Nutrient stress is a target for new antibiotics

The nucleobase analog 4-thiouracil hijacks the pyrimidine salvage pathway to inhibit Staphylococcus aureus growth

Staphylococcus aureus is a leading cause of bacterial-induced mortality due to infections that are increasingly resistant to antibiotics, highlighting the need for new therapeutic strategies to treat these drug-resistant infections. Targeting essential pathways that differ from the host, such as cell wall synthesis, has served as an effective approach for antimicrobial drug development. Nucleotides are essential building blocks for nucleic acids and the bacterial cell wall, and we hypothesized that the metabolic pathways required to obtain these molecules may represent promising antimicrobial targets. To investigate if pyrimidine metabolism could be leveraged to inhibit S. aureus growth, we tested the antimicrobial activity of the uracil derivative, 4-thiouracil (4-TU). Growth of laboratory methicillin-susceptible and resistant strains, including a methicillin-resistant clinical isolate, is inhibited by 4-TU. Based on the structural similarity between 4-TU and uracil, we hypothesized that 4-TU hijacks the pyrimidine salvage pathway for incorporation into RNA. High-performance liquid chromatography (HPLC) analysis showed 4-thiouridine (s4U) in RNA isolated from S. aureus treated with 4-TU. Isolation of 4-TU-resistant S. aureus suppressor strains revealed that mutations in uracil phosphoribosyltransferase (Upp), a component of the pyrimidine salvage pathway, confer resistance to 4-TU. HPLC analysis of RNA isolated from an S. aureus upp mutant demonstrated a lack of s4U, suggesting that upp is required for incorporation of 4-TU into RNA. Expression of Clostridioides difficile thiouracil desulfurase in S. aureus, or cotreatment with uracil and 4-TU, alleviates 4-TU toxicity. Collectively, these findings suggest that 4-TU commandeers the pyrimidine salvage pathway to inhibit S. aureus growth.

IMPORTANCE

Staphylococcus aureus is associated with greater than one million global deaths annually and is capable of infecting every human tissue. The increasing emergence of antibiotic-resistant strains emphasizes the urgent need to develop new therapeutic strategies to treat infections. Nucleoside analogs that disrupt pyrimidine or purine nucleotide metabolism serve as a promising approach for treating drug-resistant infections, as these pathways differ between host and bacteria. Here, we demonstrate that the uracil derivative 4-thiouracil (4-TU) inhibits S. aureus growth by hijacking the pyrimidine salvage pathway, leading to incorporation of 4-TU into RNA. We found that mutations in uracil phosphoribosyltransferase (upp) confer resistance to 4-TU and prevent incorporation into RNA. Expression of a thiouracil desulfurase (tudS) from Clostridioides difficile is sufficient to detoxify 4-TU and diminish 4-TU levels in RNA. Taken together, these results suggest that 4-TU-mediated disruption of pyrimidine metabolism limits S. aureus growth, which may serve as a promising therapeutic target.

Disulfiram induces redox imbalance and perturbations in central glucose catabolism and metal homeostasis to inhibit the growth of Staphylococcus aureus

Disulfiram (Antabuse®) is a prescription alcohol sobriety aid that has shown repurposing potential as an antibacterial drug for infections due to Gram-positive bacteria. In this investigation, we sought to define the principal mechanisms that disulfiram operates as a growth inhibitor of Staphylococcus aureus using differential transcriptomic, metabolomic, bioenergetic, and phenotypic growth analyses. The RNA-seq transcriptome analysis revealed that disulfiram induces oxidative stress, redox imbalance, metal acquisition, and the biosynthesis of pantothenate, coenzyme A, thiamine, menaquinone, siderophores/metallophores, and bacillithiol. The metabolomic analysis indicated that disulfiram depletes coenzyme A and attenuates the catabolism of glucose, pyruvate, and NADH. Conversely, disulfiram appeared to up-regulate arginine catabolism for ATP production and accelerate citrate consumption that was attributed to induction of siderophore biosynthesis (i.e., staphyloferrin). The bioenergetic studies further revealed that the primary metabolite of disulfiram (i.e., diethyldithiocarbamate) is likely involved in the mechanism of action as an inhibitor of oxidative phosphorylation and chelating agent of iron and other metals. In the final analysis, disulfiram inhibits the growth of S. aureus by inducing perturbations in central glucose catabolism and redox imbalance (e.g., oxidative stress). Moreover, the chelation of metal ions and antagonism of the respiratory chain by diethyldithiocarbamate are believed to contribute to the inhibition of cell replication.

Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection

Successful tuberculosis therapy requires treatment with an unwieldy multidrug combination for several months. Thus, there is a growing need to identify novel genetic vulnerabilities that can be leveraged to develop new, more effective antitubercular drugs. Consequently, recent efforts to optimize tuberculosis (TB) therapy have exploited Mycobacterium tuberculosis (Mtb) chemical genetics to identify pathways influencing antibiotic efficacy, novel mechanisms of antibiotic action, and new targets for TB drug discovery. However, the influence of the complex host environment on these interactions remains largely unknown, leaving the therapeutic potential of the identified targets unclear. In this study, we leveraged a library of conditional mutants targeting 467 essential Mtb genes to characterize the chemical-genetic interactions (CGIs) with TB drugs directly in the mouse infection model. We found that these in vivo CGIs differ significantly from those identified in vitro. Both drug-specific and drug-agnostic effects were identified, and many were preserved during treatment with a multidrug combination, suggesting numerous strategies for enhancing therapy. This work also elucidated the complex effects of pyrazinamide (PZA), a drug that relies on aspects of the infection environment for efficacy. Specifically, our work supports the importance of coenzyme A synthesis- inhibition during infection, as well as the antagonistic effect of iron limitation on PZA activity. In addition, we found that inhibition of thiamine and purine synthesis increases PZA efficacy, suggesting additional therapeutically exploitable metabolic dependencies. Our findings present a map of the unique in vivo CGIs, characterizing the mechanism of PZA activity in vivo and identifying potential targets for TB drug development.

Mechanism of Mongolian Medicine Batri-7 on Salmonella Enteritis

Purpose

Traditional Mongolian Medicine Batri-7 (BT-7) is the key Mongolian Medicine (MM) for bacterial enteritis. BT-7 is a well-known clinical MM due to its antibacterial properties. BT-7 contains plant-derived bioactive compounds, but its molecular mechanism of action remains unclear. This study explores BT-7's antibacterial compounds and therapeutic mechanism in a Salmonella enteritis mouse model.

Methods

The active components of BT-7 were detected by liquid chromatography-tandem mass spectrometry assay and identified by UPLC/Q-TOF-MS. An enteritis mouse model induced by Salmonella typhimurium was used in this study. Pathological analysis of small intestine was conducted with hematoxylin and eosin staining. The macrophage recruitment in model mice's intestines was detected by flow cytometry. Simultaneously, the Minimum Inhibitory Concentration of BT-7 was evaluated against bacterial by microbroth dilution method, BT-7 regulation of Salmonella typhimurium gene was performed by RNA-Seq methods and verified by qRT-PCR.

Results

In the LC-MS/MS assay, negative and positive-ion modes are identified for 511 and 699 compounds from BT-7, respectively. Of them, we found multiple antibacterial and anti inflammation compounds including chrysin, oroxylin A and luteolin. In vivo, we observed that treatment of mouse Salmonella enteritis with BT-7 decreases inflammation score and macrophages on intestinal tenue. In vitro, BT-7 presented the highest antibacterial activities against tested strains with MIC was 2-4 mg/mL. Meanwhile, BT-7 significantly down regulated Salmonella infection genes.

Conclusion

Twenty key anti-bacterial components were identified in the BT-7. In vivo experiment shows that orally administered BT-7 effectively reduce the inflammation of intestine in model of Salmonella-induced mouse enteritis by down regulating the infection-related virulence genes of Salmonella. Through this study, we discovered the mechanism of BT-7's dual action on the host and pathogenic bacteria. This gives inspiration for anti-infective disease research in traditional medicine and also proves that traditional medicines still have good prospects for treating infectious diseases.

