Alternatives to antibiotics-a pipeline portfolio review

Intestinal microbiota-derived d-(+)-malic acid promotes pBD1 expression via p-p38/ATF1 signaling pathway to maintain porcine intestinal health

This study aims to identify nutrients that enhance the expression of host defense peptides (HDPs) and to evaluate their application effects and regulatory mechanisms, thereby advancing the exploring of nutritional regulation of HDPs. To achieve this, we constructed 16 stable fluorescent reporter porcine epithelial cell lines, driven by promoters targeting eight porcine intestinal HDPs genes, using IPEC-1 and IPEC-J2 cells. Through untargeted metabolomics sequencing and high-throughput screening, 15 metabolites were identified as potential enhancers of pBD1 expression, with d-(+)-malic acid (DMA) emerged as the most effective candidate. Transcriptomic and western blot analysis suggested that DMA enhances pBD1 expression primarily via the p-p38/ATF1 signaling pathways. Functional studies demonstrated that DMA significantly improved intestinal barrier integrity and alleviated intestinal damage. Overall, this work successfully established promoter-driven fluorescent reporter cell lines and identified microbiota-derived metabolites enhancing pBD1 expression, such as DMA, as promising alternatives to antibiotics for maintaining porcine intestinal health.

Low-Irradiance Antimicrobial Blue Light-Bathing Therapy for Wound Infection Control

The prevalence of antibiotic resistance and tolerance in wound infection management poses a serious and growing health threat, necessitating the exploration of alternative approaches. Antimicrobial blue light therapy offers an appealing, non-pharmacological solution. However, its practical application has been hindered by the requirement for high irradiance levels (50-200 mW/cm2), which particularly raises safety concerns. Here, a light-bathing strategy is introduced that employs prolonged, continuous exposure to blue light at an irradiance range lower by more than an order of magnitude (5 mW/cm2). This method consistently applies bacteriostatic pressure, keeping wound bioburden low, all while minimizing photothermal risks. Leveraging tailor-made, wearable light-emitting patches, preclinical trials on rat models of wound infection are conducted, demonstrating its safety and efficacy for suppressing infections induced by methicillin-resistant Staphylococcus aureus (S. aureus) and multidrug-resistant Pseudomonas aeruginosa (P. aeruginosa). The results pave a new way for the application of blue light therapy in wound care.

A complete genome of an obligately lytic Pseudomonas aeruginosa bacteriophage, Minga-mokiny 4

We report the isolation of a bacteriophage with obligately lytic activity against Pseudomonas aeruginosa from wastewater. The reported phage, Minga-mokiny 4, appears to belong to the Schitoviridae family, is of the Litunavirus genus, and has a 72,362-bp genome. No known genes associated with lysogeny, bacterial resistance, or virulence were predicted.

Activation, incompatibility, and displacement of FIB replicons in E. coli

Multi-replicon sex-factor F is the archetype of the largest plasmid group in clinical Enterobacteriaceae. Such plasmids spread antimicrobial resistance (AMR) and virulence functions in commensal bacteria of humans and animals. Displacing (curing) these plasmids by blocking replication and neutralizing addiction is successful with the curing cassette on a high-copy-number vector but, with conjugative IncP-1 plasmid RK2 as vector for our "anti-F cassette", displacement of F'prolac is inefficient unless curing-plasmid copy-number is raised 1.5- to 2-fold. Here we report that it is the anti-FIB segment, originating from FIB-FII plasmid pO157, which needs potentiation. We show that the FIB replicon in F (F-FIB) is defective due to a sub-optimal rep ribosome-binding-site (rbs) but can be activated by FIB-Rep protein expressed from our anti-FIB segment joined to RK2. Deleting FIB-rep from the anti-F cassette removed the need for potentiation. A pO157-FIB single-replicon plasmid was displaced efficiently by the complete anti-F cassette without potentiation, but an F-FIB plasmid, mutated to have a pO157-like rep rbs, was not, indicating that sequence divergence between F and pO157 FIB replicons has weakened their negative cross-reactivity. Thus, raising vector copy-number slightly may be sufficient to increase displacement of plasmids similar but not identical to the sequences in the curing cassette.

Artificial Intuition and accelerating the process of antimicrobial drug discovery

New drug development is a very challenging, expensive, and usually time-consuming process. This issue is very important with regard to antimicrobials, which are affected by the global issue of the development and spread of resistance. This framework underscores the urgency of accelerating drug development processes while reducing their costs. In this context, new bioinformatics tools can provide important support for drug development by limiting and shortening in vitro evaluation of the best outcomes, thereby minimizing costs. Recently, new Artificial Intelligence (AI)-based tools have been developed for de novo design of new molecules, or for the identification of features of inhibitors among a large set of molecules that can guide rational design. With this work, we present an Artificial Intuition (AI4)-based pharmacological analysis of a series of antimicrobial compounds that are known to be active against Mycobacterium tuberculosis. The compounds have been subjected to Molecular Dynamic Simulation (MDS), and the respective outputs processed with a Quantitative Complexity Management (QCM) tool in order to determine the corresponding complexity profiles. The comparison of different analogues in each series revealed a relationship between the complexity of the various chemical moieties and their importance for the biological activity of each compound, suggesting that QCM may be a useful tool in guiding the optimization process. This first attempt to apply the tool in the field of drug development has yielded interesting results, indicating that QCM, which powers AI4, can be implemented for rational drug design in the near future.

Identifying phage Lysins through genomic analysis of prophages from Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative opportunistic pathogen, responsible for nosocomial infections worldwide. In recent years, this microorganism has acquired resistance to various antibiotics, prompting the World Health Organization (WHO) to declare carbapenem-resistant A. baumannii (CRAB) a critical priority microorganism requiring urgent attention and the development of new therapeutic options. Here, we screened for prophages in 158 genomes of A. baumannii, comprising 139 complete genomes from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), and 19 newly sequenced clinical isolates. Additionally, we conducted phylogenetic analyses of prophages, highlighting their diversity and local clustering. The analyzed genomes harbored at least two prophage regions, resulting in the identification of a total of 950 prophage regions, of which 348 were considered complete prophages through software analysis and manual curation, while the remainder may represent prophage remnants. The complete prophages ranged from 28.6 to 103.9 kbp, with an average GC content of 39%. Based on genomic similarity, only 18 complete prophages were taxonomically classified to the genus Vieuvirus. Among all identified complete prophages, we identified 166 genes encoding for putative lysins, while prophage regions that were not considered complete could also harbor putative lysins. These findings highlight the abundance of prophage-encoded lysins in A. baumannii genomes, which are promising therapeutic agents for combating A. baumannii infections, particularly in the face of rising antibiotic resistance.

Bacteriophage therapy: a possible alternative therapy against antibiotic-resistant strains of Klebsiella pneumoniae

Klebsiella pneumoniae is a notorious, Gram-negative pathogen and is a leading cause of healthcare settings and community-acquired infections. This is the commensal of human microbiota and can invade and cause infections in different body parts. The global emergence of antibiotic resistance in K. pneumoniae has become a major challenge in the whole medical community. Alternative paths to treat the infections caused by these MDR pathogens are needed as these bacteria become resistant to last-resort antibiotics like colistin. The lytic bacteriophages (phages) are the bacteria's natural predators and can rapidly eliminate the bacterial cells. Phages are abundant in nature and have recently been found to be effective tools in modern biotechnology. They can be used to control the bacterial infectious diseases. They can be manipulated easily and potentially used in therapeutics, biotechnology, and research. Several studies, both in vitro and in vivo, have demonstrated the possible applications of the lytic phages in treating K. pneumoniae superbug strains. Phage endolysins have drawn the scientific world's attention because of their involvement in phage adsorption and bacterial capsules digestion. These phage-encoded enzymes digest the polysaccharide components of bacterial cell walls by recognizing and binding them. Phage lysins, being strong biological agents, are capable of effectively and swiftly eliminating bacteria. This review summarizes the information on phages of K. pneumoniae and phage-based therapies to target their bacterial hosts.

