensional NMR (COSY, HSQC, HMBC, NOESY, and TOCSY) using material purified from an engineered Streptomyces strain optimized for production. Finally, the in vitro reconstitution of recombinant CftA catalytic activity revealed the oxidation cascade for sequential conversion of ikarugamycin to clifednamide A and clifednamide C. Our findings confirm prior genetics-based predictions on the origins of clifednamide complexity via P450s encoded in PTM BGCs and place CftA into a growing group of multifunctional P450s that tailor PTM natural products through late-stage regioselective C-H bond activation.

Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals

The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare's most potent antibiotics are becoming obsolete. Approximately two-thirds of the world's antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 104 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.

From solo to duet, intersections of natural product assembly with self-resistance

Covering: up to 2021Self-resistance mechanisms adopted by natural product producers have long been recognized and studied as a standalone system separated from the assembly machinery. However, as more examples of self-resistance have been characterized in detail, it has been revealed that self-resistance could associate with the assembly machinery to fulfill the task of biosynthesis. This review summarizes different self-resistance mechanisms showing a common feature: intersection with natural product assembly. Furthermore, their possible evolutionary origin and synthetic biology applications are discussed.

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ∼75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

Evaluation of Antibiotic Resistance of Salmonella Serotypes and Whole-Genome Sequencing of Multiresistant Strains Isolated from Food Products in Russia

Food products may be a source of Salmonella, one of the main causal agents of food poisoning, especially after the emergence of strains resistant to antimicrobial preparations. The present work dealt with investigation of the occurrence of resistance to antimicrobial preparations among S. enterica strains isolated from food. The isolates belonged to 11 serovars, among which Infantis (28%), Enteritidis (19%), and Typhimurium (13.4%) predominated. The isolates were most commonly resistant to trimethoprim/sulfamethoxazole (n = 19, 59.38%), cefazolin (n = 15, 46.86%), tetracycline (n = 13, 40.63%), and amikacin (n = 9, 28.13%). Most of the strains (68.75%) exhibited multiple resistance to commonly used antibiotics. High-throughput sequencing was used to analyse three multidrug-resistant strains (resistant to six or more antibiotics). Two of them (SZL 30 and SZL 31) belonged to S. Infantis, while one strain belonged to S. Typhimurium (SZL 38). Analysis of the genomes of the sequenced strains revealed the genes responsible for antibiotic resistance. In the genomes of strains SZL 30 and SZL 31 the genes of antibiotic resistance were shown to be localized mostly in integrons within plasmids, while most of the antibiotic resistance genes of strain SZL 38 were localized in a chromosomal island (17,949 nt). Genomes of the Salmonella strains SZL 30, SZL 31, and SZL 38 were shown to contain full-size pathogenicity islands: SPI-1, SPI-2, SPI-4, SPI-5, SPI-9, SPI-11, SPI-13, SPI-14, and CS54. Moreover, the genome of strain SZL 38 was also found to contain the full-size pathogenicity islands SPI-3, SPI-6, SPI-12, and SPI-16. The emergence of multidrug-resistant strains of various Salmonella serovars indicates that further research on the transmission pathways for these genetic determinants and monitoring of the distribution of these microorganisms are necessary.

Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics

Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics.

Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.