Arginine Regulates the Mucoid Phenotype of Hypervirulent Klebsiella pneumoniae

Hypervirulent Klebsiella pneumoniae is associated with severe community-acquired infections. Hypervirulent K. pneumoniae colonies typically exhibit a mucoid phenotype. K. pneumoniae mucoidy is influenced by a complex combination of environmental factors and genetic mechanisms. Mucoidy results from altered capsular polysaccharide chain length, yet the specific environmental cues regulating this phenotype and their impact on pathogenesis remain unclear. This study demonstrates that casamino acids enhance the mucoidy phenotype but do not affect total capsular polysaccharide levels. Through targeted screening of each amino acid present in casamino acids, we identified that arginine is necessary and sufficient to stimulate the mucoid phenotype without altering capsule abundance. Furthermore, arginine activates the rmpADC promoter, increasing rmpD transcript levels, which in turn modulates capsular polysaccharide chain length and diversity. The arginine regulator, ArgR, plays a pivotal role in this regulatory cascade since deleting argR decreases mucoidy and increases capsular polysaccharide chain length diversity. Additionally, the ∆argR mutant displays increased macrophage association and has a substantial competitive defect in the lungs of mice, suggesting a link between arginine-dependent gene regulation, immune evasion and in vivo fitness. We discovered that arginine-dependent regulation of mucoidy is conserved in four additional hypervirulent K. pneumoniae isolates likely via a conserved ARG binding box present in rmp promoters. Our findings support a model in which arginine activates ArgR and increases mucoidy in hypervirulent K. pneumoniae. As a result, it is possible that arginine-dependent regulation of mucoidy allows hypervirulent K. pneumoniae to adapt the cell surface across different niches. This study underscores the significance of arginine as a regulatory signal in bacterial virulence.

High-Throughput Discovery of Synthetic Siderophores for Trojan Horse Antibiotics

To cause infection, bacterial pathogens must overcome host immune factors and barriers to nutrient acquisition. Reproducing these aspects of host physiology in vitro has shown great promise for antibacterial drug discovery. When used as a bacterial growth medium, human serum replicates several aspects of the host environment, including innate immunity and iron limitation. We previously reported that a high-throughput chemical screen using serum as the growth medium enabled the discovery of novel growth inhibitors overlooked by conventional screens. Here, we report that a subset of compounds from this high-throughput serum screen display an unexpected growth enhancing phenotype and are enriched for synthetic siderophores. We selected 35 compounds of diverse chemical structure and quantified their ability to enhance bacterial growth in human serum. We show that many of these compounds chelate iron, suggesting they were acting as siderophores and providing iron to the bacteria. For two different pharmacophores represented among these synthetic siderophores, conjugation to the β-lactam antibiotic ampicillin imparted iron-dependent enhancement in antibacterial activity. Conjugation of the most potent growth-enhancing synthetic siderophore with the monobactam aztreonam produced MLEB-22043, a broad-spectrum antibiotic with significantly improved activity against Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. This synthetic siderophore-monobactam conjugate uses multiple TonB-dependent transporters for uptake into P. aeruginosa. Like aztreonam, MLEB-22043 demonstrated activity against metallo-β-lactamase expressing bacteria, and, when combined with the β-lactamase inhibitor avibactam, was active against clinical strains coexpressing the NDM-1 metallo-β-lactamase and serine β-lactamases. Our work shows that human serum is an effective bacterial growth medium for the high-throughput discovery of synthetic siderophores, enabling the development of novel Trojan Horse antibiotics.

Chemical-mediated virulence: the effects of host chemicals on microbial virulence and potential new antivirulence strategies

The rising antimicrobial resistance rates and declining antimicrobial discovery necessitate alternative strategies to combat multidrug-resistant pathogens. Targeting microbial virulence is an emerging area of interest. Traditionally, virulence factors were largely restricted to bacteria-derived toxins, adhesins, capsules, quorum sensing systems, secretion systems, factors required to sense, respond to, acquire, or synthesize, and utilize trace elements (such as iron and other metals) and micronutrients (such as vitamins), and other factors bacteria use to establish infection, form biofilms, or damage the host tissues and regulatory elements thereof. However, this traditional definition overlooks bacterial virulence that may be induced or influenced by host-produced metabolites or other chemicals that bacteria may encounter at the infection site. This review will discuss virulence from a non-traditional perspective, shedding light on chemical-mediated host-pathogen interactions and outlining currently available mechanistic insight into increased bacterial virulence in response to host factors. This review aims to define a possibly underestimated theme of chemically mediated host-pathogen interactions and encourage future validation and characterization of the contribution of host chemicals to microbial virulence in vivo. From this perspective, we discuss proposed antivirulence compounds and suggest new potential targets for antimicrobials that prevent chemical-mediated virulence. We also explore proposed host-targeting therapeutics reducing the level of host chemicals that induce microbial virulence, serving as virulence attenuators. Understanding the host chemical-mediated virulence may enable new antimicrobial solutions to fight multidrug-resistant pathogens.