Terramide A: a novel ironophore targeting Acinetobacter baumannii with mechanistic insights into bacterial iron deprivation

Acetobacter baumannii poses escalating clinical challenges due to its exceptional adaptability, demanding innovative antimicrobial strategies. This study pioneers an investigation into the antibacterial efficacy and molecular mechanism of Terramide A, a hydroxamate siderophore isolated from Aspergillus terreus, against notorious A. baumannii. Employing a multidisciplinary approach integrating phenotypic characterization with mechanistic interrogation, we demonstrate that Terramide A exerts significant inhibitory effects against A. baumannii and P. aeruginosa, pathogens critically dependent on siderophore-mediated iron acquisition for survival and virulence. Structural characterization underlines the hydroxamate moieties of Terramide A presumably supports its hypothesized role as a fungal siderophore, involving competitive iron sequestration and bacterial homeostasis. Subsequently, multi-omics investigation of susceptible strain AB19606 delineated a metabolic collapse cascade due to iron acquisition competition: (1) impairment of central metabolism and energy production through oxidative phosphorylation (OXPHO) inhibitions; (2) compromised stress adaptation and bacterial flexibility; (3) compensatory overactivation of siderophores biosynthesis and transportation, depleting metabolic intermediates and exacerbating stress; (4) coordinated suppression of virulence determinants, such as secretory systems and biofilm formation. These molecular derangements translated into phenotypic deficits, including quorum sensing, diminished autoinducer peptides production, and morphological/functional abnormalities. In vivo evaluation in a rat skin wound infection model further demonstrated that Terramide A promotes wound healing and mitigates inflammation, supporting its antibacterial efficacy. These findings establish Terramide A as a promising antibacterial agent and provide critical insights into iron-competitive antimicrobial strategies to exploit micro-nutrient deprivation and metabolic dysfunction. However, further research is needed to optimize the siderophore-based scaffold, clarify its mechanisms, and assess therapeutic potential.

Antibacterial Activity of Ocimum tenuiflorum against Drug Resistant Bacteria Isolated from Raw Beef

Recent empirical evidence has acknowledged raw meat, particularly beef, as a significant reservoir for diverse foodborne pathogens and drug-resistant strains, posing severe threat to consumer health. This study aimed to isolate and identify drug-resistant bacteria from raw beef samples, obtained from different butcher shops in Khulna city, Bangladesh, as well as, to determine their susceptibility pattern against Ocimum tenuiflorum extracts. Raw beef samples were randomly collected from various butcher shops, followed by the initial isolation of thirty pure bacterial isolates. Later, 16S rRNA gene amplification and analysis identified twelve distinct bacterial species from those isolates. The antimicrobial susceptibility test results revealed ten of the isolates, including Klebsiella pneumoniae, Aeromonas veronii and Enterobacter hormaechei, to exhibit multidrug resistance pattern. Amoxicillin, nitrofurantoin, and flucloxacillin were found to be ineffective against most isolates. However, the ethanolic extracts of O. tenuiflorum were found effective in inhibiting the growth of eight species at three different concentrations. Subsequent HPLC analysis of O. tenuiflorum reported the presence of five secondary metabolites epicatechin, syringic acid, rutin hydrate, p-coumaric acid, and myricetin as potent contributors to the observed antimicrobial activity. Lastly, in silico binding interaction simulations of the secondary metabolites against five relevant targets predict syringic acid and myricetin to have effective antibacterial properties, primarily mediated by better binding affinity and molecular interactions. Thus, this study identified diverse drug-resistant bacteria in raw beef and provided novel insights into the antibacterial properties of O. tenuiflorum extracts.

Nanobody-Targeted Conditional Antimicrobial Therapeutics

Conditional therapeutics that rely on disease microenvironment-specific triggers for activation are a promising strategy to improve therapeutic cargos. Among the investigated triggers, protease activity is used most often because of its dysregulation in several diseases. How to optimally fine-tune protease activation for different therapeutic cargos remains a challenge. Here, we designed nanobody-targeted conditional antimicrobial therapeutics to deliver a model therapeutic peptide and protein to the site of bacterial infection. We explored several parameters that influence proteolytic activation. We report the use of targeting nanobodies to enhance the activation of therapeutics that are otherwise activated inefficiently despite extensive optimization of the cleavable linker. Specifically, the pairing of Ly6G/C or ADAM10-targeting nanobodies with ADAM10-cleavable linkers improved activation via proximity-enabled reactivity. This study demonstrates a distinct role of active targeting in conditional therapeutic activation. More broadly, this optimization framework provides a guideline for the development of conditional therapeutics to treat various diseases in which protease activity is dysregulated.

A Novel Hepcidin Isoform Jd-Hep from the Sin Croaker Johnius dussumieri (Cuvier, 1830): Recombinant Expression and Insights into the Antibacterial Property and Modes of Action

Hepcidin is a cysteine-rich antimicrobial peptide that plays an important role in fish immunity. In the current study, we report a novel isoform of hepcidin (Jd-Hep) from Sin croaker, Johnius dussumieri, with an open reading frame (ORF) of 258 nucleotide bases that encodes 85 amino acids containing a signal peptide (24 amino acids), a prodomain (35 amino acids) and a biologically active mature peptide (26 amino acids). Phylogenetic tree analysis showed that J. dussumieri hepcidin belonged to the HAMP2 cluster of hepcidin. The tissue distribution showed that the expression of hepcidin was highest in the liver in wild-caught J. dussumieri. The mature peptide mJd-Hep was recombinantly expressed in a prokaryotic host, E. coli Rosetta-gami™B (DE3) pLysS cells, and the peptide was isolated and purified. The recombinant peptide, rJd-Hep, exhibited notable antibacterial activity against aquatic pathogens such as Aeromonas hydrophila, Vibrio parahaemolyticus, Vibrio harveyi, Vibrio alginolyticus, Vibrio proteolyticus, and Vibrio fluvialis. The mode of action of the peptide was proven to be membrane-based (pore formation and depolarization). The rJd-Hep was found to be non-hemolytic to hRBCs and non-cytotoxic to the mammalian cell line. The peptide showed 85% growth inhibition of cancer cell line, MCF-7. These findings expand our knowledge of the potential application of hepcidin in aquaculture as a therapeutic agent.

Effects of Diet Xylooligosaccharide Supplementation on Growth Performance, Carcass Characteristics, and Meat Quality of Hu Lambs

In this study, we examined the effect of xylooligosaccharide (XOS) supplementation on the growth performance, carcass characteristics, and meat quality of Hu lambs. In total, 60 Hu lambs (two months old and weighing 17.32 ± 0.81 kg) were randomly assigned to four treatment groups, each with three replicates and five lambs per replicate. The lambs were fed basal diets supplemented with 0, 1.5, 3, or 4.5 g/kg XOSs in a basal diet for 60 days, with the groups designated XOS0%, XOS1.5%, XOS3%, and XOS4.5%, respectively. The results revealed, compared to theXOS0% group, the XOS3% group presented a lower F:G during 31 to 45 d (p = 0.06). By the 60th day, the body length indices of groups XOS3% and XOS4.5% increased compared to the XOS0% group, with a significant increase observed in group XOS4.5% (p < 0.05). Additionally, the GR values of the XOS1.5%, XOS3%, and XOS4.5% groups increased significantly, and the rumen fluid pH values of the XOS3% and XOS4.5% groups increased significantly (p < 0.01). The crude fat content in the XOS1.5% and XOS4.5% groups were significantly lower (p < 0.05). The hardness, adhesiveness, elasticity, cohesiveness, and chewiness of the mutton in the XOS1.5%, XOS3%, and XOS4.5% groups were increased, although the differences were not statistically significant (p > 0.05). Correlation analysis indicates that there is a significant correlation between growth performance, carcass traits, and meat quality (p < 0.05). The factors influencing meat quality originate from the growth period and the slaughtering phase, which can be attributed to the effects of xylooligosaccharides. In conclusion, XOS had positive effects on the growth performance, carcass characteristics, and meat quality of Hu lambs. The comprehensive effect of group XOS3% was best. Considering the production cost, the 3 g/kg XOSs is identified as the optimal supplementation level for sheep.

