Antibiotic Resistance: Current Perspectives

Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study

The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.

Pillar[n]arenes in the Fight against Biofilms: Current Developments and Future Perspectives

The global surge in bacterial infections, compounded by the alarming escalation of drug-resistant strains, has evolved into a critical public health crisis. Among the challenges posed, biofilms stand out due to their formidable resistance to conventional antibiotics. This review delves into the burgeoning potential of pillar[n]arenes, distinctive macrocyclic host molecules, as promising anti-biofilm agents. The review is structured into two main sections, each dedicated to exploring distinct facets of pillar[n]arene applications. The first section scrutinizes functionalized pillar[n]arenes with a particular emphasis on cationic derivatives. This analysis reveals their significant efficacy in inhibiting biofilm formation, underscoring the pivotal role of specific chemical attributes in combating microbial communities. The second section of the review shifts its focus to inclusion complexes, elucidating how pillar[n]arenes serve as encapsulation platforms for antibiotics. This encapsulation enhances the stability of antibiotics and enables a controlled release, thereby amplifying their antibacterial activity. The examination of inclusion complexes provides valuable insights into the potential synergy between pillar[n]arenes and traditional antibiotics, offering a novel avenue for overcoming biofilm resistance. This comprehensive review highlights the escalating global threat of bacterial infections and the urgent need for innovative strategies to counteract drug-resistant biofilms. The unique properties of pillar[n]arenes, both as functionalized molecules and as inclusion complex hosts, position them as promising candidates in the quest for effective anti-biofilm agents. The exploration of their distinct mechanisms opens new avenues for research and development in the ongoing battle against bacterial infections and biofilm-related health challenges.

Antibacterial p-terphenyl and α‑pyrone derivates isolated from the marine-derived actinomycete Nocardiopsis sp. HDN154086

Assisted by OSMAC strategy, one new p-terphenyl and two new α‑pyrone derivates, namely nocarterphenyl I (1) and nocardiopyrone D-E (2-3), were obtained and characterized from the marine sediment-derived actinomycete Nocardiopsis sp. HDN154086. The structures of these compounds were determined on the basis of MS, NMR spectroscopic data and single-crystal X-ray diffraction. Compound 1 with a rare 2,2'-bithiazole structure among natural products showed promising activity against five bacteria with MIC values ranging from 0.8 to 1.6 μM and 3 exhibited notable antibacterial activity against MRSA compared the positive control ciprofloxacin.

Characterization of microbial contamination in agricultural soil: A public health perspective

Soil is widely recognized as a reservoir of microbial contaminants including antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), which are major public health concerns. Although the risks associated with soil safety in different soil habitats have been studied, the results are not comprehensive. In this study, dryland soils used for vegetable, corn, and soybean planting, and submerged soils used for rice planting and crab farming were collected and subjected to metagenomic sequencing to characterize HBPs, ARGs, and virulence factor genes (VFGs). The results showed that submerged soils had a higher abundance of HBP than dryland soils. In addition, the submerged soil microbiome acquired significantly higher levels of high-risk ARGs than the dryland soil microbiome and these ARGs were mainly assigned to bacA, sul1, and aadA genes submerged. Network analysis revealed that 11 HBPs, including Yersinia enterocolitica, Vibrio cholerae, Escherichia coli, and Leptospira interrogans, were high-risk because of their close association with ARGs, VFGs, and mobile genetic elements (MGEs). Procrustes and network analyses showed that HBPs and ARGs were more closely linked in submerged soil. This study confirms that submerged field has higher ecological environment risk and human health risk than dryland soil.

Surface-Enhanced Raman Scattering (SERS) in Combination with PCA and PLS-DA for the Evaluation of Antibacterial Activity of 1-Isopentyl-3-pentyl-1H-imidazole-3-ium Bromide against Bacillus subtilis

In the current study, surface-enhanced Raman scattering (SERS) was performed to evaluate the antibacterial activity of lab-synthesized drug (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt) and commercial drug tinidazole againstBacillus subtilis. The changes in SERS spectral features were studied for unexposed bacillus and exposed one with various dosages of drug synthesized in the lab (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt), and SERS bands were assigned associated with the drug-induced biochemical alterations in bacteria. Multivariate data analysis tools including principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) have been utilized to analyze the antibacterial activity of the imidazole derivative (lab drug). PCA was employed in differentiating all the SERS spectral data sets associated with the various doses of the lab-synthesized drug. There is clear discrimination among the spectral data sets of a bacterial strain treated with different concentrations of the drug, which are analyzed by PLS-DA with 86% area under the curve in receiver operating curve (ROC), 99% sensitivity, 100% accuracy, and 98% specificity. Various dominant spectral features are observed with a gradual increase in the different concentrations of the applied drug including 715, 850, 1002, 1132, 1237, 1396, 1416, and 1453 cm-1, which indicate the possible biochemical changes caused in bacteria during the antibacterial activity of the lab-synthesized drug. Overall, the findings show that imidazole and imidazolium compounds generated from tinidazole with various alkyl lengths in the amide substitution can be effective antibacterial agents with low cytotoxicity in humans, and these results indicate the efficiency of SERS in pharmaceuticals and biomedical applications.

Recent Development of DNA Gyrase Inhibitors: An Update

Antibiotic or antimicrobial resistance is an urgent global public health threat that occurs when bacterial or fungal infections do not respond to the drug regimen designed to treat these infections. As a result, these microbes are not evaded and continue to grow. Antibiotic resistance against natural and already-known antibiotics like Ciprofloxacin and Novobiocin can be overcome by developing an agent that can act in different ways. The success of agents like Zodiflodacin and Zenoxacin in clinical trials against DNA gyrase inhibitors that act on different sites of DNA gyrase has resulted in further exploration of this target. However, due to the emergence of bacterial resistance against these targets, there is a great need to design agents that can overcome this resistance and act with greater efficacy. This review provides information on the synthetic and natural DNA gyrase inhibitors that have been developed recently and their promising potential for combating antimicrobial resistance. The review also presents information on molecules that are in clinical trials and their current status. It also analysed the SAR studies and mechanisms of action of enlisted agents.