Bacteriophage-like Nanobiocatalysts with Spiky Topography and Dual-Atom Sites for Treating Drug-Resistant Bacteria

Overuse of antibiotics leads to the proliferation of drug-resistant bacterial strains, worsening global morbidity, and mortality rates. Bioinspired nanomaterials present a promising avenue for developing nonantibiotic strategies against drug-resistant bacteria. Here, we engineer a bacteriophage-inspired artificial nanobiocatalyst via nonstoichiometric W18O49 that features a spiky topography and synergistic dual-atom sites for combating drug-resistant bacterial infection. Benefiting from the strong interaction within the synergistic Fe-O-Mo sites, the synthesized spiky artificial nanobiocatalyst exhibits superior reactive oxygen species (ROS)-catalytic activity, attributed to the regulated adsorption affinity between the reaction intermediates and catalytic sites. The experimental and theoretical investigations demonstrate that the bioinspired biocatalyst can effectively capture and kill bacteria through its spiky morphology and potent ROS-catalytic activity, which can enable a significant reduction in bacterial viability through downregulating genes associated with biosynthesis, cellular maintenance, and respiration. In vivo experiments demonstrate that the spiky artificial biocatalyst accelerates the reconstruction of drug-resistant bacteria-infected skin wounds in rabbits, exhibiting efficacy comparable to that of vancomycin. It is expected that this bioinspired study on spiky artificial nanobiocatalysts offers a straightforward path to facilitate the development of both bionic and nonantibiotic disinfection strategies.

Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection

Successful tuberculosis therapy requires treatment with an unwieldy multidrug combination for several months. Thus, there is a growing need to identify novel genetic vulnerabilities that can be leveraged to develop new, more effective antitubercular drugs. Consequently, recent efforts to optimize TB therapy have exploited Mtb chemical genetics to identify pathways influencing antibiotic efficacy, novel mechanisms of antibiotic action, and new targets for TB drug discovery. However, the influence of the complex host environment on these interactions remains largely unknown, leaving the therapeutic potential of the identified targets unclear. In this study, we leveraged a library of conditional mutants targeting 467 essential Mtb genes to characterize the chemical-genetic interactions (CGIs) with TB drugs directly in the mouse infection model. We found that these in vivo CGIs differ significantly from those identified in vitro . Both drug-specific and drug-agnostic effects were identified, and many were preserved during treatment with a multidrug combination, suggesting numerous strategies for enhancing therapy. This work also elucidated the complex effects of pyrazinamide (PZA), a drug that relies on aspects of the infection environment for efficacy. Specifically, our work supports the importance of coenzyme A synthesis inhibition during infection, as well as the antagonistic effect of iron limitation on PZA activity. In addition, we found that inhibition of thiamine and purine synthesis increases PZA efficacy, suggesting novel therapeutically exploitable metabolic dependencies. Our findings present a map of the unique in vivo CGIs, characterizing the mechanism of PZA activity in vivo and identifying novel targets for TB drug development.

Significance

The inevitable rise of multi-drug-resistant tuberculosis underscores the urgent need for new TB drugs and novel drug targets while prioritizing synergistic drug combinations. Chemical-genetic interaction (CGI) studies have delineated bacterial pathways influencing antibiotic efficacy and uncovered druggable pathways that synergize with TB drugs. However, most studies are conducted in vitro , limiting our understanding of how the host environment influences drug-mutant interactions. Using an inducible mutant library targeting essential Mtb genes to characterize CGIs during infection, this study reveals that CGIs are both drug-specific and drug-agnostic and differ significantly from those observed in vitro . Synergistic CGIs comprised distinct metabolic pathways mediating antibiotic efficacy, revealing novel drug mechanisms of action, and defining potential drug targets that would synergize with frontline antitubercular drugs.

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.

Silversol® (a Colloidal Nanosilver Formulation) Inhibits Growth of Antibiotic-Resistant Staphylococcus aureus by Disrupting Its Physiology in Multiple Ways

Antibiotic-resistant strains of Staphylococcus aureus are being viewed as a serious threat by various public health agencies. Identifying novel targets in this important pathogen is crucial to the development of new effective antibacterial formulations. We investigated the antibacterial effect of a colloidal nanosilver formulation, Silversol®, against an antibiotic-resistant strain of S. aureus using appropriate in vitro assays. Moreover, we deciphered the molecular mechanisms underlying this formulation's anti-S. aureus activity using whole transcriptome analysis. Lower concentrations of the test formulation exerted a bacteriostatic effect against this pathogen, and higher concentrations exerted a bactericidal effect. Silversol® at sub-lethal concentration was found to disturb multiple physiological traits of S. aureus such as growth, antibiotic susceptibility, membrane permeability, efflux, protein synthesis and export, biofilm and exopolysaccharide production, etc. Transcriptome data revealed that the genes coding for transcriptional regulators, efflux machinery, transferases, β-lactam resistance, oxidoreductases, metal homeostasis, virulence factors, and arginine biosynthesis are expressed differently under the influence of the test formulation. Genes (argG and argH) involved in arginine biosynthesis emerged among the major targets of Silversol®'s antibacterial activity against S. aureus.

