Role of reactive oxygen species in antibiotic action and resistance

Antimicrobial Activity of Hydrogen Peroxide for Application in Food Safety and COVID-19 Mitigation: An Updated Review

Hydrogen peroxide (H2O2) is a well-known agent with a broad-spectrum antimicrobial activity against pathogenic bacteria, fungi, and viruses. It is a colorless liquid and commercially available in aqueous solution over a wide concentration range. It has been extensively used in the food industry by virtue of its strong oxidizing property and its ability to cause cellular oxidative damage in microbial cells. This review comprehensively documents recent research on the antimicrobial activity of H2O2 against organisms of concern for the food industry, as well as its effect against SARS-CoV-2 responsible for the COVID-19 pandemic. In addition, factors affecting the antimicrobial effectiveness of H2O2, different applications of H2O2 as a sanitizer or disinfectant in the food industry as well as safety concerns associated with H2O2 are discussed. Finally, recent efforts in enhancing the antimicrobial efficacy of H2O2 are also outlined.

Induction of ferroptosis: A new strategy for the control of bacterial infections

The continued rise of drug-resistant bacterial infections heightens a threat of a pandemic of antimicrobial resistance to the global health. The urgency of infection control against antimicrobial-resistant bacteria is evident. Ferroptosis, a newly defined form of iron-dependent cell death characterized by lipid peroxidation, has garnered substantial interest since this programmed cell death was associated with pathophysiological processes of many diseases. Exploring whether ferroptosis could be utilized in infectious diseases holds significant importance for discovering novel antimicrobial approaches. Recent years have witnessed significant progress with respect to elucidating the mechanisms that govern ferroptosis induction and its roles in bacterial pathogenesis and host-pathogen interactions. In this review, we discuss the mechanisms of targeting ferroptosis and/or iron homeostasis for the control of antimicrobial-resistant bacterial infections. These implications may inform and enable effective therapeutic strategies against pathogen infection and provide novel insights into the potential applications of ferroptosis to address the global bacterial resistance crisis.

Decoding Bacterial Persistence: Mechanisms and Strategies for Effective Eradication

The ability of pathogenic bacteria to evade antibiotic treatment is an intricate and multifaceted phenomenon. Over the years, treatment failure among patients due to determinants of antimicrobial resistance (AMR) has been the focal point for the research and development of new therapeutic agents. However, the survival of bacteria by persisting under antibiotic stress has largely been overlooked. Bacterial persisters are a subpopulation of sensitive bacterial cells exhibiting a noninheritable drug-tolerant phenotype. They are linked to the recalcitrance of infections in healthcare settings, in turn giving rise to AMR variants. The importance of bacterial persistence in recurring infections has been firmly recognized. Fundamental work over the past decade has highlighted numerous unique tolerance factors contributing to the persister phenotype in many clinically relevant pathogens. This review summarizes contributing factors that could aid in developing new strategies against bacterial antibiotic persisters.

Thymol Induces Fenton-Reaction-Dependent Ferroptosis in Vibrio parahemolyticus

Thymol has efficient bactericidal activity against a variety of pathogenic bacteria, but the bactericidal mechanism against Vibrio parahemolyticus (V. parahemolyticus) has rarely been reported. In the current study, we investigated the bactericidal mechanism of thymol against V. parahemolyticus. The Results revealed that 150 μg/mL of thymol had 99.9% bactericidal activity on V. parahemolyticus. Intracellular bursts of reactive oxygen species (ROS), Fe2+accumulation, lipid peroxidation, and DNA breakage were checked by cell staining. The exogenous addition of H2O2 and catalase promoted and alleviated thymol-induced cell death to a certain extent, respectively, and the addition of the ferroptosis inhibitor Liproxstatin-1 also alleviated thymol-induced cell death, confirming that thymol induced Fenton-reaction-dependent ferroptosis in V. parahemolyticus. Proteomic analysis revealed that relevant proteins involved in ROS production, lipid peroxidation accumulation, and DNA repair were significantly upregulated after thymol treatment. Molecular docking revealed two potential binding sites (amino acids 46H and 42F) between thymol and ferritin, and thymol could promote the release of Fe2+ from ferritin proteins through in vitro interactions analyzed. Therefore, we hypothesized that ferritin as a potential target may mediate thymol-induced ferroptosis in V. parahemolyticus. This study provides new ideas for the development of natural inhibitors for controlling V. parahemolyticus in aquatic products.

Transfer learning predicts species-specific drug interactions in emerging pathogens

Machine learning (ML) algorithms are necessary to efficiently identify potent drug combinations within a large candidate space to combat drug resistance. However, existing ML approaches cannot be applied to emerging and under-studied pathogens with limited training data. To address this, we developed a transfer learning and crowdsourcing framework (TACTIC) to train ML models on data from multiple bacteria. TACTIC was built using 2,965 drug interactions from 12 bacterial strains and outperformed traditional ML models in predicting drug interaction outcomes for species that lack training data. Top TACTIC model features revealed genetic and metabolic factors that influence cross-species and species-specific drug interaction outcomes. Upon analyzing ~600,000 predicted drug interactions across 9 metabolic environments and 18 bacterial strains, we identified a small set of drug interactions that are selectively synergistic against Gram-negative (e.g., A. baumannii) and non-tuberculous mycobacteria (NTM) pathogens. We experimentally validated synergistic drug combinations containing clarithromycin, ampicillin, and mecillinam against M. abscessus, an emerging pathogen with growing levels of antibiotic resistance. Lastly, we leveraged TACTIC to propose selectively synergistic drug combinations to treat bacterial eye infections (endophthalmitis).

Intraspecific variation in antibiotic resistance potential within E. coli

Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.

Lysis-Free Isolation and Direct Amplification of Pathogenic Bacterial DNA Using Diatom Frustules

DNA has been implicated as an important biomarker for the diagnosis of bacterial infections. Herein, we developed a streamlined methodology that uses diatom frustules (DFs) to liberate and capture bacterial DNA and allows direct downstream amplification tests without any lysis, washing, or elution steps. Unlike most conventional DNA isolation methods that rely on cell lysis to release bacterial DNA, DFs can trigger the oxidative stress response of bacterial cells to promote bacterial membrane vesicle formation and DNA release by generating reactive oxygen species in aqueous solutions. Due to the hierarchical porous structure, DFs provided high DNA capture efficiency exceeding 80% over a wide range of DNA amounts from 10 pg to 10 ng, making only 10 μg DFs sufficient for each test. Since laborious liquid handling steps are not required, the entire DNA sample preparation process using DFs can be completed within 3 min. The diagnostic use of this DF-based methodology was illustrated, which showed that the DNA of the pathogenic bacteria in serum samples was isolated by DFs and directly detected using polymerase chain reaction (PCR) at concentrations as low as 102 CFU/mL, outperforming the most used approaches based on solid-phase DNA extraction. Furthermore, most of the bacterial cells were still alive after DNA isolation using DFs, providing the possibility of recycling samples for storage and further diagnosis. The proposed DF-based methodology is anticipated to simplify bacterial infection diagnosis and be broadly applied to various medical diagnoses and biological research.

Iron efflux by IetA enhances β-lactam aztreonam resistance and is linked to oxidative stress through cellular respiration in Riemerella anatipestifer

BACKGROUND

Riemerella anatipestifer encodes an iron acquisition system, but whether it encodes the iron efflux pump and its role in antibiotic resistance are largely unknown.

