Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions

E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult

The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.

Novel cross-feeding human gut microbes metabolizing tryptophan to indole-3-propionate

Tryptophan-derived indoles produced by the gut microbiota, particularly indole-3-propionate (IPA), are key compounds associated with gastrointestinal balance and overall health. Reduced levels of IPA have been associated with inflammatory bowel disease, type 2 diabetes, and colorectal cancer. Since fiber-rich diets have been shown to promote IPA, we aimed to decipher fiber-specific effects and identify associated IPA-producing taxa in a range of healthy individuals. We cultured fecal microbiota from 16 adults with tryptophan and eight different dietary fibers and monitored community shifts by 16S rRNA gene amplicon sequencing and tryptophan-derived indoles using targeted liquid chromatography with diode array detection. The concentrations and types of indoles produced were donor-specific, with pectin strongly promoting IPA production in certain donors. IPA production was not associated with any known IPA producer but with the pectin-utilizing species Lachnospira eligens, which produced indole-3-lactate (ILA) in vitro, the IPA precursor. Supplementation of ILA in additional fecal microbiota cultures (n = 6) revealed its effective use as a substrate for IPA production. We identified a novel IPA producer, Enterocloster aldenensis, which produced IPA exclusively from ILA but not from tryptophan. Co-culture of L. eligens and E. aldenensis resulted in IPA production, providing new evidence for an ILA cross-feeding mechanism that may contribute to the IPA-promoting effects observed with pectin. Overall, we highlight the potential for targeted dietary interventions to promote beneficial gut taxa and metabolites.

Rapid High-Throughput Discovery of Molecules With Antimicrobial Activity From Natural Products Enabled by a Nanoliter Matrix SlipChip

Improper use of antibiotics has led to the development of antimicrobial resistance, or "superbugs," outpacing the discovery of new antibiotics. The lack of rapid, high-throughput screening methods is a major bottleneck in discovery novel antibiotics. Traditional methods consume significant amounts of samples, making it challenging to discover new antibiotics from limited natural product extracts. Here, a rapid, high-throughput screening method is reported for natural products with antimicrobial activity enabled by a nanoliter matrix SlipChip (nm-SlipChip). This nm-SlipChip creates a screening matrix with nanoliter droplets for 100 drug candidate-bacterium combinations. The effectiveness of candidate antibiotics is assessed by analyzing microbial phenotypic changes. This nm-SlipChip reduces sample consumption by over 5000-fold and shortens the detection time to three hours. Twenty compounds isolated from Callicarpa integerrima were tested against 10 pathogenic bacteria and identified two previously unreported clerodane diterpenes with activity against methicillin-resistant Staphylococcus aureus (MRSA). Molecular docking and fluorescence probe experiments reveals that their antimicrobial effect results from disruption of bacterial cell membranes and biofilms. The nm-SlipChip provides an effective method for discovering new antimicrobial drugs from natural sources, vital in combating antibiotic resistance.

Shear flow patterns antimicrobial gradients across bacterial populations

Bacterial populations experience chemical gradients in nature. However, most experimental systems either ignore gradients or fail to capture gradients in mechanically relevant contexts. Here, we use microfluidic experiments and biophysical simulations to explore how host-relevant shear flow affects antimicrobial gradients across communities of the highly resistant pathogen Pseudomonas aeruginosa. We discover that flow patterns gradients of three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistant P. aeruginosa cells generate local gradients by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to penetrate deeper into bacterial populations. By imaging single cells across long microfluidic channels, we observe that upstream cells protect downstream cells, and protection is abolished in higher flow regimes. Together, our results reveal that physical flow can promote antimicrobial effectiveness, which could inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials.