Antibacterial Activities of the Algal Bromophenol Methylrhodomelol Against Pseudomonas aeruginosa

Methylrhodomelol (1: ) is a bromophenol from the red alga Vertebrata lanosa that has been associated with antimicrobial properties. The aim of the current study was, therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1: exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. In addition, 1: (35 and 10 µg/mL) markedly enhanced the susceptibility of multidrug-resistant P. aeruginosa toward the aminoglycoside gentamicin, while it did not affect the viability of Vero kidney cells up to 100 µM. Finally, pyoverdine release was reduced in bacteria treated at sub-inhibitory concentration, but no effect on other virulence factors was observed. Transcriptome analysis of treated versus untreated P. aeruginosa indicated an interference of 1: with bacterial carbon and energy metabolism, which was corroborated by RT-qPCR and decreased ATP-levels in treated bacteria. In summary, the current study characterized the antibacterial properties of methylrhodomelol, revealed its potential as an adjuvant to standard antibiotics, and generated a hypothesis on its mode of action.

RNA cis-regulators are important for Streptococcus pneumoniae in vivo success

Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.

A novel antibacterial strategy for targeting the bacterial methionine biosynthesis pathway

Bacterial pathogens reprogramme their metabolic networks to support growth and establish infection at specific sites. Bacterial central metabolism has been considered attractive for developing antimicrobial drugs; however, most metabolic enzymes are conserved between humans and bacteria. This study found that blockade of methionine biosynthesis in Citrobacter rodentium and Salmonella enteritidis inhibited bacterial growth and activity of the type III secretion system, resulting in severe defects in colonization and pathogenicity. In addition, α-methyl-methionine was found to inhibit the activity of methionine biosynthetic enzyme MetA, and consequently reduce the virulence and pathogenicity of enteric pathogens. These findings highlight the crucial role of methionine in bacterial virulence, and describe a potential new drug target.

DXP Synthase Function in a Bacterial Metabolic Adaptation and Implications for Antibacterial Strategies

Pathogenic bacteria possess a remarkable ability to adapt to fluctuating host environments and cause infection. Disturbing bacterial central metabolism through inhibition of 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) has the potential to hinder bacterial adaptation, representing a new antibacterial strategy. DXPS functions at a critical metabolic branchpoint to produce the metabolite DXP, a precursor to pyridoxal-5-phosphate (PLP), thiamin diphosphate (ThDP) and isoprenoids presumed essential for metabolic adaptation in nutrient-limited host environments. However, specific roles of DXPS in bacterial adaptations that rely on vitamins or isoprenoids have not been studied. Here we investigate DXPS function in an adaptation of uropathogenic E. coli (UPEC) to d-serine (d-Ser), a bacteriostatic host metabolite that is present at high concentrations in the urinary tract. UPEC adapt to d-Ser by producing a PLP-dependent deaminase, DsdA, that converts d-Ser to pyruvate, pointing to a role for DXPS-dependent PLP synthesis in this adaptation. Using a DXPS-selective probe, butyl acetylphosphonate (BAP), and leveraging the toxic effects of d-Ser, we reveal a link between DXPS activity and d-Ser catabolism. We find that UPEC are sensitized to d-Ser and produce sustained higher levels of DsdA to catabolize d-Ser in the presence of BAP. In addition, BAP activity in the presence of d-Ser is suppressed by β-alanine, the product of aspartate decarboxylase PanD targeted by d-Ser. This BAP-dependent sensitivity to d-Ser marks a metabolic vulnerability that can be exploited to design combination therapies. As a starting point, we show that combining inhibitors of DXPS and CoA biosynthesis displays synergy against UPEC grown in urine where there is increased dependence on the TCA cycle and gluconeogenesis from amino acids. Thus, this study provides the first evidence for a DXPS-dependent metabolic adaptation in a bacterial pathogen and demonstrates how this might be leveraged for development of antibacterial strategies against clinically relevant pathogens.