OBJECTIVES

To screen and identify an iron efflux gene in R. anatipestifer and determine whether and how the iron efflux gene is involved in antibiotic resistance.

METHODS

In this study, gene knockout, streptonigrin susceptibility assay and inductively coupled plasma mass spectrometry were used to screen for the iron efflux gene ietA. The MIC measurements, scanning electron microscopy and reactive oxygen species (ROS) detection were used to verify the role of IetA in aztreonam resistance and its mechanism. Mortality and colonization assay were used to investigate the role of IetA in virulence.

RESULTS

The deletion mutant ΔietA showed heightened susceptibility to streptonigrin, and prominent intracellular iron accumulation was observed in ΔfurΔietA under excess iron conditions. Additionally, ΔietA exhibited increased sensitivity to H2O2-produced oxidative stress. Under aerobic conditions with abundant iron, ΔietA displayed increased susceptibility to the β-lactam antibiotic aztreonam due to heightened ROS production. However, the killing efficacy of aztreonam was diminished in both WT and ΔietA under anaerobic or iron restriction conditions. Further experiments demonstrated that the efficiency of aztreonam against ΔietA was dependent on respiratory complexes Ⅰ and Ⅱ. Finally, in a duckling model, ΔietA had reduced virulence compared with the WT.

CONCLUSION

Iron efflux is critical to alleviate oxidative stress damage and β-lactam aztreonam killing in R. anatipestifer, which is linked by cellular respiration.

Mechanisms of bacterial resistance to environmental silver and antimicrobial strategies for silver: A review

The good antimicrobial properties of silver make it widely used in food, medicine, and environmental applications. However, the release and accumulation of silver-based antimicrobial agents in the environment is increasing with the extensive use of silver-based antimicrobials, and the prevalence of silver-resistant bacteria is increasing. To prevent the emergence of superbugs, it is necessary to exercise rational and strict control over drug use. The mechanism of bacterial resistance to silver has not been fully elucidated, and this article provides a review of the progress of research on the mechanism of bacterial resistance to silver. The results indicate that bacterial resistance to silver can occur through inducing silver particles aggregation and Ag+ reduction, inhibiting silver contact with and entry into cells, efflux of silver particles and Ag+ in cells, and activation of damage repair mechanisms. We propose that the bacterial mechanism of silver resistance involves a combination of interrelated systems. Finally, we discuss how this information can be used to develop the next generation of silver-based antimicrobials and antimicrobial therapies. And some antimicrobial strategies are proposed such as the "Trojan Horse" - camouflage, using efflux pump inhibitors to reduce silver efflux, working with "minesweeper", immobilization of silver particles.

Role of RelA-synthesized (p)ppGpp and ROS-induced mutagenesis in de novo acquisition of antibiotic resistance in E. coli

The stringent response of bacteria to starvation and stress also fulfills a role in addressing the threat of antibiotics. Within this stringent response, (p)ppGpp, synthesized by RelA or SpoT, functions as a global alarmone. However, the effect of this (p)ppGpp on resistance development is poorly understood. Here, we show that knockout of relA or rpoS curtails resistance development against bactericidal antibiotics. The emergence of mutated genes associated with starvation and (p)ppGpp, among others, indicates the activation of stringent responses. The growth rate is decreased in ΔrelA-resistant strains due to the reduced ability to synthesize (p)ppGpp and the persistence of deacylated tRNA impeding protein synthesis. Sluggish cellular activity causes decreased production of reactive oxygen species (ROS), thereby reducing oxidative damage, leading to weakened DNA mismatch repair, potentially reducing the generation of mutations. These findings offer new targets for mitigating antibiotic resistance development, potentially achieved through inhibiting (p)ppGpp or ROS synthesis.

Effect of wheat crops on the persistence and attenuation of antibiotic resistance genes in soil after swine wastewater application

Swine wastewater (SW) application introduces antibiotic resistance genes (ARGs) into farmland soils. However, ARG attenuation in SW-fertigated soils, especially those influenced by staple crops and soil type, remains unclear. This study investigated twelve soil ARGs and one mobile genetic element (MGE) in sandy loam, loam, and silt loam soils before and after SW application in wheat-planted and unplanted soils. The results revealed an immediate increase in the abundance of ARGs in soil by two orders of magnitude above background levels following SW application. After SW application, the soil total ARG abundance was attenuated, reaching background levels at 54 days; However, more individual ARGs were detected above the detection limit than pre-application. Among the 13 genes, acc(6')-lb, tetM, and tetO tended to persist in the soil during wheat harvest. ARG half-lives were up to four times longer in wheat-planted soils than in bare soils. Wheat planting decreased the persistence of acc(6')-lb, ermB, ermF, and intI2 but increased the persistence of others such as sul1 and sul2. Soil type had no significant impact on ARG and MGE fates. Our findings emphasize the need for strategic SW application and the consideration of crop cultivation effects to mitigate ARG accumulation in farmland soils.

Antibiotic-induced ROS-mediated Fur allosterism contributes to Helicobacter pylori resistance by inhibiting arsR activation of mutS and mutY

The increasing antibiotic resistance of Helicobacter pylori primarily driven by genetic mutations poses a significant clinical challenge. Although previous research has suggested that antibiotics could induce genetic mutations in H. pylori, the molecular mechanisms regulating the antibiotic induction remain unclear. In this study, we applied various techniques (e.g., fluorescence microscopy, flow cytometry, and multifunctional microplate reader) to discover that three different types of antibiotics could induce the intracellular generation of reactive oxygen species (ROS) in H. pylori. It is well known that ROS, a critical factor contributing to bacterial drug resistance, not only induces damage to bacterial genomic DNA but also inhibits the expression of genes associated with DNA damage repair, thereby increasing the mutation rate of bacterial genes and leading to drug resistance. However, further research is needed to explore the molecular mechanisms underlying the ROS inhibition of the expression of DNA damage repair-related genes in H. pylori. In this work, we validated that ROS could trigger an allosteric change in the iron uptake regulatory protein Fur, causing its transition from apo-Fur to holo-Fur, repressing the expression of the regulatory protein ArsR, ultimately causing the down-regulation of key DNA damage repair genes (e.g., mutS and mutY); this cascade increased the genomic DNA mutation rate in H. pylori. This study unveils a novel mechanism of antibiotic-induced resistance in H. pylori, providing crucial insights for the prevention and control of antibiotic resistance in H. pylori.