Nutrient condition modulates the antibiotic tolerance of Pseudomonas aeruginosa

The variation in nutrient content across diverse environments has a significant impact on the survival and metabolism of microorganisms. In this study, we examined the influence of nutrients on the antibiotic tolerance of the PAO1 strain of Pseudomonas aeruginosa. Our findings indicate that under nutrient-rich conditions, this strain exhibited relatively high tolerance to ceftazidime, chloramphenicol, and tetracycline, but not aminoglycosides and fluoroquinolones. Transcriptome analysis revealed that genes associated with antibiotic tolerance were expressed more efficiently in nutrient-rich media, including ribosomal protein genes and multidrug efflux pump genes, which conferred higher tetracycline tolerance to the strain. Furthermore, the genes responsible for translation, biosynthesis, and oxidative phosphorylation were suppressed when nutrients were limited, resulting in decreased metabolic activity and lower sensitivity to ciprofloxacin. Artificial interference with ATP synthesis utilizing arsenate confirmed that the curtailment of energy provision bolstered the observed tolerance to ciprofloxacin. In general, our results indicate that this strain of P. aeruginosa tends to activate its intrinsic resistance mechanisms in nutrient-rich environments, thereby enhancing resistance to certain antibiotics. Conversely, in nutrient-limited environments, the strain is more likely to enter a dormant state, which enables it to tolerate antibiotics to which it would otherwise be sensitive. These findings further suggest that antibiotics released in environments with varying eutrophication levels may have divergent effects on the development of bacterial antibiotic resistance.

Surface Functionalization of Poly(lactic acid) via Deposition of Hydroxyapatite Monolayers for Biomedical Applications

The surface modification of poly(lactic acid) (PLA) using hydroxyapatite (HAP) particles via Langmuir-Blodgett (LB) and Langmuir-Schaefer (LS) approaches has been reported. The HAP monolayer was characterized at the air/water interface and deposited on three-dimensional (3D) printed poly(lactic acid). The deposition of HAP particles using the LS approach led to a larger surface coverage in comparison to the LB method, which produces a less uniform coating because of the aggregation of the particles. After the transfer of HAP on the PLA surface, the wettability values remained within the desired range. The presence of HAP on the surface of the polymer altered the topography and roughness in the nanoscale, as evidenced by the atomic force microscopy (AFM) images. This effect can be beneficial for the osteointegration of polymeric implants at an early stage, as well as for the reduction of the adherence of the microbial biofilm. Overall, the results suggest that the LS technique could be a promising approach for surface modification of PLA by hydroxyapatite with respective advantages in the biomedical field.

Effects of structural changes on antibacterial activity and cytotoxicity due to proline substitutions in chimeric peptide HnMc

Owing to the rapidly increasing emergence of multidrug-resistant pathogens, antimicrobial peptides (AMPs) are being explored as next-generation antibiotics. However, AMPs present in nature are highly toxic and exhibit low antibacterial activity. Simple modifications, such as amino acid substitution, can enhance antimicrobial activity and cell selectivity. Herein, we show that HnMc-W, substituted by the Phe1Trp analog of HnMc, a chimeric peptide, resulted in membranolytic antibacterial action and enhanced salt tolerance, whereas HnMc-WP1 with one Ser9Pro substitution resulted in a proline-kink helical structure that increased salt-tolerant antibacterial effects and reduced cytotoxicity. In addition, the HnMc-WP2 peptide, designed with a PXXP motif, had a flexible central hinge in its α-helical structure due to the introduction of two Pro and two Gln (X positions, by deletion of two Gln at positions 16 and 17) residues instead of Ser at position. HnMc-WP2 exhibited excellent antibacterial effects without cytotoxicity in vitro. Moreover, its potent antibacterial activity was demonstrated in a drug-resistant Pseudomonas aeruginosa-infected mouse model in vivo. Our findings provide valuable information for the design of peptides with high antibacterial activity and cell selectivity.

Screening of Phytochemical, Antimicrobial, and Antioxidant Properties of Juncus acutus from Northeastern Morocco

Juncus acutus, acknowledged through its indigenous nomenclature "samar", is part of the Juncaceae taxonomic lineage, bearing considerable import as a botanical reservoir harboring conceivable therapeutic attributes. Its historical precedence in traditional curative methodologies for the alleviation of infections and inflammatory conditions is notable. In the purview of Eastern traditional medicine, Juncus species seeds find application for their remedial efficacy in addressing diarrhea, while the botanical fruits are subjected to infusion processes targeting the attenuation of symptoms associated with cold manifestations. The primary objective of this study was to unravel the phytochemical composition of distinct constituents within J. acutus, specifically leaves (JALE) and roots (JARE), originating from the indigenous expanse of the Nador region in northeastern Morocco. The extraction of plant constituents was executed utilizing an ethanol-based extraction protocol. The subsequent elucidation of chemical constituents embedded within the extracts was accomplished employing analytical techniques based on high-performance liquid chromatography (HPLC). For the purpose of in vitro antioxidant evaluation, a dual approach was adopted, encompassing the radical scavenging technique employing 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the total antioxidant capacity (TAC) assay. The acquired empirical data showcase substantial radical scavenging efficacy and pronounced relative antioxidant activity. Specifically, the DPPH and TAC methods yielded values of 483.45 ± 4.07 µg/mL and 54.59 ± 2.44 µg of ascorbic acid (AA)/mL, respectively, for the leaf extracts. Correspondingly, the root extracts demonstrated values of 297.03 ± 43.3 µg/mL and 65.615 ± 0.54 µg of AA/mL for the DPPH and TAC methods. In the realm of antimicrobial evaluation, the assessment of effects was undertaken through the agar well diffusion technique. The minimum inhibitory concentration, minimum bactericidal concentration, and minimum fungicidal concentration were determined for each extract. The inhibitory influence of the ethanol extracts was observed across bacterial strains including Staphylococcus aureus, Micrococcus luteus, and Pseudomonas aeruginosa, with the notable exception of Escherichia coli. However, fungal strains such as Candida glabrata and Rhodotorula glutinis exhibited comparatively lower resistance, whereas Aspergillus niger and Penicillium digitatum exhibited heightened resistance, evincing negligible antifungal activity. An anticipatory computational assessment of pharmacokinetic parameters was conducted, complemented by the application of the Pro-tox II web tool to delineate the potential toxicity profile of compounds intrinsic to the studied extracts. The culmination of these endeavors underpins the conceivable prospects of the investigated extracts as promising candidates for oral medicinal applications.