Bactofencin A Displays a Delayed Killing Effect on a Clinical Strain of Staphylococcus aureus Which Is Greatly Accelerated in the Presence of Nisin

Background/objectives: Bacteriocins can be considered a novel source of natural alternatives to antibiotics or chemical food additives with the potential to fight against clinical and food pathogens. A number have already been commercialised as food preservatives, but they also have the potential to treat drug-resistant clinical pathogens and can play a role in immune modulation. To achieve their full potential, an understanding of their mode of action is required. Methods: Bactofencin A and nisin A were purified to homogeneity by reversed-phase HPLC and their effect on the mastitis pathogen Staphylococcus aureus DPC5246 was assessed by cell viability assays and flow cytometry. Results: We report that bactofencin A displays a delayed inhibitory effect against the mastitis pathogen, Staphylococcus aureus DPC5246, suggesting an unusual mode of action. This characteristic was clearly visible on BHI plate media, where formation of inhibition zones against the staphylococcal strain took 23 h compared to 6 h for the well-characterised nisin. This delayed killing and injury was also demonstrated using flow cytometry, where damage was evident 4 h after bacteriocin addition. Treatment with 2 μM bactofencin A resulted in approximately 20-fold higher numbers of injured and 50-fold higher numbers of dead cells when compared to untreated cells. Combining bactofencin A with the lantibiotic nisin A resulted in faster killing at lower bacteriocin concentrations. When combined in an equal ratio, the combination exhibited a 4-fold increase in inhibition compared to nisin A alone. These results demonstrate that the combination may be very effective in therapeutic applications against pathogenic staphylococci.

The efficacy of the bacteriocinogenic Enterococcus faecalis 14 in the control of induced necrotic enteritis in broilers

PURPOSE

To demonstrate the efficacy of the bacteriocinogenic Enterococcus faecalis 14 (E. faecalis 14) in the control of induced necrotic enteritis (NE) in broilers.

METHODS

Six groups of 504 broilers consisting of an infected untreated control (IUC) group, an infected and amoxicillin treated control (ITC) group, and groups receiving prophylactically (2 groups) or therapeutically (2 groups) E. faecalis 14 or its Δbac mutant were used. All groups were challenged with Clostridium perfringens 56 to induce NE. To predispose the boilers to develop subclinical NE, a high protein grower diet containing 15 % fishmeal and a coccidial inoculum were administered.

RESULTS

NE lesions were observed on D26 in all groups except ITC and those receiving prophylactically and therapeutically E. faecalis 14. On D27, only ITC and the group prophylactically treated with E. faecalis 14 (T03) were without lesions. Average body weight and daily weight gain remained lower in the treated groups compared to the ITC group, but there was a clear improvement in the period between D21 to D27, especially in the group prophylactically treated with E. faecalis 14. Specifically, the daily weight gain (DWG) in this period for group T03, was second highest after the group ITC. Metataxonomic analyses showed a positive effect of E. faecalis 14 in maintaining the diversity and richness of the intestinal microbiota, in contrast to ITC group and other conditions.

CONCLUSIONS

The results of this in vivo study demonstrated the efficacy of the prophylactic administration of the bacteriocinogenic E. faecalis 14 in preventing of the NE lesions caused by C. perfringens.

Modeling and simulation of distribution and drug resistance of major pathogens in patients with respiratory system infections

BACKGROUND

Respiratory tract infections (RTIs) are one of the leading causes of morbidity and mortality worldwide. The increase in antimicrobial resistance in respiratory pathogens poses a major challenge to the effective management of these infections.

OBJECTIVE

To investigate the distribution of major pathogens of RTIs and their antimicrobial resistance patterns in a tertiary care hospital and to develop a mathematical model to explore the relationship between pathogen distribution and antimicrobial resistance.

METHODS

Five hundred patients with RTIs were included in the study and 475 bacterial strains were isolated from their respiratory specimens. Antimicrobial susceptibility testing and analysis of influencing factors were performed. A mathematical model was developed to simulate the relationship between pathogen distribution and drug resistance.

RESULTS

The most common pathogens were Streptococcus pneumoniae (30%), Haemophilus influenzae (20%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%) and Klebsiella pneumoniae (10%). The distribution of pathogens varied according to age group and type of RTIs, with higher proportions of Pseudomonas aeruginosa and Staphylococcus aureus in hospital-acquired and ventilator-associated pneumonia. Isolated pathogens showed high and increasing rates of resistance to commonly used antibiotics. Model simulations suggest that a shift in the distribution of pathogens toward more resistant strains may lead to a significant increase in overall resistance rates, even if antibiotic use patterns remain unchanged.

CONCLUSION

This study emphasizes the importance of regular monitoring of respiratory pathogen distribution and antimicrobial resistance patterns and the need for a comprehensive approach to managing RTIs, including implementation of antibiotic stewardship programs, infection control measures, and development of new therapies.

Chloramphenicol and gentamicin reduce the evolution of resistance to phage ΦX174 by suppressing a subset of E. coli LPS mutants

Bacteriophages infect gram-negative bacteria by attaching to molecules present on the bacterial surface, often lipopolysaccharides (LPS). Modification of LPS can lead to resistance to phage infection. In addition, LPS modifications can impact antibiotic susceptibility, allowing for phage-antibiotic synergism. The evolutionary mechanism(s) behind such synergistic interactions remain largely unclear. Here, we show that the presence of antibiotics can affect the evolution of resistance to phage infection, using phage ΦX174 and Escherichia coli C. We use a collection of 34 E. coli C LPS strains, each of which is resistant to ΦX174, and has either a "rough" or "deep rough" LPS phenotype. Growth of the bacterial strains with the deep rough phenotype is inhibited at low concentrations of chloramphenicol and, to a much lesser degree, gentamicin. Treating E. coli C wild type with ΦX174 and chloramphenicol eliminates the emergence of mutants with the deep rough phenotype, and thereby slows the evolution of resistance to phage infection. At slightly lower chloramphenicol concentrations, phage resistance rates are similar to those observed at high concentrations; yet, we show that the diversity of possible mutants is much larger than at higher chloramphenicol concentrations. These data suggest that specific antibiotic concentrations can lead to synergistic phage-antibiotic interactions that disappear at higher antibiotic concentrations. Overall, we show that the change in survival of various ΦX174-resistant E. coli C mutants in the presence of antibiotics can explain the observed phage-antibiotic synergism.

A comparative guide to expression systems for phage lysin production

Phage lysins, bacteriophage-encoded enzymes tasked with degrading their host's cell wall, are increasingly investigated and engineered as novel antibacterials across diverse applications. Their rapid action, tuneable specificity, and low likelihood of resistance development make them particularly interesting. Despite numerous application-focused lysin studies, the art of their recombinant production remains relatively undiscussed. Here, we provide an overview of the available expression systems for phage lysin production and discuss key considerations guiding the choice of a suitable recombinant host. We systematically surveyed recent literature to evaluate the hosts used in the lysin field and cover various recombinant systems, including the well-known bacterial host Escherichia coli or yeast Saccharomyces cerevisiae, as well as plant, mammalian, and cell-free systems. Careful analysis of the limited studies expressing lysins in various hosts suggests a host-dependent effect on activity. Nonetheless, the multitude of available expression systems should be further leveraged to accommodate the growing interest in phage lysins and their expanding range of applications.