Supernatant of platelet-Klebsiella pneumoniae coculture induces apoptosis-like death in Klebsiella pneumoniae

Multidrug-resistant Klebsiella pneumoniae strains, especially carbapenem-resistant K. pneumoniae, have become a rapidly emerging crisis worldwide, greatly limiting current therapeutic options and posing new challenges to infection management. Therefore, it is imperative to develop novel and effective biological agents for the treatment of multidrug-resistant K. pneumoniae infections. Platelets play an important role in the development of inflammation and immune responses. The main component responsible for platelet antibacterial activity lies in the supernatant stimulated by gram-positive bacteria. However, little research has been conducted on the interaction of gram-negative bacteria with platelets. Therefore, we aimed to explore the bacteriostatic effect of the supernatant derived from platelet-K. pneumoniae coculture and the mechanism underlying this effect to further assess the potential of platelet-bacterial coculture supernatant. We conducted this study on the gram-negative bacteria K. pneumoniae and CRKP and detected turbidity changes in K. pneumoniae and CRKP cultures when grown with platelet-K. pneumoniae coculture supernatant added to the culture medium. We found that platelet-K. pneumoniae coculture supernatant significantly inhibited the growth of K. pneumoniae and CRKP in vitro. Furthermore, transfusion of platelet-K. pneumoniae coculture supernatant alleviated the symptoms of K. pneumoniae and CRKP infection in a murine model. Additionally, we observed apoptosis-like changes, such as phosphatidylserine exposure, chromosome condensation, DNA fragmentation, and overproduction of reactive oxygen species in K. pneumoniae following treatment with the supernatant. Our study demonstrates that the platelet-K. pneumoniae coculture supernatant can inhibit K. pneumoniae growth by inducing an apoptosis-like death, which is important for the antibacterial strategies development in the future.IMPORTANCEWith the widespread use of antibiotics, bacterial resistance is increasing, and a variety of multi-drug resistant Gram-negative bacteria have emerged, which brings great challenges to the treatment of infections caused by Gram-negative bacteria. Therefore, finding new strategies to inhibit Gram-negative bacteria and even multi-drug- resistant Gram-negative bacteria is crucial for treating infections caused by Gram-negative bacteria, improving the abuse of antibiotics, and maintaining the balance between bacteria and antibiotics. K. pneumoniae is a common clinical pathogen, and drug-resistant CRKP is increasingly difficult to cure, which brings great clinical challenges. In this study, we found that the platelet-K. pneumoniae coculture supernatant can inhibit K. pneumoniae growth by inducing an apoptosis-like death. This finding has inspired the development of future antimicrobial strategies, which are expected to improve the clinical treatment of Gram-negative bacteria and control the development of multidrug-resistant strains.

Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions

Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.

Methods to improve antibacterial properties of PEEK: A review

As a thermoplastic and bioinert polymer, polyether ether ketone (PEEK) serves as spine implants, femoral stems, cranial implants, and joint arthroplasty implants due to its mechanical properties resembling the cortical bone, chemical stability, and radiolucency. Although there are standards and antibiotic treatments for infection control during and after surgery, the infection risk is lowered but can not be eliminated. The antibacterial properties of PEEK implants should be improved to provide better infection control. This review includes the strategies for enhancing the antibacterial properties of PEEK in four categories: immobilization of functional materials and functional groups, forming nanocomposites, changing surface topography, and coating with antibacterial material. The measuring methods of antibacterial properties of the current studies of PEEK are explained in detail under quantitative, qualitative, andin vivomethods. The mechanisms of bacterial inhibition by reactive oxygen species generation, contact killing, trap killing, and limited bacterial adhesion on hydrophobic surfaces are explained with corresponding antibacterial compounds or techniques. The prospective analysis of the current studies is done, and dual systems combining osteogenic and antibacterial agents immobilized on the surface of PEEK are found the promising solution for a better implant design.

The Effect of the Stringent Response and Oxidative Stress Response on Fitness Costs of De Novo Acquisition of Antibiotic Resistance

Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of wild-type strains and single-gene knockout strains in stress response pathways using four different antibiotics. Throughout resistance development, the increase in minimum inhibitory concentration (MIC) is accompanied by a gradual decrease in growth rate, most pronounced in amoxicillin or kanamycin. By measuring biomass yield on glucose and whole-genome sequences at intermediate and final time points, we identified two patterns of how the stress responses affect the correlation between MIC and growth rate. First, single-gene knockout E. coli strains associated with reactive oxygen species (ROS) acquire resistance faster, and mutations related to antibiotic permeability and pumping out occur earlier. This increases the metabolic burden of resistant bacteria. Second, the ΔrelA knockout strain, which has reduced (p)ppGpp synthesis, is restricted in its stringent response, leading to diminished growth rates. The ROS-related mutagenesis and the stringent response increase metabolic burdens during resistance development, causing lower growth rates and higher fitness costs.

Regulating bacterial biofilms in food and biomedicine: unraveling mechanisms and Innovating strategies

Bacterial biofilm has brought a lot of intractable problems in food and biomedicine areas. Conventional biofilm control mainly focuses on inactivation and removal of biofilm. However, with robust construction and enhanced resistance, the established biofilm is extremely difficult to eradicate. According to the mechanism of biofilm development, biofilm formation can be modulated by intervening in the key factors and regulatory systems. Therefore, regulation of biofilm formation has been proposed as an alternative way for effective biofilm control. This review aims to provide insights into the regulation of biofilm formation in food and biomedicine. The underlying mechanisms for early-stage biofilm establishment are summarized based on the key factors and correlated regulatory networks. Recent developments and applications of novel regulatory strategies such as anti/pro-biofilm agents, nanomaterials, functionalized surface materials and physical strategies are also discussed. The current review indicates that these innovative methods have contributed to effective biofilm control in a smart, safe and eco-friendly way. However, standard methodology for regulating biofilm formation in practical use is still missing. As biofilm formation in real-world systems could be far more complicated, further studies and interdisciplinary collaboration are still needed for simulation and experiments in the industry and other open systems.

Two-Pronged Dormant Photosensitizer-Antibiotic Bacterial Inactivation: Mechanism, Dosage, and Cellular Evolution Visualized at the Single-Cell Level

Innovative therapeutic approaches are required to battle the rise of antibiotic-resistant bacterial strains. Tapping on reactive oxygen species (ROS) generation in bacteria induced by bactericidal antibiotics, here we report a two-pronged strategy for bacterial inactivation relying on the synergistic combination of a bactericidal antibiotic and newly designed dormant photosensitizers (DoPSs) that activate in the presence of ROS. Intramolecular quenching renders DoPS inert in the presence of light. ROS trapping by DoPS aborts the quenching mechanism unmasking, in equal proportions, singlet oxygen (1O2) sensitization and fluorescence emission. Juxtaposed antioxidant-prooxidant activity built within our DoPS enables (i) initial activation of a few molecules by ROS and (ii) subsequent rapid activation of all DoPS in a bacterium via a domino effect mediated by photogenerated 1O2. Bulk colony forming unit studies employing the minimum inhibitory concentration of the antibiotic illustrate rapid and selective inactivation of Escherichia coli and Pseudomonas aeruginosa only in the presence of light, antibiotic, and DoPS. Single-cell, real-time imaging studies on E. coli reveal an autocatalytic progression of DoPS activation from focal points, providing a unique amplification system for sensing. Single-cell analysis further illustrates the impact of DoPS cellular loading on the rate of DoPS activation and cell death times and on the 1O2 dosing necessary for cell death to occur. Our two-pronged therapy discriminates based on cell metabolites and has the potential to result in lower toxicity, pave the way to reduced drug resistance, and provide insightful mechanistic information about bacterial membrane response to 1O2.