Echinacoside reduces intracellular c-di-GMP levels and potentiates tobramycin activity against Pseudomonas aeruginosa biofilm aggregates

Cyclic diguanylate (c-di-GMP) is a central biofilm regulator in Pseudomonas aeruginosa, where increased intracellular levels promote biofilm formation and antibiotic tolerance. Targeting the c-di-GMP network may be a promising anti-biofilm approach, but most strategies studied so far aimed at eliminating surface-attached biofilms, while in vivo P. aeruginosa biofilms often occur as suspended aggregates. Here, the expression profile of c-di-GMP metabolism-related genes was analysed among 32 P. aeruginosa strains grown as aggregates in synthetic cystic fibrosis sputum. The diguanylate cyclase SiaD proved essential for auto-aggregation under in vivo-like conditions. Virtual screening predicted a high binding affinity of echinacoside towards the active site of SiaD. Echinacoside reduced c-di-GMP levels and aggregate sizes and potentiated tobramycin activity against aggregates in >80% of strains tested. This synergism was also observed in P. aeruginosa-infected 3-D alveolar epithelial cells and murine lungs, demonstrating echinacoside's potential as an adjunctive therapy for recalcitrant P. aeruginosa infections.

Analogue of the natural product ecumicin causes sustained growth inhibition of Mycobacterium tuberculosis under multiple growth conditions

Multi-drug-resistant Mycobacterium tuberculosis is an escalating global health problem, and a strong pipeline of novel compounds is needed to combat rising antimicrobial resistance. Ecumicin is a novel analogue of the natural antimycobacterial cyclic peptide ecumicin, with selective activity against Mycobacterium species. The activity of ecumicin∗ was compared to that of frontline tuberculosis therapies under in vitro conditions representative of niches where M. tuberculosis resides in the human lung. M. tuberculosis expressing luciferase was cultured in defined 7H9-based media containing glucose, butyrate, valerate, acidified glucose, low or high cholesterol concentrations, or intracellularly in human THP-1 and mouse RAW264.7 macrophages. Ecumicin∗ effectively killed M. tuberculosis under all assay conditions. The IC90 of ecumicin∗ was increased in acidified 7H9 media, and both IC90 and AUC90 values were increased in valerate, cholesterol, high cholesterol culture media. In time-kill assays, anti-M. tuberculosis activity of ecumicin∗ was sustained for 28 days. By comparison, IC50 and IC90 of isoniazid were decreased in butyrate and cholesterols medias, and mycobacterial regrowth occurred in glucose and cholesterol culture medias within 14 days at high isoniazid concentrations. Ecumicin∗ inhibited M. tuberculosis growth in THP-1 macrophages, and at higher IC90 in mouse RAW264.7 macrophages. Drug testing under disease-relevant conditions is important prior to in vivo examination, and ecumicin∗ has proven effective in multiple in vitro conditions typical of the lung environment of tuberculosis patients.

Metabolic engineering approaches for the biosynthesis of antibiotics

BACKGROUND

Antibiotics have been saving countless lives from deadly infectious diseases, which we now often take for granted. However, we are currently witnessing a significant rise in the emergence of multidrug-resistant (MDR) bacteria, making these infections increasingly difficult to treat in hospitals.

MAIN TEXT

The discovery and development of new antibiotic has slowed, largely due to reduced profitability, as antibiotics often lose effectiveness quickly as pathogenic bacteria evolve into MDR strains. To address this challenge, metabolic engineering has recently become crucial in developing efficient enzymes and cell factories capable of producing both existing antibiotics and a wide range of new derivatives and analogs. In this paper, we review recent tools and strategies in metabolic engineering and synthetic biology for antibiotic discovery and the efficient production of antibiotics, their derivatives, and analogs, along with representative examples.

CONCLUSION

These metabolic engineering and synthetic biology strategies offer promising potential to revitalize the discovery and development of new antibiotics, providing renewed hope in humanity's fight against MDR pathogenic bacteria.