Antiplasmodial Activity of Probiotic Limosilactobacillus fermentum YZ01 in Plasmodium berghei ANKA Infected BALB/c Mice

Malaria remains a significant global health challenge, with the deadliest infections caused by Plasmodium falciparum. In light of the escalating drug resistance and the limited effectiveness of available vaccines, innovative treatment approaches are urgently needed. This study explores the potential of the probiotic Limosilactobacillus fermentum YZ01, isolated from traditionally fermented kindirmo milk, to modify host responses to Plasmodium berghei ANKA infection. Twenty-five male BALB/c mice were grouped and administered various treatments, including probiotic-enriched yogurt alone or in combination with antibiotics. Parameters assessed included gut lactic acid bacteria (LAB) composition, parasitaemia progression, survival rates, and immune response dynamics over a 21-day postinfection period. The probiotic treatment significantly altered gut microbiota, evidenced by increased LAB counts and modulated immune responses, notably enhancing IgM and IL-4 production while reducing IFN-γ levels. Mice receiving prolonged probiotic treatment exhibited delayed parasitaemia onset, reduced mortality rates, and a more robust immune response compared to control groups. These outcomes suggest that probiotic intervention not only tempers the pathological effects of malaria but also enhances host resilience against infection. This study underscores the role of gut microbiota in infectious disease pathogenesis and supports probiotics as a promising adjunct therapy for malaria management.

High-yield, plant-based production of an antimicrobial peptide with potent activity in a mouse model

Plants offer a promising chassis for the large-scale, cost-effective production of diverse therapeutics, including antimicrobial peptides (AMPs). However, key advances will reduce production costs, including simplifying the downstream processing and purification steps. Here, using Nicotiana benthamiana plants, we present an improved modular design that enables AMPs to be secreted via the endomembrane system and sequestered in an extracellular compartment, the apoplast. Additionally, we translationally fused an AMP to a mutated small ubiquitin-like modifier sequence, thereby enhancing peptide yield and solubilizing the peptide with minimal aggregation and reduced occurrence of necrotic lesions in the plant. This strategy resulted in substantial peptide accumulation, reaching around 2.9 mg AMP per 20 g fresh weight of leaf tissue. Furthermore, the purified AMP demonstrated low collateral toxicity in primary human skin cells, killed pathogenic bacteria by permeabilizing the membrane and exhibited anti-infective efficacy in a preclinical mouse (Mus musculus) model system, reducing bacterial loads by up to three orders of magnitude. A base-case techno-economic analysis demonstrated the economic advantages and scalability of our plant-based platform. We envision that our work can establish plants as efficient bioreactors for producing preclinical-grade AMPs at a commercial scale, with the potential for clinical applications.

Conceptually innovative fluorophores for functional bioimaging

Fluorophore chemistry is at the forefront of bioimaging, revolutionizing the visualization of biological processes with unparalleled precision. From the serendipitous discovery of mauveine in 1856 to cutting-edge fluorophore engineering, this field has undergone transformative evolution. Today, the synergy of chemistry, biology, and imaging technologies has produced diverse, specialized fluorophores that enhance brightness, photostability, and targeting capabilities. This review delves into the history and innovation of fluorescent probes, showcasing their pivotal role in advancing our understanding of cellular dynamics and disease mechanisms. We highlight groundbreaking molecules and their applications, envisioning future breakthroughs that promise to redefine biomedical research and diagnostics.

Uncovering the arsenal of class II bacteriocins in salivarius streptococci

Facing the antibiotic resistance crisis, bacteriocins are considered as a promising alternative to treat bacterial infections. In the human commensal Streptococcus salivarius, the production of unmodified bacteriocins (or salivaricins) is directly controlled at the transcriptional level by quorum-sensing. To discover hidden bacteriocins, we harnessed here the unique molecular signatures of salivaricins not yet used in available computational pipelines and performed genome mining followed by orthogonal reconstitution and expression. From 100 genomes of S. salivarius, we identified more than 50 bacteriocin candidates clustered into 21 groups. Strain-based analysis of bacteriocin combinations revealed significant diversity, reflecting the plasticity of seven independent loci. Activity tests showed both narrow and broad-spectrum bacteriocins with overlapping activities against a wide panel of Gram-positive bacteria, including notorious multidrug-resistant pathogens. Overall, this work provides a search-to-test generic pipeline for bacteriocin discovery with high impact for bacterial ecology and broad applications in the food and biomedical fields.

Combating antibiotic resistance in a one health context: a plethora of frontiers

One of the most significant medical advancements of the 20th century was the discovery of antibiotics, which continue to play a vital tool in the treatment and prevention of diseases in humans and animals. However, the imprudent use of antibiotics in all fields of One-Health and concerns about antibiotic resistance among bacterial pathogens have raised interest in antibiotic use restrictions on a global scale. Despite the failure of conventional antimicrobial agents, only about 15 new antibiotics have been introduced clinically since year 2000 to date. Moreover, there has been reports of resistance to some of these new antibiotics. This has necessitated a need to search for alternative strategies to combat antimicrobial resistant pathogens. Thus, this review compiles and evaluates the approaches-natural compounds, phage treatment, and nanomaterials-that are being used and/or suggested as the potential substitutes for conventional antibiotics.

Effect of Nk-lysin peptides on bacterial growth, MIC, antimicrobial resistance, and viral activities

NK-lysins from chicken, bovine and human are used as antiviral and antibacterial agents. Gram-negative and gram-positive microorganisms, including Streptococcus pyogenes, Streptococcus mutans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella oxytoca, Shigella sonnei, Klebsiella pneumoniae and Salmonella typhimurium, are susceptible to NK-lysin treatment. The presence of dominant TEM-1 gene was noted in all untreated and treated bacteria, while TOHO-1 gene was absent in all bacteria. Importantly, β-lactamase genes CTX-M-1, CTX-M-8, and CTX-M-9 genes were detected in untreated bacterial strains; however, none of these were found in any bacterial strains following treatment with NK-lysin peptides. NK-lysin peptides are also used to test for inhibition of infectivity, which ranged from 50 to 90% depending on NK-lysin species. Chicken, bo vine and human NK-lysin peptides are demonstrated herein to have antibacterial activity and antiviral activity against Rotavirus (strain SA-11). On the basis of the comparison between these peptides, potent antiviral activity of bovine NK-lysin against Rotavirus (strain SA-11) is particularly evident, inhibiting infection by up to 90%. However, growth was also significantly inhibited by chicken and human NK-lysin peptides, restricted by 80 and 50%, respectively. This study provided a novel treatment using NK-lysin peptides to inhibit expression of β-lactamase genes in β-lactam antibiotic-resistant bacterial infections.

Consumer acceptance of bacteriophage technology for microbial control

As global concerns and awareness of the threat posed by antimicrobial resistance (AMR) grow, the One Health initiative provides a framework to advance public understanding of and willingness to address AMR. The use of bacteriophages as a non-antibiotic means to control bacterial infections aligns with this framework, but it is unknown whether the use of new antibiotic alternatives, and bacteriophages in particular, will find acceptance among consumers. Within the context of poultry production and consumption, we sampled 1497 Pakistani consumers studying their knowledge of and familiarity with antibiotics, bacteriophages and AMR, whether they perceived AMR as a threat, and their willingness to accept alternative microbial control technologies. Additionally, we tested the impact information about bacteriophages had on the different concepts as well as respondents' perception of different chicken quality attributes. Using both Probit and Multivariate Probit models we found that familiarity with antibiotics and bacteriophages is significantly associated with the acceptance of alternative microbial control technologies and perceptions of resulting products. Moreover, we find that providing information about the technology does not significantly alter respondent's perception of most quality attributes.