A high-throughput and low-waste viability assay for microbes

Counting viable cells is a universal practice in microbiology. The colony-forming unit (CFU) assay has remained the gold standard to measure viability across disciplines, but it is time-intensive and resource-consuming. Here we describe the geometric viability assay (GVA) that replicates CFU measurements over 6 orders of magnitude while reducing over 10-fold the time and consumables required. GVA computes a sample's viable cell count on the basis of the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with Gram-positive and Gram-negative planktonic bacteria (Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis), biofilms and fungi (Saccharomyces cerevisiae). Laborious CFU experiments such as checkerboard assays, treatment time-courses and drug screens against slow-growing cells are simplified by GVA. The ease and low cost of GVA evinces that it can replace existing viability assays and enable viability measurements at previously impractical scales.

Escherichia coli K-12 Transcriptomics for Assessing the Mechanism of Action of High-Power Ultrasound

An investigation into the mechanisms of action on bacteria involving exposure to stress factors was conducted in this study. The effects of ultrasound on Escherichia coli K-12 MG1655 and its isogenic mutant, ∆gadW, under high power ultrasound treatments (26 kHz) were screened and identified by analysing their transcriptome differences between primary and secondary sequential treatments using RNA-Seq. This also helped to assess any developed protection for cells between different generations. According to our results, 1825 genes of all tested conditions were expressed, playing different roles in the cell. The expression of these genes is associated with DNA damage, cell membrane integrity, and also metabolic effects. The studied strains also showed different differential expressed genes (DEGs), with some genes being directly responsible for defence mechanisms, while others play an indirect effect due to cell damage. A gradual decrease in the expression of the genes, as we moved from just one cycle of ultrasound treatment to sequential treatment, was evident from a heat map analysis of the results. Overall, E. coli K-12 builds a self-protection mechanism by increasing the expression of genes involved in the respiration for increased growth, and production of flagellum and pili. It can be concluded that high power ultrasound is a technology that triggers several different defence mechanisms which directly link to E. coli.

Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E. coli

Antibiotic-resistant bacteria severely threaten human health. Besides spontaneous mutations generated by endogenous factors, the resistance might also originate from mutations induced by certain antibiotics, such as the fluoroquinolones. Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems. However, the relative contributions of these molecular mechanisms remain unclear, hindering understanding of the generation of resistant pathogens. Here, using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains, as well as those of the strains deficient for the mismatch repair (MMR) and the oxidative damage repair pathways, we find that the SOS response is the major mutagenesis contributor in mutation elevation, responsible for ~ 30-50% of the total base-pair substitution (BPS) mutation-rate elevation upon treatment with sublethal levels of norfloxacin (0 ~ 50 ng/mL). We further estimate the significance of the effects on other mutational features of these mechanisms (i.e., transversions, structural variations, and mutation spectrum) in E. coli using linear models. The SOS response plays a positive role in all three mutational features (mutation rates of BPSs, transversions, structural variations) and affects the mutational spectrum. The repair systems significantly reduce the BPS mutation rate and the transversion rate, regardless of whether antibiotics are present, while significantly increasing the structural variation rate in E. coli. Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00185-y.

Implication of Mn-cofactored superoxide dismutase in the tolerance of swarmer Pseudomonas aeruginosa to polymixin, ciprofloxacin and meropenem antibiotics

The protective role of superoxide dismutase (Sod) against oxidative stress, resulting from the common antibiotic pathway of action, has been studied in the wild type and mutant strains of swarmer Pseudomonas aeruginosa, lacking Cytosolic Mn-Sod (sodM), Fe-Sod (sodB) or both Sods (sodMB).Our results showed that inactivation of sodB genes leads to significant motility defects and tolerance to meropenem. This resistance is correlated with a greater membrane unsaturation as well as an effective intervention of Mn-Sod isoform, in antibiotic tolerance.Moreover, loss of Mn-Sod in sodM mutant, leads to polymixin intolerance and is correlated with membrane unsaturation. Effectivelty, sodM mutant showed an enhanced swarming motility and a conserved rhamnolipid production. Whereas, in the double mutant sodMB, ciprofloxacin tolerance would be linked to an increase in the percentage of saturated fatty acids in the membrane, even in the absence of superoxide dismutase activity.The overall results showed that Mn-Sod has a protective role in the tolerance to antibiotics, in swarmer P.aeruginosa strain. It has been further shown that Sod intervention in antibiotic tolerance is through change in membrane fatty acid composition.

Activation of multiple stress responses in Staphylococcus aureus substantially lowers the minimal inhibitory concentration when combining two novel antibiotic drug candidates

The past few decades have been plagued by an increasing number of infections caused by antibiotic resistant bacteria. To mitigate the rise in untreatable infections, we need new antibiotics with novel targets and drug combinations that reduce resistance development. The novel β-clamp targeting antimicrobial peptide BTP-001 was recently shown to have a strong additive effect in combination with the halogenated pyrrolopyrimidine JK-274. In this study, the molecular basis for this effect was examined by a comprehensive proteomic and metabolomic study of the individual and combined effects on Staphylococcus aureus. We found that JK-274 reduced activation of several TCA cycle enzymes, likely via increasing the cellular nitric oxide stress, and BTP-001 induced oxidative stress in addition to inhibiting replication, translation, and DNA repair processes. Analysis indicated that several proteins linked to stress were only activated in the combination and not in the single treatments. These results suggest that the strong additive effect is due to the activation of multiple stress responses that can only be triggered by the combined effect of the individual mechanisms. Importantly, the combination dose required to eradicate S. aureus was well tolerated and did not affect cell viability of immortalized human keratinocyte cells, suggesting a species-specific response. Our findings demonstrate the potential of JK-274 and BTP-001 as antibiotic drug candidates and warrant further studies.

Returning to Nature for the Next Generation of Antimicrobial Therapeutics

Antibiotics found in and inspired by nature are life-saving cures for bacterial infections and have enabled modern medicine. However, the rise in resistance necessitates the discovery and development of novel antibiotics and alternative treatment strategies to prevent the return to a pre-antibiotic era. Once again, nature can serve as a source for new therapies in the form of natural product antibiotics and microbiota-based therapies. Screening of soil bacteria, particularly actinomycetes, identified most of the antibiotics used in the clinic today, but the rediscovery of existing molecules prompted a shift away from natural product discovery. Next-generation sequencing technologies and bioinformatics advances have revealed the untapped metabolic potential harbored within the genomes of environmental microbes. In this review, we first highlight current strategies for mining this untapped chemical space, including approaches to activate silent biosynthetic gene clusters and in situ culturing methods. Next, we describe how using live microbes in microbiota-based therapies can simultaneously leverage many of the diverse antimicrobial mechanisms found in nature to treat disease and the impressive efficacy of fecal microbiome transplantation and bacterial consortia on infection. Nature-provided antibiotics are some of the most important drugs in human history, and new technologies and approaches show that nature will continue to offer valuable inspiration for the next generation of antibacterial therapeutics.

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis

Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N²-methyladenosine (m²A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.

Fighting bacterial pathogens with carbon nanotubes: focused review of recent progress

The fast and global spread of bacterial resistance to currently available antibiotics results in a great and urgent need for alternative antibacterial agents and therapeutic strategies. Recent studies on the application of nanomaterials as antimicrobial agents have demonstrated their potential for the management of infectious diseases. Among the diverse palette of nanomaterials currently used in biomedical applications, carbon nanotubes (CNTs) have gained massive interest given their many valuable properties, such as high thermal and electrical conductivity, tensile strength, flexibility convenient aspect ratio, and low fabrication costs. All these features are augmented by facile conjugation with functional groups. CNTs are currently available in many configurations, with two main categories being single-walled and multi-walled CNTs, depending on the number of rolled-up single-layer carbon atoms sheets making up the nanostructure. Both classes have been identified over the past years as promising antibacterial agents but the current level of understanding of their efficiency still harbors many pending questions. This mini-review surveys recent progress on the topic of antibacterial effects of CNTs and examines the proposed mechanisms of action(s) of different CNT typologies, placing the main focus on past studies addressing the antibacterial activity on Staphylococcus aureus and Escherichia coli, two prototypical Gram-positive and Gram-negative pathogens, respectively.