Tale of Twin Bifunctional Second Messenger (p)ppGpp Synthetases and Their Function in Mycobacteria

M. tuberculosis, an etiological agent of tuberculosis, requires a long treatment regimen due to its ability to respond to stress and persist inside the host. The second messenger (p)ppGpp-mediated stress response plays a critical role in such long-term survival, persistence, and antibiotic tolerance which may also lead to the emergence of multiple drug resistance. In mycobacteria, (pp)pGpp molecules are synthesized predominantly by two bifunctional enzymes-long RSH-Rel and short SAS-RelZ. The long RSH-Rel is a major (p)ppGpp synthetase and hydrolase. How it switches its activity from synthesis to hydrolysis remains unclear. RelMtb mutant has been reported to be defective in biofilm formation, cell wall function, and persister cell formation. The survival of such mutants has also been observed to be compromised in infection models. In M. smegmatis, short SAS-RelZ has RNase HII activity in addition to (pp)Gpp synthesis activity. The RNase HII function of RelZ has been implicated in resolving replication-transcription conflicts by degrading R-loops. However, the mechanism and regulatory aspects of such a regulation remain elusive. In this article, we have discussed (p)ppGpp metabolism and its role in managing the stress response network of mycobacteria, which is responsible for long-term survival inside the host, making it an important therapeutic target.

Resveratrol as an Inhibitor of the NorA Efflux Pump and Resistance Modulator in Staphylococcus aureus

Staphylococcus aureus can exhibit resistance to various antibiotics. Among its resistance mechanisms, the active efflux of antibiotics can be seen as relevant. This study aimed to evaluate the ability of resveratrol to modulate norfloxacin resistance in S. aureus. The antimicrobial activity of resveratrol was assessed using the broth microdilution method to determine the minimum inhibitory concentration (MIC). Then, the modulatory effect of resveratrol was evaluated using the MIC determination for the antibiotic or ethidium bromide in the presence and absence of resveratrol at a sub-MIC level. The MIC of norfloxacin against S. aureus SA1199B (NorA-overexpressing strain) decreased 16-fold when in the presence of resveratrol, with a similar behavior being observed for ethidium bromide. An evaluation of the ethidium bromide accumulation was also performed, showing that in the presence of resveratrol, the SA1199B strain had augmented fluorescence due to the accumulation of ethidium bromide. Altogether, the results suggested that resveratrol may act by inhibiting NorA. These in vitro data were supported by docking results, with interactions between resveratrol and the NorA efflux pump predicted to be favorable. Our findings demonstrated that resveratrol may modulate norfloxacin resistance through the inhibition of NorA, increasing the effectiveness of this antibiotic against S. aureus.

C-4-Modified Isotetrones Prevent Biofilm Growth and Persister Cell Resuscitation in Mycobacterium smegmatis

Hyperphosphorylated nucleotide (p)ppGpp, synthesized by Rel protein, regulates the stringent response pathway responsible for biofilm and persister cell growth in mycobacteria. The discovery of vitamin C as an inhibitor of Rel protein activities raises the prospect of tetrone lactones to prevent such pathways. The closely related isotetrone lactone derivatives are identified herein as inhibitors of the above processes in a mycobacterium. Synthesis and biochemical evaluations show that an isotetrone possessing phenyl substituent at C-4 inhibit the biofilm formation at 400 μg mL^-1, 84 h post-exposure, followed by moderate inhibition by the isotetrone possessing the p-hydroxyphenyl substituent. The latter isotetrone inhibits the growth of persister cells at 400 μg mL^-1 f.c. when monitored for 2 weeks, under PBS starvation. Isotetrones also potentiate the inhibition of antibiotic-tolerant regrowth of cells by ciprofloxacin (0.75 μg mL^-1) and thus act as bioenhancers. Molecular dynamics studies show that isotetrone derivatives bind to the Rel_Msm protein more efficiently than vitamin C at a binding site possessing serine, threonine, lysine, and arginine.

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

Antimicrobial resistance in Klebsiella pneumoniae: identification of bacterial DNA adenine methyltransferase as a novel drug target from hypothetical proteins using subtractive genomics

Klebsiella pneumoniae is a gram-negative bacterium that is known for causing infection innosocomial settings. As reported by the World Health Organization, carbapenem-resistantEnterobacteriaceae, a category that includes K. pneumoniae, are classified as an urgentthreat, and the greatest concern is that these bacterial pathogens may acquire genetictraits that make them resistant towards antibiotics. The last class of antibiotics, carbapenems, are not able to combat these bacterial pathogens, allowing them to clonally expandantibiotic-resistant strains. Most antibiotics target essential pathways of bacterial cells;however, these targets are no longer susceptible to antibiotics. Hence, in our study, we focused on a hypothetical protein in K. pneumoniae that contains a DNA methylation proteindomain, suggesting a new potential site as a drug target. DNA methylation regulates theattenuation of bacterial virulence. We integrated computational-aided drug design by using a bioinformatics approach to perform subtractive genomics, virtual screening, and fingerprint similarity search. We identified a new potential drug, koenimbine, which could bea novel antibiotic.

Enzymatic Synthesis of Vancomycin-Modified DNA

Many potent antibiotics fail to treat bacterial infections due to emergence of drug-resistant strains. This surge of antimicrobial resistance (AMR) calls in for the development of alternative strategies and methods for the development of drugs with restored bactericidal activities. In this context, we surmised that identifying aptamers using nucleotides connected to antibiotics will lead to chemically modified aptameric species capable of restoring the original binding activity of the drugs and hence produce active antibiotic species that could be used to combat AMR. Here, we report the synthesis of a modified nucleoside triphosphate equipped with a vancomycin moiety on the nucleobase. We demonstrate that this nucleotide analogue is suitable for polymerase-mediated synthesis of modified DNA and, importantly, highlight its compatibility with the SELEX methodology. These results pave the way for bacterial-SELEX for the identification of vancomycin-modified aptamers.

Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects

Antimicrobial peptides (AMPs) are a diverse class of short, often cationic biological molecules that present promising opportunities in the development of new therapeutics to combat antimicrobial resistance. Newly developed in silico methods offer the ability to rapidly discover numerous novel AMPs with a variety of physiochemical properties. Herein, using the rAMPage AMP discovery pipeline, we bioinformatically identified 51 AMP candidates from amphibia and insect RNA-seq data and present their in-depth characterization. The studied AMPs demonstrate activity against a panel of bacterial pathogens and have undetected or low toxicity to red blood cells and human cultured cells. Amino acid sequence analysis revealed that 30 of these bioactive peptides belong to either the Brevinin-1, Brevinin-2, Nigrocin-2, or Apidaecin AMP families. Prediction of three-dimensional structures using ColabFold indicated an association between peptides predicted to adopt a helical structure and broad-spectrum antibacterial activity against the Gram-negative and Gram-positive species tested in our panel. These findings highlight the utility of associating the diverse sequences of novel AMPs with their estimated peptide structures in categorizing AMPs and predicting their antimicrobial activity.

Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli

Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.

Fluoroquinolones Hybrid Molecules as Promising Antibacterial Agents in the Fight against Antibacterial Resistance

The emergence of bacterial resistance has motivated researchers to discover new antibacterial agents. Nowadays, fluoroquinolones keep their status as one of the essential classes of antibacterial agents. The new generations of fluoroquinolones are valuable therapeutic tools with a spectrum of activity, including Gram-positive, Gram-negative, and atypical bacteria. This review article surveys the design of fluoroquinolone hybrids with other antibacterial agents or active compounds and underlines the new hybrids' antibacterial properties. Antibiotic fluoroquinolone hybrids have several advantages over combined antibiotic therapy. Thus, some challenges related to joining two different molecules are under study. Structurally, the obtained hybrids may contain a cleavable or non-cleavable linker, an essential element for their pharmacokinetic properties and mechanism of action. The design of hybrids seems to provide promising antibacterial agents helpful in the fight against more virulent and resistant strains. These hybrid structures have proven superior antibacterial activity and less susceptibility to bacterial resistance than the component molecules. In addition, fluoroquinolone hybrids have demonstrated other biological effects such as anti-HIV, antifungal, antiplasmodic/antimalarial, and antitumor activity. Many fluoroquinolone hybrids are in various phases of clinical trials, raising hopes that new antibacterial agents will be approved shortly.

In-biofilm generation of nitric oxide using a magnetically-targetable cascade-reaction container for eradication of infectious biofilms

Cascade-reaction chemistry can generate reactive-oxygen-species that can be used for the eradication of infectious biofilms. However, suitable and sufficient oxygen sources are not always available near an infection site, while the reactive-oxygen-species generated are short-lived. Therefore, we developed a magnetic cascade-reaction container composed of mesoporous Fe₃O₄@SiO₂ nanoparticles containing glucose-oxidase and l-arginine for generation of reactive-oxygen-species. Glucose-oxidase was conjugated with APTES facilitating coupling to Fe₃O₄@SiO₂ nanoparticles and generation of H₂O₂ from glucose. l-arginine was loaded into the nanoparticles to generate NO from the H₂O₂ generated. Using an externally-applied magnetic field, cascade-reaction containers could be homogeneously distributed across the depth of an infectious biofilm. Cascade-reaction containers with coupled glucose-oxidase were effective in killing planktonic, Gram-positive and Gram-negative bacteria. Additional efficacy of the l-arginine based second cascade-reaction was only observed when H₂O₂ as well as NO were generated in-biofilm. In vivo accumulation of cascade-reaction containers inside abdominal Staphylococcus aureus biofilms upon magnetic targeting was observed real-time in living mice through an implanted, intra-vital window. Moreover, vancomycin-resistant, abdominal S. aureus biofilms could be eradicated consuming solely endogenous glucose, without any glucose addition. Herewith, a new, non-antibiotic-based infection-control strategy has been provided, constituting a welcome addendum to the shrinking clinical armamentarium to control antibiotic-resistant bacterial infections.

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Fe₃O₄@SiO₂ NPs can be used as magnetically-targetable cascade-reaction containers.

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Mesoporous Fe₃O₄@SiO₂ NPs with GOx/l-arginine consume glucose to yield H₂O₂ and NO.

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Fe₃O₄@SiO₂ cascade-reaction containers are magnetically targetable to biofilm in vivo.

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In-biofilm generation of ROS is essential for killing biofilm bacteria.

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Fe₃O₄@SiO₂ NPs with GOx/l-arginine eradicate biofilms using only endogenous glucose.

Functional analysis of Escherichia coli K12 toxin-antitoxin systems as novel drug targets using a network biology approach

Bacterial resistance to various drugs and antibiotics has become a significant issue in the fight against infectious diseases. Due to the presence of diverse toxin-antitoxin (TA) systems, bacteria undergo adaptive metabolic alterations and can tolerate the effects of drugs and antibiotics. Bacterial TA systems are unique and can be therapeutic targets for developing new antimicrobial agents, owing to their ability to influence bacterial fate. With this background, our study aims to identify novel drug targets against Escherichia coli K12 MG1655 antitoxin using homology modelling approach. In this study, the protein-protein interaction network of 87 E. coli K12 MG1655 TA systems identified through literature mining was screened for the identification of hub proteins. The model evaluation, assessment, and homology modelling of the hub proteins were evaluated. Furthermore, computer-aided mathematical models of selected phytochemicals have been tested against the identified hub proteins. The TA system was functionally enriched in regulation of cell growth, negative regulation of cell growth, regulation of mRNA stability, mRNA catabolic process and RNA phosphodiester bond hydrolysis. RelE, RelB, MazE, MazF, MqsR, MqsA, and YoeB were identified as hub proteins. The robustness and superior quality of the RelB and MazE modelled structure were discovered by model evaluation, quality assessment criteria, and homology modelling of hub proteins. Clorobiocin was found to be a strong inhibitor by docking these modelled structures. Clorobiocin could be utilized as an antibacterial agent against multidrug resistant E. coli which may inactivate antitoxins and cause programmed cell death.

Modeling Polygenic Antibiotic Resistance Evolution in Biofilms

The recalcitrance of biofilms to antimicrobials is a multi-factorial phenomenon, including genetic, physical, and physiological changes. Individually, they often cannot account for biofilm recalcitrance. However, their combination can increase the minimal inhibitory concentration of antibiotics needed to kill bacterial cells by three orders of magnitude, explaining bacterial survival under otherwise lethal drug treatment. The relative contributions of these factors depend on the specific antibiotics, bacterial strain, as well as environmental and growth conditions. An emerging population genetic property—increased biofilm genetic diversity—further enhances biofilm recalcitrance. Here, we develop a polygenic model of biofilm recalcitrance accounting for multiple phenotypic mechanisms proposed to explain biofilm recalcitrance. The model can be used to generate predictions about the emergence of resistance—its timing and population genetic consequences. We use the model to simulate various treatments and experimental setups. Our simulations predict that the evolution of resistance is impaired in biofilms at low antimicrobial concentrations while it is facilitated at higher concentrations. In scenarios that allow bacteria exchange between planktonic and biofilm compartments, the evolution of resistance is further facilitated compared to scenarios without exchange. We compare these predictions to published experimental observations.