Rumicidins are a family of mammalian host-defense peptides plugging the 70S ribosome exit tunnel

The antimicrobial resistance crisis along with challenges of antimicrobial discovery revealed the vital necessity to develop new antibiotics. Many of the animal proline-rich antimicrobial peptides (PrAMPs) inhibit the process of bacterial translation. Genome projects allowed to identify immune-related genes encoding animal host defense peptides. Here, using genome mining approach, we discovered a family of proline-rich cathelicidins, named rumicidins. The genes encoding these peptides are widespread among ruminant mammals. Biochemical studies indicated that rumicidins effectively inhibited the elongation stage of bacterial translation. The cryo-EM structure of the Escherichia coli 70S ribosome in complex with one of the representatives of the family revealed that the binding site of rumicidins span the ribosomal A-site cleft and the nascent peptide exit tunnel interacting with its constriction point by the conservative Trp23-Phe24 dyad. Bacterial resistance to rumicidins is mediated by knockout of the SbmA transporter or modification of the MacAB-TolC efflux pump. A wide spectrum of antibacterial activity, a high efficacy in the animal infection model, and lack of adverse effects towards human cells in vitro make rumicidins promising molecular scaffolds for development of ribosome-targeting antibiotics.

Therapeutic potential of compound extract from Dracocephalum Rupestre Hance and Berberidis Radix against Salmonella-induced lamb diarrhea

Lamb diarrhea is primarily induced by bacterial infections, causing great economic and health challenges. Traditional antibiotic treatments raise concerns over drug resistance and environmental contamination. We explored the therapeutic potential of a compound extract from Dracocephalum rupestre Hance and Berberidis Radix against Salmonella-induced diarrhea in lamb. Twenty-five five-week-old Kunming mice (20 ± 5 g) were used. A controlled laboratory experiment, combing histological examinations, serum cytokine level analysis, gut microbiota composition analysis, and short-chain fatty acid quantification were conducted. Results demonstrated significant reparative effects on intestinal mucosal damage of the compound. Compound treatment notably reduced serum levels of inflammatory cytokines (IL-6, IL-8, sigA, and TNF-α), indicating an anti-inflammatory effect. Gene expression analysis of mucosal repair markers (PCNA, TGF, and EGFR) confirmed the positive impacts on intestinal recovery processes after treatment. Microbiota analysis revealed concentration-dependent alterations in gut microbial composition, with a notable increase in beneficial bacterial genera such as Muribaculum and Prevotella, suggesting the role of the compound in promoting gut health. Additionally, short-chain fatty acid analysis indicated an increase in beneficial acids, which are critical for the gut and overall health. This investigation highlights the potential therapeutic benefits of Dracocephalum rupestre Hance combining Berberidis Radix in lamb with Salmonella-induced diarrhea.

Rifabutin: a repurposed antibiotic with high potential against planktonic and biofilm staphylococcal clinical isolates

Staphylococcus aureus poses a significant threat as an opportunistic pathogen in humans, and animal medicine, particularly in the context of hospital-acquired infections (HAIs). Effective treatment is a significant challenge, contributing substantially to the global health burden. While antibiotic therapy remains the primary approach for staphylococcal infections, its efficacy is often compromised by the emergence of resistant strains and biofilm formation. The anticipated solution is the discovery and development of new antibacterial agents. However, this is a time consuming and expensive process with limited success rates. One potential alternative for addressing this challenge is the repurposing of existing antibiotics. This study investigated the potential of rifabutin (RFB) as a repurposed antibiotic for treating S. aureus infections. The minimum inhibitory concentration (MIC) of rifabutin was assessed by the broth microdilution method, in parallel to vancomycin, against 114 clinical isolates in planktonic form. The minimum biofilm inhibitory concentration (MBIC50) was determined by an adaptation of the broth microdilution method, followed by MTT assay, against a subset of selected 40 clinical isolates organized in biofilms. The study demonstrated that RFB MIC ranged from 0.002 to 6.250 μg/mL with a MIC50 of 0.013 μg/mL. RFB also demonstrated high anti-biofilm activity in the subset of 40 clinical isolates, with confirmed biofilm formation, with no significant MBIC50 differences observed between the MSSA and MRSA strains, in contrast to that observed for the VAN. These results highlight the promising efficacy of RFB against staphylococcal clinical isolates with different resistance patterns, whether in planktonic and biofilm forms.

Enhancing Antimicrobial Peptide Activity through Modifications of Charge, Hydrophobicity, and Structure

Antimicrobial peptides (AMPs) are emerging as a promising alternative to traditional antibiotics due to their ability to disturb bacterial membranes and/or their intracellular processes, offering a potential solution to the growing problem of antimicrobial resistance. AMP effectiveness is governed by factors such as net charge, hydrophobicity, and the ability to form amphipathic secondary structures. When properly balanced, these characteristics enable AMPs to selectively target bacterial membranes while sparing eukaryotic cells. This review focuses on the roles of positive charge, hydrophobicity, and structure in influencing AMP activity and toxicity, and explores strategies to optimize them for enhanced therapeutic potential. We highlight the delicate balance between these properties and how various modifications, including amino acid substitutions, peptide tagging, or lipid conjugation, can either enhance or impair AMP performance. Notably, an increase in these parameters does not always yield the best results; sometimes, a slight reduction in charge, hydrophobicity, or structural stability improves the overall AMP therapeutic potential. Understanding these complex interactions is key to developing AMPs with greater antimicrobial activity and reduced toxicity, making them viable candidates in the fight against antibiotic-resistant bacteria.

High-throughput screening identification of apigenin that reverses the colistin resistance of mcr-1-positive pathogens

The plasmid-mediated gene mcr-1 that makes bacteria resistant to the antibiotic colistin is spreading quickly, which means that colistin is no longer working well to treat Gram-negative bacterial infections. Herein, we utilized a computer-aided high-throughput screening drugs method to identify the natural product apigenin, a potential mcr-protein inhibitor, which effectively enhanced the antimicrobial activity of colistin. Several assays, including a checkerboard minimum inhibitory concentration assay, a time-kill assay, the combined disk test, molecular simulation dynamics, and animal infection models assay, were conducted to verify whether apigenin enhanced the ability of colistin to fight Gram-negative bacterial infections. The results showed that apigenin improved the antimicrobial activity of colistin against multidrug-resistant Enterobacteriaceae infection. Moreover, apigenin not only did not increase the toxic effect of colistin but also had the ability to effectively inhibit the frequency of bacterial resistance mutations to colistin. Studies clearly elucidated that apigenin could interfere with the thermal stability of the protein by binding to the mcr-1 protein. Additionally, the combination of apigenin and colistin could exert multiple effects, including disrupting bacterial membranes, the generation of bacterial nitric oxide and reactive oxygen species, as well as inhibiting bacterial adenosine triphosphate production. Furthermore, the addition of apigenin was able to significantly inhibit colistin-stimulated high expression levels of the bacterial mcr-1 gene. Finally, apigenin exhibited a characteristic anti-inflammatory effect while enhancing the antimicrobial activity of colistin against mcr-1-positive Escherichia coli (E. coli) infected animals. In conclusion, as a potential lead compound, apigenin is promising in combination with colistin in the future treatment of mcr-1-positive E. coli infections.IMPORTANCEThis study found that apigenin was able to inhibit the activity of the mcr-1 protein using a high-throughput virtual screening method. Apigenin effectively enhanced the antimicrobial activity of colistin against multidrug-resistant Enterobacteriaceae, including mcr-1-positive strains, in vitro and in vivo. This study will provide new options and strategies for the future treatment of multidrug-resistant pathogen infections.

Protein Immobilization on Bacterial Cellulose for Biomedical Application

New carriers for protein immobilization are objects of interest in various fields of biomedicine. Immobilization is a technique used to stabilize and provide physical support for biological micro- and macromolecules and whole cells. Special efforts have been made to develop new materials for protein immobilization that are non-toxic to both the body and the environment, inexpensive, readily available, and easy to modify. Currently, biodegradable and non-toxic polymers, including cellulose, are widely used for protein immobilization. Bacterial cellulose (BC) is a natural polymer with excellent biocompatibility, purity, high porosity, high water uptake capacity, non-immunogenicity, and ease of production and modification. BC is composed of glucose units and does not contain lignin or hemicellulose, which is an advantage allowing the avoidance of the chemical purification step before use. Recently, BC-protein composites have been developed as wound dressings, tissue engineering scaffolds, three-dimensional (3D) cell culture systems, drug delivery systems, and enzyme immobilization matrices. Proteins or peptides are often added to polymeric scaffolds to improve their biocompatibility and biological, physical-chemical, and mechanical properties. To broaden BC applications, various ex situ and in situ modifications of native BC are used to improve its properties for a specific application. In vivo studies showed that several BC-protein composites exhibited excellent biocompatibility, demonstrated prolonged treatment time, and increased the survival of animals. Today, there are several patents and commercial BC-based composites for wounds and vascular grafts. Therefore, further research on BC-protein composites has great prospects. This review focuses on the major advances in protein immobilization on BC for biomedical applications.