Nonsteroidal anti-inflammatory drug diclofenac accelerates the emergence of antibiotic resistance via mutagenesis

Overuse of antimicrobial agents are generally considered to be a key factor in the occurrence of antibiotic resistance bacteria (ARB). Nevertheless, it is unclear whether ARB can be induced by non-antibiotic chemicals such as nonsteroidal anti-inflammatory drug (NSAID). Thus, the objective of this study is to investigate whether NSAID diclofenac (DCF) promote the emergence of antibiotic resistance in Escherichia coli K12 MG1655. Our results suggested that DCF induced the occurrence of ARB which showed hereditary stability of resistance. Meanwhile, gene variation was identified on chromosome of the ARB, and DCF can cause bacterial oxidative stress and SOS response. Subsequently, transcriptional levels of antioxidant (soxS, sodA, sodC, gor, katG, ahpF) and SOS (recA, lexA, uvrA, uvrB, ruvA, ruvB, dinB, umuC, polB) system-related genes were enhanced. However, the expression of related genes cannot be increased in high-dosage treatment compared with low-dosage samples because of cytotoxicity and cellular damage. Simultaneously, high-dosage DCF decreased the mutation frequency but enhanced the resistance of mutants. Our findings expand our knowledge of the promoting effect on the emergence of ARB caused by DCF. More attention and regulations should be given to these potential ecological and health risks for widespread DCF.

Metal-based nanomaterials as antimicrobial agents: A novel driveway to accelerate the aggravation of antibiotic resistance

The consequences of antibiotic tolerance directly affect human health and result in socioeconomic loss. Nanomaterials as antimicrobial agents are considered a promising alternative to antibiotics and have been blended with various medical applications. However, with increasing evidence that metal-based nanomaterials may induce antibiotic tolerance, there is an urgent need to scrutinize how nanomaterial-induced microbial adaption affects the evolution and spread of antibiotic tolerance. Accordingly, within this investigation, we summarized the principal factors influencing the resistance development exposed to metal-based nanomaterials, including physicochemical properties, exposure scenario, as well as bacterial response. Furthermore, the mechanisms of metal-based nanomaterial-induced antibiotic resistance development were comprehensively elucidated from acquired resistance by horizontal transfer of antibiotic resistance genes (ARGs), intrinsic resistance by genetic mutation or upregulated resistance-related gene expression, and adaptive resistance by global evolution. Overall, our review raises concerns about the safety of nanomaterials as antimicrobial agents, which will facilitate assistance in the safe development of antibiotic-free antibacterial strategies.

Bacterial metabolism and susceptibility to cell wall-active antibiotics

Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.

Enhanced alginate-like exopolymers recovery from algal-bacterial aerobic granular sludge: Optimal cultivation condition and contribution of bacteria and microalgae during the transport/storage period

Extracting alginate-like exopolymers (ALE) is a promising approach for valuable resources recovery from excess algal-bacterial aerobic granular sludge (AGS) to achieve circular bioeconomy and environmental sustainability in wastewater treatment plants (WWTPs). In this study, six batch cultivation tests were conducted to investigate the optimal cultivation duration or transport/storage period, light intensity, and temperature for algal-bacterial AGS after sampling and before further processing or ALE extraction. At a light intensity of 5 klux, the highest ALE content (36.33 mg/g-VSS) was detected at a low temperature of 10°C, which increased by 300% from its original level after 6-h cultivation. Results from levofloxacin (LVX) exposure and dark condition imply that microalgae contributed more to ALE synthesis in the algal-bacterial granules. This work not only provides a better understanding of the mechanisms involved in ALE biosynthesis but also offers useful guidance for maintaining or improving ALE recovery after algal-bacterial biomass sampling.

Vitamin K3 (Menadione) is a multifunctional microbicide acting as a photosensitizer and synergizing with blue light to kill drug-resistant bacteria in biofilms

Cutaneous bacterial wound infections typically involve gram-positive cocci such as Staphylococcus aureus (SA) and usually become biofilm infections. Bacteria in biofilms may be 100-1000-fold more resistant to an antibiotic than the clinical laboratory minimal inhibitory concentration (MIC) for that antibiotic, contributing to antimicrobial resistance (AMR). AMR is a growing global threat to humanity. One pathogen-antibiotic resistant combination, methicillin-resistant SA (MRSA) caused more deaths globally than any other such combination in a recent worldwide statistical review. Many wound infections are accessible to light. Antimicrobial phototherapy, and particularly antimicrobial blue light therapy (aBL) is an innovative non-antibiotic approach often overlooked as a possible alternative or adjunctive therapy to reduce antibiotic use. We therefore focused on aBL treatment of biofilm infections, especially MRSA, focusing on in vitro and ex vivo porcine skin models of bacterial biofilm infections. Since aBL is microbicidal through the generation of reactive oxygen species (ROS), we hypothesized that menadione (Vitamin K3), a multifunctional ROS generator, might enhance aBL. Our studies suggest that menadione can synergize with aBL to increase both ROS and microbicidal effects, acting as a photosensitizer as well as an ROS recycler in the treatment of biofilm infections. Vitamin K3/menadione has been given orally and intravenously worldwide to thousands of patients. We conclude that menadione/Vitamin K3 can be used as an adjunct to antimicrobial blue light therapy, increasing the effectiveness of this modality in the treatment of biofilm infections, thereby presenting a potential alternative to antibiotic therapy, to which biofilm infections are so resistant.

The oxidative nuclease activity of human cytochrome c with mutations in Ω-loop C/D

Natural and artificial nucleases have extensive applications in biotechnology and biomedicine. The exploration of protein with potential DNA cleavage activity also inspires the design of artificial nuclease and helps to understand the physiological process of DNA damage. In this study, we engineered four human cytochrome c (Cyt c) mutants (N52S, N52A, I81N, and I81D Cyt c), which showed enhanced DNA cleavage activity and degradation in comparison with WT Cyt c, especially under acidic conditions. The mechanism assays revealed that the superoxide (O₂^•-) plays an important role in the nuclease reaction. The kinetic assays showed that the peroxidase activity of the I81D Cyt c mutant enhanced up to 9-fold at pH 5. This study suggests that the mutations of Ile81 and Asn52 in Ω-loop C/D are critical for the nuclease activity of Cyt c, which may have physiological significance in DNA damage and potential applications in biomedicine.