Antimicrobial Potential of Endophytic Fungi From Artemisia argyi and Bioactive Metabolites From Diaporthe sp. AC1

Endophytic fungi of medicinal plants are important sources of active natural products. In this study, 26 fungi were isolated from Artemisia argyi, which were belonging to eight genera, namely, Alternaria, Fusarium, Chaetomium, Phoma, Diaporthe, Trichoderma, Gibberella, and Colletotrichum. The antimicrobial activities of all fungal extracts were tested by using the cup-plate method against Staphylococcus aureus, Salmonella enteritidis, and Fusarium graminearum. The results demonstrated that 25 extracts (96%) exhibited inhibitory activity against at least one of the tested pathogenic microorganisms. The strain Diaporthe sp. AC1, which showed good antimicrobial activity and high yield of crude extract from fermentation, was selected for the study of secondary metabolites. The crude extract of strain AC1 was purified by silica gel column chromatography, Sephadex LH-20 gel column chromatography, and HPLC, and finally, a new compound phomopsolide G (1), together with three known phomopsolides (2–4) and four other known compounds (5–8), was obtained. The structures of the compounds were elucidated by NMR and/or HR-MS spectroscopy. Microdilution method and MTT colorimetry were used to determine the bioactivity of the compounds. The study demonstrated that the new compound 1 had moderate antifungal activity against F. graminearum, Fusarium moniliforme, and Botrytis cinerea and weak antibacterial activity against Staphylococcus aureus. Compound 1 also showed weak cytotoxicity against HepG2, A549, and MDA-MB-231, with IC50 values of 89.91, 107.65, and 53.97 μM. Additionally, other compounds also exhibited antimicrobial and/or cytotoxic activities. The findings provided the basis for searching drug and agricultural lead compounds from A. argyi-associated fungi resources.

Nanomaterials-Based Combinatorial Therapy as a Strategy to Combat Antibiotic Resistance

Since the discovery of antibiotics, humanity has been able to cope with the battle against bacterial infections. However, the inappropriate use of antibiotics, the lack of innovation in therapeutic agents, and other factors have allowed the emergence of new bacterial strains resistant to multiple antibiotic treatments, causing a crisis in the health sector. Furthermore, the World Health Organization has listed a series of pathogens (ESKAPE group) that have acquired new and varied resistance to different antibiotics families. Therefore, the scientific community has prioritized designing and developing novel treatments to combat these ESKAPE pathogens and other emergent multidrug-resistant bacteria. One of the solutions is the use of combinatorial therapies. Combinatorial therapies seek to enhance the effects of individual treatments at lower doses, bringing the advantage of being, in most cases, much less harmful to patients. Among the new developments in combinatorial therapies, nanomaterials have gained significant interest. Some of the most promising nanotherapeutics include polymers, inorganic nanoparticles, and antimicrobial peptides due to their bactericidal and nanocarrier properties. Therefore, this review focuses on discussing the state-of-the-art of the most significant advances and concludes with a perspective on the future developments of nanotherapeutic combinatorial treatments that target bacterial infections.

Gallium(III)-Mediated Dual-Cross-Linked Alginate Hydrogels with Antibacterial Properties for Promoting Infected Wound Healing

The metal gallium has enormous promise in fighting infections by disrupting bacterial iron metabolism via a "Trojan horse" trick. It is well worth trying to study the potential of gallium-mediated hydrogel for treating infected wounds. Herein, on the basis of a conventional gelation strategy of sodium alginate combined with metal ions, Ga³⁺ has been innovatively given a dual role in a dual-cross-linked hydrogel. It acts nor only as a cross-linking agent to form a hydrogel material but also as a therapeutic agent to slow-release and continuously treat infected wounds. Further photo-cross-linking is introduced to improve the mechanical properties of the hydrogel. Thus, a new gallium ionic- and photo-dual-cross-linked alginate hydrogel, with broad-spectrum antimicrobial activity and strengthened mechanical performance, for the treatment of infected wounds is reported. The morphology, degradability, swelling behavior, rheological properties, and gallium release kinetics together indicated the homogeneous and the strengthened mechanical performance of this hydrogel but did not impede the release of gallium ions. Interestingly, in vitro and in vivo results also demonstrated its favorable biocompatibility, reduced bacterial growth, and accelerated infected wound healing, making the gallium-incorporated hydrogel an ideal antimicrobial dressing.

Multicomponent Peptide Hydrogels as an Innovative Platform for Cell-Based Tissue Engineering in the Dental Pulp

In light of the increasing levels of antibiotic resistance, nanomaterials and novel biologics are urgently required to manage bacterial infections. To date, commercially available self-assembling peptide hydrogels have not been studied extensively for their ability to inhibit micro-organisms relevant to tissue engineering sites such as dental root canals. In this work, we assess the biocompatibility of dental pulp stem/stromal cells with commercially available multicomponent peptide hydrogels. We also determine the effects of dental pulp stem/stromal cell (DPSC) culture in hydrogels on growth factor/cytokine expression. Furthermore, to investigate novel aspects of self-assembling peptide hydrogels, we determine their antimicrobial activity against the oral pathogens Staphylococcus aureus, Enterococcus faecalis, and Fusobacterium nucleatum. We show that self-assembling peptide hydrogels and hydrogels functionalized with the adhesion motif Arg-Gly-Asp (RGD) are biocompatible with DPSCs, and that cells grown in 3D hydrogel cultures produce a discrete secretome compared with 2D-cultured cells. Furthermore, we show that soluble peptides and assembled hydrogels have antimicrobial effects against oral pathogens. Given their antibacterial activity against oral pathogens, biocompatibility with dental pulp stem/stromal cells and enhancement of an angiogenic secretome, multicomponent peptide hydrogels hold promise for translational use.