DeepMineLys: Deep mining of phage lysins from human microbiome

Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.

Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries

Bacteriophages are promising alternatives to traditional antimicrobial treatment of bacterial infections. To further increase the potential of phages, efficient engineering methods are needed. This study investigates an approach to phage engineering based on phage rebooting and compares selected methods of assembly and rebooting of phage genomes. GG assembly of phage genomes and subsequent rebooting by cell-free transcription-translation reactions yielded the most efficient phage engineering and allowed production of a proof-of-concept T7 phage library of 1.8 × 107 phages. We obtained 7.5 × 106 different phages, demonstrating generation of large and diverse libraries suitable for high-throughput screening of mutant phenotypes. Implementing versatile and high-throughput phage engineering methods allows vastly accelerated and improved phage engineering, bringing us closer to applying effective phages to treat infections in the clinic.

Multi-year analysis of the global preclinical antibacterial pipeline: trends and gaps

Antimicrobial resistance (AMR) is a major global health threat estimated to have caused the deaths of 1.27 million people in 2019, which is more than HIV/AIDS and malaria deaths combined. AMR also has significant consequences on the global economy. If not properly addressed, AMR could immensely impact the world's economy, further increasing the poverty burden in low- and middle-income countries. To mitigate the risk of a post-antibiotic society, where the ability to effectively treat common bacterial infections is being severely threatened, it is necessary to establish a continuous supply of new and novel antibacterial medicines. However, there are gaps in the current pipeline that will prove difficult to address, given the time required to develop new agents. To understand the status of upstream antibiotic development and the challenges faced by drug developers in the early development stage, the World Health Organization has regularly assessed the preclinical and clinical antibacterial development pipeline. The review identifies potential new classes of antibiotics or novel mechanisms of action that can better address resistant bacterial strains. This proactive approach is necessary to stay ahead of evolving resistance patterns and to support the availability of effective treatment options. This review examines the trends in preclinical development and attempts to identify gaps and potential opportunities to overcome the numerous hurdles in the early stages of the antibacterial research and development space.

Differential Age-Based Response Induced by a Commercial Probiotic Supplementation in Pastured Goats

The potential benefit of probiotics in small ruminant production systems has largely been unexplored. We evaluated the effect of a goat commercial probiotic on health and performance indicators in pastured goats from birth until 10 months. We randomly allocated 26 newborn nursing goat kids to two groups: a control group that received saline and a treatment group that received a commercial probiotic paste orally. We evaluated select observable health indicators (inappetence, diarrhea, coughing), weight, immunity (IgA, IgG, and innate immune response), total protein, hematocrit (HCT), total lactic acid bacteria (LAB), total coliforms, and prevalence of Escherichia coli (E. coli) primary virulence genes (stx1, stx2, and eae) during the experimental period. The results revealed no significant differences in the health indicators, LAB count, and total E. coli count. Prevalence of stx1 at 1 week of age and both stx1 and stx2 genes 4 months post-weaning was significantly (P < 0.05) higher in probiotic-supplemented goats. Probiotic supplementation significantly (P < 0.05) increased the total protein and IgA 1 month post-supplementation during the pre-weaning period and innate immune markers 2 days post-weaning. The HCT in probiotic-supplemented goats was significantly (P < 0.05) higher at 1 and 2 months post-weaning. The growth rate was not affected by probiotic supplementation in pre- and peri-weaned goats but was significantly (P < 0.05) lowered in goats older than 4 months in the supplemented group. In this pastured goat production study, there were mixed responses to a commercial probiotic in healthy goats based on age. The study suggests that early daily probiotic supplementation in pre-weaned pastured goats may have immune stimulation benefits, but in older healthy animals, post-weaning net benefits are unclear and further research is recommended.

Multiple resistance factors collectively promote inoculum-dependent dynamic survival during antimicrobial peptide exposure in Enterobacter cloacae

Antimicrobial peptides (AMPs) are a promising tool with which to fight rising antibiotic resistance. However, pathogenic bacteria are equipped with several AMP defense mechanisms, whose contributions to AMP resistance are often poorly defined. Here, we evaluate the genetic determinants of resistance to an insect AMP, cecropin B, in the opportunistic pathogen Enterobacter cloacae. Single-cell analysis of E. cloacae's response to cecropin revealed marked heterogeneity in cell survival, phenotypically reminiscent of heteroresistance (the ability of a subpopulation to grow in the presence of supra-MIC concentration of antimicrobial). The magnitude of this response was highly dependent on initial E. cloacae inoculum. We identified 3 genetic factors which collectively contribute to E. cloacae resistance in response to the AMP cecropin: The PhoPQ-two-component system, OmpT-mediated proteolytic cleavage of cecropin, and Rcs-mediated membrane stress response. Altogether, our data suggest that multiple, independent mechanisms contribute to AMP resistance in E. cloacae.

Photosensitizer-Amplified Antimicrobial Materials for Broad-Spectrum Ablation of Resistant Pathogens in Ocular Infections

The emergence of multidrug resistant (MDR) pathogens and the scarcity of new potent antibiotics and antifungals are one of the biggest threats to human health. Antimicrobial photodynamic therapy (aPDT) combines light and photosensitizers to kill drug-resistant pathogens; however, there are limited materials that can effectively ablate different classes of infective pathogens. In the present work, a new class of benzodiazole-paired materials is designed as highly potent PDT agents with broad-spectrum antimicrobial activity upon illumination with nontoxic light. The results mechanistically demonstrate that the energy transfer and electron transfer between nonphotosensitive and photosensitive benzodiazole moieties embedded within pathogen-binding peptide sequences result in increased singlet oxygen generation and enhanced phototoxicity. Chemical optimization renders PEP3 as a novel PDT agent with remarkable activity against MDR bacteria and fungi as well as pathogens at different stages of development (e.g., biofilms, spores, and fungal hyphae), which also prove effective in an ex vivo porcine model of microbial keratitis. The chemical modularity of this strategy and its general compatibility with peptide-based targeting agents will accelerate the design of highly photosensitive materials for antimicrobial PDT.

Triton X-100 counteracts antibiotic resistance of Enterococcus faecalis: An in vitro study

OBJECTIVES

The high prevalence of antibiotic-resistant bacteria poses a threat to the global public health. The appropriate use of adjuvants to restore the antimicrobial activity of antibiotics against resistant bacteria could be an effective strategy for combating antibiotic resistance. In this study, we investigated the counteraction of Triton X-100 (TX-100) and the mechanisms underlying the antibiotic resistance of Enterococcus faecalis (E. faecalis).

METHODS

Standard, wild-type (WT), and induced antibiotic-resistant E. faecalis strains were used in this study. In vitro antibacterial experiments were conducted to evaluate the antimicrobial activities of gentamicin sulfate and ciprofloxacin hydrochloride in the presence and absence of 0.02 % TX-100 against both planktonic and biofilm bacteria. Transcriptomic and untargeted metabolomic analyses were performed to explore the molecular mechanisms of TX-100 as an antibiotic adjuvant. Additionally, membrane permeability, membrane potential, glycolysis-related enzyme activity, intracellular adenosine triphosphate (ATP), and expression levels of virulence genes were assessed. The biocompatibility of different drug combinations was also evaluated.