Ultrasound-assisted blue light killing Vibrio parahaemolyticus to improve salmon preservation

Vibrio parahaemolyticus is a typical marine bacterium, which often contaminates seafood and poses a health risk to consumers. Some non-thermal sterilization technologies, such as ultrasonic field (UF) and blue light (BL) irradiation, have been widely used in clinical practice due to their efficiency, safety, and avoidance of drug resistance, but their application in food preservation has not been extensively studied. This study aims to investigate the effect of BL on V. parahaemolyticus in culture media and in ready-to-eat fresh salmon, and to evaluate the killing effectiveness of the UF combined with BL treatment on V. parahaemolyticus. The results showed that BL irradiation at 216 J/cm2 was effective in causing cell death (close to 100%), cell shrinkage and reactive oxygen species (ROS) burst in V. parahaemolyticus. Application of imidazole (IMZ), an inhibitor of ROS generation, attenuated the cell death induced by BL, indicating that ROS were involved in the bactericidal effects of BL on V. parahaemolyticus. Furthermore, UF for 15 min enhanced the bactericidal effect of BL at 216 J/cm2 on V. parahaemolyticus, with the bactericidal rate of 98.81%. In addition, BL sterilization did not affect the color and quality of salmon, and the additive UF treatment for 15 min did not significant impact on the color of salmon. These results suggest that BL or UF combined with BL treatment has potential for salmon preservation, however, it is crucial to strictly control the intensity of BL and the duration of UF treatment to prevent reducing the freshness and brightness of salmon.

Recent progress in the use of purple non-sulfur bacteria as probiotics in aquaculture

The use of probiotics in aquaculture is widely recognized as an ecological and cost-effective approach to raising healthy, pathogen-tolerant aquatic animals, including fish and shrimp. In particular for shrimp, probiotics are viewed as a promising countermeasure to the recent severe damage to the shrimp industry by bacterial and viral pathogens. Purple non-sulfur bacteria (PNSB) are Gram-negative, non-pathogenic bacteria with wide application potential in agriculture, wastewater treatment, and bioenergy/biomaterials production. In aquaculture, lactic bacteria and Bacillus are the major probiotic bacteria used, but PNSB, like Rhodopseudomonas and Rhodobacter, are also used. In this review, we summarize the previous work on the use of PNSB in aquaculture, overview the previous studies on the stimulation of innate immunity of shrimp by various probiotic microorganisms, and also share our results in the probiotic performance of Rhodovulum sulfidophilum KKMI01, a marine PNSB, which showed a superior effect in promotion of growth and stimulation of immunity in shrimp at a quite low concentration of 1 × 10³ cfu (colony forming unit)/ml in rearing water.

Fluoroquinolone Residues in the Environment Rapidly Induce Heritable Fluoroquinolone Resistance in Escherichia coli

Extensive antibiotic use increases the environmental presence of their residues and may accelerate the development of antibiotic resistance, although this remains poorly understood at environmentally relevant concentrations. Herein, susceptible Escherichia coli K12 was continuously exposed to five antibiotics at such concentrations for 100 days. The de novo-evolved mutants rapidly obtained fluoroquinolone resistance within 10 days, as indicated by the 4- and 16-fold augmentation of minimum inhibitory concentrations against enrofloxacin and ciprofloxacin, respectively. Moreover, the mutants maintained heritable fluoroquinolone resistance after the withdrawal of antibiotics for 30 days. Genomic analysis identified Asp87Gly or Ser83Leu substitutions in the gyrA gene in the mutants. Transcriptomics data showed that the transcriptional response of the mutants to fluoroquinolones was primarily involved in biofilm formation, cellular motility, porin, oxidative stress defense, and energy metabolism. Homologous recombination and molecular docking revealed that mutations of gyrA primarily mainly conferred fluoroquinolone resistance, while mutations at different positions of gyrA likely endowed different fluoroquinolone resistance levels. Collectively, this study revealed that environmentally relevant concentrations of antibiotics could rapidly induce heritable antibiotic resistance; therefore, the discharge of antibiotics into the environment should be rigorously controlled to prevent the development of antibiotic resistance.

Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review

The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.

Heat shock potentiates aminoglycosides against gram-negative bacteria by enhancing antibiotic uptake, protein aggregation, and ROS

The potentiation of antibiotics is a promising strategy for combatting antibiotic-resistant/tolerant bacteria. Herein, we report that a 5-min sublethal heat shock enhances the bactericidal actions of aminoglycoside antibiotics by six orders of magnitude against both exponential- and stationary-phase Escherichia coli. This combined treatment also effectively kills various E. coli persisters, E. coli clinical isolates, and numerous gram-negative but not gram-positive bacteria and enables aminoglycosides at 5% of minimum inhibitory concentrations to eradicate multidrug-resistant pathogens Acinetobacter baumannii and Klebsiella pneumoniae. Mechanistically, the potentiation is achieved comprehensively by heat shock-enhanced proton motive force that thus promotes the bacterial uptake of aminoglycosides, as well as by increasing irreversible protein aggregation and reactive oxygen species that further augment the downstream lethality of aminoglycosides. Consistently, protonophores, chemical chaperones, antioxidants, and anaerobic culturing abolish heat shock-enhanced aminoglycoside lethality. We also demonstrate as a proof of concept that infrared irradiation- or photothermal nanosphere-induced thermal treatments potentiate aminoglycoside killing of Pseudomonas aeruginosa in a mouse acute skin wound model. Our study advances the understanding of the mechanism of actions of aminoglycosides and demonstrates a high potential for thermal ablation in curing bacterial infections when combined with aminoglycosides.

An injectable multifunctional hydrogel for eradication of bacterial biofilms and wound healing

Wound treatment is largely influenced by pre-existing hypoxic microenvironments and biofilms, which can severely diminish the efficacy of phototherapy, suggesting the importance of multifunctional nanoplatforms for synergistic treatment of wound infections. Here, we developed a multifunctional injectable hydrogel (PSPG hydrogel) by loading photothermal sensitive sodium nitroprusside (SNP) into Pt-modified porphyrin metal organic framework (PCN) and in situ modification of gold particles to form a near-infrared (NIR) light-triggered all-in-one phototherapeutic nanoplatform. The Pt-modified nanoplatform exhibits a remarkable catalase-like behavior and promotes the continuous decomposition of endogenous H₂O₂ into O₂, thereby enhancing the photodynamic therapy (PDT) effect under hypoxia. Under dual NIR irradiation, PSPG hydrogel can not only produce hyperthermia (η=89.21%) but also generate reactive oxygen species and trigger NO release, contributing jointly to removal of biofilms and disruption of the cell membranes of methicillin-resistant Staphylococcus aureus (MRSA) and Escherichia coli (E. coli). In vivo experiments demonstrated a 99.9% reduction in bacterial burden on wounds. Additionally, PSPG hydrogel can accelerate MRSA-infected and Pseudomonas aeruginosa-infected (P. aeruginosa-infected) wound healing by promoting angiogenesis, collagen deposition, and suppressing inflammatory responses. Furthermore, in vitro and in vivo experiments revealed that PSPG hydrogel has good cytocompatibility. Overall, we proposed an antimicrobial strategy to eliminate bacteria through the synergistic effects of gas-photodynamic-photothermal killing, alleviating hypoxia in the bacterial infection microenvironment, and inhibiting biofilms, offering a new way against antimicrobial resistance and biofilm-associated infections. STATEMENT OF SIGNIFICANCE: The NIR light-triggered multifunctional injectable hydrogel nanoplatform (PSPG hydrogel) based on Pt-decorated gold nanoparticles with sodium nitroprusside (SNP)-loading porphyrin metal organic framework (PCN) as inner templates can efficiently perform photothermal conversion (η=89.21%) to trigger NO release from SNP, while continuously regulating the hypoxic microenvironment at the bacterial infection site through Pt-induced self-oxygenation, achieving efficient sterilization and removal of biofilm by synergistic PDT and PTT phototherapy. In vivo and in vitro experiments demonstrated that the PSPG hydrogel has significant anti-biofilm, antibacterial, and inflammatory regulatory functions. This study proposed an antimicrobial strategy to eliminate bacteria through the synergistic effects of gas-photodynamic-photothermal killing, alleviating hypoxia in the bacterial infection microenvironment, and inhibiting biofilms.