Scale-adaptive Deep Model for Bacterial Raman Spectra Identification

The combination of Raman spectroscopy and deep learning technology provides an automatic, rapid, and accurate scheme for the clinical diagnosis of pathogenic bacteria. However, the accuracy of existing deep learning methods is still limited because of the single and fixed scales of deep neural networks. We propose a deep neural network that can learn multi-scale features of Raman spectra by using the automatic combination of multi-receptive fields of convolutional layers. This model is based on the expert knowledge that the discrimination information of Raman spectra is composed of multi-scale spectral peaks. We enhance the interpretability of the model by visualizing the activated wavenumbers of the bacterial spectrum that can be used for reference in related work. Compared with existing state-of-the-art methods, the proposed method achieves higher accuracy and efficiency for bacterial identification on isolate-level, empiric-treatment-level, and antibiotic-resistance-level tasks. The clinical bacterial identification task requires significantly fewer patient samples to achieve similar accuracy. Therefore, this method has tremendous potential for the identification of clinical pathogenic bacteria, antibiotic susceptibility testing, and prescription guidance.

A Cell Membrane Fluorogenic Probe for Gram-Positive Bacteria Imaging and Real-Time Tracking of Bacterial Viability

Bacterial infections are a global healthcare problem, resulting in serious clinical morbidities and mortality. Real-time monitoring of live bacteria by fluorescent imaging technology has potential in diagnosis of bacterial infections, elucidating antimicrobial agents' mode of action, assessing drug toxicity, and examining bacterial antimicrobial resistance. In this work, a naphthalimide-derived fluorescent probe ZTRS-BP was developed for wash-free Gram-positive bacteria imaging. The probe aggregated in aqueous solutions and exhibited aggregation-caused fluorescence quenching (ACQ). The interaction with Gram-positive bacteria cell walls would selectively disaggregate the probe and the liberated probes were dispersed on the outside of the bacteria cell walls to achieve surface fluorescence imaging. There were no such interactions with Gram-negative bacteria, which indicates that selective binding and imaging of Gram-positive bacteria was achieved. The binding of zinc ions by ZTRS-BP can enhance the fluorescent signals on the bacterial surface by inhibiting the process of photoinduced electron transfer. ZTRS-BP-Zn(II) complex was an excellent dye to discriminate mixed Gram-positive and Gram-negative bacteria. Also, live and dead bacteria can be differentially imaged by ZTRS-BP-Zn(II). Furthermore, ZTRS-BP-Zn(II) was used for real-time monitoring bacteria viability such as B. cereus treated with antibiotic vancomycin.

Fluorescence Spectroscopy and Chemometrics: A Simple and Easy Way for the Monitoring of Fluoroquinolone Mixture Degradation

In this work, fluorescence excitation-emission matrices (EEMs), in combination with the chemometric tool and parallel factor analysis (PARAFAC), have been proposed as an unexplored methodology to follow the removal of the fluorescent contaminants of emerging concern, fluoroquinolones (FQs). Ofloxacin, enrofloxacin, and sarafloxacin were degraded by different advanced oxidation processes employing simulated sunlight (hν): photolysis, H₂O₂/hν, and photo-Fenton. All experiments were performed in ultrapure water at three different pH values: 2.8, 5.0, and 7.0. With the obvious advantage of multivariate analysis methods, EEM-PARAFAC allowed the monitoring of degradation from the overall substances (original and formed ones) through simultaneous, rapid, and cost-efficient fluorescence spectroscopy determinations. A five-component model was found to best fit the experimental data, allowing us to (i) describe the decay of the fluorescence signals of the three parent pollutants, (ii) follow the kinetics profile of FQ-like byproducts with similar EEM fingerprints than the original FQs, and (iii) observe the formation of two families of reaction intermediates with completely different EEMs. Results were finally correlated with high pressure liquid chromatography, total organic carbon, and toxicity tests on Escherichia coli, showing good agreement with all the studied techniques.

Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O-Acetylserine Sulfhydrylase as a Colistin Adjuvant

Antibacterial adjuvants are of great significance, since they allow the therapeutic dose of conventional antibiotics to be lowered and reduce the insurgence of antibiotic resistance. Herein, we report that an O-acetylserine sulfhydrylase (OASS) inhibitor can be used as a colistin adjuvant to treat infections caused by Gram-positive and Gram-negative pathogens. A compound that binds OASS with a nM dissociation constant was tested as an adjuvant of colistin against six critical pathogens responsible for infections spreading worldwide, Escherichia coli, Salmonella enterica serovar Typhimurium, Klebisiella pneumoniae, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Staphylococcus pseudintermedius. The compound showed promising synergistic or additive activities against all of them. Knockout experiments confirmed the intracellular target engagement supporting the proposed mechanism of action. Moreover, compound toxicity was evaluated by means of its hemolytic activity against sheep defibrinated blood cells, showing a good safety profile. The 3D structure of the compound in complex with OASS was determined at 1.2 Å resolution by macromolecular crystallography, providing for the first time structural insights about the nature of the interaction between the enzyme and this class of competitive inhibitors. Our results provide a robust proof of principle supporting OASS as a potential nonessential antibacterial target to develop a new class of adjuvants and the structural basis for further structure-activity relationship studies.

Synthesis and evaluation of the antibiotic-adjuvant activity of carbohydrate-based phosphoramidate derivatives

Phosphoramidates are becoming increasingly recognized as molecular targets for therapeutic development. Their biological functions are significantly influenced by their inherent properties such as reactivity, as well as the P-N backbone which allows for structural diversity. In this study we report the synthesis of novel carbohydrate-based phosphoramidate derivatives via the Staudinger-phosphite reaction; along with an evaluation of their adjuvant activity in combination with popular antibiotics. Our targets involved variation in both the sugar residue as well as the identity of the phosphoramidate. Moderate to excellent yields of these derivatives were obtained. Notable adjuvant activity was observed with the halogenated phosphoramidates. For the fluorinated glucose derivative in particular, a remarkable 32-fold decrease in the MIC of Ampicillin was obtained against Methicillin-resistant S. aureus.