RESULTS

A substantially low TX-100 concentration improved the antimicrobial effects of gentamicin sulfate or ciprofloxacin hydrochloride against antibiotic-resistant E. faecalis. Mechanistic studies demonstrated that TX-100 increased cell membrane permeability and dissipated membrane potential. Moreover, antibiotic resistance and pathogenicity of E. faecalis were attenuated by TX-100 via downregulation of the ABC transporter, phosphotransferase system (PTS), and ATP supply.

CONCLUSIONS

TX-100 enhanced the antimicrobial activity of gentamicin sulfate and ciprofloxacin hydrochloride at a low concentration by improving antibiotic susceptibility and attenuating antibiotic resistance and pathogenicity of E. faecalis.

CLINICAL SIGNIFICANCE

These findings provide a theoretical basis for developing new root canal disinfectants that can reduce antibiotic resistance.

The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is severely constrained by random peptide mixtures

The prevalence of antibiotic-resistant pathogens has become a major threat to public health, requiring swift initiatives for discovering new strategies to control bacterial infections. Hence, antibiotic stewardship and rapid diagnostics, but also the development, and prudent use, of novel effective antimicrobial agents are paramount. Ideally, these agents should be less likely to select for resistance in pathogens than currently available conventional antimicrobials. The usage of antimicrobial peptides (AMPs), key components of the innate immune response, and combination therapies, have been proposed as strategies to diminish the emergence of resistance. Herein, we investigated whether newly developed random antimicrobial peptide mixtures (RPMs) can significantly reduce the risk of resistance evolution in vitro to that of single sequence AMPs, using the ESKAPE pathogen Pseudomonas aeruginosa (P. aeruginosa) as a model gram-negative bacterium. Infections of this pathogen are difficult to treat due the inherent resistance to many drug classes, enhanced by the capacity to form biofilms. P. aeruginosa was experimentally evolved in the presence of AMPs or RPMs, subsequentially assessing the extent of resistance evolution and cross-resistance/collateral sensitivity between treatments. Furthermore, the fitness costs of resistance on bacterial growth were studied and whole-genome sequencing used to investigate which mutations could be candidates for causing resistant phenotypes. Lastly, changes in the pharmacodynamics of the evolved bacterial strains were examined. Our findings suggest that using RPMs bears a much lower risk of resistance evolution compared to AMPs and mostly prevents cross-resistance development to other treatments, while maintaining (or even improving) drug sensitivity. This strengthens the case for using random cocktails of AMPs in favour of single AMPs, against which resistance evolved in vitro, providing an alternative to classic antibiotics worth pursuing.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Phage K exposure generates phage-neutralizing activity in a rabbit model-humoral receptiveness may impact efficacy of phage therapy

Phage therapy has not been established in the clinical routine, in part due to uncertainties concerning efficacy and immunogenicity. Here, three rabbits were immunized against staphylococcal phage K to assess viral potency in the presence of immunized serum. Three rabbits received weekly intramuscular injections of ~1010±1 pfu/mL phage K. Phage K-specific IgG formation was measured by an enzyme-linked immunosorbent assay (ELISA); phage inactivation was assessed by calculating K-rates. Using transmission electron microscopy (TEM) and immunogold labeling, antibody binding to phage K was visualized. This was numerically assessed by objective imaging analysis comparing the relative distances of each gold particle to the nearest phage head and tail structure. Immunization led to a strong IgG response, plateauing 7 days after the last phage injection. There was no significant correlation between K-rate and antibody titer over time. TEM showed IgG binding to the head structure of phage K. Image analysis showed a significant reduction in relative distances between antibodies and phage head structures when comparing samples from day 0 and day 28 (P < 0.0001). These results suggest that while individual serum analysis for antibodies against therapeutic phage bears consideration prior to and with prolonged therapy, during phage application, the formation of specific antibodies against phage may only partially explain decreased phage potency in the presence of immunized serum. Instead, other factors may contribute to an individual's "humoral receptiveness" to phage therapy. Future investigations should be directed toward the identification of the humoral factors that have the most significant predictive value on phage potency in vivo.

Biodistribution of Native and Nanoformulated Innate Defense Regulator Peptide 1002

Innate defense regulator-1002 (IDR-1002) is a synthetic peptide with promising immunomodulatory and antibiofilm properties. An appreciable body of work exists around its mechanism of action at the cellular and molecular level, along with its efficacy across several infection and inflammation models. However, little is known about its absorption, distribution, and excretion in live organisms. Here, we performed a comprehensive biodistribution assessment with a gallium-67 radiolabeled derivative of IDR-1002 using nuclear tracing techniques. Various dose levels of the radiotracer (2-40 mg/kg) were administered into the blood, peritoneal cavity, and subcutaneous tissue, or instilled into the lungs. The peptide was well tolerated at all subcutaneous and intraperitoneal doses, although higher levels were associated with delayed absorption kinetics and precipitation of the peptide within the tissues. Low intratracheal doses were rapidly absorbed systemically, and small increases in the dose level were lethal. Intravenous doses were rapidly cleared from the blood at lower levels, and upon escalation, were toxic with a high proportion of the dose accumulating within the lung tissue. To improve biocompatibility and prolong its circulation within the blood, IDR-1002 was further formulated onto high molecular weight hyperbranched polyglycerol (HPG) polymers. Constructs prepared at 5:1 and 10:1 peptide-to-polymer ratios were colloidally stable, maintained the biological profile of the peptide payload and helped reduce red blood cell lysis. The 5:1 construct circulated well in the blood, but higher peptide loading was associated with rapid clearance by the reticuloendothelial system. Many peptides face pharmacokinetic and biocompatibility challenges, but formulations such as those with HPG have the potential to overcome these limitations.

Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46

Background

Endolysins are phage-encoded lytic enzymes that degrade bacterial peptidoglycan at the end of phage lytic cycles to release new phage particles. These enzymes are being explored as an alternative to small-molecule antibiotics.

Methods

The crystal structure of KTN6 Gp46 was determined and compared with a ColabFold model. Cleavage specificity was examined using a peptidoglycan digest and reversed-phase high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS).

Results

The structure of KTN6 Gp46 could be determined at 1.4 Å resolution, and key differences in loops of the putative peptidoglycan binding domain were identified in comparison with its closest known homologue, the endolysin of phage SPN1S. Reversed-phase HPLC/MS analysis of the reaction products following peptidoglycan digestion confirmed the muramidase activity of Gp46, consistent with structural predictions.

Conclusion

These insights into the structure and function of endolysins further expand the toolbox for endolysin engineering and explore their potential in enzyme-based antibacterial design strategies.

Pharmacokinetics, tissue distribution, bioavailability and excretion of the anti-virulence drug Fluorothiazinon in rats and rabbits

Growing antimicrobial resistance has accelerated the development of anti-virulence drugs to suppress bacterial toxicity without affecting cell viability. Fluorothiazinon (FT), an anti-virulence, type three secretion system and flagella motility inhibitor which has shown promise to suppress drug-resistant pathogens having the potential to enhance the efficacy of commonly prescribed antibiotics when used in combination. In this study we characterized the pharmacokinetics, tissue distribution, bioavailability and excretion of FT in rats and rabbits. FT presented a dose-proportional linear increase in the blood of rats. Tissue distribution profiling confirmed that FT distributes to all organs being substantially higher than in the blood of rats. The bioavailability of FT was higher when administered with starch than with water implying FT should be ideally dosed with food. FT was primarily excreted in the feces in rats and rabbits while negligible amounts are recovered from the urine.