Revisiting Host-Pathogen Interactions in Cystic Fibrosis Lungs in the Era of CFTR Modulators

Cystic fibrosis transmembrane conductance regulator (CFTR) modulators, a new series of therapeutics that correct and potentiate some classes of mutations of the CFTR, have provided a great therapeutic advantage to people with cystic fibrosis (pwCF). The main hindrances of the present CFTR modulators are related to their limitations in reducing chronic lung bacterial infection and inflammation, the main causes of pulmonary tissue damage and progressive respiratory insufficiency, particularly in adults with CF. Here, the most debated issues of the pulmonary bacterial infection and inflammatory processes in pwCF are revisited. Special attention is given to the mechanisms favoring the bacterial infection of pwCF, the progressive adaptation of Pseudomonas aeruginosa and its interplay with Staphylococcus aureus, the cross-talk among bacteria, the bronchial epithelial cells and the phagocytes of the host immune defenses. The most recent findings of the effect of CFTR modulators on bacterial infection and the inflammatory process are also presented to provide critical hints towards the identification of relevant therapeutic targets to overcome the respiratory pathology of pwCF.

Re-sensitization of Multidrug-Resistant and Colistin-Resistant Gram-Negative Bacteria to Colistin by Povarov/Doebner-Derived Compounds

Colistin, typically viewed as the antibiotic of last resort to treat infections caused by multidrug-resistant (MDR) Gram-negative bacteria, had fallen out of favor due to toxicity issues. The recent increase in clinical usage of colistin has resulted in colistin-resistant isolates becoming more common. To counter this threat, we have investigated previously reported compounds, HSD07 and HSD17, and developed 13 compounds with more desirable drug-like properties for colistin sensitization against 16 colistin-resistant bacterial strains, three of which harbor the plasmid-borne mobile colistin resistance (mcr-1). Lead compound HSD1624, which has a lower LogDpH7.4 (2.46) compared to HSD07 (>5.58), reduces the minimum inhibitory concentration (MIC) of colistin against Pseudomonas aeruginosa strain TRPA161 to 0.03 μg/mL from 1024 μg/mL (34,000-fold reduction). Checkerboard assays revealed that HSD1624 and analogues are also synergistic with colistin against colistin-resistant strains of Escherichia coli, Acinetobacter baumannii, and Klebsiella pneumoniae. Preliminary mechanism of action studies indicate that HSD1624 exerts its action differently depending on the bacterial species. Time-kill studies suggested that HSD1624 in combination with 0.5 μg/mL colistin was bactericidal to extended-spectrum beta-lactamase (ESBL)-producing E. coli, as well as to E. coli harboring mcr-1, while against P. aeruginosa TRPA161, the combination was bacteriostatic. Mechanistically, HSD1624 increased membrane permeability in K. pneumoniae harboring a plasmid containing the mcr-1 gene but did not increase radical oxygen species (ROS), while a combination of 15 μM HSD1624 and 0.5 μg/mL colistin significantly increased ROS in P. aeruginosa TRPA161. HSD1624 was not toxic to mammalian red blood cells (up to 226 μM).

Antimycobacterial Compound of Cynoglossum lanceolatum Forsk.: Bioassay Guided Isolation, Molecular Docking, Synthesis of Analogs, and a Plausible Mechanism of Action

Tuberculosis (TB) remains a major threat to human health. Due to the prevalence of drug-resistant Mycobacterium tuberculosis (Mtb), it is urgent to discover drugs with new mechanisms of action (MOA) to ensure effectiveness against strains that are resistant to existing TB drugs. Cynoglossum lanceolatum Forsk was used to treat TB in Traditional Chinese Medicine. In this article, shikonin, the anti-Mtb active component, was obtained from the whole herb extract of C. lanceolatum by bioassay-guided isolation. Using the microplate alamar blue assay (MABA), the minimum inhibitory concentration (MIC) of shikonin against Mtb was determined to be 128 μg/mL. In order to obtain a more efficient anti-Mtb molecule, (E)-1-(6-bromo-2,3-dihydrochromen-4-ylidene)thiosemicarbazide was synthesized based on the scaffold of shikonin, which exhibited potent activity against Mtb (MIC=4 μg/mL). These results highlight that both naphthalene-1,4-dione and chroman-4-one are pharmacophores with activities against Mtb. To investigate a plausible mechanism of action, the molecular docking was firstly performed against catalase-peroxidase enzyme (KatG) of Mtb using AutoDock 4 software. The results demonstrated that both shikonin and (E)-1-(6-bromo-2,3-dihydrochromen-4-ylidene)thiosemicarbazide could bind to the active site of Mtb KatG. KatG enzyme activity and intracellular reactive oxygen species (ROS) levels in Mtb cells were then measured by ultraviolet spectrophotometric method and fluorescence microplate reader assay, respectively. The experiments confirmed that above compounds could inhibit the catalytic activity of Mtb KatG, and cause the ROS accumulation in Mtb cells. Therefore, inhibition of KatG may be a novel mechanism of action for these two compounds to fight against Mtb.

Antibacterial and antibiofilm mechanisms of carbon dots: a review

Due to the increasing bacterial resistance to conventional antibiotics, developing safe and effective approaches to combat infections caused by bacteria and biofilms has become an urgent clinical problem. Recently, carbon dots (CDs) have received great attention as a promising alternative to conventional antimicrobial agents due to their excellent antimicrobial efficacy and biocompatibility. Although CDs have been widely used in the field of antibacterial applications, their antibacterial and antibiofilm mechanisms have not been systematically discussed. This review provides a systematic overview on the complicated mechanisms of antibacterial and antibiofilm CDs based on recent development.

Enzymatic and proteomic exploration into the inhibitory activities of lemongrass and lemon essential oils against Botrytis cinerea (causative pathogen of gray mold)

Introduction

Essential oils (EOs) have been demonstrated as efficacious against B. cinerea. However, the underpinning enzymatic and proteomic mechanism for these inhibitory effects is not entirely clear.

Methods

Thus, this study examined the effects of lemon (Le) and lemongrass (Lg) EOs (individually and in combination) against B. cinerea based on enzymatic and proteomic analyses. Proteomics data are available via ProteomeXchange with identifier PXD038894.