Establishment of a 3D-Printed Tissue-on-a-Chip Model for Live Imaging of Bacterial Infections

Despite advances in healthcare, bacterial pathogens remain a severe global health threat, exacerbated by rising antibiotic resistance. Lower respiratory tract infections, with their high death toll, are of particular concern. Accurately replicating host-pathogen interactions in laboratory models is crucial for understanding these diseases and evaluating new therapies. In this communication, we briefly present existing in vivo models for cystic fibrosis and their limitations in replicating human respiratory infections. We then present a novel, 3D-printed, cytocompatible microfluidic lung-on-a-chip device, designed to simulate the human lung environment, and with possible use in recapitulating general infectious diseases.Our device enables the colonisation of fully differentiated lung epithelia at an air-liquid interface with Pseudomonas aeruginosa, a key pathogen in many severe infections. By incorporating dynamic flow, we replicate the clearance of bacterial toxins and planktonic cells, simulating both acute and chronic infections. This platform supports real-time monitoring of therapeutic interventions, mimics repeated drug administrations as in clinical settings, and facilitates the analysis of colony-forming units and cytokine secretion over time. Our findings indicate that this lung-on-a-chip device has significant potential for advancing infectious disease research, in optimizing treatment strategies against infections and in developing novel treatments.

Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane

The sophisticated envelope of Gram-negative bacteria modulates the uptake of small molecules in a side-chain-sensitive manner. Despite intensive theoretical and experimental investigations, a general set of pathways underpinning antibiotic uptake has not been identified. This manuscript discusses the passive influx versus active efflux of antibiotics, considering the responsible membrane proteins and the transported molecules. Recent methods have analyzed drug transport across the bacterial membrane in order to understand their activity. The combination of in vitro, in cellulo and in silico methods shed light on the key, mainly electrostatic, interactions between the molecule surface, porins and transporters during permeation. A key factor is the relationship between the dose of an active compound near its target and its antibacterial activity during the critical early window. Today, methodology breakthroughs provide fruitful tools to precisely dissect drug transport, identify key steps in drug resistance associated with membrane impermeability and efflux, and highlight key parameters to generate more effective drugs.

The contribution of porins to enterobacterial drug resistance

In Enterobacteriaceae, susceptibility to cephalosporins and carbapenems is often associated with membrane and enzymatic barrier resistance. For about 20 years, a large number of Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae presenting ß-lactam resistance have been isolated from medical clinics. In addition, some of the resistant isolates exhibited alterations in the outer membrane porin OmpC-OmpF orthologues, resulting in the complete absence of gene expression, replacement by another porin or mutations affecting channel properties. Interestingly, for mutations reported in OmpC-OmpF orthologues, major changes in pore function were found to be present in the gene encoding for OmpC. The alterations were located in the constriction region of the porin and the resulting amino acid substitutions were found to induce severe restriction of the lumen diameter and/or alteration of the electrostatic field that governs the diffusion of charged molecules. This functional adaptation through porins maintains the entry of solutes necessary for bacterial growth but critically controls the influx of harmful molecules such as β-lactams at a reduced cost. The data recently published show the importance of understanding the underlying parameters affecting the uptake of antibiotics by infectious bacteria. Furthermore, the development of reliable methods to measure the concentration of antibiotics within bacterial cells is key to combat impermeability-resistance mechanisms.

Recreating chronic respiratory infections in vitro using physiologically relevant models

Despite the need for effective treatments against chronic respiratory infections (often caused by pathogenic biofilms), only a few new antimicrobials have been introduced to the market in recent decades. Although different factors impede the successful advancement of antimicrobial candidates from the bench to the clinic, a major driver is the use of poorly predictive model systems in preclinical research. To bridge this translational gap, significant efforts have been made to develop physiologically relevant models capable of recapitulating the key aspects of the airway microenvironment that are known to influence infection dynamics and antimicrobial activity in vivo In this review, we provide an overview of state-of-the-art cell culture platforms and ex vivo models that have been used to model chronic (biofilm-associated) airway infections, including air-liquid interfaces, three-dimensional cultures obtained with rotating-wall vessel bioreactors, lung-on-a-chips and ex vivo pig lungs. Our focus is on highlighting the advantages of these infection models over standard (abiotic) biofilm methods by describing studies that have benefited from these platforms to investigate chronic bacterial infections and explore novel antibiofilm strategies. Furthermore, we discuss the challenges that still need to be overcome to ensure the widespread application of in vivo-like infection models in antimicrobial drug development, suggesting possible directions for future research. Bearing in mind that no single model is able to faithfully capture the full complexity of the (infected) airways, we emphasise the importance of informed model selection in order to generate clinically relevant experimental data.