Resistance to bacteriophage incurs a cost to virulence in drug-resistant Acinetobacter baumannii

Introduction . Acinetobacter baumannii is a critical priority pathogen for novel antimicrobials (World Health Organization) because of the rise in nosocomial infections and its ability to evolve resistance to last resort antibiotics. A. baumannii is thus a priority target for phage therapeutics. Two strains of a novel, virulent bacteriophage (LemonAid and Tonic) able to infect carbapenem-resistant A. baumannii (strain NCTC 13420), were isolated from environmental water samples collected through a citizen science programme.Gap statement. Phage-host coevolution can lead to emergence of host resistance, with a concomitant reduction in the virulence of host bacteria; a potential benefit to phage therapy applications.Methodology. In vitro and in vivo assays, genomics and microscopy techniques were used to characterize the phages; determine mechanisms and impact of phage resistance on host virulence, and the efficacy of the phages against A. baumannii.Results. A. baumannii developed resistance to both viruses, LemonAid and Tonic. Resistance came at a cost to virulence, with the resistant variants causing significantly reduced mortality in a Galleria mellonella larval in vivo model. A replicated 8 bp insertion increased in frequency (~40 % higher frequency than in the wild-type) within phage-resistant A. baumannii mutants, putatively resulting in early truncation of a protein of unknown function. Evidence from comparative genomics and an adsorption assay suggests this protein acts as a novel phage receptor site in A. baumannii. We find no evidence linking resistance to changes in capsule structure, a known virulence factor. LemonAid efficiently suppressed growth of A. baumanni in vitro across a wide range of titres. However, in vivo, while survival of A. baumannii infected larvae significantly increased with both remedial and prophylactic treatment with LemonAid (107 p.f.u. ml-1), the effect was weak and not sufficient to save larvae from morbidity and mortality.Conclusion. While LemonAid and Tonic did not prove effective as a treatment in a Galleria larvae model, there is potential to harness their ability to attenuate virulence in drug-resistant A. baumannii.

Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications

Antimicrobial peptides (AMPs) constitute a group of small molecular peptides that exhibit a wide range of antimicrobial activity. These peptides are abundantly present in the innate immune system of various organisms. Given the rise of multidrug-resistant bacteria, microbiological studies have identified AMPs as potential natural antibiotics. In the context of antimicrobial resistance across various human pathogens, AMPs hold considerable promise for clinical applications. However, numerous challenges exist in the detection of AMPs, particularly by immunological and molecular biological methods, especially when studying of newly discovered AMPs in proteomics. This review outlines the current status of AMPs research and the strategies employed in their development, considering resent discoveries and methodologies. Subsequently, we focus on the advanced techniques of mass spectrometry for the quantification of AMPs in diverse samples, and analyzes their application, advantages, and limitations. Additionally, we propose suggestions for the future development of tandem mass spectrometry for the detection of AMPs.

Biocontrol of multidrug resistant pathogens isolated from fish farms using silver nanoparticles combined with hydrogen peroxide insight to its modulatory effect

This study was divided into two parts. The first part involved the isolation, and detection of the prevalence and antimicrobial resistance profile of Aeromonas hydrophila, Pseudomonas aeruginosa, and Vibrio species from Nile tilapia fish and marine aquatic water. One hundred freshly dead Nile tilapia fish were collected from freshwater aquaculture fish farms located in Al-Abbassah district, Sharkia Governorate, and 100 samples of marine aquatic water were collected from fish farms in Port Said. The second part of the study focused on determining the in vitro inhibitory effect of dual-combination of AgNPs-H2O2 on bacterial growth and its down regulatory effect on crucial virulence factors using RT-PCR. The highest levels of A. hydrophila and P. aeruginosa were detected in 43%, and 34% of Nile tilapia fish samples, respectively. Meanwhile, the highest level of Vibrio species was found in 37% of marine water samples. Additionally, most of the isolated A. hydrophila, P. aeruginosa and Vibrio species exhibited a multi-drug resistance profile. The MIC and MBC results indicated a bactericidal effect of AgNPs-H2O2. Furthermore, a transcriptional modulation effect of AgNPs-H2O2 on the virulence-associated genes resulted in a significant down-regulation of aerA, exoU, and trh genes in A. hydrophila, P. aeruginosa, and Vibrio spp., respectively. The findings of this study suggest the effectiveness of AgNPs-H2O2 against drug resistant pathogens related to aquaculture.

Antimicrobial susceptibility of mastitis pathogens isolated from North American dairy cattle, 2011-2022

A total of 10,890 bacterial isolates of Streptococcus dysgalactiae, Streptococcus uberis, Staphylococcus aureus and Escherichia coli isolated as etiological agents from dairy cows with mastitis by 29 veterinary laboratories across North America between 2011 and 2022 were tested for in vitro antimicrobial susceptibility by broth microdilution to ampicillin, cefoperazone, ceftiofur, cephalothin, erythromycin, oxacillin, penicillin-novobiocin and pirlimycin according to CLSI standards. Using available clinical breakpoints, antimicrobial resistance among S. dysgalactiae (n = 2406) was low for penicillin-novobiocin (0% resistance), ceftiofur (0.1%), erythromycin (3.2%) and pirlimycin (4.6%). Among S. uberis (n = 2398), resistance was low for ampicillin (0%) and ceftiofur (0.2%) and moderate for erythromycin (11.9%) and pirlimycin (18.4%). For S. aureus (n = 3194), resistance was low for penicillin-novobiocin (0%), ceftiofur (0.1%), oxacillin (0.2%), erythromycin (0.7%), cefoperazone (1.2%) and pirlimycin (2.8%). For E. coli (n = 2892), resistance was low for ceftiofur (2.8%) and cefoperazone (3.4%) and moderate for ampicillin (9.2%). Overall, the results indicate that mastitis pathogens in the United States and Canada have not shown any substantial changes in the in vitro susceptibility to antimicrobial drugs over the 12 years of the study, or among that of the proceeding survey from 2002-2010. The data support the conclusion that resistance to common antimicrobial drugs among mastitis pathogens, even to drugs that have been used in dairies for mastitis management for many years, continues to remain low.

The global burden of antimicrobial resistance - urinary tract infections

Antimicrobial resistance (AMR) has emerged as a significant global healthcare problem. Antibiotic use has accelerated the physiologic process of AMR, particularly in Gram-negative pathogens. Urinary tract infections (UTIs) are predominantly of a Gram-negative nature. Uropathogens are evolutionarily highly adapted and selected strains with specific virulence factors, suggesting common mechanisms in how bacterial cells acquire virulence and AMR factors. The simultaneous increase in resistance and virulence is a complex and context-dependent phenomenon. Among known AMR mechanisms, the plenitude of different β-lactamases is especially prominent. The risk for AMR in UTIs varies in different patient populations. A history of antibiotic consumption and the physiology of urinary flow are major factors that shape AMR prevalence. The urinary tract is in close crosstalk with the microbiome of other compartments, including the gut and genital tracts. In addition, pharmacokinetic properties and the physiochemical composition of urinary compartments can contribute to the emergence of AMR. Alternatives to antibiotic treatment and a broader approach to address bacterial infections are needed. Among the various alternatives studied, antimicrobial peptides and bacteriophage treatment appear to be highly promising approaches. We herein summarize the present knowledge of clinical and microbiological AMR in UTIs and discuss innovative approaches, namely new risk prediction tools and the use of non-antibiotic approaches to defend against uropathogenic microbes.

Multiple resistance factors collectively promote inoculum-dependent dynamic survival during antimicrobial peptide exposure in Enterobacter cloacae

Antimicrobial peptides (AMPs) are a promising tool with which to fight rising antibiotic resistance. However, pathogenic bacteria are equipped with several AMP defense mechanisms, whose contributions to AMP resistance are often poorly defined. Here, we evaluate the genetic determinants of resistance to an insect AMP, cecropin B, in the opportunistic pathogen Enterobacter cloacae. Single-cell analysis of E. cloacae's response to cecropin revealed marked heterogeneity in cell survival, phenotypically reminiscent of heteroresistance (the ability of a subpopulation to grow in the presence of supra-MIC concentration of antimicrobial). The magnitude of this response was highly dependent on initial E. cloacae inoculum. We identified 3 genetic factors which collectively contribute to E. cloacae resistance in response to the AMP cecropin: The PhoPQ-two-component system, OmpT-mediated proteolytic cleavage of cecropin, and Rcs-mediated membrane stress response. Altogether, this evidence suggests that multiple, independent mechanisms contribute to AMP resistance in E. cloacae.