Research on the Impact and Mechanism for the Inhibition of Micrococcus Catalase Activity by Typical Tetracyclines

As potential inhibitors target to biological enzymes, antibiotics may have certain impacts on the biochemical treatment process. With micrococcus catalase (CAT) served as the target molecule, the impact and inhibition mechanism for typical tetracyclines (TCs) were evaluated. Toxicity experiments showed that TCs had significant inhibition on CAT in the sequence of tetracycline>chlortetracycline>oxytetracycline>doxycycline. To clarify the inhibition mechanism between TCs and CAT which was explored with the assistance of fluorescence spectroscopy and MOE molecule simulation. According to fluorescence analysis, TCs quenched the fluorescence signal of CAT by the mode of static quenching. Combined with toxicity data, it could be presumed that TCs combined with the catalytic active center and thus inhibited CAT. Above presumption was further verified by the molecular simulation data. When TCs combined with the catalytic center of CAT, the compounds have increased combination areas and prominent energy change (compared with the compounds formed by TCs and noncatalytic center recommend by MOE software). IBM SPSS statistics showed that TC toxicity positively correlated with the hydrogen bonds such as O¹³→Glu₂₅₂, O¹←Arg₁₉₅, and O⁶→Asp₂₄₉, but negatively correlated with the hydrogen bonds such as O¹⁰→Pro₃₆₃, O¹⁰→Lys₄₅₅, and O¹² → Asn₁₂₇. TC toxicity also positively correlated with the ion bonds ofN⁴-Glu₂₅₂, but negatively correlated with the ion bonds of N⁴-Asp₃₇₉. Hydrogen bonds and ion bonds for above key sites were closely related to the inhibition effect of TCs on CAT.

Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria.

Pleiotropic Effects of Bacterial Small Alarmone Synthetases: Underscoring the Dual-Domain Small Alarmone Synthetases in Mycobacterium smegmatis

The nucleotide alarmone (p)ppGpp, signaling the stringent response, is known for more than 5 decades. The cellular turnover of the alarmone is regulated by RelA/SpoT homolog (RSH) superfamily of enzymes. There are long RSHs (RelA, SpoT, and Rel) and short RSHs [small alarmone synthetases (SAS) and small alarmone hydrolases (SAH)]. Long RSHs are multidomain proteins with (p)ppGpp synthesis, hydrolysis, and regulatory functions. Short RSHs are single-domain proteins with a single (p)ppGpp synthesis/hydrolysis function with few exceptions having two domains. Mycobacterial RelZ is a dual-domain SAS with RNase HII and the (p)ppGpp synthetase activity. SAS is known to impact multiple cellular functions independently and in accordance with the long RSH. Few SAS in bacteria including RelZ synthesize pGpp, the third small alarmone, along with the conventional (p)ppGpp. SAS can act as an RNA-binding protein for the negative allosteric inhibition of (p)ppGpp synthesis. Here, we initially recap the important features and molecular functions of different SAS that are previously characterized to understand the obligation for the “alarmone pool” produced by the long and short RSHs. Then, we focus on the RelZ, especially the combined functions of RNase HII and (p)ppGpp synthesis from a single polypeptide to connect with the recent findings of SAS as an RNA-binding protein. Finally, we conclude with the possibilities of using single-stranded RNA (ssRNA) as an additional therapeutic strategy to combat the persistent infections by inhibiting the redundant (p)ppGpp synthetases.

Tackling Multidrug Resistance in Streptococci - From Novel Biotherapeutic Strategies to Nanomedicines

The pyogenic streptococci group includes pathogenic species for humans and other animals and has been associated with enduring morbidity and high mortality. The main reason for the treatment failure of streptococcal infections is the increased resistance to antibiotics. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been raising with a significant impact to public health and veterinary industry. The rise of antibiotic-resistant streptococci has been associated to diverse mechanisms, such as efflux pumps and modifications of the antimicrobial target. Among streptococci, antibiotic resistance emerges from previously sensitive populations as result of horizontal gene transfer or chromosomal point mutations due to excessive use of antimicrobials. Streptococci strains are also recognized as biofilm producers. The increased resistance of biofilms to antibiotics among streptococci promote persistent infection, which comprise circa 80% of microbial infections in humans. Therefore, to overcome drug resistance, new strategies, including new antibacterial and antibiofilm agents, have been studied. Interestingly, the use of systems based on nanoparticles have been applied to tackle infection and reduce the emergence of drug resistance. Herein, we present a synopsis of mechanisms associated to drug resistance in (pyogenic) streptococci and discuss some innovative strategies as alternative to conventional antibiotics, such as bacteriocins, bacteriophage, and phage lysins, and metal nanoparticles. We shall provide focused discussion on the advantages and limitations of agents considering application, efficacy and safety in the context of impact to the host and evolution of bacterial resistance.

Magnetotactic T-Budbots to Kill-n-Clean Biofilms

Treatment of persistent biofilm infections has turned out to be a formidable challenge even with broad-spectrum antibiotic therapies. In this direction, intelligent micromachines may serve as active mechanical means to dislodge such deleterious bacterial communities. Herein, we have designed biocompatible micromotors from tea buds, namely, T-Budbots, which shows the capacity to be magnetically driven on a biofilm matrix and remove or fragment biofilms with precision, as a part of the proposed non-invasive "Kill-n-Clean" strategy. In a way, we present a bactericidal robotic platform decorated with magnetite nanoparticles aimed at clearing in vitro biofilms present on the surfaces. We have also shown that the smart porous T-Budbots can integrate antibiotic ciprofloxacin due to electrostatic interaction on their surface to increase their antibacterial efficacy against dreadful pathogenic bacterial communities of Pseudomonas aeruginosa and Staphylococcus aureus. It is noteworthy that the release of this drug can be controlled by tuning the surrounding pH of the T-Budbots. For example, while the acidic environment of the biofilm facilitates the release of antibiotics from the porous T-Budbots, the drug release was rather minimal at higher pH. The work represents a first step in the involvement of a plant-based microbot exhibiting magneto-robotic therapeutic properties, providing a non-invasive and safe approach to dismantle harmful biofilm infections.

Antimicrobial resistance three ways: healthcare crisis, major concepts and the relevance of biofilms

Worldwide, infections are resuming their role as highly effective killing diseases, as current treatments are failing to respond to the growing problem of antimicrobial resistance (AMR). The social and economic burden of AMR seems ever rising, with health- and research-related organizations rushing to collaborate on a worldwide scale to find effective solutions. Resistant bacteria are spreading even in first-world nations, being found not only in healthcare-related settings, but also in food and in the environment. In this minireview, the impact of AMR in healthcare systems and the major bacteria behind it are highlighted. Ecological aspects of AMR evolution and the complexity of its molecular mechanisms are explained. Major concepts, such as intrinsic, acquired and adaptive resistance, as well as tolerance and heteroresistance, are also clarified. More importantly, the problematic of biofilms and their role in AMR, namely their main resistance and tolerance mechanisms, are elucidated. Finally, some of the most promising anti-biofilm strategies being investigated are reviewed. Much is still to be done regarding the study of AMR and the discovery of new anti-biofilm strategies. Gladly, considerable research on this topic is generated every day and increasingly concerted actions are being engaged globally to try and tackle this problem.