Preserving the efficacy of antibiotics to tackle antibiotic resistance

Different international agencies recognize that antibiotic resistance is one of the most severe human health problems that humankind is facing. Traditionally, the introduction of new antibiotics solved this problem but various scientific and economic reasons have led to a shortage of novel antibiotics at the pipeline. This situation makes mandatory the implementation of approaches to preserve the efficacy of current antibiotics. The concept is not novel, but the only action taken for such preservation had been the 'prudent' use of antibiotics, trying to reduce the selection pressure by reducing the amount of antibiotics. However, even if antibiotics are used only when needed, this will be insufficient because resistance is the inescapable outcome of antibiotics' use. A deeper understanding of the alterations in the bacterial physiology upon acquisition of resistance and during infection will help to design improved strategies to treat bacterial infections. In this article, we discuss the interconnection between antibiotic resistance (and antibiotic activity) and bacterial metabolism, particularly in vivo, when bacteria are causing infection. We discuss as well how understanding evolutionary trade-offs, as collateral sensitivity, associated with the acquisition of resistance may help to define evolution-based therapeutic strategies to fight antibiotic resistance and to preserve currently used antibiotics.

Fluid flow overcomes antimicrobial resistance by boosting delivery

Antimicrobial resistance is an emerging global threat to humanity. As resistance outpaces development, new perspectives are required. For decades, scientists have prioritized chemical optimization, while largely ignoring the physical process of delivery. Here, we used biophysical simulations and microfluidic experiments to explore how fluid flow delivers antimicrobials into communities of the highly resistant pathogen Pseudomonas aeruginosa . We discover that increasing flow overcomes bacterial resistance towards three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistant P. aeruginosa cells generate local zones of depletion by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to regain effectiveness against resistant bacteria. Additionally, we discover that cells on the edge of a community shield internal cells, and cell-cell shielding is abolished in higher flow regimes. Collectively, our quantitative experiments reveal the unexpected result that physical flow and chemical dosage are equally important to antimicrobial effectiveness. Thus, our results should inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials, and could represent a new strategy to combat antimicrobial resistance.

Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders

Accumulating evidence suggests that gut microbiota alterations influence brain function and could serve as diagnostic biomarkers and therapeutic targets. The potential of using fecal microbiota signatures to aid autism spectrum disorder (ASD) detection is still not fully explored. Here, we assessed the potential of different levels of microbial markers (taxonomy and genome) in distinguishing children with ASD from age and gender-matched typically developing peers (n = 598, ASD vs TD = 273 vs 325). A combined microbial taxa and metagenome-assembled genome (MAG) markers showed a better performance than either microbial taxa or microbial MAGs alone for detecting ASD. A machine-learning model comprising 5 bacterial taxa and 44 microbial MAG markers (2 viral MAGs and 42 bacterial MAGs) achieved an area under the receiving operator curve (AUROC) of 0.886 in the discovery cohort and 0.734 in an independent validation cohort. Furthermore, the identified biomarkers and predicted ASD risk score also significantly correlated with the core symptoms measured by the Social Responsiveness Scale-2 (SRS-2). The microbiome panel showed a superior classification performance in younger children (≤6 years old) with an AUROC of 0.845 than older children (>6 years). The model was broadly applicable to subjects across genders, with or without gastrointestinal tract symptoms (constipation and diarrhea) and with or without psychiatric comorbidities (attention deficit and hyperactivity disorder and anxiety). This study highlights the potential clinical validity of fecal microbiome to aid in ASD diagnosis and will facilitate studies to understand the association of disturbance of human gut microbiota and ASD symptom severity.