Results and discussion

Both EOs (individually and in combination) displayed abilities to induce scavenging as observed with the reduction of H2O2. Measured malondialdehyde (MDA) and superoxide dismutase (SOD) activity were increased in all EOs treated B. cinerea mycelia compared to the control. Ascorbate peroxidase (APX) activity was highest in Lg treated B. cinerea (206% increase), followed by combined (Le + Lg) treatment with 73% compared to the untreated control. Based on GC-MS analysis, the number of volatile compounds identified in lemon and lemongrass EOs were 7 and 10, respectively. Major chemical constituent of lemon EO was d-limonene (71%), while lemongrass EO was a-citral (50.1%). Based on the interrogated LC-MS data, 42 distinct proteins were identified, and 13 of these proteins were unique with 1, 8, and 4 found in Le-, Lg-, and (Le + Lg) EOs treated B. cinerea, respectively, and none in control. Overall, 72% of identified proteins were localized within cellular anatomical entity, and 28% in protein-complexes. Proteins involved in translation initiation, antioxidant activity, protein macromolecule adaptor activity and microtubule motor activity were only identified in the Lg and (Le + Lg) EOs treated B. cinerea mycelia, which was consistent with their APX activities.

Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater

The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.

High Throughput Viability Assay for Microbiology

Counting viable cells is a universal practice in microbiology. The colony forming unit (CFU) assay has remained the gold standard to measure viability across disciplines; however, it is time-intensive and resource-consuming. Herein, we describe the Geometric Viability Assay (GVA) that replicates CFU measurements over 6-orders of magnitude while reducing over 10-fold the time and consumables. GVA computes a sample's viable cell count based on the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with gram-positive and -negative planktonic bacteria, biofilms, and yeast. Laborious CFU experiments such as checkerboard assays, treatment time-courses, and drug screens against slow-growing cells are simplified by GVA. We therefore screened a drug library against exponential and stationary phase E. coli leading to the discovery of the ROS-mediated, bactericidal mechanism of diphenyliodonium. The ease and low cost of GVA evinces it can accelerate existing viability assays and enable measurements at previously impractical scales.

Extracellular polymeric substances-antibiotics interaction in activated sludge: A review

Antibiotics, the most frequently prescribed drugs, have been widely applied to prevent or cure human and veterinary diseases and have undoubtedly led to massive releases into sewer networks and wastewater treatment systems, a hotspot where the occurrence and transformation of antibiotic resistance take place. Extracellular polymeric substances (EPS), biopolymers secreted via microbial activity, play an important role in cell adhesion, nutrient retention, and toxicity resistance. However, the potential roles of sludge EPS related to the resistance and removal of antibiotics are still unclear. This work summarizes the composition and physicochemical characteristics of state-of-the-art microbial EPS, highlights the critical role of EPS in antibiotics removal, evaluates their defense performances under different antibiotics exposures, and analyzes the typical factors that could affect the sorption and biotransformation behavior of antibiotics. Next, interactions between microbial EPS and antibiotic resistance genes are analyzed. Future perspectives, especially the engineering application of microbial EPS for antibiotics toxicity detection and defense, are also emphatically stressed.

Yeast Mannan-Rich Fraction Modulates Endogenous Reactive Oxygen Species Generation and Antibiotic Sensitivity in Resistant E. coli

Mannan-rich fraction (MRF) isolated from Saccharomyces cerevisiae has been studied for its beneficial impact on animal intestinal health. Herein, we examined how MRF affected the formation of reactive oxygen species (ROS), impacting antibiotic susceptibility in resistant Escherichia coli through the modulation of bacterial metabolism. The role of MRF in effecting proteomic change was examined using a proteomics-based approach. The results showed that MRF, when combined with bactericidal antibiotic treatment, increased ROS production in resistant E. coli by 59.29 ± 4.03% compared to the control (p ≤ 0.05). We further examined the effect of MRF alone and in combination with antibiotic treatment on E. coli growth and explored how MRF potentiates bacterial susceptibility to antibiotics via proteomic changes in key metabolic pathways. Herein we demonstrated that MRF supplementation in the growth media of ampicillin-resistant E. coli had a significant impact on the normal translational control of the central metabolic pathways, including those involved in the glycolysis-TCA cycle (p ≤ 0.05).

MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway

Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats. The role of the N-acyl homoserine lactone (AHL)-mediated signaling pathway, which is widespread in gram-negative bacteria, in the bacterial resistance process should be studied in depth. Here, we report a degrading enzyme of AHLs, MomL, that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism. The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response. The degradation of AHLs by MomL results in the inability of LasR to activate relA, which, in turn, stops the activation of downstream rpoS. Further results show that rpoS directly regulates the type VI secretion system H2-T6SS. Under MomL treatment, inactivated RpoS fails to regulate H2-T6SS; therefore, the expression of effector phospholipase A is reduced, and the adaptability of bacteria to antibiotics is weakened. MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria. Therefore, this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.

Loss of outer membrane protein A (OmpA) impairs the survival of Salmonella Typhimurium by inducing membrane damage in the presence of ceftazidime and meropenem

OBJECTIVES

Salmonella enterica serovar Typhimurium is one of the significant non-typhoidal Salmonella serovars that causes gastroenteritis. The rapid development of antimicrobial resistance necessitates studying new antimicrobials and their therapeutic targets in this pathogen. Our study aimed to investigate the role of four prominent outer membrane porins of S. Typhimurium, namely OmpA, OmpC, OmpD and OmpF, in developing resistance against ceftazidime and meropenem.

METHODS

The antibiotic-mediated inhibition of bacterial growth was determined by measuring the absorbance and the resazurin assay. DiBAC4 (Bis-(1,3-Dibutylbarbituric Acid)Trimethine Oxonol), 2,7-dichlorodihydrofluoroscein diacetate (DCFDA) and propidium iodide were used to determine the outer membrane depolarization, reactive oxygen species (ROS) generation and subsequent killing of Salmonella. The expression of oxidative stress-response and efflux pump genes was quantified by quantitative RT-qPCR. HPLC was done to determine the amount of antibiotics that entered the bacteria. The damage to the bacterial outer membrane was studied by confocal and atomic force microscopy. The in vivo efficacy of ceftazidime and meropenem were tested in the C57BL/6 mouse model.

RESULTS

Deleting ompA reduced the survival of Salmonella in the presence of ceftazidime and meropenem. Massive outer membrane depolarization and reduced expression of oxidative stress-response genes in S. Typhimurium ΔompA hampered its growth in the presence of antibiotics. The enhanced uptake of antibiotics and decreased expression of efflux pump genes in S. Typhimurium ΔompA resulted in damage to the bacterial outer membrane. The clearance of the S. Typhimurium ΔompA from C57BL/6 mice with ceftazidime treatment proved the role of OmpA in rendering protection against β-lactam antibiotics.

CONCLUSIONS

OmpA protects S. Typhimurium from two broad-spectrum β-lactam antibiotics, ceftazidime and meropenem, by maintaining the stability of the outer membrane.

The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain

CRISPR-associated Rossmann fold (CARF) domain signaling underpins modulation of CRISPR-Cas nucleases; however, the RtcR CARF domain controls expression of two conserved RNA repair enzymes, cyclase RtcA and ligase RtcB. Here, we demonstrate that RtcAB are required for RtcR-dependent transcription activation and directly bind to RtcR CARF. RtcAB catalytic activity is not required for complex formation with CARF, but is essential yet not sufficient for RtcRAB-dependent transcription activation, implying the need for an additional RNA repair-dependent activating signal. This signal differs from oligoadenylates, a known ligand of CARF domains, and instead appears to originate from the translation apparatus: RtcB repairs a tmRNA that rescues stalled ribosomes and increases translation elongation speed. Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mechanism to regulate RNA repair required for a functioning translation apparatus.