Prevalence and distribution analysis of antibiotic resistance genes in a large-scale aquaculture environment

This study examined the profiles of antibiotic resistance genes (ARGs) in water and sediments from one large-scale freshwater pond farming system. A qPCR array was used to quantify ARGs (16S, Tetx, Tetw, TetG, Intll, and Sull) and microbial community structure was analyzed by 16S rRNA gene sequencing. A large number of ARGs (2 8 8) were detected. The ARG richness of the sediments was significantly higher than that of water and an average of 15 more genes were detected (p < 0.01). Sediment samples showed significantly higher taxonomic diversity and higher abundance of Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. A significant correlation was observed between antibiotic resistance genes and breeding periods. The taxonomic diversity of the samples in ponds was significantly higher than that in ditch samples (p < 0.05), suggesting that pond farming systems could act as a local reservoir to spread ARGs into aquatic environments of rural communities.

Interplay between Supramolecular and Coordination Interactions in Synthetic Amphiphiles: Triggering Metal Starvation and Anchorage onto MRSA Cell Surface

The present work highlights the implications of supramolecular interaction and metal coordination on the self-assembly behavior and bactericidal potential of salicaldehyde-(C1) and napthaldehyde-based (C2) amphiphiles against methicillin-resistant Staphylococcus aureus (MRSA). LB trough and atomic force microscope (AFM) analysis indicated the propensity of the amphiphiles to form a monolayer as well as spherical aggregates, with the critical micelle concentration (CMC) for C2 (7.0 μM) being lower than C1 (18.5 μM) in water. Formation of an amphiphile-metal complex was evidenced by ESI-MS, FTIR, FETEM-EDX, and ITC analysis. Growth of S. aureus MRSA 100 cells was remarkably impaired in the presence of 5.0 μM C1 or 20 μM C2 as compared to free cells or cells grown in the presence of equivalent levels of amphiphile-metal complexes, suggesting that the amphiphiles perhaps sequester metal and induce metal starvation in MRSA. C1 and C2 rendered superior membrane damage in MRSA and were less toxic to human embryonic kidney (HEK 293) cells as compared to their metal complexes. C1 and C2 rendered a dose-dependent inhibition of S. aureus biofilm formation, while revival of biofilm upon Zn(II) addition suggested that zinc starvation rendered by the amphiphiles may induce biofilm inhibition. C1 imposed a concentration-dependent metal starvation response in MRSA as there was an upregulation of the cntL gene and downregulation of cntA gene, which are involved in synthesis of the zincophore staphylopine (Stp) and transport of the Stp-Zn complex, respectively. ITC analysis revealed that binding of C1 and C2 to staphylococcal lipoteichoic acid (LTA) was stronger than the corresponding Zn(II) complexes, which perhaps accounted for the higher bactericidal potency of the amphiphiles. The study provides a fundamental understanding on how the chemistry-driven multimodal interaction of the amphiphile translates into growth inhibition and metal starvation in MRSA and advances the idea of combating drug resistance in pathogenic bacteria through amphiphiles, which are pluri-active.

Clinical Mutations That Partially Activate the Stringent Response Confer Multidrug Tolerance in Staphylococcus aureus

Antibiotic tolerance is an underappreciated antibiotic escape strategy that is associated with recurrent and relapsing infections, as well as acting as a precursor to resistance. Tolerance describes the ability of a bacterial population to survive transient exposure to an otherwise lethal concentration of antibiotic without exhibiting an elevated MIC. It is detected in time-kill assays as a lower rate of killing than a susceptible strain and can be quantified by the metric minimum duration for killing (MDK). The molecular mechanisms behind tolerance are varied, but activation of the stringent response (SR) via gene knockouts and/or chemical induction has long been associated with tolerance. More recently, two Gram-positive clinical isolates from persistent bacteremias were found to bear mutations in the SR controller, Rel, that caused elevated levels of the alarmone (p)ppGpp. Here, we show that introduction of either of these mutations into Staphylococcus aureus confers tolerance to five different classes of antibiotic as a result of (p)ppGpp-mediated growth defects (longer lag time and/or lower growth rate). The degree of tolerance is related to the severity of the growth defect and ranges from a 1.5- to 3.1-fold increase in MDK. Two classes of proposed SR inhibitor were unable to reverse or reduce this tolerance. Our findings reveal the significance of SR-activating mutations in terms of tolerance and clinical treatment failures. The panel of strains reported here provide a clinically relevant model of tolerance for further investigation of its link to resistance development, as well as potential validation of high-throughput tolerance screens.

Design, characterization, and evaluation of antibacterial gels, Boc-D-Phe-γ4-L-Phe-PEA/chitosan and Boc-L-Phe-γ4-L-Phe-PEA/chitosan, for biomaterial-related infections

Self-assembled peptide gels have generated interest as antibacterial materials to prevent biomaterial-related infections but these peptides are often associated with poor proteolytic stability. Efforts have been made to stabilize peptides by incorporating non-natural amino acids and/or linkages but complexation with polymers have not been explored. Therefore, we developed self-assembled peptide/chitosan gels, Boc-D-Phe-γ⁴-L-Phe-PEA (NH007)/chitosan and Boc-L-Phe-γ⁴-L-Phe-PEA (NH009)/chitosan, by complexing dipeptide NH007 or NH009 with chitosan in DMSO:acetic acid. The gels were characterized using SEM, FTIR, contact angle, and rheology data and found to exhibit excellent viscoelastic and self-healing characteristics. Complexation with chitosan led to an increase in stability against proteolytic degradation. Peptide/chitosan gels showed broad spectrum antibacterial activities against Gram-negative and Gram-positive bacteria, such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis at a high inoculum of 10⁷-10⁸ cfu/mL. NH007/chitosan gels showed 70-75% inhibition, whereas NH009/chitosan showed 78-81% inhibition and NH009/chitosan gels, in particular, showed strong antibacterial activity against pathogenic strain of P. aeruginosa. A unique feature of these gels is that the antibacterial activities did not decrease gradually but were sustained for up to 48 h. The mechanistic studies using SEM and HR-TEM indicated interaction of gels with bacterial membrane components, leading to cell lysis. The MTT and LDH assays indicated >90% cell viability and only 8-10% toxicity towards NIH 3T3 fibroblast cells. Thus, peptide/chitosan gels developed in the present work showed improved proteolytic stability and sustained antibacterial activities and, therefore, may be used for preventing biomaterial-related infections.